Starting phenix.real_space_refine on Sat Aug 8 06:55:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g9t_29878/08_2026/8g9t_29878.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g9t_29878/08_2026/8g9t_29878.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8g9t_29878/08_2026/8g9t_29878.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g9t_29878/08_2026/8g9t_29878.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8g9t_29878/08_2026/8g9t_29878.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g9t_29878/08_2026/8g9t_29878.map" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.060 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 P 43 5.49 5 S 110 5.16 5 C 16729 2.51 5 N 4769 2.21 5 O 5153 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 224 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 26804 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 583 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 1, 'TRANS': 68} Chain: "B" Number of atoms: 2206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2206 Classifications: {'peptide': 275} Link IDs: {'PTRANS': 8, 'TRANS': 266} Chain breaks: 1 Chain: "C" Number of atoms: 2241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2241 Classifications: {'peptide': 280} Link IDs: {'PTRANS': 8, 'TRANS': 271} Chain breaks: 1 Chain: "D" Number of atoms: 2214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 2214 Classifications: {'peptide': 276} Link IDs: {'PTRANS': 8, 'TRANS': 267} Chain breaks: 1 Chain: "E" Number of atoms: 2225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 2225 Classifications: {'peptide': 278} Link IDs: {'PTRANS': 8, 'TRANS': 269} Chain breaks: 1 Chain: "F" Number of atoms: 2097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2097 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 8, 'TRANS': 252} Chain breaks: 1 Chain: "G" Number of atoms: 1007 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 1007 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 4, 'TRANS': 119} Chain: "H" Number of atoms: 1955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1955 Classifications: {'peptide': 242} Link IDs: {'PTRANS': 5, 'TRANS': 236} Chain breaks: 2 Chain: "I" Number of atoms: 1007 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 1007 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 4, 'TRANS': 119} Chain: "J" Number of atoms: 1007 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 1007 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 4, 'TRANS': 119} Chain: "K" Number of atoms: 4559 Number of conformers: 1 Conformer: "" Number of residues, atoms: 582, 4559 Classifications: {'peptide': 582} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 1, 'PTRANS': 21, 'TRANS': 559} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "M" Number of atoms: 2101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 2101 Classifications: {'peptide': 263} Link IDs: {'PTRANS': 8, 'TRANS': 254} Chain breaks: 1 Chain: "N" Number of atoms: 1674 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1674 Classifications: {'peptide': 205} Link IDs: {'PTRANS': 11, 'TRANS': 193} Chain: "O" Number of atoms: 921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 921 Classifications: {'RNA': 43} Modifications used: {'rna2p_pur': 10, 'rna2p_pyr': 13, 'rna3p_pur': 14, 'rna3p_pyr': 6} Link IDs: {'rna2p': 22, 'rna3p': 20} Chain: "L" Number of atoms: 1007 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 1007 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 4, 'TRANS': 119} Time building chain proxies: 5.01, per 1000 atoms: 0.19 Number of scatterers: 26804 At special positions: 0 Unit cell: (108.697, 116.142, 203.993, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 110 16.00 P 43 15.00 O 5153 8.00 N 4769 7.00 C 16729 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.11 Conformation dependent library (CDL) restraints added in 1.2 seconds 6368 Ramachandran restraints generated. 3184 Oldfield, 0 Emsley, 3184 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5976 Finding SS restraints... Secondary structure from input PDB file: 114 helices and 41 sheets defined 43.3% alpha, 15.0% beta 0 base pairs and 12 stacking pairs defined. Time for finding SS restraints: 3.56 Creating SS restraints... Processing helix chain 'A' and resid 135 through 147 Processing helix chain 'A' and resid 161 through 163 No H-bonds generated for 'chain 'A' and resid 161 through 163' Processing helix chain 'A' and resid 164 through 169 removed outlier: 3.722A pdb=" N TYR A 168 " --> pdb=" O GLU A 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 58 removed outlier: 3.537A pdb=" N LEU B 46 " --> pdb=" O THR B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 82 Processing helix chain 'B' and resid 83 through 88 removed outlier: 3.536A pdb=" N GLY B 88 " --> pdb=" O GLU B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 106 Processing helix chain 'B' and resid 106 through 112 Processing helix chain 'B' and resid 185 through 193 removed outlier: 3.505A pdb=" N GLN B 191 " --> pdb=" O HIS B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 209 Processing helix chain 'B' and resid 210 through 213 Processing helix chain 'B' and resid 239 through 247 removed outlier: 3.554A pdb=" N ILE B 247 " --> pdb=" O LEU B 243 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 262 No H-bonds generated for 'chain 'B' and resid 260 through 262' Processing helix chain 'B' and resid 272 through 276 removed outlier: 4.297A pdb=" N GLU B 275 " --> pdb=" O ASN B 272 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 58 Processing helix chain 'C' and resid 72 through 81 Processing helix chain 'C' and resid 92 through 106 removed outlier: 4.033A pdb=" N GLU C 96 " --> pdb=" O GLY C 92 " (cutoff:3.500A) Processing helix chain 'C' and resid 106 through 113 Processing helix chain 'C' and resid 185 through 193 removed outlier: 4.578A pdb=" N GLN C 191 " --> pdb=" O HIS C 187 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N THR C 192 " --> pdb=" O PHE C 188 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 209 Processing helix chain 'C' and resid 239 through 246 removed outlier: 3.514A pdb=" N LEU C 243 " --> pdb=" O PRO C 239 " (cutoff:3.500A) Processing helix chain 'D' and resid 42 through 58 removed outlier: 4.032A pdb=" N LYS D 49 " --> pdb=" O CYS D 45 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 83 removed outlier: 4.515A pdb=" N ALA D 80 " --> pdb=" O LEU D 76 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLN D 83 " --> pdb=" O GLU D 79 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 88 removed outlier: 4.123A pdb=" N GLY D 88 " --> pdb=" O GLU D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 106 removed outlier: 3.940A pdb=" N THR D 95 " --> pdb=" O LYS D 91 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N GLU D 96 " --> pdb=" O GLY D 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 106 through 112 Processing helix chain 'D' and resid 185 through 190 Processing helix chain 'D' and resid 195 through 213 removed outlier: 5.397A pdb=" N PHE D 210 " --> pdb=" O LEU D 206 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N ASP D 211 " --> pdb=" O VAL D 207 " (cutoff:3.500A) Processing helix chain 'D' and resid 239 through 246 Processing helix chain 'E' and resid 42 through 58 Processing helix chain 'E' and resid 72 through 82 Processing helix chain 'E' and resid 90 through 106 removed outlier: 4.336A pdb=" N THR E 95 " --> pdb=" O LYS E 91 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N GLU E 96 " --> pdb=" O GLY E 92 " (cutoff:3.500A) Processing helix chain 'E' and resid 106 through 112 Processing helix chain 'E' and resid 185 through 193 Processing helix chain 'E' and resid 195 through 210 removed outlier: 4.489A pdb=" N PHE E 210 " --> pdb=" O LEU E 206 " (cutoff:3.500A) Processing helix chain 'E' and resid 211 through 213 No H-bonds generated for 'chain 'E' and resid 211 through 213' Processing helix chain 'E' and resid 239 through 247 Processing helix chain 'E' and resid 260 through 262 No H-bonds generated for 'chain 'E' and resid 260 through 262' Processing helix chain 'E' and resid 272 through 276 Processing helix chain 'F' and resid 42 through 58 removed outlier: 3.609A pdb=" N LEU F 46 " --> pdb=" O THR F 42 " (cutoff:3.500A) Processing helix chain 'F' and resid 72 through 82 Processing helix chain 'F' and resid 93 through 106 Processing helix chain 'F' and resid 106 through 112 removed outlier: 3.609A pdb=" N ARG F 110 " --> pdb=" O TYR F 106 " (cutoff:3.500A) Processing helix chain 'F' and resid 185 through 190 Processing helix chain 'F' and resid 195 through 209 Processing helix chain 'F' and resid 239 through 247 Processing helix chain 'F' and resid 260 through 262 No H-bonds generated for 'chain 'F' and resid 260 through 262' Processing helix chain 'F' and resid 272 through 276 removed outlier: 4.455A pdb=" N GLU F 275 " --> pdb=" O ASN F 272 " (cutoff:3.500A) Processing helix chain 'G' and resid 9 through 29 Processing helix chain 'G' and resid 35 through 47 removed outlier: 6.547A pdb=" N GLY G 42 " --> pdb=" O ASP G 38 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N SER G 43 " --> pdb=" O ARG G 39 " (cutoff:3.500A) Processing helix chain 'G' and resid 47 through 66 removed outlier: 4.071A pdb=" N VAL G 51 " --> pdb=" O THR G 47 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N THR G 54 " --> pdb=" O ALA G 50 " (cutoff:3.500A) Proline residue: G 60 - end of helix Processing helix chain 'G' and resid 68 through 86 removed outlier: 3.532A pdb=" N ALA G 72 " --> pdb=" O PHE G 68 " (cutoff:3.500A) Processing helix chain 'G' and resid 94 through 114 Processing helix chain 'G' and resid 116 through 124 removed outlier: 3.759A pdb=" N ASN G 120 " --> pdb=" O ASP G 116 " (cutoff:3.500A) Processing helix chain 'H' and resid 42 through 58 Processing helix chain 'H' and resid 72 through 82 Processing helix chain 'H' and resid 91 through 106 Processing helix chain 'H' and resid 106 through 112 Processing helix chain 'H' and resid 185 through 193 Processing helix chain 'H' and resid 195 through 209 Processing helix chain 'H' and resid 210 through 214 Processing helix chain 'H' and resid 239 through 246 Processing helix chain 'H' and resid 260 through 262 No H-bonds generated for 'chain 'H' and resid 260 through 262' Processing helix chain 'H' and resid 272 through 276 removed outlier: 4.177A pdb=" N THR H 276 " --> pdb=" O LEU H 273 " (cutoff:3.500A) Processing helix chain 'I' and resid 9 through 29 Processing helix chain 'I' and resid 35 through 47 removed outlier: 6.546A pdb=" N GLY I 42 " --> pdb=" O ASP I 38 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N SER I 43 " --> pdb=" O ARG I 39 " (cutoff:3.500A) Processing helix chain 'I' and resid 47 through 66 removed outlier: 4.071A pdb=" N VAL I 51 " --> pdb=" O THR I 47 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N THR I 54 " --> pdb=" O ALA I 50 " (cutoff:3.500A) Proline residue: I 60 - end of helix Processing helix chain 'I' and resid 68 through 86 removed outlier: 3.531A pdb=" N ALA I 72 " --> pdb=" O PHE I 68 " (cutoff:3.500A) Processing helix chain 'I' and resid 94 through 114 Processing helix chain 'I' and resid 116 through 124 removed outlier: 3.759A pdb=" N ASN I 120 " --> pdb=" O ASP I 116 " (cutoff:3.500A) Processing helix chain 'J' and resid 9 through 29 Processing helix chain 'J' and resid 35 through 47 removed outlier: 6.547A pdb=" N GLY J 42 " --> pdb=" O ASP J 38 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N SER J 43 " --> pdb=" O ARG J 39 " (cutoff:3.500A) Processing helix chain 'J' and resid 47 through 66 removed outlier: 4.071A pdb=" N VAL J 51 " --> pdb=" O THR J 47 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N THR J 54 " --> pdb=" O ALA J 50 " (cutoff:3.500A) Proline residue: J 60 - end of helix Processing helix chain 'J' and resid 68 through 86 removed outlier: 3.530A pdb=" N ALA J 72 " --> pdb=" O PHE J 68 " (cutoff:3.500A) Processing helix chain 'J' and resid 94 through 114 Processing helix chain 'J' and resid 116 through 124 removed outlier: 3.759A pdb=" N ASN J 120 " --> pdb=" O ASP J 116 " (cutoff:3.500A) Processing helix chain 'K' and resid 2 through 16 Processing helix chain 'K' and resid 73 through 77 Processing helix chain 'K' and resid 84 through 89 Processing helix chain 'K' and resid 97 through 118 Processing helix chain 'K' and resid 121 through 133 Processing helix chain 'K' and resid 134 through 144 removed outlier: 4.009A pdb=" N VAL K 140 " --> pdb=" O GLU K 136 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N GLN K 142 " --> pdb=" O SER K 138 " (cutoff:3.500A) Processing helix chain 'K' and resid 172 through 190 Processing helix chain 'K' and resid 243 through 260 Processing helix chain 'K' and resid 282 through 290 removed outlier: 4.501A pdb=" N SER K 287 " --> pdb=" O GLU K 283 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N MET K 288 " --> pdb=" O SER K 284 " (cutoff:3.500A) Processing helix chain 'K' and resid 299 through 302 Processing helix chain 'K' and resid 303 through 311 Processing helix chain 'K' and resid 347 through 361 Processing helix chain 'K' and resid 376 through 384 Processing helix chain 'K' and resid 397 through 408 Processing helix chain 'K' and resid 412 through 427 Processing helix chain 'K' and resid 430 through 447 Processing helix chain 'K' and resid 468 through 486 removed outlier: 4.103A pdb=" N LEU K 474 " --> pdb=" O VAL K 470 " (cutoff:3.500A) Processing helix chain 'K' and resid 493 through 504 removed outlier: 7.152A pdb=" N GLY K 499 " --> pdb=" O ASP K 495 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N SER K 500 " --> pdb=" O ARG K 496 " (cutoff:3.500A) Processing helix chain 'K' and resid 504 through 522 removed outlier: 3.683A pdb=" N VAL K 508 " --> pdb=" O THR K 504 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N THR K 511 " --> pdb=" O ALA K 507 " (cutoff:3.500A) Proline residue: K 517 - end of helix removed outlier: 3.640A pdb=" N LYS K 522 " --> pdb=" O HIS K 518 " (cutoff:3.500A) Processing helix chain 'K' and resid 525 through 543 removed outlier: 3.646A pdb=" N HIS K 542 " --> pdb=" O GLN K 538 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N CYS K 543 " --> pdb=" O ILE K 539 " (cutoff:3.500A) Processing helix chain 'K' and resid 551 through 571 Processing helix chain 'K' and resid 573 through 582 Processing helix chain 'M' and resid 42 through 58 Processing helix chain 'M' and resid 96 through 106 Processing helix chain 'M' and resid 106 through 113 removed outlier: 3.648A pdb=" N ARG M 110 " --> pdb=" O TYR M 106 " (cutoff:3.500A) Processing helix chain 'M' and resid 185 through 192 Processing helix chain 'M' and resid 195 through 213 removed outlier: 5.635A pdb=" N PHE M 210 " --> pdb=" O LEU M 206 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N ASP M 211 " --> pdb=" O VAL M 207 " (cutoff:3.500A) Processing helix chain 'M' and resid 239 through 246 Processing helix chain 'M' and resid 260 through 262 No H-bonds generated for 'chain 'M' and resid 260 through 262' Processing helix chain 'M' and resid 271 through 276 removed outlier: 3.933A pdb=" N GLU M 274 " --> pdb=" O LYS M 271 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N THR M 276 " --> pdb=" O LEU M 273 " (cutoff:3.500A) Processing helix chain 'N' and resid 30 through 42 Processing helix chain 'N' and resid 117 through 131 Processing helix chain 'L' and resid 9 through 29 Processing helix chain 'L' and resid 35 through 47 removed outlier: 6.546A pdb=" N GLY L 42 " --> pdb=" O ASP L 38 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N SER L 43 " --> pdb=" O ARG L 39 " (cutoff:3.500A) Processing helix chain 'L' and resid 47 through 66 removed outlier: 4.071A pdb=" N VAL L 51 " --> pdb=" O THR L 47 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N THR L 54 " --> pdb=" O ALA L 50 " (cutoff:3.500A) Proline residue: L 60 - end of helix Processing helix chain 'L' and resid 68 through 86 removed outlier: 3.531A pdb=" N ALA L 72 " --> pdb=" O PHE L 68 " (cutoff:3.500A) Processing helix chain 'L' and resid 94 through 114 Processing helix chain 'L' and resid 116 through 124 removed outlier: 3.759A pdb=" N ASN L 120 " --> pdb=" O ASP L 116 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 156 through 159 Processing sheet with id=AA2, first strand: chain 'B' and resid 40 through 41 Processing sheet with id=AA3, first strand: chain 'B' and resid 40 through 41 removed outlier: 5.749A pdb=" N ARG B 6 " --> pdb=" O GLU B 230 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N GLU B 230 " --> pdb=" O ARG B 6 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ASP B 8 " --> pdb=" O VAL B 228 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N VAL B 228 " --> pdb=" O ASP B 8 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N VAL B 10 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N LEU B 226 " --> pdb=" O VAL B 10 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N LEU B 12 " --> pdb=" O ARG B 224 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N GLN B 220 " --> pdb=" O GLN B 16 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU B 278 " --> pdb=" O GLU B 230 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 114 through 115 Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 149 Processing sheet with id=AA6, first strand: chain 'B' and resid 248 through 251 Processing sheet with id=AA7, first strand: chain 'C' and resid 31 through 32 removed outlier: 3.811A pdb=" N ARG C 31 " --> pdb=" O LEU C 40 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N GLY C 39 " --> pdb=" O SER C 136 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 31 through 32 removed outlier: 3.811A pdb=" N ARG C 31 " --> pdb=" O LEU C 40 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N GLY C 39 " --> pdb=" O SER C 136 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ASP C 14 " --> pdb=" O ALA C 223 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N ALA C 223 " --> pdb=" O ASP C 14 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 145 through 147 removed outlier: 3.741A pdb=" N HIS C 145 " --> pdb=" O LYS C 170 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 247 through 251 Processing sheet with id=AB2, first strand: chain 'D' and resid 32 through 33 removed outlier: 4.820A pdb=" N GLY D 39 " --> pdb=" O SER D 136 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 32 through 33 removed outlier: 4.820A pdb=" N GLY D 39 " --> pdb=" O SER D 136 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N GLY D 176 " --> pdb=" O VAL D 15 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N VAL D 15 " --> pdb=" O GLY D 176 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N ARG D 6 " --> pdb=" O GLU D 230 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N GLU D 230 " --> pdb=" O ARG D 6 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ASP D 8 " --> pdb=" O VAL D 228 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N VAL D 228 " --> pdb=" O ASP D 8 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N VAL D 10 " --> pdb=" O LEU D 226 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N LEU D 226 " --> pdb=" O VAL D 10 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N LEU D 12 " --> pdb=" O ARG D 224 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 145 through 147 removed outlier: 3.728A pdb=" N HIS D 145 " --> pdb=" O LYS D 170 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 247 through 251 Processing sheet with id=AB6, first strand: chain 'E' and resid 129 through 131 Processing sheet with id=AB7, first strand: chain 'E' and resid 40 through 41 Processing sheet with id=AB8, first strand: chain 'E' and resid 22 through 23 removed outlier: 3.548A pdb=" N LEU E 29 " --> pdb=" O ASP E 23 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 114 through 115 Processing sheet with id=AC1, first strand: chain 'E' and resid 145 through 147 removed outlier: 3.826A pdb=" N HIS E 145 " --> pdb=" O LYS E 170 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 248 through 251 removed outlier: 3.776A pdb=" N GLN E 248 " --> pdb=" O SER E 267 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 40 through 41 removed outlier: 3.789A pdb=" N ARG F 135 " --> pdb=" O ARG F 179 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 40 through 41 removed outlier: 3.789A pdb=" N ARG F 135 " --> pdb=" O ARG F 179 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N ASP F 8 " --> pdb=" O VAL F 228 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N VAL F 228 " --> pdb=" O ASP F 8 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N VAL F 10 " --> pdb=" O LEU F 226 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N LEU F 226 " --> pdb=" O VAL F 10 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N LEU F 12 " --> pdb=" O ARG F 224 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 17 through 18 Processing sheet with id=AC6, first strand: chain 'F' and resid 114 through 115 Processing sheet with id=AC7, first strand: chain 'F' and resid 248 through 251 Processing sheet with id=AC8, first strand: chain 'H' and resid 32 through 33 removed outlier: 4.862A pdb=" N GLY H 39 " --> pdb=" O SER H 136 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'H' and resid 32 through 33 removed outlier: 4.862A pdb=" N GLY H 39 " --> pdb=" O SER H 136 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'H' and resid 114 through 115 removed outlier: 3.784A pdb=" N VAL H 125 " --> pdb=" O ALA H 114 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 247 through 251 Processing sheet with id=AD3, first strand: chain 'K' and resid 25 through 26 Processing sheet with id=AD4, first strand: chain 'K' and resid 29 through 30 removed outlier: 3.607A pdb=" N ILE K 30 " --> pdb=" O ARG K 59 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ARG K 59 " --> pdb=" O ILE K 30 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'K' and resid 44 through 47 Processing sheet with id=AD6, first strand: chain 'K' and resid 324 through 325 Processing sheet with id=AD7, first strand: chain 'K' and resid 330 through 333 Processing sheet with id=AD8, first strand: chain 'M' and resid 40 through 41 removed outlier: 3.955A pdb=" N ARG M 135 " --> pdb=" O ARG M 179 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLY M 176 " --> pdb=" O VAL M 15 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ASP M 14 " --> pdb=" O ALA M 223 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N ALA M 223 " --> pdb=" O ASP M 14 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'M' and resid 114 through 115 Processing sheet with id=AE1, first strand: chain 'M' and resid 143 through 147 removed outlier: 4.273A pdb=" N HIS M 145 " --> pdb=" O LYS M 170 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'M' and resid 247 through 251 Processing sheet with id=AE3, first strand: chain 'N' and resid 23 through 24 removed outlier: 6.957A pdb=" N ARG N 23 " --> pdb=" O MET N 93 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N LEU N 95 " --> pdb=" O ARG N 23 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ASP N 10 " --> pdb=" O ASP N 97 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ALA N 99 " --> pdb=" O SER N 8 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N SER N 8 " --> pdb=" O ALA N 99 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N ARG N 101 " --> pdb=" O GLU N 6 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N GLU N 6 " --> pdb=" O ARG N 101 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N HIS N 103 " --> pdb=" O ILE N 4 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ILE N 4 " --> pdb=" O HIS N 103 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ILE N 4 " --> pdb=" O LEU N 152 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'N' and resid 62 through 70 removed outlier: 7.119A pdb=" N ALA N 99 " --> pdb=" O ILE N 56 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N ILE N 56 " --> pdb=" O ALA N 99 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N ARG N 101 " --> pdb=" O ILE N 54 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N ILE N 54 " --> pdb=" O ARG N 101 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N HIS N 103 " --> pdb=" O LEU N 52 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'N' and resid 170 through 171 1175 hydrogen bonds defined for protein. 3315 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 12 stacking parallelities Total time for adding SS restraints: 4.86 Time building geometry restraints manager: 2.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 6494 1.32 - 1.45: 6182 1.45 - 1.57: 14484 1.57 - 1.69: 86 1.69 - 1.81: 184 Bond restraints: 27430 Sorted by residual: bond pdb=" CB ARG D 48 " pdb=" CG ARG D 48 " ideal model delta sigma weight residual 1.520 1.280 0.240 3.00e-02 1.11e+03 6.41e+01 bond pdb=" CA LEU C 279 " pdb=" CB LEU C 279 " ideal model delta sigma weight residual 1.526 1.406 0.120 1.53e-02 4.27e+03 6.14e+01 bond pdb=" N7 G O 4 " pdb=" C5 G O 4 " ideal model delta sigma weight residual 1.388 1.344 0.044 6.00e-03 2.78e+04 5.46e+01 bond pdb=" C6 G O 4 " pdb=" N1 G O 4 " ideal model delta sigma weight residual 1.391 1.340 0.051 7.00e-03 2.04e+04 5.29e+01 bond pdb=" C8 G O 4 " pdb=" N7 G O 4 " ideal model delta sigma weight residual 1.305 1.270 0.035 6.00e-03 2.78e+04 3.35e+01 ... (remaining 27425 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.10: 36840 5.10 - 10.19: 312 10.19 - 15.29: 40 15.29 - 20.39: 0 20.39 - 25.49: 2 Bond angle restraints: 37194 Sorted by residual: angle pdb=" C1' G O 4 " pdb=" N9 G O 4 " pdb=" C8 G O 4 " ideal model delta sigma weight residual 127.00 112.01 14.99 1.30e+00 5.92e-01 1.33e+02 angle pdb=" C1' G O 4 " pdb=" N9 G O 4 " pdb=" C4 G O 4 " ideal model delta sigma weight residual 126.50 141.30 -14.80 1.30e+00 5.92e-01 1.30e+02 angle pdb=" N7 G O 4 " pdb=" C5 G O 4 " pdb=" C6 G O 4 " ideal model delta sigma weight residual 130.40 123.63 6.77 6.00e-01 2.78e+00 1.27e+02 angle pdb=" CG ARG D 48 " pdb=" CD ARG D 48 " pdb=" NE ARG D 48 " ideal model delta sigma weight residual 112.00 87.19 24.81 2.20e+00 2.07e-01 1.27e+02 angle pdb=" N1 G O 4 " pdb=" C2 G O 4 " pdb=" N2 G O 4 " ideal model delta sigma weight residual 116.20 106.81 9.39 9.00e-01 1.23e+00 1.09e+02 ... (remaining 37189 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.34: 15939 34.34 - 68.67: 479 68.67 - 103.01: 69 103.01 - 137.34: 7 137.34 - 171.68: 2 Dihedral angle restraints: 16496 sinusoidal: 7206 harmonic: 9290 Sorted by residual: dihedral pdb=" C5' G O 4 " pdb=" C4' G O 4 " pdb=" C3' G O 4 " pdb=" O3' G O 4 " ideal model delta sinusoidal sigma weight residual 147.00 90.57 56.43 1 8.00e+00 1.56e-02 6.71e+01 dihedral pdb=" CA LYS K 234 " pdb=" C LYS K 234 " pdb=" N GLU K 235 " pdb=" CA GLU K 235 " ideal model delta harmonic sigma weight residual 180.00 139.30 40.70 0 5.00e+00 4.00e-02 6.63e+01 dihedral pdb=" CA ASN K 333 " pdb=" C ASN K 333 " pdb=" N SER K 334 " pdb=" CA SER K 334 " ideal model delta harmonic sigma weight residual 180.00 -141.26 -38.74 0 5.00e+00 4.00e-02 6.00e+01 ... (remaining 16493 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.136: 3878 0.136 - 0.271: 134 0.271 - 0.407: 8 0.407 - 0.542: 1 0.542 - 0.678: 2 Chirality restraints: 4023 Sorted by residual: chirality pdb=" CG LEU D 73 " pdb=" CB LEU D 73 " pdb=" CD1 LEU D 73 " pdb=" CD2 LEU D 73 " both_signs ideal model delta sigma weight residual False -2.59 -1.91 -0.68 2.00e-01 2.50e+01 1.15e+01 chirality pdb=" C1' G O 4 " pdb=" O4' G O 4 " pdb=" C2' G O 4 " pdb=" N9 G O 4 " both_signs ideal model delta sigma weight residual False 2.44 1.79 0.64 2.00e-01 2.50e+01 1.03e+01 chirality pdb=" CB ILE N 202 " pdb=" CA ILE N 202 " pdb=" CG1 ILE N 202 " pdb=" CG2 ILE N 202 " both_signs ideal model delta sigma weight residual False 2.64 2.19 0.46 2.00e-01 2.50e+01 5.18e+00 ... (remaining 4020 not shown) Planarity restraints: 4752 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL D 173 " 0.120 5.00e-02 4.00e+02 1.69e-01 4.54e+01 pdb=" N PRO D 174 " -0.291 5.00e-02 4.00e+02 pdb=" CA PRO D 174 " 0.089 5.00e-02 4.00e+02 pdb=" CD PRO D 174 " 0.082 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS D 49 " 0.021 2.00e-02 2.50e+03 4.29e-02 1.84e+01 pdb=" C LYS D 49 " -0.074 2.00e-02 2.50e+03 pdb=" O LYS D 49 " 0.028 2.00e-02 2.50e+03 pdb=" N VAL D 50 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 183 " -0.022 2.00e-02 2.50e+03 3.19e-02 1.78e+01 pdb=" CG PHE B 183 " 0.072 2.00e-02 2.50e+03 pdb=" CD1 PHE B 183 " -0.033 2.00e-02 2.50e+03 pdb=" CD2 PHE B 183 " -0.016 2.00e-02 2.50e+03 pdb=" CE1 PHE B 183 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 PHE B 183 " -0.011 2.00e-02 2.50e+03 pdb=" CZ PHE B 183 " 0.005 2.00e-02 2.50e+03 ... (remaining 4749 not shown) Histogram of nonbonded interaction distances: 1.67 - 2.32: 193 2.32 - 2.96: 16976 2.96 - 3.61: 47908 3.61 - 4.25: 74077 4.25 - 4.90: 117853 Nonbonded interactions: 257007 Sorted by model distance: nonbonded pdb=" NH2 ARG D 48 " pdb=" OP2 G O 26 " model vdw 1.669 3.120 nonbonded pdb=" O ARG E 48 " pdb=" NH1 ARG E 48 " model vdw 2.011 3.120 nonbonded pdb=" NH1 ARG C 48 " pdb=" OD1 ASN C 52 " model vdw 2.015 3.120 nonbonded pdb=" OE1 GLU H 38 " pdb=" OG SER H 136 " model vdw 2.023 3.040 nonbonded pdb=" OG SER F 260 " pdb=" OD1 ASP F 262 " model vdw 2.037 3.040 ... (remaining 257002 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'B' and (resid 2 through 19 or resid 31 through 74 or resid 95 through 14 \ 0 or resid 171 through 284)) selection = (chain 'C' and (resid 2 through 19 or resid 31 through 74 or resid 95 through 14 \ 0 or resid 171 through 284)) selection = (chain 'D' and (resid 2 through 19 or resid 31 through 74 or resid 95 through 14 \ 0 or resid 171 through 284)) selection = (chain 'E' and (resid 2 through 19 or resid 31 through 74 or resid 95 through 14 \ 0 or resid 171 through 284)) selection = (chain 'F' and (resid 2 through 19 or resid 31 through 74 or resid 95 through 14 \ 0 or resid 171 through 284)) selection = (chain 'H' and (resid 2 through 74 or resid 95 through 284)) selection = (chain 'M' and (resid 2 through 19 or resid 31 through 140 or resid 171 through \ 284)) } ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'J' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.420 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 25.210 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 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 : 0.013 0.240 27430 Z= 0.661 Angle : 1.330 25.485 37194 Z= 0.769 Chirality : 0.066 0.678 4023 Planarity : 0.007 0.169 4752 Dihedral : 17.276 171.678 10520 Min Nonbonded Distance : 1.669 Molprobity Statistics. All-atom Clashscore : 58.96 Ramachandran Plot: Outliers : 0.09 % Allowed : 14.04 % Favored : 85.87 % Rotamer: Outliers : 2.61 % Allowed : 1.67 % Favored : 95.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.57 (0.13), residues: 3184 helix: -1.85 (0.13), residues: 1236 sheet: -2.69 (0.24), residues: 384 loop : -2.71 (0.14), residues: 1564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.047 0.002 ARG D 48 TYR 0.042 0.005 TYR C 7 PHE 0.072 0.004 PHE B 183 TRP 0.053 0.006 TRP L 77 HIS 0.029 0.003 HIS C 214 Details of bonding type rmsd/Z covalent geometry : bond 0.01319 / 0.66 (27430) covalent geometry : angle 1.33024 / 0.77 (37194) hydrogen bonds : bond 0.18718 / 12.71 ( 1148) hydrogen bonds : angle 9.00116 / 6.42 ( 3315) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6368 Ramachandran restraints generated. 3184 Oldfield, 0 Emsley, 3184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6368 Ramachandran restraints generated. 3184 Oldfield, 0 Emsley, 3184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 904 residues out of total 2762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 832 time to evaluate : 0.824 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 144 ASP cc_start: 0.8403 (m-30) cc_final: 0.8145 (m-30) REVERT: B 82 GLU cc_start: 0.7780 (tm-30) cc_final: 0.7333 (tm-30) REVERT: B 183 PHE cc_start: 0.8049 (m-10) cc_final: 0.7321 (m-10) REVERT: B 263 ASP cc_start: 0.8035 (m-30) cc_final: 0.7777 (m-30) REVERT: C 4 GLU cc_start: 0.7791 (tp30) cc_final: 0.7554 (tp30) REVERT: C 25 ASP cc_start: 0.7711 (m-30) cc_final: 0.7319 (m-30) REVERT: C 72 ILE cc_start: 0.8824 (mm) cc_final: 0.8589 (mm) REVERT: C 75 ASN cc_start: 0.8433 (m110) cc_final: 0.7985 (m-40) REVERT: C 156 LYS cc_start: 0.8526 (ttpp) cc_final: 0.8292 (tttm) REVERT: C 209 MET cc_start: 0.6932 (ptm) cc_final: 0.6680 (ptm) REVERT: D 263 ASP cc_start: 0.8616 (m-30) cc_final: 0.8264 (m-30) REVERT: E 101 TYR cc_start: 0.8044 (t80) cc_final: 0.7772 (t80) REVERT: E 167 MET cc_start: 0.8840 (mtm) cc_final: 0.8625 (mtp) REVERT: E 171 PHE cc_start: 0.8656 (m-80) cc_final: 0.8223 (m-80) REVERT: E 204 GLN cc_start: 0.8084 (tm130) cc_final: 0.7519 (tm-30) REVERT: E 233 ASN cc_start: 0.8215 (m-40) cc_final: 0.7918 (m-40) REVERT: E 241 ASP cc_start: 0.7245 (t70) cc_final: 0.6700 (t0) REVERT: F 40 LEU cc_start: 0.7679 (tp) cc_final: 0.7310 (tp) REVERT: F 72 ILE cc_start: 0.8290 (mm) cc_final: 0.6734 (mm) REVERT: F 108 ASP cc_start: 0.7638 (t0) cc_final: 0.7358 (t0) REVERT: F 137 ILE cc_start: 0.9459 (mm) cc_final: 0.9139 (mm) REVERT: F 141 MET cc_start: 0.8235 (ttm) cc_final: 0.7861 (ttt) REVERT: F 144 GLU cc_start: 0.7449 (pp20) cc_final: 0.7226 (pp20) REVERT: F 170 LYS cc_start: 0.7766 (ttmm) cc_final: 0.7555 (ttmt) REVERT: G 10 ILE cc_start: 0.8936 (OUTLIER) cc_final: 0.8735 (tp) REVERT: G 17 LEU cc_start: 0.8994 (tt) cc_final: 0.8787 (tt) REVERT: G 56 MET cc_start: 0.9012 (mmm) cc_final: 0.8738 (tmm) REVERT: G 77 TRP cc_start: 0.7854 (t60) cc_final: 0.7060 (t60) REVERT: G 105 TYR cc_start: 0.8764 (t80) cc_final: 0.7703 (t80) REVERT: G 108 GLU cc_start: 0.8156 (mm-30) cc_final: 0.7873 (mm-30) REVERT: G 111 PHE cc_start: 0.8128 (t80) cc_final: 0.7805 (t80) REVERT: G 122 PHE cc_start: 0.7259 (t80) cc_final: 0.6987 (t80) REVERT: H 11 PHE cc_start: 0.7956 (t80) cc_final: 0.7399 (t80) REVERT: H 55 GLN cc_start: 0.9201 (mm110) cc_final: 0.8994 (mm-40) REVERT: H 58 GLN cc_start: 0.8822 (tp-100) cc_final: 0.8170 (tp-100) REVERT: H 96 GLU cc_start: 0.8388 (tp30) cc_final: 0.7963 (tp30) REVERT: H 100 GLN cc_start: 0.7660 (mp-120) cc_final: 0.6897 (mm110) REVERT: H 102 MET cc_start: 0.8794 (mmp) cc_final: 0.8138 (mmp) REVERT: H 204 GLN cc_start: 0.8410 (mp10) cc_final: 0.8132 (mp10) REVERT: H 206 LEU cc_start: 0.9400 (mt) cc_final: 0.8911 (mt) REVERT: H 248 GLN cc_start: 0.7332 (mp10) cc_final: 0.6978 (tm-30) REVERT: H 267 SER cc_start: 0.8765 (p) cc_final: 0.8508 (p) REVERT: H 272 ASN cc_start: 0.9119 (t0) cc_final: 0.8903 (t0) REVERT: I 18 PHE cc_start: 0.8687 (t80) cc_final: 0.8465 (t80) REVERT: I 22 GLU cc_start: 0.8599 (tm-30) cc_final: 0.7884 (tm-30) REVERT: I 23 LYS cc_start: 0.8751 (OUTLIER) cc_final: 0.8288 (tppt) REVERT: I 84 GLU cc_start: 0.8228 (OUTLIER) cc_final: 0.7738 (tp30) REVERT: I 108 GLU cc_start: 0.8755 (mm-30) cc_final: 0.8430 (mm-30) REVERT: I 110 GLN cc_start: 0.8437 (tp40) cc_final: 0.8028 (tp40) REVERT: I 121 LEU cc_start: 0.8026 (OUTLIER) cc_final: 0.7717 (tp) REVERT: J 9 ASP cc_start: 0.8414 (t0) cc_final: 0.8106 (t0) REVERT: J 27 GLU cc_start: 0.8197 (mt-10) cc_final: 0.7896 (mt-10) REVERT: J 52 PHE cc_start: 0.8134 (m-10) cc_final: 0.7158 (m-80) REVERT: J 56 MET cc_start: 0.8807 (mmm) cc_final: 0.8168 (tmm) REVERT: J 71 ARG cc_start: 0.8025 (OUTLIER) cc_final: 0.6830 (tpp80) REVERT: J 77 TRP cc_start: 0.7756 (t60) cc_final: 0.7536 (t60) REVERT: J 105 TYR cc_start: 0.8896 (t80) cc_final: 0.8375 (t80) REVERT: J 119 LYS cc_start: 0.8736 (OUTLIER) cc_final: 0.8317 (ttpp) REVERT: J 120 ASN cc_start: 0.8065 (m110) cc_final: 0.7248 (m-40) REVERT: J 123 ASN cc_start: 0.7747 (m110) cc_final: 0.7339 (m-40) REVERT: K 16 SER cc_start: 0.7730 (t) cc_final: 0.7494 (p) REVERT: K 23 GLU cc_start: 0.6975 (tm-30) cc_final: 0.6574 (tm-30) REVERT: K 61 PHE cc_start: 0.8252 (m-10) cc_final: 0.8011 (m-10) REVERT: K 156 ASN cc_start: 0.8008 (m110) cc_final: 0.7634 (m110) REVERT: K 508 VAL cc_start: 0.8542 (m) cc_final: 0.8207 (p) REVERT: M 16 GLN cc_start: 0.7734 (mm-40) cc_final: 0.7529 (mm-40) REVERT: M 35 GLN cc_start: 0.8108 (mp10) cc_final: 0.7861 (mp10) REVERT: M 221 MET cc_start: 0.8568 (ttt) cc_final: 0.8040 (ttt) REVERT: M 263 ASP cc_start: 0.8076 (m-30) cc_final: 0.7619 (m-30) REVERT: M 277 LYS cc_start: 0.8104 (mppt) cc_final: 0.7888 (mppt) REVERT: N 68 ASN cc_start: 0.7796 (t0) cc_final: 0.7592 (t0) REVERT: N 93 MET cc_start: 0.7439 (ttp) cc_final: 0.7179 (ttp) REVERT: L 17 LEU cc_start: 0.9424 (tt) cc_final: 0.9074 (tt) REVERT: L 103 ILE cc_start: 0.7827 (tt) cc_final: 0.6517 (tt) REVERT: L 107 HIS cc_start: 0.7386 (m90) cc_final: 0.6552 (m90) outliers start: 72 outliers final: 21 residues processed: 865 average time/residue: 0.1869 time to fit residues: 257.5133 Evaluate side-chains 662 residues out of total 2762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 635 time to evaluate : 1.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 10 ILE Chi-restraints excluded: chain G residue 13 VAL Chi-restraints excluded: chain G residue 58 LEU Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 124 GLU Chi-restraints excluded: chain I residue 5 ARG Chi-restraints excluded: chain I residue 8 GLN Chi-restraints excluded: chain I residue 13 VAL Chi-restraints excluded: chain I residue 23 LYS Chi-restraints excluded: chain I residue 58 LEU Chi-restraints excluded: chain I residue 76 GLN Chi-restraints excluded: chain I residue 84 GLU Chi-restraints excluded: chain I residue 109 THR Chi-restraints excluded: chain I residue 121 LEU Chi-restraints excluded: chain I residue 124 GLU Chi-restraints excluded: chain J residue 5 ARG Chi-restraints excluded: chain J residue 10 ILE Chi-restraints excluded: chain J residue 71 ARG Chi-restraints excluded: chain J residue 73 VAL Chi-restraints excluded: chain J residue 109 THR Chi-restraints excluded: chain J residue 119 LYS Chi-restraints excluded: chain J residue 124 GLU Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 71 ARG Chi-restraints excluded: chain L residue 76 GLN Chi-restraints excluded: chain L residue 109 THR Chi-restraints excluded: chain L residue 119 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 197 optimal weight: 0.5980 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 0.7980 chunk 261 optimal weight: 0.7980 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 0.0170 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 0.8980 chunk 183 optimal weight: 0.6980 chunk 298 optimal weight: 0.7980 overall best weight: 0.5818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 153 ASN ** B 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 58 GLN ** B 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 62 HIS ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 181 HIS ** E 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 63 HIS F 233 ASN ** G 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 76 GLN ** G 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 120 ASN H 81 HIS ** H 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 220 GLN H 231 HIS H 272 ASN ** I 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 120 ASN J 8 GLN J 62 HIS ** K 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 555 GLN ** M 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 58 GLN M 74 ASN ** M 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 61 GLN ** N 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 74 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.152512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.120027 restraints weight = 46957.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.124445 restraints weight = 20701.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.127283 restraints weight = 11944.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.128989 restraints weight = 8258.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 58)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.130204 restraints weight = 6519.717| |-----------------------------------------------------------------------------| r_work (final): 0.3922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.2227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.109 27430 Z= 0.275 Angle : 0.968 15.857 37194 Z= 0.512 Chirality : 0.055 0.629 4023 Planarity : 0.008 0.131 4752 Dihedral : 15.360 175.256 4257 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 38.35 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.61 % Favored : 90.33 % Rotamer: Outliers : 2.97 % Allowed : 14.24 % Favored : 82.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.00 (0.13), residues: 3184 helix: -1.20 (0.13), residues: 1263 sheet: -2.62 (0.24), residues: 374 loop : -2.50 (0.14), residues: 1547 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG N 128 TYR 0.037 0.004 TYR L 106 PHE 0.033 0.003 PHE K 264 TRP 0.059 0.004 TRP I 77 HIS 0.018 0.002 HIS C 214 Details of bonding type rmsd/Z covalent geometry : bond 0.00618 / 0.28 (27430) covalent geometry : angle 0.96761 / 0.51 (37194) hydrogen bonds : bond 0.06476 / 4.25 ( 1148) hydrogen bonds : angle 7.50586 / 5.37 ( 3315) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6368 Ramachandran restraints generated. 3184 Oldfield, 0 Emsley, 3184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6368 Ramachandran restraints generated. 3184 Oldfield, 0 Emsley, 3184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 921 residues out of total 2762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 839 time to evaluate : 1.080 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 ASN cc_start: 0.7966 (t0) cc_final: 0.7400 (t0) REVERT: A 144 ASP cc_start: 0.8521 (m-30) cc_final: 0.8259 (m-30) REVERT: A 167 GLN cc_start: 0.8260 (tm-30) cc_final: 0.7500 (tm-30) REVERT: B 40 LEU cc_start: 0.9121 (mt) cc_final: 0.8870 (mt) REVERT: B 141 MET cc_start: 0.7057 (mmt) cc_final: 0.6716 (mmt) REVERT: B 175 TYR cc_start: 0.8609 (t80) cc_final: 0.7950 (t80) REVERT: B 183 PHE cc_start: 0.7912 (m-10) cc_final: 0.6903 (m-10) REVERT: C 4 GLU cc_start: 0.7834 (tp30) cc_final: 0.7597 (tp30) REVERT: C 48 ARG cc_start: 0.7751 (tpt90) cc_final: 0.7435 (tpt90) REVERT: C 72 ILE cc_start: 0.8822 (mm) cc_final: 0.8416 (mm) REVERT: C 75 ASN cc_start: 0.8419 (m110) cc_final: 0.8099 (m-40) REVERT: C 124 GLN cc_start: 0.7638 (mt0) cc_final: 0.7053 (mt0) REVERT: C 156 LYS cc_start: 0.8736 (ttpp) cc_final: 0.8514 (tttm) REVERT: C 175 TYR cc_start: 0.9144 (t80) cc_final: 0.8757 (t80) REVERT: C 191 GLN cc_start: 0.8099 (tt0) cc_final: 0.7792 (tt0) REVERT: C 209 MET cc_start: 0.7401 (ptm) cc_final: 0.7043 (ttp) REVERT: C 218 ARG cc_start: 0.8058 (mpt90) cc_final: 0.7795 (mpt90) REVERT: C 220 GLN cc_start: 0.7875 (tm-30) cc_final: 0.7001 (tm-30) REVERT: C 226 LEU cc_start: 0.8625 (tp) cc_final: 0.8382 (tp) REVERT: D 48 ARG cc_start: 0.7395 (mtt90) cc_final: 0.6701 (ttt90) REVERT: D 146 SER cc_start: 0.8163 (m) cc_final: 0.7843 (m) REVERT: D 244 PHE cc_start: 0.8942 (m-10) cc_final: 0.8664 (m-10) REVERT: D 260 SER cc_start: 0.9109 (p) cc_final: 0.8887 (p) REVERT: E 56 MET cc_start: 0.7831 (mtm) cc_final: 0.7516 (mtm) REVERT: E 79 GLU cc_start: 0.7561 (tm-30) cc_final: 0.7010 (tm-30) REVERT: E 101 TYR cc_start: 0.7943 (t80) cc_final: 0.7695 (t80) REVERT: E 204 GLN cc_start: 0.7686 (tm130) cc_final: 0.7229 (tm-30) REVERT: E 221 MET cc_start: 0.8135 (mtm) cc_final: 0.7726 (mtm) REVERT: E 226 LEU cc_start: 0.8882 (tp) cc_final: 0.8483 (tp) REVERT: E 233 ASN cc_start: 0.8308 (m-40) cc_final: 0.7900 (m-40) REVERT: E 241 ASP cc_start: 0.7146 (t70) cc_final: 0.6617 (t0) REVERT: F 72 ILE cc_start: 0.8130 (mm) cc_final: 0.7828 (mm) REVERT: F 108 ASP cc_start: 0.7682 (t0) cc_final: 0.7336 (t0) REVERT: F 141 MET cc_start: 0.8307 (ttm) cc_final: 0.7790 (ttt) REVERT: F 218 ARG cc_start: 0.6560 (ptp-170) cc_final: 0.6356 (ptp-110) REVERT: G 56 MET cc_start: 0.8939 (mmm) cc_final: 0.8464 (mmm) REVERT: G 77 TRP cc_start: 0.8100 (t60) cc_final: 0.7431 (t60) REVERT: G 93 LEU cc_start: 0.8391 (tp) cc_final: 0.8075 (tp) REVERT: G 97 GLN cc_start: 0.8386 (tt0) cc_final: 0.8034 (mm-40) REVERT: G 105 TYR cc_start: 0.8461 (t80) cc_final: 0.8224 (t80) REVERT: G 122 PHE cc_start: 0.7534 (t80) cc_final: 0.7122 (t80) REVERT: H 11 PHE cc_start: 0.7924 (t80) cc_final: 0.7526 (t80) REVERT: H 96 GLU cc_start: 0.8635 (tp30) cc_final: 0.8388 (tp30) REVERT: H 178 TYR cc_start: 0.6970 (m-80) cc_final: 0.6654 (m-10) REVERT: H 181 HIS cc_start: 0.7884 (m-70) cc_final: 0.7484 (m-70) REVERT: H 206 LEU cc_start: 0.9406 (mt) cc_final: 0.8995 (mt) REVERT: H 261 PHE cc_start: 0.7434 (t80) cc_final: 0.7012 (t80) REVERT: H 272 ASN cc_start: 0.8902 (OUTLIER) cc_final: 0.8523 (t0) REVERT: I 22 GLU cc_start: 0.8688 (tm-30) cc_final: 0.7936 (tm-30) REVERT: I 23 LYS cc_start: 0.8716 (tppt) cc_final: 0.8239 (tppt) REVERT: I 39 ARG cc_start: 0.8252 (mtp180) cc_final: 0.7950 (mtm180) REVERT: I 40 TYR cc_start: 0.8290 (m-80) cc_final: 0.7984 (m-80) REVERT: I 84 GLU cc_start: 0.8359 (tp30) cc_final: 0.7993 (tp30) REVERT: I 87 GLN cc_start: 0.9175 (tt0) cc_final: 0.8710 (tm-30) REVERT: I 108 GLU cc_start: 0.8690 (mm-30) cc_final: 0.8224 (mm-30) REVERT: I 121 LEU cc_start: 0.8298 (OUTLIER) cc_final: 0.8040 (tp) REVERT: J 23 LYS cc_start: 0.8768 (mmmt) cc_final: 0.8311 (tppp) REVERT: J 52 PHE cc_start: 0.8178 (m-10) cc_final: 0.7329 (m-80) REVERT: J 65 LYS cc_start: 0.8945 (mttp) cc_final: 0.8669 (mmtm) REVERT: J 77 TRP cc_start: 0.8320 (t60) cc_final: 0.8097 (t60) REVERT: J 97 GLN cc_start: 0.8127 (mm-40) cc_final: 0.7354 (mm-40) REVERT: J 105 TYR cc_start: 0.9014 (t80) cc_final: 0.8536 (t80) REVERT: J 108 GLU cc_start: 0.8445 (mm-30) cc_final: 0.8234 (mm-30) REVERT: J 120 ASN cc_start: 0.8229 (m110) cc_final: 0.7384 (m-40) REVERT: J 123 ASN cc_start: 0.7955 (m110) cc_final: 0.7742 (m-40) REVERT: K 16 SER cc_start: 0.7921 (t) cc_final: 0.7394 (p) REVERT: K 23 GLU cc_start: 0.7211 (tm-30) cc_final: 0.6715 (tm-30) REVERT: K 82 TRP cc_start: 0.8694 (p-90) cc_final: 0.8133 (p-90) REVERT: K 156 ASN cc_start: 0.7951 (m110) cc_final: 0.7702 (m110) REVERT: K 285 LEU cc_start: 0.9340 (mt) cc_final: 0.9078 (mp) REVERT: K 309 LYS cc_start: 0.8667 (tppt) cc_final: 0.8454 (ttmm) REVERT: K 392 ASN cc_start: 0.8483 (t0) cc_final: 0.8017 (t0) REVERT: K 397 LEU cc_start: 0.7473 (OUTLIER) cc_final: 0.7243 (mm) REVERT: K 403 ASP cc_start: 0.7693 (OUTLIER) cc_final: 0.7009 (t70) REVERT: M 21 ASN cc_start: 0.8160 (p0) cc_final: 0.7804 (p0) REVERT: M 102 MET cc_start: 0.5842 (mtt) cc_final: 0.5375 (mtp) REVERT: M 130 GLN cc_start: 0.7258 (OUTLIER) cc_final: 0.6744 (tt0) REVERT: M 198 ASP cc_start: 0.7611 (m-30) cc_final: 0.6891 (m-30) REVERT: M 204 GLN cc_start: 0.8383 (tm-30) cc_final: 0.8092 (tm-30) REVERT: M 212 HIS cc_start: 0.6824 (m-70) cc_final: 0.6255 (m-70) REVERT: M 221 MET cc_start: 0.8438 (ttt) cc_final: 0.7811 (ttt) REVERT: M 263 ASP cc_start: 0.8130 (m-30) cc_final: 0.7745 (m-30) REVERT: N 26 TYR cc_start: 0.8708 (m-80) cc_final: 0.8104 (m-80) REVERT: N 63 THR cc_start: 0.8838 (t) cc_final: 0.8410 (p) REVERT: N 76 GLU cc_start: 0.6817 (mm-30) cc_final: 0.6234 (mm-30) REVERT: N 151 LEU cc_start: 0.8800 (tt) cc_final: 0.8494 (tt) REVERT: N 152 LEU cc_start: 0.8429 (mp) cc_final: 0.8159 (mp) REVERT: L 56 MET cc_start: 0.7769 (mmm) cc_final: 0.7349 (mmm) REVERT: L 103 ILE cc_start: 0.8026 (tt) cc_final: 0.7727 (tt) REVERT: L 107 HIS cc_start: 0.7442 (m90) cc_final: 0.6991 (m90) outliers start: 82 outliers final: 41 residues processed: 864 average time/residue: 0.1883 time to fit residues: 259.9595 Evaluate side-chains 744 residues out of total 2762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 698 time to evaluate : 1.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 ASN Chi-restraints excluded: chain A residue 176 SER Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain C residue 167 MET Chi-restraints excluded: chain D residue 10 VAL Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain F residue 21 ASN Chi-restraints excluded: chain F residue 32 ILE Chi-restraints excluded: chain F residue 95 THR Chi-restraints excluded: chain G residue 10 ILE Chi-restraints excluded: chain G residue 13 VAL Chi-restraints excluded: chain G residue 49 ILE Chi-restraints excluded: chain G residue 88 ARG Chi-restraints excluded: chain G residue 120 ASN Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain H residue 229 PHE Chi-restraints excluded: chain H residue 272 ASN Chi-restraints excluded: chain I residue 13 VAL Chi-restraints excluded: chain I residue 20 VAL Chi-restraints excluded: chain I residue 36 ILE Chi-restraints excluded: chain I residue 57 ARG Chi-restraints excluded: chain I residue 76 GLN Chi-restraints excluded: chain I residue 120 ASN Chi-restraints excluded: chain I residue 121 LEU Chi-restraints excluded: chain J residue 10 ILE Chi-restraints excluded: chain J residue 29 ASN Chi-restraints excluded: chain J residue 95 LEU Chi-restraints excluded: chain J residue 96 GLU Chi-restraints excluded: chain K residue 198 THR Chi-restraints excluded: chain K residue 330 LEU Chi-restraints excluded: chain K residue 397 LEU Chi-restraints excluded: chain K residue 403 ASP Chi-restraints excluded: chain K residue 430 THR Chi-restraints excluded: chain K residue 512 LEU Chi-restraints excluded: chain M residue 42 THR Chi-restraints excluded: chain M residue 125 VAL Chi-restraints excluded: chain M residue 130 GLN Chi-restraints excluded: chain M residue 272 ASN Chi-restraints excluded: chain N residue 37 ILE Chi-restraints excluded: chain N residue 192 PHE Chi-restraints excluded: chain N residue 201 VAL Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 76 GLN Chi-restraints excluded: chain L residue 84 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 64 optimal weight: 0.9990 chunk 125 optimal weight: 4.9990 chunk 221 optimal weight: 3.9990 chunk 134 optimal weight: 2.9990 chunk 321 optimal weight: 8.9990 chunk 311 optimal weight: 5.9990 chunk 131 optimal weight: 0.8980 chunk 82 optimal weight: 0.9980 chunk 116 optimal weight: 5.9990 chunk 119 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 55 GLN C 62 HIS C 83 GLN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 130 GLN ** E 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 97 GLN ** G 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 272 ASN ** I 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 8 GLN ** J 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 74 ASN M 187 HIS ** M 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.149841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.117296 restraints weight = 46917.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.121692 restraints weight = 20715.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.124494 restraints weight = 11966.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 59)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.126262 restraints weight = 8303.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.127258 restraints weight = 6551.223| |-----------------------------------------------------------------------------| r_work (final): 0.3903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.2847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 27430 Z= 0.264 Angle : 0.873 11.627 37194 Z= 0.463 Chirality : 0.052 0.586 4023 Planarity : 0.006 0.080 4752 Dihedral : 15.033 179.048 4205 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 34.36 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.58 % Favored : 90.36 % Rotamer: Outliers : 3.70 % Allowed : 18.80 % Favored : 77.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.80 (0.14), residues: 3184 helix: -0.98 (0.13), residues: 1284 sheet: -2.79 (0.23), residues: 401 loop : -2.34 (0.15), residues: 1499 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 224 TYR 0.036 0.003 TYR J 106 PHE 0.043 0.003 PHE M 229 TRP 0.049 0.003 TRP I 77 HIS 0.020 0.002 HIS C 214 Details of bonding type rmsd/Z covalent geometry : bond 0.00597 / 0.26 (27430) covalent geometry : angle 0.87318 / 0.46 (37194) hydrogen bonds : bond 0.05651 / 3.72 ( 1148) hydrogen bonds : angle 7.09601 / 5.09 ( 3315) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6368 Ramachandran restraints generated. 3184 Oldfield, 0 Emsley, 3184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6368 Ramachandran restraints generated. 3184 Oldfield, 0 Emsley, 3184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 876 residues out of total 2762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 774 time to evaluate : 1.052 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 ASN cc_start: 0.8143 (t0) cc_final: 0.7539 (t0) REVERT: A 144 ASP cc_start: 0.8545 (m-30) cc_final: 0.8258 (m-30) REVERT: A 164 GLU cc_start: 0.7923 (tp30) cc_final: 0.7215 (tp30) REVERT: A 165 TRP cc_start: 0.8597 (m-10) cc_final: 0.8389 (m100) REVERT: A 167 GLN cc_start: 0.8340 (tm-30) cc_final: 0.6714 (tm-30) REVERT: A 168 TYR cc_start: 0.7556 (m-80) cc_final: 0.6785 (m-80) REVERT: B 40 LEU cc_start: 0.8928 (mt) cc_final: 0.8589 (mt) REVERT: B 110 ARG cc_start: 0.7781 (mtm-85) cc_final: 0.7567 (mtm-85) REVERT: B 130 GLN cc_start: 0.7556 (tp40) cc_final: 0.7246 (tp40) REVERT: B 175 TYR cc_start: 0.8696 (t80) cc_final: 0.7927 (t80) REVERT: B 183 PHE cc_start: 0.8302 (m-80) cc_final: 0.7620 (m-10) REVERT: C 4 GLU cc_start: 0.7495 (tp30) cc_final: 0.7181 (tp30) REVERT: C 43 ASP cc_start: 0.8154 (p0) cc_final: 0.7881 (p0) REVERT: C 110 ARG cc_start: 0.7753 (ptm160) cc_final: 0.6976 (ptm160) REVERT: C 218 ARG cc_start: 0.8286 (mpt90) cc_final: 0.7944 (mpt90) REVERT: C 220 GLN cc_start: 0.7882 (tm-30) cc_final: 0.6600 (tm-30) REVERT: C 222 ASN cc_start: 0.8323 (m110) cc_final: 0.6498 (m110) REVERT: C 226 LEU cc_start: 0.8625 (tp) cc_final: 0.8413 (tp) REVERT: D 36 THR cc_start: 0.8282 (OUTLIER) cc_final: 0.7872 (p) REVERT: D 102 MET cc_start: 0.8153 (mmt) cc_final: 0.7650 (mmt) REVERT: D 116 MET cc_start: 0.8765 (mmt) cc_final: 0.8464 (mmm) REVERT: D 134 SER cc_start: 0.8042 (p) cc_final: 0.6689 (t) REVERT: D 218 ARG cc_start: 0.7163 (mtt-85) cc_final: 0.6945 (mtt-85) REVERT: D 244 PHE cc_start: 0.8985 (m-10) cc_final: 0.8467 (m-10) REVERT: D 255 VAL cc_start: 0.8823 (t) cc_final: 0.8562 (p) REVERT: E 79 GLU cc_start: 0.7542 (tm-30) cc_final: 0.6944 (tm-30) REVERT: E 204 GLN cc_start: 0.7726 (tm130) cc_final: 0.7301 (tm-30) REVERT: E 221 MET cc_start: 0.8409 (OUTLIER) cc_final: 0.8105 (mtm) REVERT: E 226 LEU cc_start: 0.8918 (tp) cc_final: 0.8500 (tp) REVERT: E 233 ASN cc_start: 0.8234 (m-40) cc_final: 0.7833 (m-40) REVERT: E 241 ASP cc_start: 0.7040 (t70) cc_final: 0.6548 (t0) REVERT: E 265 LEU cc_start: 0.9033 (tp) cc_final: 0.8522 (pp) REVERT: F 72 ILE cc_start: 0.8313 (mm) cc_final: 0.7976 (mm) REVERT: F 108 ASP cc_start: 0.7729 (t0) cc_final: 0.7357 (t0) REVERT: F 141 MET cc_start: 0.8285 (ttm) cc_final: 0.7720 (ttt) REVERT: G 16 ARG cc_start: 0.8717 (tpt-90) cc_final: 0.8398 (tpt-90) REVERT: G 17 LEU cc_start: 0.9155 (tt) cc_final: 0.8586 (pp) REVERT: G 56 MET cc_start: 0.9010 (mmm) cc_final: 0.8807 (mmm) REVERT: G 57 ARG cc_start: 0.8452 (ttm-80) cc_final: 0.7492 (ttm110) REVERT: G 58 LEU cc_start: 0.8054 (tp) cc_final: 0.7594 (tp) REVERT: G 68 PHE cc_start: 0.7710 (t80) cc_final: 0.7421 (t80) REVERT: G 77 TRP cc_start: 0.8261 (t60) cc_final: 0.7686 (t60) REVERT: G 88 ARG cc_start: 0.8002 (OUTLIER) cc_final: 0.7115 (ttp80) REVERT: G 94 ASN cc_start: 0.8576 (p0) cc_final: 0.6943 (p0) REVERT: G 97 GLN cc_start: 0.8439 (OUTLIER) cc_final: 0.7954 (mt0) REVERT: G 98 GLN cc_start: 0.8035 (tt0) cc_final: 0.7382 (tt0) REVERT: G 108 GLU cc_start: 0.8429 (mm-30) cc_final: 0.8213 (mm-30) REVERT: G 111 PHE cc_start: 0.8135 (t80) cc_final: 0.7803 (t80) REVERT: H 11 PHE cc_start: 0.7577 (t80) cc_final: 0.7086 (t80) REVERT: H 102 MET cc_start: 0.8906 (mmm) cc_final: 0.7996 (mmm) REVERT: H 126 ARG cc_start: 0.7223 (ttt-90) cc_final: 0.6504 (ttt-90) REVERT: H 178 TYR cc_start: 0.7091 (m-80) cc_final: 0.6359 (m-10) REVERT: H 181 HIS cc_start: 0.7988 (m-70) cc_final: 0.7763 (m90) REVERT: H 206 LEU cc_start: 0.9414 (mt) cc_final: 0.8983 (mt) REVERT: H 246 ARG cc_start: 0.7281 (mmt90) cc_final: 0.6621 (mmm-85) REVERT: H 261 PHE cc_start: 0.7458 (t80) cc_final: 0.7116 (t80) REVERT: H 272 ASN cc_start: 0.8817 (OUTLIER) cc_final: 0.8319 (t0) REVERT: I 8 GLN cc_start: 0.8294 (tp40) cc_final: 0.7968 (mm110) REVERT: I 18 PHE cc_start: 0.8824 (t80) cc_final: 0.8488 (t80) REVERT: I 22 GLU cc_start: 0.8752 (tm-30) cc_final: 0.7908 (tm-30) REVERT: I 23 LYS cc_start: 0.8758 (tppt) cc_final: 0.8150 (tppt) REVERT: I 39 ARG cc_start: 0.8010 (mtp180) cc_final: 0.7641 (mtp180) REVERT: I 56 MET cc_start: 0.8822 (mmm) cc_final: 0.8354 (mmm) REVERT: I 57 ARG cc_start: 0.7833 (OUTLIER) cc_final: 0.7479 (mtt90) REVERT: I 77 TRP cc_start: 0.8388 (t60) cc_final: 0.8026 (t60) REVERT: I 81 GLN cc_start: 0.8931 (OUTLIER) cc_final: 0.8632 (mp10) REVERT: I 84 GLU cc_start: 0.8409 (tp30) cc_final: 0.8010 (tp30) REVERT: I 87 GLN cc_start: 0.9117 (tt0) cc_final: 0.8611 (tm-30) REVERT: I 88 ARG cc_start: 0.7568 (ttp80) cc_final: 0.6743 (tmm-80) REVERT: I 97 GLN cc_start: 0.8290 (pt0) cc_final: 0.8048 (pt0) REVERT: I 123 ASN cc_start: 0.8587 (m110) cc_final: 0.8345 (m110) REVERT: I 124 GLU cc_start: 0.8447 (pp20) cc_final: 0.8150 (pp20) REVERT: J 23 LYS cc_start: 0.8897 (mmmt) cc_final: 0.8662 (tppp) REVERT: J 27 GLU cc_start: 0.8075 (mt-10) cc_final: 0.7063 (mt-10) REVERT: J 52 PHE cc_start: 0.8145 (m-10) cc_final: 0.7571 (m-80) REVERT: J 65 LYS cc_start: 0.9120 (mttp) cc_final: 0.8726 (mmtm) REVERT: J 71 ARG cc_start: 0.8651 (tpt170) cc_final: 0.7749 (tpt170) REVERT: J 78 GLU cc_start: 0.8778 (tp30) cc_final: 0.8216 (tp30) REVERT: J 98 GLN cc_start: 0.8580 (tt0) cc_final: 0.8367 (tt0) REVERT: J 105 TYR cc_start: 0.8920 (t80) cc_final: 0.8484 (t80) REVERT: J 116 ASP cc_start: 0.7496 (t0) cc_final: 0.6986 (t0) REVERT: K 23 GLU cc_start: 0.7544 (tm-30) cc_final: 0.6972 (tm-30) REVERT: K 82 TRP cc_start: 0.8551 (p-90) cc_final: 0.7950 (p-90) REVERT: K 156 ASN cc_start: 0.7881 (m110) cc_final: 0.7487 (m-40) REVERT: K 250 TYR cc_start: 0.7909 (OUTLIER) cc_final: 0.6687 (p90) REVERT: K 285 LEU cc_start: 0.9308 (mt) cc_final: 0.9049 (mp) REVERT: K 309 LYS cc_start: 0.8602 (tppt) cc_final: 0.8377 (ttmm) REVERT: K 342 TRP cc_start: 0.7950 (t-100) cc_final: 0.7737 (t-100) REVERT: K 427 GLN cc_start: 0.8194 (mm-40) cc_final: 0.7950 (mm110) REVERT: M 102 MET cc_start: 0.5849 (mtt) cc_final: 0.5625 (mtt) REVERT: M 130 GLN cc_start: 0.7317 (tt0) cc_final: 0.6981 (tt0) REVERT: M 198 ASP cc_start: 0.7645 (m-30) cc_final: 0.7154 (m-30) REVERT: M 204 GLN cc_start: 0.8438 (tm-30) cc_final: 0.8134 (tm-30) REVERT: M 221 MET cc_start: 0.8351 (ttt) cc_final: 0.7930 (ttt) REVERT: M 277 LYS cc_start: 0.7942 (mppt) cc_final: 0.7641 (mppt) REVERT: N 26 TYR cc_start: 0.8540 (m-80) cc_final: 0.7897 (m-80) REVERT: N 63 THR cc_start: 0.8937 (t) cc_final: 0.8505 (p) REVERT: N 146 PRO cc_start: 0.9217 (Cg_endo) cc_final: 0.8982 (Cg_exo) REVERT: L 40 TYR cc_start: 0.8494 (m-10) cc_final: 0.7925 (m-80) REVERT: L 56 MET cc_start: 0.7794 (mmm) cc_final: 0.7388 (mmm) REVERT: L 76 GLN cc_start: 0.8689 (mp10) cc_final: 0.8423 (mm110) REVERT: L 96 GLU cc_start: 0.8140 (pm20) cc_final: 0.7872 (pm20) outliers start: 102 outliers final: 59 residues processed: 827 average time/residue: 0.1847 time to fit residues: 243.5628 Evaluate side-chains 760 residues out of total 2762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 693 time to evaluate : 0.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 153 ASN Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 167 MET Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain D residue 10 VAL Chi-restraints excluded: chain D residue 36 THR Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 48 ARG Chi-restraints excluded: chain D residue 69 GLU Chi-restraints excluded: chain E residue 134 SER Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 203 TRP Chi-restraints excluded: chain E residue 207 VAL Chi-restraints excluded: chain E residue 221 MET Chi-restraints excluded: chain F residue 21 ASN Chi-restraints excluded: chain F residue 32 ILE Chi-restraints excluded: chain F residue 40 LEU Chi-restraints excluded: chain F residue 124 GLN Chi-restraints excluded: chain G residue 10 ILE Chi-restraints excluded: chain G residue 13 VAL Chi-restraints excluded: chain G residue 49 ILE Chi-restraints excluded: chain G residue 88 ARG Chi-restraints excluded: chain G residue 97 GLN Chi-restraints excluded: chain H residue 42 THR Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain H residue 132 THR Chi-restraints excluded: chain H residue 229 PHE Chi-restraints excluded: chain H residue 253 ASP Chi-restraints excluded: chain H residue 272 ASN Chi-restraints excluded: chain H residue 276 THR Chi-restraints excluded: chain I residue 13 VAL Chi-restraints excluded: chain I residue 25 GLN Chi-restraints excluded: chain I residue 36 ILE Chi-restraints excluded: chain I residue 57 ARG Chi-restraints excluded: chain I residue 81 GLN Chi-restraints excluded: chain J residue 96 GLU Chi-restraints excluded: chain K residue 89 LEU Chi-restraints excluded: chain K residue 250 TYR Chi-restraints excluded: chain K residue 257 LEU Chi-restraints excluded: chain K residue 266 ILE Chi-restraints excluded: chain K residue 269 VAL Chi-restraints excluded: chain K residue 306 THR Chi-restraints excluded: chain K residue 330 LEU Chi-restraints excluded: chain K residue 403 ASP Chi-restraints excluded: chain K residue 430 THR Chi-restraints excluded: chain K residue 458 MET Chi-restraints excluded: chain K residue 481 ILE Chi-restraints excluded: chain K residue 512 LEU Chi-restraints excluded: chain M residue 42 THR Chi-restraints excluded: chain M residue 46 LEU Chi-restraints excluded: chain M residue 180 CYS Chi-restraints excluded: chain M residue 209 MET Chi-restraints excluded: chain M residue 272 ASN Chi-restraints excluded: chain M residue 276 THR Chi-restraints excluded: chain N residue 21 VAL Chi-restraints excluded: chain N residue 30 THR Chi-restraints excluded: chain N residue 37 ILE Chi-restraints excluded: chain N residue 70 VAL Chi-restraints excluded: chain N residue 133 GLN Chi-restraints excluded: chain N residue 159 LEU Chi-restraints excluded: chain N residue 192 PHE Chi-restraints excluded: chain N residue 201 VAL Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 84 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 107 optimal weight: 2.9990 chunk 301 optimal weight: 1.9990 chunk 170 optimal weight: 3.9990 chunk 79 optimal weight: 0.9980 chunk 139 optimal weight: 0.2980 chunk 182 optimal weight: 4.9990 chunk 186 optimal weight: 0.9990 chunk 236 optimal weight: 1.9990 chunk 209 optimal weight: 7.9990 chunk 169 optimal weight: 0.0770 chunk 259 optimal weight: 1.9990 overall best weight: 0.8742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 153 ASN ** B 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 35 GLN ** B 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 52 ASN E 63 HIS ** E 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 100 GLN ** H 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 272 ASN I 33 ASN I 62 HIS I 120 ASN J 8 GLN J 62 HIS ** J 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 74 ASN ** M 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 123 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.153819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.121010 restraints weight = 46924.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.125506 restraints weight = 20954.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 62)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.128375 restraints weight = 12141.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.130181 restraints weight = 8398.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.131202 restraints weight = 6598.556| |-----------------------------------------------------------------------------| r_work (final): 0.3934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.3299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 27430 Z= 0.228 Angle : 0.840 12.484 37194 Z= 0.441 Chirality : 0.051 0.558 4023 Planarity : 0.006 0.061 4752 Dihedral : 14.787 177.472 4195 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 32.70 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.17 % Favored : 90.80 % Rotamer: Outliers : 4.28 % Allowed : 20.58 % Favored : 75.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.67 (0.14), residues: 3184 helix: -0.85 (0.13), residues: 1284 sheet: -2.78 (0.24), residues: 383 loop : -2.28 (0.15), residues: 1517 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 224 TYR 0.030 0.003 TYR E 178 PHE 0.030 0.003 PHE A 132 TRP 0.041 0.004 TRP L 77 HIS 0.023 0.002 HIS C 214 Details of bonding type rmsd/Z covalent geometry : bond 0.00515 / 0.23 (27430) covalent geometry : angle 0.83990 / 0.44 (37194) hydrogen bonds : bond 0.05209 / 3.42 ( 1148) hydrogen bonds : angle 6.94557 / 4.99 ( 3315) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6368 Ramachandran restraints generated. 3184 Oldfield, 0 Emsley, 3184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6368 Ramachandran restraints generated. 3184 Oldfield, 0 Emsley, 3184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 881 residues out of total 2762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 763 time to evaluate : 1.146 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 PHE cc_start: 0.8222 (OUTLIER) cc_final: 0.6664 (t80) REVERT: A 126 ASN cc_start: 0.8185 (t0) cc_final: 0.7553 (t0) REVERT: A 164 GLU cc_start: 0.7948 (tp30) cc_final: 0.7540 (tp30) REVERT: A 167 GLN cc_start: 0.8412 (tm-30) cc_final: 0.7369 (tm-30) REVERT: B 102 MET cc_start: 0.7616 (OUTLIER) cc_final: 0.7235 (mtt) REVERT: B 130 GLN cc_start: 0.7491 (tp40) cc_final: 0.7225 (tp40) REVERT: B 141 MET cc_start: 0.6958 (mmt) cc_final: 0.6606 (mmt) REVERT: B 175 TYR cc_start: 0.8572 (t80) cc_final: 0.7932 (t80) REVERT: B 183 PHE cc_start: 0.8311 (m-80) cc_final: 0.7301 (m-10) REVERT: B 279 LEU cc_start: 0.8527 (tt) cc_final: 0.8308 (tt) REVERT: C 4 GLU cc_start: 0.7424 (tp30) cc_final: 0.7046 (tp30) REVERT: C 43 ASP cc_start: 0.8040 (p0) cc_final: 0.7780 (p0) REVERT: C 67 ILE cc_start: 0.8381 (OUTLIER) cc_final: 0.8055 (mm) REVERT: C 124 GLN cc_start: 0.7724 (mt0) cc_final: 0.7134 (mt0) REVERT: C 220 GLN cc_start: 0.7792 (tm-30) cc_final: 0.6392 (tm-30) REVERT: C 243 LEU cc_start: 0.7984 (mt) cc_final: 0.7643 (mt) REVERT: C 256 GLU cc_start: 0.7588 (tm-30) cc_final: 0.7205 (tm-30) REVERT: D 76 LEU cc_start: 0.8590 (mt) cc_final: 0.8368 (mt) REVERT: D 102 MET cc_start: 0.8118 (mmt) cc_final: 0.7864 (mmt) REVERT: D 144 GLU cc_start: 0.7615 (tp30) cc_final: 0.6923 (tp30) REVERT: D 150 MET cc_start: 0.6110 (ptm) cc_final: 0.5809 (ptt) REVERT: D 244 PHE cc_start: 0.8964 (m-10) cc_final: 0.8747 (m-10) REVERT: D 264 TYR cc_start: 0.8386 (m-10) cc_final: 0.8101 (m-80) REVERT: E 17 ASP cc_start: 0.8324 (t70) cc_final: 0.7383 (t0) REVERT: E 79 GLU cc_start: 0.7598 (tm-30) cc_final: 0.7175 (tm-30) REVERT: E 204 GLN cc_start: 0.7684 (tm130) cc_final: 0.7014 (tm-30) REVERT: E 221 MET cc_start: 0.8462 (OUTLIER) cc_final: 0.8245 (mtm) REVERT: E 226 LEU cc_start: 0.8825 (tp) cc_final: 0.8396 (tp) REVERT: E 233 ASN cc_start: 0.8302 (m-40) cc_final: 0.7908 (m-40) REVERT: E 241 ASP cc_start: 0.7054 (t70) cc_final: 0.6626 (t0) REVERT: E 265 LEU cc_start: 0.9035 (tp) cc_final: 0.8778 (tt) REVERT: F 72 ILE cc_start: 0.8308 (mm) cc_final: 0.7962 (mm) REVERT: F 135 ARG cc_start: 0.8602 (mmm-85) cc_final: 0.8269 (mmm-85) REVERT: F 141 MET cc_start: 0.7943 (ttm) cc_final: 0.7707 (ttp) REVERT: F 218 ARG cc_start: 0.6818 (ptp90) cc_final: 0.6587 (ptp90) REVERT: G 68 PHE cc_start: 0.7942 (t80) cc_final: 0.7677 (t80) REVERT: G 77 TRP cc_start: 0.8128 (t60) cc_final: 0.7646 (t60) REVERT: G 88 ARG cc_start: 0.8134 (OUTLIER) cc_final: 0.7181 (ttp80) REVERT: G 94 ASN cc_start: 0.8674 (p0) cc_final: 0.8239 (p0) REVERT: G 103 ILE cc_start: 0.8960 (OUTLIER) cc_final: 0.8221 (tt) REVERT: G 107 HIS cc_start: 0.8513 (m90) cc_final: 0.7962 (m90) REVERT: G 110 GLN cc_start: 0.7693 (tp-100) cc_final: 0.7244 (tp-100) REVERT: G 121 LEU cc_start: 0.8476 (mt) cc_final: 0.8181 (pp) REVERT: G 122 PHE cc_start: 0.7770 (t80) cc_final: 0.7250 (t80) REVERT: G 124 GLU cc_start: 0.8784 (OUTLIER) cc_final: 0.8510 (pm20) REVERT: H 11 PHE cc_start: 0.7540 (t80) cc_final: 0.6959 (t80) REVERT: H 56 MET cc_start: 0.8652 (ptm) cc_final: 0.8397 (ptm) REVERT: H 81 HIS cc_start: 0.8574 (OUTLIER) cc_final: 0.7955 (t-90) REVERT: H 102 MET cc_start: 0.8867 (mmm) cc_final: 0.8093 (mmm) REVERT: H 178 TYR cc_start: 0.7143 (m-80) cc_final: 0.6503 (m-10) REVERT: H 181 HIS cc_start: 0.8085 (m-70) cc_final: 0.7487 (m-70) REVERT: H 261 PHE cc_start: 0.7644 (t80) cc_final: 0.7321 (t80) REVERT: H 272 ASN cc_start: 0.8868 (OUTLIER) cc_final: 0.8469 (t0) REVERT: I 22 GLU cc_start: 0.8818 (tm-30) cc_final: 0.7967 (tm-30) REVERT: I 23 LYS cc_start: 0.8846 (tppt) cc_final: 0.8587 (tppt) REVERT: I 39 ARG cc_start: 0.8057 (mtp180) cc_final: 0.7579 (mtp180) REVERT: I 56 MET cc_start: 0.8827 (mmm) cc_final: 0.8245 (mmm) REVERT: I 77 TRP cc_start: 0.8643 (t60) cc_final: 0.7911 (t60) REVERT: I 78 GLU cc_start: 0.9372 (tp30) cc_final: 0.9077 (tp30) REVERT: I 81 GLN cc_start: 0.8975 (OUTLIER) cc_final: 0.8173 (mp10) REVERT: I 84 GLU cc_start: 0.8466 (tp30) cc_final: 0.8039 (tp30) REVERT: I 88 ARG cc_start: 0.7759 (ttp80) cc_final: 0.6948 (tmm-80) REVERT: I 96 GLU cc_start: 0.8491 (OUTLIER) cc_final: 0.7892 (pm20) REVERT: I 123 ASN cc_start: 0.8617 (m110) cc_final: 0.8270 (m-40) REVERT: J 18 PHE cc_start: 0.8670 (t80) cc_final: 0.8153 (t80) REVERT: J 23 LYS cc_start: 0.8844 (mmmt) cc_final: 0.8574 (tppp) REVERT: J 27 GLU cc_start: 0.7985 (mt-10) cc_final: 0.7751 (mt-10) REVERT: J 52 PHE cc_start: 0.8095 (m-10) cc_final: 0.7704 (m-80) REVERT: J 65 LYS cc_start: 0.8999 (mttp) cc_final: 0.8658 (mmtm) REVERT: J 71 ARG cc_start: 0.8790 (tpt170) cc_final: 0.8499 (tpt170) REVERT: J 78 GLU cc_start: 0.8888 (tp30) cc_final: 0.8400 (tp30) REVERT: J 98 GLN cc_start: 0.8618 (tt0) cc_final: 0.8290 (tp40) REVERT: J 105 TYR cc_start: 0.8840 (t80) cc_final: 0.8336 (t80) REVERT: J 120 ASN cc_start: 0.7980 (m-40) cc_final: 0.7568 (p0) REVERT: K 23 GLU cc_start: 0.7505 (tm-30) cc_final: 0.7000 (tm-30) REVERT: K 82 TRP cc_start: 0.8465 (p-90) cc_final: 0.7918 (p-90) REVERT: K 250 TYR cc_start: 0.7896 (OUTLIER) cc_final: 0.6614 (p90) REVERT: K 285 LEU cc_start: 0.9306 (mt) cc_final: 0.9068 (mp) REVERT: K 288 MET cc_start: 0.7850 (mtm) cc_final: 0.7606 (ptp) REVERT: K 299 GLU cc_start: 0.7675 (tm-30) cc_final: 0.7447 (tm-30) REVERT: K 436 LEU cc_start: 0.9066 (tp) cc_final: 0.8813 (tp) REVERT: K 503 SER cc_start: 0.8299 (m) cc_final: 0.7979 (p) REVERT: M 102 MET cc_start: 0.5965 (mtt) cc_final: 0.5764 (mtt) REVERT: M 130 GLN cc_start: 0.7233 (OUTLIER) cc_final: 0.6808 (tt0) REVERT: M 198 ASP cc_start: 0.7645 (m-30) cc_final: 0.7111 (m-30) REVERT: M 204 GLN cc_start: 0.8301 (tm-30) cc_final: 0.7945 (tm-30) REVERT: M 277 LYS cc_start: 0.7967 (mppt) cc_final: 0.7586 (mppt) REVERT: N 26 TYR cc_start: 0.8550 (m-80) cc_final: 0.7745 (m-80) REVERT: N 63 THR cc_start: 0.8968 (t) cc_final: 0.8504 (p) REVERT: N 68 ASN cc_start: 0.8141 (t0) cc_final: 0.7690 (t0) REVERT: N 100 TYR cc_start: 0.8624 (m-80) cc_final: 0.8010 (m-80) REVERT: L 17 LEU cc_start: 0.9361 (tt) cc_final: 0.8857 (pp) REVERT: L 40 TYR cc_start: 0.8726 (m-10) cc_final: 0.8212 (m-80) REVERT: L 76 GLN cc_start: 0.8709 (mp10) cc_final: 0.8398 (mm110) REVERT: L 96 GLU cc_start: 0.8054 (pm20) cc_final: 0.7765 (pm20) REVERT: L 124 GLU cc_start: 0.5965 (OUTLIER) cc_final: 0.5761 (pm20) outliers start: 118 outliers final: 68 residues processed: 825 average time/residue: 0.1898 time to fit residues: 248.6070 Evaluate side-chains 765 residues out of total 2762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 683 time to evaluate : 1.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 PHE Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 102 MET Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 109 ILE Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 133 PHE Chi-restraints excluded: chain C residue 215 SER Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain D residue 10 VAL Chi-restraints excluded: chain D residue 45 CYS Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 69 GLU Chi-restraints excluded: chain E residue 52 ASN Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 203 TRP Chi-restraints excluded: chain E residue 221 MET Chi-restraints excluded: chain F residue 21 ASN Chi-restraints excluded: chain F residue 32 ILE Chi-restraints excluded: chain F residue 40 LEU Chi-restraints excluded: chain F residue 67 ILE Chi-restraints excluded: chain F residue 124 GLN Chi-restraints excluded: chain G residue 10 ILE Chi-restraints excluded: chain G residue 13 VAL Chi-restraints excluded: chain G residue 49 ILE Chi-restraints excluded: chain G residue 88 ARG Chi-restraints excluded: chain G residue 95 LEU Chi-restraints excluded: chain G residue 103 ILE Chi-restraints excluded: chain G residue 120 ASN Chi-restraints excluded: chain G residue 124 GLU Chi-restraints excluded: chain H residue 81 HIS Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain H residue 132 THR Chi-restraints excluded: chain H residue 228 VAL Chi-restraints excluded: chain H residue 229 PHE Chi-restraints excluded: chain H residue 253 ASP Chi-restraints excluded: chain H residue 266 VAL Chi-restraints excluded: chain H residue 272 ASN Chi-restraints excluded: chain H residue 276 THR Chi-restraints excluded: chain I residue 13 VAL Chi-restraints excluded: chain I residue 20 VAL Chi-restraints excluded: chain I residue 25 GLN Chi-restraints excluded: chain I residue 57 ARG Chi-restraints excluded: chain I residue 58 LEU Chi-restraints excluded: chain I residue 81 GLN Chi-restraints excluded: chain I residue 96 GLU Chi-restraints excluded: chain K residue 89 LEU Chi-restraints excluded: chain K residue 198 THR Chi-restraints excluded: chain K residue 250 TYR Chi-restraints excluded: chain K residue 257 LEU Chi-restraints excluded: chain K residue 266 ILE Chi-restraints excluded: chain K residue 269 VAL Chi-restraints excluded: chain K residue 306 THR Chi-restraints excluded: chain K residue 330 LEU Chi-restraints excluded: chain K residue 403 ASP Chi-restraints excluded: chain K residue 430 THR Chi-restraints excluded: chain K residue 458 MET Chi-restraints excluded: chain K residue 481 ILE Chi-restraints excluded: chain M residue 42 THR Chi-restraints excluded: chain M residue 46 LEU Chi-restraints excluded: chain M residue 130 GLN Chi-restraints excluded: chain M residue 166 THR Chi-restraints excluded: chain M residue 180 CYS Chi-restraints excluded: chain M residue 209 MET Chi-restraints excluded: chain M residue 272 ASN Chi-restraints excluded: chain N residue 21 VAL Chi-restraints excluded: chain N residue 30 THR Chi-restraints excluded: chain N residue 37 ILE Chi-restraints excluded: chain N residue 70 VAL Chi-restraints excluded: chain N residue 133 GLN Chi-restraints excluded: chain N residue 159 LEU Chi-restraints excluded: chain N residue 172 LEU Chi-restraints excluded: chain N residue 192 PHE Chi-restraints excluded: chain N residue 201 VAL Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 81 GLN Chi-restraints excluded: chain L residue 84 GLU Chi-restraints excluded: chain L residue 124 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 69 optimal weight: 7.9990 chunk 243 optimal weight: 0.7980 chunk 218 optimal weight: 4.9990 chunk 253 optimal weight: 2.9990 chunk 260 optimal weight: 3.9990 chunk 64 optimal weight: 0.0170 chunk 149 optimal weight: 0.7980 chunk 183 optimal weight: 0.8980 chunk 294 optimal weight: 0.4980 chunk 266 optimal weight: 0.7980 chunk 279 optimal weight: 0.9980 overall best weight: 0.5818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 124 GLN ** C 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 120 ASN H 58 GLN ** H 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 272 ASN ** I 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 8 GLN ** J 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 74 GLN ** K 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 383 ASN ** K 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 52 ASN M 74 ASN ** M 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 166 GLN ** N 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 98 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 = 0.4227 r_free = 0.4227 target = 0.156180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.123455 restraints weight = 46603.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.127970 restraints weight = 20835.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.130836 restraints weight = 12052.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 58)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.132675 restraints weight = 8343.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.133709 restraints weight = 6546.731| |-----------------------------------------------------------------------------| r_work (final): 0.3970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.3699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.089 27430 Z= 0.208 Angle : 0.821 14.913 37194 Z= 0.431 Chirality : 0.051 0.532 4023 Planarity : 0.006 0.074 4752 Dihedral : 14.666 175.498 4195 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 31.07 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.86 % Favored : 91.11 % Rotamer: Outliers : 4.71 % Allowed : 21.38 % Favored : 73.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.56 (0.14), residues: 3184 helix: -0.74 (0.14), residues: 1282 sheet: -2.76 (0.24), residues: 374 loop : -2.25 (0.15), residues: 1528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 48 TYR 0.030 0.003 TYR E 178 PHE 0.030 0.003 PHE G 111 TRP 0.056 0.003 TRP J 77 HIS 0.021 0.002 HIS C 214 Details of bonding type rmsd/Z covalent geometry : bond 0.00475 / 0.21 (27430) covalent geometry : angle 0.82108 / 0.43 (37194) hydrogen bonds : bond 0.04961 / 3.26 ( 1148) hydrogen bonds : angle 6.82353 / 4.90 ( 3315) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6368 Ramachandran restraints generated. 3184 Oldfield, 0 Emsley, 3184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6368 Ramachandran restraints generated. 3184 Oldfield, 0 Emsley, 3184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 882 residues out of total 2762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 752 time to evaluate : 1.068 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 PHE cc_start: 0.8269 (OUTLIER) cc_final: 0.6629 (t80) REVERT: A 126 ASN cc_start: 0.7983 (t0) cc_final: 0.7329 (t0) REVERT: A 164 GLU cc_start: 0.8042 (tp30) cc_final: 0.7148 (tp30) REVERT: A 167 GLN cc_start: 0.8436 (tm-30) cc_final: 0.6699 (tm-30) REVERT: A 168 TYR cc_start: 0.7216 (m-80) cc_final: 0.6650 (m-80) REVERT: B 102 MET cc_start: 0.7604 (OUTLIER) cc_final: 0.7289 (mtt) REVERT: B 130 GLN cc_start: 0.7541 (tp40) cc_final: 0.7300 (tp40) REVERT: B 141 MET cc_start: 0.6802 (mmt) cc_final: 0.6396 (mmt) REVERT: B 175 TYR cc_start: 0.8571 (t80) cc_final: 0.7971 (t80) REVERT: B 183 PHE cc_start: 0.8252 (m-80) cc_final: 0.7371 (m-10) REVERT: B 201 LEU cc_start: 0.8224 (OUTLIER) cc_final: 0.7969 (mm) REVERT: B 241 ASP cc_start: 0.7964 (t0) cc_final: 0.7494 (t0) REVERT: C 48 ARG cc_start: 0.7599 (tpt90) cc_final: 0.7331 (tpt90) REVERT: C 67 ILE cc_start: 0.8417 (OUTLIER) cc_final: 0.8009 (mm) REVERT: C 110 ARG cc_start: 0.7544 (ptm160) cc_final: 0.7323 (ptm160) REVERT: C 124 GLN cc_start: 0.7604 (mt0) cc_final: 0.6928 (mt0) REVERT: C 146 SER cc_start: 0.7994 (t) cc_final: 0.7632 (t) REVERT: C 220 GLN cc_start: 0.7631 (tm-30) cc_final: 0.6259 (tm-30) REVERT: C 222 ASN cc_start: 0.8207 (m110) cc_final: 0.6165 (m110) REVERT: C 243 LEU cc_start: 0.8041 (OUTLIER) cc_final: 0.7684 (mt) REVERT: C 256 GLU cc_start: 0.7543 (tm-30) cc_final: 0.7094 (tm-30) REVERT: C 279 LEU cc_start: 0.8103 (OUTLIER) cc_final: 0.7903 (tp) REVERT: D 35 GLN cc_start: 0.8271 (mm-40) cc_final: 0.7752 (tp40) REVERT: D 36 THR cc_start: 0.7926 (OUTLIER) cc_final: 0.7597 (p) REVERT: E 17 ASP cc_start: 0.8339 (t70) cc_final: 0.7820 (t0) REVERT: E 79 GLU cc_start: 0.7611 (tm-30) cc_final: 0.7051 (tm-30) REVERT: E 167 MET cc_start: 0.8933 (mtm) cc_final: 0.8683 (mtp) REVERT: E 204 GLN cc_start: 0.7809 (tm130) cc_final: 0.7149 (tm-30) REVERT: E 226 LEU cc_start: 0.8660 (tp) cc_final: 0.8253 (tp) REVERT: E 233 ASN cc_start: 0.8286 (m-40) cc_final: 0.7905 (m-40) REVERT: E 241 ASP cc_start: 0.7017 (t70) cc_final: 0.6607 (t0) REVERT: E 265 LEU cc_start: 0.9020 (tp) cc_final: 0.8747 (tt) REVERT: F 40 LEU cc_start: 0.8144 (OUTLIER) cc_final: 0.7725 (tp) REVERT: F 48 ARG cc_start: 0.7283 (tpm170) cc_final: 0.6579 (tpm170) REVERT: F 49 LYS cc_start: 0.8858 (mmmt) cc_final: 0.8534 (mtpp) REVERT: F 72 ILE cc_start: 0.8313 (mm) cc_final: 0.7940 (mm) REVERT: F 115 VAL cc_start: 0.9342 (OUTLIER) cc_final: 0.8912 (m) REVERT: F 135 ARG cc_start: 0.8504 (mmm-85) cc_final: 0.8284 (tpp-160) REVERT: F 172 THR cc_start: 0.7964 (m) cc_final: 0.7058 (p) REVERT: F 209 MET cc_start: 0.6498 (tmm) cc_final: 0.6225 (tmm) REVERT: F 213 ASP cc_start: 0.7934 (OUTLIER) cc_final: 0.7212 (t70) REVERT: F 218 ARG cc_start: 0.6874 (ptp90) cc_final: 0.6655 (ptp90) REVERT: G 17 LEU cc_start: 0.9268 (tt) cc_final: 0.8653 (pp) REVERT: G 68 PHE cc_start: 0.7928 (t80) cc_final: 0.7611 (t80) REVERT: G 71 ARG cc_start: 0.8609 (mmm-85) cc_final: 0.8335 (mmm-85) REVERT: G 77 TRP cc_start: 0.8161 (t60) cc_final: 0.7887 (t60) REVERT: G 88 ARG cc_start: 0.8063 (OUTLIER) cc_final: 0.7075 (ttp80) REVERT: G 94 ASN cc_start: 0.8642 (p0) cc_final: 0.8152 (p0) REVERT: G 96 GLU cc_start: 0.8987 (pm20) cc_final: 0.8756 (pm20) REVERT: G 103 ILE cc_start: 0.8936 (OUTLIER) cc_final: 0.8063 (tt) REVERT: G 107 HIS cc_start: 0.8437 (m90) cc_final: 0.7954 (m90) REVERT: G 111 PHE cc_start: 0.8075 (t80) cc_final: 0.7630 (t80) REVERT: G 122 PHE cc_start: 0.7839 (t80) cc_final: 0.7288 (t80) REVERT: H 11 PHE cc_start: 0.7414 (t80) cc_final: 0.6866 (t80) REVERT: H 81 HIS cc_start: 0.8496 (OUTLIER) cc_final: 0.7850 (t-90) REVERT: H 102 MET cc_start: 0.8767 (mmm) cc_final: 0.7960 (mmm) REVERT: H 126 ARG cc_start: 0.6609 (ttt-90) cc_final: 0.6281 (ttt-90) REVERT: H 178 TYR cc_start: 0.6957 (m-80) cc_final: 0.6263 (m-10) REVERT: H 181 HIS cc_start: 0.7704 (m-70) cc_final: 0.7411 (m-70) REVERT: H 206 LEU cc_start: 0.9413 (mt) cc_final: 0.8991 (mt) REVERT: H 208 ASN cc_start: 0.8584 (m110) cc_final: 0.7457 (t0) REVERT: H 212 HIS cc_start: 0.7581 (t-90) cc_final: 0.6928 (t70) REVERT: H 261 PHE cc_start: 0.7640 (t80) cc_final: 0.7322 (t80) REVERT: H 272 ASN cc_start: 0.8918 (OUTLIER) cc_final: 0.8471 (t0) REVERT: I 8 GLN cc_start: 0.8188 (tp40) cc_final: 0.7949 (mm110) REVERT: I 18 PHE cc_start: 0.8722 (t80) cc_final: 0.8376 (t80) REVERT: I 21 LEU cc_start: 0.8872 (mp) cc_final: 0.8628 (mp) REVERT: I 22 GLU cc_start: 0.8870 (tm-30) cc_final: 0.8194 (tm-30) REVERT: I 23 LYS cc_start: 0.8809 (tppt) cc_final: 0.8550 (tppt) REVERT: I 56 MET cc_start: 0.8656 (mmm) cc_final: 0.8316 (mmm) REVERT: I 77 TRP cc_start: 0.8575 (t60) cc_final: 0.7831 (t60) REVERT: I 78 GLU cc_start: 0.9290 (tp30) cc_final: 0.8945 (tp30) REVERT: I 81 GLN cc_start: 0.9028 (OUTLIER) cc_final: 0.8647 (mp10) REVERT: I 84 GLU cc_start: 0.8602 (tp30) cc_final: 0.8109 (tp30) REVERT: I 96 GLU cc_start: 0.8488 (OUTLIER) cc_final: 0.7993 (pm20) REVERT: I 113 PHE cc_start: 0.8109 (m-10) cc_final: 0.7771 (m-10) REVERT: I 119 LYS cc_start: 0.9274 (ptmm) cc_final: 0.8888 (ptmm) REVERT: I 123 ASN cc_start: 0.8624 (m110) cc_final: 0.8237 (m110) REVERT: J 18 PHE cc_start: 0.8700 (t80) cc_final: 0.8076 (t80) REVERT: J 23 LYS cc_start: 0.8799 (mmmt) cc_final: 0.8599 (tppp) REVERT: J 25 GLN cc_start: 0.7886 (tt0) cc_final: 0.7507 (tt0) REVERT: J 52 PHE cc_start: 0.8031 (m-10) cc_final: 0.7772 (m-80) REVERT: J 64 ASN cc_start: 0.8002 (m110) cc_final: 0.7801 (m-40) REVERT: J 65 LYS cc_start: 0.9066 (mttp) cc_final: 0.8739 (mmtm) REVERT: J 78 GLU cc_start: 0.8887 (tp30) cc_final: 0.8474 (tp30) REVERT: J 91 ASN cc_start: 0.8568 (m-40) cc_final: 0.7996 (m-40) REVERT: J 105 TYR cc_start: 0.8879 (t80) cc_final: 0.8292 (t80) REVERT: J 115 LYS cc_start: 0.5418 (mmtt) cc_final: 0.5069 (mmtt) REVERT: K 23 GLU cc_start: 0.7471 (tm-30) cc_final: 0.6890 (tm-30) REVERT: K 82 TRP cc_start: 0.8500 (p-90) cc_final: 0.8056 (p-90) REVERT: K 156 ASN cc_start: 0.8034 (m110) cc_final: 0.7647 (m110) REVERT: K 250 TYR cc_start: 0.7894 (OUTLIER) cc_final: 0.6456 (p90) REVERT: K 281 LEU cc_start: 0.8521 (mp) cc_final: 0.8173 (mp) REVERT: K 436 LEU cc_start: 0.9041 (tp) cc_final: 0.8826 (tp) REVERT: K 453 MET cc_start: 0.6547 (mmp) cc_final: 0.6232 (mmp) REVERT: K 526 GLU cc_start: 0.7563 (mm-30) cc_final: 0.6770 (tp30) REVERT: M 16 GLN cc_start: 0.7280 (mm-40) cc_final: 0.6864 (tp40) REVERT: M 130 GLN cc_start: 0.7229 (OUTLIER) cc_final: 0.6906 (tt0) REVERT: M 198 ASP cc_start: 0.7625 (m-30) cc_final: 0.7062 (m-30) REVERT: M 204 GLN cc_start: 0.8283 (tm-30) cc_final: 0.7910 (tm-30) REVERT: M 209 MET cc_start: 0.8028 (OUTLIER) cc_final: 0.7771 (ptt) REVERT: M 277 LYS cc_start: 0.7886 (mppt) cc_final: 0.7433 (mppt) REVERT: N 7 ILE cc_start: 0.8365 (mp) cc_final: 0.8022 (mm) REVERT: N 26 TYR cc_start: 0.8408 (m-80) cc_final: 0.7486 (m-80) REVERT: N 63 THR cc_start: 0.8892 (t) cc_final: 0.8450 (p) REVERT: N 68 ASN cc_start: 0.7999 (t0) cc_final: 0.7652 (t0) REVERT: N 89 GLN cc_start: 0.8356 (OUTLIER) cc_final: 0.7878 (mt0) REVERT: N 100 TYR cc_start: 0.8531 (m-80) cc_final: 0.7980 (m-80) REVERT: L 40 TYR cc_start: 0.8839 (m-10) cc_final: 0.8035 (m-80) REVERT: L 76 GLN cc_start: 0.8726 (mp10) cc_final: 0.8384 (mm110) REVERT: L 96 GLU cc_start: 0.8267 (pm20) cc_final: 0.7934 (pm20) REVERT: L 124 GLU cc_start: 0.6174 (OUTLIER) cc_final: 0.5825 (pm20) outliers start: 130 outliers final: 66 residues processed: 821 average time/residue: 0.1687 time to fit residues: 221.3844 Evaluate side-chains 781 residues out of total 2762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 694 time to evaluate : 0.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 PHE Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 102 MET Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain C residue 32 ILE Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 109 ILE Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 133 PHE Chi-restraints excluded: chain C residue 215 SER Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 279 LEU Chi-restraints excluded: chain D residue 36 THR Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain E residue 134 SER Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 203 TRP Chi-restraints excluded: chain E residue 259 ARG Chi-restraints excluded: chain F residue 21 ASN Chi-restraints excluded: chain F residue 32 ILE Chi-restraints excluded: chain F residue 40 LEU Chi-restraints excluded: chain F residue 67 ILE Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 124 GLN Chi-restraints excluded: chain F residue 213 ASP Chi-restraints excluded: chain G residue 10 ILE Chi-restraints excluded: chain G residue 49 ILE Chi-restraints excluded: chain G residue 81 GLN Chi-restraints excluded: chain G residue 88 ARG Chi-restraints excluded: chain G residue 95 LEU Chi-restraints excluded: chain G residue 103 ILE Chi-restraints excluded: chain G residue 120 ASN Chi-restraints excluded: chain H residue 81 HIS Chi-restraints excluded: chain H residue 132 THR Chi-restraints excluded: chain H residue 187 HIS Chi-restraints excluded: chain H residue 191 GLN Chi-restraints excluded: chain H residue 228 VAL Chi-restraints excluded: chain H residue 229 PHE Chi-restraints excluded: chain H residue 253 ASP Chi-restraints excluded: chain H residue 272 ASN Chi-restraints excluded: chain H residue 276 THR Chi-restraints excluded: chain I residue 13 VAL Chi-restraints excluded: chain I residue 20 VAL Chi-restraints excluded: chain I residue 25 GLN Chi-restraints excluded: chain I residue 81 GLN Chi-restraints excluded: chain I residue 96 GLU Chi-restraints excluded: chain K residue 89 LEU Chi-restraints excluded: chain K residue 250 TYR Chi-restraints excluded: chain K residue 257 LEU Chi-restraints excluded: chain K residue 266 ILE Chi-restraints excluded: chain K residue 269 VAL Chi-restraints excluded: chain K residue 306 THR Chi-restraints excluded: chain K residue 328 LEU Chi-restraints excluded: chain K residue 330 LEU Chi-restraints excluded: chain K residue 383 ASN Chi-restraints excluded: chain K residue 403 ASP Chi-restraints excluded: chain K residue 478 LEU Chi-restraints excluded: chain K residue 518 HIS Chi-restraints excluded: chain M residue 42 THR Chi-restraints excluded: chain M residue 125 VAL Chi-restraints excluded: chain M residue 130 GLN Chi-restraints excluded: chain M residue 166 THR Chi-restraints excluded: chain M residue 209 MET Chi-restraints excluded: chain M residue 272 ASN Chi-restraints excluded: chain M residue 276 THR Chi-restraints excluded: chain N residue 21 VAL Chi-restraints excluded: chain N residue 30 THR Chi-restraints excluded: chain N residue 37 ILE Chi-restraints excluded: chain N residue 70 VAL Chi-restraints excluded: chain N residue 89 GLN Chi-restraints excluded: chain N residue 133 GLN Chi-restraints excluded: chain N residue 159 LEU Chi-restraints excluded: chain N residue 192 PHE Chi-restraints excluded: chain N residue 201 VAL Chi-restraints excluded: chain L residue 81 GLN Chi-restraints excluded: chain L residue 84 GLU Chi-restraints excluded: chain L residue 124 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 231 optimal weight: 0.6980 chunk 44 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 132 optimal weight: 0.9980 chunk 80 optimal weight: 3.9990 chunk 306 optimal weight: 8.9990 chunk 55 optimal weight: 0.8980 chunk 305 optimal weight: 0.6980 chunk 319 optimal weight: 7.9990 chunk 296 optimal weight: 0.8980 chunk 45 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 58 GLN E 75 ASN E 187 HIS ** E 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 74 GLN ** G 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 55 GLN ** H 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 272 ASN ** I 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 8 GLN ** J 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 123 ASN ** K 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 368 ASN ** K 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.156812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.123730 restraints weight = 47039.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.128275 restraints weight = 20950.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.131169 restraints weight = 12157.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 61)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.133019 restraints weight = 8451.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 56)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.134147 restraints weight = 6651.636| |-----------------------------------------------------------------------------| r_work (final): 0.3971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.3970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 27430 Z= 0.215 Angle : 0.831 17.129 37194 Z= 0.432 Chirality : 0.051 0.529 4023 Planarity : 0.006 0.065 4752 Dihedral : 14.570 174.209 4193 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 31.07 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.14 % Favored : 90.83 % Rotamer: Outliers : 4.86 % Allowed : 22.61 % Favored : 72.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.52 (0.14), residues: 3184 helix: -0.69 (0.14), residues: 1269 sheet: -2.68 (0.24), residues: 378 loop : -2.24 (0.15), residues: 1537 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG I 57 TYR 0.033 0.003 TYR J 106 PHE 0.037 0.003 PHE G 111 TRP 0.079 0.003 TRP J 77 HIS 0.024 0.002 HIS C 214 Details of bonding type rmsd/Z covalent geometry : bond 0.00489 / 0.21 (27430) covalent geometry : angle 0.83068 / 0.43 (37194) hydrogen bonds : bond 0.04873 / 3.22 ( 1148) hydrogen bonds : angle 6.72299 / 4.82 ( 3315) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6368 Ramachandran restraints generated. 3184 Oldfield, 0 Emsley, 3184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6368 Ramachandran restraints generated. 3184 Oldfield, 0 Emsley, 3184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 874 residues out of total 2762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 740 time to evaluate : 0.988 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 PHE cc_start: 0.8260 (OUTLIER) cc_final: 0.6728 (t80) REVERT: A 126 ASN cc_start: 0.7998 (t0) cc_final: 0.7238 (t0) REVERT: A 164 GLU cc_start: 0.7945 (tp30) cc_final: 0.7073 (tp30) REVERT: A 167 GLN cc_start: 0.8294 (tm-30) cc_final: 0.6551 (tm-30) REVERT: A 168 TYR cc_start: 0.7386 (m-80) cc_final: 0.6838 (m-80) REVERT: B 8 ASP cc_start: 0.8263 (OUTLIER) cc_final: 0.7651 (t0) REVERT: B 141 MET cc_start: 0.6730 (mmt) cc_final: 0.6354 (mmt) REVERT: B 175 TYR cc_start: 0.8532 (t80) cc_final: 0.8221 (t80) REVERT: B 183 PHE cc_start: 0.8226 (m-80) cc_final: 0.7694 (m-10) REVERT: B 201 LEU cc_start: 0.8253 (OUTLIER) cc_final: 0.7965 (mm) REVERT: B 241 ASP cc_start: 0.7743 (t0) cc_final: 0.7246 (t0) REVERT: C 11 PHE cc_start: 0.7667 (t80) cc_final: 0.7320 (t80) REVERT: C 67 ILE cc_start: 0.8414 (OUTLIER) cc_final: 0.7961 (mm) REVERT: C 124 GLN cc_start: 0.7650 (mt0) cc_final: 0.6998 (mt0) REVERT: C 146 SER cc_start: 0.7970 (t) cc_final: 0.7749 (t) REVERT: C 220 GLN cc_start: 0.7717 (tm-30) cc_final: 0.6448 (tm-30) REVERT: C 222 ASN cc_start: 0.8210 (m110) cc_final: 0.6054 (m110) REVERT: C 243 LEU cc_start: 0.8040 (OUTLIER) cc_final: 0.7752 (mt) REVERT: C 256 GLU cc_start: 0.7584 (tm-30) cc_final: 0.7155 (tm-30) REVERT: C 271 LYS cc_start: 0.8565 (mmmt) cc_final: 0.8306 (mmmt) REVERT: D 35 GLN cc_start: 0.8331 (mm-40) cc_final: 0.7830 (tp40) REVERT: D 36 THR cc_start: 0.7929 (OUTLIER) cc_final: 0.7625 (p) REVERT: D 54 ILE cc_start: 0.8296 (mm) cc_final: 0.7877 (pt) REVERT: D 144 GLU cc_start: 0.7502 (tp30) cc_final: 0.7275 (tp30) REVERT: E 17 ASP cc_start: 0.8372 (t70) cc_final: 0.7807 (t0) REVERT: E 79 GLU cc_start: 0.7831 (tm-30) cc_final: 0.7411 (tm-30) REVERT: E 167 MET cc_start: 0.8932 (mtm) cc_final: 0.8671 (mtp) REVERT: E 204 GLN cc_start: 0.7832 (tm130) cc_final: 0.7195 (tm-30) REVERT: E 226 LEU cc_start: 0.8656 (tp) cc_final: 0.8247 (tp) REVERT: E 233 ASN cc_start: 0.8246 (m-40) cc_final: 0.7942 (m-40) REVERT: E 241 ASP cc_start: 0.7028 (t70) cc_final: 0.6605 (t0) REVERT: F 40 LEU cc_start: 0.8148 (OUTLIER) cc_final: 0.7842 (tp) REVERT: F 72 ILE cc_start: 0.8327 (mm) cc_final: 0.7979 (mm) REVERT: F 135 ARG cc_start: 0.8471 (mmm-85) cc_final: 0.8260 (tpp-160) REVERT: F 141 MET cc_start: 0.8511 (ttp) cc_final: 0.8173 (ttt) REVERT: F 172 THR cc_start: 0.7876 (m) cc_final: 0.6886 (p) REVERT: F 213 ASP cc_start: 0.7953 (OUTLIER) cc_final: 0.7428 (t0) REVERT: G 8 GLN cc_start: 0.8452 (mm110) cc_final: 0.8069 (mm-40) REVERT: G 56 MET cc_start: 0.8740 (mmm) cc_final: 0.8457 (mmm) REVERT: G 68 PHE cc_start: 0.7922 (t80) cc_final: 0.7587 (t80) REVERT: G 88 ARG cc_start: 0.8039 (OUTLIER) cc_final: 0.6927 (ttp80) REVERT: G 94 ASN cc_start: 0.8528 (p0) cc_final: 0.8217 (p0) REVERT: G 96 GLU cc_start: 0.8907 (pm20) cc_final: 0.8604 (pm20) REVERT: G 103 ILE cc_start: 0.8670 (OUTLIER) cc_final: 0.7688 (tt) REVERT: G 110 GLN cc_start: 0.7490 (tp-100) cc_final: 0.7127 (tp-100) REVERT: G 122 PHE cc_start: 0.8020 (t80) cc_final: 0.7449 (t80) REVERT: H 11 PHE cc_start: 0.7586 (t80) cc_final: 0.6886 (t80) REVERT: H 81 HIS cc_start: 0.8436 (OUTLIER) cc_final: 0.7811 (t-90) REVERT: H 102 MET cc_start: 0.8833 (mmm) cc_final: 0.8147 (mmm) REVERT: H 126 ARG cc_start: 0.6633 (ttt-90) cc_final: 0.5686 (ttt-90) REVERT: H 178 TYR cc_start: 0.6979 (m-80) cc_final: 0.6283 (m-10) REVERT: H 181 HIS cc_start: 0.7717 (m-70) cc_final: 0.7448 (m-70) REVERT: H 206 LEU cc_start: 0.9396 (mt) cc_final: 0.8982 (mt) REVERT: H 208 ASN cc_start: 0.8602 (m110) cc_final: 0.7480 (t0) REVERT: H 212 HIS cc_start: 0.7503 (t-90) cc_final: 0.6923 (t70) REVERT: H 261 PHE cc_start: 0.7649 (t80) cc_final: 0.7362 (t80) REVERT: H 272 ASN cc_start: 0.8888 (OUTLIER) cc_final: 0.8436 (t0) REVERT: I 8 GLN cc_start: 0.8190 (tp40) cc_final: 0.7949 (mm110) REVERT: I 22 GLU cc_start: 0.8700 (tm-30) cc_final: 0.8041 (tm-30) REVERT: I 23 LYS cc_start: 0.8786 (tppt) cc_final: 0.8541 (tppt) REVERT: I 77 TRP cc_start: 0.8590 (t60) cc_final: 0.7933 (t60) REVERT: I 78 GLU cc_start: 0.9341 (tp30) cc_final: 0.9056 (tp30) REVERT: I 81 GLN cc_start: 0.9047 (OUTLIER) cc_final: 0.8481 (mp10) REVERT: I 84 GLU cc_start: 0.8598 (tp30) cc_final: 0.8124 (tp30) REVERT: I 88 ARG cc_start: 0.8039 (tmm-80) cc_final: 0.6957 (tmm-80) REVERT: I 96 GLU cc_start: 0.8539 (OUTLIER) cc_final: 0.7972 (pm20) REVERT: I 113 PHE cc_start: 0.8005 (m-10) cc_final: 0.7496 (m-10) REVERT: I 119 LYS cc_start: 0.9263 (ptmm) cc_final: 0.8864 (ptmm) REVERT: I 123 ASN cc_start: 0.8612 (m110) cc_final: 0.8196 (m110) REVERT: J 18 PHE cc_start: 0.8755 (t80) cc_final: 0.8113 (t80) REVERT: J 25 GLN cc_start: 0.7914 (tt0) cc_final: 0.7539 (tt0) REVERT: J 64 ASN cc_start: 0.7936 (m110) cc_final: 0.7693 (m-40) REVERT: J 65 LYS cc_start: 0.9087 (mttp) cc_final: 0.8742 (mmtm) REVERT: J 78 GLU cc_start: 0.8890 (tp30) cc_final: 0.8441 (tp30) REVERT: J 80 ARG cc_start: 0.8442 (mtm-85) cc_final: 0.8166 (mtm-85) REVERT: J 88 ARG cc_start: 0.7330 (OUTLIER) cc_final: 0.6814 (tpt90) REVERT: J 105 TYR cc_start: 0.8928 (t80) cc_final: 0.8387 (t80) REVERT: J 108 GLU cc_start: 0.8206 (mt-10) cc_final: 0.7873 (mt-10) REVERT: K 12 ARG cc_start: 0.8085 (mmp80) cc_final: 0.7783 (mmp80) REVERT: K 23 GLU cc_start: 0.7495 (tm-30) cc_final: 0.6880 (tm-30) REVERT: K 82 TRP cc_start: 0.8512 (p-90) cc_final: 0.7957 (p-90) REVERT: K 156 ASN cc_start: 0.8092 (m110) cc_final: 0.7464 (m-40) REVERT: K 250 TYR cc_start: 0.7898 (OUTLIER) cc_final: 0.6368 (p90) REVERT: K 281 LEU cc_start: 0.8577 (mp) cc_final: 0.8229 (mp) REVERT: K 436 LEU cc_start: 0.9080 (tp) cc_final: 0.8841 (tp) REVERT: K 453 MET cc_start: 0.6065 (mmp) cc_final: 0.5840 (mmp) REVERT: K 496 ARG cc_start: 0.7972 (OUTLIER) cc_final: 0.7671 (mtm180) REVERT: K 526 GLU cc_start: 0.7533 (mm-30) cc_final: 0.6706 (tp30) REVERT: M 130 GLN cc_start: 0.7264 (OUTLIER) cc_final: 0.6975 (tt0) REVERT: M 183 PHE cc_start: 0.8906 (m-80) cc_final: 0.8311 (m-80) REVERT: M 204 GLN cc_start: 0.8305 (tm-30) cc_final: 0.7934 (tm-30) REVERT: M 277 LYS cc_start: 0.7817 (mppt) cc_final: 0.7427 (mppt) REVERT: N 25 SER cc_start: 0.8737 (m) cc_final: 0.8456 (m) REVERT: N 26 TYR cc_start: 0.8522 (m-80) cc_final: 0.7597 (m-80) REVERT: N 68 ASN cc_start: 0.8022 (t0) cc_final: 0.7737 (t0) REVERT: N 100 TYR cc_start: 0.8555 (m-80) cc_final: 0.7980 (m-80) REVERT: N 106 PHE cc_start: 0.8654 (p90) cc_final: 0.8201 (p90) REVERT: N 133 GLN cc_start: 0.7514 (OUTLIER) cc_final: 0.6858 (mm110) REVERT: L 24 ILE cc_start: 0.8973 (mt) cc_final: 0.8715 (mt) REVERT: L 40 TYR cc_start: 0.8457 (m-10) cc_final: 0.7894 (m-80) REVERT: L 56 MET cc_start: 0.7230 (mmm) cc_final: 0.6221 (tmm) REVERT: L 76 GLN cc_start: 0.8769 (OUTLIER) cc_final: 0.8424 (mm110) REVERT: L 96 GLU cc_start: 0.8296 (pm20) cc_final: 0.8037 (pm20) outliers start: 134 outliers final: 75 residues processed: 811 average time/residue: 0.1792 time to fit residues: 231.4158 Evaluate side-chains 776 residues out of total 2762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 681 time to evaluate : 1.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 PHE Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain B residue 8 ASP Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 43 ASP Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 102 MET Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 209 MET Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain C residue 32 ILE Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 109 ILE Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 215 SER Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain D residue 36 THR Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 48 ARG Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain E residue 134 SER Chi-restraints excluded: chain E residue 143 LEU Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 203 TRP Chi-restraints excluded: chain F residue 21 ASN Chi-restraints excluded: chain F residue 32 ILE Chi-restraints excluded: chain F residue 40 LEU Chi-restraints excluded: chain F residue 67 ILE Chi-restraints excluded: chain F residue 118 THR Chi-restraints excluded: chain F residue 213 ASP Chi-restraints excluded: chain G residue 10 ILE Chi-restraints excluded: chain G residue 49 ILE Chi-restraints excluded: chain G residue 81 GLN Chi-restraints excluded: chain G residue 88 ARG Chi-restraints excluded: chain G residue 95 LEU Chi-restraints excluded: chain G residue 103 ILE Chi-restraints excluded: chain G residue 124 GLU Chi-restraints excluded: chain H residue 81 HIS Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain H residue 132 THR Chi-restraints excluded: chain H residue 187 HIS Chi-restraints excluded: chain H residue 228 VAL Chi-restraints excluded: chain H residue 229 PHE Chi-restraints excluded: chain H residue 253 ASP Chi-restraints excluded: chain H residue 266 VAL Chi-restraints excluded: chain H residue 272 ASN Chi-restraints excluded: chain H residue 276 THR Chi-restraints excluded: chain I residue 81 GLN Chi-restraints excluded: chain I residue 96 GLU Chi-restraints excluded: chain J residue 58 LEU Chi-restraints excluded: chain J residue 88 ARG Chi-restraints excluded: chain J residue 98 GLN Chi-restraints excluded: chain K residue 89 LEU Chi-restraints excluded: chain K residue 195 CYS Chi-restraints excluded: chain K residue 250 TYR Chi-restraints excluded: chain K residue 257 LEU Chi-restraints excluded: chain K residue 266 ILE Chi-restraints excluded: chain K residue 269 VAL Chi-restraints excluded: chain K residue 306 THR Chi-restraints excluded: chain K residue 330 LEU Chi-restraints excluded: chain K residue 386 LEU Chi-restraints excluded: chain K residue 403 ASP Chi-restraints excluded: chain K residue 458 MET Chi-restraints excluded: chain K residue 478 LEU Chi-restraints excluded: chain K residue 496 ARG Chi-restraints excluded: chain M residue 42 THR Chi-restraints excluded: chain M residue 46 LEU Chi-restraints excluded: chain M residue 125 VAL Chi-restraints excluded: chain M residue 130 GLN Chi-restraints excluded: chain M residue 166 THR Chi-restraints excluded: chain M residue 180 CYS Chi-restraints excluded: chain M residue 272 ASN Chi-restraints excluded: chain M residue 276 THR Chi-restraints excluded: chain N residue 21 VAL Chi-restraints excluded: chain N residue 30 THR Chi-restraints excluded: chain N residue 37 ILE Chi-restraints excluded: chain N residue 70 VAL Chi-restraints excluded: chain N residue 133 GLN Chi-restraints excluded: chain N residue 159 LEU Chi-restraints excluded: chain N residue 172 LEU Chi-restraints excluded: chain N residue 192 PHE Chi-restraints excluded: chain N residue 201 VAL Chi-restraints excluded: chain L residue 45 SER Chi-restraints excluded: chain L residue 76 GLN Chi-restraints excluded: chain L residue 81 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 8 optimal weight: 0.0980 chunk 20 optimal weight: 0.9980 chunk 238 optimal weight: 0.3980 chunk 150 optimal weight: 6.9990 chunk 88 optimal weight: 0.9990 chunk 44 optimal weight: 0.7980 chunk 104 optimal weight: 5.9990 chunk 97 optimal weight: 0.1980 chunk 156 optimal weight: 3.9990 chunk 123 optimal weight: 2.9990 chunk 203 optimal weight: 4.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 ASN ** B 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 74 GLN ** G 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 120 ASN H 272 ASN ** I 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 97 GLN I 98 GLN J 8 GLN ** J 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 137 GLN ** N 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 25 GLN ** L 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.159472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.127039 restraints weight = 46619.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.131531 restraints weight = 20801.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.134379 restraints weight = 12053.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 58)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.136225 restraints weight = 8359.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.137172 restraints weight = 6558.544| |-----------------------------------------------------------------------------| r_work (final): 0.4012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.4285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 27430 Z= 0.200 Angle : 0.841 18.040 37194 Z= 0.436 Chirality : 0.051 0.517 4023 Planarity : 0.006 0.156 4752 Dihedral : 14.521 173.099 4192 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 30.34 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.86 % Favored : 91.11 % Rotamer: Outliers : 4.31 % Allowed : 24.57 % Favored : 71.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.46 (0.14), residues: 3184 helix: -0.66 (0.14), residues: 1264 sheet: -2.67 (0.24), residues: 371 loop : -2.17 (0.15), residues: 1549 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG I 57 TYR 0.041 0.003 TYR J 106 PHE 0.045 0.003 PHE K 42 TRP 0.099 0.003 TRP J 77 HIS 0.025 0.002 HIS C 214 Details of bonding type rmsd/Z covalent geometry : bond 0.00461 / 0.20 (27430) covalent geometry : angle 0.84075 / 0.44 (37194) hydrogen bonds : bond 0.04747 / 3.13 ( 1148) hydrogen bonds : angle 6.68626 / 4.80 ( 3315) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6368 Ramachandran restraints generated. 3184 Oldfield, 0 Emsley, 3184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6368 Ramachandran restraints generated. 3184 Oldfield, 0 Emsley, 3184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 853 residues out of total 2762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 734 time to evaluate : 0.968 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 PHE cc_start: 0.7968 (OUTLIER) cc_final: 0.6565 (t80) REVERT: A 126 ASN cc_start: 0.7886 (t0) cc_final: 0.7563 (t0) REVERT: A 164 GLU cc_start: 0.7969 (tp30) cc_final: 0.7311 (tp30) REVERT: A 167 GLN cc_start: 0.8290 (tm-30) cc_final: 0.6471 (tm-30) REVERT: A 168 TYR cc_start: 0.7250 (m-80) cc_final: 0.6690 (m-80) REVERT: A 169 GLU cc_start: 0.7889 (tt0) cc_final: 0.7621 (tt0) REVERT: B 8 ASP cc_start: 0.8117 (OUTLIER) cc_final: 0.7536 (t0) REVERT: B 141 MET cc_start: 0.6567 (mmt) cc_final: 0.6128 (mmt) REVERT: B 183 PHE cc_start: 0.8168 (m-80) cc_final: 0.7860 (m-10) REVERT: B 201 LEU cc_start: 0.8226 (OUTLIER) cc_final: 0.7932 (mm) REVERT: B 241 ASP cc_start: 0.7690 (t70) cc_final: 0.7363 (t70) REVERT: C 67 ILE cc_start: 0.8440 (OUTLIER) cc_final: 0.7951 (mm) REVERT: C 124 GLN cc_start: 0.7618 (mt0) cc_final: 0.7013 (mt0) REVERT: C 146 SER cc_start: 0.7847 (t) cc_final: 0.7493 (t) REVERT: C 243 LEU cc_start: 0.8158 (OUTLIER) cc_final: 0.7869 (mt) REVERT: C 256 GLU cc_start: 0.7554 (tm-30) cc_final: 0.7169 (tm-30) REVERT: C 279 LEU cc_start: 0.7943 (OUTLIER) cc_final: 0.7708 (tp) REVERT: D 35 GLN cc_start: 0.8388 (mm-40) cc_final: 0.7916 (tp40) REVERT: D 36 THR cc_start: 0.7886 (OUTLIER) cc_final: 0.7588 (p) REVERT: D 150 MET cc_start: 0.5557 (ppp) cc_final: 0.4859 (ppp) REVERT: D 245 LYS cc_start: 0.8252 (mmtp) cc_final: 0.7915 (mmtp) REVERT: E 17 ASP cc_start: 0.7786 (t70) cc_final: 0.6692 (t0) REVERT: E 79 GLU cc_start: 0.7780 (tm-30) cc_final: 0.7359 (tm-30) REVERT: E 167 MET cc_start: 0.8793 (mtm) cc_final: 0.8547 (mtp) REVERT: E 204 GLN cc_start: 0.7865 (tm130) cc_final: 0.7275 (tm-30) REVERT: E 224 ARG cc_start: 0.7779 (tpp-160) cc_final: 0.7438 (tpp-160) REVERT: E 226 LEU cc_start: 0.8624 (tp) cc_final: 0.8295 (tp) REVERT: E 233 ASN cc_start: 0.8108 (m-40) cc_final: 0.7892 (m-40) REVERT: E 241 ASP cc_start: 0.7061 (t70) cc_final: 0.6711 (t0) REVERT: F 25 ASP cc_start: 0.7500 (OUTLIER) cc_final: 0.6479 (t0) REVERT: F 48 ARG cc_start: 0.6958 (tpm170) cc_final: 0.5942 (tpm170) REVERT: F 72 ILE cc_start: 0.8168 (mm) cc_final: 0.7825 (mm) REVERT: F 141 MET cc_start: 0.8500 (ttp) cc_final: 0.8111 (ttt) REVERT: F 172 THR cc_start: 0.7892 (m) cc_final: 0.7068 (p) REVERT: F 213 ASP cc_start: 0.7495 (OUTLIER) cc_final: 0.7230 (t0) REVERT: G 8 GLN cc_start: 0.8273 (mm110) cc_final: 0.7966 (mm-40) REVERT: G 17 LEU cc_start: 0.9162 (OUTLIER) cc_final: 0.8382 (pp) REVERT: G 57 ARG cc_start: 0.8547 (ttm110) cc_final: 0.8259 (ttm110) REVERT: G 68 PHE cc_start: 0.8131 (t80) cc_final: 0.7732 (t80) REVERT: G 88 ARG cc_start: 0.7990 (OUTLIER) cc_final: 0.6865 (ttp80) REVERT: G 94 ASN cc_start: 0.8594 (p0) cc_final: 0.8252 (p0) REVERT: G 96 GLU cc_start: 0.8908 (pm20) cc_final: 0.8547 (pm20) REVERT: G 97 GLN cc_start: 0.8686 (tt0) cc_final: 0.8198 (tp40) REVERT: G 106 TYR cc_start: 0.8427 (m-80) cc_final: 0.8025 (m-80) REVERT: G 122 PHE cc_start: 0.8099 (t80) cc_final: 0.7883 (t80) REVERT: H 11 PHE cc_start: 0.7548 (t80) cc_final: 0.6891 (t80) REVERT: H 81 HIS cc_start: 0.8490 (OUTLIER) cc_final: 0.7843 (t-90) REVERT: H 102 MET cc_start: 0.8905 (mmm) cc_final: 0.8175 (mmm) REVERT: H 178 TYR cc_start: 0.6792 (m-80) cc_final: 0.6193 (m-10) REVERT: H 206 LEU cc_start: 0.9376 (mt) cc_final: 0.8977 (mt) REVERT: H 208 ASN cc_start: 0.8602 (m110) cc_final: 0.7480 (t0) REVERT: H 212 HIS cc_start: 0.7594 (t-90) cc_final: 0.7090 (t-90) REVERT: H 261 PHE cc_start: 0.7645 (t80) cc_final: 0.7370 (t80) REVERT: H 272 ASN cc_start: 0.8889 (OUTLIER) cc_final: 0.8452 (t0) REVERT: I 17 LEU cc_start: 0.9195 (tt) cc_final: 0.8881 (tp) REVERT: I 21 LEU cc_start: 0.8742 (mp) cc_final: 0.8456 (mp) REVERT: I 22 GLU cc_start: 0.8662 (tm-30) cc_final: 0.8050 (tm-30) REVERT: I 23 LYS cc_start: 0.8775 (tppt) cc_final: 0.8486 (tppt) REVERT: I 57 ARG cc_start: 0.8229 (ttm-80) cc_final: 0.7931 (ttm-80) REVERT: I 77 TRP cc_start: 0.8528 (t60) cc_final: 0.7970 (t60) REVERT: I 78 GLU cc_start: 0.9303 (tp30) cc_final: 0.9050 (tp30) REVERT: I 81 GLN cc_start: 0.8914 (OUTLIER) cc_final: 0.8488 (mp10) REVERT: I 84 GLU cc_start: 0.8570 (tp30) cc_final: 0.8005 (tp30) REVERT: I 96 GLU cc_start: 0.8537 (OUTLIER) cc_final: 0.7949 (pm20) REVERT: I 110 GLN cc_start: 0.8113 (tp40) cc_final: 0.7906 (tp40) REVERT: I 113 PHE cc_start: 0.7961 (m-10) cc_final: 0.7407 (m-10) REVERT: I 119 LYS cc_start: 0.9228 (ptmm) cc_final: 0.8780 (ptmm) REVERT: I 123 ASN cc_start: 0.8625 (m110) cc_final: 0.8204 (m110) REVERT: J 18 PHE cc_start: 0.8780 (t80) cc_final: 0.8380 (t80) REVERT: J 25 GLN cc_start: 0.8051 (tt0) cc_final: 0.7719 (tt0) REVERT: J 64 ASN cc_start: 0.7874 (m110) cc_final: 0.7614 (m-40) REVERT: J 65 LYS cc_start: 0.9090 (mttp) cc_final: 0.8740 (mmtm) REVERT: J 88 ARG cc_start: 0.7339 (OUTLIER) cc_final: 0.6859 (tpt90) REVERT: K 12 ARG cc_start: 0.8048 (mmp80) cc_final: 0.7710 (mmp80) REVERT: K 23 GLU cc_start: 0.7401 (tm-30) cc_final: 0.6794 (tm-30) REVERT: K 69 ARG cc_start: 0.6896 (mmt180) cc_final: 0.6161 (mpt180) REVERT: K 82 TRP cc_start: 0.8420 (p-90) cc_final: 0.7845 (p-90) REVERT: K 156 ASN cc_start: 0.8057 (m110) cc_final: 0.7436 (m-40) REVERT: K 250 TYR cc_start: 0.7837 (OUTLIER) cc_final: 0.6656 (p90) REVERT: K 281 LEU cc_start: 0.8496 (mp) cc_final: 0.8234 (mp) REVERT: K 282 GLU cc_start: 0.8487 (tm-30) cc_final: 0.8164 (tm-30) REVERT: K 421 ARG cc_start: 0.8452 (ttm-80) cc_final: 0.8250 (ttm-80) REVERT: K 436 LEU cc_start: 0.9077 (tp) cc_final: 0.8816 (tp) REVERT: K 453 MET cc_start: 0.6049 (mmp) cc_final: 0.5783 (mmp) REVERT: K 496 ARG cc_start: 0.7810 (mtm180) cc_final: 0.7565 (mtm180) REVERT: K 565 GLU cc_start: 0.7954 (mm-30) cc_final: 0.7694 (mm-30) REVERT: M 16 GLN cc_start: 0.7135 (mm-40) cc_final: 0.6892 (tp40) REVERT: M 204 GLN cc_start: 0.8217 (tm-30) cc_final: 0.7760 (tm-30) REVERT: M 277 LYS cc_start: 0.7758 (mppt) cc_final: 0.7383 (mppt) REVERT: N 7 ILE cc_start: 0.8330 (mp) cc_final: 0.7886 (mm) REVERT: N 26 TYR cc_start: 0.8492 (m-80) cc_final: 0.7563 (m-80) REVERT: N 66 ARG cc_start: 0.7803 (mtp180) cc_final: 0.7529 (mtp85) REVERT: N 68 ASN cc_start: 0.7961 (t0) cc_final: 0.7712 (t0) REVERT: N 100 TYR cc_start: 0.8478 (m-80) cc_final: 0.7905 (m-80) REVERT: L 40 TYR cc_start: 0.8598 (m-10) cc_final: 0.7859 (m-80) REVERT: L 56 MET cc_start: 0.7348 (mmm) cc_final: 0.6337 (tmm) REVERT: L 96 GLU cc_start: 0.8284 (pm20) cc_final: 0.8023 (pm20) outliers start: 119 outliers final: 76 residues processed: 794 average time/residue: 0.1748 time to fit residues: 219.1767 Evaluate side-chains 788 residues out of total 2762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 695 time to evaluate : 1.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 PHE Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain B residue 8 ASP Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 43 ASP Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 102 MET Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain C residue 32 ILE Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 109 ILE Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 214 HIS Chi-restraints excluded: chain C residue 215 SER Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 279 LEU Chi-restraints excluded: chain D residue 36 THR Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 48 ARG Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 69 GLU Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 134 SER Chi-restraints excluded: chain E residue 143 LEU Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 203 TRP Chi-restraints excluded: chain E residue 259 ARG Chi-restraints excluded: chain F residue 21 ASN Chi-restraints excluded: chain F residue 25 ASP Chi-restraints excluded: chain F residue 32 ILE Chi-restraints excluded: chain F residue 40 LEU Chi-restraints excluded: chain F residue 67 ILE Chi-restraints excluded: chain F residue 124 GLN Chi-restraints excluded: chain F residue 213 ASP Chi-restraints excluded: chain G residue 10 ILE Chi-restraints excluded: chain G residue 17 LEU Chi-restraints excluded: chain G residue 49 ILE Chi-restraints excluded: chain G residue 81 GLN Chi-restraints excluded: chain G residue 88 ARG Chi-restraints excluded: chain G residue 95 LEU Chi-restraints excluded: chain G residue 120 ASN Chi-restraints excluded: chain G residue 124 GLU Chi-restraints excluded: chain H residue 81 HIS Chi-restraints excluded: chain H residue 187 HIS Chi-restraints excluded: chain H residue 228 VAL Chi-restraints excluded: chain H residue 229 PHE Chi-restraints excluded: chain H residue 253 ASP Chi-restraints excluded: chain H residue 266 VAL Chi-restraints excluded: chain H residue 272 ASN Chi-restraints excluded: chain H residue 276 THR Chi-restraints excluded: chain I residue 58 LEU Chi-restraints excluded: chain I residue 76 GLN Chi-restraints excluded: chain I residue 81 GLN Chi-restraints excluded: chain I residue 96 GLU Chi-restraints excluded: chain J residue 58 LEU Chi-restraints excluded: chain J residue 88 ARG Chi-restraints excluded: chain J residue 98 GLN Chi-restraints excluded: chain K residue 29 GLU Chi-restraints excluded: chain K residue 32 PHE Chi-restraints excluded: chain K residue 89 LEU Chi-restraints excluded: chain K residue 195 CYS Chi-restraints excluded: chain K residue 250 TYR Chi-restraints excluded: chain K residue 266 ILE Chi-restraints excluded: chain K residue 306 THR Chi-restraints excluded: chain K residue 330 LEU Chi-restraints excluded: chain K residue 403 ASP Chi-restraints excluded: chain K residue 458 MET Chi-restraints excluded: chain M residue 42 THR Chi-restraints excluded: chain M residue 125 VAL Chi-restraints excluded: chain M residue 131 LEU Chi-restraints excluded: chain M residue 166 THR Chi-restraints excluded: chain M residue 180 CYS Chi-restraints excluded: chain M residue 272 ASN Chi-restraints excluded: chain M residue 276 THR Chi-restraints excluded: chain N residue 21 VAL Chi-restraints excluded: chain N residue 30 THR Chi-restraints excluded: chain N residue 37 ILE Chi-restraints excluded: chain N residue 70 VAL Chi-restraints excluded: chain N residue 133 GLN Chi-restraints excluded: chain N residue 159 LEU Chi-restraints excluded: chain N residue 172 LEU Chi-restraints excluded: chain N residue 192 PHE Chi-restraints excluded: chain N residue 201 VAL Chi-restraints excluded: chain L residue 25 GLN Chi-restraints excluded: chain L residue 81 GLN Chi-restraints excluded: chain L residue 84 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 280 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 134 optimal weight: 3.9990 chunk 178 optimal weight: 0.8980 chunk 247 optimal weight: 1.9990 chunk 318 optimal weight: 0.4980 chunk 224 optimal weight: 0.9980 chunk 171 optimal weight: 30.0000 chunk 109 optimal weight: 5.9990 chunk 36 optimal weight: 1.9990 chunk 249 optimal weight: 0.5980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 181 HIS ** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 123 ASN H 272 ASN ** I 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 97 GLN J 8 GLN ** J 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 85 HIS ** K 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 187 HIS ** M 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 25 GLN L 98 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.157648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.124879 restraints weight = 47190.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.129393 restraints weight = 21014.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.132287 restraints weight = 12168.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.134071 restraints weight = 8423.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 62)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.135262 restraints weight = 6624.112| |-----------------------------------------------------------------------------| r_work (final): 0.3990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.4390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 27430 Z= 0.227 Angle : 0.854 18.462 37194 Z= 0.442 Chirality : 0.052 0.534 4023 Planarity : 0.006 0.147 4752 Dihedral : 14.489 173.310 4192 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 31.62 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.98 % Favored : 90.99 % Rotamer: Outliers : 4.06 % Allowed : 25.25 % Favored : 70.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.43 (0.14), residues: 3184 helix: -0.66 (0.14), residues: 1260 sheet: -2.59 (0.25), residues: 383 loop : -2.14 (0.15), residues: 1541 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG F 126 TYR 0.049 0.003 TYR A 125 PHE 0.037 0.003 PHE F 188 TRP 0.112 0.003 TRP J 77 HIS 0.023 0.002 HIS C 214 Details of bonding type rmsd/Z covalent geometry : bond 0.00526 / 0.23 (27430) covalent geometry : angle 0.85421 / 0.44 (37194) hydrogen bonds : bond 0.04759 / 3.15 ( 1148) hydrogen bonds : angle 6.63026 / 4.76 ( 3315) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6368 Ramachandran restraints generated. 3184 Oldfield, 0 Emsley, 3184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6368 Ramachandran restraints generated. 3184 Oldfield, 0 Emsley, 3184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 809 residues out of total 2762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 697 time to evaluate : 1.136 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 PHE cc_start: 0.8091 (OUTLIER) cc_final: 0.6686 (t80) REVERT: A 126 ASN cc_start: 0.7933 (t0) cc_final: 0.7606 (t0) REVERT: A 164 GLU cc_start: 0.8057 (tp30) cc_final: 0.7688 (tp30) REVERT: A 167 GLN cc_start: 0.8295 (tm-30) cc_final: 0.6374 (tm-30) REVERT: A 168 TYR cc_start: 0.7289 (m-80) cc_final: 0.6757 (m-80) REVERT: A 169 GLU cc_start: 0.7872 (tt0) cc_final: 0.7557 (tt0) REVERT: B 116 MET cc_start: 0.8253 (mmt) cc_final: 0.7935 (mtt) REVERT: B 183 PHE cc_start: 0.8289 (m-80) cc_final: 0.7792 (m-80) REVERT: B 201 LEU cc_start: 0.8217 (OUTLIER) cc_final: 0.7918 (mm) REVERT: B 241 ASP cc_start: 0.7818 (t70) cc_final: 0.7473 (t70) REVERT: C 11 PHE cc_start: 0.7814 (t80) cc_final: 0.7583 (t80) REVERT: C 67 ILE cc_start: 0.8441 (OUTLIER) cc_final: 0.7910 (mm) REVERT: C 146 SER cc_start: 0.7759 (t) cc_final: 0.7484 (t) REVERT: C 243 LEU cc_start: 0.8051 (OUTLIER) cc_final: 0.7795 (mt) REVERT: C 256 GLU cc_start: 0.7390 (tm-30) cc_final: 0.7019 (tm-30) REVERT: C 279 LEU cc_start: 0.8025 (OUTLIER) cc_final: 0.7804 (tp) REVERT: D 35 GLN cc_start: 0.8452 (mm-40) cc_final: 0.8053 (tp40) REVERT: D 36 THR cc_start: 0.7942 (OUTLIER) cc_final: 0.7641 (p) REVERT: D 144 GLU cc_start: 0.7377 (tp30) cc_final: 0.7081 (tp30) REVERT: D 150 MET cc_start: 0.5621 (ppp) cc_final: 0.4916 (ppp) REVERT: D 218 ARG cc_start: 0.7709 (OUTLIER) cc_final: 0.7407 (tpp-160) REVERT: D 245 LYS cc_start: 0.8229 (mmtp) cc_final: 0.7917 (mmtp) REVERT: E 17 ASP cc_start: 0.7759 (t70) cc_final: 0.6610 (t0) REVERT: E 79 GLU cc_start: 0.7836 (tm-30) cc_final: 0.7330 (tm-30) REVERT: E 150 MET cc_start: 0.8461 (mmm) cc_final: 0.8129 (mtm) REVERT: E 167 MET cc_start: 0.8783 (mtm) cc_final: 0.8524 (mtp) REVERT: E 204 GLN cc_start: 0.7913 (tm130) cc_final: 0.7273 (tm-30) REVERT: E 226 LEU cc_start: 0.8681 (tp) cc_final: 0.8352 (tp) REVERT: E 233 ASN cc_start: 0.8097 (m-40) cc_final: 0.7870 (m-40) REVERT: E 241 ASP cc_start: 0.7054 (t70) cc_final: 0.6735 (t0) REVERT: F 25 ASP cc_start: 0.7301 (OUTLIER) cc_final: 0.6417 (t0) REVERT: F 48 ARG cc_start: 0.6993 (tpm170) cc_final: 0.5937 (tpm170) REVERT: F 72 ILE cc_start: 0.8172 (mm) cc_final: 0.7833 (mm) REVERT: F 126 ARG cc_start: 0.7639 (mtp-110) cc_final: 0.7357 (ttt90) REVERT: F 141 MET cc_start: 0.8543 (ttp) cc_final: 0.8176 (ttt) REVERT: F 213 ASP cc_start: 0.7557 (OUTLIER) cc_final: 0.6968 (t0) REVERT: G 8 GLN cc_start: 0.8196 (mm110) cc_final: 0.7962 (mm-40) REVERT: G 57 ARG cc_start: 0.8597 (ttm110) cc_final: 0.8260 (ttm110) REVERT: G 68 PHE cc_start: 0.8146 (t80) cc_final: 0.7756 (t80) REVERT: G 71 ARG cc_start: 0.8464 (mmm-85) cc_final: 0.8164 (mmm-85) REVERT: G 88 ARG cc_start: 0.8002 (OUTLIER) cc_final: 0.6905 (ttp80) REVERT: G 94 ASN cc_start: 0.8670 (p0) cc_final: 0.8226 (p0) REVERT: G 96 GLU cc_start: 0.8917 (pm20) cc_final: 0.8511 (pm20) REVERT: G 97 GLN cc_start: 0.8529 (tt0) cc_final: 0.8089 (tp40) REVERT: G 106 TYR cc_start: 0.8501 (m-80) cc_final: 0.8139 (m-80) REVERT: G 110 GLN cc_start: 0.7593 (tp40) cc_final: 0.7323 (tp-100) REVERT: G 122 PHE cc_start: 0.8107 (t80) cc_final: 0.7834 (t80) REVERT: H 102 MET cc_start: 0.8860 (mmm) cc_final: 0.8256 (mmm) REVERT: H 178 TYR cc_start: 0.6809 (m-80) cc_final: 0.6243 (m-10) REVERT: H 190 LYS cc_start: 0.8784 (mttm) cc_final: 0.8410 (mttp) REVERT: H 206 LEU cc_start: 0.9379 (mt) cc_final: 0.8831 (tt) REVERT: H 208 ASN cc_start: 0.8689 (m110) cc_final: 0.7698 (t0) REVERT: H 261 PHE cc_start: 0.7667 (t80) cc_final: 0.7401 (t80) REVERT: H 272 ASN cc_start: 0.8918 (t160) cc_final: 0.8706 (t0) REVERT: I 18 PHE cc_start: 0.8683 (t80) cc_final: 0.8305 (t80) REVERT: I 22 GLU cc_start: 0.8739 (tm-30) cc_final: 0.8189 (tm-30) REVERT: I 23 LYS cc_start: 0.8820 (tppt) cc_final: 0.8604 (tppt) REVERT: I 77 TRP cc_start: 0.8265 (t60) cc_final: 0.8004 (t60) REVERT: I 78 GLU cc_start: 0.9232 (tp30) cc_final: 0.9002 (tp30) REVERT: I 84 GLU cc_start: 0.8547 (tp30) cc_final: 0.8027 (tp30) REVERT: I 96 GLU cc_start: 0.8555 (OUTLIER) cc_final: 0.7887 (pm20) REVERT: I 113 PHE cc_start: 0.7875 (m-10) cc_final: 0.7473 (m-10) REVERT: I 119 LYS cc_start: 0.9208 (ptmm) cc_final: 0.8752 (ptmm) REVERT: I 123 ASN cc_start: 0.8651 (m110) cc_final: 0.8234 (m110) REVERT: J 18 PHE cc_start: 0.8722 (t80) cc_final: 0.8317 (t80) REVERT: J 25 GLN cc_start: 0.7972 (tt0) cc_final: 0.7651 (tt0) REVERT: J 64 ASN cc_start: 0.7890 (m110) cc_final: 0.7577 (m-40) REVERT: J 65 LYS cc_start: 0.9125 (mttp) cc_final: 0.8765 (mmtm) REVERT: J 77 TRP cc_start: 0.7206 (t60) cc_final: 0.6851 (t60) REVERT: J 78 GLU cc_start: 0.8752 (tp30) cc_final: 0.8547 (tp30) REVERT: J 80 ARG cc_start: 0.8358 (mtm-85) cc_final: 0.8101 (mtm-85) REVERT: J 88 ARG cc_start: 0.7339 (OUTLIER) cc_final: 0.6729 (tpt90) REVERT: J 91 ASN cc_start: 0.8587 (m-40) cc_final: 0.7991 (m-40) REVERT: K 12 ARG cc_start: 0.8067 (mmp80) cc_final: 0.7720 (mmp80) REVERT: K 23 GLU cc_start: 0.7442 (tm-30) cc_final: 0.6821 (tm-30) REVERT: K 69 ARG cc_start: 0.6752 (mmt180) cc_final: 0.6118 (mpt180) REVERT: K 250 TYR cc_start: 0.7968 (OUTLIER) cc_final: 0.6534 (p90) REVERT: K 273 CYS cc_start: 0.8315 (t) cc_final: 0.8111 (m) REVERT: K 281 LEU cc_start: 0.8493 (mp) cc_final: 0.8231 (mp) REVERT: K 282 GLU cc_start: 0.8553 (tm-30) cc_final: 0.8200 (tm-30) REVERT: K 436 LEU cc_start: 0.9119 (tp) cc_final: 0.8866 (tp) REVERT: K 453 MET cc_start: 0.6151 (mmp) cc_final: 0.5836 (mmp) REVERT: K 496 ARG cc_start: 0.7845 (OUTLIER) cc_final: 0.7481 (mtm180) REVERT: K 513 MET cc_start: 0.8528 (tpp) cc_final: 0.8151 (mmm) REVERT: K 565 GLU cc_start: 0.7997 (mm-30) cc_final: 0.7761 (mm-30) REVERT: M 16 GLN cc_start: 0.7169 (mm-40) cc_final: 0.6959 (tp40) REVERT: M 150 MET cc_start: 0.6981 (mmp) cc_final: 0.6643 (mmm) REVERT: M 198 ASP cc_start: 0.7783 (m-30) cc_final: 0.7443 (m-30) REVERT: M 204 GLN cc_start: 0.8270 (tm-30) cc_final: 0.7814 (tm-30) REVERT: M 277 LYS cc_start: 0.7752 (mppt) cc_final: 0.7357 (mppt) REVERT: N 66 ARG cc_start: 0.7827 (mtp180) cc_final: 0.7480 (mtp85) REVERT: N 68 ASN cc_start: 0.8003 (t0) cc_final: 0.7773 (t0) REVERT: N 100 TYR cc_start: 0.8551 (m-80) cc_final: 0.7901 (m-80) REVERT: L 40 TYR cc_start: 0.8633 (m-10) cc_final: 0.8051 (m-80) REVERT: L 56 MET cc_start: 0.7367 (mmm) cc_final: 0.6321 (tmm) REVERT: L 76 GLN cc_start: 0.8558 (mm110) cc_final: 0.8257 (mm-40) REVERT: L 96 GLU cc_start: 0.8283 (pm20) cc_final: 0.8025 (pm20) outliers start: 112 outliers final: 79 residues processed: 755 average time/residue: 0.1851 time to fit residues: 219.9798 Evaluate side-chains 769 residues out of total 2762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 676 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 PHE Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 43 ASP Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 209 MET Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 32 ILE Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 109 ILE Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 215 SER Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 279 LEU Chi-restraints excluded: chain D residue 36 THR Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 48 ARG Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain D residue 69 GLU Chi-restraints excluded: chain D residue 209 MET Chi-restraints excluded: chain D residue 214 HIS Chi-restraints excluded: chain D residue 218 ARG Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 134 SER Chi-restraints excluded: chain E residue 143 LEU Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 203 TRP Chi-restraints excluded: chain E residue 259 ARG Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 21 ASN Chi-restraints excluded: chain F residue 25 ASP Chi-restraints excluded: chain F residue 32 ILE Chi-restraints excluded: chain F residue 40 LEU Chi-restraints excluded: chain F residue 67 ILE Chi-restraints excluded: chain F residue 118 THR Chi-restraints excluded: chain F residue 124 GLN Chi-restraints excluded: chain F residue 213 ASP Chi-restraints excluded: chain G residue 10 ILE Chi-restraints excluded: chain G residue 17 LEU Chi-restraints excluded: chain G residue 49 ILE Chi-restraints excluded: chain G residue 81 GLN Chi-restraints excluded: chain G residue 88 ARG Chi-restraints excluded: chain G residue 95 LEU Chi-restraints excluded: chain H residue 187 HIS Chi-restraints excluded: chain H residue 228 VAL Chi-restraints excluded: chain H residue 229 PHE Chi-restraints excluded: chain H residue 253 ASP Chi-restraints excluded: chain H residue 266 VAL Chi-restraints excluded: chain H residue 276 THR Chi-restraints excluded: chain I residue 58 LEU Chi-restraints excluded: chain I residue 96 GLU Chi-restraints excluded: chain J residue 58 LEU Chi-restraints excluded: chain J residue 88 ARG Chi-restraints excluded: chain J residue 98 GLN Chi-restraints excluded: chain K residue 29 GLU Chi-restraints excluded: chain K residue 32 PHE Chi-restraints excluded: chain K residue 195 CYS Chi-restraints excluded: chain K residue 250 TYR Chi-restraints excluded: chain K residue 266 ILE Chi-restraints excluded: chain K residue 269 VAL Chi-restraints excluded: chain K residue 306 THR Chi-restraints excluded: chain K residue 328 LEU Chi-restraints excluded: chain K residue 330 LEU Chi-restraints excluded: chain K residue 458 MET Chi-restraints excluded: chain K residue 496 ARG Chi-restraints excluded: chain M residue 42 THR Chi-restraints excluded: chain M residue 131 LEU Chi-restraints excluded: chain M residue 166 THR Chi-restraints excluded: chain M residue 180 CYS Chi-restraints excluded: chain M residue 272 ASN Chi-restraints excluded: chain M residue 276 THR Chi-restraints excluded: chain N residue 21 VAL Chi-restraints excluded: chain N residue 30 THR Chi-restraints excluded: chain N residue 37 ILE Chi-restraints excluded: chain N residue 70 VAL Chi-restraints excluded: chain N residue 133 GLN Chi-restraints excluded: chain N residue 159 LEU Chi-restraints excluded: chain N residue 172 LEU Chi-restraints excluded: chain N residue 192 PHE Chi-restraints excluded: chain N residue 201 VAL Chi-restraints excluded: chain L residue 25 GLN Chi-restraints excluded: chain L residue 81 GLN Chi-restraints excluded: chain L residue 84 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 0 optimal weight: 5.9990 chunk 316 optimal weight: 3.9990 chunk 229 optimal weight: 0.0060 chunk 65 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 203 optimal weight: 0.8980 chunk 172 optimal weight: 0.9980 chunk 63 optimal weight: 0.5980 chunk 16 optimal weight: 2.9990 chunk 107 optimal weight: 0.8980 chunk 56 optimal weight: 0.9990 overall best weight: 0.6796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 ASN ** B 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 97 GLN I 98 GLN J 8 GLN ** J 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 74 GLN J 85 HIS ** K 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 137 GLN ** L 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 98 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.159069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.126470 restraints weight = 46803.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.131014 restraints weight = 20836.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.133929 restraints weight = 12017.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.135742 restraints weight = 8310.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.136966 restraints weight = 6528.006| |-----------------------------------------------------------------------------| r_work (final): 0.4019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.4602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 27430 Z= 0.208 Angle : 0.870 19.295 37194 Z= 0.448 Chirality : 0.053 0.525 4023 Planarity : 0.006 0.126 4752 Dihedral : 14.485 172.481 4192 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 30.95 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.98 % Favored : 90.99 % Rotamer: Outliers : 3.88 % Allowed : 25.80 % Favored : 70.33 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.40 (0.14), residues: 3184 helix: -0.63 (0.14), residues: 1259 sheet: -2.55 (0.26), residues: 360 loop : -2.16 (0.14), residues: 1565 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG F 126 TYR 0.055 0.003 TYR A 125 PHE 0.053 0.002 PHE F 188 TRP 0.087 0.003 TRP J 77 HIS 0.022 0.002 HIS C 214 Details of bonding type rmsd/Z covalent geometry : bond 0.00483 / 0.21 (27430) covalent geometry : angle 0.87006 / 0.45 (37194) hydrogen bonds : bond 0.04764 / 3.14 ( 1148) hydrogen bonds : angle 6.60723 / 4.74 ( 3315) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6368 Ramachandran restraints generated. 3184 Oldfield, 0 Emsley, 3184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6368 Ramachandran restraints generated. 3184 Oldfield, 0 Emsley, 3184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 822 residues out of total 2762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 715 time to evaluate : 1.103 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 PHE cc_start: 0.8021 (OUTLIER) cc_final: 0.6733 (t80) REVERT: A 164 GLU cc_start: 0.8077 (tp30) cc_final: 0.7671 (tp30) REVERT: A 167 GLN cc_start: 0.8234 (tm-30) cc_final: 0.6254 (tm-30) REVERT: A 168 TYR cc_start: 0.7235 (m-80) cc_final: 0.6704 (m-80) REVERT: A 169 GLU cc_start: 0.7897 (tt0) cc_final: 0.7548 (tp30) REVERT: B 183 PHE cc_start: 0.8258 (m-80) cc_final: 0.8033 (m-10) REVERT: B 201 LEU cc_start: 0.8287 (OUTLIER) cc_final: 0.7992 (mm) REVERT: B 241 ASP cc_start: 0.7770 (t70) cc_final: 0.7157 (t0) REVERT: C 67 ILE cc_start: 0.8339 (OUTLIER) cc_final: 0.7859 (mm) REVERT: C 103 CYS cc_start: 0.8098 (m) cc_final: 0.7851 (m) REVERT: C 146 SER cc_start: 0.7486 (t) cc_final: 0.7178 (t) REVERT: C 243 LEU cc_start: 0.8210 (OUTLIER) cc_final: 0.7928 (mt) REVERT: C 256 GLU cc_start: 0.7308 (tm-30) cc_final: 0.6981 (tm-30) REVERT: C 279 LEU cc_start: 0.7968 (OUTLIER) cc_final: 0.7749 (tp) REVERT: D 35 GLN cc_start: 0.8434 (mm-40) cc_final: 0.7775 (tp-100) REVERT: D 36 THR cc_start: 0.7881 (OUTLIER) cc_final: 0.7590 (p) REVERT: D 150 MET cc_start: 0.5730 (ppp) cc_final: 0.5045 (ppp) REVERT: D 245 LYS cc_start: 0.8159 (mmtp) cc_final: 0.7774 (mmtp) REVERT: E 17 ASP cc_start: 0.7695 (t70) cc_final: 0.6553 (t0) REVERT: E 79 GLU cc_start: 0.7858 (tm-30) cc_final: 0.7587 (tm-30) REVERT: E 167 MET cc_start: 0.8713 (mtm) cc_final: 0.8425 (mtp) REVERT: E 204 GLN cc_start: 0.7846 (tm130) cc_final: 0.7267 (tm-30) REVERT: E 226 LEU cc_start: 0.8644 (tp) cc_final: 0.8306 (tp) REVERT: E 241 ASP cc_start: 0.7077 (t70) cc_final: 0.6764 (t0) REVERT: F 25 ASP cc_start: 0.7010 (OUTLIER) cc_final: 0.6603 (t70) REVERT: F 48 ARG cc_start: 0.7224 (tpm170) cc_final: 0.6216 (tpm170) REVERT: F 72 ILE cc_start: 0.8143 (mm) cc_final: 0.7814 (mm) REVERT: F 124 GLN cc_start: 0.8433 (OUTLIER) cc_final: 0.7974 (mt0) REVERT: F 141 MET cc_start: 0.8537 (ttp) cc_final: 0.8296 (ttt) REVERT: F 172 THR cc_start: 0.7870 (m) cc_final: 0.7530 (m) REVERT: G 8 GLN cc_start: 0.8291 (mm110) cc_final: 0.8078 (mm-40) REVERT: G 68 PHE cc_start: 0.8167 (t80) cc_final: 0.7765 (t80) REVERT: G 71 ARG cc_start: 0.8631 (mmm-85) cc_final: 0.8268 (mmm-85) REVERT: G 97 GLN cc_start: 0.8639 (tt0) cc_final: 0.8129 (tp40) REVERT: G 106 TYR cc_start: 0.8477 (m-80) cc_final: 0.8140 (m-80) REVERT: G 110 GLN cc_start: 0.7563 (tp40) cc_final: 0.7175 (tp-100) REVERT: H 81 HIS cc_start: 0.8425 (OUTLIER) cc_final: 0.7832 (t-90) REVERT: H 102 MET cc_start: 0.8913 (mmm) cc_final: 0.8169 (mmm) REVERT: H 178 TYR cc_start: 0.6790 (m-80) cc_final: 0.6217 (m-10) REVERT: H 208 ASN cc_start: 0.8637 (m110) cc_final: 0.7623 (t0) REVERT: H 261 PHE cc_start: 0.7758 (t80) cc_final: 0.7500 (t80) REVERT: H 272 ASN cc_start: 0.8859 (t160) cc_final: 0.8647 (t0) REVERT: I 18 PHE cc_start: 0.8694 (t80) cc_final: 0.8415 (t80) REVERT: I 22 GLU cc_start: 0.8703 (tm-30) cc_final: 0.8102 (tm-30) REVERT: I 23 LYS cc_start: 0.8846 (tppt) cc_final: 0.8599 (tppt) REVERT: I 74 GLN cc_start: 0.8536 (pt0) cc_final: 0.7724 (mt0) REVERT: I 77 TRP cc_start: 0.8310 (t60) cc_final: 0.7845 (t60) REVERT: I 78 GLU cc_start: 0.9216 (tp30) cc_final: 0.8983 (tp30) REVERT: I 81 GLN cc_start: 0.8940 (OUTLIER) cc_final: 0.8291 (mp10) REVERT: I 84 GLU cc_start: 0.8563 (tp30) cc_final: 0.7965 (tp30) REVERT: I 96 GLU cc_start: 0.8561 (OUTLIER) cc_final: 0.7894 (pm20) REVERT: I 113 PHE cc_start: 0.7859 (m-10) cc_final: 0.7442 (m-10) REVERT: I 119 LYS cc_start: 0.9212 (ptmm) cc_final: 0.8690 (ptmm) REVERT: I 123 ASN cc_start: 0.8684 (m110) cc_final: 0.8264 (m110) REVERT: J 18 PHE cc_start: 0.8725 (t80) cc_final: 0.8387 (t80) REVERT: J 25 GLN cc_start: 0.8082 (tt0) cc_final: 0.7812 (tt0) REVERT: J 64 ASN cc_start: 0.7830 (m110) cc_final: 0.7532 (m-40) REVERT: J 80 ARG cc_start: 0.8376 (mtm-85) cc_final: 0.8046 (mtm-85) REVERT: J 88 ARG cc_start: 0.7375 (OUTLIER) cc_final: 0.6964 (tmt170) REVERT: J 91 ASN cc_start: 0.8562 (m-40) cc_final: 0.8053 (m-40) REVERT: K 12 ARG cc_start: 0.8036 (mmp80) cc_final: 0.7662 (mmp80) REVERT: K 250 TYR cc_start: 0.7871 (OUTLIER) cc_final: 0.6513 (p90) REVERT: K 281 LEU cc_start: 0.8341 (mp) cc_final: 0.8081 (mp) REVERT: K 282 GLU cc_start: 0.8517 (tm-30) cc_final: 0.8232 (tm-30) REVERT: K 421 ARG cc_start: 0.8626 (ttm-80) cc_final: 0.8376 (ttm-80) REVERT: K 428 LYS cc_start: 0.8642 (ttpt) cc_final: 0.8408 (ttpp) REVERT: K 436 LEU cc_start: 0.9091 (tp) cc_final: 0.8815 (tp) REVERT: K 453 MET cc_start: 0.6245 (mmp) cc_final: 0.5941 (mmp) REVERT: K 496 ARG cc_start: 0.7831 (OUTLIER) cc_final: 0.7502 (mtm180) REVERT: M 150 MET cc_start: 0.6826 (mmp) cc_final: 0.6617 (mmm) REVERT: M 198 ASP cc_start: 0.7808 (m-30) cc_final: 0.7313 (m-30) REVERT: M 204 GLN cc_start: 0.8176 (tm-30) cc_final: 0.7687 (tm-30) REVERT: M 230 GLU cc_start: 0.7739 (tt0) cc_final: 0.7326 (tt0) REVERT: M 263 ASP cc_start: 0.7504 (m-30) cc_final: 0.7299 (m-30) REVERT: N 7 ILE cc_start: 0.8387 (mp) cc_final: 0.7940 (mm) REVERT: N 22 GLU cc_start: 0.7717 (mm-30) cc_final: 0.7125 (mm-30) REVERT: N 26 TYR cc_start: 0.8677 (m-80) cc_final: 0.7669 (m-80) REVERT: N 66 ARG cc_start: 0.7804 (mtp180) cc_final: 0.7454 (mtp85) REVERT: N 97 ASP cc_start: 0.7583 (m-30) cc_final: 0.7045 (p0) REVERT: N 100 TYR cc_start: 0.8473 (m-80) cc_final: 0.7827 (m-80) REVERT: N 133 GLN cc_start: 0.7417 (OUTLIER) cc_final: 0.6768 (mm110) REVERT: L 40 TYR cc_start: 0.8633 (m-10) cc_final: 0.8146 (m-80) REVERT: L 56 MET cc_start: 0.7370 (mmm) cc_final: 0.6329 (tmm) REVERT: L 76 GLN cc_start: 0.8613 (mm110) cc_final: 0.8310 (mm110) REVERT: L 96 GLU cc_start: 0.8281 (pm20) cc_final: 0.8049 (pm20) outliers start: 107 outliers final: 77 residues processed: 772 average time/residue: 0.1756 time to fit residues: 212.7890 Evaluate side-chains 776 residues out of total 2762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 684 time to evaluate : 0.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 PHE Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 43 ASP Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 209 MET Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain C residue 32 ILE Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 109 ILE Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 214 HIS Chi-restraints excluded: chain C residue 215 SER Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 279 LEU Chi-restraints excluded: chain D residue 36 THR Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 48 ARG Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 69 GLU Chi-restraints excluded: chain D residue 209 MET Chi-restraints excluded: chain D residue 218 ARG Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 134 SER Chi-restraints excluded: chain E residue 143 LEU Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 203 TRP Chi-restraints excluded: chain E residue 259 ARG Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 21 ASN Chi-restraints excluded: chain F residue 25 ASP Chi-restraints excluded: chain F residue 32 ILE Chi-restraints excluded: chain F residue 40 LEU Chi-restraints excluded: chain F residue 67 ILE Chi-restraints excluded: chain F residue 124 GLN Chi-restraints excluded: chain G residue 10 ILE Chi-restraints excluded: chain G residue 17 LEU Chi-restraints excluded: chain G residue 49 ILE Chi-restraints excluded: chain G residue 81 GLN Chi-restraints excluded: chain G residue 88 ARG Chi-restraints excluded: chain G residue 95 LEU Chi-restraints excluded: chain H residue 81 HIS Chi-restraints excluded: chain H residue 187 HIS Chi-restraints excluded: chain H residue 228 VAL Chi-restraints excluded: chain H residue 229 PHE Chi-restraints excluded: chain H residue 253 ASP Chi-restraints excluded: chain H residue 266 VAL Chi-restraints excluded: chain H residue 276 THR Chi-restraints excluded: chain I residue 76 GLN Chi-restraints excluded: chain I residue 81 GLN Chi-restraints excluded: chain I residue 96 GLU Chi-restraints excluded: chain J residue 58 LEU Chi-restraints excluded: chain J residue 88 ARG Chi-restraints excluded: chain J residue 98 GLN Chi-restraints excluded: chain K residue 29 GLU Chi-restraints excluded: chain K residue 32 PHE Chi-restraints excluded: chain K residue 89 LEU Chi-restraints excluded: chain K residue 195 CYS Chi-restraints excluded: chain K residue 250 TYR Chi-restraints excluded: chain K residue 266 ILE Chi-restraints excluded: chain K residue 269 VAL Chi-restraints excluded: chain K residue 306 THR Chi-restraints excluded: chain K residue 330 LEU Chi-restraints excluded: chain K residue 393 LEU Chi-restraints excluded: chain K residue 403 ASP Chi-restraints excluded: chain K residue 458 MET Chi-restraints excluded: chain K residue 496 ARG Chi-restraints excluded: chain M residue 42 THR Chi-restraints excluded: chain M residue 131 LEU Chi-restraints excluded: chain M residue 166 THR Chi-restraints excluded: chain M residue 180 CYS Chi-restraints excluded: chain M residue 276 THR Chi-restraints excluded: chain N residue 21 VAL Chi-restraints excluded: chain N residue 30 THR Chi-restraints excluded: chain N residue 37 ILE Chi-restraints excluded: chain N residue 70 VAL Chi-restraints excluded: chain N residue 133 GLN Chi-restraints excluded: chain N residue 159 LEU Chi-restraints excluded: chain N residue 171 MET Chi-restraints excluded: chain N residue 172 LEU Chi-restraints excluded: chain N residue 192 PHE Chi-restraints excluded: chain N residue 201 VAL Chi-restraints excluded: chain L residue 25 GLN Chi-restraints excluded: chain L residue 81 GLN Chi-restraints excluded: chain L residue 84 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 82 optimal weight: 0.7980 chunk 302 optimal weight: 5.9990 chunk 18 optimal weight: 0.6980 chunk 46 optimal weight: 0.8980 chunk 124 optimal weight: 7.9990 chunk 141 optimal weight: 5.9990 chunk 221 optimal weight: 5.9990 chunk 263 optimal weight: 4.9990 chunk 65 optimal weight: 1.9990 chunk 239 optimal weight: 2.9990 chunk 167 optimal weight: 9.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 130 GLN B 222 ASN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 123 ASN ** I 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 97 GLN I 98 GLN J 8 GLN ** J 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 85 HIS ** K 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 187 HIS ** M 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 272 ASN ** N 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 89 GLN ** N 194 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 = 0.4231 r_free = 0.4231 target = 0.156688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.123867 restraints weight = 47089.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.128309 restraints weight = 21179.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.131123 restraints weight = 12337.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.132955 restraints weight = 8579.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.134025 restraints weight = 6746.582| |-----------------------------------------------------------------------------| r_work (final): 0.3957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.4638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.092 27430 Z= 0.266 Angle : 0.920 20.176 37194 Z= 0.473 Chirality : 0.054 0.553 4023 Planarity : 0.006 0.109 4752 Dihedral : 14.452 171.837 4192 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 32.47 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.58 % Favored : 90.39 % Rotamer: Outliers : 3.66 % Allowed : 26.96 % Favored : 69.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.49 (0.14), residues: 3184 helix: -0.73 (0.14), residues: 1276 sheet: -2.59 (0.25), residues: 364 loop : -2.19 (0.15), residues: 1544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG F 126 TYR 0.046 0.003 TYR A 125 PHE 0.061 0.003 PHE F 188 TRP 0.147 0.004 TRP J 77 HIS 0.020 0.002 HIS C 214 Details of bonding type rmsd/Z covalent geometry : bond 0.00617 / 0.27 (27430) covalent geometry : angle 0.91967 / 0.47 (37194) hydrogen bonds : bond 0.04868 / 3.21 ( 1148) hydrogen bonds : angle 6.65135 / 4.76 ( 3315) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6368 Ramachandran restraints generated. 3184 Oldfield, 0 Emsley, 3184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6368 Ramachandran restraints generated. 3184 Oldfield, 0 Emsley, 3184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 796 residues out of total 2762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 695 time to evaluate : 0.973 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 PHE cc_start: 0.7998 (OUTLIER) cc_final: 0.6678 (t80) REVERT: A 164 GLU cc_start: 0.8074 (tp30) cc_final: 0.7776 (tp30) REVERT: A 167 GLN cc_start: 0.8277 (tm-30) cc_final: 0.6546 (tm-30) REVERT: A 168 TYR cc_start: 0.7353 (m-80) cc_final: 0.6899 (m-80) REVERT: B 124 GLN cc_start: 0.7412 (mp10) cc_final: 0.6874 (mp10) REVERT: B 175 TYR cc_start: 0.8341 (t80) cc_final: 0.8100 (t80) REVERT: B 201 LEU cc_start: 0.8299 (OUTLIER) cc_final: 0.7985 (mm) REVERT: B 241 ASP cc_start: 0.7831 (t70) cc_final: 0.7238 (t0) REVERT: B 259 ARG cc_start: 0.7858 (mtp180) cc_final: 0.7603 (mtp180) REVERT: C 67 ILE cc_start: 0.8410 (OUTLIER) cc_final: 0.7970 (mm) REVERT: C 91 LYS cc_start: 0.8598 (ttmt) cc_final: 0.8355 (mmmt) REVERT: C 103 CYS cc_start: 0.8320 (m) cc_final: 0.7964 (m) REVERT: C 110 ARG cc_start: 0.7573 (ptm160) cc_final: 0.6960 (ptm160) REVERT: C 146 SER cc_start: 0.7627 (t) cc_final: 0.7318 (t) REVERT: C 256 GLU cc_start: 0.7302 (tm-30) cc_final: 0.7018 (tm-30) REVERT: D 35 GLN cc_start: 0.8505 (mm-40) cc_final: 0.7865 (tp-100) REVERT: D 36 THR cc_start: 0.8074 (OUTLIER) cc_final: 0.7720 (p) REVERT: D 143 LEU cc_start: 0.8773 (mt) cc_final: 0.8523 (mt) REVERT: D 144 GLU cc_start: 0.7589 (tp30) cc_final: 0.7325 (tp30) REVERT: D 150 MET cc_start: 0.5961 (ppp) cc_final: 0.5029 (ppp) REVERT: D 245 LYS cc_start: 0.8093 (mmtp) cc_final: 0.7680 (mmtp) REVERT: E 17 ASP cc_start: 0.7775 (t70) cc_final: 0.6622 (t0) REVERT: E 79 GLU cc_start: 0.7857 (tm-30) cc_final: 0.7460 (tm-30) REVERT: E 178 TYR cc_start: 0.8107 (m-80) cc_final: 0.7635 (m-10) REVERT: E 204 GLN cc_start: 0.7912 (tm130) cc_final: 0.7306 (tm-30) REVERT: E 226 LEU cc_start: 0.8695 (tp) cc_final: 0.8340 (tp) REVERT: E 241 ASP cc_start: 0.7109 (t70) cc_final: 0.6811 (t0) REVERT: F 25 ASP cc_start: 0.7067 (OUTLIER) cc_final: 0.6571 (t70) REVERT: F 48 ARG cc_start: 0.6973 (tpm170) cc_final: 0.5839 (tpm170) REVERT: F 72 ILE cc_start: 0.8206 (mm) cc_final: 0.7862 (mm) REVERT: F 102 MET cc_start: 0.8793 (mmm) cc_final: 0.7877 (mpp) REVERT: F 141 MET cc_start: 0.8539 (ttp) cc_final: 0.8299 (ttt) REVERT: G 8 GLN cc_start: 0.8294 (mm110) cc_final: 0.8078 (mm-40) REVERT: G 16 ARG cc_start: 0.8761 (ttt180) cc_final: 0.7412 (ttt-90) REVERT: G 68 PHE cc_start: 0.8213 (t80) cc_final: 0.7797 (t80) REVERT: G 71 ARG cc_start: 0.8799 (mmm-85) cc_final: 0.8456 (mmm-85) REVERT: G 106 TYR cc_start: 0.8534 (m-80) cc_final: 0.8132 (m-80) REVERT: G 110 GLN cc_start: 0.7635 (tp40) cc_final: 0.7371 (tp-100) REVERT: G 122 PHE cc_start: 0.8087 (t80) cc_final: 0.7656 (t80) REVERT: H 102 MET cc_start: 0.8872 (mmm) cc_final: 0.8384 (mmm) REVERT: H 178 TYR cc_start: 0.6739 (m-80) cc_final: 0.6283 (m-10) REVERT: H 208 ASN cc_start: 0.8668 (m110) cc_final: 0.7639 (t0) REVERT: H 261 PHE cc_start: 0.7886 (t80) cc_final: 0.7625 (t80) REVERT: I 18 PHE cc_start: 0.8726 (t80) cc_final: 0.8507 (t80) REVERT: I 22 GLU cc_start: 0.8709 (tm-30) cc_final: 0.8154 (tm-30) REVERT: I 23 LYS cc_start: 0.8954 (tppt) cc_final: 0.8636 (tppt) REVERT: I 74 GLN cc_start: 0.8678 (pt0) cc_final: 0.7695 (mt0) REVERT: I 77 TRP cc_start: 0.8359 (t60) cc_final: 0.7936 (t60) REVERT: I 78 GLU cc_start: 0.9245 (tp30) cc_final: 0.8988 (tp30) REVERT: I 81 GLN cc_start: 0.8916 (OUTLIER) cc_final: 0.8461 (mp10) REVERT: I 84 GLU cc_start: 0.8553 (tp30) cc_final: 0.8079 (tp30) REVERT: I 96 GLU cc_start: 0.8502 (OUTLIER) cc_final: 0.7873 (pm20) REVERT: I 113 PHE cc_start: 0.7892 (m-10) cc_final: 0.7468 (m-10) REVERT: I 119 LYS cc_start: 0.9161 (ptmm) cc_final: 0.8653 (ptmm) REVERT: I 123 ASN cc_start: 0.8738 (m110) cc_final: 0.8323 (m110) REVERT: J 18 PHE cc_start: 0.8767 (t80) cc_final: 0.8424 (t80) REVERT: J 25 GLN cc_start: 0.8134 (tt0) cc_final: 0.7833 (tt0) REVERT: J 64 ASN cc_start: 0.7977 (m110) cc_final: 0.7630 (m-40) REVERT: J 65 LYS cc_start: 0.9087 (mttt) cc_final: 0.8680 (mmtm) REVERT: J 80 ARG cc_start: 0.8369 (mtm-85) cc_final: 0.8077 (mtm-85) REVERT: J 88 ARG cc_start: 0.7583 (OUTLIER) cc_final: 0.7128 (tmt170) REVERT: J 91 ASN cc_start: 0.8581 (m-40) cc_final: 0.8067 (m-40) REVERT: J 108 GLU cc_start: 0.8598 (mt-10) cc_final: 0.8003 (mt-10) REVERT: K 12 ARG cc_start: 0.8060 (mmp80) cc_final: 0.7699 (mmp80) REVERT: K 250 TYR cc_start: 0.7940 (OUTLIER) cc_final: 0.6471 (p90) REVERT: K 281 LEU cc_start: 0.8355 (mp) cc_final: 0.8072 (mp) REVERT: K 282 GLU cc_start: 0.8646 (tm-30) cc_final: 0.8259 (tm-30) REVERT: K 428 LYS cc_start: 0.8653 (ttpt) cc_final: 0.8392 (ttpp) REVERT: K 436 LEU cc_start: 0.9107 (tp) cc_final: 0.8776 (tp) REVERT: K 453 MET cc_start: 0.6225 (mmp) cc_final: 0.5886 (mmp) REVERT: K 496 ARG cc_start: 0.7773 (OUTLIER) cc_final: 0.7419 (mtm180) REVERT: K 534 TRP cc_start: 0.9068 (t60) cc_final: 0.8634 (t60) REVERT: M 16 GLN cc_start: 0.7533 (mm-40) cc_final: 0.7254 (tp40) REVERT: M 102 MET cc_start: 0.5988 (mtp) cc_final: 0.5754 (mtp) REVERT: M 150 MET cc_start: 0.7005 (mmp) cc_final: 0.6743 (mmm) REVERT: M 198 ASP cc_start: 0.7832 (m-30) cc_final: 0.7368 (m-30) REVERT: M 204 GLN cc_start: 0.8258 (tm-30) cc_final: 0.7716 (tm-30) REVERT: M 259 ARG cc_start: 0.7368 (mtm110) cc_final: 0.7077 (mtm110) REVERT: N 7 ILE cc_start: 0.8435 (mp) cc_final: 0.8017 (mm) REVERT: N 22 GLU cc_start: 0.7785 (mm-30) cc_final: 0.7378 (mm-30) REVERT: N 66 ARG cc_start: 0.7910 (mtp180) cc_final: 0.7643 (mtp85) REVERT: N 133 GLN cc_start: 0.7501 (OUTLIER) cc_final: 0.6790 (mm110) REVERT: L 40 TYR cc_start: 0.8703 (m-10) cc_final: 0.8202 (m-80) REVERT: L 56 MET cc_start: 0.7430 (mmm) cc_final: 0.6433 (tmm) REVERT: L 76 GLN cc_start: 0.8510 (mm110) cc_final: 0.8221 (mm110) REVERT: L 96 GLU cc_start: 0.8289 (pm20) cc_final: 0.8027 (pm20) outliers start: 101 outliers final: 76 residues processed: 747 average time/residue: 0.1742 time to fit residues: 204.8490 Evaluate side-chains 766 residues out of total 2762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 679 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 PHE Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 43 ASP Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 130 GLN Chi-restraints excluded: chain B residue 150 MET Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 209 MET Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 32 ILE Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 109 ILE Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 215 SER Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain D residue 36 THR Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 69 GLU Chi-restraints excluded: chain D residue 209 MET Chi-restraints excluded: chain D residue 218 ARG Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 134 SER Chi-restraints excluded: chain E residue 143 LEU Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 203 TRP Chi-restraints excluded: chain E residue 259 ARG Chi-restraints excluded: chain F residue 21 ASN Chi-restraints excluded: chain F residue 25 ASP Chi-restraints excluded: chain F residue 32 ILE Chi-restraints excluded: chain F residue 40 LEU Chi-restraints excluded: chain F residue 67 ILE Chi-restraints excluded: chain G residue 10 ILE Chi-restraints excluded: chain G residue 17 LEU Chi-restraints excluded: chain G residue 49 ILE Chi-restraints excluded: chain G residue 81 GLN Chi-restraints excluded: chain G residue 88 ARG Chi-restraints excluded: chain G residue 95 LEU Chi-restraints excluded: chain H residue 187 HIS Chi-restraints excluded: chain H residue 228 VAL Chi-restraints excluded: chain H residue 253 ASP Chi-restraints excluded: chain H residue 266 VAL Chi-restraints excluded: chain H residue 276 THR Chi-restraints excluded: chain I residue 58 LEU Chi-restraints excluded: chain I residue 66 LEU Chi-restraints excluded: chain I residue 76 GLN Chi-restraints excluded: chain I residue 81 GLN Chi-restraints excluded: chain I residue 96 GLU Chi-restraints excluded: chain J residue 58 LEU Chi-restraints excluded: chain J residue 88 ARG Chi-restraints excluded: chain J residue 98 GLN Chi-restraints excluded: chain K residue 29 GLU Chi-restraints excluded: chain K residue 32 PHE Chi-restraints excluded: chain K residue 195 CYS Chi-restraints excluded: chain K residue 250 TYR Chi-restraints excluded: chain K residue 266 ILE Chi-restraints excluded: chain K residue 269 VAL Chi-restraints excluded: chain K residue 306 THR Chi-restraints excluded: chain K residue 330 LEU Chi-restraints excluded: chain K residue 393 LEU Chi-restraints excluded: chain K residue 403 ASP Chi-restraints excluded: chain K residue 458 MET Chi-restraints excluded: chain K residue 496 ARG Chi-restraints excluded: chain M residue 42 THR Chi-restraints excluded: chain M residue 166 THR Chi-restraints excluded: chain M residue 180 CYS Chi-restraints excluded: chain M residue 276 THR Chi-restraints excluded: chain N residue 21 VAL Chi-restraints excluded: chain N residue 30 THR Chi-restraints excluded: chain N residue 37 ILE Chi-restraints excluded: chain N residue 42 LEU Chi-restraints excluded: chain N residue 70 VAL Chi-restraints excluded: chain N residue 133 GLN Chi-restraints excluded: chain N residue 159 LEU Chi-restraints excluded: chain N residue 172 LEU Chi-restraints excluded: chain N residue 192 PHE Chi-restraints excluded: chain N residue 201 VAL Chi-restraints excluded: chain L residue 81 GLN Chi-restraints excluded: chain L residue 84 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 201 optimal weight: 3.9990 chunk 269 optimal weight: 0.2980 chunk 155 optimal weight: 4.9990 chunk 128 optimal weight: 4.9990 chunk 261 optimal weight: 0.7980 chunk 185 optimal weight: 0.8980 chunk 195 optimal weight: 0.0020 chunk 55 optimal weight: 1.9990 chunk 307 optimal weight: 7.9990 chunk 158 optimal weight: 0.8980 chunk 14 optimal weight: 0.6980 overall best weight: 0.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 124 GLN ** F 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 6 ASN ** G 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 97 GLN I 98 GLN ** J 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 85 HIS ** K 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.156966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.125028 restraints weight = 47053.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 67)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.129419 restraints weight = 20944.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.132217 restraints weight = 12097.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 61)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.134010 restraints weight = 8359.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.134962 restraints weight = 6543.745| |-----------------------------------------------------------------------------| r_work (final): 0.3970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.4671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.339 27430 Z= 0.312 Angle : 1.016 59.152 37194 Z= 0.539 Chirality : 0.053 0.549 4023 Planarity : 0.006 0.109 4752 Dihedral : 14.445 171.856 4192 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 37.49 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.61 % Favored : 90.36 % Rotamer: Outliers : 3.51 % Allowed : 26.81 % Favored : 69.67 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.48 (0.14), residues: 3184 helix: -0.72 (0.14), residues: 1276 sheet: -2.59 (0.25), residues: 364 loop : -2.20 (0.15), residues: 1544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG G 16 TYR 0.075 0.003 TYR N 26 PHE 0.056 0.003 PHE F 188 TRP 0.133 0.004 TRP J 77 HIS 0.021 0.002 HIS M 214 Details of bonding type rmsd/Z covalent geometry : bond 0.00720 / 0.31 (27430) covalent geometry : angle 1.01553 / 0.54 (37194) hydrogen bonds : bond 0.04876 / 3.22 ( 1148) hydrogen bonds : angle 6.65480 / 4.76 ( 3315) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6075.59 seconds wall clock time: 105 minutes 56.19 seconds (6356.19 seconds total)