Starting phenix.real_space_refine on Sun May 25 07:41:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g9t_29878/05_2025/8g9t_29878.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g9t_29878/05_2025/8g9t_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8g9t_29878/05_2025/8g9t_29878.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g9t_29878/05_2025/8g9t_29878.map" model { file = "/net/cci-nas-00/data/ceres_data/8g9t_29878/05_2025/8g9t_29878.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g9t_29878/05_2025/8g9t_29878.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.060 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): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 15.04, per 1000 atoms: 0.56 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: 8.20 Conformation dependent library (CDL) restraints added in 3.6 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: 10.52 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: 9.89 Time building geometry restraints manager: 9.39 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=" C ALA K 239 " pdb=" N PHE K 240 " ideal model delta sigma weight residual 1.328 1.233 0.095 1.67e-02 3.59e+03 3.22e+01 bond pdb=" C VAL D 173 " pdb=" N PRO D 174 " ideal model delta sigma weight residual 1.335 1.266 0.069 1.30e-02 5.92e+03 2.80e+01 bond pdb=" CA PHE C 183 " pdb=" CB PHE C 183 " ideal model delta sigma weight residual 1.523 1.459 0.064 1.35e-02 5.49e+03 2.22e+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=" 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=" O3' A O 25 " pdb=" P G O 26 " pdb=" OP2 G O 26 " ideal model delta sigma weight residual 108.00 82.51 25.49 3.00e+00 1.11e-01 7.22e+01 angle pdb=" CA PRO D 174 " pdb=" N PRO D 174 " pdb=" CD PRO D 174 " ideal model delta sigma weight residual 112.00 101.24 10.76 1.40e+00 5.10e-01 5.91e+01 angle pdb=" C CYS K 149 " pdb=" N ALA K 150 " pdb=" CA ALA K 150 " ideal model delta sigma weight residual 121.90 113.57 8.33 1.26e+00 6.30e-01 4.37e+01 angle pdb=" C ARG D 48 " pdb=" N LYS D 49 " pdb=" CA LYS D 49 " ideal model delta sigma weight residual 120.28 111.78 8.50 1.44e+00 4.82e-01 3.48e+01 ... (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: 1.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.990 Check model and map are aligned: 0.180 Set scattering table: 0.250 Process input model: 68.690 Find NCS groups from input model: 1.070 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 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= 0.615 Angle : 1.326 25.485 37194 Z= 0.704 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.053 0.006 TRP L 77 HIS 0.029 0.003 HIS C 214 PHE 0.072 0.004 PHE B 183 TYR 0.042 0.005 TYR C 7 ARG 0.047 0.002 ARG D 48 Details of bonding type rmsd hydrogen bonds : bond 0.18718 ( 1148) hydrogen bonds : angle 9.00116 ( 3315) covalent geometry : bond 0.01318 (27430) covalent geometry : angle 1.32558 (37194) *********************** 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 : 2.842 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: 0.7778 (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: 0.8588 (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: 0.8291 (tttm) REVERT: C 209 MET cc_start: 0.6932 (ptm) cc_final: 0.6681 (ptm) REVERT: D 263 ASP cc_start: 0.8616 (m-30) cc_final: 0.8265 (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: 0.8624 (mtp) REVERT: E 171 PHE cc_start: 0.8656 (m-80) cc_final: 0.8224 (m-80) REVERT: E 204 GLN cc_start: 0.8084 (tm130) cc_final: 0.7520 (tm-30) REVERT: E 233 ASN cc_start: 0.8215 (m-40) cc_final: 0.7917 (m-40) REVERT: E 241 ASP cc_start: 0.7245 (t70) cc_final: 0.6703 (t0) REVERT: F 40 LEU cc_start: 0.7679 (tp) cc_final: 0.7311 (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: 0.7862 (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 56 MET cc_start: 0.9012 (mmm) cc_final: 0.8738 (tmm) REVERT: G 77 TRP cc_start: 0.7854 (t60) cc_final: 0.7061 (t60) REVERT: G 105 TYR cc_start: 0.8764 (t80) cc_final: 0.7705 (t80) REVERT: G 111 PHE cc_start: 0.8128 (t80) cc_final: 0.7796 (t80) REVERT: G 122 PHE cc_start: 0.7259 (t80) cc_final: 0.6986 (t80) REVERT: H 11 PHE cc_start: 0.7956 (t80) cc_final: 0.7398 (t80) REVERT: H 55 GLN cc_start: 0.9201 (mm110) cc_final: 0.8993 (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: 0.7962 (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: 0.8766 (p) cc_final: 0.8509 (p) REVERT: H 272 ASN cc_start: 0.9119 (t0) cc_final: 0.8903 (t0) REVERT: I 18 PHE cc_start: 0.8686 (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: 0.8286 (tppt) REVERT: I 84 GLU cc_start: 0.8228 (OUTLIER) cc_final: 0.7736 (tp30) REVERT: I 108 GLU cc_start: 0.8755 (mm-30) cc_final: 0.8427 (mm-30) REVERT: I 110 GLN cc_start: 0.8437 (tp40) cc_final: 0.8042 (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: 0.8107 (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: 0.8169 (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: 0.7535 (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: 0.7338 (m-40) REVERT: K 16 SER cc_start: 0.7730 (t) cc_final: 0.7495 (p) REVERT: K 23 GLU cc_start: 0.6976 (tm-30) cc_final: 0.6574 (tm-30) REVERT: K 156 ASN cc_start: 0.8008 (m110) cc_final: 0.7633 (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: 0.7528 (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: 0.7618 (m-30) REVERT: M 277 LYS cc_start: 0.8104 (mppt) cc_final: 0.7889 (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: 0.7177 (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: 0.6516 (tt) REVERT: L 107 HIS cc_start: 0.7386 (m90) cc_final: 0.6553 (m90) outliers start: 72 outliers final: 21 residues processed: 865 average time/residue: 0.3783 time to fit residues: 511.5013 Evaluate side-chains 660 residues out of total 2762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 634 time to evaluate : 2.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 271 optimal weight: 0.0670 chunk 244 optimal weight: 0.8980 chunk 135 optimal weight: 3.9990 chunk 83 optimal weight: 0.8980 chunk 164 optimal weight: 4.9990 chunk 130 optimal weight: 1.9990 chunk 252 optimal weight: 0.6980 chunk 97 optimal weight: 5.9990 chunk 153 optimal weight: 0.9990 chunk 187 optimal weight: 0.1980 chunk 292 optimal weight: 0.9980 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 ** 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 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 ** 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 ** G 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 120 ASN H 58 GLN H 81 HIS ** H 100 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 220 GLN H 231 HIS H 272 ASN ** I 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 555 GLN ** M 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 74 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 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: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.154196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.122026 restraints weight = 46559.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.126451 restraints weight = 20469.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.129299 restraints weight = 11798.200| |-----------------------------------------------------------------------------| r_work (final): 0.3908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 moved from start: 0.2489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.088 27430 Z= 0.238 Angle : 0.927 14.866 37194 Z= 0.484 Chirality : 0.053 0.337 4023 Planarity : 0.007 0.123 4752 Dihedral : 15.297 177.772 4255 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 35.52 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.20 % Favored : 90.73 % Rotamer: Outliers : 2.93 % Allowed : 13.84 % Favored : 83.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.78 (0.14), residues: 3184 helix: -0.95 (0.13), residues: 1259 sheet: -2.66 (0.24), residues: 367 loop : -2.39 (0.14), residues: 1558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.003 TRP I 77 HIS 0.014 0.002 HIS C 214 PHE 0.034 0.003 PHE B 183 TYR 0.033 0.003 TYR L 106 ARG 0.013 0.001 ARG B 224 Details of bonding type rmsd hydrogen bonds : bond 0.06009 ( 1148) hydrogen bonds : angle 7.26481 ( 3315) covalent geometry : bond 0.00536 (27430) covalent geometry : angle 0.92748 (37194) *********************** 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 942 residues out of total 2762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 861 time to evaluate : 2.877 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: A 117 THR cc_start: 0.9348 (p) cc_final: 0.8979 (p) REVERT: A 126 ASN cc_start: 0.8121 (t0) cc_final: 0.7516 (t0) REVERT: A 144 ASP cc_start: 0.8515 (m-30) cc_final: 0.8262 (m-30) REVERT: A 165 TRP cc_start: 0.8523 (m-10) cc_final: 0.8288 (m100) REVERT: A 167 GLN cc_start: 0.8242 (tm-30) cc_final: 0.7023 (tm-30) REVERT: A 168 TYR cc_start: 0.7565 (m-80) cc_final: 0.6893 (m-80) REVERT: B 40 LEU cc_start: 0.9011 (mt) cc_final: 0.8773 (mt) REVERT: B 141 MET cc_start: 0.7119 (mmt) cc_final: 0.6771 (mmt) REVERT: B 175 TYR cc_start: 0.8610 (t80) cc_final: 0.8034 (t80) REVERT: B 183 PHE cc_start: 0.8106 (m-10) cc_final: 0.7037 (m-10) REVERT: C 4 GLU cc_start: 0.7706 (tp30) cc_final: 0.7456 (tp30) REVERT: C 124 GLN cc_start: 0.7681 (mt0) cc_final: 0.7167 (mt0) REVERT: C 156 LYS cc_start: 0.8778 (ttpp) cc_final: 0.8533 (tttm) REVERT: C 175 TYR cc_start: 0.9146 (t80) cc_final: 0.8826 (t80) REVERT: C 191 GLN cc_start: 0.8227 (tt0) cc_final: 0.7955 (tt0) REVERT: C 209 MET cc_start: 0.7162 (ptm) cc_final: 0.6769 (ttm) REVERT: C 220 GLN cc_start: 0.7804 (tm-30) cc_final: 0.6865 (tm-30) REVERT: C 226 LEU cc_start: 0.8653 (tp) cc_final: 0.8424 (tp) REVERT: D 116 MET cc_start: 0.8859 (mmt) cc_final: 0.8481 (mmm) REVERT: D 244 PHE cc_start: 0.9021 (m-10) cc_final: 0.8597 (m-10) REVERT: E 56 MET cc_start: 0.7850 (mtm) cc_final: 0.7615 (mtm) REVERT: E 79 GLU cc_start: 0.7573 (tm-30) cc_final: 0.7001 (tm-30) REVERT: E 184 ILE cc_start: 0.8720 (mm) cc_final: 0.8470 (mm) REVERT: E 204 GLN cc_start: 0.7702 (tm130) cc_final: 0.7242 (tm-30) REVERT: E 221 MET cc_start: 0.8363 (mtm) cc_final: 0.7967 (mtm) REVERT: E 226 LEU cc_start: 0.8804 (tp) cc_final: 0.8496 (tp) REVERT: E 233 ASN cc_start: 0.8262 (m-40) cc_final: 0.7892 (m-40) REVERT: E 241 ASP cc_start: 0.7136 (t70) cc_final: 0.6640 (t0) REVERT: F 19 ASN cc_start: 0.7280 (t0) cc_final: 0.7075 (t0) REVERT: F 72 ILE cc_start: 0.8299 (mm) cc_final: 0.7955 (mm) REVERT: F 81 HIS cc_start: 0.8290 (m170) cc_final: 0.8086 (m170) REVERT: F 108 ASP cc_start: 0.7691 (t0) cc_final: 0.7352 (t0) REVERT: F 141 MET cc_start: 0.8248 (ttm) cc_final: 0.7763 (ttt) REVERT: G 9 ASP cc_start: 0.8425 (t0) cc_final: 0.8099 (m-30) REVERT: G 76 GLN cc_start: 0.9062 (mm-40) cc_final: 0.8861 (mm110) REVERT: G 77 TRP cc_start: 0.8101 (t60) cc_final: 0.7393 (t60) REVERT: G 88 ARG cc_start: 0.7943 (OUTLIER) cc_final: 0.7091 (ttp80) REVERT: G 105 TYR cc_start: 0.8475 (t80) cc_final: 0.8257 (t80) REVERT: G 107 HIS cc_start: 0.8524 (m90) cc_final: 0.8306 (m90) REVERT: G 121 LEU cc_start: 0.8230 (mt) cc_final: 0.7896 (mt) REVERT: G 122 PHE cc_start: 0.7606 (t80) cc_final: 0.7109 (t80) REVERT: H 11 PHE cc_start: 0.7589 (t80) cc_final: 0.7032 (t80) REVERT: H 96 GLU cc_start: 0.8752 (tp30) cc_final: 0.8500 (tp30) REVERT: H 126 ARG cc_start: 0.7044 (ttt-90) cc_final: 0.6434 (tmt170) REVERT: H 178 TYR cc_start: 0.7111 (m-80) cc_final: 0.6685 (m-80) REVERT: H 181 HIS cc_start: 0.7937 (m-70) cc_final: 0.7734 (m-70) REVERT: H 191 GLN cc_start: 0.9195 (OUTLIER) cc_final: 0.8906 (pm20) REVERT: H 206 LEU cc_start: 0.9404 (mt) cc_final: 0.8976 (mt) REVERT: H 246 ARG cc_start: 0.7238 (mmt90) cc_final: 0.6593 (mmm-85) REVERT: H 261 PHE cc_start: 0.7430 (t80) cc_final: 0.7030 (t80) REVERT: H 272 ASN cc_start: 0.8921 (OUTLIER) cc_final: 0.8483 (t0) REVERT: I 22 GLU cc_start: 0.8722 (tm-30) cc_final: 0.7985 (tm-30) REVERT: I 23 LYS cc_start: 0.8767 (tppt) cc_final: 0.8276 (tppt) REVERT: I 76 GLN cc_start: 0.8395 (mp10) cc_final: 0.7936 (mm-40) REVERT: I 84 GLU cc_start: 0.8470 (tp30) cc_final: 0.8184 (tp30) REVERT: I 87 GLN cc_start: 0.9140 (tt0) cc_final: 0.8610 (tm-30) REVERT: I 88 ARG cc_start: 0.7551 (ttp80) cc_final: 0.6639 (tmm-80) REVERT: I 94 ASN cc_start: 0.8105 (p0) cc_final: 0.7315 (p0) REVERT: I 121 LEU cc_start: 0.8266 (OUTLIER) cc_final: 0.8008 (tp) REVERT: J 18 PHE cc_start: 0.8825 (t80) cc_final: 0.8295 (t80) REVERT: J 23 LYS cc_start: 0.8694 (mmmt) cc_final: 0.8241 (tppp) REVERT: J 52 PHE cc_start: 0.8096 (m-10) cc_final: 0.7513 (m-80) REVERT: J 64 ASN cc_start: 0.8082 (m-40) cc_final: 0.7882 (m-40) REVERT: J 65 LYS cc_start: 0.9035 (mttp) cc_final: 0.8613 (mmtm) REVERT: J 77 TRP cc_start: 0.8379 (t60) cc_final: 0.8177 (t60) REVERT: J 97 GLN cc_start: 0.8181 (mm-40) cc_final: 0.7440 (mm-40) REVERT: J 98 GLN cc_start: 0.8773 (tt0) cc_final: 0.8558 (tt0) REVERT: J 100 LEU cc_start: 0.8841 (OUTLIER) cc_final: 0.8532 (mt) REVERT: J 105 TYR cc_start: 0.8879 (t80) cc_final: 0.8498 (t80) REVERT: J 116 ASP cc_start: 0.7246 (t0) cc_final: 0.6983 (t0) REVERT: J 120 ASN cc_start: 0.8156 (m110) cc_final: 0.7715 (m-40) REVERT: K 16 SER cc_start: 0.7975 (t) cc_final: 0.7352 (p) REVERT: K 23 GLU cc_start: 0.7475 (tm-30) cc_final: 0.6972 (tm-30) REVERT: K 82 TRP cc_start: 0.8559 (p-90) cc_final: 0.7974 (p-90) REVERT: K 156 ASN cc_start: 0.8037 (m110) cc_final: 0.7658 (m-40) REVERT: K 285 LEU cc_start: 0.9339 (mt) cc_final: 0.9069 (mp) REVERT: K 309 LYS cc_start: 0.8547 (tppt) cc_final: 0.8313 (ttmm) REVERT: K 403 ASP cc_start: 0.7391 (OUTLIER) cc_final: 0.6839 (t70) REVERT: K 565 GLU cc_start: 0.7354 (mm-30) cc_final: 0.6089 (mm-30) REVERT: M 21 ASN cc_start: 0.8060 (p0) cc_final: 0.7714 (p0) REVERT: M 55 GLN cc_start: 0.8676 (tt0) cc_final: 0.8382 (tt0) REVERT: M 102 MET cc_start: 0.6083 (mtt) cc_final: 0.5716 (mtp) REVERT: M 116 MET cc_start: 0.8832 (mmt) cc_final: 0.8553 (mmt) REVERT: M 130 GLN cc_start: 0.7226 (OUTLIER) cc_final: 0.6700 (tt0) REVERT: M 178 TYR cc_start: 0.8222 (m-80) cc_final: 0.8020 (m-80) REVERT: M 198 ASP cc_start: 0.7666 (m-30) cc_final: 0.7084 (m-30) REVERT: M 204 GLN cc_start: 0.8424 (tm-30) cc_final: 0.8137 (tm-30) REVERT: M 212 HIS cc_start: 0.6894 (m-70) cc_final: 0.6322 (m-70) REVERT: M 221 MET cc_start: 0.8419 (ttt) cc_final: 0.7790 (ttt) REVERT: M 263 ASP cc_start: 0.7798 (m-30) cc_final: 0.7529 (m-30) REVERT: M 277 LYS cc_start: 0.7893 (mppt) cc_final: 0.7554 (mppt) REVERT: N 7 ILE cc_start: 0.8622 (mt) cc_final: 0.8410 (mm) REVERT: N 26 TYR cc_start: 0.8554 (m-80) cc_final: 0.8092 (m-80) REVERT: N 56 ILE cc_start: 0.8709 (mm) cc_final: 0.8507 (mm) REVERT: N 63 THR cc_start: 0.8946 (t) cc_final: 0.8538 (p) REVERT: N 100 TYR cc_start: 0.8519 (m-80) cc_final: 0.8128 (m-80) REVERT: L 17 LEU cc_start: 0.9357 (tt) cc_final: 0.9002 (tt) REVERT: L 40 TYR cc_start: 0.8662 (m-10) cc_final: 0.8374 (m-10) REVERT: L 56 MET cc_start: 0.7924 (mmm) cc_final: 0.7581 (mmm) REVERT: L 74 GLN cc_start: 0.6978 (mt0) cc_final: 0.6753 (mt0) REVERT: L 103 ILE cc_start: 0.8416 (tt) cc_final: 0.8084 (tt) REVERT: L 107 HIS cc_start: 0.7484 (m90) cc_final: 0.7020 (m90) outliers start: 81 outliers final: 35 residues processed: 889 average time/residue: 0.3797 time to fit residues: 526.6135 Evaluate side-chains 746 residues out of total 2762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 704 time to evaluate : 2.877 ------------------------------------------------------------------------------- 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 276 THR Chi-restraints excluded: chain D residue 10 VAL Chi-restraints excluded: chain D residue 45 CYS Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain F residue 21 ASN Chi-restraints excluded: chain F residue 32 ILE Chi-restraints excluded: chain 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 191 GLN Chi-restraints excluded: chain H residue 229 PHE Chi-restraints excluded: chain H residue 272 ASN Chi-restraints excluded: chain H residue 276 THR Chi-restraints excluded: chain I residue 13 VAL Chi-restraints excluded: chain I residue 20 VAL Chi-restraints excluded: chain I residue 57 ARG Chi-restraints excluded: chain I residue 121 LEU Chi-restraints excluded: chain J residue 96 GLU Chi-restraints excluded: chain J residue 100 LEU Chi-restraints excluded: chain K residue 198 THR Chi-restraints excluded: chain K residue 306 THR Chi-restraints excluded: chain K residue 330 LEU Chi-restraints excluded: chain K residue 403 ASP Chi-restraints excluded: chain K residue 430 THR Chi-restraints excluded: chain 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 109 THR 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 16 optimal weight: 2.9990 chunk 307 optimal weight: 3.9990 chunk 295 optimal weight: 0.7980 chunk 191 optimal weight: 0.6980 chunk 253 optimal weight: 0.9980 chunk 277 optimal weight: 0.8980 chunk 221 optimal weight: 4.9990 chunk 283 optimal weight: 6.9990 chunk 308 optimal weight: 2.9990 chunk 274 optimal weight: 2.9990 chunk 280 optimal weight: 4.9990 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 ASN ** B 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 55 GLN C 62 HIS ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 52 ASN ** 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 ** 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 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 33 ASN ** I 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 8 GLN ** J 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 52 ASN ** M 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 61 GLN ** N 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 98 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.152485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.119494 restraints weight = 47159.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.123875 restraints weight = 20995.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 69)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.126720 restraints weight = 12235.539| |-----------------------------------------------------------------------------| r_work (final): 0.3866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.3128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 27430 Z= 0.259 Angle : 0.850 11.196 37194 Z= 0.444 Chirality : 0.050 0.330 4023 Planarity : 0.006 0.066 4752 Dihedral : 14.788 174.011 4195 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 33.22 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.77 % Favored : 90.20 % Rotamer: Outliers : 3.59 % Allowed : 18.91 % Favored : 77.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.61 (0.14), residues: 3184 helix: -0.75 (0.14), residues: 1278 sheet: -2.77 (0.24), residues: 388 loop : -2.28 (0.15), residues: 1518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.003 TRP I 77 HIS 0.020 0.002 HIS C 214 PHE 0.036 0.003 PHE G 111 TYR 0.033 0.003 TYR J 106 ARG 0.011 0.001 ARG B 224 Details of bonding type rmsd hydrogen bonds : bond 0.05356 ( 1148) hydrogen bonds : angle 6.92123 ( 3315) covalent geometry : bond 0.00585 (27430) covalent geometry : angle 0.84974 (37194) *********************** 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 849 residues out of total 2762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 750 time to evaluate : 3.223 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: 0.8484 (OUTLIER) cc_final: 0.6115 (t80) REVERT: A 126 ASN cc_start: 0.8191 (t0) cc_final: 0.7565 (t0) REVERT: A 144 ASP cc_start: 0.8550 (m-30) cc_final: 0.8279 (m-30) REVERT: A 155 TYR cc_start: 0.8540 (m-80) cc_final: 0.8216 (m-80) REVERT: A 165 TRP cc_start: 0.8576 (m-10) cc_final: 0.8310 (m100) REVERT: A 167 GLN cc_start: 0.8505 (tm-30) cc_final: 0.7727 (tm-30) REVERT: A 168 TYR cc_start: 0.7706 (m-80) cc_final: 0.7343 (m-80) REVERT: B 40 LEU cc_start: 0.8988 (mt) cc_final: 0.8722 (mt) REVERT: B 69 GLU cc_start: 0.6751 (tm-30) cc_final: 0.6496 (tm-30) REVERT: B 175 TYR cc_start: 0.8623 (t80) cc_final: 0.8064 (t80) REVERT: B 183 PHE cc_start: 0.8412 (m-80) cc_final: 0.7531 (m-10) REVERT: C 4 GLU cc_start: 0.7494 (tp30) cc_final: 0.7131 (tp30) REVERT: C 156 LYS cc_start: 0.8834 (ttpp) cc_final: 0.8598 (tttm) REVERT: C 220 GLN cc_start: 0.7932 (tm-30) cc_final: 0.6679 (tm-30) REVERT: C 256 GLU cc_start: 0.7453 (tm-30) cc_final: 0.7232 (tm-30) REVERT: D 36 THR cc_start: 0.8083 (OUTLIER) cc_final: 0.7720 (p) REVERT: D 46 LEU cc_start: 0.8015 (tt) cc_final: 0.7721 (tp) REVERT: D 169 ARG cc_start: 0.8054 (mtm-85) cc_final: 0.7836 (mtm-85) REVERT: D 244 PHE cc_start: 0.9000 (m-10) cc_final: 0.8663 (m-10) REVERT: E 79 GLU cc_start: 0.7706 (tm-30) cc_final: 0.7351 (tm-30) REVERT: E 101 TYR cc_start: 0.7932 (t80) cc_final: 0.7729 (t80) REVERT: E 184 ILE cc_start: 0.8786 (mm) cc_final: 0.8531 (mm) REVERT: E 204 GLN cc_start: 0.7763 (tm130) cc_final: 0.7324 (tm-30) REVERT: E 221 MET cc_start: 0.8401 (mtm) cc_final: 0.8113 (mtm) REVERT: E 226 LEU cc_start: 0.8606 (tp) cc_final: 0.8294 (tp) REVERT: E 233 ASN cc_start: 0.8322 (m-40) cc_final: 0.7931 (m-40) REVERT: E 241 ASP cc_start: 0.7040 (t70) cc_final: 0.6607 (t0) REVERT: E 265 LEU cc_start: 0.9044 (tp) cc_final: 0.8767 (tt) REVERT: F 72 ILE cc_start: 0.8279 (mm) cc_final: 0.7917 (mm) REVERT: F 108 ASP cc_start: 0.7791 (t0) cc_final: 0.7336 (t0) REVERT: F 141 MET cc_start: 0.8204 (ttm) cc_final: 0.7817 (ttt) REVERT: F 172 THR cc_start: 0.8059 (m) cc_final: 0.7016 (p) REVERT: G 9 ASP cc_start: 0.8380 (t0) cc_final: 0.8088 (m-30) REVERT: G 16 ARG cc_start: 0.8848 (tpt-90) cc_final: 0.8465 (tpt-90) REVERT: G 57 ARG cc_start: 0.8533 (ttm-80) cc_final: 0.8309 (ttm110) REVERT: G 58 LEU cc_start: 0.8146 (tp) cc_final: 0.7701 (tp) REVERT: G 68 PHE cc_start: 0.8266 (t80) cc_final: 0.8037 (t80) REVERT: G 71 ARG cc_start: 0.8579 (mmm160) cc_final: 0.8288 (mmm-85) REVERT: G 77 TRP cc_start: 0.8152 (t60) cc_final: 0.7450 (t60) REVERT: G 88 ARG cc_start: 0.7895 (OUTLIER) cc_final: 0.6944 (ttp80) REVERT: G 94 ASN cc_start: 0.8603 (p0) cc_final: 0.8352 (p0) REVERT: G 97 GLN cc_start: 0.8546 (tt0) cc_final: 0.8179 (tp40) REVERT: G 98 GLN cc_start: 0.7973 (tt0) cc_final: 0.7659 (tm-30) REVERT: G 103 ILE cc_start: 0.8958 (OUTLIER) cc_final: 0.8271 (tt) REVERT: G 107 HIS cc_start: 0.8487 (m90) cc_final: 0.8047 (m90) REVERT: G 110 GLN cc_start: 0.7724 (tp-100) cc_final: 0.7302 (tp-100) REVERT: G 111 PHE cc_start: 0.8141 (t80) cc_final: 0.7677 (t80) REVERT: G 122 PHE cc_start: 0.7827 (t80) cc_final: 0.7272 (t80) REVERT: H 11 PHE cc_start: 0.7541 (t80) cc_final: 0.6979 (t80) REVERT: H 81 HIS cc_start: 0.8522 (OUTLIER) cc_final: 0.7807 (t-90) REVERT: H 102 MET cc_start: 0.8856 (mmm) cc_final: 0.7971 (mmm) REVERT: H 178 TYR cc_start: 0.7122 (m-80) cc_final: 0.6380 (m-10) REVERT: H 181 HIS cc_start: 0.8108 (m-70) cc_final: 0.7639 (m-70) REVERT: H 261 PHE cc_start: 0.7619 (t80) cc_final: 0.7267 (t80) REVERT: H 272 ASN cc_start: 0.8848 (t0) cc_final: 0.8471 (t0) REVERT: I 22 GLU cc_start: 0.8800 (tm-30) cc_final: 0.8003 (tm-30) REVERT: I 23 LYS cc_start: 0.8798 (tppt) cc_final: 0.8178 (tppt) REVERT: I 71 ARG cc_start: 0.8870 (mmm160) cc_final: 0.8596 (mmm160) REVERT: I 77 TRP cc_start: 0.8106 (t60) cc_final: 0.7541 (t60) REVERT: I 81 GLN cc_start: 0.8930 (OUTLIER) cc_final: 0.8496 (mp10) REVERT: I 84 GLU cc_start: 0.8550 (tp30) cc_final: 0.8137 (tp30) REVERT: I 87 GLN cc_start: 0.9135 (tt0) cc_final: 0.8592 (tm-30) REVERT: I 88 ARG cc_start: 0.7722 (ttp80) cc_final: 0.6861 (tmm-80) REVERT: J 18 PHE cc_start: 0.8785 (t80) cc_final: 0.8121 (t80) REVERT: J 23 LYS cc_start: 0.8827 (mmmt) cc_final: 0.8583 (tppp) REVERT: J 52 PHE cc_start: 0.8092 (m-10) cc_final: 0.7509 (m-80) REVERT: J 65 LYS cc_start: 0.9128 (mttp) cc_final: 0.8735 (mmtm) REVERT: J 78 GLU cc_start: 0.9033 (tp30) cc_final: 0.8389 (tp30) REVERT: J 91 ASN cc_start: 0.8544 (m-40) cc_final: 0.8014 (m-40) REVERT: J 105 TYR cc_start: 0.8921 (t80) cc_final: 0.8413 (t80) REVERT: J 108 GLU cc_start: 0.8153 (mm-30) cc_final: 0.7946 (mm-30) REVERT: J 116 ASP cc_start: 0.7454 (t0) cc_final: 0.7073 (t0) REVERT: J 120 ASN cc_start: 0.8369 (m110) cc_final: 0.7679 (m-40) REVERT: J 123 ASN cc_start: 0.8277 (m-40) cc_final: 0.8075 (m-40) REVERT: J 124 GLU cc_start: 0.7942 (pp20) cc_final: 0.7717 (pp20) REVERT: K 82 TRP cc_start: 0.8554 (p-90) cc_final: 0.7964 (p-90) REVERT: K 156 ASN cc_start: 0.8073 (m110) cc_final: 0.7581 (m-40) REVERT: K 250 TYR cc_start: 0.7948 (OUTLIER) cc_final: 0.6601 (p90) REVERT: K 285 LEU cc_start: 0.9321 (mt) cc_final: 0.9072 (mp) REVERT: K 288 MET cc_start: 0.7860 (mtm) cc_final: 0.7587 (ptp) REVERT: K 309 LYS cc_start: 0.8630 (tppt) cc_final: 0.8387 (ttmm) REVERT: K 436 LEU cc_start: 0.8933 (mt) cc_final: 0.8439 (tp) REVERT: K 503 SER cc_start: 0.8347 (m) cc_final: 0.8067 (p) REVERT: M 19 ASN cc_start: 0.8026 (t0) cc_final: 0.7824 (t0) REVERT: M 102 MET cc_start: 0.6156 (mtt) cc_final: 0.5853 (mtt) REVERT: M 130 GLN cc_start: 0.7391 (OUTLIER) cc_final: 0.7042 (tt0) REVERT: M 204 GLN cc_start: 0.8476 (tm-30) cc_final: 0.8201 (tm-30) REVERT: M 209 MET cc_start: 0.7909 (ttp) cc_final: 0.7427 (ttp) REVERT: M 221 MET cc_start: 0.8412 (ttt) cc_final: 0.7946 (ttt) REVERT: M 277 LYS cc_start: 0.7868 (mppt) cc_final: 0.7490 (mppt) REVERT: N 26 TYR cc_start: 0.8582 (m-80) cc_final: 0.7919 (m-80) REVERT: N 63 THR cc_start: 0.8974 (t) cc_final: 0.8502 (p) REVERT: L 17 LEU cc_start: 0.9376 (tt) cc_final: 0.8663 (pp) REVERT: L 40 TYR cc_start: 0.8610 (m-10) cc_final: 0.8101 (m-80) REVERT: L 76 GLN cc_start: 0.8787 (mp10) cc_final: 0.8465 (mm110) REVERT: L 103 ILE cc_start: 0.8470 (tt) cc_final: 0.7991 (tt) REVERT: L 107 HIS cc_start: 0.6691 (m90) cc_final: 0.5996 (m90) outliers start: 99 outliers final: 57 residues processed: 801 average time/residue: 0.3866 time to fit residues: 484.9355 Evaluate side-chains 743 residues out of total 2762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 678 time to evaluate : 3.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 PHE 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 109 ILE Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain D residue 10 VAL Chi-restraints excluded: chain D residue 36 THR Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 45 CYS Chi-restraints excluded: chain D residue 260 SER Chi-restraints excluded: chain E residue 52 ASN Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 207 VAL Chi-restraints excluded: chain F residue 21 ASN Chi-restraints excluded: chain F residue 32 ILE Chi-restraints excluded: chain F residue 40 LEU Chi-restraints excluded: chain F residue 124 GLN Chi-restraints excluded: chain G residue 10 ILE Chi-restraints excluded: chain G residue 13 VAL Chi-restraints excluded: chain G residue 49 ILE Chi-restraints excluded: chain G residue 88 ARG Chi-restraints excluded: chain G residue 95 LEU Chi-restraints excluded: chain G residue 103 ILE Chi-restraints excluded: chain H residue 42 THR Chi-restraints excluded: chain H residue 81 HIS Chi-restraints excluded: chain H residue 132 THR Chi-restraints excluded: chain H residue 212 HIS Chi-restraints excluded: chain H residue 229 PHE Chi-restraints excluded: chain H residue 253 ASP 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 58 LEU Chi-restraints excluded: chain I residue 81 GLN 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 308 TYR Chi-restraints excluded: chain K residue 330 LEU Chi-restraints excluded: chain K residue 403 ASP Chi-restraints excluded: chain K residue 430 THR Chi-restraints excluded: chain K residue 458 MET Chi-restraints excluded: chain K residue 481 ILE Chi-restraints excluded: chain M residue 42 THR Chi-restraints excluded: chain M residue 46 LEU Chi-restraints excluded: chain M residue 125 VAL Chi-restraints excluded: chain M residue 130 GLN Chi-restraints excluded: chain M residue 272 ASN Chi-restraints excluded: chain N residue 21 VAL Chi-restraints excluded: chain N residue 30 THR Chi-restraints excluded: chain N residue 37 ILE Chi-restraints excluded: chain N residue 70 VAL Chi-restraints excluded: chain N residue 133 GLN Chi-restraints excluded: chain N residue 159 LEU Chi-restraints excluded: chain N residue 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 309 optimal weight: 6.9990 chunk 245 optimal weight: 0.6980 chunk 113 optimal weight: 0.9990 chunk 270 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 233 optimal weight: 5.9990 chunk 307 optimal weight: 3.9990 chunk 219 optimal weight: 0.9990 chunk 193 optimal weight: 10.0000 chunk 14 optimal weight: 0.9990 chunk 123 optimal weight: 1.9990 overall best weight: 0.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 ASN ** B 181 HIS ** 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 28 ASN ** 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** ** G 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 55 GLN H 100 GLN ** H 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 97 GLN J 8 GLN ** J 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 383 ASN ** K 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 518 HIS ** 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 61 GLN ** N 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.153905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.121075 restraints weight = 46828.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.125568 restraints weight = 20687.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.128446 restraints weight = 11951.912| |-----------------------------------------------------------------------------| r_work (final): 0.3906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.3672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 27430 Z= 0.219 Angle : 0.806 12.257 37194 Z= 0.421 Chirality : 0.050 0.301 4023 Planarity : 0.006 0.069 4752 Dihedral : 14.596 171.997 4193 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 30.99 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.05 % Favored : 90.92 % Rotamer: Outliers : 4.28 % Allowed : 20.04 % Favored : 75.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.47 (0.14), residues: 3184 helix: -0.60 (0.14), residues: 1272 sheet: -2.76 (0.24), residues: 376 loop : -2.22 (0.15), residues: 1536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP J 77 HIS 0.026 0.002 HIS C 214 PHE 0.034 0.003 PHE G 111 TYR 0.039 0.003 TYR K 440 ARG 0.022 0.001 ARG I 57 Details of bonding type rmsd hydrogen bonds : bond 0.04943 ( 1148) hydrogen bonds : angle 6.75709 ( 3315) covalent geometry : bond 0.00495 (27430) covalent geometry : angle 0.80628 (37194) *********************** 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 883 residues out of total 2762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 765 time to evaluate : 3.130 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 PHE cc_start: 0.8183 (OUTLIER) cc_final: 0.6062 (t80) REVERT: A 126 ASN cc_start: 0.8196 (t0) cc_final: 0.7566 (t0) REVERT: A 164 GLU cc_start: 0.8332 (tp30) cc_final: 0.7781 (tp30) REVERT: A 165 TRP cc_start: 0.8535 (m-10) cc_final: 0.8208 (m100) REVERT: A 167 GLN cc_start: 0.8559 (tm-30) cc_final: 0.7750 (tm-30) REVERT: B 35 GLN cc_start: 0.7715 (mt0) cc_final: 0.7130 (mt0) REVERT: B 40 LEU cc_start: 0.8964 (mt) cc_final: 0.8633 (mt) REVERT: B 141 MET cc_start: 0.6937 (mmt) cc_final: 0.6527 (mmt) REVERT: B 175 TYR cc_start: 0.8564 (t80) cc_final: 0.8096 (t80) REVERT: B 183 PHE cc_start: 0.8155 (m-80) cc_final: 0.7887 (m-80) REVERT: C 67 ILE cc_start: 0.8432 (OUTLIER) cc_final: 0.8008 (mm) REVERT: C 146 SER cc_start: 0.8267 (t) cc_final: 0.7927 (t) REVERT: C 220 GLN cc_start: 0.7794 (tm-30) cc_final: 0.6545 (tm-30) REVERT: C 256 GLU cc_start: 0.7580 (tm-30) cc_final: 0.7337 (tm-30) REVERT: D 35 GLN cc_start: 0.8444 (mm-40) cc_final: 0.8120 (tp-100) REVERT: D 36 THR cc_start: 0.7966 (OUTLIER) cc_final: 0.7652 (p) REVERT: D 46 LEU cc_start: 0.7864 (tt) cc_final: 0.7612 (tt) REVERT: D 150 MET cc_start: 0.5436 (ptm) cc_final: 0.5064 (ppp) REVERT: D 244 PHE cc_start: 0.8991 (m-10) cc_final: 0.8586 (m-10) REVERT: E 17 ASP cc_start: 0.8367 (t70) cc_final: 0.7885 (t0) REVERT: E 79 GLU cc_start: 0.7704 (tm-30) cc_final: 0.7106 (tm-30) REVERT: E 116 MET cc_start: 0.8053 (mmt) cc_final: 0.7338 (mmt) REVERT: E 167 MET cc_start: 0.8792 (mtm) cc_final: 0.8524 (mtp) REVERT: E 184 ILE cc_start: 0.8726 (OUTLIER) cc_final: 0.8417 (mm) REVERT: E 204 GLN cc_start: 0.7772 (tm130) cc_final: 0.7049 (tm-30) REVERT: E 221 MET cc_start: 0.8315 (OUTLIER) cc_final: 0.7493 (mtm) REVERT: E 233 ASN cc_start: 0.8241 (m-40) cc_final: 0.7866 (m-40) REVERT: E 241 ASP cc_start: 0.7007 (t70) cc_final: 0.6696 (t0) REVERT: E 264 TYR cc_start: 0.8650 (OUTLIER) cc_final: 0.8429 (m-10) REVERT: F 40 LEU cc_start: 0.8230 (OUTLIER) cc_final: 0.7842 (tp) REVERT: F 72 ILE cc_start: 0.8182 (mm) cc_final: 0.7801 (mm) REVERT: F 108 ASP cc_start: 0.7908 (t0) cc_final: 0.7425 (t0) REVERT: F 141 MET cc_start: 0.7840 (ttm) cc_final: 0.7627 (ttp) REVERT: G 9 ASP cc_start: 0.8249 (t0) cc_final: 0.7835 (m-30) REVERT: G 17 LEU cc_start: 0.9161 (tt) cc_final: 0.8612 (pp) REVERT: G 68 PHE cc_start: 0.8141 (t80) cc_final: 0.7820 (t80) REVERT: G 71 ARG cc_start: 0.8560 (mmm160) cc_final: 0.8088 (mmm-85) REVERT: G 77 TRP cc_start: 0.8247 (t60) cc_final: 0.8011 (t60) REVERT: G 94 ASN cc_start: 0.8631 (p0) cc_final: 0.8381 (p0) REVERT: G 103 ILE cc_start: 0.8942 (OUTLIER) cc_final: 0.8192 (tt) REVERT: G 107 HIS cc_start: 0.8462 (m90) cc_final: 0.8130 (m90) REVERT: G 110 GLN cc_start: 0.7622 (tp-100) cc_final: 0.7203 (tp-100) REVERT: G 122 PHE cc_start: 0.8158 (t80) cc_final: 0.7510 (t80) REVERT: H 11 PHE cc_start: 0.7561 (t80) cc_final: 0.6881 (t80) REVERT: H 81 HIS cc_start: 0.8266 (OUTLIER) cc_final: 0.7477 (t-90) REVERT: H 86 VAL cc_start: 0.8357 (OUTLIER) cc_final: 0.7742 (p) REVERT: H 102 MET cc_start: 0.8890 (mmm) cc_final: 0.7985 (mmm) REVERT: H 126 ARG cc_start: 0.7266 (ttt-90) cc_final: 0.7060 (ttt-90) REVERT: H 178 TYR cc_start: 0.7107 (m-80) cc_final: 0.6364 (m-10) REVERT: H 191 GLN cc_start: 0.9081 (OUTLIER) cc_final: 0.8864 (pp30) REVERT: H 206 LEU cc_start: 0.9411 (mt) cc_final: 0.8958 (mt) REVERT: H 261 PHE cc_start: 0.7636 (t80) cc_final: 0.7306 (t80) REVERT: H 272 ASN cc_start: 0.8853 (t0) cc_final: 0.8643 (t0) REVERT: I 22 GLU cc_start: 0.8871 (tm-30) cc_final: 0.8191 (tm-30) REVERT: I 23 LYS cc_start: 0.8875 (tppt) cc_final: 0.8561 (tppt) REVERT: I 71 ARG cc_start: 0.8809 (mmm160) cc_final: 0.8565 (mmm160) REVERT: I 77 TRP cc_start: 0.8447 (t60) cc_final: 0.7493 (t60) REVERT: I 81 GLN cc_start: 0.9085 (OUTLIER) cc_final: 0.8561 (mp10) REVERT: I 84 GLU cc_start: 0.8546 (tp30) cc_final: 0.8098 (tp30) REVERT: I 87 GLN cc_start: 0.9098 (tt0) cc_final: 0.8618 (tm-30) REVERT: I 88 ARG cc_start: 0.7892 (ttp80) cc_final: 0.7248 (tmm-80) REVERT: I 96 GLU cc_start: 0.8425 (OUTLIER) cc_final: 0.8063 (pm20) REVERT: I 109 THR cc_start: 0.8119 (m) cc_final: 0.7446 (p) REVERT: I 113 PHE cc_start: 0.8072 (m-80) cc_final: 0.7658 (m-10) REVERT: I 123 ASN cc_start: 0.8569 (m110) cc_final: 0.8165 (m110) REVERT: J 18 PHE cc_start: 0.8753 (t80) cc_final: 0.8147 (t80) REVERT: J 52 PHE cc_start: 0.8055 (m-10) cc_final: 0.7590 (m-80) REVERT: J 57 ARG cc_start: 0.8752 (mtm110) cc_final: 0.8384 (mtm-85) REVERT: J 77 TRP cc_start: 0.8087 (t60) cc_final: 0.7713 (t60) REVERT: J 78 GLU cc_start: 0.8922 (tp30) cc_final: 0.8472 (tp30) REVERT: J 91 ASN cc_start: 0.8573 (m-40) cc_final: 0.7995 (m-40) REVERT: J 98 GLN cc_start: 0.8572 (tt0) cc_final: 0.8302 (tp40) REVERT: J 115 LYS cc_start: 0.5376 (mmtt) cc_final: 0.5102 (mmtt) REVERT: J 116 ASP cc_start: 0.7388 (t0) cc_final: 0.6955 (t0) REVERT: J 120 ASN cc_start: 0.8124 (m110) cc_final: 0.7564 (m-40) REVERT: K 250 TYR cc_start: 0.7894 (OUTLIER) cc_final: 0.6675 (p90) REVERT: K 281 LEU cc_start: 0.8483 (mp) cc_final: 0.8107 (mp) REVERT: K 309 LYS cc_start: 0.8555 (tppt) cc_final: 0.8303 (ttpp) REVERT: K 503 SER cc_start: 0.8467 (m) cc_final: 0.8266 (p) REVERT: K 526 GLU cc_start: 0.7462 (mm-30) cc_final: 0.6716 (tp30) REVERT: M 147 ILE cc_start: 0.9160 (pt) cc_final: 0.8913 (mt) REVERT: M 204 GLN cc_start: 0.8301 (tm-30) cc_final: 0.7951 (tm-30) REVERT: M 221 MET cc_start: 0.8243 (ttt) cc_final: 0.8011 (ttt) REVERT: M 277 LYS cc_start: 0.7833 (mppt) cc_final: 0.7465 (mppt) REVERT: N 26 TYR cc_start: 0.8476 (m-80) cc_final: 0.7635 (m-80) REVERT: N 63 THR cc_start: 0.8915 (t) cc_final: 0.8473 (p) REVERT: N 68 ASN cc_start: 0.8202 (t0) cc_final: 0.7740 (t0) REVERT: N 152 LEU cc_start: 0.8517 (mp) cc_final: 0.8184 (mp) REVERT: N 171 MET cc_start: 0.7158 (mtm) cc_final: 0.6524 (mtm) REVERT: L 17 LEU cc_start: 0.8991 (tt) cc_final: 0.8656 (tt) REVERT: L 24 ILE cc_start: 0.8874 (mt) cc_final: 0.8669 (mp) REVERT: L 35 THR cc_start: 0.8573 (t) cc_final: 0.8302 (t) REVERT: L 40 TYR cc_start: 0.8751 (m-10) cc_final: 0.8349 (m-80) REVERT: L 76 GLN cc_start: 0.8777 (OUTLIER) cc_final: 0.8458 (mm110) outliers start: 118 outliers final: 57 residues processed: 826 average time/residue: 0.3832 time to fit residues: 497.5103 Evaluate side-chains 754 residues out of total 2762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 682 time to evaluate : 3.042 ------------------------------------------------------------------------------- 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 32 ILE Chi-restraints excluded: chain B residue 44 VAL 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 268 VAL Chi-restraints excluded: chain C residue 276 THR 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 184 ILE 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 E residue 264 TYR Chi-restraints excluded: chain F residue 21 ASN Chi-restraints excluded: chain F residue 32 ILE Chi-restraints excluded: chain F residue 40 LEU Chi-restraints excluded: chain F residue 124 GLN Chi-restraints excluded: chain 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 95 LEU Chi-restraints excluded: chain G residue 103 ILE Chi-restraints excluded: chain G residue 124 GLU Chi-restraints excluded: chain H residue 81 HIS Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain H residue 132 THR Chi-restraints excluded: chain H residue 187 HIS Chi-restraints excluded: chain H residue 191 GLN Chi-restraints excluded: chain H residue 228 VAL Chi-restraints excluded: chain H residue 229 PHE Chi-restraints excluded: chain H residue 253 ASP Chi-restraints excluded: chain H residue 266 VAL Chi-restraints excluded: chain H residue 276 THR Chi-restraints excluded: chain I residue 13 VAL Chi-restraints excluded: chain I residue 81 GLN Chi-restraints excluded: chain I residue 96 GLU 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 269 VAL Chi-restraints excluded: chain K residue 306 THR Chi-restraints excluded: chain K residue 308 TYR Chi-restraints excluded: chain K residue 330 LEU Chi-restraints excluded: chain K residue 383 ASN Chi-restraints excluded: chain K residue 403 ASP Chi-restraints excluded: chain K residue 478 LEU Chi-restraints excluded: chain 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 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 76 GLN Chi-restraints excluded: chain L residue 81 GLN Chi-restraints excluded: chain L residue 84 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 24 optimal weight: 1.9990 chunk 262 optimal weight: 0.6980 chunk 273 optimal weight: 0.0970 chunk 73 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 chunk 148 optimal weight: 5.9990 chunk 317 optimal weight: 1.9990 chunk 146 optimal weight: 7.9990 chunk 33 optimal weight: 0.0980 chunk 119 optimal weight: 0.8980 chunk 277 optimal weight: 0.6980 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** ** B 220 GLN ** 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 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 234 ASN ** F 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 62 HIS ** 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 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 61 GLN ** N 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 98 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.158079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.124585 restraints weight = 46700.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.129201 restraints weight = 20887.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.132054 restraints weight = 12131.846| |-----------------------------------------------------------------------------| r_work (final): 0.3967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.4167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 27430 Z= 0.190 Angle : 0.792 13.863 37194 Z= 0.411 Chirality : 0.049 0.317 4023 Planarity : 0.006 0.074 4752 Dihedral : 14.441 170.476 4191 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 29.03 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.73 % Favored : 91.24 % Rotamer: Outliers : 4.49 % Allowed : 21.45 % Favored : 74.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.39 (0.14), residues: 3184 helix: -0.54 (0.14), residues: 1265 sheet: -2.71 (0.24), residues: 376 loop : -2.19 (0.14), residues: 1543 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 182 HIS 0.027 0.002 HIS C 214 PHE 0.035 0.002 PHE G 111 TYR 0.038 0.003 TYR J 106 ARG 0.013 0.001 ARG C 280 Details of bonding type rmsd hydrogen bonds : bond 0.04684 ( 1148) hydrogen bonds : angle 6.65043 ( 3315) covalent geometry : bond 0.00431 (27430) covalent geometry : angle 0.79210 (37194) *********************** 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 878 residues out of total 2762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 754 time to evaluate : 3.140 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 ASN cc_start: 0.7975 (t0) cc_final: 0.7516 (t0) REVERT: A 133 TRP cc_start: 0.7542 (t-100) cc_final: 0.6856 (t-100) REVERT: A 155 TYR cc_start: 0.8414 (m-80) cc_final: 0.8067 (m-80) REVERT: A 164 GLU cc_start: 0.8325 (tp30) cc_final: 0.7442 (tp30) REVERT: A 165 TRP cc_start: 0.8531 (m-10) cc_final: 0.8216 (m100) REVERT: A 167 GLN cc_start: 0.8860 (tm-30) cc_final: 0.7435 (tm-30) REVERT: A 168 TYR cc_start: 0.7427 (m-80) cc_final: 0.6578 (m-10) REVERT: B 8 ASP cc_start: 0.7703 (t70) cc_final: 0.7468 (t0) REVERT: B 141 MET cc_start: 0.6653 (mmt) cc_final: 0.6244 (mmt) REVERT: B 175 TYR cc_start: 0.8420 (t80) cc_final: 0.8084 (t80) REVERT: B 201 LEU cc_start: 0.8203 (OUTLIER) cc_final: 0.7923 (mm) REVERT: B 241 ASP cc_start: 0.7857 (t70) cc_final: 0.7615 (t70) REVERT: B 259 ARG cc_start: 0.7741 (mtp180) cc_final: 0.7524 (mtm110) REVERT: C 48 ARG cc_start: 0.7593 (tpt90) cc_final: 0.7323 (tpt90) REVERT: C 67 ILE cc_start: 0.8424 (OUTLIER) cc_final: 0.7867 (mm) REVERT: C 103 CYS cc_start: 0.8179 (m) cc_final: 0.7820 (m) REVERT: C 110 ARG cc_start: 0.7400 (ptm160) cc_final: 0.7039 (ptm160) REVERT: C 146 SER cc_start: 0.8202 (t) cc_final: 0.7927 (t) REVERT: C 220 GLN cc_start: 0.7652 (tm-30) cc_final: 0.6071 (tm-30) REVERT: C 222 ASN cc_start: 0.8191 (m110) cc_final: 0.6058 (m110) REVERT: C 243 LEU cc_start: 0.7870 (OUTLIER) cc_final: 0.7530 (mt) REVERT: C 256 GLU cc_start: 0.7546 (tm-30) cc_final: 0.7302 (tm-30) REVERT: D 35 GLN cc_start: 0.8483 (mm-40) cc_final: 0.8212 (tp-100) REVERT: D 36 THR cc_start: 0.7858 (OUTLIER) cc_final: 0.7592 (p) REVERT: D 134 SER cc_start: 0.8066 (p) cc_final: 0.7228 (t) REVERT: D 141 MET cc_start: 0.8135 (mtp) cc_final: 0.7844 (mtp) REVERT: D 150 MET cc_start: 0.4978 (ptm) cc_final: 0.4775 (ppp) REVERT: D 227 TYR cc_start: 0.8361 (m-80) cc_final: 0.8132 (m-80) REVERT: E 79 GLU cc_start: 0.7808 (tm-30) cc_final: 0.7393 (tm-30) REVERT: E 116 MET cc_start: 0.8347 (mmt) cc_final: 0.7874 (mmt) REVERT: E 144 GLU cc_start: 0.7869 (mt-10) cc_final: 0.7644 (mt-10) REVERT: E 167 MET cc_start: 0.8681 (mtm) cc_final: 0.8436 (mtp) REVERT: E 184 ILE cc_start: 0.8777 (OUTLIER) cc_final: 0.8420 (mm) REVERT: E 233 ASN cc_start: 0.8129 (m-40) cc_final: 0.7807 (m-40) REVERT: E 241 ASP cc_start: 0.7079 (t70) cc_final: 0.6767 (t0) REVERT: E 264 TYR cc_start: 0.8649 (OUTLIER) cc_final: 0.8395 (m-10) REVERT: F 25 ASP cc_start: 0.7503 (OUTLIER) cc_final: 0.6634 (t0) REVERT: F 40 LEU cc_start: 0.8137 (OUTLIER) cc_final: 0.7870 (mp) REVERT: F 48 ARG cc_start: 0.7195 (tpt170) cc_final: 0.6800 (tpm170) REVERT: F 72 ILE cc_start: 0.8142 (mm) cc_final: 0.7765 (mm) REVERT: F 172 THR cc_start: 0.7690 (m) cc_final: 0.7421 (m) REVERT: F 187 HIS cc_start: 0.7902 (OUTLIER) cc_final: 0.7533 (p90) REVERT: G 9 ASP cc_start: 0.8159 (t0) cc_final: 0.7905 (m-30) REVERT: G 68 PHE cc_start: 0.8203 (t80) cc_final: 0.7809 (t80) REVERT: G 94 ASN cc_start: 0.8605 (p0) cc_final: 0.8324 (p0) REVERT: G 97 GLN cc_start: 0.8590 (tt0) cc_final: 0.8232 (tp40) REVERT: G 103 ILE cc_start: 0.8714 (OUTLIER) cc_final: 0.7679 (tt) REVERT: G 122 PHE cc_start: 0.8109 (t80) cc_final: 0.7730 (t80) REVERT: H 11 PHE cc_start: 0.7433 (t80) cc_final: 0.6782 (t80) REVERT: H 86 VAL cc_start: 0.8300 (OUTLIER) cc_final: 0.6571 (p) REVERT: H 102 MET cc_start: 0.8965 (mmm) cc_final: 0.8178 (mmm) REVERT: H 126 ARG cc_start: 0.7214 (ttt-90) cc_final: 0.6452 (ttt-90) REVERT: H 178 TYR cc_start: 0.6924 (m-80) cc_final: 0.6331 (m-10) REVERT: H 191 GLN cc_start: 0.9038 (OUTLIER) cc_final: 0.8744 (pp30) REVERT: H 206 LEU cc_start: 0.9383 (mt) cc_final: 0.8971 (mt) REVERT: H 208 ASN cc_start: 0.8723 (m110) cc_final: 0.7378 (t0) REVERT: H 261 PHE cc_start: 0.7643 (t80) cc_final: 0.7327 (t80) REVERT: H 272 ASN cc_start: 0.9003 (t0) cc_final: 0.8591 (t0) REVERT: I 18 PHE cc_start: 0.8731 (t80) cc_final: 0.8470 (t80) REVERT: I 22 GLU cc_start: 0.8767 (tm-30) cc_final: 0.8077 (tm-30) REVERT: I 23 LYS cc_start: 0.8833 (tppt) cc_final: 0.8585 (tppt) REVERT: I 56 MET cc_start: 0.8663 (mmm) cc_final: 0.8378 (mmm) REVERT: I 77 TRP cc_start: 0.8248 (t60) cc_final: 0.7437 (t60) REVERT: I 81 GLN cc_start: 0.9017 (OUTLIER) cc_final: 0.8624 (mp10) REVERT: I 84 GLU cc_start: 0.8566 (tp30) cc_final: 0.8008 (tp30) REVERT: I 87 GLN cc_start: 0.9087 (tt0) cc_final: 0.8559 (tm-30) REVERT: I 96 GLU cc_start: 0.8486 (OUTLIER) cc_final: 0.7903 (pm20) REVERT: I 109 THR cc_start: 0.8193 (m) cc_final: 0.7464 (p) REVERT: I 113 PHE cc_start: 0.7999 (m-80) cc_final: 0.7491 (m-10) REVERT: I 119 LYS cc_start: 0.9052 (ptmm) cc_final: 0.8813 (ptmm) REVERT: I 123 ASN cc_start: 0.8581 (m110) cc_final: 0.8153 (m110) REVERT: J 18 PHE cc_start: 0.8718 (t80) cc_final: 0.8200 (t80) REVERT: J 57 ARG cc_start: 0.8749 (mtm110) cc_final: 0.8384 (mtm-85) REVERT: J 78 GLU cc_start: 0.8923 (tp30) cc_final: 0.8411 (tp30) REVERT: J 85 HIS cc_start: 0.8000 (m170) cc_final: 0.7700 (m170) REVERT: J 91 ASN cc_start: 0.8558 (m-40) cc_final: 0.8046 (m-40) REVERT: J 98 GLN cc_start: 0.8478 (tt0) cc_final: 0.8230 (tp40) REVERT: J 115 LYS cc_start: 0.5813 (mmtt) cc_final: 0.5437 (mttt) REVERT: J 116 ASP cc_start: 0.7140 (t0) cc_final: 0.6671 (t0) REVERT: J 120 ASN cc_start: 0.8133 (m110) cc_final: 0.7413 (m-40) REVERT: K 12 ARG cc_start: 0.8142 (mmp80) cc_final: 0.7809 (mmp80) REVERT: K 250 TYR cc_start: 0.7869 (OUTLIER) cc_final: 0.6443 (p90) REVERT: K 309 LYS cc_start: 0.8416 (tppt) cc_final: 0.8138 (ttpp) REVERT: K 436 LEU cc_start: 0.8964 (tp) cc_final: 0.8696 (tp) REVERT: K 504 THR cc_start: 0.8646 (m) cc_final: 0.8039 (p) REVERT: K 526 GLU cc_start: 0.7354 (mm-30) cc_final: 0.6620 (tp30) REVERT: M 7 TYR cc_start: 0.7960 (m-80) cc_final: 0.7726 (m-80) REVERT: M 16 GLN cc_start: 0.7328 (mm-40) cc_final: 0.7046 (tp40) REVERT: M 54 ILE cc_start: 0.8929 (mm) cc_final: 0.8717 (mm) REVERT: M 130 GLN cc_start: 0.7441 (OUTLIER) cc_final: 0.7213 (tt0) REVERT: M 147 ILE cc_start: 0.9105 (pt) cc_final: 0.8879 (mt) REVERT: M 204 GLN cc_start: 0.8281 (tm-30) cc_final: 0.7893 (tm-30) REVERT: M 209 MET cc_start: 0.7923 (OUTLIER) cc_final: 0.7708 (ptt) REVERT: M 277 LYS cc_start: 0.7763 (mppt) cc_final: 0.7438 (mppt) REVERT: N 7 ILE cc_start: 0.8240 (OUTLIER) cc_final: 0.7926 (mm) REVERT: N 66 ARG cc_start: 0.7846 (mtp180) cc_final: 0.7593 (mtp85) REVERT: N 68 ASN cc_start: 0.7910 (t0) cc_final: 0.7405 (t0) REVERT: N 76 GLU cc_start: 0.6941 (mm-30) cc_final: 0.5365 (mm-30) REVERT: N 116 ASP cc_start: 0.6892 (p0) cc_final: 0.6669 (p0) REVERT: N 152 LEU cc_start: 0.8477 (mp) cc_final: 0.8217 (mp) REVERT: N 171 MET cc_start: 0.6952 (mtm) cc_final: 0.6620 (mtm) REVERT: L 21 LEU cc_start: 0.8147 (OUTLIER) cc_final: 0.7855 (mt) REVERT: L 24 ILE cc_start: 0.8950 (mt) cc_final: 0.8716 (mp) REVERT: L 35 THR cc_start: 0.8462 (t) cc_final: 0.8229 (t) REVERT: L 40 TYR cc_start: 0.8800 (m-10) cc_final: 0.8312 (m-80) REVERT: L 56 MET cc_start: 0.7309 (mmm) cc_final: 0.6369 (tmm) REVERT: L 76 GLN cc_start: 0.8691 (OUTLIER) cc_final: 0.8343 (mm-40) REVERT: L 81 GLN cc_start: 0.8471 (OUTLIER) cc_final: 0.8222 (mm-40) outliers start: 124 outliers final: 60 residues processed: 818 average time/residue: 0.3979 time to fit residues: 508.0476 Evaluate side-chains 786 residues out of total 2762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 705 time to evaluate : 3.080 ------------------------------------------------------------------------------- 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 32 ILE Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain C residue 32 ILE Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 109 ILE Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 156 LYS Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain D residue 36 THR Chi-restraints excluded: chain D residue 45 CYS Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 109 ILE Chi-restraints excluded: chain D residue 260 SER Chi-restraints excluded: chain E residue 109 ILE Chi-restraints excluded: chain E residue 134 SER Chi-restraints excluded: chain E residue 184 ILE 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 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 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 95 LEU Chi-restraints excluded: chain G residue 103 ILE Chi-restraints excluded: chain G residue 124 GLU Chi-restraints excluded: chain H residue 86 VAL 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 253 ASP Chi-restraints excluded: chain H residue 276 THR Chi-restraints excluded: chain I residue 58 LEU Chi-restraints excluded: chain I residue 81 GLN Chi-restraints excluded: chain I residue 96 GLU Chi-restraints excluded: chain K residue 195 CYS Chi-restraints excluded: chain K residue 250 TYR Chi-restraints excluded: chain K residue 266 ILE Chi-restraints excluded: chain K residue 269 VAL Chi-restraints excluded: chain K residue 306 THR Chi-restraints excluded: chain K residue 330 LEU Chi-restraints excluded: chain K residue 403 ASP Chi-restraints excluded: chain K residue 478 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 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 7 ILE 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 21 LEU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 303 optimal weight: 1.9990 chunk 142 optimal weight: 8.9990 chunk 87 optimal weight: 0.9980 chunk 130 optimal weight: 5.9990 chunk 167 optimal weight: 3.9990 chunk 140 optimal weight: 1.9990 chunk 249 optimal weight: 0.5980 chunk 96 optimal weight: 0.9980 chunk 74 optimal weight: 0.0060 chunk 206 optimal weight: 10.0000 chunk 91 optimal weight: 0.5980 overall best weight: 0.6396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** ** B 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 62 HIS ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 83 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** ** F 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 123 ASN ** H 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 62 HIS 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 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 74 GLN J 81 GLN ** K 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 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 ** L 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.158883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.126150 restraints weight = 47060.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.130725 restraints weight = 20943.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.133623 restraints weight = 12083.330| |-----------------------------------------------------------------------------| r_work (final): 0.3975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.4489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 27430 Z= 0.194 Angle : 0.792 10.563 37194 Z= 0.410 Chirality : 0.049 0.319 4023 Planarity : 0.005 0.080 4752 Dihedral : 14.351 169.649 4190 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 29.07 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.14 % Favored : 90.83 % Rotamer: Outliers : 4.64 % Allowed : 22.57 % Favored : 72.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.36 (0.14), residues: 3184 helix: -0.54 (0.14), residues: 1287 sheet: -2.66 (0.24), residues: 376 loop : -2.17 (0.15), residues: 1521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP G 77 HIS 0.024 0.002 HIS C 214 PHE 0.038 0.003 PHE M 112 TYR 0.038 0.003 TYR A 125 ARG 0.009 0.001 ARG B 224 Details of bonding type rmsd hydrogen bonds : bond 0.04620 ( 1148) hydrogen bonds : angle 6.58392 ( 3315) covalent geometry : bond 0.00443 (27430) covalent geometry : angle 0.79165 (37194) *********************** 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 875 residues out of total 2762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 747 time to evaluate : 3.192 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: 0.7999 (OUTLIER) cc_final: 0.6156 (t80) REVERT: A 126 ASN cc_start: 0.8003 (t0) cc_final: 0.7662 (t0) REVERT: A 133 TRP cc_start: 0.7417 (t-100) cc_final: 0.6858 (t-100) REVERT: A 155 TYR cc_start: 0.8405 (m-80) cc_final: 0.8074 (m-80) REVERT: A 164 GLU cc_start: 0.8321 (tp30) cc_final: 0.7378 (tp30) REVERT: A 165 TRP cc_start: 0.8546 (m-10) cc_final: 0.8237 (m100) REVERT: A 167 GLN cc_start: 0.8938 (tm-30) cc_final: 0.7306 (tm-30) REVERT: A 168 TYR cc_start: 0.7434 (m-80) cc_final: 0.6553 (m-10) REVERT: A 169 GLU cc_start: 0.7717 (tt0) cc_final: 0.7395 (tt0) REVERT: B 8 ASP cc_start: 0.7678 (t70) cc_final: 0.7427 (t0) REVERT: B 141 MET cc_start: 0.6583 (mmt) cc_final: 0.6204 (mmt) REVERT: B 175 TYR cc_start: 0.8417 (t80) cc_final: 0.8109 (t80) REVERT: B 201 LEU cc_start: 0.8322 (OUTLIER) cc_final: 0.8015 (mm) REVERT: C 11 PHE cc_start: 0.7779 (t80) cc_final: 0.7501 (t80) REVERT: C 67 ILE cc_start: 0.8491 (OUTLIER) cc_final: 0.7970 (mm) REVERT: C 103 CYS cc_start: 0.8071 (m) cc_final: 0.7775 (m) REVERT: C 110 ARG cc_start: 0.7410 (ptm160) cc_final: 0.7072 (ptm160) REVERT: C 138 ASP cc_start: 0.6299 (m-30) cc_final: 0.6093 (m-30) REVERT: C 146 SER cc_start: 0.7918 (t) cc_final: 0.7544 (t) REVERT: C 220 GLN cc_start: 0.7817 (tm-30) cc_final: 0.6478 (tm-30) REVERT: C 243 LEU cc_start: 0.7923 (OUTLIER) cc_final: 0.7630 (mt) REVERT: C 256 GLU cc_start: 0.7329 (tm-30) cc_final: 0.6929 (tm-30) REVERT: C 271 LYS cc_start: 0.8496 (mmmt) cc_final: 0.8206 (mmmt) REVERT: D 21 ASN cc_start: 0.7388 (t0) cc_final: 0.7079 (t0) REVERT: D 35 GLN cc_start: 0.8493 (mm-40) cc_final: 0.8024 (tp40) REVERT: D 36 THR cc_start: 0.7957 (OUTLIER) cc_final: 0.7643 (p) REVERT: D 48 ARG cc_start: 0.6861 (OUTLIER) cc_final: 0.5938 (ttm-80) REVERT: D 141 MET cc_start: 0.8088 (mtp) cc_final: 0.7811 (mtm) REVERT: D 227 TYR cc_start: 0.8361 (m-80) cc_final: 0.8119 (m-80) REVERT: E 79 GLU cc_start: 0.7808 (tm-30) cc_final: 0.7468 (tm-30) REVERT: E 101 TYR cc_start: 0.7995 (t80) cc_final: 0.7759 (t80) REVERT: E 116 MET cc_start: 0.8187 (mmt) cc_final: 0.7885 (mmt) REVERT: E 141 MET cc_start: 0.7360 (OUTLIER) cc_final: 0.7151 (tpp) REVERT: E 144 GLU cc_start: 0.7998 (mt-10) cc_final: 0.7783 (mt-10) REVERT: E 167 MET cc_start: 0.8603 (mtm) cc_final: 0.8327 (mtp) REVERT: E 184 ILE cc_start: 0.8521 (OUTLIER) cc_final: 0.8155 (mm) REVERT: E 233 ASN cc_start: 0.8077 (m-40) cc_final: 0.7793 (m-40) REVERT: E 241 ASP cc_start: 0.7144 (t70) cc_final: 0.6826 (t0) REVERT: F 25 ASP cc_start: 0.7437 (OUTLIER) cc_final: 0.6582 (t0) REVERT: F 72 ILE cc_start: 0.8225 (mm) cc_final: 0.7864 (mm) REVERT: F 172 THR cc_start: 0.7697 (m) cc_final: 0.7309 (m) REVERT: F 187 HIS cc_start: 0.7672 (OUTLIER) cc_final: 0.6882 (p90) REVERT: F 209 MET cc_start: 0.6652 (tmm) cc_final: 0.6443 (tmm) REVERT: G 9 ASP cc_start: 0.7994 (t0) cc_final: 0.7650 (m-30) REVERT: G 68 PHE cc_start: 0.8107 (t80) cc_final: 0.7750 (t80) REVERT: G 71 ARG cc_start: 0.8757 (mmm160) cc_final: 0.8171 (mmm-85) REVERT: G 94 ASN cc_start: 0.8692 (p0) cc_final: 0.8076 (p0) REVERT: G 106 TYR cc_start: 0.8270 (m-80) cc_final: 0.7552 (m-80) REVERT: G 110 GLN cc_start: 0.7378 (tp-100) cc_final: 0.7045 (tp-100) REVERT: G 122 PHE cc_start: 0.8121 (t80) cc_final: 0.7601 (t80) REVERT: H 102 MET cc_start: 0.9034 (mmm) cc_final: 0.8477 (mmm) REVERT: H 126 ARG cc_start: 0.7441 (ttt-90) cc_final: 0.6892 (ttt-90) REVERT: H 178 TYR cc_start: 0.6765 (m-80) cc_final: 0.6288 (m-10) REVERT: H 190 LYS cc_start: 0.8670 (mttm) cc_final: 0.8346 (mttp) REVERT: H 191 GLN cc_start: 0.8898 (OUTLIER) cc_final: 0.8663 (pp30) REVERT: H 208 ASN cc_start: 0.8803 (m110) cc_final: 0.7714 (t0) REVERT: H 261 PHE cc_start: 0.7752 (t80) cc_final: 0.7481 (t80) REVERT: H 272 ASN cc_start: 0.8920 (t0) cc_final: 0.8476 (t0) REVERT: I 18 PHE cc_start: 0.8710 (t80) cc_final: 0.8492 (t80) REVERT: I 21 LEU cc_start: 0.8815 (mp) cc_final: 0.8603 (mp) REVERT: I 22 GLU cc_start: 0.8768 (tm-30) cc_final: 0.8066 (tm-30) REVERT: I 23 LYS cc_start: 0.8878 (tppt) cc_final: 0.8607 (tppt) REVERT: I 56 MET cc_start: 0.8819 (mmm) cc_final: 0.8521 (mmm) REVERT: I 77 TRP cc_start: 0.8186 (t60) cc_final: 0.7414 (t60) REVERT: I 80 ARG cc_start: 0.8081 (mtp180) cc_final: 0.7667 (mtp-110) REVERT: I 81 GLN cc_start: 0.8966 (OUTLIER) cc_final: 0.8323 (mp10) REVERT: I 84 GLU cc_start: 0.8577 (tp30) cc_final: 0.7991 (tp30) REVERT: I 87 GLN cc_start: 0.8973 (tt0) cc_final: 0.8484 (tm-30) REVERT: I 91 ASN cc_start: 0.8886 (t0) cc_final: 0.8360 (t0) REVERT: I 96 GLU cc_start: 0.8504 (OUTLIER) cc_final: 0.7860 (pm20) REVERT: I 109 THR cc_start: 0.8261 (m) cc_final: 0.7480 (p) REVERT: I 119 LYS cc_start: 0.9070 (ptmm) cc_final: 0.8780 (ptmm) REVERT: I 123 ASN cc_start: 0.8613 (m110) cc_final: 0.8191 (m110) REVERT: J 18 PHE cc_start: 0.8761 (t80) cc_final: 0.8191 (t80) REVERT: J 57 ARG cc_start: 0.8761 (mtm110) cc_final: 0.8439 (mtm-85) REVERT: J 62 HIS cc_start: 0.8103 (m90) cc_final: 0.7731 (m-70) REVERT: J 78 GLU cc_start: 0.8844 (tp30) cc_final: 0.8341 (tp30) REVERT: J 80 ARG cc_start: 0.8373 (mtm-85) cc_final: 0.8099 (ttm-80) REVERT: J 81 GLN cc_start: 0.8582 (OUTLIER) cc_final: 0.8377 (mp-120) REVERT: J 85 HIS cc_start: 0.8168 (m170) cc_final: 0.7861 (m170) REVERT: J 91 ASN cc_start: 0.8585 (m-40) cc_final: 0.8088 (m-40) REVERT: J 108 GLU cc_start: 0.8124 (mt-10) cc_final: 0.7795 (mt-10) REVERT: J 116 ASP cc_start: 0.7208 (t0) cc_final: 0.6858 (t0) REVERT: J 123 ASN cc_start: 0.8411 (m-40) cc_final: 0.8138 (m-40) REVERT: K 12 ARG cc_start: 0.8053 (mmp80) cc_final: 0.7800 (mmp80) REVERT: K 46 GLU cc_start: 0.8640 (tm-30) cc_final: 0.8381 (tm-30) REVERT: K 82 TRP cc_start: 0.8387 (p-90) cc_final: 0.7818 (p-90) REVERT: K 250 TYR cc_start: 0.7810 (OUTLIER) cc_final: 0.6526 (p90) REVERT: K 277 LYS cc_start: 0.9240 (tppt) cc_final: 0.8772 (mmtm) REVERT: K 309 LYS cc_start: 0.8397 (tppt) cc_final: 0.8021 (ttpp) REVERT: K 436 LEU cc_start: 0.8977 (tp) cc_final: 0.8709 (tp) REVERT: K 504 THR cc_start: 0.8640 (m) cc_final: 0.8246 (p) REVERT: M 16 GLN cc_start: 0.7272 (mm-40) cc_final: 0.7058 (tp40) REVERT: M 102 MET cc_start: 0.6402 (mtp) cc_final: 0.6063 (mtp) REVERT: M 175 TYR cc_start: 0.8360 (t80) cc_final: 0.8004 (t80) REVERT: M 183 PHE cc_start: 0.9034 (m-80) cc_final: 0.8629 (m-80) REVERT: M 198 ASP cc_start: 0.7818 (m-30) cc_final: 0.7476 (m-30) REVERT: M 204 GLN cc_start: 0.8261 (tm-30) cc_final: 0.7648 (tm-30) REVERT: M 221 MET cc_start: 0.7520 (ttt) cc_final: 0.7199 (mtp) REVERT: M 259 ARG cc_start: 0.7365 (mtm110) cc_final: 0.7117 (mtm110) REVERT: M 277 LYS cc_start: 0.7716 (mppt) cc_final: 0.7379 (mppt) REVERT: N 68 ASN cc_start: 0.7979 (t0) cc_final: 0.7517 (t0) REVERT: N 133 GLN cc_start: 0.7323 (OUTLIER) cc_final: 0.6906 (mm110) REVERT: L 21 LEU cc_start: 0.8173 (OUTLIER) cc_final: 0.7966 (mp) REVERT: L 24 ILE cc_start: 0.8954 (mt) cc_final: 0.8727 (mp) REVERT: L 35 THR cc_start: 0.8637 (t) cc_final: 0.8433 (t) REVERT: L 40 TYR cc_start: 0.8631 (m-10) cc_final: 0.8218 (m-80) REVERT: L 56 MET cc_start: 0.7573 (mmm) cc_final: 0.6292 (tmm) REVERT: L 76 GLN cc_start: 0.8753 (OUTLIER) cc_final: 0.8505 (mm110) REVERT: L 81 GLN cc_start: 0.8430 (OUTLIER) cc_final: 0.8212 (mm-40) outliers start: 128 outliers final: 68 residues processed: 820 average time/residue: 0.3864 time to fit residues: 498.0394 Evaluate side-chains 778 residues out of total 2762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 691 time to evaluate : 3.278 ------------------------------------------------------------------------------- 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 201 LEU Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain C residue 5 LYS Chi-restraints excluded: chain C residue 32 ILE Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 109 ILE Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 133 PHE Chi-restraints excluded: chain C residue 156 LYS Chi-restraints excluded: chain C residue 177 LEU 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 109 ILE Chi-restraints excluded: chain D residue 260 SER Chi-restraints excluded: chain E residue 125 VAL Chi-restraints excluded: chain E residue 134 SER Chi-restraints excluded: chain E residue 141 MET Chi-restraints excluded: chain E residue 143 LEU Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain E residue 184 ILE 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 25 ASP Chi-restraints excluded: chain F residue 32 ILE 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 95 LEU 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 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 58 LEU Chi-restraints excluded: chain I residue 81 GLN Chi-restraints excluded: chain I residue 96 GLU Chi-restraints excluded: chain J residue 81 GLN Chi-restraints excluded: chain K residue 195 CYS Chi-restraints excluded: chain K residue 250 TYR Chi-restraints excluded: chain K residue 266 ILE Chi-restraints excluded: chain K residue 269 VAL Chi-restraints excluded: chain K residue 306 THR Chi-restraints excluded: chain K residue 330 LEU Chi-restraints excluded: chain K residue 383 ASN Chi-restraints excluded: chain K residue 393 LEU Chi-restraints excluded: chain K residue 403 ASP Chi-restraints excluded: chain K residue 430 THR Chi-restraints excluded: chain M residue 42 THR Chi-restraints excluded: chain M residue 46 LEU 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 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 21 LEU Chi-restraints excluded: chain L residue 76 GLN Chi-restraints excluded: chain L residue 81 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 81 optimal weight: 2.9990 chunk 278 optimal weight: 0.8980 chunk 128 optimal weight: 3.9990 chunk 142 optimal weight: 0.7980 chunk 76 optimal weight: 0.7980 chunk 45 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 247 optimal weight: 0.8980 chunk 194 optimal weight: 1.9990 chunk 258 optimal weight: 2.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** ** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 123 ASN 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 81 GLN ** K 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 58 GLN ** M 204 GLN ** 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** ** 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 = 0.4130 r_free = 0.4130 target = 0.153080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.115637 restraints weight = 47857.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.120103 restraints weight = 21681.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 61)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.122973 restraints weight = 12812.812| |-----------------------------------------------------------------------------| r_work (final): 0.3948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.4654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 27430 Z= 0.225 Angle : 0.806 10.765 37194 Z= 0.418 Chirality : 0.050 0.360 4023 Planarity : 0.005 0.058 4752 Dihedral : 14.307 169.303 4190 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 30.02 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.36 % Favored : 90.61 % Rotamer: Outliers : 3.91 % Allowed : 24.24 % Favored : 71.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.31 (0.14), residues: 3184 helix: -0.51 (0.14), residues: 1280 sheet: -2.62 (0.25), residues: 366 loop : -2.13 (0.15), residues: 1538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.003 TRP J 77 HIS 0.024 0.002 HIS C 214 PHE 0.042 0.003 PHE H 183 TYR 0.042 0.003 TYR A 125 ARG 0.009 0.001 ARG B 224 Details of bonding type rmsd hydrogen bonds : bond 0.04626 ( 1148) hydrogen bonds : angle 6.56129 ( 3315) covalent geometry : bond 0.00516 (27430) covalent geometry : angle 0.80555 (37194) *********************** 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 831 residues out of total 2762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 723 time to evaluate : 2.805 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: 0.8082 (OUTLIER) cc_final: 0.6182 (t80) REVERT: A 126 ASN cc_start: 0.7936 (t0) cc_final: 0.7611 (t0) REVERT: A 133 TRP cc_start: 0.7222 (t-100) cc_final: 0.6859 (t-100) REVERT: A 153 ASN cc_start: 0.6966 (m-40) cc_final: 0.6644 (m-40) REVERT: A 155 TYR cc_start: 0.8352 (m-80) cc_final: 0.8002 (m-80) REVERT: A 164 GLU cc_start: 0.8300 (tp30) cc_final: 0.7387 (tp30) REVERT: A 165 TRP cc_start: 0.8563 (m-10) cc_final: 0.8285 (m100) REVERT: A 167 GLN cc_start: 0.8867 (tm-30) cc_final: 0.7244 (tm-30) REVERT: A 168 TYR cc_start: 0.7498 (m-80) cc_final: 0.6571 (m-10) REVERT: A 169 GLU cc_start: 0.7677 (tt0) cc_final: 0.7297 (tt0) REVERT: B 141 MET cc_start: 0.6719 (mmt) cc_final: 0.6493 (mmt) REVERT: B 183 PHE cc_start: 0.7522 (m-10) cc_final: 0.7313 (m-10) REVERT: B 259 ARG cc_start: 0.7563 (mtm110) cc_final: 0.7350 (mtm180) REVERT: C 43 ASP cc_start: 0.8040 (p0) cc_final: 0.7801 (p0) REVERT: C 67 ILE cc_start: 0.8462 (OUTLIER) cc_final: 0.7910 (mm) REVERT: C 103 CYS cc_start: 0.8121 (m) cc_final: 0.7883 (m) REVERT: C 110 ARG cc_start: 0.7458 (ptm160) cc_final: 0.7146 (ptm160) REVERT: C 133 PHE cc_start: 0.8231 (OUTLIER) cc_final: 0.7113 (t80) REVERT: C 146 SER cc_start: 0.7978 (t) cc_final: 0.7703 (t) REVERT: C 256 GLU cc_start: 0.7267 (tm-30) cc_final: 0.6926 (tm-30) REVERT: C 271 LYS cc_start: 0.8377 (mmmt) cc_final: 0.8044 (mmtm) REVERT: D 21 ASN cc_start: 0.7491 (t0) cc_final: 0.7228 (t0) REVERT: D 35 GLN cc_start: 0.8420 (mm-40) cc_final: 0.8018 (tp40) REVERT: D 36 THR cc_start: 0.7931 (OUTLIER) cc_final: 0.7655 (p) REVERT: D 48 ARG cc_start: 0.7018 (OUTLIER) cc_final: 0.5904 (ttm-80) REVERT: D 54 ILE cc_start: 0.8407 (mm) cc_final: 0.7829 (pt) REVERT: D 227 TYR cc_start: 0.8426 (m-80) cc_final: 0.8155 (m-80) REVERT: E 17 ASP cc_start: 0.7977 (t70) cc_final: 0.7156 (t0) REVERT: E 56 MET cc_start: 0.8588 (ttp) cc_final: 0.8268 (ttp) REVERT: E 79 GLU cc_start: 0.7795 (tm-30) cc_final: 0.7297 (tm-30) REVERT: E 101 TYR cc_start: 0.7887 (t80) cc_final: 0.7644 (t80) REVERT: E 116 MET cc_start: 0.8313 (mmt) cc_final: 0.7867 (mmt) REVERT: E 144 GLU cc_start: 0.7951 (mt-10) cc_final: 0.7720 (mt-10) REVERT: E 169 ARG cc_start: 0.8273 (mtp85) cc_final: 0.8045 (mtp180) REVERT: E 184 ILE cc_start: 0.8491 (OUTLIER) cc_final: 0.8140 (mm) REVERT: E 241 ASP cc_start: 0.7123 (t70) cc_final: 0.6770 (t0) REVERT: F 25 ASP cc_start: 0.7190 (OUTLIER) cc_final: 0.6284 (t0) REVERT: F 72 ILE cc_start: 0.8216 (mm) cc_final: 0.7895 (mm) REVERT: F 145 HIS cc_start: 0.8684 (m-70) cc_final: 0.8342 (m-70) REVERT: F 187 HIS cc_start: 0.7437 (OUTLIER) cc_final: 0.6642 (p90) REVERT: F 209 MET cc_start: 0.6791 (tmm) cc_final: 0.6406 (tmm) REVERT: G 68 PHE cc_start: 0.8085 (t80) cc_final: 0.7740 (t80) REVERT: G 71 ARG cc_start: 0.8731 (mmm160) cc_final: 0.8397 (mtp85) REVERT: G 94 ASN cc_start: 0.8570 (p0) cc_final: 0.8089 (p0) REVERT: G 122 PHE cc_start: 0.8275 (t80) cc_final: 0.7826 (t80) REVERT: H 102 MET cc_start: 0.8972 (mmm) cc_final: 0.8479 (mmm) REVERT: H 178 TYR cc_start: 0.6727 (m-80) cc_final: 0.6366 (m-10) REVERT: H 190 LYS cc_start: 0.8694 (mttm) cc_final: 0.8382 (mttp) REVERT: H 191 GLN cc_start: 0.8861 (OUTLIER) cc_final: 0.8582 (pp30) REVERT: H 206 LEU cc_start: 0.9300 (mt) cc_final: 0.9031 (mt) REVERT: H 208 ASN cc_start: 0.8774 (m110) cc_final: 0.7695 (t0) REVERT: H 261 PHE cc_start: 0.7771 (t80) cc_final: 0.7505 (t80) REVERT: H 272 ASN cc_start: 0.8801 (t0) cc_final: 0.8404 (t0) REVERT: I 22 GLU cc_start: 0.8713 (tm-30) cc_final: 0.8139 (tm-30) REVERT: I 56 MET cc_start: 0.8710 (mmm) cc_final: 0.8499 (mmm) REVERT: I 77 TRP cc_start: 0.8215 (t60) cc_final: 0.6937 (t60) REVERT: I 80 ARG cc_start: 0.8131 (mtp180) cc_final: 0.7124 (mtm-85) REVERT: I 81 GLN cc_start: 0.8936 (OUTLIER) cc_final: 0.8207 (mp10) REVERT: I 84 GLU cc_start: 0.8518 (tp30) cc_final: 0.8062 (tp30) REVERT: I 87 GLN cc_start: 0.8955 (tt0) cc_final: 0.8423 (tm-30) REVERT: I 91 ASN cc_start: 0.8724 (t0) cc_final: 0.8219 (t0) REVERT: I 96 GLU cc_start: 0.8492 (OUTLIER) cc_final: 0.7838 (pm20) REVERT: I 109 THR cc_start: 0.8247 (m) cc_final: 0.7515 (p) REVERT: I 113 PHE cc_start: 0.7969 (m-10) cc_final: 0.7598 (m-10) REVERT: I 119 LYS cc_start: 0.9073 (ptmm) cc_final: 0.8829 (ptmm) REVERT: I 123 ASN cc_start: 0.8648 (m110) cc_final: 0.8228 (m110) REVERT: J 18 PHE cc_start: 0.8901 (t80) cc_final: 0.8468 (t80) REVERT: J 62 HIS cc_start: 0.8138 (m90) cc_final: 0.7805 (m-70) REVERT: J 78 GLU cc_start: 0.8662 (tp30) cc_final: 0.8289 (tp30) REVERT: J 88 ARG cc_start: 0.7332 (OUTLIER) cc_final: 0.6967 (tmt170) REVERT: J 91 ASN cc_start: 0.8457 (m-40) cc_final: 0.7999 (m-40) REVERT: J 116 ASP cc_start: 0.6943 (t0) cc_final: 0.6334 (t0) REVERT: J 123 ASN cc_start: 0.8414 (m-40) cc_final: 0.8205 (m-40) REVERT: K 46 GLU cc_start: 0.8583 (tm-30) cc_final: 0.8351 (tm-30) REVERT: K 250 TYR cc_start: 0.7930 (OUTLIER) cc_final: 0.6715 (p90) REVERT: K 277 LYS cc_start: 0.9041 (tppt) cc_final: 0.8765 (mmtm) REVERT: K 281 LEU cc_start: 0.8375 (mp) cc_final: 0.8081 (mp) REVERT: K 309 LYS cc_start: 0.8383 (tppt) cc_final: 0.8082 (ttpp) REVERT: K 436 LEU cc_start: 0.9069 (tp) cc_final: 0.8846 (tp) REVERT: K 504 THR cc_start: 0.8737 (m) cc_final: 0.8318 (p) REVERT: K 513 MET cc_start: 0.8782 (mmm) cc_final: 0.8419 (tpp) REVERT: M 16 GLN cc_start: 0.7426 (mm-40) cc_final: 0.7160 (tp40) REVERT: M 19 ASN cc_start: 0.8076 (t0) cc_final: 0.7792 (t0) REVERT: M 56 MET cc_start: 0.8153 (ttm) cc_final: 0.7504 (tmm) REVERT: M 102 MET cc_start: 0.6233 (mtp) cc_final: 0.5439 (mtp) REVERT: M 175 TYR cc_start: 0.8303 (t80) cc_final: 0.8003 (t80) REVERT: M 198 ASP cc_start: 0.7657 (m-30) cc_final: 0.7280 (m-30) REVERT: M 204 GLN cc_start: 0.8265 (tm-30) cc_final: 0.7771 (tm-30) REVERT: M 277 LYS cc_start: 0.7683 (mppt) cc_final: 0.7422 (mppt) REVERT: N 68 ASN cc_start: 0.7986 (t0) cc_final: 0.7629 (t0) REVERT: N 76 GLU cc_start: 0.6827 (mm-30) cc_final: 0.6542 (tp30) REVERT: N 133 GLN cc_start: 0.7574 (OUTLIER) cc_final: 0.7097 (mm110) REVERT: N 171 MET cc_start: 0.7268 (mtm) cc_final: 0.6690 (mtm) REVERT: N 193 TYR cc_start: 0.7763 (t80) cc_final: 0.7473 (t80) REVERT: L 21 LEU cc_start: 0.8151 (OUTLIER) cc_final: 0.7931 (mp) REVERT: L 24 ILE cc_start: 0.8954 (mt) cc_final: 0.8717 (mp) REVERT: L 25 GLN cc_start: 0.8486 (OUTLIER) cc_final: 0.8170 (tt0) REVERT: L 40 TYR cc_start: 0.8621 (m-10) cc_final: 0.8212 (m-80) REVERT: L 56 MET cc_start: 0.7809 (mmm) cc_final: 0.6409 (tmm) REVERT: L 96 GLU cc_start: 0.8344 (pm20) cc_final: 0.8075 (pm20) outliers start: 108 outliers final: 72 residues processed: 784 average time/residue: 0.3789 time to fit residues: 466.9166 Evaluate side-chains 780 residues out of total 2762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 692 time to evaluate : 2.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 PHE Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 187 HIS Chi-restraints excluded: chain B residue 209 MET Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain C residue 5 LYS Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 32 ILE Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 109 ILE Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 133 PHE Chi-restraints excluded: chain C residue 156 LYS 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 109 ILE Chi-restraints excluded: chain D residue 260 SER Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain E residue 125 VAL Chi-restraints excluded: chain E residue 134 SER Chi-restraints excluded: chain E residue 143 LEU Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain E residue 184 ILE 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 25 ASP Chi-restraints excluded: chain F residue 32 ILE Chi-restraints excluded: chain F residue 67 ILE Chi-restraints excluded: chain F residue 187 HIS Chi-restraints excluded: chain G residue 49 ILE Chi-restraints excluded: chain G residue 81 GLN Chi-restraints excluded: chain G residue 88 ARG Chi-restraints excluded: chain G residue 95 LEU Chi-restraints excluded: chain H residue 187 HIS Chi-restraints excluded: chain H residue 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 20 VAL Chi-restraints excluded: chain I residue 58 LEU Chi-restraints excluded: chain I residue 81 GLN Chi-restraints excluded: chain I residue 96 GLU Chi-restraints excluded: chain J residue 58 LEU Chi-restraints excluded: chain J residue 88 ARG Chi-restraints excluded: chain J residue 98 GLN Chi-restraints excluded: chain K residue 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 387 ASP Chi-restraints excluded: chain K residue 393 LEU Chi-restraints excluded: chain K residue 403 ASP 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 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 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 21 LEU Chi-restraints excluded: chain L residue 25 GLN Chi-restraints excluded: chain L residue 81 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 63 optimal weight: 0.7980 chunk 260 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 chunk 187 optimal weight: 2.9990 chunk 216 optimal weight: 5.9990 chunk 251 optimal weight: 2.9990 chunk 23 optimal weight: 0.6980 chunk 238 optimal weight: 4.9990 chunk 137 optimal weight: 8.9990 chunk 316 optimal weight: 7.9990 chunk 182 optimal weight: 1.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 16 GLN ** 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** B 222 ASN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 130 GLN ** 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 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 97 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 J 8 GLN ** J 61 HIS ** 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 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 58 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** M 272 ASN ** N 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 89 GLN ** L 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.153888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.119748 restraints weight = 47644.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.124180 restraints weight = 21682.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.126976 restraints weight = 12833.537| |-----------------------------------------------------------------------------| r_work (final): 0.3866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.4641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.099 27430 Z= 0.297 Angle : 0.861 11.513 37194 Z= 0.447 Chirality : 0.053 0.392 4023 Planarity : 0.006 0.146 4752 Dihedral : 14.339 171.062 4190 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 32.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.99 % Favored : 90.01 % Rotamer: Outliers : 4.42 % Allowed : 24.35 % Favored : 71.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.35 (0.14), residues: 3184 helix: -0.55 (0.14), residues: 1267 sheet: -2.49 (0.25), residues: 378 loop : -2.16 (0.15), residues: 1539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.088 0.003 TRP J 77 HIS 0.025 0.002 HIS C 214 PHE 0.041 0.003 PHE M 112 TYR 0.040 0.003 TYR B 175 ARG 0.010 0.001 ARG D 246 Details of bonding type rmsd hydrogen bonds : bond 0.04843 ( 1148) hydrogen bonds : angle 6.59506 ( 3315) covalent geometry : bond 0.00672 (27430) covalent geometry : angle 0.86086 (37194) *********************** 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 827 residues out of total 2762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 705 time to evaluate : 3.235 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: 0.8062 (OUTLIER) cc_final: 0.6244 (t80) REVERT: A 133 TRP cc_start: 0.7512 (t-100) cc_final: 0.7023 (t-100) REVERT: A 164 GLU cc_start: 0.8505 (tp30) cc_final: 0.8134 (tp30) REVERT: A 165 TRP cc_start: 0.8617 (m-10) cc_final: 0.8285 (m100) REVERT: A 167 GLN cc_start: 0.8905 (tm-30) cc_final: 0.7889 (tm-30) REVERT: A 168 TYR cc_start: 0.7582 (m-80) cc_final: 0.7165 (m-10) REVERT: A 169 GLU cc_start: 0.7806 (tt0) cc_final: 0.7427 (tt0) REVERT: B 70 LYS cc_start: 0.7425 (OUTLIER) cc_final: 0.6952 (mttp) REVERT: B 83 GLN cc_start: 0.8742 (mm-40) cc_final: 0.7966 (mm-40) REVERT: B 141 MET cc_start: 0.6821 (mmt) cc_final: 0.6588 (mmt) REVERT: B 175 TYR cc_start: 0.8296 (t80) cc_final: 0.7957 (t80) REVERT: B 183 PHE cc_start: 0.7575 (m-10) cc_final: 0.7342 (m-10) REVERT: B 241 ASP cc_start: 0.7889 (t70) cc_final: 0.7573 (t70) REVERT: C 67 ILE cc_start: 0.8510 (OUTLIER) cc_final: 0.8030 (mm) REVERT: C 103 CYS cc_start: 0.8324 (m) cc_final: 0.7977 (m) REVERT: C 110 ARG cc_start: 0.7591 (ptm160) cc_final: 0.7305 (ptm160) REVERT: C 133 PHE cc_start: 0.8326 (OUTLIER) cc_final: 0.6380 (t80) REVERT: C 146 SER cc_start: 0.8345 (t) cc_final: 0.8065 (t) REVERT: C 256 GLU cc_start: 0.7386 (tm-30) cc_final: 0.7032 (tm-30) REVERT: C 271 LYS cc_start: 0.8552 (mmmt) cc_final: 0.8304 (mmtm) REVERT: D 21 ASN cc_start: 0.7731 (t0) cc_final: 0.7145 (t0) REVERT: D 35 GLN cc_start: 0.8641 (mm-40) cc_final: 0.8233 (tp40) REVERT: D 36 THR cc_start: 0.8139 (OUTLIER) cc_final: 0.7792 (p) REVERT: D 54 ILE cc_start: 0.8524 (mm) cc_final: 0.7840 (pt) REVERT: E 79 GLU cc_start: 0.7842 (tm-30) cc_final: 0.7386 (tm-30) REVERT: E 101 TYR cc_start: 0.8077 (t80) cc_final: 0.7839 (t80) REVERT: E 116 MET cc_start: 0.8370 (mmt) cc_final: 0.8124 (mmt) REVERT: E 141 MET cc_start: 0.7409 (OUTLIER) cc_final: 0.6912 (tpp) REVERT: E 167 MET cc_start: 0.8722 (mtm) cc_final: 0.8502 (mtp) REVERT: E 169 ARG cc_start: 0.8394 (mtp85) cc_final: 0.8053 (mtp180) REVERT: E 184 ILE cc_start: 0.8643 (OUTLIER) cc_final: 0.8292 (mm) REVERT: E 221 MET cc_start: 0.7901 (mtm) cc_final: 0.7441 (mtm) REVERT: E 241 ASP cc_start: 0.7072 (t70) cc_final: 0.6742 (t0) REVERT: F 19 ASN cc_start: 0.7329 (t0) cc_final: 0.7121 (t0) REVERT: F 25 ASP cc_start: 0.7206 (OUTLIER) cc_final: 0.6283 (t0) REVERT: F 72 ILE cc_start: 0.8187 (mm) cc_final: 0.7826 (mm) REVERT: F 145 HIS cc_start: 0.8634 (m-70) cc_final: 0.8349 (m170) REVERT: F 172 THR cc_start: 0.7732 (m) cc_final: 0.7476 (m) REVERT: F 187 HIS cc_start: 0.7620 (OUTLIER) cc_final: 0.6952 (p90) REVERT: F 209 MET cc_start: 0.7043 (tmm) cc_final: 0.6607 (tmm) REVERT: G 23 LYS cc_start: 0.8068 (mmtp) cc_final: 0.7866 (tttt) REVERT: G 57 ARG cc_start: 0.8759 (ttm-80) cc_final: 0.7990 (ttm110) REVERT: G 68 PHE cc_start: 0.8138 (t80) cc_final: 0.7719 (t80) REVERT: G 71 ARG cc_start: 0.8717 (mmm160) cc_final: 0.8294 (mmm-85) REVERT: G 108 GLU cc_start: 0.8306 (mm-30) cc_final: 0.7944 (mt-10) REVERT: G 110 GLN cc_start: 0.7291 (tp-100) cc_final: 0.6806 (tp-100) REVERT: H 102 MET cc_start: 0.9068 (mmm) cc_final: 0.8530 (mmm) REVERT: H 178 TYR cc_start: 0.6823 (m-80) cc_final: 0.6401 (m-10) REVERT: H 190 LYS cc_start: 0.8757 (mttm) cc_final: 0.8379 (mttp) REVERT: H 206 LEU cc_start: 0.9282 (mt) cc_final: 0.9017 (mt) REVERT: H 208 ASN cc_start: 0.8801 (m110) cc_final: 0.7645 (t0) REVERT: H 261 PHE cc_start: 0.7859 (t80) cc_final: 0.7609 (t80) REVERT: I 21 LEU cc_start: 0.8829 (mp) cc_final: 0.8623 (mp) REVERT: I 22 GLU cc_start: 0.8836 (tm-30) cc_final: 0.8295 (tm-30) REVERT: I 56 MET cc_start: 0.8903 (mmm) cc_final: 0.8700 (mmm) REVERT: I 77 TRP cc_start: 0.8372 (t60) cc_final: 0.7098 (t60) REVERT: I 80 ARG cc_start: 0.8314 (mtp180) cc_final: 0.7303 (mtm-85) REVERT: I 81 GLN cc_start: 0.8902 (OUTLIER) cc_final: 0.8110 (mp10) REVERT: I 84 GLU cc_start: 0.8614 (tp30) cc_final: 0.8196 (tp30) REVERT: I 91 ASN cc_start: 0.8936 (t0) cc_final: 0.8408 (t0) REVERT: I 96 GLU cc_start: 0.8485 (OUTLIER) cc_final: 0.7860 (pm20) REVERT: I 109 THR cc_start: 0.8297 (m) cc_final: 0.7528 (p) REVERT: I 119 LYS cc_start: 0.9105 (ptmm) cc_final: 0.8835 (ptmm) REVERT: I 123 ASN cc_start: 0.8792 (m110) cc_final: 0.8299 (m110) REVERT: J 18 PHE cc_start: 0.8904 (t80) cc_final: 0.8396 (t80) REVERT: J 61 HIS cc_start: 0.8432 (t-90) cc_final: 0.8040 (t-90) REVERT: J 62 HIS cc_start: 0.8281 (m90) cc_final: 0.8049 (m-70) REVERT: J 78 GLU cc_start: 0.8914 (tp30) cc_final: 0.8489 (tp30) REVERT: J 80 ARG cc_start: 0.8143 (mtm-85) cc_final: 0.7724 (ttm-80) REVERT: J 88 ARG cc_start: 0.7688 (OUTLIER) cc_final: 0.7348 (tmt170) REVERT: J 91 ASN cc_start: 0.8597 (m-40) cc_final: 0.8128 (m-40) REVERT: J 108 GLU cc_start: 0.8597 (mt-10) cc_final: 0.8100 (mt-10) REVERT: J 116 ASP cc_start: 0.7388 (t0) cc_final: 0.6993 (t0) REVERT: K 46 GLU cc_start: 0.8631 (tm-30) cc_final: 0.8331 (tm-30) REVERT: K 250 TYR cc_start: 0.8052 (OUTLIER) cc_final: 0.6555 (p90) REVERT: K 295 ASP cc_start: 0.8668 (t0) cc_final: 0.8319 (t0) REVERT: K 309 LYS cc_start: 0.8379 (tppt) cc_final: 0.7971 (ttpp) REVERT: K 436 LEU cc_start: 0.9075 (tp) cc_final: 0.8814 (tp) REVERT: K 513 MET cc_start: 0.8873 (mmm) cc_final: 0.8524 (tpp) REVERT: M 16 GLN cc_start: 0.7372 (mm-40) cc_final: 0.7145 (tp40) REVERT: M 56 MET cc_start: 0.8296 (ttm) cc_final: 0.7562 (tmm) REVERT: M 102 MET cc_start: 0.6445 (mtp) cc_final: 0.5602 (mtp) REVERT: M 198 ASP cc_start: 0.8044 (m-30) cc_final: 0.7561 (m-30) REVERT: M 204 GLN cc_start: 0.8334 (OUTLIER) cc_final: 0.7814 (tm-30) REVERT: N 63 THR cc_start: 0.9003 (t) cc_final: 0.8563 (p) REVERT: N 68 ASN cc_start: 0.7926 (t0) cc_final: 0.7397 (t0) REVERT: N 76 GLU cc_start: 0.6992 (mm-30) cc_final: 0.6624 (tp30) REVERT: N 100 TYR cc_start: 0.8754 (m-80) cc_final: 0.8374 (m-80) REVERT: L 24 ILE cc_start: 0.8975 (mt) cc_final: 0.8741 (mp) REVERT: L 25 GLN cc_start: 0.8553 (OUTLIER) cc_final: 0.8245 (tt0) REVERT: L 40 TYR cc_start: 0.8673 (m-10) cc_final: 0.8219 (m-80) REVERT: L 56 MET cc_start: 0.7769 (mmm) cc_final: 0.6351 (tmm) outliers start: 122 outliers final: 85 residues processed: 775 average time/residue: 0.3893 time to fit residues: 474.6734 Evaluate side-chains 780 residues out of total 2762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 680 time to evaluate : 2.875 ------------------------------------------------------------------------------- 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 70 LYS Chi-restraints excluded: chain B residue 150 MET Chi-restraints excluded: chain B residue 187 HIS Chi-restraints excluded: chain B residue 209 MET Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain C residue 5 LYS Chi-restraints excluded: chain C residue 15 VAL 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 131 LEU Chi-restraints excluded: chain C residue 133 PHE 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 69 GLU Chi-restraints excluded: chain D residue 260 SER Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain E residue 32 ILE Chi-restraints excluded: chain E residue 65 ILE Chi-restraints excluded: chain E residue 125 VAL Chi-restraints excluded: chain E residue 134 SER Chi-restraints excluded: chain E residue 141 MET Chi-restraints excluded: chain E residue 143 LEU Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain E residue 180 CYS Chi-restraints excluded: chain E residue 184 ILE 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 67 ILE Chi-restraints excluded: chain F residue 187 HIS 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 H residue 42 THR Chi-restraints excluded: chain H residue 66 PHE Chi-restraints excluded: chain H residue 132 THR Chi-restraints excluded: chain H residue 187 HIS 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 20 VAL Chi-restraints excluded: chain I residue 58 LEU Chi-restraints excluded: chain I residue 81 GLN Chi-restraints excluded: chain I residue 96 GLU Chi-restraints excluded: chain I residue 124 GLU Chi-restraints excluded: chain J residue 24 ILE Chi-restraints excluded: chain J residue 58 LEU Chi-restraints excluded: chain J residue 88 ARG Chi-restraints excluded: chain J residue 98 GLN Chi-restraints excluded: chain K residue 32 PHE Chi-restraints excluded: chain K residue 195 CYS Chi-restraints excluded: chain K residue 226 LEU Chi-restraints excluded: chain K residue 250 TYR Chi-restraints excluded: chain K residue 257 LEU Chi-restraints excluded: chain K residue 266 ILE Chi-restraints excluded: chain K residue 269 VAL Chi-restraints excluded: chain K residue 306 THR Chi-restraints excluded: chain K residue 330 LEU Chi-restraints excluded: chain K residue 387 ASP Chi-restraints excluded: chain K residue 393 LEU Chi-restraints excluded: chain K residue 403 ASP Chi-restraints excluded: chain K residue 430 THR Chi-restraints excluded: chain K residue 466 ASP 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 137 ILE Chi-restraints excluded: chain M residue 166 THR Chi-restraints excluded: chain M residue 180 CYS Chi-restraints excluded: chain M residue 204 GLN Chi-restraints excluded: chain M residue 209 MET 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 25 GLN Chi-restraints excluded: chain L residue 81 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 99 optimal weight: 0.9990 chunk 130 optimal weight: 0.9990 chunk 199 optimal weight: 0.9980 chunk 241 optimal weight: 0.6980 chunk 70 optimal weight: 5.9990 chunk 233 optimal weight: 0.2980 chunk 148 optimal weight: 9.9990 chunk 49 optimal weight: 0.0970 chunk 297 optimal weight: 7.9990 chunk 35 optimal weight: 0.5980 chunk 56 optimal weight: 0.8980 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 52 ASN ** 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** ** D 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 52 ASN E 58 GLN E 75 ASN ** 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 97 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 8 GLN ** 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 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 518 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 58 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** ** M 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.160992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.127750 restraints weight = 47253.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.132339 restraints weight = 21225.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.135291 restraints weight = 12368.425| |-----------------------------------------------------------------------------| r_work (final): 0.3977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 moved from start: 0.5113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.088 27430 Z= 0.195 Angle : 0.839 15.314 37194 Z= 0.435 Chirality : 0.052 0.438 4023 Planarity : 0.006 0.059 4752 Dihedral : 14.285 167.000 4190 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 30.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.01 % Favored : 90.99 % Rotamer: Outliers : 3.84 % Allowed : 25.33 % Favored : 70.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.38 (0.14), residues: 3184 helix: -0.59 (0.14), residues: 1268 sheet: -2.48 (0.25), residues: 391 loop : -2.17 (0.15), residues: 1525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.109 0.003 TRP J 77 HIS 0.027 0.002 HIS C 214 PHE 0.043 0.003 PHE M 112 TYR 0.036 0.002 TYR B 175 ARG 0.010 0.001 ARG B 224 Details of bonding type rmsd hydrogen bonds : bond 0.04575 ( 1148) hydrogen bonds : angle 6.58152 ( 3315) covalent geometry : bond 0.00452 (27430) covalent geometry : angle 0.83911 (37194) *********************** 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 843 residues out of total 2762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 737 time to evaluate : 2.949 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: 0.7928 (OUTLIER) cc_final: 0.6192 (t80) REVERT: A 125 TYR cc_start: 0.7652 (t80) cc_final: 0.7269 (t80) REVERT: A 153 ASN cc_start: 0.7117 (m-40) cc_final: 0.6906 (m-40) REVERT: A 155 TYR cc_start: 0.8384 (m-80) cc_final: 0.7955 (m-80) REVERT: A 164 GLU cc_start: 0.8456 (tp30) cc_final: 0.7794 (tp30) REVERT: A 165 TRP cc_start: 0.8603 (m-10) cc_final: 0.8246 (m100) REVERT: A 167 GLN cc_start: 0.8822 (tm-30) cc_final: 0.7562 (tm-30) REVERT: A 168 TYR cc_start: 0.7317 (m-80) cc_final: 0.6736 (m-10) REVERT: A 169 GLU cc_start: 0.7698 (tt0) cc_final: 0.7229 (tt0) REVERT: B 70 LYS cc_start: 0.7286 (OUTLIER) cc_final: 0.6875 (mttp) REVERT: B 83 GLN cc_start: 0.8469 (mm-40) cc_final: 0.7745 (mm-40) REVERT: B 175 TYR cc_start: 0.8139 (t80) cc_final: 0.7740 (t80) REVERT: B 241 ASP cc_start: 0.7610 (t70) cc_final: 0.7222 (t70) REVERT: C 67 ILE cc_start: 0.8370 (OUTLIER) cc_final: 0.7838 (mm) REVERT: C 91 LYS cc_start: 0.8668 (pptt) cc_final: 0.8378 (ttmt) REVERT: C 133 PHE cc_start: 0.8118 (OUTLIER) cc_final: 0.7794 (m-80) REVERT: C 146 SER cc_start: 0.7751 (t) cc_final: 0.7413 (t) REVERT: C 256 GLU cc_start: 0.7246 (tm-30) cc_final: 0.6895 (tm-30) REVERT: C 271 LYS cc_start: 0.8448 (mmmt) cc_final: 0.8209 (mmtm) REVERT: D 21 ASN cc_start: 0.7407 (t0) cc_final: 0.7100 (t0) REVERT: D 35 GLN cc_start: 0.8478 (mm-40) cc_final: 0.8095 (tp40) REVERT: D 36 THR cc_start: 0.7889 (OUTLIER) cc_final: 0.7596 (p) REVERT: D 48 ARG cc_start: 0.6772 (OUTLIER) cc_final: 0.5380 (ttm-80) REVERT: D 227 TYR cc_start: 0.8374 (m-80) cc_final: 0.8162 (m-80) REVERT: D 244 PHE cc_start: 0.8598 (m-10) cc_final: 0.8055 (m-10) REVERT: E 16 GLN cc_start: 0.8425 (tp40) cc_final: 0.8045 (tp40) REVERT: E 56 MET cc_start: 0.8247 (ttp) cc_final: 0.7474 (ttp) REVERT: E 79 GLU cc_start: 0.7908 (tm-30) cc_final: 0.7192 (tm-30) REVERT: E 116 MET cc_start: 0.8306 (mmt) cc_final: 0.8099 (mmt) REVERT: E 138 ASP cc_start: 0.7679 (m-30) cc_final: 0.6670 (m-30) REVERT: E 141 MET cc_start: 0.7329 (OUTLIER) cc_final: 0.6786 (tpp) REVERT: E 148 THR cc_start: 0.7433 (p) cc_final: 0.7166 (p) REVERT: E 167 MET cc_start: 0.8400 (mtm) cc_final: 0.8099 (mtp) REVERT: E 169 ARG cc_start: 0.8331 (mtp85) cc_final: 0.8127 (mtp180) REVERT: E 184 ILE cc_start: 0.8609 (OUTLIER) cc_final: 0.8284 (mm) REVERT: E 221 MET cc_start: 0.7783 (mtm) cc_final: 0.7290 (mtm) REVERT: E 226 LEU cc_start: 0.8107 (tp) cc_final: 0.7880 (tp) REVERT: E 241 ASP cc_start: 0.7107 (t70) cc_final: 0.6809 (t0) REVERT: F 25 ASP cc_start: 0.6999 (OUTLIER) cc_final: 0.6150 (t0) REVERT: F 72 ILE cc_start: 0.8192 (mm) cc_final: 0.7810 (mm) REVERT: F 124 GLN cc_start: 0.8511 (OUTLIER) cc_final: 0.8264 (mt0) REVERT: F 187 HIS cc_start: 0.7348 (OUTLIER) cc_final: 0.6750 (p90) REVERT: F 209 MET cc_start: 0.6896 (tmm) cc_final: 0.6639 (tmm) REVERT: G 9 ASP cc_start: 0.7276 (m-30) cc_final: 0.6743 (m-30) REVERT: G 17 LEU cc_start: 0.9060 (OUTLIER) cc_final: 0.8445 (pp) REVERT: G 57 ARG cc_start: 0.8654 (ttm-80) cc_final: 0.7954 (ttm110) REVERT: G 68 PHE cc_start: 0.8129 (t80) cc_final: 0.7742 (t80) REVERT: G 106 TYR cc_start: 0.8433 (m-80) cc_final: 0.7981 (m-80) REVERT: G 110 GLN cc_start: 0.7299 (tp-100) cc_final: 0.6946 (tp40) REVERT: H 8 ASP cc_start: 0.6046 (p0) cc_final: 0.5452 (p0) REVERT: H 102 MET cc_start: 0.9139 (mmm) cc_final: 0.8586 (mmm) REVERT: H 178 TYR cc_start: 0.6718 (m-80) cc_final: 0.6289 (m-10) REVERT: H 206 LEU cc_start: 0.9099 (mt) cc_final: 0.8793 (mt) REVERT: H 208 ASN cc_start: 0.8784 (m110) cc_final: 0.7682 (t0) REVERT: H 261 PHE cc_start: 0.7752 (t80) cc_final: 0.7510 (t80) REVERT: H 272 ASN cc_start: 0.8552 (t0) cc_final: 0.8230 (m110) REVERT: I 22 GLU cc_start: 0.8820 (tm-30) cc_final: 0.8247 (tm-30) REVERT: I 77 TRP cc_start: 0.8256 (t60) cc_final: 0.7042 (t60) REVERT: I 80 ARG cc_start: 0.8014 (mtp180) cc_final: 0.7231 (mtm-85) REVERT: I 81 GLN cc_start: 0.8713 (OUTLIER) cc_final: 0.8196 (mp10) REVERT: I 84 GLU cc_start: 0.8530 (tp30) cc_final: 0.8155 (tp30) REVERT: I 86 CYS cc_start: 0.8808 (t) cc_final: 0.8151 (p) REVERT: I 91 ASN cc_start: 0.8891 (t0) cc_final: 0.8618 (t0) REVERT: I 96 GLU cc_start: 0.8482 (OUTLIER) cc_final: 0.7797 (pm20) REVERT: I 109 THR cc_start: 0.8197 (m) cc_final: 0.7376 (p) REVERT: I 119 LYS cc_start: 0.9045 (ptmm) cc_final: 0.8717 (ptmm) REVERT: I 123 ASN cc_start: 0.8809 (m110) cc_final: 0.8297 (m110) REVERT: J 9 ASP cc_start: 0.7873 (t0) cc_final: 0.7362 (t0) REVERT: J 18 PHE cc_start: 0.8824 (t80) cc_final: 0.8459 (t80) REVERT: J 57 ARG cc_start: 0.8757 (mtm180) cc_final: 0.8391 (mtm-85) REVERT: J 62 HIS cc_start: 0.8292 (m90) cc_final: 0.7866 (m-70) REVERT: J 78 GLU cc_start: 0.8746 (tp30) cc_final: 0.8467 (tp30) REVERT: J 80 ARG cc_start: 0.8080 (mtm-85) cc_final: 0.7688 (tpp80) REVERT: J 91 ASN cc_start: 0.8551 (m-40) cc_final: 0.8145 (m-40) REVERT: J 116 ASP cc_start: 0.7372 (t0) cc_final: 0.7100 (t0) REVERT: K 46 GLU cc_start: 0.8598 (tm-30) cc_final: 0.8321 (tm-30) REVERT: K 65 LYS cc_start: 0.9180 (mppt) cc_final: 0.8847 (mtmm) REVERT: K 250 TYR cc_start: 0.7798 (OUTLIER) cc_final: 0.6266 (p90) REVERT: K 309 LYS cc_start: 0.8316 (tppt) cc_final: 0.7922 (ttpp) REVERT: K 504 THR cc_start: 0.8776 (m) cc_final: 0.8384 (p) REVERT: M 16 GLN cc_start: 0.7337 (mm-40) cc_final: 0.7065 (tp40) REVERT: M 53 PHE cc_start: 0.9028 (t80) cc_final: 0.8776 (t80) REVERT: M 56 MET cc_start: 0.8150 (ttm) cc_final: 0.7676 (ttm) REVERT: M 198 ASP cc_start: 0.7818 (m-30) cc_final: 0.7356 (m-30) REVERT: M 204 GLN cc_start: 0.8302 (OUTLIER) cc_final: 0.7621 (tm-30) REVERT: N 63 THR cc_start: 0.8922 (t) cc_final: 0.8508 (p) REVERT: L 24 ILE cc_start: 0.8969 (mt) cc_final: 0.8731 (mp) REVERT: L 25 GLN cc_start: 0.8522 (OUTLIER) cc_final: 0.8233 (tt0) REVERT: L 40 TYR cc_start: 0.8658 (m-10) cc_final: 0.8183 (m-80) REVERT: L 56 MET cc_start: 0.7784 (mmm) cc_final: 0.6356 (tmm) REVERT: L 76 GLN cc_start: 0.8368 (mm110) cc_final: 0.8041 (mm110) REVERT: L 96 GLU cc_start: 0.8340 (pm20) cc_final: 0.8031 (pm20) outliers start: 106 outliers final: 70 residues processed: 792 average time/residue: 0.3886 time to fit residues: 482.4339 Evaluate side-chains 777 residues out of total 2762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 690 time to evaluate : 2.990 ------------------------------------------------------------------------------- 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 44 VAL Chi-restraints excluded: chain B residue 70 LYS Chi-restraints excluded: chain B residue 150 MET Chi-restraints excluded: chain B residue 187 HIS Chi-restraints excluded: chain B residue 209 MET Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain C residue 5 LYS Chi-restraints excluded: chain C residue 8 ASP 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 214 HIS 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 260 SER Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain E residue 65 ILE Chi-restraints excluded: chain E residue 125 VAL Chi-restraints excluded: chain E residue 134 SER Chi-restraints excluded: chain E residue 141 MET Chi-restraints excluded: chain E residue 143 LEU Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 184 ILE 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 67 ILE Chi-restraints excluded: chain F residue 124 GLN Chi-restraints excluded: chain F residue 187 HIS 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 H residue 66 PHE Chi-restraints excluded: chain H residue 132 THR Chi-restraints excluded: chain H residue 187 HIS 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 58 LEU Chi-restraints excluded: chain I residue 81 GLN Chi-restraints excluded: chain I residue 96 GLU Chi-restraints excluded: chain J residue 98 GLN Chi-restraints excluded: chain K residue 32 PHE Chi-restraints excluded: chain K residue 195 CYS Chi-restraints excluded: chain K residue 226 LEU Chi-restraints excluded: chain K residue 250 TYR Chi-restraints excluded: chain K residue 257 LEU Chi-restraints excluded: chain K residue 266 ILE Chi-restraints excluded: chain K residue 269 VAL Chi-restraints excluded: chain K residue 306 THR Chi-restraints excluded: chain K residue 330 LEU Chi-restraints excluded: chain K residue 343 HIS Chi-restraints excluded: chain K residue 387 ASP Chi-restraints excluded: chain K residue 393 LEU Chi-restraints excluded: chain K residue 403 ASP Chi-restraints excluded: chain K residue 430 THR Chi-restraints excluded: chain M residue 42 THR Chi-restraints excluded: chain M residue 46 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 204 GLN 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 25 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 103 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 227 optimal weight: 1.9990 chunk 299 optimal weight: 0.5980 chunk 40 optimal weight: 0.3980 chunk 115 optimal weight: 6.9990 chunk 317 optimal weight: 9.9990 chunk 42 optimal weight: 8.9990 chunk 170 optimal weight: 10.0000 chunk 262 optimal weight: 0.9990 chunk 252 optimal weight: 0.8980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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 124 GLN ** B 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 83 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** ** D 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 62 HIS ** E 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 16 GLN ** F 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 85 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** ** G 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 97 GLN J 8 GLN ** 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 427 GLN ** K 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 544 GLN ** M 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 86 ASN ** 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 = 0.4144 r_free = 0.4144 target = 0.154196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.117672 restraints weight = 47732.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 63)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.122032 restraints weight = 21761.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.124850 restraints weight = 12862.949| |-----------------------------------------------------------------------------| r_work (final): 0.3960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.5256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.103 27430 Z= 0.226 Angle : 0.873 17.639 37194 Z= 0.451 Chirality : 0.052 0.418 4023 Planarity : 0.006 0.070 4752 Dihedral : 14.255 167.107 4190 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 30.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.08 % Favored : 90.92 % Rotamer: Outliers : 3.41 % Allowed : 26.67 % Favored : 69.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.38 (0.14), residues: 3184 helix: -0.63 (0.14), residues: 1269 sheet: -2.49 (0.25), residues: 392 loop : -2.13 (0.15), residues: 1523 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.112 0.003 TRP J 77 HIS 0.030 0.002 HIS C 214 PHE 0.047 0.003 PHE D 183 TYR 0.030 0.003 TYR B 175 ARG 0.012 0.001 ARG C 280 Details of bonding type rmsd hydrogen bonds : bond 0.04662 ( 1148) hydrogen bonds : angle 6.60501 ( 3315) covalent geometry : bond 0.00525 (27430) covalent geometry : angle 0.87265 (37194) ********************** 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 795 residues out of total 2762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 701 time to evaluate : 3.045 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: 0.7763 (OUTLIER) cc_final: 0.6287 (t80) REVERT: A 153 ASN cc_start: 0.7044 (m-40) cc_final: 0.6720 (m-40) REVERT: A 155 TYR cc_start: 0.8363 (m-80) cc_final: 0.7956 (m-80) REVERT: A 164 GLU cc_start: 0.8269 (tp30) cc_final: 0.7740 (tp30) REVERT: A 167 GLN cc_start: 0.8825 (tm-30) cc_final: 0.7598 (tm-30) REVERT: A 168 TYR cc_start: 0.7226 (m-80) cc_final: 0.6623 (m-10) REVERT: A 169 GLU cc_start: 0.7718 (tt0) cc_final: 0.7474 (tp30) REVERT: B 70 LYS cc_start: 0.7219 (OUTLIER) cc_final: 0.6816 (mttp) REVERT: B 83 GLN cc_start: 0.8154 (mm-40) cc_final: 0.7621 (mm-40) REVERT: B 175 TYR cc_start: 0.8154 (t80) cc_final: 0.7649 (t80) REVERT: B 241 ASP cc_start: 0.7567 (t70) cc_final: 0.7280 (t70) REVERT: B 279 LEU cc_start: 0.8042 (tt) cc_final: 0.7689 (tt) REVERT: C 67 ILE cc_start: 0.8371 (OUTLIER) cc_final: 0.7759 (mm) REVERT: C 91 LYS cc_start: 0.8617 (pptt) cc_final: 0.8343 (mmmt) REVERT: C 133 PHE cc_start: 0.8441 (OUTLIER) cc_final: 0.8086 (m-80) REVERT: C 146 SER cc_start: 0.7625 (t) cc_final: 0.7347 (t) REVERT: C 256 GLU cc_start: 0.7060 (tm-30) cc_final: 0.6819 (tm-30) REVERT: D 35 GLN cc_start: 0.8346 (mm-40) cc_final: 0.8042 (tp40) REVERT: D 36 THR cc_start: 0.7792 (OUTLIER) cc_final: 0.7575 (p) REVERT: D 138 ASP cc_start: 0.7698 (t0) cc_final: 0.7279 (m-30) REVERT: D 209 MET cc_start: 0.7652 (mmm) cc_final: 0.7118 (mmm) REVERT: E 56 MET cc_start: 0.8203 (ttp) cc_final: 0.7753 (ttp) REVERT: E 79 GLU cc_start: 0.7484 (tm-30) cc_final: 0.6957 (tm-30) REVERT: E 116 MET cc_start: 0.8363 (mmt) cc_final: 0.8103 (mmp) REVERT: E 138 ASP cc_start: 0.7606 (m-30) cc_final: 0.6693 (m-30) REVERT: E 148 THR cc_start: 0.7437 (p) cc_final: 0.7202 (p) REVERT: E 150 MET cc_start: 0.8281 (mmm) cc_final: 0.7574 (mmm) REVERT: E 169 ARG cc_start: 0.8191 (mtp85) cc_final: 0.7808 (mtp-110) REVERT: E 184 ILE cc_start: 0.8480 (OUTLIER) cc_final: 0.8173 (mm) REVERT: E 221 MET cc_start: 0.7629 (mtm) cc_final: 0.7134 (mtm) REVERT: E 226 LEU cc_start: 0.8163 (tp) cc_final: 0.7907 (tp) REVERT: F 19 ASN cc_start: 0.7773 (t0) cc_final: 0.7503 (t0) REVERT: F 72 ILE cc_start: 0.8255 (mm) cc_final: 0.7933 (mm) REVERT: F 95 THR cc_start: 0.8311 (p) cc_final: 0.8039 (t) REVERT: F 102 MET cc_start: 0.9037 (mmt) cc_final: 0.8826 (mmt) REVERT: F 124 GLN cc_start: 0.8385 (OUTLIER) cc_final: 0.8029 (mt0) REVERT: F 187 HIS cc_start: 0.7446 (OUTLIER) cc_final: 0.6796 (p90) REVERT: F 209 MET cc_start: 0.7055 (tmm) cc_final: 0.6657 (tmm) REVERT: G 23 LYS cc_start: 0.8056 (tptt) cc_final: 0.7421 (tttt) REVERT: G 68 PHE cc_start: 0.8058 (t80) cc_final: 0.7696 (t80) REVERT: G 71 ARG cc_start: 0.8646 (mtp85) cc_final: 0.8231 (mtp85) REVERT: G 106 TYR cc_start: 0.8578 (m-80) cc_final: 0.8184 (m-80) REVERT: G 110 GLN cc_start: 0.7375 (tp-100) cc_final: 0.7023 (tp40) REVERT: H 6 ARG cc_start: 0.8795 (ttp80) cc_final: 0.8323 (ttt180) REVERT: H 41 VAL cc_start: 0.8833 (m) cc_final: 0.8525 (p) REVERT: H 102 MET cc_start: 0.8933 (mmm) cc_final: 0.8600 (mmm) REVERT: H 190 LYS cc_start: 0.8709 (mttm) cc_final: 0.8374 (mttp) REVERT: H 206 LEU cc_start: 0.9201 (mt) cc_final: 0.8912 (mt) REVERT: H 208 ASN cc_start: 0.8760 (m110) cc_final: 0.7698 (t0) REVERT: H 261 PHE cc_start: 0.7850 (t80) cc_final: 0.7647 (t80) REVERT: I 22 GLU cc_start: 0.8700 (tm-30) cc_final: 0.8148 (tm-30) REVERT: I 65 LYS cc_start: 0.8834 (mttp) cc_final: 0.8525 (mttt) REVERT: I 74 GLN cc_start: 0.8650 (pt0) cc_final: 0.8103 (mp10) REVERT: I 77 TRP cc_start: 0.8260 (t60) cc_final: 0.7105 (t60) REVERT: I 80 ARG cc_start: 0.8219 (mtp180) cc_final: 0.7276 (mtm-85) REVERT: I 84 GLU cc_start: 0.8130 (tp30) cc_final: 0.7771 (tp30) REVERT: I 86 CYS cc_start: 0.8693 (t) cc_final: 0.7994 (p) REVERT: I 91 ASN cc_start: 0.8724 (t0) cc_final: 0.8503 (t0) REVERT: I 96 GLU cc_start: 0.8396 (OUTLIER) cc_final: 0.7738 (pm20) REVERT: I 98 GLN cc_start: 0.8840 (tt0) cc_final: 0.8631 (tt0) REVERT: I 109 THR cc_start: 0.8141 (m) cc_final: 0.7369 (p) REVERT: I 113 PHE cc_start: 0.7350 (m-10) cc_final: 0.6396 (m-10) REVERT: I 119 LYS cc_start: 0.9059 (ptmm) cc_final: 0.8650 (ptmm) REVERT: I 123 ASN cc_start: 0.8803 (m110) cc_final: 0.8320 (m110) REVERT: J 9 ASP cc_start: 0.7893 (t0) cc_final: 0.7408 (t0) REVERT: J 18 PHE cc_start: 0.8899 (t80) cc_final: 0.8466 (t80) REVERT: J 57 ARG cc_start: 0.8680 (mtm180) cc_final: 0.8344 (mtm-85) REVERT: J 91 ASN cc_start: 0.8405 (m-40) cc_final: 0.8091 (m-40) REVERT: J 108 GLU cc_start: 0.8452 (mt-10) cc_final: 0.8009 (mt-10) REVERT: J 116 ASP cc_start: 0.7193 (t0) cc_final: 0.6897 (t0) REVERT: K 46 GLU cc_start: 0.8487 (tm-30) cc_final: 0.8254 (tm-30) REVERT: K 170 CYS cc_start: 0.9062 (m) cc_final: 0.8858 (m) REVERT: K 250 TYR cc_start: 0.7904 (OUTLIER) cc_final: 0.6450 (p90) REVERT: K 295 ASP cc_start: 0.8355 (t0) cc_final: 0.8005 (t0) REVERT: K 309 LYS cc_start: 0.8207 (tppt) cc_final: 0.7821 (ttpp) REVERT: K 395 SER cc_start: 0.7043 (t) cc_final: 0.6607 (p) REVERT: K 504 THR cc_start: 0.8744 (m) cc_final: 0.8392 (p) REVERT: K 513 MET cc_start: 0.8774 (mmm) cc_final: 0.8432 (tpp) REVERT: M 16 GLN cc_start: 0.7324 (mm-40) cc_final: 0.7118 (tp40) REVERT: M 53 PHE cc_start: 0.8973 (t80) cc_final: 0.8746 (t80) REVERT: M 56 MET cc_start: 0.8125 (ttm) cc_final: 0.7801 (ttm) REVERT: M 175 TYR cc_start: 0.8333 (t80) cc_final: 0.7977 (t80) REVERT: M 198 ASP cc_start: 0.7381 (m-30) cc_final: 0.7059 (m-30) REVERT: M 204 GLN cc_start: 0.8276 (OUTLIER) cc_final: 0.7713 (tm-30) REVERT: N 63 THR cc_start: 0.8962 (t) cc_final: 0.8571 (p) REVERT: L 24 ILE cc_start: 0.9037 (mt) cc_final: 0.8804 (mp) REVERT: L 25 GLN cc_start: 0.8575 (OUTLIER) cc_final: 0.8267 (tt0) REVERT: L 40 TYR cc_start: 0.8530 (m-10) cc_final: 0.8131 (m-80) REVERT: L 56 MET cc_start: 0.7803 (mmm) cc_final: 0.6359 (tmm) REVERT: L 76 GLN cc_start: 0.8439 (mm110) cc_final: 0.8084 (mm110) outliers start: 94 outliers final: 68 residues processed: 748 average time/residue: 0.3943 time to fit residues: 467.1707 Evaluate side-chains 765 residues out of total 2762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 685 time to evaluate : 2.825 ------------------------------------------------------------------------------- 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 44 VAL Chi-restraints excluded: chain B residue 70 LYS Chi-restraints excluded: chain B residue 150 MET Chi-restraints excluded: chain B residue 187 HIS Chi-restraints excluded: chain B residue 209 MET Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain C residue 5 LYS Chi-restraints excluded: chain C residue 8 ASP Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 32 ILE Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 77 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 268 VAL 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 260 SER Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain E residue 65 ILE Chi-restraints excluded: chain E residue 125 VAL Chi-restraints excluded: chain E residue 134 SER Chi-restraints excluded: chain E residue 143 LEU Chi-restraints excluded: chain E residue 144 GLU Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 184 ILE Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 203 TRP Chi-restraints excluded: chain E residue 259 ARG Chi-restraints excluded: chain F residue 21 ASN Chi-restraints excluded: chain F residue 32 ILE Chi-restraints excluded: chain F residue 124 GLN Chi-restraints excluded: chain F residue 187 HIS 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 H residue 66 PHE Chi-restraints excluded: chain H residue 132 THR Chi-restraints excluded: chain H residue 187 HIS Chi-restraints excluded: chain H residue 212 HIS 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 23 LYS Chi-restraints excluded: chain I residue 58 LEU Chi-restraints excluded: chain I residue 96 GLU Chi-restraints excluded: chain J residue 98 GLN Chi-restraints excluded: chain K residue 32 PHE Chi-restraints excluded: chain K residue 195 CYS Chi-restraints excluded: chain K residue 226 LEU Chi-restraints excluded: chain K residue 250 TYR Chi-restraints excluded: chain K residue 257 LEU Chi-restraints excluded: chain K residue 266 ILE Chi-restraints excluded: chain K residue 306 THR Chi-restraints excluded: chain K residue 330 LEU Chi-restraints excluded: chain K residue 387 ASP Chi-restraints excluded: chain K residue 393 LEU Chi-restraints excluded: chain K residue 403 ASP Chi-restraints excluded: chain M residue 42 THR Chi-restraints excluded: chain M residue 131 LEU Chi-restraints excluded: chain M residue 166 THR Chi-restraints excluded: chain M residue 180 CYS Chi-restraints excluded: chain M residue 204 GLN 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 201 VAL Chi-restraints excluded: chain L residue 25 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 181 optimal weight: 3.9990 chunk 316 optimal weight: 9.9990 chunk 110 optimal weight: 1.9990 chunk 215 optimal weight: 0.9990 chunk 236 optimal weight: 0.6980 chunk 126 optimal weight: 0.9990 chunk 151 optimal weight: 0.7980 chunk 300 optimal weight: 0.9980 chunk 119 optimal weight: 0.9980 chunk 13 optimal weight: 0.8980 chunk 171 optimal weight: 5.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 83 GLN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 214 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 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 97 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 J 8 GLN ** J 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 85 HIS ** 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 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.154831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.118266 restraints weight = 47617.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.122640 restraints weight = 21705.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.125431 restraints weight = 12851.370| |-----------------------------------------------------------------------------| r_work (final): 0.3992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.5417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 27430 Z= 0.218 Angle : 0.873 18.114 37194 Z= 0.450 Chirality : 0.053 0.423 4023 Planarity : 0.006 0.058 4752 Dihedral : 14.269 166.638 4190 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 30.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.42 % Favored : 90.58 % Rotamer: Outliers : 3.62 % Allowed : 26.41 % Favored : 69.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.36 (0.14), residues: 3184 helix: -0.63 (0.14), residues: 1260 sheet: -2.39 (0.26), residues: 382 loop : -2.13 (0.15), residues: 1542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.095 0.004 TRP J 77 HIS 0.028 0.002 HIS C 214 PHE 0.044 0.003 PHE M 112 TYR 0.032 0.003 TYR J 40 ARG 0.019 0.001 ARG C 110 Details of bonding type rmsd hydrogen bonds : bond 0.04714 ( 1148) hydrogen bonds : angle 6.63381 ( 3315) covalent geometry : bond 0.00506 (27430) covalent geometry : angle 0.87279 (37194) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11360.54 seconds wall clock time: 199 minutes 11.42 seconds (11951.42 seconds total)