Starting phenix.real_space_refine on Sun Jul 5 07:55:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g9t_29878/07_2026/8g9t_29878.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g9t_29878/07_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_29878/07_2026/8g9t_29878.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g9t_29878/07_2026/8g9t_29878.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8g9t_29878/07_2026/8g9t_29878.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g9t_29878/07_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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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: 5.53, per 1000 atoms: 0.21 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: 2.44 Conformation dependent library (CDL) restraints added in 1.1 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: 3.53 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: 5.51 Time building geometry restraints manager: 3.16 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: 3883 0.136 - 0.271: 128 0.271 - 0.407: 9 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 1.04e+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: 1.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.470 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 27.690 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.960 ------------------------------------------------------------------------------- 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= 0.654 Angle : 1.326 25.485 37194 Z= 0.759 Chirality : 0.065 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 0.01318 / 0.65 (27430) covalent geometry : angle 1.32558 / 0.76 (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 : 1.070 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: 0.1915 time to fit residues: 262.5096 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 : 1.078 ------------------------------------------------------------------------------- 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** ** 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 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 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: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.152016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.119925 restraints weight = 46993.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.124370 restraints weight = 22015.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.126742 restraints weight = 12053.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.127972 restraints weight = 8709.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.128135 restraints weight = 7255.150| |-----------------------------------------------------------------------------| r_work (final): 0.3894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.2159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.110 27430 Z= 0.273 Angle : 0.960 16.512 37194 Z= 0.510 Chirality : 0.054 0.366 4023 Planarity : 0.008 0.136 4752 Dihedral : 15.419 179.140 4257 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 38.65 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.80 % Favored : 90.14 % Rotamer: Outliers : 2.86 % Allowed : 14.13 % Favored : 83.01 % 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: -3.02 (0.13), residues: 3184 helix: -1.23 (0.13), residues: 1269 sheet: -2.66 (0.24), residues: 376 loop : -2.49 (0.14), residues: 1539 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG N 128 TYR 0.038 0.004 TYR L 106 PHE 0.033 0.003 PHE K 264 TRP 0.052 0.003 TRP I 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 0.95995 / 0.51 (37194) hydrogen bonds : bond 0.06616 / 4.36 ( 1148) hydrogen bonds : angle 7.51363 / 5.38 ( 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 918 residues out of total 2762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 839 time to evaluate : 1.338 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: A 126 ASN cc_start: 0.7907 (t0) cc_final: 0.7351 (t0) REVERT: A 144 ASP cc_start: 0.8533 (m-30) cc_final: 0.8275 (m-30) REVERT: A 167 GLN cc_start: 0.8271 (tm-30) cc_final: 0.7512 (tm-30) REVERT: B 40 LEU cc_start: 0.9131 (mt) cc_final: 0.8895 (mt) REVERT: B 141 MET cc_start: 0.7056 (mmt) cc_final: 0.6709 (mmt) REVERT: B 175 TYR cc_start: 0.8616 (t80) cc_final: 0.7971 (t80) REVERT: B 183 PHE cc_start: 0.7966 (m-10) cc_final: 0.7392 (m-80) REVERT: C 4 GLU cc_start: 0.7838 (tp30) cc_final: 0.7621 (tp30) REVERT: C 72 ILE cc_start: 0.8822 (mm) cc_final: 0.8421 (mm) REVERT: C 75 ASN cc_start: 0.8436 (m110) cc_final: 0.8117 (m-40) REVERT: C 124 GLN cc_start: 0.7659 (mt0) cc_final: 0.7064 (mt0) REVERT: C 150 MET cc_start: 0.6514 (ttp) cc_final: 0.5798 (ttp) REVERT: C 156 LYS cc_start: 0.8833 (ttpp) cc_final: 0.8595 (tttm) REVERT: C 175 TYR cc_start: 0.9131 (t80) cc_final: 0.8840 (t80) REVERT: C 191 GLN cc_start: 0.8091 (tt0) cc_final: 0.7782 (tt0) REVERT: C 204 GLN cc_start: 0.7844 (mt0) cc_final: 0.7465 (mt0) REVERT: C 214 HIS cc_start: 0.7406 (m170) cc_final: 0.7197 (m170) REVERT: C 220 GLN cc_start: 0.7899 (tm-30) cc_final: 0.7049 (tm-30) REVERT: C 226 LEU cc_start: 0.8629 (tp) cc_final: 0.8374 (tp) REVERT: D 146 SER cc_start: 0.8166 (m) cc_final: 0.7873 (m) REVERT: D 244 PHE cc_start: 0.9017 (m-10) cc_final: 0.8655 (m-10) REVERT: D 260 SER cc_start: 0.9092 (p) cc_final: 0.8860 (p) REVERT: E 79 GLU cc_start: 0.7622 (tm-30) cc_final: 0.7017 (tm-30) REVERT: E 101 TYR cc_start: 0.8013 (t80) cc_final: 0.7677 (t80) REVERT: E 204 GLN cc_start: 0.7709 (tm130) cc_final: 0.7234 (tm-30) REVERT: E 221 MET cc_start: 0.8113 (mtm) cc_final: 0.7730 (mtm) REVERT: E 226 LEU cc_start: 0.8894 (tp) cc_final: 0.8500 (tp) REVERT: E 233 ASN cc_start: 0.8362 (m-40) cc_final: 0.7913 (m-40) REVERT: E 241 ASP cc_start: 0.7158 (t70) cc_final: 0.6636 (t0) REVERT: F 19 ASN cc_start: 0.7289 (t0) cc_final: 0.6792 (t0) REVERT: F 72 ILE cc_start: 0.8022 (mm) cc_final: 0.7678 (mm) REVERT: F 108 ASP cc_start: 0.7742 (t0) cc_final: 0.7365 (t0) REVERT: F 116 MET cc_start: 0.8285 (tpp) cc_final: 0.8041 (tpt) REVERT: F 124 GLN cc_start: 0.8309 (mt0) cc_final: 0.8054 (mt0) REVERT: F 141 MET cc_start: 0.8336 (ttm) cc_final: 0.7768 (ttt) REVERT: G 40 TYR cc_start: 0.8154 (m-80) cc_final: 0.7910 (m-80) REVERT: G 56 MET cc_start: 0.9009 (mmm) cc_final: 0.8736 (mmm) REVERT: G 77 TRP cc_start: 0.8066 (t60) cc_final: 0.7356 (t60) REVERT: G 93 LEU cc_start: 0.8362 (tp) cc_final: 0.8058 (tp) REVERT: G 97 GLN cc_start: 0.8374 (tt0) cc_final: 0.8007 (mm-40) REVERT: G 105 TYR cc_start: 0.8398 (t80) cc_final: 0.7975 (t80) REVERT: G 122 PHE cc_start: 0.7547 (t80) cc_final: 0.7187 (t80) REVERT: H 11 PHE cc_start: 0.7805 (t80) cc_final: 0.7422 (t80) REVERT: H 96 GLU cc_start: 0.8700 (tp30) cc_final: 0.8459 (tp30) REVERT: H 178 TYR cc_start: 0.7072 (m-80) cc_final: 0.6723 (m-10) REVERT: H 181 HIS cc_start: 0.7807 (m-70) cc_final: 0.7406 (m-70) REVERT: H 206 LEU cc_start: 0.9428 (mt) cc_final: 0.9044 (mt) REVERT: H 261 PHE cc_start: 0.7511 (t80) cc_final: 0.7084 (t80) REVERT: H 272 ASN cc_start: 0.9042 (OUTLIER) cc_final: 0.8650 (t0) REVERT: I 22 GLU cc_start: 0.8706 (tm-30) cc_final: 0.7966 (tm-30) REVERT: I 23 LYS cc_start: 0.8686 (tppt) cc_final: 0.8237 (tppt) REVERT: I 39 ARG cc_start: 0.8304 (mtp180) cc_final: 0.7563 (mtp180) REVERT: I 76 GLN cc_start: 0.8567 (OUTLIER) cc_final: 0.8299 (mm-40) REVERT: I 84 GLU cc_start: 0.8431 (tp30) cc_final: 0.8111 (tp30) REVERT: I 87 GLN cc_start: 0.9187 (tt0) cc_final: 0.8697 (tm-30) REVERT: I 108 GLU cc_start: 0.8714 (mm-30) cc_final: 0.8260 (mm-30) REVERT: I 113 PHE cc_start: 0.8240 (m-80) cc_final: 0.8008 (m-10) REVERT: I 121 LEU cc_start: 0.8307 (OUTLIER) cc_final: 0.8078 (tp) REVERT: J 23 LYS cc_start: 0.8818 (mmmt) cc_final: 0.8554 (mmmt) REVERT: J 52 PHE cc_start: 0.8183 (m-10) cc_final: 0.7346 (m-80) REVERT: J 65 LYS cc_start: 0.8904 (mttp) cc_final: 0.8585 (mmtm) REVERT: J 77 TRP cc_start: 0.8343 (t60) cc_final: 0.8047 (t60) REVERT: J 97 GLN cc_start: 0.8123 (mm-40) cc_final: 0.7318 (mm-40) REVERT: J 105 TYR cc_start: 0.9020 (t80) cc_final: 0.8509 (t80) REVERT: J 120 ASN cc_start: 0.8213 (m110) cc_final: 0.7748 (m-40) REVERT: K 16 SER cc_start: 0.8012 (t) cc_final: 0.7491 (p) REVERT: K 23 GLU cc_start: 0.7370 (tm-30) cc_final: 0.6870 (tm-30) REVERT: K 82 TRP cc_start: 0.8646 (p-90) cc_final: 0.8045 (p-90) REVERT: K 156 ASN cc_start: 0.8150 (m110) cc_final: 0.7897 (m110) REVERT: K 285 LEU cc_start: 0.9369 (mt) cc_final: 0.9102 (mp) REVERT: K 309 LYS cc_start: 0.8729 (tppt) cc_final: 0.8479 (ttmm) REVERT: K 343 HIS cc_start: 0.7022 (m90) cc_final: 0.6822 (m90) REVERT: K 392 ASN cc_start: 0.8500 (t0) cc_final: 0.8030 (t0) REVERT: K 403 ASP cc_start: 0.7714 (OUTLIER) cc_final: 0.6781 (t70) REVERT: M 21 ASN cc_start: 0.8197 (p0) cc_final: 0.7847 (p0) REVERT: M 102 MET cc_start: 0.6032 (mtt) cc_final: 0.5703 (mtp) REVERT: M 130 GLN cc_start: 0.7270 (OUTLIER) cc_final: 0.6765 (tt0) REVERT: M 198 ASP cc_start: 0.7772 (m-30) cc_final: 0.7136 (m-30) REVERT: M 204 GLN cc_start: 0.8394 (tm-30) cc_final: 0.8130 (tm-30) REVERT: M 212 HIS cc_start: 0.6867 (m-70) cc_final: 0.6307 (m-70) REVERT: M 221 MET cc_start: 0.8448 (ttt) cc_final: 0.7850 (ttt) REVERT: M 263 ASP cc_start: 0.8132 (m-30) cc_final: 0.7745 (m-30) REVERT: M 277 LYS cc_start: 0.7951 (mppt) cc_final: 0.7724 (mppt) REVERT: N 26 TYR cc_start: 0.8667 (m-80) cc_final: 0.8058 (m-80) REVERT: N 63 THR cc_start: 0.8873 (t) cc_final: 0.8444 (p) REVERT: N 68 ASN cc_start: 0.7962 (t0) cc_final: 0.7735 (t0) REVERT: N 69 GLU cc_start: 0.7098 (tt0) cc_final: 0.6888 (tt0) REVERT: N 76 GLU cc_start: 0.6938 (mm-30) cc_final: 0.6303 (mm-30) REVERT: N 151 LEU cc_start: 0.8814 (tt) cc_final: 0.8518 (tt) REVERT: N 152 LEU cc_start: 0.8430 (mp) cc_final: 0.8159 (mp) REVERT: L 103 ILE cc_start: 0.7967 (tt) cc_final: 0.7630 (tt) REVERT: L 107 HIS cc_start: 0.7553 (m90) cc_final: 0.7047 (m90) outliers start: 79 outliers final: 38 residues processed: 862 average time/residue: 0.1864 time to fit residues: 256.7205 Evaluate side-chains 752 residues out of total 2762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 709 time to evaluate : 1.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 153 ASN Chi-restraints excluded: chain A residue 176 SER 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 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 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 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: 0.8980 chunk 125 optimal weight: 7.9990 chunk 221 optimal weight: 3.9990 chunk 134 optimal weight: 1.9990 chunk 321 optimal weight: 10.0000 chunk 311 optimal weight: 5.9990 chunk 131 optimal weight: 6.9990 chunk 82 optimal weight: 2.9990 chunk 116 optimal weight: 4.9990 chunk 119 optimal weight: 0.7980 chunk 17 optimal weight: 0.5980 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** C 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 52 ASN 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 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** I 97 GLN J 8 GLN ** J 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 64 ASN ** 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 333 ASN ** 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 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 91 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.148920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.115603 restraints weight = 47090.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.120017 restraints weight = 20880.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.122798 restraints weight = 12146.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.124621 restraints weight = 8486.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.125583 restraints weight = 6701.296| |-----------------------------------------------------------------------------| r_work (final): 0.3875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.2772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.080 27430 Z= 0.287 Angle : 0.879 11.752 37194 Z= 0.467 Chirality : 0.052 0.346 4023 Planarity : 0.007 0.084 4752 Dihedral : 15.072 178.227 4205 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 35.82 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.86 % Favored : 90.08 % Rotamer: Outliers : 3.95 % Allowed : 18.73 % Favored : 77.32 % 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: -2.81 (0.14), residues: 3184 helix: -0.98 (0.13), residues: 1278 sheet: -2.77 (0.24), residues: 392 loop : -2.36 (0.15), residues: 1514 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 0.042 0.003 PHE M 229 TRP 0.052 0.003 TRP I 77 HIS 0.015 0.002 HIS B 214 Details of bonding type rmsd/Z covalent geometry : bond 0.00639 / 0.29 (27430) covalent geometry : angle 0.87874 / 0.47 (37194) hydrogen bonds : bond 0.05737 / 3.78 ( 1148) hydrogen bonds : angle 7.12842 / 5.12 ( 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 874 residues out of total 2762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 765 time to evaluate : 1.069 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 117 THR cc_start: 0.9413 (p) cc_final: 0.9161 (p) REVERT: A 126 ASN cc_start: 0.8187 (t0) cc_final: 0.7437 (t0) REVERT: A 144 ASP cc_start: 0.8566 (m-30) cc_final: 0.8285 (m-30) REVERT: A 155 TYR cc_start: 0.8732 (m-80) cc_final: 0.8516 (m-80) REVERT: A 164 GLU cc_start: 0.7948 (tp30) cc_final: 0.7734 (tp30) REVERT: B 130 GLN cc_start: 0.7632 (tp40) cc_final: 0.7370 (tp40) REVERT: B 175 TYR cc_start: 0.8742 (t80) cc_final: 0.8074 (t80) REVERT: B 183 PHE cc_start: 0.8253 (m-80) cc_final: 0.7403 (m-10) REVERT: C 4 GLU cc_start: 0.7546 (tp30) cc_final: 0.7238 (tp30) REVERT: C 43 ASP cc_start: 0.8092 (p0) cc_final: 0.7795 (p0) REVERT: C 124 GLN cc_start: 0.7721 (mt0) cc_final: 0.6939 (mt0) REVERT: C 209 MET cc_start: 0.7070 (ttp) cc_final: 0.6703 (ttm) REVERT: C 220 GLN cc_start: 0.7959 (tm-30) cc_final: 0.6666 (tm-30) REVERT: C 222 ASN cc_start: 0.8304 (m110) cc_final: 0.6410 (m110) REVERT: C 226 LEU cc_start: 0.8246 (tp) cc_final: 0.7913 (tp) REVERT: D 36 THR cc_start: 0.8165 (OUTLIER) cc_final: 0.7771 (p) REVERT: D 102 MET cc_start: 0.8185 (mmt) cc_final: 0.7654 (mmt) REVERT: D 116 MET cc_start: 0.8660 (mmt) cc_final: 0.8439 (mmm) REVERT: D 169 ARG cc_start: 0.8282 (mtm-85) cc_final: 0.7943 (mtm-85) REVERT: D 244 PHE cc_start: 0.8893 (m-10) cc_final: 0.8599 (m-10) REVERT: D 246 ARG cc_start: 0.8759 (mtm110) cc_final: 0.8327 (mtm-85) REVERT: D 255 VAL cc_start: 0.8867 (t) cc_final: 0.8614 (p) REVERT: D 264 TYR cc_start: 0.8399 (m-10) cc_final: 0.8191 (m-80) REVERT: E 79 GLU cc_start: 0.7551 (tm-30) cc_final: 0.6949 (tm-30) REVERT: E 204 GLN cc_start: 0.7734 (tm130) cc_final: 0.7084 (tm-30) REVERT: E 221 MET cc_start: 0.8426 (OUTLIER) cc_final: 0.8103 (mtm) REVERT: E 226 LEU cc_start: 0.8993 (tp) cc_final: 0.8582 (tp) REVERT: E 233 ASN cc_start: 0.8274 (m-40) cc_final: 0.7852 (m-40) REVERT: E 241 ASP cc_start: 0.7004 (t70) cc_final: 0.6510 (t0) REVERT: E 265 LEU cc_start: 0.9012 (tp) cc_final: 0.8507 (pp) REVERT: F 19 ASN cc_start: 0.7594 (t0) cc_final: 0.7160 (t0) REVERT: F 72 ILE cc_start: 0.8315 (mm) cc_final: 0.7978 (mm) REVERT: F 108 ASP cc_start: 0.7760 (t0) cc_final: 0.7353 (t0) REVERT: F 141 MET cc_start: 0.8293 (ttm) cc_final: 0.7726 (ttt) REVERT: G 16 ARG cc_start: 0.8727 (tpt-90) cc_final: 0.8386 (tpt-90) REVERT: G 56 MET cc_start: 0.9011 (mmm) cc_final: 0.8795 (mmm) REVERT: G 57 ARG cc_start: 0.8447 (ttm-80) cc_final: 0.7453 (ttm110) REVERT: G 58 LEU cc_start: 0.8065 (tp) cc_final: 0.7588 (tp) REVERT: G 68 PHE cc_start: 0.7989 (t80) cc_final: 0.7691 (t80) REVERT: G 71 ARG cc_start: 0.8709 (mmm160) cc_final: 0.8269 (mmm-85) REVERT: G 77 TRP cc_start: 0.8246 (t60) cc_final: 0.7662 (t60) REVERT: G 88 ARG cc_start: 0.8016 (OUTLIER) cc_final: 0.7116 (ttp80) REVERT: G 94 ASN cc_start: 0.8586 (p0) cc_final: 0.7925 (p0) REVERT: G 98 GLN cc_start: 0.7977 (tt0) cc_final: 0.7368 (tt0) REVERT: G 105 TYR cc_start: 0.8531 (t80) cc_final: 0.8325 (t80) REVERT: G 111 PHE cc_start: 0.8134 (t80) cc_final: 0.7801 (t80) REVERT: H 11 PHE cc_start: 0.7580 (t80) cc_final: 0.7132 (t80) REVERT: H 102 MET cc_start: 0.8946 (mmm) cc_final: 0.8054 (mmm) REVERT: H 126 ARG cc_start: 0.7108 (ttt-90) cc_final: 0.6686 (ttt-90) REVERT: H 178 TYR cc_start: 0.6975 (m-80) cc_final: 0.6169 (m-10) REVERT: H 181 HIS cc_start: 0.7986 (m-70) cc_final: 0.7481 (m-70) REVERT: H 246 ARG cc_start: 0.7313 (mmt90) cc_final: 0.6685 (mmm-85) REVERT: H 261 PHE cc_start: 0.7499 (t80) cc_final: 0.7144 (t80) REVERT: H 272 ASN cc_start: 0.8854 (OUTLIER) cc_final: 0.8475 (t0) REVERT: I 8 GLN cc_start: 0.8287 (tp40) cc_final: 0.7940 (mm110) REVERT: I 18 PHE cc_start: 0.8835 (t80) cc_final: 0.8542 (t80) REVERT: I 22 GLU cc_start: 0.8748 (tm-30) cc_final: 0.7960 (tm-30) REVERT: I 23 LYS cc_start: 0.8836 (tppt) cc_final: 0.8192 (tppt) REVERT: I 56 MET cc_start: 0.8837 (mmm) cc_final: 0.8384 (mmm) REVERT: I 57 ARG cc_start: 0.7870 (OUTLIER) cc_final: 0.7589 (mtt90) REVERT: I 77 TRP cc_start: 0.8438 (t60) cc_final: 0.7938 (t60) REVERT: I 81 GLN cc_start: 0.8866 (OUTLIER) cc_final: 0.8394 (mp10) REVERT: I 84 GLU cc_start: 0.8440 (tp30) cc_final: 0.8033 (tp30) REVERT: I 87 GLN cc_start: 0.9121 (tt0) cc_final: 0.8619 (tm-30) REVERT: I 88 ARG cc_start: 0.7612 (ttp80) cc_final: 0.6760 (tmm-80) REVERT: I 113 PHE cc_start: 0.8265 (m-80) cc_final: 0.8023 (m-80) REVERT: I 119 LYS cc_start: 0.9077 (ptmm) cc_final: 0.8734 (ptmm) REVERT: I 123 ASN cc_start: 0.8609 (m110) cc_final: 0.8377 (m110) REVERT: I 124 GLU cc_start: 0.8480 (pp20) cc_final: 0.8172 (pp20) REVERT: J 52 PHE cc_start: 0.8184 (m-10) cc_final: 0.7543 (m-80) REVERT: J 65 LYS cc_start: 0.9110 (mttp) cc_final: 0.8697 (mmtm) REVERT: J 78 GLU cc_start: 0.8973 (tp30) cc_final: 0.8189 (tp30) REVERT: J 100 LEU cc_start: 0.8633 (OUTLIER) cc_final: 0.8405 (mt) REVERT: J 105 TYR cc_start: 0.8990 (t80) cc_final: 0.8469 (t80) REVERT: J 108 GLU cc_start: 0.8113 (mm-30) cc_final: 0.7622 (mt-10) REVERT: J 116 ASP cc_start: 0.7490 (t0) cc_final: 0.6994 (t0) REVERT: J 120 ASN cc_start: 0.8303 (m110) cc_final: 0.7130 (m-40) REVERT: K 23 GLU cc_start: 0.7608 (tm-30) cc_final: 0.7023 (tm-30) REVERT: K 82 TRP cc_start: 0.8591 (p-90) cc_final: 0.7969 (p-90) REVERT: K 156 ASN cc_start: 0.7960 (m110) cc_final: 0.7534 (m-40) REVERT: K 250 TYR cc_start: 0.7954 (OUTLIER) cc_final: 0.6749 (p90) REVERT: K 285 LEU cc_start: 0.9337 (mt) cc_final: 0.9073 (mp) REVERT: K 299 GLU cc_start: 0.7691 (tm-30) cc_final: 0.7486 (tm-30) REVERT: K 309 LYS cc_start: 0.8625 (tppt) cc_final: 0.8396 (ttmm) REVERT: K 342 TRP cc_start: 0.8080 (t-100) cc_final: 0.7725 (t-100) REVERT: K 343 HIS cc_start: 0.7127 (m90) cc_final: 0.6817 (m90) REVERT: K 403 ASP cc_start: 0.7438 (OUTLIER) cc_final: 0.6651 (t70) REVERT: K 427 GLN cc_start: 0.8244 (mm-40) cc_final: 0.7982 (mm110) REVERT: K 436 LEU cc_start: 0.9052 (mt) cc_final: 0.8616 (tp) REVERT: M 102 MET cc_start: 0.5862 (mtt) cc_final: 0.5622 (mtt) REVERT: M 130 GLN cc_start: 0.7344 (tt0) cc_final: 0.6970 (tt0) REVERT: M 147 ILE cc_start: 0.9100 (pt) cc_final: 0.8811 (mt) REVERT: M 198 ASP cc_start: 0.7683 (m-30) cc_final: 0.7205 (m-30) REVERT: M 204 GLN cc_start: 0.8495 (tm-30) cc_final: 0.8215 (tm-30) REVERT: M 209 MET cc_start: 0.8257 (ttp) cc_final: 0.8016 (ttp) REVERT: M 221 MET cc_start: 0.8382 (ttt) cc_final: 0.7955 (ttt) REVERT: M 277 LYS cc_start: 0.7974 (mppt) cc_final: 0.7742 (mppt) REVERT: N 26 TYR cc_start: 0.8586 (m-80) cc_final: 0.7959 (m-80) REVERT: N 63 THR cc_start: 0.8884 (t) cc_final: 0.8453 (p) REVERT: N 68 ASN cc_start: 0.7978 (t0) cc_final: 0.7593 (t0) REVERT: N 69 GLU cc_start: 0.7223 (tt0) cc_final: 0.6919 (tt0) REVERT: N 137 GLN cc_start: 0.7973 (tp40) cc_final: 0.7479 (tp40) REVERT: L 40 TYR cc_start: 0.8520 (m-10) cc_final: 0.8042 (m-80) REVERT: L 76 GLN cc_start: 0.8668 (mp10) cc_final: 0.8425 (mm110) REVERT: L 96 GLU cc_start: 0.8147 (pm20) cc_final: 0.7885 (pm20) outliers start: 109 outliers final: 64 residues processed: 820 average time/residue: 0.1854 time to fit residues: 243.1041 Evaluate side-chains 757 residues out of total 2762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 684 time to evaluate : 1.125 ------------------------------------------------------------------------------- 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 32 ILE Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 109 ILE 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 C residue 276 THR Chi-restraints excluded: chain D residue 10 VAL Chi-restraints excluded: chain D residue 36 THR Chi-restraints excluded: chain D residue 45 CYS 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 180 CYS 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 67 ILE 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 91 ASN Chi-restraints excluded: chain J residue 96 GLU Chi-restraints excluded: chain J residue 100 LEU Chi-restraints excluded: chain K residue 89 LEU 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 381 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 K residue 555 GLN 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 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: 3.9990 chunk 170 optimal weight: 5.9990 chunk 79 optimal weight: 0.5980 chunk 139 optimal weight: 2.9990 chunk 182 optimal weight: 0.8980 chunk 186 optimal weight: 0.8980 chunk 236 optimal weight: 0.7980 chunk 209 optimal weight: 10.0000 chunk 169 optimal weight: 0.7980 chunk 259 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 153 ASN 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 ** C 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 55 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 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 97 GLN ** G 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 120 ASN H 100 GLN ** H 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 272 ASN I 33 ASN I 62 HIS I 97 GLN I 120 ASN 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 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** ** M 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 123 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.153223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.119890 restraints weight = 46991.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.124422 restraints weight = 21031.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.127302 restraints weight = 12217.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.129091 restraints weight = 8487.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 60)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.130279 restraints weight = 6696.237| |-----------------------------------------------------------------------------| r_work (final): 0.3914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.3212 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= 0.229 Angle : 0.836 12.752 37194 Z= 0.442 Chirality : 0.051 0.335 4023 Planarity : 0.006 0.078 4752 Dihedral : 14.855 175.438 4195 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 32.91 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.17 % Favored : 90.77 % Rotamer: Outliers : 4.42 % Allowed : 20.22 % Favored : 75.36 % 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: -2.72 (0.14), residues: 3184 helix: -0.87 (0.13), residues: 1287 sheet: -2.82 (0.24), residues: 387 loop : -2.33 (0.15), residues: 1510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 280 TYR 0.030 0.003 TYR J 106 PHE 0.030 0.003 PHE M 229 TRP 0.041 0.003 TRP L 77 HIS 0.020 0.002 HIS C 214 Details of bonding type rmsd/Z covalent geometry : bond 0.00523 / 0.23 (27430) covalent geometry : angle 0.83599 / 0.44 (37194) hydrogen bonds : bond 0.05261 / 3.46 ( 1148) hydrogen bonds : angle 7.00489 / 5.02 ( 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 878 residues out of total 2762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 756 time to evaluate : 1.046 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 119 PHE cc_start: 0.8237 (OUTLIER) cc_final: 0.6555 (t80) REVERT: A 126 ASN cc_start: 0.8189 (t0) cc_final: 0.7475 (t0) REVERT: A 144 ASP cc_start: 0.8430 (m-30) cc_final: 0.8139 (m-30) REVERT: A 164 GLU cc_start: 0.7978 (tp30) cc_final: 0.7295 (tp30) REVERT: A 167 GLN cc_start: 0.8690 (tm-30) cc_final: 0.7457 (tm-30) REVERT: A 168 TYR cc_start: 0.7907 (m-80) cc_final: 0.7208 (m-10) REVERT: B 102 MET cc_start: 0.7622 (OUTLIER) cc_final: 0.7253 (mtt) REVERT: B 141 MET cc_start: 0.6917 (mmt) cc_final: 0.6511 (mmt) REVERT: B 175 TYR cc_start: 0.8601 (t80) cc_final: 0.7956 (t80) REVERT: B 183 PHE cc_start: 0.8057 (m-80) cc_final: 0.6962 (m-10) REVERT: B 279 LEU cc_start: 0.8313 (tt) cc_final: 0.8067 (tt) REVERT: C 4 GLU cc_start: 0.7490 (tp30) cc_final: 0.7131 (tp30) REVERT: C 43 ASP cc_start: 0.8060 (p0) cc_final: 0.7804 (p0) REVERT: C 67 ILE cc_start: 0.8369 (OUTLIER) cc_final: 0.7958 (mm) REVERT: C 220 GLN cc_start: 0.7845 (tm-30) cc_final: 0.6548 (tm-30) REVERT: C 256 GLU cc_start: 0.7628 (tm-30) cc_final: 0.7368 (tm-30) REVERT: D 35 GLN cc_start: 0.8335 (mm-40) cc_final: 0.8044 (tp-100) REVERT: D 48 ARG cc_start: 0.6560 (OUTLIER) cc_final: 0.5978 (mtm-85) REVERT: D 102 MET cc_start: 0.8119 (mmt) cc_final: 0.7844 (mmt) REVERT: D 169 ARG cc_start: 0.8243 (mtm-85) cc_final: 0.8027 (mtm-85) REVERT: D 246 ARG cc_start: 0.8583 (mtm110) cc_final: 0.8226 (mtm-85) REVERT: E 79 GLU cc_start: 0.7596 (tm-30) cc_final: 0.7179 (tm-30) REVERT: E 204 GLN cc_start: 0.7730 (tm130) cc_final: 0.7032 (tm-30) REVERT: E 209 MET cc_start: 0.8120 (ttp) cc_final: 0.7522 (ttp) REVERT: E 221 MET cc_start: 0.8433 (OUTLIER) cc_final: 0.7609 (mtm) REVERT: E 226 LEU cc_start: 0.8878 (tp) cc_final: 0.8477 (tp) REVERT: E 233 ASN cc_start: 0.8271 (m-40) cc_final: 0.7895 (m-40) REVERT: E 241 ASP cc_start: 0.7029 (t70) cc_final: 0.6576 (t0) REVERT: E 265 LEU cc_start: 0.9043 (tp) cc_final: 0.8780 (tt) REVERT: F 19 ASN cc_start: 0.7214 (t0) cc_final: 0.6918 (t0) REVERT: F 48 ARG cc_start: 0.7159 (tpt170) cc_final: 0.6919 (tpm170) REVERT: F 72 ILE cc_start: 0.8306 (mm) cc_final: 0.7967 (mm) REVERT: F 108 ASP cc_start: 0.7817 (t0) cc_final: 0.7414 (t0) REVERT: F 116 MET cc_start: 0.8517 (tpp) cc_final: 0.8268 (tpp) REVERT: F 141 MET cc_start: 0.7981 (ttm) cc_final: 0.7716 (ttp) REVERT: F 172 THR cc_start: 0.7975 (m) cc_final: 0.6929 (p) REVERT: G 16 ARG cc_start: 0.8540 (tpt-90) cc_final: 0.8228 (tpt-90) REVERT: G 68 PHE cc_start: 0.8033 (t80) cc_final: 0.7719 (t80) REVERT: G 71 ARG cc_start: 0.8720 (mmm160) cc_final: 0.8180 (mmm-85) REVERT: G 77 TRP cc_start: 0.8132 (t60) cc_final: 0.7286 (t60) REVERT: G 78 GLU cc_start: 0.8604 (tp30) cc_final: 0.8380 (tp30) REVERT: G 88 ARG cc_start: 0.8056 (OUTLIER) cc_final: 0.7120 (ttp80) REVERT: G 94 ASN cc_start: 0.8542 (p0) cc_final: 0.8047 (p0) REVERT: G 96 GLU cc_start: 0.8939 (pm20) cc_final: 0.8707 (pm20) REVERT: G 103 ILE cc_start: 0.8958 (OUTLIER) cc_final: 0.8223 (tt) REVERT: G 107 HIS cc_start: 0.8504 (m90) cc_final: 0.7954 (m90) REVERT: G 110 GLN cc_start: 0.7699 (tp-100) cc_final: 0.7389 (tp-100) REVERT: G 122 PHE cc_start: 0.7901 (t80) cc_final: 0.7470 (t80) REVERT: H 11 PHE cc_start: 0.7529 (t80) cc_final: 0.6980 (t80) REVERT: H 81 HIS cc_start: 0.8571 (OUTLIER) cc_final: 0.7957 (t-90) REVERT: H 102 MET cc_start: 0.8869 (mmm) cc_final: 0.8096 (mmm) REVERT: H 126 ARG cc_start: 0.7202 (ttt-90) cc_final: 0.6564 (tmt170) REVERT: H 178 TYR cc_start: 0.7110 (m-80) cc_final: 0.6537 (m-10) REVERT: H 179 ARG cc_start: 0.7057 (ttt90) cc_final: 0.6689 (ttt90) REVERT: H 181 HIS cc_start: 0.7983 (m-70) cc_final: 0.7463 (m-70) REVERT: H 261 PHE cc_start: 0.7637 (t80) cc_final: 0.7309 (t80) REVERT: H 272 ASN cc_start: 0.8853 (t160) cc_final: 0.8455 (t0) REVERT: I 18 PHE cc_start: 0.8832 (t80) cc_final: 0.8516 (t80) REVERT: I 22 GLU cc_start: 0.8844 (tm-30) cc_final: 0.8027 (tm-30) REVERT: I 23 LYS cc_start: 0.8897 (tppt) cc_final: 0.8448 (tppt) REVERT: I 56 MET cc_start: 0.8827 (mmm) cc_final: 0.8245 (mmm) REVERT: I 84 GLU cc_start: 0.8470 (tp30) cc_final: 0.8073 (tp30) REVERT: I 88 ARG cc_start: 0.7658 (ttp80) cc_final: 0.6791 (tmm-80) REVERT: I 96 GLU cc_start: 0.8468 (OUTLIER) cc_final: 0.7980 (pm20) REVERT: I 123 ASN cc_start: 0.8618 (m110) cc_final: 0.8241 (m-40) REVERT: J 27 GLU cc_start: 0.7958 (mt-10) cc_final: 0.7736 (mt-10) REVERT: J 52 PHE cc_start: 0.8122 (m-10) cc_final: 0.7655 (m-80) REVERT: J 71 ARG cc_start: 0.8772 (tpm170) cc_final: 0.8563 (tpt170) REVERT: J 77 TRP cc_start: 0.8087 (t60) cc_final: 0.7844 (t60) REVERT: J 78 GLU cc_start: 0.9084 (tp30) cc_final: 0.8453 (tp30) REVERT: J 105 TYR cc_start: 0.8857 (t80) cc_final: 0.8352 (t80) REVERT: J 116 ASP cc_start: 0.7414 (t0) cc_final: 0.7025 (t0) REVERT: J 120 ASN cc_start: 0.7798 (m110) cc_final: 0.7394 (m-40) REVERT: K 23 GLU cc_start: 0.7598 (tm-30) cc_final: 0.7031 (tm-30) REVERT: K 82 TRP cc_start: 0.8530 (p-90) cc_final: 0.7941 (p-90) REVERT: K 156 ASN cc_start: 0.7963 (m110) cc_final: 0.7493 (m-40) REVERT: K 161 LEU cc_start: 0.8585 (OUTLIER) cc_final: 0.8235 (tt) REVERT: K 250 TYR cc_start: 0.7869 (OUTLIER) cc_final: 0.6624 (p90) REVERT: K 285 LEU cc_start: 0.9314 (mt) cc_final: 0.9062 (mp) REVERT: K 288 MET cc_start: 0.7791 (mtm) cc_final: 0.7532 (ptp) REVERT: K 299 GLU cc_start: 0.7684 (tm-30) cc_final: 0.7473 (tm-30) REVERT: K 343 HIS cc_start: 0.7007 (m90) cc_final: 0.6406 (m90) REVERT: K 403 ASP cc_start: 0.7319 (OUTLIER) cc_final: 0.6385 (t70) REVERT: K 415 LEU cc_start: 0.8920 (OUTLIER) cc_final: 0.8677 (tt) REVERT: K 421 ARG cc_start: 0.8506 (OUTLIER) cc_final: 0.7947 (mtm-85) REVERT: K 427 GLN cc_start: 0.8111 (mm-40) cc_final: 0.7622 (mp10) REVERT: K 436 LEU cc_start: 0.8995 (mt) cc_final: 0.8502 (tp) REVERT: M 130 GLN cc_start: 0.7281 (OUTLIER) cc_final: 0.6914 (tt0) REVERT: M 147 ILE cc_start: 0.9053 (pt) cc_final: 0.8834 (mt) REVERT: M 198 ASP cc_start: 0.7650 (m-30) cc_final: 0.7121 (m-30) REVERT: M 204 GLN cc_start: 0.8386 (tm-30) cc_final: 0.8051 (tm-30) REVERT: M 277 LYS cc_start: 0.7842 (mppt) cc_final: 0.7531 (mppt) REVERT: N 26 TYR cc_start: 0.8554 (m-80) cc_final: 0.7751 (m-80) REVERT: N 63 THR cc_start: 0.8998 (t) cc_final: 0.8500 (p) REVERT: N 68 ASN cc_start: 0.7942 (t0) cc_final: 0.7591 (t0) REVERT: N 89 GLN cc_start: 0.8491 (OUTLIER) cc_final: 0.8126 (mt0) REVERT: N 100 TYR cc_start: 0.8591 (m-80) cc_final: 0.7967 (m-80) REVERT: N 171 MET cc_start: 0.7559 (mtm) cc_final: 0.7092 (mtm) REVERT: L 17 LEU cc_start: 0.9206 (tt) cc_final: 0.8813 (pp) REVERT: L 40 TYR cc_start: 0.8777 (m-10) cc_final: 0.8209 (m-80) REVERT: L 52 PHE cc_start: 0.7010 (m-80) cc_final: 0.6692 (m-80) REVERT: L 76 GLN cc_start: 0.8704 (mp10) cc_final: 0.8382 (mm110) REVERT: L 96 GLU cc_start: 0.8069 (pm20) cc_final: 0.7774 (pm20) REVERT: L 107 HIS cc_start: 0.6565 (m90) cc_final: 0.6041 (m170) REVERT: L 124 GLU cc_start: 0.6109 (OUTLIER) cc_final: 0.5906 (pm20) outliers start: 122 outliers final: 64 residues processed: 815 average time/residue: 0.1913 time to fit residues: 247.1943 Evaluate side-chains 753 residues out of total 2762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 672 time to evaluate : 1.133 ------------------------------------------------------------------------------- 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 44 VAL Chi-restraints excluded: chain B residue 102 MET Chi-restraints excluded: chain C residue 46 LEU 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 228 VAL Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain D residue 10 VAL Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 45 CYS 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 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 103 ILE Chi-restraints excluded: chain G residue 120 ASN Chi-restraints excluded: chain H residue 81 HIS Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain H residue 228 VAL Chi-restraints excluded: chain H residue 229 PHE 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 96 GLU Chi-restraints excluded: chain J residue 64 ASN Chi-restraints excluded: chain K residue 89 LEU Chi-restraints excluded: chain K residue 161 LEU Chi-restraints excluded: chain K residue 198 THR 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 403 ASP Chi-restraints excluded: chain K residue 415 LEU Chi-restraints excluded: chain K residue 421 ARG Chi-restraints excluded: chain K residue 430 THR 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 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 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 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: 0.9990 chunk 243 optimal weight: 0.6980 chunk 218 optimal weight: 4.9990 chunk 253 optimal weight: 0.9990 chunk 260 optimal weight: 3.9990 chunk 64 optimal weight: 0.3980 chunk 149 optimal weight: 0.9990 chunk 183 optimal weight: 0.9990 chunk 294 optimal weight: 0.8980 chunk 266 optimal weight: 0.6980 chunk 279 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 128 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 ** 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** ** D 181 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** ** 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 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 97 GLN J 8 GLN ** J 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 123 ASN ** K 521 ASN ** 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 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** ** L 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 98 GLN ** 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 = 0.4210 r_free = 0.4210 target = 0.154791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.121738 restraints weight = 46906.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.126212 restraints weight = 20953.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.129062 restraints weight = 12152.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 68)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.130892 restraints weight = 8420.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.131964 restraints weight = 6614.554| |-----------------------------------------------------------------------------| r_work (final): 0.3943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.3535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 27430 Z= 0.222 Angle : 0.825 14.119 37194 Z= 0.435 Chirality : 0.050 0.329 4023 Planarity : 0.006 0.069 4752 Dihedral : 14.735 174.152 4195 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 32.23 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.30 % Favored : 90.67 % Rotamer: Outliers : 4.82 % Allowed : 21.20 % Favored : 73.99 % 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: -2.63 (0.14), residues: 3184 helix: -0.78 (0.14), residues: 1288 sheet: -2.84 (0.24), residues: 386 loop : -2.28 (0.15), residues: 1510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 224 TYR 0.030 0.003 TYR E 178 PHE 0.037 0.003 PHE G 111 TRP 0.023 0.002 TRP A 165 HIS 0.026 0.002 HIS C 214 Details of bonding type rmsd/Z covalent geometry : bond 0.00513 / 0.22 (27430) covalent geometry : angle 0.82549 / 0.43 (37194) hydrogen bonds : bond 0.05080 / 3.35 ( 1148) hydrogen bonds : angle 6.89487 / 4.95 ( 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 876 residues out of total 2762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 743 time to evaluate : 1.141 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: A 119 PHE cc_start: 0.8251 (OUTLIER) cc_final: 0.6710 (t80) REVERT: A 126 ASN cc_start: 0.8229 (t0) cc_final: 0.7444 (t0) REVERT: A 164 GLU cc_start: 0.7938 (tp30) cc_final: 0.7533 (tp30) REVERT: A 167 GLN cc_start: 0.8779 (tm-30) cc_final: 0.7702 (tm-30) REVERT: A 168 TYR cc_start: 0.7732 (m-80) cc_final: 0.7140 (m-10) REVERT: B 102 MET cc_start: 0.7614 (OUTLIER) cc_final: 0.7291 (mtt) REVERT: B 141 MET cc_start: 0.6902 (mmt) cc_final: 0.6527 (mmt) REVERT: B 175 TYR cc_start: 0.8591 (t80) cc_final: 0.7977 (t80) REVERT: B 183 PHE cc_start: 0.7794 (m-80) cc_final: 0.6870 (m-10) REVERT: B 201 LEU cc_start: 0.8269 (OUTLIER) cc_final: 0.7974 (mm) REVERT: B 259 ARG cc_start: 0.7644 (mtp180) cc_final: 0.7418 (mtp180) REVERT: C 67 ILE cc_start: 0.8444 (OUTLIER) cc_final: 0.7910 (mm) REVERT: C 103 CYS cc_start: 0.8294 (m) cc_final: 0.8001 (m) REVERT: C 110 ARG cc_start: 0.7654 (ptm160) cc_final: 0.6803 (ptm160) REVERT: C 146 SER cc_start: 0.8265 (t) cc_final: 0.7909 (t) REVERT: C 220 GLN cc_start: 0.7686 (tm-30) cc_final: 0.6283 (tm-30) REVERT: C 256 GLU cc_start: 0.7641 (tm-30) cc_final: 0.7387 (tm-30) REVERT: D 35 GLN cc_start: 0.8394 (mm-40) cc_final: 0.7984 (tp-100) REVERT: D 36 THR cc_start: 0.7986 (OUTLIER) cc_final: 0.7651 (p) REVERT: D 102 MET cc_start: 0.8039 (mmt) cc_final: 0.7793 (mmt) REVERT: D 134 SER cc_start: 0.7709 (p) cc_final: 0.7029 (t) REVERT: D 138 ASP cc_start: 0.8438 (t0) cc_final: 0.8201 (t0) REVERT: D 169 ARG cc_start: 0.8089 (mtm-85) cc_final: 0.7712 (mtm-85) REVERT: D 246 ARG cc_start: 0.8500 (mtm110) cc_final: 0.8108 (mtm-85) REVERT: E 17 ASP cc_start: 0.8333 (t70) cc_final: 0.7786 (t0) REVERT: E 79 GLU cc_start: 0.7626 (tm-30) cc_final: 0.7178 (tm-30) REVERT: E 116 MET cc_start: 0.8184 (tpp) cc_final: 0.7807 (mmt) REVERT: E 204 GLN cc_start: 0.7835 (tm130) cc_final: 0.7244 (tm-30) REVERT: E 209 MET cc_start: 0.7950 (ttp) cc_final: 0.7428 (ttp) REVERT: E 226 LEU cc_start: 0.8769 (tp) cc_final: 0.8381 (tp) REVERT: E 233 ASN cc_start: 0.8225 (m-40) cc_final: 0.7855 (m-40) REVERT: E 241 ASP cc_start: 0.7099 (t70) cc_final: 0.6650 (t0) REVERT: E 265 LEU cc_start: 0.9031 (tp) cc_final: 0.8762 (tt) REVERT: F 48 ARG cc_start: 0.7173 (tpt170) cc_final: 0.6803 (tpm170) REVERT: F 72 ILE cc_start: 0.8314 (mm) cc_final: 0.7974 (mm) REVERT: F 116 MET cc_start: 0.8465 (tpp) cc_final: 0.8253 (tpp) REVERT: F 135 ARG cc_start: 0.8425 (mmm-85) cc_final: 0.8121 (tpp-160) REVERT: F 172 THR cc_start: 0.7961 (m) cc_final: 0.7088 (p) REVERT: F 187 HIS cc_start: 0.8192 (OUTLIER) cc_final: 0.7736 (p90) REVERT: F 209 MET cc_start: 0.6728 (tmm) cc_final: 0.6491 (tmm) REVERT: G 8 GLN cc_start: 0.8370 (mm-40) cc_final: 0.8139 (mm110) REVERT: G 16 ARG cc_start: 0.8789 (ttt-90) cc_final: 0.8403 (tpt-90) REVERT: G 17 LEU cc_start: 0.9264 (tt) cc_final: 0.8663 (pp) REVERT: G 68 PHE cc_start: 0.8069 (t80) cc_final: 0.7695 (t80) REVERT: G 71 ARG cc_start: 0.8726 (mmm160) cc_final: 0.8199 (mmm-85) REVERT: G 88 ARG cc_start: 0.8092 (OUTLIER) cc_final: 0.7115 (ttp80) REVERT: G 94 ASN cc_start: 0.8682 (p0) cc_final: 0.8064 (p0) REVERT: G 96 GLU cc_start: 0.8984 (pm20) cc_final: 0.8675 (pm20) REVERT: G 98 GLN cc_start: 0.8330 (tt0) cc_final: 0.7191 (tm-30) REVERT: G 103 ILE cc_start: 0.8950 (OUTLIER) cc_final: 0.8086 (tt) REVERT: G 107 HIS cc_start: 0.8495 (m90) cc_final: 0.7990 (m90) REVERT: G 122 PHE cc_start: 0.7837 (t80) cc_final: 0.7394 (t80) REVERT: H 11 PHE cc_start: 0.7582 (t80) cc_final: 0.6922 (t80) REVERT: H 81 HIS cc_start: 0.8568 (OUTLIER) cc_final: 0.7963 (t-90) REVERT: H 102 MET cc_start: 0.8833 (mmm) cc_final: 0.8064 (mmm) REVERT: H 178 TYR cc_start: 0.7126 (m-80) cc_final: 0.6452 (m-10) REVERT: H 181 HIS cc_start: 0.8063 (m-70) cc_final: 0.7460 (m-70) REVERT: H 191 GLN cc_start: 0.9253 (OUTLIER) cc_final: 0.9023 (pp30) REVERT: H 206 LEU cc_start: 0.9424 (mt) cc_final: 0.8995 (mt) REVERT: H 208 ASN cc_start: 0.8573 (m110) cc_final: 0.7456 (t0) REVERT: H 261 PHE cc_start: 0.7652 (t80) cc_final: 0.7317 (t80) REVERT: I 22 GLU cc_start: 0.8873 (tm-30) cc_final: 0.8178 (tm-30) REVERT: I 23 LYS cc_start: 0.8839 (tppt) cc_final: 0.8451 (tppt) REVERT: I 56 MET cc_start: 0.8981 (mmm) cc_final: 0.8606 (mmm) REVERT: I 77 TRP cc_start: 0.8654 (t60) cc_final: 0.7778 (t60) REVERT: I 81 GLN cc_start: 0.9037 (OUTLIER) cc_final: 0.8658 (mp10) REVERT: I 84 GLU cc_start: 0.8490 (tp30) cc_final: 0.8103 (tp30) REVERT: I 96 GLU cc_start: 0.8429 (pm20) cc_final: 0.7938 (pm20) REVERT: I 113 PHE cc_start: 0.8361 (m-80) cc_final: 0.8030 (m-10) REVERT: I 119 LYS cc_start: 0.9273 (ptmm) cc_final: 0.8827 (ptmm) REVERT: I 123 ASN cc_start: 0.8664 (m110) cc_final: 0.8281 (m110) REVERT: J 27 GLU cc_start: 0.7854 (mt-10) cc_final: 0.7518 (mt-10) REVERT: J 52 PHE cc_start: 0.8095 (m-10) cc_final: 0.7725 (m-80) REVERT: J 71 ARG cc_start: 0.8785 (tpt170) cc_final: 0.8289 (tpt170) REVERT: J 77 TRP cc_start: 0.8074 (t60) cc_final: 0.7840 (t60) REVERT: J 78 GLU cc_start: 0.9018 (tp30) cc_final: 0.8326 (tp30) REVERT: J 105 TYR cc_start: 0.8784 (t80) cc_final: 0.8253 (t80) REVERT: J 108 GLU cc_start: 0.8216 (mm-30) cc_final: 0.7944 (mm-30) REVERT: J 115 LYS cc_start: 0.5485 (mmtt) cc_final: 0.5192 (mmtt) REVERT: J 116 ASP cc_start: 0.7377 (t0) cc_final: 0.7074 (t0) REVERT: K 23 GLU cc_start: 0.7523 (tm-30) cc_final: 0.6962 (tm-30) REVERT: K 82 TRP cc_start: 0.8497 (p-90) cc_final: 0.7942 (p-90) REVERT: K 156 ASN cc_start: 0.8020 (m110) cc_final: 0.7497 (m110) REVERT: K 250 TYR cc_start: 0.7874 (OUTLIER) cc_final: 0.6439 (p90) REVERT: K 281 LEU cc_start: 0.8572 (mp) cc_final: 0.8211 (mp) REVERT: K 427 GLN cc_start: 0.7958 (mm-40) cc_final: 0.7721 (mp10) REVERT: K 453 MET cc_start: 0.6521 (mmp) cc_final: 0.6214 (mmp) REVERT: K 515 LEU cc_start: 0.8720 (mt) cc_final: 0.8468 (mt) REVERT: K 526 GLU cc_start: 0.7561 (mm-30) cc_final: 0.6648 (tp30) REVERT: M 16 GLN cc_start: 0.7369 (mm-40) cc_final: 0.6957 (tp40) REVERT: M 54 ILE cc_start: 0.8959 (mm) cc_final: 0.8743 (mm) REVERT: M 130 GLN cc_start: 0.7313 (OUTLIER) cc_final: 0.6941 (tt0) REVERT: M 147 ILE cc_start: 0.9203 (pt) cc_final: 0.8921 (mt) REVERT: M 204 GLN cc_start: 0.8285 (tm-30) cc_final: 0.7924 (tm-30) REVERT: M 277 LYS cc_start: 0.7801 (mppt) cc_final: 0.7503 (mppt) REVERT: N 26 TYR cc_start: 0.8469 (m-80) cc_final: 0.7593 (m-80) REVERT: N 63 THR cc_start: 0.8941 (t) cc_final: 0.8503 (p) REVERT: N 68 ASN cc_start: 0.7832 (t0) cc_final: 0.7396 (t0) REVERT: N 69 GLU cc_start: 0.7678 (mt-10) cc_final: 0.7088 (mt-10) REVERT: N 76 GLU cc_start: 0.6774 (mm-30) cc_final: 0.6548 (mm-30) REVERT: N 89 GLN cc_start: 0.8381 (OUTLIER) cc_final: 0.8074 (mt0) REVERT: N 100 TYR cc_start: 0.8564 (m-80) cc_final: 0.7996 (m-80) REVERT: L 40 TYR cc_start: 0.8839 (m-10) cc_final: 0.8194 (m-80) REVERT: L 52 PHE cc_start: 0.6784 (m-80) cc_final: 0.6547 (m-10) REVERT: L 56 MET cc_start: 0.7054 (mmm) cc_final: 0.6305 (tmm) REVERT: L 76 GLN cc_start: 0.8727 (mp10) cc_final: 0.8371 (mm110) REVERT: L 96 GLU cc_start: 0.8137 (pm20) cc_final: 0.7834 (pm20) REVERT: L 124 GLU cc_start: 0.6260 (OUTLIER) cc_final: 0.5893 (pm20) outliers start: 133 outliers final: 69 residues processed: 818 average time/residue: 0.1905 time to fit residues: 248.1790 Evaluate side-chains 779 residues out of total 2762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 695 time to evaluate : 1.076 ------------------------------------------------------------------------------- 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 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 46 LEU 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 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 45 CYS Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain E residue 52 ASN Chi-restraints excluded: chain E residue 109 ILE 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 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 F residue 187 HIS Chi-restraints excluded: chain G residue 10 ILE 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 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 212 HIS Chi-restraints excluded: chain H residue 228 VAL Chi-restraints excluded: chain H residue 229 PHE Chi-restraints excluded: chain H residue 266 VAL 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 K residue 89 LEU Chi-restraints excluded: chain K residue 91 TYR 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 430 THR Chi-restraints excluded: chain K residue 458 MET Chi-restraints excluded: chain K residue 478 LEU 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 137 ILE 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 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: 6.9990 chunk 44 optimal weight: 0.0970 chunk 12 optimal weight: 2.9990 chunk 132 optimal weight: 0.0020 chunk 80 optimal weight: 0.9990 chunk 306 optimal weight: 6.9990 chunk 55 optimal weight: 2.9990 chunk 305 optimal weight: 4.9990 chunk 319 optimal weight: 5.9990 chunk 296 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 overall best weight: 0.8192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 128 GLN ** 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 ** 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 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 120 ASN H 55 GLN H 58 GLN ** H 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 8 GLN ** J 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 74 GLN J 123 ASN ** K 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 383 ASN ** 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 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 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 74 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 = 0.4216 r_free = 0.4216 target = 0.155354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.121703 restraints weight = 47043.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.126267 restraints weight = 21094.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.129169 restraints weight = 12296.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.131044 restraints weight = 8571.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.132094 restraints weight = 6762.509| |-----------------------------------------------------------------------------| r_work (final): 0.3950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.3853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 27430 Z= 0.218 Angle : 0.828 17.366 37194 Z= 0.434 Chirality : 0.051 0.326 4023 Planarity : 0.006 0.175 4752 Dihedral : 14.632 173.074 4193 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 30.86 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.17 % Favored : 90.80 % Rotamer: Outliers : 4.71 % Allowed : 22.25 % Favored : 73.04 % 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: -2.56 (0.14), residues: 3184 helix: -0.72 (0.14), residues: 1281 sheet: -2.65 (0.24), residues: 373 loop : -2.29 (0.15), residues: 1530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG I 57 TYR 0.041 0.003 TYR K 440 PHE 0.036 0.003 PHE G 111 TRP 0.016 0.002 TRP A 165 HIS 0.026 0.002 HIS C 214 Details of bonding type rmsd/Z covalent geometry : bond 0.00503 / 0.22 (27430) covalent geometry : angle 0.82798 / 0.43 (37194) hydrogen bonds : bond 0.04900 / 3.22 ( 1148) hydrogen bonds : angle 6.78239 / 4.87 ( 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 883 residues out of total 2762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 753 time to evaluate : 1.081 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: A 119 PHE cc_start: 0.8232 (OUTLIER) cc_final: 0.6652 (t80) REVERT: A 126 ASN cc_start: 0.8189 (t0) cc_final: 0.7344 (t0) REVERT: A 164 GLU cc_start: 0.7992 (tp30) cc_final: 0.7368 (tp30) REVERT: A 167 GLN cc_start: 0.8919 (tm-30) cc_final: 0.7576 (tm-30) REVERT: A 168 TYR cc_start: 0.7842 (m-80) cc_final: 0.7199 (m-10) REVERT: B 7 TYR cc_start: 0.8050 (m-80) cc_final: 0.7717 (m-80) REVERT: B 141 MET cc_start: 0.6862 (mmt) cc_final: 0.6443 (mmt) REVERT: B 175 TYR cc_start: 0.8569 (t80) cc_final: 0.8304 (t80) REVERT: B 183 PHE cc_start: 0.8047 (m-80) cc_final: 0.7440 (m-10) REVERT: B 241 ASP cc_start: 0.7861 (t0) cc_final: 0.7366 (t0) REVERT: C 11 PHE cc_start: 0.7735 (t80) cc_final: 0.7405 (t80) REVERT: C 67 ILE cc_start: 0.8419 (OUTLIER) cc_final: 0.7906 (mm) REVERT: C 103 CYS cc_start: 0.8246 (m) cc_final: 0.7942 (m) REVERT: C 110 ARG cc_start: 0.7615 (ptm160) cc_final: 0.6795 (ptm160) REVERT: C 126 ARG cc_start: 0.6356 (ttp-110) cc_final: 0.6130 (ttp-110) REVERT: C 146 SER cc_start: 0.7844 (t) cc_final: 0.7544 (t) REVERT: C 188 PHE cc_start: 0.5783 (t80) cc_final: 0.5455 (t80) REVERT: C 220 GLN cc_start: 0.7773 (tm-30) cc_final: 0.6420 (tm-30) REVERT: C 243 LEU cc_start: 0.8085 (OUTLIER) cc_final: 0.7767 (mt) REVERT: C 256 GLU cc_start: 0.7596 (tm-30) cc_final: 0.7117 (tm-30) REVERT: C 279 LEU cc_start: 0.8485 (tp) cc_final: 0.8261 (tp) REVERT: D 35 GLN cc_start: 0.8418 (mm-40) cc_final: 0.7899 (tp40) REVERT: D 36 THR cc_start: 0.7926 (OUTLIER) cc_final: 0.7614 (p) REVERT: D 54 ILE cc_start: 0.8377 (mm) cc_final: 0.7940 (pt) REVERT: D 169 ARG cc_start: 0.8098 (mtm-85) cc_final: 0.7640 (mtm-85) REVERT: D 227 TYR cc_start: 0.8427 (m-80) cc_final: 0.8194 (m-80) REVERT: D 245 LYS cc_start: 0.8367 (mmtp) cc_final: 0.8105 (mmtp) REVERT: D 246 ARG cc_start: 0.8512 (mtm110) cc_final: 0.8242 (mtm-85) REVERT: E 17 ASP cc_start: 0.7922 (t70) cc_final: 0.7657 (t0) REVERT: E 79 GLU cc_start: 0.7646 (tm-30) cc_final: 0.7070 (tm-30) REVERT: E 101 TYR cc_start: 0.7942 (t80) cc_final: 0.7705 (t80) REVERT: E 116 MET cc_start: 0.8070 (tpp) cc_final: 0.7104 (mpp) REVERT: E 150 MET cc_start: 0.8551 (mmm) cc_final: 0.8301 (mmm) REVERT: E 167 MET cc_start: 0.8905 (mtm) cc_final: 0.8668 (mtp) REVERT: E 204 GLN cc_start: 0.7826 (tm130) cc_final: 0.7238 (tm-30) REVERT: E 209 MET cc_start: 0.7781 (ttp) cc_final: 0.7242 (ttp) REVERT: E 226 LEU cc_start: 0.8727 (tp) cc_final: 0.8327 (tp) REVERT: E 233 ASN cc_start: 0.8190 (m-40) cc_final: 0.7837 (m-40) REVERT: E 241 ASP cc_start: 0.7058 (t70) cc_final: 0.6638 (t0) REVERT: E 265 LEU cc_start: 0.9024 (tp) cc_final: 0.8741 (tt) REVERT: F 25 ASP cc_start: 0.7471 (OUTLIER) cc_final: 0.6520 (t0) REVERT: F 72 ILE cc_start: 0.8351 (mm) cc_final: 0.8007 (mm) REVERT: F 116 MET cc_start: 0.8400 (tpp) cc_final: 0.8156 (tpp) REVERT: F 135 ARG cc_start: 0.8456 (mmm-85) cc_final: 0.8141 (tpp-160) REVERT: F 141 MET cc_start: 0.8630 (ttp) cc_final: 0.8379 (ttt) REVERT: F 172 THR cc_start: 0.7884 (m) cc_final: 0.6902 (p) REVERT: F 187 HIS cc_start: 0.7925 (OUTLIER) cc_final: 0.7615 (p90) REVERT: F 209 MET cc_start: 0.6688 (tmm) cc_final: 0.6331 (tmm) REVERT: G 8 GLN cc_start: 0.8348 (mm-40) cc_final: 0.8130 (mm110) REVERT: G 56 MET cc_start: 0.8758 (mmm) cc_final: 0.8441 (mmm) REVERT: G 68 PHE cc_start: 0.8076 (t80) cc_final: 0.7703 (t80) REVERT: G 71 ARG cc_start: 0.8674 (mmm160) cc_final: 0.8210 (mmm-85) REVERT: G 88 ARG cc_start: 0.8025 (OUTLIER) cc_final: 0.6977 (ttp80) REVERT: G 94 ASN cc_start: 0.8852 (p0) cc_final: 0.8623 (p0) REVERT: G 103 ILE cc_start: 0.8726 (OUTLIER) cc_final: 0.7768 (tt) REVERT: G 110 GLN cc_start: 0.7542 (tp-100) cc_final: 0.7165 (tp-100) REVERT: G 111 PHE cc_start: 0.8005 (t80) cc_final: 0.7792 (t80) REVERT: G 121 LEU cc_start: 0.8397 (mt) cc_final: 0.8149 (pp) REVERT: G 122 PHE cc_start: 0.8059 (t80) cc_final: 0.7531 (t80) REVERT: H 11 PHE cc_start: 0.7408 (t80) cc_final: 0.6810 (t80) REVERT: H 81 HIS cc_start: 0.8456 (OUTLIER) cc_final: 0.7949 (t-90) REVERT: H 102 MET cc_start: 0.8862 (mmm) cc_final: 0.8071 (mmm) REVERT: H 178 TYR cc_start: 0.6976 (m-80) cc_final: 0.6241 (m-10) REVERT: H 181 HIS cc_start: 0.7694 (m-70) cc_final: 0.7429 (m-70) REVERT: H 191 GLN cc_start: 0.9194 (OUTLIER) cc_final: 0.8965 (pp30) REVERT: H 206 LEU cc_start: 0.9405 (mt) cc_final: 0.8979 (mt) REVERT: H 208 ASN cc_start: 0.8612 (m110) cc_final: 0.7491 (t0) REVERT: H 261 PHE cc_start: 0.7668 (t80) cc_final: 0.7364 (t80) REVERT: I 18 PHE cc_start: 0.8702 (t80) cc_final: 0.8322 (t80) REVERT: I 21 LEU cc_start: 0.8780 (mp) cc_final: 0.8520 (mp) REVERT: I 22 GLU cc_start: 0.8695 (tm-30) cc_final: 0.8014 (tm-30) REVERT: I 23 LYS cc_start: 0.8931 (tppt) cc_final: 0.8591 (tppt) REVERT: I 27 GLU cc_start: 0.7466 (mt-10) cc_final: 0.7164 (mt-10) REVERT: I 77 TRP cc_start: 0.8577 (t60) cc_final: 0.7848 (t60) REVERT: I 81 GLN cc_start: 0.8972 (OUTLIER) cc_final: 0.8506 (mp10) REVERT: I 84 GLU cc_start: 0.8559 (tp30) cc_final: 0.8108 (tp30) REVERT: I 88 ARG cc_start: 0.8158 (tmm-80) cc_final: 0.7065 (tmm-80) REVERT: I 96 GLU cc_start: 0.8515 (OUTLIER) cc_final: 0.7886 (pm20) REVERT: I 119 LYS cc_start: 0.9245 (ptmm) cc_final: 0.8857 (ptmm) REVERT: I 123 ASN cc_start: 0.8684 (m110) cc_final: 0.8271 (m110) REVERT: J 52 PHE cc_start: 0.7995 (m-10) cc_final: 0.7712 (m-80) REVERT: J 77 TRP cc_start: 0.8060 (t60) cc_final: 0.7762 (t60) REVERT: J 78 GLU cc_start: 0.8904 (tp30) cc_final: 0.8364 (tp30) REVERT: J 80 ARG cc_start: 0.8385 (mtm-85) cc_final: 0.8146 (ttm-80) REVERT: J 88 ARG cc_start: 0.7412 (OUTLIER) cc_final: 0.6860 (tpt90) REVERT: J 98 GLN cc_start: 0.8428 (tt0) cc_final: 0.7820 (tp40) REVERT: J 105 TYR cc_start: 0.8855 (t80) cc_final: 0.8362 (t80) REVERT: J 115 LYS cc_start: 0.5494 (mmtt) cc_final: 0.5217 (mmtt) REVERT: J 116 ASP cc_start: 0.7497 (t0) cc_final: 0.7253 (t0) REVERT: J 120 ASN cc_start: 0.8082 (p0) cc_final: 0.7745 (p0) REVERT: J 123 ASN cc_start: 0.7596 (m110) cc_final: 0.7303 (m110) REVERT: K 12 ARG cc_start: 0.8123 (mmp80) cc_final: 0.7819 (mmp80) REVERT: K 23 GLU cc_start: 0.7516 (tm-30) cc_final: 0.6884 (tm-30) REVERT: K 82 TRP cc_start: 0.8500 (p-90) cc_final: 0.7926 (p-90) REVERT: K 141 MET cc_start: 0.2664 (tpt) cc_final: 0.2105 (tpt) REVERT: K 250 TYR cc_start: 0.7828 (OUTLIER) cc_final: 0.6641 (p90) REVERT: K 281 LEU cc_start: 0.8580 (mp) cc_final: 0.8226 (mp) REVERT: K 420 LEU cc_start: 0.8826 (OUTLIER) cc_final: 0.8583 (mm) REVERT: K 421 ARG cc_start: 0.8646 (OUTLIER) cc_final: 0.8322 (ttm-80) REVERT: K 453 MET cc_start: 0.6497 (mmp) cc_final: 0.6175 (mmp) REVERT: K 496 ARG cc_start: 0.7979 (OUTLIER) cc_final: 0.7695 (mtm180) REVERT: K 515 LEU cc_start: 0.8635 (mt) cc_final: 0.8396 (mt) REVERT: K 526 GLU cc_start: 0.7574 (mm-30) cc_final: 0.6723 (tp30) REVERT: M 16 GLN cc_start: 0.7350 (mm-40) cc_final: 0.6934 (tp40) REVERT: M 54 ILE cc_start: 0.8939 (mm) cc_final: 0.8710 (mm) REVERT: M 130 GLN cc_start: 0.7318 (OUTLIER) cc_final: 0.6969 (tt0) REVERT: M 147 ILE cc_start: 0.9190 (pt) cc_final: 0.8866 (mt) REVERT: M 204 GLN cc_start: 0.8265 (tm-30) cc_final: 0.7884 (tm-30) REVERT: M 277 LYS cc_start: 0.7785 (mppt) cc_final: 0.7496 (mppt) REVERT: N 26 TYR cc_start: 0.8642 (m-80) cc_final: 0.7748 (m-80) REVERT: N 68 ASN cc_start: 0.7863 (t0) cc_final: 0.7318 (t0) REVERT: N 69 GLU cc_start: 0.7541 (mt-10) cc_final: 0.7120 (mt-10) REVERT: N 76 GLU cc_start: 0.7099 (mm-30) cc_final: 0.6196 (mm-30) REVERT: N 89 GLN cc_start: 0.8387 (OUTLIER) cc_final: 0.8036 (mt0) REVERT: N 100 TYR cc_start: 0.8505 (m-80) cc_final: 0.7944 (m-80) REVERT: N 106 PHE cc_start: 0.8692 (p90) cc_final: 0.8190 (p90) REVERT: N 151 LEU cc_start: 0.8895 (tt) cc_final: 0.8667 (tt) REVERT: N 152 LEU cc_start: 0.8608 (mp) cc_final: 0.8335 (mp) REVERT: L 40 TYR cc_start: 0.8546 (m-10) cc_final: 0.7908 (m-80) REVERT: L 56 MET cc_start: 0.7374 (mmm) cc_final: 0.6433 (tmm) REVERT: L 76 GLN cc_start: 0.8728 (mp10) cc_final: 0.8362 (mm110) REVERT: L 96 GLU cc_start: 0.8250 (pm20) cc_final: 0.7892 (pm20) REVERT: L 98 GLN cc_start: 0.7848 (tt0) cc_final: 0.7431 (pt0) REVERT: L 124 GLU cc_start: 0.6201 (OUTLIER) cc_final: 0.5849 (pm20) outliers start: 130 outliers final: 74 residues processed: 823 average time/residue: 0.1913 time to fit residues: 249.9237 Evaluate side-chains 797 residues out of total 2762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 703 time to evaluate : 1.061 ------------------------------------------------------------------------------- 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 43 ASP Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 102 MET Chi-restraints excluded: chain B residue 130 GLN Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain C residue 32 ILE Chi-restraints excluded: chain C residue 46 LEU 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 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 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 109 ILE 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 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 187 HIS 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 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 191 GLN Chi-restraints excluded: chain H residue 212 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 13 VAL Chi-restraints excluded: chain I residue 20 VAL 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 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 383 ASN Chi-restraints excluded: chain K residue 403 ASP Chi-restraints excluded: chain K residue 420 LEU Chi-restraints excluded: chain K residue 421 ARG 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 125 VAL Chi-restraints excluded: chain M residue 130 GLN Chi-restraints excluded: chain M residue 137 ILE 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 45 SER Chi-restraints excluded: chain L residue 81 GLN Chi-restraints excluded: chain L residue 93 LEU Chi-restraints excluded: chain L residue 124 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 8 optimal weight: 0.5980 chunk 20 optimal weight: 0.8980 chunk 238 optimal weight: 2.9990 chunk 150 optimal weight: 8.9990 chunk 88 optimal weight: 0.7980 chunk 44 optimal weight: 0.6980 chunk 104 optimal weight: 10.0000 chunk 97 optimal weight: 0.6980 chunk 156 optimal weight: 1.9990 chunk 123 optimal weight: 0.9990 chunk 203 optimal weight: 4.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 128 GLN ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 220 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 52 ASN ** 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** ** G 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 98 GLN J 8 GLN ** J 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 62 HIS ** 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 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 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.156673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.122817 restraints weight = 46678.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.127386 restraints weight = 21027.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.130281 restraints weight = 12266.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 68)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.132136 restraints weight = 8565.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.133189 restraints weight = 6774.628| |-----------------------------------------------------------------------------| r_work (final): 0.3953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.4101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 27430 Z= 0.214 Angle : 0.833 17.349 37194 Z= 0.436 Chirality : 0.051 0.504 4023 Planarity : 0.006 0.075 4752 Dihedral : 14.585 172.358 4193 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 31.41 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.30 % Favored : 90.67 % Rotamer: Outliers : 4.13 % Allowed : 23.84 % Favored : 72.03 % 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: -2.51 (0.14), residues: 3184 helix: -0.68 (0.14), residues: 1273 sheet: -2.57 (0.25), residues: 370 loop : -2.28 (0.14), residues: 1541 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG I 57 TYR 0.037 0.003 TYR H 101 PHE 0.034 0.002 PHE G 111 TRP 0.015 0.002 TRP H 203 HIS 0.023 0.002 HIS C 214 Details of bonding type rmsd/Z covalent geometry : bond 0.00494 / 0.21 (27430) covalent geometry : angle 0.83319 / 0.44 (37194) hydrogen bonds : bond 0.04863 / 3.23 ( 1148) hydrogen bonds : angle 6.73238 / 4.82 ( 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 846 residues out of total 2762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 732 time to evaluate : 1.089 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: A 119 PHE cc_start: 0.8207 (OUTLIER) cc_final: 0.6693 (t80) REVERT: A 126 ASN cc_start: 0.8150 (t0) cc_final: 0.7272 (t0) REVERT: A 164 GLU cc_start: 0.8028 (tp30) cc_final: 0.7355 (tp30) REVERT: A 167 GLN cc_start: 0.8871 (tm-30) cc_final: 0.7481 (tm-30) REVERT: A 168 TYR cc_start: 0.7763 (m-80) cc_final: 0.7120 (m-10) REVERT: B 7 TYR cc_start: 0.8109 (m-80) cc_final: 0.7873 (m-80) REVERT: B 141 MET cc_start: 0.6719 (mmt) cc_final: 0.6338 (mmt) REVERT: B 183 PHE cc_start: 0.7999 (m-80) cc_final: 0.7762 (m-10) REVERT: B 201 LEU cc_start: 0.8219 (OUTLIER) cc_final: 0.7948 (mm) REVERT: B 241 ASP cc_start: 0.7836 (t70) cc_final: 0.7474 (t0) REVERT: C 11 PHE cc_start: 0.7710 (t80) cc_final: 0.7355 (t80) REVERT: C 67 ILE cc_start: 0.8406 (OUTLIER) cc_final: 0.7832 (mm) REVERT: C 103 CYS cc_start: 0.8450 (m) cc_final: 0.8132 (m) REVERT: C 110 ARG cc_start: 0.7578 (ptm160) cc_final: 0.7257 (ptm160) REVERT: C 146 SER cc_start: 0.7650 (t) cc_final: 0.7300 (t) REVERT: C 220 GLN cc_start: 0.7637 (tm-30) cc_final: 0.6149 (tm-30) REVERT: C 222 ASN cc_start: 0.8259 (m110) cc_final: 0.6064 (m110) REVERT: C 243 LEU cc_start: 0.8030 (OUTLIER) cc_final: 0.7753 (mt) REVERT: C 256 GLU cc_start: 0.7609 (tm-30) cc_final: 0.7118 (tm-30) REVERT: C 271 LYS cc_start: 0.8471 (mmmt) cc_final: 0.8226 (mmmt) REVERT: D 35 GLN cc_start: 0.8491 (mm-40) cc_final: 0.8002 (tp40) REVERT: D 36 THR cc_start: 0.7900 (OUTLIER) cc_final: 0.7588 (p) REVERT: D 48 ARG cc_start: 0.6939 (OUTLIER) cc_final: 0.6040 (ttm-80) REVERT: D 169 ARG cc_start: 0.8104 (mtm-85) cc_final: 0.7606 (mtm-85) REVERT: D 227 TYR cc_start: 0.8389 (m-80) cc_final: 0.8132 (m-80) REVERT: D 245 LYS cc_start: 0.8346 (mmtp) cc_final: 0.8050 (mmtp) REVERT: D 246 ARG cc_start: 0.8509 (mtm110) cc_final: 0.8219 (mtm-85) REVERT: E 17 ASP cc_start: 0.7944 (t70) cc_final: 0.7640 (t0) REVERT: E 79 GLU cc_start: 0.7661 (tm-30) cc_final: 0.7212 (tm-30) REVERT: E 101 TYR cc_start: 0.7998 (t80) cc_final: 0.7767 (t80) REVERT: E 116 MET cc_start: 0.8083 (tpp) cc_final: 0.7196 (mpp) REVERT: E 167 MET cc_start: 0.8861 (mtm) cc_final: 0.8588 (mtp) REVERT: E 204 GLN cc_start: 0.7802 (tm130) cc_final: 0.7235 (tm-30) REVERT: E 209 MET cc_start: 0.7772 (ttp) cc_final: 0.7250 (ttp) REVERT: E 226 LEU cc_start: 0.8677 (tp) cc_final: 0.8301 (tp) REVERT: E 233 ASN cc_start: 0.8185 (m-40) cc_final: 0.7860 (m-40) REVERT: E 234 ASN cc_start: 0.8265 (m-40) cc_final: 0.8021 (m-40) REVERT: E 241 ASP cc_start: 0.7083 (t70) cc_final: 0.6764 (t0) REVERT: F 25 ASP cc_start: 0.7451 (OUTLIER) cc_final: 0.6520 (t0) REVERT: F 72 ILE cc_start: 0.8235 (mm) cc_final: 0.7843 (mm) REVERT: F 135 ARG cc_start: 0.8413 (mmm-85) cc_final: 0.8114 (tpp-160) REVERT: F 141 MET cc_start: 0.8437 (ttp) cc_final: 0.8092 (ttt) REVERT: F 172 THR cc_start: 0.7942 (m) cc_final: 0.7088 (p) REVERT: F 187 HIS cc_start: 0.7870 (OUTLIER) cc_final: 0.7363 (p90) REVERT: F 209 MET cc_start: 0.6775 (tmm) cc_final: 0.6308 (tmm) REVERT: G 56 MET cc_start: 0.8730 (mmm) cc_final: 0.8414 (mmm) REVERT: G 68 PHE cc_start: 0.8103 (t80) cc_final: 0.7758 (t80) REVERT: G 71 ARG cc_start: 0.8676 (mmm160) cc_final: 0.8226 (mmm-85) REVERT: G 88 ARG cc_start: 0.7977 (OUTLIER) cc_final: 0.6901 (ttp80) REVERT: G 106 TYR cc_start: 0.8192 (m-80) cc_final: 0.7930 (m-80) REVERT: G 121 LEU cc_start: 0.8321 (mt) cc_final: 0.7998 (pp) REVERT: G 122 PHE cc_start: 0.7991 (t80) cc_final: 0.7424 (t80) REVERT: H 11 PHE cc_start: 0.7505 (t80) cc_final: 0.6860 (t80) REVERT: H 81 HIS cc_start: 0.8627 (OUTLIER) cc_final: 0.7978 (t-90) REVERT: H 102 MET cc_start: 0.9037 (mmm) cc_final: 0.8432 (mmm) REVERT: H 178 TYR cc_start: 0.6985 (m-80) cc_final: 0.6270 (m-10) REVERT: H 181 HIS cc_start: 0.7732 (m-70) cc_final: 0.7437 (m-70) REVERT: H 206 LEU cc_start: 0.9393 (mt) cc_final: 0.8993 (mt) REVERT: H 208 ASN cc_start: 0.8632 (m110) cc_final: 0.7511 (t0) REVERT: H 261 PHE cc_start: 0.7679 (t80) cc_final: 0.7384 (t80) REVERT: I 18 PHE cc_start: 0.8609 (t80) cc_final: 0.8310 (t80) REVERT: I 21 LEU cc_start: 0.8796 (mp) cc_final: 0.8575 (mp) REVERT: I 22 GLU cc_start: 0.8689 (tm-30) cc_final: 0.8025 (tm-30) REVERT: I 23 LYS cc_start: 0.8911 (tppt) cc_final: 0.8646 (tppt) REVERT: I 57 ARG cc_start: 0.7482 (tpp80) cc_final: 0.7251 (tpp80) REVERT: I 77 TRP cc_start: 0.8469 (t60) cc_final: 0.7767 (t60) REVERT: I 81 GLN cc_start: 0.9038 (OUTLIER) cc_final: 0.8644 (mp10) REVERT: I 84 GLU cc_start: 0.8581 (tp30) cc_final: 0.8154 (tp30) REVERT: I 96 GLU cc_start: 0.8521 (OUTLIER) cc_final: 0.7869 (pm20) REVERT: I 113 PHE cc_start: 0.8028 (m-10) cc_final: 0.7541 (m-10) REVERT: I 119 LYS cc_start: 0.9251 (ptmm) cc_final: 0.8892 (ptmm) REVERT: I 123 ASN cc_start: 0.8706 (m110) cc_final: 0.8296 (m110) REVERT: J 52 PHE cc_start: 0.7945 (m-10) cc_final: 0.7728 (m-80) REVERT: J 78 GLU cc_start: 0.8909 (tp30) cc_final: 0.8320 (tp30) REVERT: J 80 ARG cc_start: 0.8334 (mtm-85) cc_final: 0.8133 (mtm-85) REVERT: J 88 ARG cc_start: 0.7467 (OUTLIER) cc_final: 0.6946 (tpt90) REVERT: J 98 GLN cc_start: 0.8404 (tt0) cc_final: 0.7866 (tp40) REVERT: J 105 TYR cc_start: 0.8830 (t80) cc_final: 0.8307 (t80) REVERT: J 108 GLU cc_start: 0.8219 (mm-30) cc_final: 0.7656 (mt-10) REVERT: J 115 LYS cc_start: 0.5829 (mmtt) cc_final: 0.5589 (mmtt) REVERT: J 116 ASP cc_start: 0.7315 (t0) cc_final: 0.7000 (t0) REVERT: J 120 ASN cc_start: 0.8072 (p0) cc_final: 0.7820 (p0) REVERT: K 12 ARG cc_start: 0.8094 (mmp80) cc_final: 0.7793 (mmp80) REVERT: K 23 GLU cc_start: 0.7480 (tm-30) cc_final: 0.6853 (tm-30) REVERT: K 59 ARG cc_start: 0.9079 (mpp80) cc_final: 0.8857 (mpp80) REVERT: K 82 TRP cc_start: 0.8498 (p-90) cc_final: 0.7890 (p-90) REVERT: K 250 TYR cc_start: 0.7918 (OUTLIER) cc_final: 0.6410 (p90) REVERT: K 281 LEU cc_start: 0.8537 (mp) cc_final: 0.8261 (mp) REVERT: K 420 LEU cc_start: 0.8846 (OUTLIER) cc_final: 0.8623 (mm) REVERT: K 421 ARG cc_start: 0.8695 (OUTLIER) cc_final: 0.8357 (ttm-80) REVERT: K 453 MET cc_start: 0.6352 (mmp) cc_final: 0.6103 (mmp) REVERT: K 460 LEU cc_start: 0.6489 (OUTLIER) cc_final: 0.5947 (tt) REVERT: K 526 GLU cc_start: 0.7544 (mm-30) cc_final: 0.6703 (tp30) REVERT: M 54 ILE cc_start: 0.8877 (mm) cc_final: 0.8650 (mm) REVERT: M 102 MET cc_start: 0.6084 (mtp) cc_final: 0.5459 (mtp) REVERT: M 130 GLN cc_start: 0.7254 (OUTLIER) cc_final: 0.7021 (tt0) REVERT: M 204 GLN cc_start: 0.8273 (tm-30) cc_final: 0.7863 (tm-30) REVERT: M 221 MET cc_start: 0.8445 (mtp) cc_final: 0.8188 (ttt) REVERT: M 277 LYS cc_start: 0.7728 (mppt) cc_final: 0.7478 (mppt) REVERT: N 7 ILE cc_start: 0.8167 (mp) cc_final: 0.7817 (mm) REVERT: N 26 TYR cc_start: 0.8697 (m-80) cc_final: 0.7786 (m-80) REVERT: N 68 ASN cc_start: 0.7867 (t0) cc_final: 0.7213 (t0) REVERT: N 69 GLU cc_start: 0.7554 (mt-10) cc_final: 0.6998 (tt0) REVERT: N 89 GLN cc_start: 0.8332 (OUTLIER) cc_final: 0.8118 (mt0) REVERT: N 100 TYR cc_start: 0.8518 (m-80) cc_final: 0.7837 (m-80) REVERT: N 106 PHE cc_start: 0.8498 (p90) cc_final: 0.8244 (p90) REVERT: N 151 LEU cc_start: 0.8867 (tt) cc_final: 0.8641 (tt) REVERT: N 152 LEU cc_start: 0.8604 (mp) cc_final: 0.8300 (mp) REVERT: L 40 TYR cc_start: 0.8671 (m-10) cc_final: 0.7933 (m-80) REVERT: L 56 MET cc_start: 0.7280 (mmm) cc_final: 0.6349 (tmm) REVERT: L 76 GLN cc_start: 0.8642 (mp10) cc_final: 0.8271 (mm110) REVERT: L 96 GLU cc_start: 0.8265 (pm20) cc_final: 0.7996 (pm20) REVERT: L 124 GLU cc_start: 0.6215 (OUTLIER) cc_final: 0.5886 (pm20) outliers start: 114 outliers final: 71 residues processed: 791 average time/residue: 0.1939 time to fit residues: 242.3907 Evaluate side-chains 777 residues out of total 2762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 686 time to evaluate : 1.145 ------------------------------------------------------------------------------- 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 32 ILE 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 257 VAL Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain C residue 32 ILE Chi-restraints excluded: chain C residue 46 LEU 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 177 LEU 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 D residue 36 THR Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 45 CYS Chi-restraints excluded: chain D residue 48 ARG Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain E residue 109 ILE 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 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 187 HIS 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 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 20 VAL 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 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 403 ASP Chi-restraints excluded: chain K residue 420 LEU Chi-restraints excluded: chain K residue 421 ARG Chi-restraints excluded: chain K residue 458 MET Chi-restraints excluded: chain K residue 460 LEU Chi-restraints excluded: chain M residue 46 LEU Chi-restraints excluded: chain M residue 130 GLN Chi-restraints excluded: chain M residue 137 ILE 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 171 MET 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 81 GLN Chi-restraints excluded: chain L residue 84 GLU Chi-restraints excluded: chain L residue 124 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 280 optimal weight: 4.9990 chunk 3 optimal weight: 1.9990 chunk 134 optimal weight: 0.5980 chunk 178 optimal weight: 0.9990 chunk 247 optimal weight: 4.9990 chunk 318 optimal weight: 5.9990 chunk 224 optimal weight: 2.9990 chunk 171 optimal weight: 20.0000 chunk 109 optimal weight: 5.9990 chunk 36 optimal weight: 0.2980 chunk 249 optimal weight: 0.5980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 128 GLN ** 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 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 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** ** 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 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 120 ASN ** H 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 97 GLN J 8 GLN ** J 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 74 GLN ** J 85 HIS ** 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 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 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 25 GLN ** L 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.156919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.123657 restraints weight = 47219.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.128183 restraints weight = 21150.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.131072 restraints weight = 12297.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.132917 restraints weight = 8530.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.133979 restraints weight = 6716.093| |-----------------------------------------------------------------------------| r_work (final): 0.3977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.4315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 27430 Z= 0.219 Angle : 0.837 18.078 37194 Z= 0.438 Chirality : 0.051 0.490 4023 Planarity : 0.006 0.074 4752 Dihedral : 14.546 171.550 4192 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 31.26 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.36 % Favored : 90.61 % Rotamer: Outliers : 4.49 % Allowed : 24.17 % Favored : 71.34 % 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: -2.44 (0.14), residues: 3184 helix: -0.60 (0.14), residues: 1259 sheet: -2.56 (0.25), residues: 364 loop : -2.24 (0.14), residues: 1561 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG I 57 TYR 0.043 0.003 TYR B 175 PHE 0.040 0.003 PHE M 13 TRP 0.070 0.003 TRP J 77 HIS 0.026 0.002 HIS C 214 Details of bonding type rmsd/Z covalent geometry : bond 0.00502 / 0.22 (27430) covalent geometry : angle 0.83732 / 0.44 (37194) hydrogen bonds : bond 0.04759 / 3.15 ( 1148) hydrogen bonds : angle 6.68727 / 4.79 ( 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 837 residues out of total 2762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 713 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: A 119 PHE cc_start: 0.7964 (OUTLIER) cc_final: 0.6444 (t80) REVERT: A 126 ASN cc_start: 0.8260 (t0) cc_final: 0.7387 (t0) REVERT: A 164 GLU cc_start: 0.8049 (tp30) cc_final: 0.7283 (tp30) REVERT: A 167 GLN cc_start: 0.8777 (tm-30) cc_final: 0.7065 (tm-30) REVERT: A 168 TYR cc_start: 0.7646 (m-80) cc_final: 0.6720 (m-10) REVERT: A 169 GLU cc_start: 0.7763 (tt0) cc_final: 0.7436 (tt0) REVERT: B 141 MET cc_start: 0.6370 (mmt) cc_final: 0.5916 (mmt) REVERT: B 183 PHE cc_start: 0.7988 (m-80) cc_final: 0.7767 (m-80) REVERT: B 201 LEU cc_start: 0.8302 (OUTLIER) cc_final: 0.8027 (mm) REVERT: B 241 ASP cc_start: 0.7848 (t70) cc_final: 0.7248 (t0) REVERT: C 11 PHE cc_start: 0.7746 (t80) cc_final: 0.7427 (t80) REVERT: C 67 ILE cc_start: 0.8376 (OUTLIER) cc_final: 0.7768 (mm) REVERT: C 103 CYS cc_start: 0.8469 (m) cc_final: 0.8146 (m) REVERT: C 110 ARG cc_start: 0.7549 (ptm160) cc_final: 0.7313 (ptm160) REVERT: C 126 ARG cc_start: 0.5949 (ttp-110) cc_final: 0.5722 (ttp-110) REVERT: C 146 SER cc_start: 0.7717 (t) cc_final: 0.7377 (t) REVERT: C 220 GLN cc_start: 0.7694 (tm-30) cc_final: 0.6110 (tm-30) REVERT: C 222 ASN cc_start: 0.8241 (m110) cc_final: 0.5965 (m110) REVERT: C 243 LEU cc_start: 0.7954 (OUTLIER) cc_final: 0.7567 (mt) REVERT: C 256 GLU cc_start: 0.7400 (tm-30) cc_final: 0.6940 (tm-30) REVERT: C 271 LYS cc_start: 0.8442 (mmmt) cc_final: 0.8205 (mmmt) REVERT: D 35 GLN cc_start: 0.8474 (mm-40) cc_final: 0.7958 (tp40) REVERT: D 36 THR cc_start: 0.7876 (OUTLIER) cc_final: 0.7639 (p) REVERT: D 48 ARG cc_start: 0.6925 (OUTLIER) cc_final: 0.5718 (ttm-80) REVERT: D 169 ARG cc_start: 0.8079 (mtm-85) cc_final: 0.7623 (mtm-85) REVERT: D 227 TYR cc_start: 0.8398 (m-80) cc_final: 0.8117 (m-80) REVERT: D 245 LYS cc_start: 0.8155 (mmtp) cc_final: 0.7952 (mmtp) REVERT: E 17 ASP cc_start: 0.7704 (t70) cc_final: 0.7345 (t0) REVERT: E 79 GLU cc_start: 0.7754 (tm-30) cc_final: 0.7280 (tm-30) REVERT: E 116 MET cc_start: 0.8155 (tpp) cc_final: 0.7376 (mpp) REVERT: E 150 MET cc_start: 0.8294 (mmm) cc_final: 0.7911 (mmm) REVERT: E 167 MET cc_start: 0.8865 (mtm) cc_final: 0.8600 (mtp) REVERT: E 204 GLN cc_start: 0.7826 (tm130) cc_final: 0.7288 (tm-30) REVERT: E 209 MET cc_start: 0.7785 (ttp) cc_final: 0.7236 (ttp) REVERT: E 226 LEU cc_start: 0.8696 (tp) cc_final: 0.8337 (tp) REVERT: E 233 ASN cc_start: 0.8129 (m-40) cc_final: 0.7821 (m-40) REVERT: E 234 ASN cc_start: 0.8245 (m-40) cc_final: 0.8002 (m-40) REVERT: E 241 ASP cc_start: 0.7149 (t70) cc_final: 0.6824 (t0) REVERT: E 264 TYR cc_start: 0.8519 (OUTLIER) cc_final: 0.8249 (m-10) REVERT: F 25 ASP cc_start: 0.7468 (OUTLIER) cc_final: 0.6603 (t0) REVERT: F 72 ILE cc_start: 0.8147 (mm) cc_final: 0.7805 (mm) REVERT: F 135 ARG cc_start: 0.8517 (mmm-85) cc_final: 0.7987 (tpp-160) REVERT: F 141 MET cc_start: 0.8527 (ttp) cc_final: 0.8194 (ttt) REVERT: F 187 HIS cc_start: 0.7743 (OUTLIER) cc_final: 0.7278 (p90) REVERT: F 209 MET cc_start: 0.6899 (tmm) cc_final: 0.6629 (tmm) REVERT: G 8 GLN cc_start: 0.8249 (mm110) cc_final: 0.7695 (mm-40) REVERT: G 23 LYS cc_start: 0.8285 (mmtp) cc_final: 0.8082 (mmtp) REVERT: G 68 PHE cc_start: 0.8030 (t80) cc_final: 0.7683 (t80) REVERT: G 88 ARG cc_start: 0.7995 (OUTLIER) cc_final: 0.6898 (ttp80) REVERT: G 96 GLU cc_start: 0.8938 (pm20) cc_final: 0.8648 (pm20) REVERT: G 106 TYR cc_start: 0.8301 (m-80) cc_final: 0.7961 (m-80) REVERT: G 110 GLN cc_start: 0.7324 (tp-100) cc_final: 0.7006 (tp-100) REVERT: G 120 ASN cc_start: 0.8619 (OUTLIER) cc_final: 0.8227 (m110) REVERT: G 122 PHE cc_start: 0.8122 (t80) cc_final: 0.7861 (t80) REVERT: H 11 PHE cc_start: 0.7560 (t80) cc_final: 0.6867 (t80) REVERT: H 35 GLN cc_start: 0.7937 (tp40) cc_final: 0.7722 (tp40) REVERT: H 81 HIS cc_start: 0.8549 (OUTLIER) cc_final: 0.7932 (t-90) REVERT: H 102 MET cc_start: 0.9008 (mmm) cc_final: 0.8400 (mmm) REVERT: H 178 TYR cc_start: 0.6801 (m-80) cc_final: 0.6186 (m-10) REVERT: H 206 LEU cc_start: 0.9392 (mt) cc_final: 0.8977 (mt) REVERT: H 208 ASN cc_start: 0.8704 (m110) cc_final: 0.7692 (t0) REVERT: H 261 PHE cc_start: 0.7703 (t80) cc_final: 0.7414 (t80) REVERT: I 16 ARG cc_start: 0.8772 (OUTLIER) cc_final: 0.8252 (ttt90) REVERT: I 22 GLU cc_start: 0.8704 (tm-30) cc_final: 0.8157 (tm-30) REVERT: I 74 GLN cc_start: 0.9005 (pt0) cc_final: 0.8785 (mt0) REVERT: I 77 TRP cc_start: 0.8449 (t60) cc_final: 0.7750 (t60) REVERT: I 81 GLN cc_start: 0.9095 (OUTLIER) cc_final: 0.8577 (mp10) REVERT: I 84 GLU cc_start: 0.8559 (tp30) cc_final: 0.7896 (tp30) REVERT: I 91 ASN cc_start: 0.8848 (t0) cc_final: 0.8341 (t0) REVERT: I 96 GLU cc_start: 0.8579 (OUTLIER) cc_final: 0.7831 (pm20) REVERT: I 108 GLU cc_start: 0.8049 (mt-10) cc_final: 0.7714 (mm-30) REVERT: I 113 PHE cc_start: 0.8088 (m-10) cc_final: 0.7516 (m-10) REVERT: I 119 LYS cc_start: 0.9248 (ptmm) cc_final: 0.8917 (ptmm) REVERT: I 123 ASN cc_start: 0.8693 (m110) cc_final: 0.8293 (m110) REVERT: J 52 PHE cc_start: 0.7937 (m-10) cc_final: 0.7720 (m-80) REVERT: J 71 ARG cc_start: 0.8674 (tpt170) cc_final: 0.8043 (tpt170) REVERT: J 77 TRP cc_start: 0.7879 (t60) cc_final: 0.7497 (t60) REVERT: J 78 GLU cc_start: 0.8844 (tp30) cc_final: 0.8401 (tp30) REVERT: J 88 ARG cc_start: 0.7568 (OUTLIER) cc_final: 0.6940 (tpt90) REVERT: J 91 ASN cc_start: 0.8593 (m-40) cc_final: 0.8007 (m-40) REVERT: J 98 GLN cc_start: 0.8407 (tt0) cc_final: 0.7895 (tp40) REVERT: J 105 TYR cc_start: 0.8853 (t80) cc_final: 0.8391 (t80) REVERT: J 108 GLU cc_start: 0.8129 (mm-30) cc_final: 0.7715 (mt-10) REVERT: J 116 ASP cc_start: 0.7330 (t0) cc_final: 0.6965 (t0) REVERT: J 120 ASN cc_start: 0.8035 (p0) cc_final: 0.7696 (p0) REVERT: J 123 ASN cc_start: 0.7842 (m110) cc_final: 0.7585 (m-40) REVERT: K 12 ARG cc_start: 0.8084 (mmp80) cc_final: 0.7795 (mmp80) REVERT: K 69 ARG cc_start: 0.6856 (mmt180) cc_final: 0.6178 (mpt180) REVERT: K 250 TYR cc_start: 0.7898 (OUTLIER) cc_final: 0.6498 (p90) REVERT: K 281 LEU cc_start: 0.8509 (mp) cc_final: 0.8265 (mp) REVERT: K 282 GLU cc_start: 0.8489 (tm-30) cc_final: 0.8182 (tm-30) REVERT: K 421 ARG cc_start: 0.8749 (OUTLIER) cc_final: 0.8207 (mtm-85) REVERT: K 460 LEU cc_start: 0.6470 (OUTLIER) cc_final: 0.5948 (tt) REVERT: M 16 GLN cc_start: 0.7432 (mm-40) cc_final: 0.7178 (tp40) REVERT: M 48 ARG cc_start: 0.8579 (tpp-160) cc_final: 0.8355 (tpp-160) REVERT: M 54 ILE cc_start: 0.8869 (mm) cc_final: 0.8635 (mm) REVERT: M 56 MET cc_start: 0.7969 (ttm) cc_final: 0.7360 (ttp) REVERT: M 147 ILE cc_start: 0.9257 (pt) cc_final: 0.8893 (mt) REVERT: M 150 MET cc_start: 0.7137 (mmp) cc_final: 0.6849 (mmm) REVERT: M 178 TYR cc_start: 0.8295 (m-80) cc_final: 0.8077 (m-80) REVERT: M 198 ASP cc_start: 0.7750 (m-30) cc_final: 0.7253 (m-30) REVERT: M 204 GLN cc_start: 0.8289 (tm-30) cc_final: 0.7857 (tm-30) REVERT: M 277 LYS cc_start: 0.7702 (mppt) cc_final: 0.7479 (mppt) REVERT: N 68 ASN cc_start: 0.7926 (t0) cc_final: 0.7323 (t0) REVERT: N 100 TYR cc_start: 0.8539 (m-80) cc_final: 0.7808 (m-80) REVERT: N 106 PHE cc_start: 0.8489 (p90) cc_final: 0.8288 (p90) REVERT: N 151 LEU cc_start: 0.8847 (tt) cc_final: 0.8614 (tt) REVERT: N 152 LEU cc_start: 0.8682 (mp) cc_final: 0.8410 (mp) REVERT: L 40 TYR cc_start: 0.8710 (m-10) cc_final: 0.7942 (m-80) REVERT: L 56 MET cc_start: 0.7361 (mmm) cc_final: 0.6397 (tmm) REVERT: L 76 GLN cc_start: 0.8677 (mp10) cc_final: 0.8303 (mm110) REVERT: L 96 GLU cc_start: 0.8251 (pm20) cc_final: 0.7969 (pm20) REVERT: L 98 GLN cc_start: 0.7852 (tt0) cc_final: 0.7539 (pt0) REVERT: L 124 GLU cc_start: 0.6048 (OUTLIER) cc_final: 0.5722 (pm20) outliers start: 124 outliers final: 77 residues processed: 774 average time/residue: 0.1941 time to fit residues: 237.4599 Evaluate side-chains 777 residues out of total 2762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 680 time to evaluate : 1.066 ------------------------------------------------------------------------------- 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 32 ILE 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 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 46 LEU 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 177 LEU 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 45 CYS 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 109 ILE 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 E residue 264 TYR 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 187 HIS 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 98 GLN Chi-restraints excluded: chain G residue 120 ASN 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 266 VAL Chi-restraints excluded: chain H residue 276 THR Chi-restraints excluded: chain I residue 16 ARG Chi-restraints excluded: chain I residue 20 VAL 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 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 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 421 ARG Chi-restraints excluded: chain K residue 460 LEU Chi-restraints excluded: chain K residue 515 LEU Chi-restraints excluded: chain M residue 46 LEU 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 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 17 LEU Chi-restraints excluded: chain L residue 45 SER Chi-restraints excluded: chain L residue 81 GLN Chi-restraints excluded: chain L residue 124 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: 7.9990 chunk 229 optimal weight: 0.4980 chunk 65 optimal weight: 2.9990 chunk 59 optimal weight: 0.5980 chunk 203 optimal weight: 4.9990 chunk 172 optimal weight: 0.9990 chunk 63 optimal weight: 0.5980 chunk 16 optimal weight: 0.9990 chunk 107 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 128 GLN ** 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 181 HIS ** 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** ** F 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 123 ASN ** H 124 GLN ** 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 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 368 ASN ** K 521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 55 GLN ** 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** ** N 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 98 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.158520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.124865 restraints weight = 46994.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.129426 restraints weight = 21110.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.132381 restraints weight = 12346.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.134185 restraints weight = 8602.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 57)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.135399 restraints weight = 6809.700| |-----------------------------------------------------------------------------| r_work (final): 0.3996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.4480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 27430 Z= 0.212 Angle : 0.863 18.969 37194 Z= 0.447 Chirality : 0.052 0.487 4023 Planarity : 0.006 0.142 4752 Dihedral : 14.517 171.033 4192 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 31.12 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.23 % Favored : 90.70 % Rotamer: Outliers : 4.06 % Allowed : 25.58 % Favored : 70.36 % 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: -2.44 (0.14), residues: 3184 helix: -0.63 (0.14), residues: 1261 sheet: -2.62 (0.25), residues: 367 loop : -2.20 (0.14), residues: 1556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG K 496 TYR 0.038 0.003 TYR J 106 PHE 0.037 0.002 PHE H 183 TRP 0.055 0.003 TRP J 77 HIS 0.025 0.002 HIS C 214 Details of bonding type rmsd/Z covalent geometry : bond 0.00491 / 0.21 (27430) covalent geometry : angle 0.86266 / 0.45 (37194) hydrogen bonds : bond 0.04755 / 3.14 ( 1148) hydrogen bonds : angle 6.67421 / 4.79 ( 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 841 residues out of total 2762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 729 time to evaluate : 1.016 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 119 PHE cc_start: 0.7884 (OUTLIER) cc_final: 0.6443 (t80) REVERT: A 126 ASN cc_start: 0.8237 (t0) cc_final: 0.7327 (t0) REVERT: A 164 GLU cc_start: 0.7967 (tp30) cc_final: 0.7251 (tp30) REVERT: A 167 GLN cc_start: 0.8782 (tm-30) cc_final: 0.6750 (tm-30) REVERT: A 168 TYR cc_start: 0.7645 (m-80) cc_final: 0.6736 (m-10) REVERT: A 169 GLU cc_start: 0.7790 (tt0) cc_final: 0.7456 (tt0) REVERT: B 110 ARG cc_start: 0.7633 (mtm-85) cc_final: 0.7192 (mtm-85) REVERT: B 141 MET cc_start: 0.6522 (mmt) cc_final: 0.6321 (mmt) REVERT: B 183 PHE cc_start: 0.8004 (m-80) cc_final: 0.7780 (m-10) REVERT: B 198 ASP cc_start: 0.7677 (m-30) cc_final: 0.7081 (m-30) REVERT: B 201 LEU cc_start: 0.8279 (OUTLIER) cc_final: 0.7984 (mm) REVERT: B 241 ASP cc_start: 0.7804 (t70) cc_final: 0.7221 (t0) REVERT: C 11 PHE cc_start: 0.7907 (t80) cc_final: 0.7544 (t80) REVERT: C 67 ILE cc_start: 0.8292 (OUTLIER) cc_final: 0.7749 (mm) REVERT: C 103 CYS cc_start: 0.8425 (m) cc_final: 0.8136 (m) REVERT: C 110 ARG cc_start: 0.7518 (ptm160) cc_final: 0.7272 (ptm160) REVERT: C 124 GLN cc_start: 0.7628 (mt0) cc_final: 0.6869 (mt0) REVERT: C 138 ASP cc_start: 0.6294 (m-30) cc_final: 0.6085 (m-30) REVERT: C 146 SER cc_start: 0.7562 (t) cc_final: 0.7315 (t) REVERT: C 191 GLN cc_start: 0.8339 (tt0) cc_final: 0.8101 (tt0) REVERT: C 220 GLN cc_start: 0.7771 (tm-30) cc_final: 0.6174 (tm-30) REVERT: C 222 ASN cc_start: 0.8155 (m110) cc_final: 0.5769 (m110) REVERT: C 243 LEU cc_start: 0.8158 (OUTLIER) cc_final: 0.7789 (mt) REVERT: C 256 GLU cc_start: 0.7352 (tm-30) cc_final: 0.6910 (tm-30) REVERT: C 271 LYS cc_start: 0.8494 (mmmt) cc_final: 0.8258 (mmmt) REVERT: D 35 GLN cc_start: 0.8509 (mm-40) cc_final: 0.7938 (tp40) REVERT: D 36 THR cc_start: 0.7879 (OUTLIER) cc_final: 0.7614 (p) REVERT: D 48 ARG cc_start: 0.6892 (OUTLIER) cc_final: 0.5193 (ttm-80) REVERT: D 150 MET cc_start: 0.6220 (ppp) cc_final: 0.5313 (ppp) REVERT: D 169 ARG cc_start: 0.8041 (mtm-85) cc_final: 0.7623 (mtm-85) REVERT: D 227 TYR cc_start: 0.8358 (m-80) cc_final: 0.8077 (m-80) REVERT: E 17 ASP cc_start: 0.7698 (t70) cc_final: 0.7283 (t0) REVERT: E 79 GLU cc_start: 0.7829 (tm-30) cc_final: 0.7476 (tm-30) REVERT: E 116 MET cc_start: 0.8131 (tpp) cc_final: 0.7432 (mpp) REVERT: E 150 MET cc_start: 0.8297 (mmm) cc_final: 0.8008 (mmm) REVERT: E 167 MET cc_start: 0.8827 (mtm) cc_final: 0.8568 (mtp) REVERT: E 204 GLN cc_start: 0.7771 (tm130) cc_final: 0.7296 (tm-30) REVERT: E 209 MET cc_start: 0.7819 (ttp) cc_final: 0.7310 (ttp) REVERT: E 226 LEU cc_start: 0.8658 (tp) cc_final: 0.8306 (tp) REVERT: E 233 ASN cc_start: 0.8116 (m-40) cc_final: 0.7808 (m-40) REVERT: E 241 ASP cc_start: 0.7123 (t70) cc_final: 0.6805 (t0) REVERT: E 264 TYR cc_start: 0.8534 (OUTLIER) cc_final: 0.8286 (m-10) REVERT: F 25 ASP cc_start: 0.7481 (OUTLIER) cc_final: 0.6587 (t0) REVERT: F 72 ILE cc_start: 0.8076 (mm) cc_final: 0.7746 (mm) REVERT: F 102 MET cc_start: 0.9072 (mmm) cc_final: 0.8863 (mmm) REVERT: F 135 ARG cc_start: 0.8485 (mmm-85) cc_final: 0.7977 (tpp-160) REVERT: F 141 MET cc_start: 0.8463 (ttp) cc_final: 0.8169 (ttt) REVERT: F 172 THR cc_start: 0.7818 (m) cc_final: 0.7493 (m) REVERT: F 187 HIS cc_start: 0.7852 (OUTLIER) cc_final: 0.7341 (p90) REVERT: F 209 MET cc_start: 0.6943 (tmm) cc_final: 0.6662 (tmm) REVERT: G 68 PHE cc_start: 0.8046 (t80) cc_final: 0.7691 (t80) REVERT: G 106 TYR cc_start: 0.8260 (m-80) cc_final: 0.7974 (m-80) REVERT: G 124 GLU cc_start: 0.8819 (OUTLIER) cc_final: 0.8430 (pm20) REVERT: H 81 HIS cc_start: 0.8447 (OUTLIER) cc_final: 0.7850 (t-90) REVERT: H 102 MET cc_start: 0.9091 (mmm) cc_final: 0.8403 (mmm) REVERT: H 178 TYR cc_start: 0.6813 (m-80) cc_final: 0.6231 (m-10) REVERT: H 206 LEU cc_start: 0.9372 (mt) cc_final: 0.8828 (tt) REVERT: H 208 ASN cc_start: 0.8651 (m110) cc_final: 0.7620 (t0) REVERT: H 261 PHE cc_start: 0.7818 (t80) cc_final: 0.7550 (t80) REVERT: I 16 ARG cc_start: 0.8844 (OUTLIER) cc_final: 0.8197 (ttt90) REVERT: I 18 PHE cc_start: 0.8780 (t80) cc_final: 0.8424 (t80) REVERT: I 22 GLU cc_start: 0.8797 (tm-30) cc_final: 0.8244 (tm-30) REVERT: I 74 GLN cc_start: 0.8966 (pt0) cc_final: 0.7712 (mt0) REVERT: I 77 TRP cc_start: 0.8439 (t60) cc_final: 0.7771 (t60) REVERT: I 81 GLN cc_start: 0.8967 (OUTLIER) cc_final: 0.8596 (mp10) REVERT: I 84 GLU cc_start: 0.8609 (tp30) cc_final: 0.7994 (tp30) REVERT: I 91 ASN cc_start: 0.8736 (t0) cc_final: 0.8225 (t0) REVERT: I 96 GLU cc_start: 0.8566 (OUTLIER) cc_final: 0.7812 (pm20) REVERT: I 108 GLU cc_start: 0.8227 (mt-10) cc_final: 0.7704 (mt-10) REVERT: I 109 THR cc_start: 0.8439 (m) cc_final: 0.7523 (p) REVERT: I 113 PHE cc_start: 0.7697 (m-10) cc_final: 0.7351 (m-10) REVERT: I 119 LYS cc_start: 0.9223 (ptmm) cc_final: 0.8754 (ptmm) REVERT: I 123 ASN cc_start: 0.8738 (m110) cc_final: 0.8292 (m110) REVERT: J 8 GLN cc_start: 0.7970 (tp40) cc_final: 0.7751 (tp-100) REVERT: J 39 ARG cc_start: 0.7982 (mtp85) cc_final: 0.7650 (mmm-85) REVERT: J 71 ARG cc_start: 0.8706 (tpt170) cc_final: 0.8075 (tpt170) REVERT: J 78 GLU cc_start: 0.8924 (tp30) cc_final: 0.8408 (tp30) REVERT: J 80 ARG cc_start: 0.8242 (mtm-85) cc_final: 0.7789 (tpp80) REVERT: J 84 GLU cc_start: 0.8363 (tp30) cc_final: 0.8114 (tp30) REVERT: J 88 ARG cc_start: 0.7472 (OUTLIER) cc_final: 0.6986 (tmt170) REVERT: J 91 ASN cc_start: 0.8590 (m-40) cc_final: 0.8064 (m-40) REVERT: J 98 GLN cc_start: 0.8306 (tt0) cc_final: 0.7830 (tp40) REVERT: J 116 ASP cc_start: 0.7180 (t0) cc_final: 0.6771 (t0) REVERT: J 119 LYS cc_start: 0.8552 (ttpp) cc_final: 0.8248 (mtpp) REVERT: J 120 ASN cc_start: 0.7980 (p0) cc_final: 0.7606 (p0) REVERT: J 123 ASN cc_start: 0.7740 (m110) cc_final: 0.7445 (m110) REVERT: K 12 ARG cc_start: 0.8065 (mmp80) cc_final: 0.7716 (mmp80) REVERT: K 82 TRP cc_start: 0.8376 (p-90) cc_final: 0.7774 (p-90) REVERT: K 250 TYR cc_start: 0.7852 (OUTLIER) cc_final: 0.6275 (p90) REVERT: K 281 LEU cc_start: 0.8475 (mp) cc_final: 0.8235 (mp) REVERT: K 282 GLU cc_start: 0.8496 (tm-30) cc_final: 0.8197 (tm-30) REVERT: K 398 ILE cc_start: 0.8893 (mt) cc_final: 0.8681 (mp) REVERT: K 460 LEU cc_start: 0.6407 (OUTLIER) cc_final: 0.5890 (tt) REVERT: M 48 ARG cc_start: 0.8605 (tpp-160) cc_final: 0.8354 (tpp-160) REVERT: M 56 MET cc_start: 0.7885 (ttm) cc_final: 0.7312 (ttp) REVERT: M 147 ILE cc_start: 0.9241 (pt) cc_final: 0.8895 (mt) REVERT: M 178 TYR cc_start: 0.8332 (m-80) cc_final: 0.8124 (m-80) REVERT: M 183 PHE cc_start: 0.9066 (m-80) cc_final: 0.8766 (m-80) REVERT: M 198 ASP cc_start: 0.7738 (m-30) cc_final: 0.7248 (m-30) REVERT: M 204 GLN cc_start: 0.8279 (tm-30) cc_final: 0.7816 (tm-30) REVERT: M 259 ARG cc_start: 0.7338 (mtm110) cc_final: 0.6981 (mtm110) REVERT: M 277 LYS cc_start: 0.7658 (mppt) cc_final: 0.7437 (mppt) REVERT: N 68 ASN cc_start: 0.7742 (t0) cc_final: 0.7150 (t0) REVERT: N 97 ASP cc_start: 0.7558 (m-30) cc_final: 0.7011 (p0) REVERT: N 100 TYR cc_start: 0.8516 (m-80) cc_final: 0.7768 (m-80) REVERT: N 137 GLN cc_start: 0.7579 (tp-100) cc_final: 0.7047 (tt0) REVERT: N 152 LEU cc_start: 0.8505 (mp) cc_final: 0.8259 (mp) REVERT: L 40 TYR cc_start: 0.8707 (m-10) cc_final: 0.7837 (m-80) REVERT: L 56 MET cc_start: 0.7347 (mmm) cc_final: 0.6380 (tmm) REVERT: L 76 GLN cc_start: 0.8738 (OUTLIER) cc_final: 0.8506 (mm110) REVERT: L 96 GLU cc_start: 0.8250 (pm20) cc_final: 0.7965 (pm20) REVERT: L 98 GLN cc_start: 0.7867 (OUTLIER) cc_final: 0.7553 (pt0) outliers start: 112 outliers final: 71 residues processed: 784 average time/residue: 0.1870 time to fit residues: 230.9098 Evaluate side-chains 780 residues out of total 2762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 690 time to evaluate : 1.046 ------------------------------------------------------------------------------- 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 32 ILE 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 102 MET Chi-restraints excluded: chain B residue 201 LEU 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 46 LEU Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 86 VAL 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 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 45 CYS 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 109 ILE 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 E residue 264 TYR 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 187 HIS 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 98 GLN 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 266 VAL Chi-restraints excluded: chain H residue 276 THR Chi-restraints excluded: chain I residue 16 ARG Chi-restraints excluded: chain I residue 20 VAL 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 88 ARG 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 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 393 LEU Chi-restraints excluded: chain K residue 403 ASP Chi-restraints excluded: chain K residue 460 LEU 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 M residue 276 THR 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 76 GLN Chi-restraints excluded: chain L residue 81 GLN Chi-restraints excluded: chain L residue 98 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 82 optimal weight: 2.9990 chunk 302 optimal weight: 0.0270 chunk 18 optimal weight: 3.9990 chunk 46 optimal weight: 0.5980 chunk 124 optimal weight: 0.0060 chunk 141 optimal weight: 1.9990 chunk 221 optimal weight: 4.9990 chunk 263 optimal weight: 0.6980 chunk 65 optimal weight: 0.7980 chunk 239 optimal weight: 0.0770 chunk 167 optimal weight: 7.9990 overall best weight: 0.2812 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 58 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** E 75 ASN ** E 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 222 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** ** G 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 97 GLN I 98 GLN J 64 ASN J 74 GLN J 85 HIS ** K 343 HIS ** 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 55 GLN ** 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 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 74 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 = 0.4294 r_free = 0.4294 target = 0.161906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.129704 restraints weight = 46912.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.134271 restraints weight = 20829.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.137055 restraints weight = 11990.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 58)----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.138993 restraints weight = 8349.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.139729 restraints weight = 6506.540| |-----------------------------------------------------------------------------| r_work (final): 0.4045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.4779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 27430 Z= 0.196 Angle : 0.887 19.530 37194 Z= 0.459 Chirality : 0.052 0.486 4023 Planarity : 0.006 0.092 4752 Dihedral : 14.484 168.971 4192 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 30.50 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.73 % Favored : 91.21 % Rotamer: Outliers : 3.55 % Allowed : 26.78 % Favored : 69.67 % 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: -2.46 (0.14), residues: 3184 helix: -0.71 (0.14), residues: 1265 sheet: -2.51 (0.26), residues: 355 loop : -2.20 (0.14), residues: 1564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG K 496 TYR 0.059 0.003 TYR K 440 PHE 0.041 0.003 PHE I 52 TRP 0.133 0.004 TRP J 77 HIS 0.030 0.002 HIS C 214 Details of bonding type rmsd/Z covalent geometry : bond 0.00455 / 0.20 (27430) covalent geometry : angle 0.88737 / 0.46 (37194) hydrogen bonds : bond 0.04798 / 3.17 ( 1148) hydrogen bonds : angle 6.72550 / 4.82 ( 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 849 residues out of total 2762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 751 time to evaluate : 1.091 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: 0.7927 (OUTLIER) cc_final: 0.6601 (t80) REVERT: A 126 ASN cc_start: 0.8242 (t0) cc_final: 0.7317 (t0) REVERT: A 164 GLU cc_start: 0.7934 (tp30) cc_final: 0.7588 (tp30) REVERT: A 167 GLN cc_start: 0.8784 (tm-30) cc_final: 0.6701 (tm-30) REVERT: A 168 TYR cc_start: 0.7485 (m-80) cc_final: 0.6541 (m-10) REVERT: A 169 GLU cc_start: 0.7806 (tt0) cc_final: 0.7586 (tp30) REVERT: A 179 GLU cc_start: 0.7873 (tm-30) cc_final: 0.7294 (tt0) REVERT: B 241 ASP cc_start: 0.7645 (t70) cc_final: 0.7070 (t0) REVERT: C 11 PHE cc_start: 0.7949 (t80) cc_final: 0.7675 (t80) REVERT: C 48 ARG cc_start: 0.7447 (tpt90) cc_final: 0.5948 (tpt90) REVERT: C 67 ILE cc_start: 0.8321 (OUTLIER) cc_final: 0.6209 (mm) REVERT: C 124 GLN cc_start: 0.7529 (mt0) cc_final: 0.6836 (mt0) REVERT: C 126 ARG cc_start: 0.5740 (ttp-110) cc_final: 0.5440 (ttp-110) REVERT: C 138 ASP cc_start: 0.6157 (m-30) cc_final: 0.5948 (m-30) REVERT: C 146 SER cc_start: 0.7320 (t) cc_final: 0.7051 (t) REVERT: C 191 GLN cc_start: 0.8248 (tt0) cc_final: 0.8029 (tt0) REVERT: C 218 ARG cc_start: 0.8158 (mpt90) cc_final: 0.7928 (mpt-90) REVERT: C 243 LEU cc_start: 0.8108 (OUTLIER) cc_final: 0.7868 (mt) REVERT: C 256 GLU cc_start: 0.7219 (tm-30) cc_final: 0.6847 (tm-30) REVERT: C 271 LYS cc_start: 0.8409 (mmmt) cc_final: 0.8077 (mmtm) REVERT: D 35 GLN cc_start: 0.8452 (mm-40) cc_final: 0.7905 (tp40) REVERT: D 36 THR cc_start: 0.7856 (OUTLIER) cc_final: 0.7611 (p) REVERT: D 48 ARG cc_start: 0.6672 (OUTLIER) cc_final: 0.5235 (ttm-80) REVERT: D 76 LEU cc_start: 0.7935 (mt) cc_final: 0.7527 (mt) REVERT: D 102 MET cc_start: 0.8086 (mmt) cc_final: 0.7590 (mmt) REVERT: D 116 MET cc_start: 0.8176 (mtp) cc_final: 0.7422 (mtp) REVERT: D 169 ARG cc_start: 0.7951 (mtm-85) cc_final: 0.7560 (mtm-85) REVERT: D 227 TYR cc_start: 0.8235 (m-80) cc_final: 0.7920 (m-80) REVERT: E 17 ASP cc_start: 0.7647 (t70) cc_final: 0.7271 (t0) REVERT: E 79 GLU cc_start: 0.7839 (tm-30) cc_final: 0.7496 (tm-30) REVERT: E 116 MET cc_start: 0.8030 (tpp) cc_final: 0.7359 (mpp) REVERT: E 167 MET cc_start: 0.8731 (mtm) cc_final: 0.8462 (mtp) REVERT: E 204 GLN cc_start: 0.7742 (tm130) cc_final: 0.7304 (tm-30) REVERT: E 209 MET cc_start: 0.7793 (OUTLIER) cc_final: 0.7312 (ttp) REVERT: E 226 LEU cc_start: 0.8614 (tp) cc_final: 0.8311 (tp) REVERT: E 233 ASN cc_start: 0.7925 (m-40) cc_final: 0.7718 (m-40) REVERT: E 241 ASP cc_start: 0.7061 (t70) cc_final: 0.6793 (t0) REVERT: E 264 TYR cc_start: 0.8443 (OUTLIER) cc_final: 0.8209 (m-10) REVERT: F 25 ASP cc_start: 0.7070 (OUTLIER) cc_final: 0.6194 (t0) REVERT: F 72 ILE cc_start: 0.8158 (mm) cc_final: 0.7826 (mm) REVERT: F 102 MET cc_start: 0.9071 (mmm) cc_final: 0.8839 (mmm) REVERT: F 124 GLN cc_start: 0.8266 (OUTLIER) cc_final: 0.7914 (mt0) REVERT: F 135 ARG cc_start: 0.8375 (mmm-85) cc_final: 0.7986 (tpp-160) REVERT: F 141 MET cc_start: 0.8389 (ttp) cc_final: 0.8053 (ttt) REVERT: F 187 HIS cc_start: 0.7754 (OUTLIER) cc_final: 0.7209 (p90) REVERT: F 209 MET cc_start: 0.6978 (tmm) cc_final: 0.6707 (tmm) REVERT: G 68 PHE cc_start: 0.8042 (t80) cc_final: 0.7669 (t80) REVERT: G 71 ARG cc_start: 0.8921 (mmm160) cc_final: 0.8479 (mmm-85) REVERT: G 98 GLN cc_start: 0.8411 (OUTLIER) cc_final: 0.7931 (tm-30) REVERT: G 106 TYR cc_start: 0.8360 (m-80) cc_final: 0.8053 (m-80) REVERT: G 108 GLU cc_start: 0.8309 (mm-30) cc_final: 0.8085 (mt-10) REVERT: G 110 GLN cc_start: 0.6874 (tp-100) cc_final: 0.6620 (tp-100) REVERT: G 122 PHE cc_start: 0.8089 (t80) cc_final: 0.7741 (t80) REVERT: G 124 GLU cc_start: 0.8804 (OUTLIER) cc_final: 0.8427 (pm20) REVERT: H 7 TYR cc_start: 0.8365 (m-80) cc_final: 0.8161 (m-80) REVERT: H 81 HIS cc_start: 0.8537 (OUTLIER) cc_final: 0.7919 (t-90) REVERT: H 102 MET cc_start: 0.9084 (mmm) cc_final: 0.8632 (mmm) REVERT: H 178 TYR cc_start: 0.6759 (m-80) cc_final: 0.6184 (m-10) REVERT: H 208 ASN cc_start: 0.8688 (m110) cc_final: 0.7725 (t0) REVERT: H 261 PHE cc_start: 0.7749 (t80) cc_final: 0.7496 (t80) REVERT: I 18 PHE cc_start: 0.8632 (t80) cc_final: 0.8348 (t80) REVERT: I 22 GLU cc_start: 0.8670 (tm-30) cc_final: 0.8108 (tm-30) REVERT: I 39 ARG cc_start: 0.7923 (ptm160) cc_final: 0.7601 (mtm110) REVERT: I 74 GLN cc_start: 0.8923 (pt0) cc_final: 0.7675 (mt0) REVERT: I 77 TRP cc_start: 0.8285 (t60) cc_final: 0.7798 (t60) REVERT: I 81 GLN cc_start: 0.8968 (OUTLIER) cc_final: 0.8546 (mp10) REVERT: I 84 GLU cc_start: 0.8582 (tp30) cc_final: 0.8048 (tp30) REVERT: I 96 GLU cc_start: 0.8619 (OUTLIER) cc_final: 0.7973 (pm20) REVERT: I 109 THR cc_start: 0.8424 (m) cc_final: 0.7640 (p) REVERT: I 113 PHE cc_start: 0.7560 (m-10) cc_final: 0.7350 (m-10) REVERT: I 119 LYS cc_start: 0.9191 (ptmm) cc_final: 0.8727 (ptmm) REVERT: I 123 ASN cc_start: 0.8714 (m110) cc_final: 0.8270 (m110) REVERT: J 39 ARG cc_start: 0.7919 (mtp85) cc_final: 0.7661 (mmm-85) REVERT: J 78 GLU cc_start: 0.8833 (tp30) cc_final: 0.8416 (tp30) REVERT: J 91 ASN cc_start: 0.8509 (m-40) cc_final: 0.8035 (m-40) REVERT: J 98 GLN cc_start: 0.8231 (tt0) cc_final: 0.7799 (tp40) REVERT: J 116 ASP cc_start: 0.7070 (t0) cc_final: 0.6627 (t0) REVERT: K 12 ARG cc_start: 0.7995 (mmp80) cc_final: 0.7789 (mmp80) REVERT: K 82 TRP cc_start: 0.8328 (p-90) cc_final: 0.7704 (p-90) REVERT: K 250 TYR cc_start: 0.7790 (OUTLIER) cc_final: 0.6327 (p90) REVERT: K 281 LEU cc_start: 0.8287 (mp) cc_final: 0.8031 (mp) REVERT: K 282 GLU cc_start: 0.8468 (tm-30) cc_final: 0.8241 (tm-30) REVERT: K 421 ARG cc_start: 0.8549 (ttm110) cc_final: 0.7758 (mtm-85) REVERT: K 428 LYS cc_start: 0.8672 (ttpt) cc_final: 0.8424 (ttpp) REVERT: K 460 LEU cc_start: 0.6138 (OUTLIER) cc_final: 0.5606 (tt) REVERT: K 504 THR cc_start: 0.8655 (m) cc_final: 0.8279 (p) REVERT: M 48 ARG cc_start: 0.8490 (tpp-160) cc_final: 0.8284 (tpp-160) REVERT: M 56 MET cc_start: 0.7820 (ttm) cc_final: 0.7210 (ttp) REVERT: M 116 MET cc_start: 0.9026 (mmt) cc_final: 0.8811 (mmt) REVERT: M 147 ILE cc_start: 0.9241 (pt) cc_final: 0.8896 (mt) REVERT: M 198 ASP cc_start: 0.7685 (m-30) cc_final: 0.7197 (m-30) REVERT: M 204 GLN cc_start: 0.8163 (tm-30) cc_final: 0.7545 (tm-30) REVERT: N 7 ILE cc_start: 0.7994 (mp) cc_final: 0.7706 (mm) REVERT: N 68 ASN cc_start: 0.7776 (t0) cc_final: 0.7217 (t0) REVERT: N 100 TYR cc_start: 0.8414 (m-80) cc_final: 0.7565 (m-80) REVERT: N 133 GLN cc_start: 0.7555 (OUTLIER) cc_final: 0.7204 (mm110) REVERT: N 152 LEU cc_start: 0.8428 (mp) cc_final: 0.8197 (mp) REVERT: N 171 MET cc_start: 0.7535 (mtm) cc_final: 0.7022 (mtt) REVERT: L 23 LYS cc_start: 0.8888 (tppt) cc_final: 0.8674 (ttpt) REVERT: L 40 TYR cc_start: 0.8716 (m-10) cc_final: 0.7842 (m-80) REVERT: L 56 MET cc_start: 0.7405 (mmm) cc_final: 0.6476 (tmm) REVERT: L 76 GLN cc_start: 0.8724 (OUTLIER) cc_final: 0.8494 (mm110) REVERT: L 96 GLU cc_start: 0.8061 (pm20) cc_final: 0.7761 (pm20) outliers start: 98 outliers final: 64 residues processed: 796 average time/residue: 0.1931 time to fit residues: 241.5463 Evaluate side-chains 782 residues out of total 2762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 699 time to evaluate : 1.132 ------------------------------------------------------------------------------- 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 32 ILE 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 257 VAL Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain C residue 5 LYS Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 32 ILE Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 86 VAL 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 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 45 CYS Chi-restraints excluded: chain D residue 48 ARG Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain E residue 134 SER Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 209 MET Chi-restraints excluded: chain E residue 259 ARG Chi-restraints excluded: chain E residue 264 TYR 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 187 HIS 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 88 ARG Chi-restraints excluded: chain G residue 95 LEU Chi-restraints excluded: chain G residue 98 GLN 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 266 VAL Chi-restraints excluded: chain H residue 276 THR 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 74 GLN 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 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 393 LEU Chi-restraints excluded: chain K residue 403 ASP Chi-restraints excluded: chain K residue 460 LEU 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 209 MET Chi-restraints excluded: chain M residue 272 ASN Chi-restraints excluded: chain M residue 276 THR 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 137 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 76 GLN Chi-restraints excluded: chain L residue 81 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 201 optimal weight: 2.9990 chunk 269 optimal weight: 1.9990 chunk 155 optimal weight: 10.0000 chunk 128 optimal weight: 2.9990 chunk 261 optimal weight: 0.5980 chunk 185 optimal weight: 0.8980 chunk 195 optimal weight: 0.5980 chunk 55 optimal weight: 3.9990 chunk 307 optimal weight: 6.9990 chunk 158 optimal weight: 9.9990 chunk 14 optimal weight: 0.6980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 181 HIS ** 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 154 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** ** G 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 91 ASN ** 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 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 97 GLN I 98 GLN ** J 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 85 HIS ** K 343 HIS ** 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 55 GLN ** 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 61 GLN ** N 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 89 GLN ** N 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 98 GLN ** 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 = 0.4169 r_free = 0.4169 target = 0.156268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.120033 restraints weight = 47796.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.124489 restraints weight = 21754.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 74)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.127339 restraints weight = 12819.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.129045 restraints weight = 9024.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 62)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.130228 restraints weight = 7232.226| |-----------------------------------------------------------------------------| r_work (final): 0.4036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.4834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.332 27430 Z= 0.346 Angle : 1.016 65.893 37194 Z= 0.573 Chirality : 0.053 0.693 4023 Planarity : 0.009 0.305 4752 Dihedral : 14.476 168.963 4192 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 39.85 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.70 % Favored : 91.24 % Rotamer: Outliers : 3.51 % Allowed : 27.17 % Favored : 69.31 % Cbeta Deviations : 0.10 % 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: -2.46 (0.14), residues: 3184 helix: -0.71 (0.14), residues: 1265 sheet: -2.51 (0.26), residues: 355 loop : -2.19 (0.15), residues: 1564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG F 259 TYR 0.046 0.003 TYR K 440 PHE 0.048 0.003 PHE H 11 TRP 0.102 0.005 TRP J 77 HIS 0.030 0.002 HIS C 214 Details of bonding type rmsd/Z covalent geometry : bond 0.00754 / 0.35 (27430) covalent geometry : angle 1.01599 / 0.57 (37194) hydrogen bonds : bond 0.04802 / 3.17 ( 1148) hydrogen bonds : angle 6.72567 / 4.82 ( 3315) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6277.53 seconds wall clock time: 124 minutes 18.45 seconds (7458.45 seconds total)