Starting phenix.real_space_refine on Mon Jun 23 00:17:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g9t_29878/06_2025/8g9t_29878.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g9t_29878/06_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_29878/06_2025/8g9t_29878.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g9t_29878/06_2025/8g9t_29878.map" model { file = "/net/cci-nas-00/data/ceres_data/8g9t_29878/06_2025/8g9t_29878.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g9t_29878/06_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-5710/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: 14.64, per 1000 atoms: 0.55 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: 6.82 Conformation dependent library (CDL) restraints added in 3.2 seconds 6368 Ramachandran restraints generated. 3184 Oldfield, 0 Emsley, 3184 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5976 Finding SS restraints... Secondary structure from input PDB file: 114 helices and 41 sheets defined 43.3% alpha, 15.0% beta 0 base pairs and 12 stacking pairs defined. Time for finding SS restraints: 9.28 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: 10.44 Time building geometry restraints manager: 8.06 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: 1.090 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: 0.920 Check model and map are aligned: 0.180 Set scattering table: 0.220 Process input model: 64.730 Find NCS groups from input model: 1.080 Set up NCS constraints: 0.130 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: 0.020 Load rotamer database and sin/cos tables:3.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.490 ------------------------------------------------------------------------------- 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 : 3.000 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: 0.3983 time to fit residues: 539.2129 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 : 2.950 ------------------------------------------------------------------------------- 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 = 55)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.122010 restraints weight = 46559.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.126444 restraints weight = 20493.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.129270 restraints weight = 11812.601| |-----------------------------------------------------------------------------| 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 : 2.850 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: 0.8120 (t0) cc_final: 0.7514 (t0) REVERT: A 144 ASP cc_start: 0.8516 (m-30) cc_final: 0.8263 (m-30) REVERT: A 165 TRP cc_start: 0.8522 (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: 0.7566 (m-80) cc_final: 0.6894 (m-80) REVERT: B 40 LEU cc_start: 0.9011 (mt) cc_final: 0.8773 (mt) REVERT: B 141 MET cc_start: 0.7116 (mmt) cc_final: 0.6774 (mmt) REVERT: B 175 TYR cc_start: 0.8608 (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: 0.7708 (tp30) cc_final: 0.7457 (tp30) REVERT: C 124 GLN cc_start: 0.7681 (mt0) cc_final: 0.7165 (mt0) REVERT: C 156 LYS cc_start: 0.8779 (ttpp) cc_final: 0.8533 (tttm) REVERT: C 175 TYR cc_start: 0.9147 (t80) cc_final: 0.8827 (t80) REVERT: C 191 GLN cc_start: 0.8228 (tt0) cc_final: 0.7955 (tt0) REVERT: C 209 MET cc_start: 0.7165 (ptm) cc_final: 0.6770 (ttm) REVERT: C 220 GLN cc_start: 0.7804 (tm-30) cc_final: 0.6865 (tm-30) REVERT: C 226 LEU cc_start: 0.8654 (tp) cc_final: 0.8424 (tp) REVERT: D 116 MET cc_start: 0.8860 (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: 0.7849 (mtm) cc_final: 0.7612 (mtm) REVERT: E 79 GLU cc_start: 0.7573 (tm-30) cc_final: 0.7002 (tm-30) REVERT: E 184 ILE cc_start: 0.8719 (mm) cc_final: 0.8469 (mm) REVERT: E 204 GLN cc_start: 0.7704 (tm130) cc_final: 0.7243 (tm-30) REVERT: E 221 MET cc_start: 0.8363 (mtm) cc_final: 0.7967 (mtm) REVERT: E 226 LEU cc_start: 0.8803 (tp) cc_final: 0.8496 (tp) REVERT: E 233 ASN cc_start: 0.8263 (m-40) cc_final: 0.7893 (m-40) REVERT: E 241 ASP cc_start: 0.7137 (t70) cc_final: 0.6640 (t0) REVERT: F 19 ASN cc_start: 0.7280 (t0) cc_final: 0.7076 (t0) REVERT: F 72 ILE cc_start: 0.8299 (mm) cc_final: 0.7954 (mm) REVERT: F 81 HIS cc_start: 0.8291 (m170) cc_final: 0.8086 (m170) REVERT: F 108 ASP cc_start: 0.7692 (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: 0.8426 (t0) cc_final: 0.8100 (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: 0.8258 (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: 0.7897 (mt) REVERT: G 122 PHE cc_start: 0.7606 (t80) cc_final: 0.7111 (t80) REVERT: H 11 PHE cc_start: 0.7588 (t80) cc_final: 0.7032 (t80) REVERT: H 96 GLU cc_start: 0.8751 (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: 0.7113 (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: 0.8977 (mt) REVERT: H 246 ARG cc_start: 0.7239 (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: 0.8920 (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: 0.8396 (mp10) cc_final: 0.7936 (mm-40) REVERT: I 84 GLU cc_start: 0.8471 (tp30) cc_final: 0.8185 (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: 0.8104 (p0) cc_final: 0.7315 (p0) REVERT: I 121 LEU cc_start: 0.8265 (OUTLIER) cc_final: 0.8007 (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: 0.8242 (tppp) REVERT: J 52 PHE cc_start: 0.8096 (m-10) cc_final: 0.7514 (m-80) REVERT: J 64 ASN cc_start: 0.8083 (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: 0.8533 (mt) REVERT: J 105 TYR cc_start: 0.8879 (t80) cc_final: 0.8499 (t80) REVERT: J 116 ASP cc_start: 0.7246 (t0) cc_final: 0.6983 (t0) REVERT: J 120 ASN cc_start: 0.8157 (m110) cc_final: 0.7715 (m-40) REVERT: K 16 SER cc_start: 0.7975 (t) cc_final: 0.7353 (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: 0.7975 (p-90) REVERT: K 156 ASN cc_start: 0.8036 (m110) cc_final: 0.7657 (m-40) REVERT: K 285 LEU cc_start: 0.9339 (mt) cc_final: 0.9069 (mp) REVERT: K 309 LYS cc_start: 0.8549 (tppt) cc_final: 0.8314 (ttmm) REVERT: K 403 ASP cc_start: 0.7391 (OUTLIER) cc_final: 0.6840 (t70) REVERT: K 565 GLU cc_start: 0.7355 (mm-30) cc_final: 0.6089 (mm-30) REVERT: M 21 ASN cc_start: 0.8060 (p0) cc_final: 0.7713 (p0) REVERT: M 55 GLN cc_start: 0.8676 (tt0) cc_final: 0.8382 (tt0) REVERT: M 102 MET cc_start: 0.6088 (mtt) cc_final: 0.5716 (mtp) REVERT: M 116 MET cc_start: 0.8831 (mmt) cc_final: 0.8552 (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: 0.7669 (m-30) cc_final: 0.7087 (m-30) REVERT: M 204 GLN cc_start: 0.8424 (tm-30) cc_final: 0.8137 (tm-30) REVERT: M 212 HIS cc_start: 0.6895 (m-70) cc_final: 0.6323 (m-70) REVERT: M 221 MET cc_start: 0.8420 (ttt) cc_final: 0.7790 (ttt) REVERT: M 263 ASP cc_start: 0.7798 (m-30) cc_final: 0.7530 (m-30) REVERT: M 277 LYS cc_start: 0.7892 (mppt) cc_final: 0.7553 (mppt) REVERT: N 7 ILE cc_start: 0.8621 (mt) cc_final: 0.8410 (mm) REVERT: N 26 TYR cc_start: 0.8553 (m-80) cc_final: 0.8092 (m-80) REVERT: N 56 ILE cc_start: 0.8709 (mm) cc_final: 0.8506 (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: 0.7485 (m90) cc_final: 0.7021 (m90) outliers start: 81 outliers final: 35 residues processed: 889 average time/residue: 0.3912 time to fit residues: 545.2852 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 : 2.984 ------------------------------------------------------------------------------- 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: 0.5980 chunk 253 optimal weight: 0.9980 chunk 277 optimal weight: 0.6980 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: 1.2182 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 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 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.152647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.119732 restraints weight = 47094.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.124149 restraints weight = 20933.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.126971 restraints weight = 12160.344| |-----------------------------------------------------------------------------| r_work (final): 0.3872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.3125 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= 0.254 Angle : 0.853 11.317 37194 Z= 0.446 Chirality : 0.051 0.328 4023 Planarity : 0.006 0.065 4752 Dihedral : 14.801 174.159 4195 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 32.87 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.55 % Favored : 90.42 % Rotamer: Outliers : 3.55 % Allowed : 18.95 % 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: -0.77 (0.14), residues: 1278 sheet: -2.76 (0.24), residues: 388 loop : -2.29 (0.15), residues: 1518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.003 TRP I 77 HIS 0.024 0.002 HIS C 214 PHE 0.036 0.003 PHE G 111 TYR 0.035 0.003 TYR K 440 ARG 0.012 0.001 ARG K 496 Details of bonding type rmsd hydrogen bonds : bond 0.05372 ( 1148) hydrogen bonds : angle 6.92866 ( 3315) covalent geometry : bond 0.00574 (27430) covalent geometry : angle 0.85348 (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 858 residues out of total 2762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 760 time to evaluate : 2.822 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 PHE cc_start: 0.8460 (OUTLIER) cc_final: 0.6067 (t80) REVERT: A 126 ASN cc_start: 0.8201 (t0) cc_final: 0.7561 (t0) REVERT: A 144 ASP cc_start: 0.8548 (m-30) cc_final: 0.8277 (m-30) REVERT: A 155 TYR cc_start: 0.8545 (m-80) cc_final: 0.8222 (m-80) REVERT: A 165 TRP cc_start: 0.8574 (m-10) cc_final: 0.8306 (m100) REVERT: A 167 GLN cc_start: 0.8495 (tm-30) cc_final: 0.7819 (tm-30) REVERT: A 168 TYR cc_start: 0.7708 (m-80) cc_final: 0.7479 (m-80) REVERT: B 40 LEU cc_start: 0.8966 (mt) cc_final: 0.8698 (mt) REVERT: B 69 GLU cc_start: 0.6800 (tm-30) cc_final: 0.6453 (tm-30) REVERT: B 175 TYR cc_start: 0.8618 (t80) cc_final: 0.8045 (t80) REVERT: B 183 PHE cc_start: 0.8416 (m-80) cc_final: 0.7642 (m-10) REVERT: C 4 GLU cc_start: 0.7515 (tp30) cc_final: 0.7144 (tp30) REVERT: C 156 LYS cc_start: 0.8843 (ttpp) cc_final: 0.8602 (tttm) REVERT: C 220 GLN cc_start: 0.7941 (tm-30) cc_final: 0.6651 (tm-30) REVERT: C 222 ASN cc_start: 0.8271 (m110) cc_final: 0.6329 (m110) REVERT: C 226 LEU cc_start: 0.8560 (tp) cc_final: 0.8297 (tp) REVERT: C 256 GLU cc_start: 0.7449 (tm-30) cc_final: 0.7225 (tm-30) REVERT: D 36 THR cc_start: 0.8082 (OUTLIER) cc_final: 0.7713 (p) REVERT: D 46 LEU cc_start: 0.7989 (tt) cc_final: 0.7697 (tp) REVERT: D 169 ARG cc_start: 0.8066 (mtm-85) cc_final: 0.7845 (mtm-85) REVERT: D 244 PHE cc_start: 0.9000 (m-10) cc_final: 0.8667 (m-10) REVERT: E 79 GLU cc_start: 0.7708 (tm-30) cc_final: 0.7212 (tm-30) REVERT: E 101 TYR cc_start: 0.7934 (t80) cc_final: 0.7675 (t80) REVERT: E 184 ILE cc_start: 0.8791 (mm) cc_final: 0.8541 (mm) REVERT: E 204 GLN cc_start: 0.7741 (tm130) cc_final: 0.7025 (tm-30) REVERT: E 221 MET cc_start: 0.8419 (mtm) cc_final: 0.8122 (mtm) REVERT: E 226 LEU cc_start: 0.8567 (tp) cc_final: 0.8259 (tp) REVERT: E 233 ASN cc_start: 0.8333 (m-40) cc_final: 0.7934 (m-40) REVERT: E 241 ASP cc_start: 0.7046 (t70) cc_final: 0.6615 (t0) REVERT: E 265 LEU cc_start: 0.9033 (tp) cc_final: 0.8507 (pp) REVERT: F 72 ILE cc_start: 0.8275 (mm) cc_final: 0.7910 (mm) REVERT: F 108 ASP cc_start: 0.7790 (t0) cc_final: 0.7337 (t0) REVERT: F 141 MET cc_start: 0.8170 (ttm) cc_final: 0.7801 (ttt) REVERT: F 172 THR cc_start: 0.8062 (m) cc_final: 0.6995 (p) REVERT: G 9 ASP cc_start: 0.8385 (t0) cc_final: 0.8073 (m-30) REVERT: G 16 ARG cc_start: 0.8819 (tpt-90) cc_final: 0.8442 (tpt-90) REVERT: G 57 ARG cc_start: 0.8510 (ttm-80) cc_final: 0.8284 (ttm110) REVERT: G 58 LEU cc_start: 0.8053 (tp) cc_final: 0.7603 (tp) REVERT: G 68 PHE cc_start: 0.8299 (t80) cc_final: 0.8006 (t80) REVERT: G 77 TRP cc_start: 0.8146 (t60) cc_final: 0.7431 (t60) REVERT: G 94 ASN cc_start: 0.8602 (p0) cc_final: 0.8349 (p0) REVERT: G 97 GLN cc_start: 0.8548 (tt0) cc_final: 0.8279 (tp40) REVERT: G 98 GLN cc_start: 0.7939 (tt0) cc_final: 0.7659 (tm-30) REVERT: G 103 ILE cc_start: 0.8951 (OUTLIER) cc_final: 0.8432 (tt) REVERT: G 107 HIS cc_start: 0.8483 (m90) cc_final: 0.7839 (m90) REVERT: G 110 GLN cc_start: 0.7713 (tp-100) cc_final: 0.7292 (tp-100) REVERT: G 111 PHE cc_start: 0.8128 (t80) cc_final: 0.7660 (t80) REVERT: G 122 PHE cc_start: 0.7819 (t80) cc_final: 0.7284 (t80) REVERT: H 11 PHE cc_start: 0.7529 (t80) cc_final: 0.6972 (t80) REVERT: H 81 HIS cc_start: 0.8489 (OUTLIER) cc_final: 0.7907 (t-90) REVERT: H 102 MET cc_start: 0.8826 (mmm) cc_final: 0.7838 (mmm) REVERT: H 178 TYR cc_start: 0.7129 (m-80) cc_final: 0.6385 (m-10) REVERT: H 181 HIS cc_start: 0.8076 (m-70) cc_final: 0.7613 (m-70) REVERT: H 261 PHE cc_start: 0.7615 (t80) cc_final: 0.7265 (t80) REVERT: I 21 LEU cc_start: 0.8885 (mp) cc_final: 0.8683 (mp) REVERT: I 22 GLU cc_start: 0.8790 (tm-30) cc_final: 0.8002 (tm-30) REVERT: I 23 LYS cc_start: 0.8789 (tppt) cc_final: 0.8173 (tppt) REVERT: I 71 ARG cc_start: 0.8865 (mmm160) cc_final: 0.8586 (mmm160) REVERT: I 77 TRP cc_start: 0.8073 (t60) cc_final: 0.7552 (t60) REVERT: I 81 GLN cc_start: 0.8940 (OUTLIER) cc_final: 0.8489 (mp10) REVERT: I 84 GLU cc_start: 0.8565 (tp30) cc_final: 0.8151 (tp30) REVERT: I 87 GLN cc_start: 0.9143 (tt0) cc_final: 0.8638 (tm-30) REVERT: I 88 ARG cc_start: 0.7715 (ttp80) cc_final: 0.6837 (tmm-80) REVERT: I 113 PHE cc_start: 0.8231 (m-80) cc_final: 0.7789 (m-80) REVERT: I 119 LYS cc_start: 0.9133 (ptmm) cc_final: 0.8633 (ptmm) REVERT: I 123 ASN cc_start: 0.8532 (m110) cc_final: 0.8191 (m-40) REVERT: J 18 PHE cc_start: 0.8773 (t80) cc_final: 0.8074 (t80) REVERT: J 23 LYS cc_start: 0.8870 (mmmt) cc_final: 0.8641 (tppp) REVERT: J 52 PHE cc_start: 0.8088 (m-10) cc_final: 0.7512 (m-80) REVERT: J 65 LYS cc_start: 0.9122 (mttp) cc_final: 0.8726 (mmtm) REVERT: J 78 GLU cc_start: 0.9040 (tp30) cc_final: 0.8390 (tp30) REVERT: J 80 ARG cc_start: 0.8162 (mtm-85) cc_final: 0.7940 (mmm-85) REVERT: J 91 ASN cc_start: 0.8552 (m-40) cc_final: 0.8016 (m-40) REVERT: J 105 TYR cc_start: 0.8915 (t80) cc_final: 0.8302 (t80) REVERT: J 108 GLU cc_start: 0.8175 (mm-30) cc_final: 0.7951 (mm-30) REVERT: J 116 ASP cc_start: 0.7468 (t0) cc_final: 0.7083 (t0) REVERT: J 120 ASN cc_start: 0.8372 (m110) cc_final: 0.7685 (m-40) REVERT: J 123 ASN cc_start: 0.8263 (m-40) cc_final: 0.8061 (m-40) REVERT: J 124 GLU cc_start: 0.7953 (pp20) cc_final: 0.7718 (pp20) REVERT: K 82 TRP cc_start: 0.8540 (p-90) cc_final: 0.7955 (p-90) REVERT: K 156 ASN cc_start: 0.8082 (m110) cc_final: 0.7600 (m-40) REVERT: K 250 TYR cc_start: 0.7949 (OUTLIER) cc_final: 0.6627 (p90) REVERT: K 285 LEU cc_start: 0.9328 (mt) cc_final: 0.9077 (mp) REVERT: K 288 MET cc_start: 0.7880 (mtm) cc_final: 0.7605 (ptp) REVERT: K 309 LYS cc_start: 0.8636 (tppt) cc_final: 0.8390 (ttmm) REVERT: K 436 LEU cc_start: 0.8927 (mt) cc_final: 0.8478 (tp) REVERT: K 503 SER cc_start: 0.8372 (m) cc_final: 0.8084 (p) REVERT: M 102 MET cc_start: 0.6185 (mtt) cc_final: 0.5890 (mtt) REVERT: M 130 GLN cc_start: 0.7378 (tt0) cc_final: 0.7029 (tt0) REVERT: M 204 GLN cc_start: 0.8473 (tm-30) cc_final: 0.8181 (tm-30) REVERT: M 209 MET cc_start: 0.7986 (ttp) cc_final: 0.7497 (ttp) REVERT: M 221 MET cc_start: 0.8425 (ttt) cc_final: 0.7944 (ttt) REVERT: M 277 LYS cc_start: 0.7919 (mppt) cc_final: 0.7645 (mppt) REVERT: N 26 TYR cc_start: 0.8578 (m-80) cc_final: 0.7917 (m-80) REVERT: N 63 THR cc_start: 0.8962 (t) cc_final: 0.8497 (p) REVERT: L 17 LEU cc_start: 0.9380 (tt) cc_final: 0.8437 (tt) REVERT: L 40 TYR cc_start: 0.8617 (m-10) cc_final: 0.8245 (m-80) REVERT: L 76 GLN cc_start: 0.8774 (mp10) cc_final: 0.8448 (mm110) REVERT: L 103 ILE cc_start: 0.8467 (tt) cc_final: 0.8002 (tt) REVERT: L 107 HIS cc_start: 0.6690 (m90) cc_final: 0.5987 (m90) outliers start: 98 outliers final: 57 residues processed: 809 average time/residue: 0.3890 time to fit residues: 493.3265 Evaluate side-chains 739 residues out of total 2762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 676 time to evaluate : 2.862 ------------------------------------------------------------------------------- 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 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 198 THR Chi-restraints excluded: chain K residue 250 TYR Chi-restraints excluded: chain K residue 257 LEU Chi-restraints excluded: chain K residue 266 ILE Chi-restraints excluded: chain K residue 269 VAL Chi-restraints excluded: chain K residue 306 THR Chi-restraints excluded: chain K residue 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 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 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: 0.8980 chunk 113 optimal weight: 0.9980 chunk 270 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 233 optimal weight: 5.9990 chunk 307 optimal weight: 3.9990 chunk 219 optimal weight: 0.9990 chunk 193 optimal weight: 9.9990 chunk 14 optimal weight: 0.7980 chunk 123 optimal weight: 3.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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 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** N 61 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.154587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.121808 restraints weight = 47123.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.126294 restraints weight = 20953.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.129168 restraints weight = 12149.777| |-----------------------------------------------------------------------------| r_work (final): 0.3903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 0.3648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 27430 Z= 0.220 Angle : 0.811 11.974 37194 Z= 0.422 Chirality : 0.050 0.303 4023 Planarity : 0.006 0.073 4752 Dihedral : 14.605 172.094 4193 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 31.16 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.92 % Favored : 91.05 % Rotamer: Outliers : 4.20 % Allowed : 20.40 % Favored : 75.40 % 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: -2.48 (0.14), residues: 3184 helix: -0.64 (0.14), residues: 1272 sheet: -2.77 (0.24), residues: 376 loop : -2.20 (0.15), residues: 1536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP J 77 HIS 0.025 0.002 HIS C 214 PHE 0.035 0.002 PHE G 111 TYR 0.038 0.003 TYR J 106 ARG 0.010 0.001 ARG B 224 Details of bonding type rmsd hydrogen bonds : bond 0.05001 ( 1148) hydrogen bonds : angle 6.77329 ( 3315) covalent geometry : bond 0.00497 (27430) covalent geometry : angle 0.81058 (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 879 residues out of total 2762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 763 time to evaluate : 3.236 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: 0.8200 (OUTLIER) cc_final: 0.6025 (t80) REVERT: A 126 ASN cc_start: 0.8186 (t0) cc_final: 0.7561 (t0) REVERT: A 164 GLU cc_start: 0.8240 (tp30) cc_final: 0.7773 (tp30) REVERT: A 165 TRP cc_start: 0.8531 (m-10) cc_final: 0.8196 (m100) REVERT: A 167 GLN cc_start: 0.8532 (tm-30) cc_final: 0.7666 (tm-30) REVERT: A 168 TYR cc_start: 0.7507 (m-80) cc_final: 0.7196 (m-80) REVERT: B 35 GLN cc_start: 0.7706 (mt0) cc_final: 0.7120 (mt0) REVERT: B 40 LEU cc_start: 0.8967 (mt) cc_final: 0.8651 (mt) REVERT: B 69 GLU cc_start: 0.6567 (tm-30) cc_final: 0.6366 (tm-30) REVERT: B 141 MET cc_start: 0.6917 (mmt) cc_final: 0.6500 (mmt) REVERT: B 175 TYR cc_start: 0.8549 (t80) cc_final: 0.8102 (t80) REVERT: B 183 PHE cc_start: 0.8316 (m-80) cc_final: 0.8039 (m-80) REVERT: C 67 ILE cc_start: 0.8424 (OUTLIER) cc_final: 0.7990 (mm) REVERT: C 146 SER cc_start: 0.8249 (t) cc_final: 0.7881 (t) REVERT: C 220 GLN cc_start: 0.7813 (tm-30) cc_final: 0.6570 (tm-30) REVERT: C 226 LEU cc_start: 0.8082 (tp) cc_final: 0.7741 (tp) REVERT: C 256 GLU cc_start: 0.7579 (tm-30) cc_final: 0.7333 (tm-30) REVERT: D 35 GLN cc_start: 0.8402 (mm-40) cc_final: 0.8090 (tp-100) REVERT: D 36 THR cc_start: 0.7956 (OUTLIER) cc_final: 0.7651 (p) REVERT: D 150 MET cc_start: 0.5439 (ptm) cc_final: 0.5124 (ppp) REVERT: D 244 PHE cc_start: 0.8983 (m-10) cc_final: 0.8557 (m-10) REVERT: E 17 ASP cc_start: 0.8353 (t70) cc_final: 0.7859 (t0) REVERT: E 79 GLU cc_start: 0.7765 (tm-30) cc_final: 0.7215 (tm-30) REVERT: E 101 TYR cc_start: 0.7938 (t80) cc_final: 0.7691 (t80) REVERT: E 167 MET cc_start: 0.8794 (mtm) cc_final: 0.8542 (mtp) REVERT: E 184 ILE cc_start: 0.8746 (mm) cc_final: 0.8450 (mm) REVERT: E 204 GLN cc_start: 0.7764 (tm130) cc_final: 0.7087 (tm-30) REVERT: E 221 MET cc_start: 0.8320 (OUTLIER) cc_final: 0.7511 (mtm) REVERT: E 233 ASN cc_start: 0.8230 (m-40) cc_final: 0.7865 (m-40) REVERT: E 241 ASP cc_start: 0.7012 (t70) cc_final: 0.6703 (t0) REVERT: F 40 LEU cc_start: 0.8206 (OUTLIER) cc_final: 0.7831 (tp) REVERT: F 72 ILE cc_start: 0.8193 (mm) cc_final: 0.7813 (mm) REVERT: F 108 ASP cc_start: 0.7892 (t0) cc_final: 0.7411 (t0) REVERT: F 141 MET cc_start: 0.7835 (ttm) cc_final: 0.7629 (ttp) REVERT: G 9 ASP cc_start: 0.8269 (t0) cc_final: 0.7809 (m-30) REVERT: G 12 TYR cc_start: 0.8357 (t80) cc_final: 0.7928 (t80) REVERT: G 68 PHE cc_start: 0.8124 (t80) cc_final: 0.7815 (t80) REVERT: G 71 ARG cc_start: 0.8575 (mmm160) cc_final: 0.8092 (mmm-85) REVERT: G 77 TRP cc_start: 0.8251 (t60) cc_final: 0.7817 (t60) REVERT: G 94 ASN cc_start: 0.8640 (p0) cc_final: 0.6422 (p0) REVERT: G 97 GLN cc_start: 0.8459 (tt0) cc_final: 0.8121 (mt0) REVERT: G 110 GLN cc_start: 0.7637 (tp-100) cc_final: 0.7214 (tp-100) REVERT: G 111 PHE cc_start: 0.8236 (t80) cc_final: 0.7997 (t80) REVERT: G 121 LEU cc_start: 0.8435 (mt) cc_final: 0.8080 (pp) REVERT: G 122 PHE cc_start: 0.8084 (t80) cc_final: 0.7424 (t80) REVERT: H 11 PHE cc_start: 0.7563 (t80) cc_final: 0.6865 (t80) REVERT: H 102 MET cc_start: 0.8908 (mmm) cc_final: 0.8143 (mmm) REVERT: H 126 ARG cc_start: 0.7274 (ttt-90) cc_final: 0.7053 (ttt-90) REVERT: H 178 TYR cc_start: 0.7082 (m-80) cc_final: 0.6353 (m-10) REVERT: H 191 GLN cc_start: 0.9081 (OUTLIER) cc_final: 0.8859 (pp30) REVERT: H 206 LEU cc_start: 0.9408 (mt) cc_final: 0.8962 (mt) REVERT: H 261 PHE cc_start: 0.7611 (t80) cc_final: 0.7286 (t80) REVERT: I 22 GLU cc_start: 0.8889 (tm-30) cc_final: 0.8249 (tm-30) REVERT: I 23 LYS cc_start: 0.8886 (tppt) cc_final: 0.8518 (tppt) REVERT: I 71 ARG cc_start: 0.8814 (mmm160) cc_final: 0.8566 (mmm160) REVERT: I 77 TRP cc_start: 0.8452 (t60) cc_final: 0.7495 (t60) REVERT: I 81 GLN cc_start: 0.9093 (OUTLIER) cc_final: 0.8564 (mp10) REVERT: I 84 GLU cc_start: 0.8598 (tp30) cc_final: 0.8188 (tp30) REVERT: I 87 GLN cc_start: 0.9122 (tt0) cc_final: 0.8667 (tm-30) REVERT: I 88 ARG cc_start: 0.7856 (ttp80) cc_final: 0.7189 (tmm-80) REVERT: I 96 GLU cc_start: 0.8412 (OUTLIER) cc_final: 0.7996 (pm20) REVERT: I 109 THR cc_start: 0.8133 (m) cc_final: 0.7696 (t) REVERT: I 119 LYS cc_start: 0.9132 (ptmm) cc_final: 0.8713 (ptmm) REVERT: I 123 ASN cc_start: 0.8590 (m110) cc_final: 0.8180 (m110) REVERT: J 18 PHE cc_start: 0.8753 (t80) cc_final: 0.8147 (t80) REVERT: J 52 PHE cc_start: 0.8039 (m-10) cc_final: 0.7680 (m-80) REVERT: J 57 ARG cc_start: 0.8749 (mtm110) cc_final: 0.8386 (mtm-85) REVERT: J 77 TRP cc_start: 0.8047 (t60) cc_final: 0.7781 (t60) REVERT: J 78 GLU cc_start: 0.8921 (tp30) cc_final: 0.8477 (tp30) REVERT: J 85 HIS cc_start: 0.7842 (m170) cc_final: 0.7603 (m170) REVERT: J 91 ASN cc_start: 0.8559 (m-40) cc_final: 0.7991 (m-40) REVERT: J 98 GLN cc_start: 0.8580 (tt0) cc_final: 0.8264 (tp40) REVERT: J 115 LYS cc_start: 0.5358 (mmtt) cc_final: 0.5067 (mmtt) REVERT: J 116 ASP cc_start: 0.7550 (t0) cc_final: 0.7134 (t0) REVERT: J 120 ASN cc_start: 0.8129 (m110) cc_final: 0.7486 (m-40) REVERT: J 123 ASN cc_start: 0.8176 (m-40) cc_final: 0.7911 (m-40) REVERT: K 250 TYR cc_start: 0.7902 (OUTLIER) cc_final: 0.6693 (p90) REVERT: K 281 LEU cc_start: 0.8481 (mp) cc_final: 0.8103 (mp) REVERT: K 309 LYS cc_start: 0.8538 (tppt) cc_final: 0.8296 (ttpp) REVERT: K 526 GLU cc_start: 0.7465 (mm-30) cc_final: 0.6713 (tp30) REVERT: M 55 GLN cc_start: 0.8619 (tt0) cc_final: 0.8389 (tt0) REVERT: M 102 MET cc_start: 0.6240 (mtt) cc_final: 0.6036 (mtt) REVERT: M 130 GLN cc_start: 0.7336 (OUTLIER) cc_final: 0.6996 (tt0) REVERT: M 147 ILE cc_start: 0.9143 (pt) cc_final: 0.8902 (mt) REVERT: M 204 GLN cc_start: 0.8310 (tm-30) cc_final: 0.7973 (tm-30) REVERT: M 221 MET cc_start: 0.8276 (ttt) cc_final: 0.8062 (ttt) REVERT: M 277 LYS cc_start: 0.7822 (mppt) cc_final: 0.7463 (mppt) REVERT: N 26 TYR cc_start: 0.8587 (m-80) cc_final: 0.7737 (m-80) REVERT: N 63 THR cc_start: 0.8926 (t) cc_final: 0.8477 (p) REVERT: N 68 ASN cc_start: 0.8191 (t0) cc_final: 0.7729 (t0) REVERT: N 152 LEU cc_start: 0.8508 (mp) cc_final: 0.8176 (mp) REVERT: L 17 LEU cc_start: 0.9125 (tt) cc_final: 0.8727 (pp) REVERT: L 35 THR cc_start: 0.8596 (t) cc_final: 0.8366 (t) REVERT: L 40 TYR cc_start: 0.8749 (m-10) cc_final: 0.7925 (m-80) REVERT: L 52 PHE cc_start: 0.6341 (m-10) cc_final: 0.5561 (m-10) REVERT: L 76 GLN cc_start: 0.8662 (OUTLIER) cc_final: 0.8265 (mm110) outliers start: 116 outliers final: 62 residues processed: 826 average time/residue: 0.4069 time to fit residues: 533.1917 Evaluate side-chains 749 residues out of total 2762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 676 time to evaluate : 4.541 ------------------------------------------------------------------------------- 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 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 146 SER Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 203 TRP Chi-restraints excluded: chain E residue 221 MET Chi-restraints excluded: chain F residue 21 ASN Chi-restraints excluded: chain F residue 32 ILE Chi-restraints excluded: chain F residue 40 LEU Chi-restraints excluded: chain F residue 67 ILE Chi-restraints excluded: chain F residue 124 GLN Chi-restraints excluded: chain 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 120 ASN Chi-restraints excluded: chain G residue 124 GLU 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 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 25 GLN Chi-restraints excluded: chain I residue 81 GLN Chi-restraints excluded: chain I residue 96 GLU 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 383 ASN 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 125 VAL Chi-restraints excluded: chain M residue 130 GLN Chi-restraints excluded: chain M residue 166 THR Chi-restraints excluded: chain M residue 209 MET Chi-restraints excluded: chain M residue 272 ASN Chi-restraints excluded: chain M residue 276 THR Chi-restraints excluded: chain N residue 21 VAL Chi-restraints excluded: chain N residue 30 THR Chi-restraints excluded: chain N residue 37 ILE Chi-restraints excluded: chain N residue 70 VAL Chi-restraints excluded: chain N residue 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 24 optimal weight: 0.8980 chunk 262 optimal weight: 1.9990 chunk 273 optimal weight: 0.2980 chunk 73 optimal weight: 1.9990 chunk 44 optimal weight: 0.6980 chunk 148 optimal weight: 5.9990 chunk 317 optimal weight: 8.9990 chunk 146 optimal weight: 7.9990 chunk 33 optimal weight: 2.9990 chunk 119 optimal weight: 0.8980 chunk 277 optimal weight: 2.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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** ** C 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 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** G 120 ASN H 55 GLN ** 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** L 98 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.156206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.122392 restraints weight = 46737.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.126950 restraints weight = 20998.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 61)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.129865 restraints weight = 12258.960| |-----------------------------------------------------------------------------| r_work (final): 0.3912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.4027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 27430 Z= 0.218 Angle : 0.804 10.659 37194 Z= 0.417 Chirality : 0.050 0.512 4023 Planarity : 0.006 0.074 4752 Dihedral : 14.477 171.606 4190 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 30.50 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.30 % Favored : 90.67 % Rotamer: Outliers : 4.78 % Allowed : 21.27 % Favored : 73.95 % 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: -2.42 (0.14), residues: 3184 helix: -0.57 (0.14), residues: 1274 sheet: -2.72 (0.24), residues: 369 loop : -2.20 (0.14), residues: 1541 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 182 HIS 0.027 0.002 HIS C 214 PHE 0.032 0.003 PHE G 111 TYR 0.038 0.003 TYR J 106 ARG 0.015 0.001 ARG C 280 Details of bonding type rmsd hydrogen bonds : bond 0.04751 ( 1148) hydrogen bonds : angle 6.67061 ( 3315) covalent geometry : bond 0.00495 (27430) covalent geometry : angle 0.80363 (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 874 residues out of total 2762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 742 time to evaluate : 3.208 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 ASN cc_start: 0.8159 (t0) cc_final: 0.7431 (t0) REVERT: A 155 TYR cc_start: 0.8484 (m-80) cc_final: 0.8115 (m-80) REVERT: A 164 GLU cc_start: 0.8373 (tp30) cc_final: 0.7939 (tp30) REVERT: A 165 TRP cc_start: 0.8541 (m-10) cc_final: 0.8190 (m100) REVERT: A 167 GLN cc_start: 0.8509 (tm-30) cc_final: 0.7621 (tm-30) REVERT: A 168 TYR cc_start: 0.7477 (m-80) cc_final: 0.7092 (m-80) REVERT: B 8 ASP cc_start: 0.7735 (t70) cc_final: 0.7527 (t0) REVERT: B 78 ASP cc_start: 0.7236 (m-30) cc_final: 0.6985 (m-30) REVERT: B 83 GLN cc_start: 0.8720 (mm-40) cc_final: 0.8490 (mm-40) REVERT: B 141 MET cc_start: 0.6889 (mmt) cc_final: 0.6481 (mmt) REVERT: B 171 PHE cc_start: 0.8414 (m-80) cc_final: 0.8205 (m-80) REVERT: B 175 TYR cc_start: 0.8514 (t80) cc_final: 0.8093 (t80) REVERT: B 183 PHE cc_start: 0.8227 (m-80) cc_final: 0.7960 (m-10) REVERT: B 201 LEU cc_start: 0.8213 (OUTLIER) cc_final: 0.7911 (mm) REVERT: C 48 ARG cc_start: 0.7690 (tpt90) cc_final: 0.7407 (tpt90) REVERT: C 67 ILE cc_start: 0.8440 (OUTLIER) cc_final: 0.7885 (mm) REVERT: C 103 CYS cc_start: 0.8327 (m) cc_final: 0.7959 (m) REVERT: C 110 ARG cc_start: 0.7473 (ptm160) cc_final: 0.7102 (ptm160) REVERT: C 146 SER cc_start: 0.8287 (t) cc_final: 0.7976 (t) REVERT: C 147 ILE cc_start: 0.8207 (mt) cc_final: 0.7883 (mm) REVERT: C 220 GLN cc_start: 0.7803 (tm-30) cc_final: 0.6364 (tm-30) REVERT: C 226 LEU cc_start: 0.8104 (tp) cc_final: 0.7818 (tp) REVERT: C 243 LEU cc_start: 0.7946 (OUTLIER) cc_final: 0.7578 (mt) REVERT: C 256 GLU cc_start: 0.7584 (tm-30) cc_final: 0.7148 (tm-30) REVERT: D 35 GLN cc_start: 0.8449 (mm-40) cc_final: 0.7988 (tp40) REVERT: D 36 THR cc_start: 0.8056 (OUTLIER) cc_final: 0.7707 (p) REVERT: D 46 LEU cc_start: 0.7961 (tt) cc_final: 0.7743 (tp) REVERT: D 116 MET cc_start: 0.8549 (mmm) cc_final: 0.8334 (mmm) REVERT: D 134 SER cc_start: 0.8064 (p) cc_final: 0.7835 (t) REVERT: D 141 MET cc_start: 0.8273 (mtp) cc_final: 0.8053 (mtp) REVERT: D 150 MET cc_start: 0.5327 (ptm) cc_final: 0.4872 (ppp) REVERT: D 244 PHE cc_start: 0.8927 (m-10) cc_final: 0.8421 (m-10) REVERT: E 79 GLU cc_start: 0.7815 (tm-30) cc_final: 0.7286 (tm-30) REVERT: E 167 MET cc_start: 0.8749 (mtm) cc_final: 0.8511 (mtp) REVERT: E 184 ILE cc_start: 0.8750 (OUTLIER) cc_final: 0.8461 (mm) REVERT: E 233 ASN cc_start: 0.8192 (m-40) cc_final: 0.7839 (m-40) REVERT: E 241 ASP cc_start: 0.7184 (t70) cc_final: 0.6866 (t0) REVERT: F 25 ASP cc_start: 0.7534 (OUTLIER) cc_final: 0.6610 (t0) REVERT: F 40 LEU cc_start: 0.8192 (OUTLIER) cc_final: 0.7839 (mp) REVERT: F 72 ILE cc_start: 0.8132 (mm) cc_final: 0.7779 (mm) REVERT: F 116 MET cc_start: 0.8464 (tpp) cc_final: 0.8255 (tpt) REVERT: F 172 THR cc_start: 0.7675 (m) cc_final: 0.7411 (m) REVERT: G 9 ASP cc_start: 0.8206 (t0) cc_final: 0.7945 (m-30) REVERT: G 68 PHE cc_start: 0.8180 (t80) cc_final: 0.7816 (t80) REVERT: G 71 ARG cc_start: 0.8556 (mmm160) cc_final: 0.8047 (mmm-85) REVERT: G 77 TRP cc_start: 0.8234 (t60) cc_final: 0.7962 (t60) REVERT: G 94 ASN cc_start: 0.8603 (p0) cc_final: 0.8319 (p0) REVERT: G 97 GLN cc_start: 0.8571 (tt0) cc_final: 0.8234 (tp40) REVERT: G 110 GLN cc_start: 0.7556 (tp-100) cc_final: 0.7265 (tp-100) REVERT: G 111 PHE cc_start: 0.8209 (t80) cc_final: 0.7842 (t80) REVERT: G 121 LEU cc_start: 0.8399 (mt) cc_final: 0.8144 (pp) REVERT: G 122 PHE cc_start: 0.8036 (t80) cc_final: 0.7431 (t80) REVERT: H 11 PHE cc_start: 0.7480 (t80) cc_final: 0.6823 (t80) REVERT: H 81 HIS cc_start: 0.8611 (OUTLIER) cc_final: 0.7856 (t-90) REVERT: H 102 MET cc_start: 0.8935 (mmm) cc_final: 0.8202 (mmm) REVERT: H 126 ARG cc_start: 0.7247 (ttt-90) cc_final: 0.6973 (ttt-90) REVERT: H 178 TYR cc_start: 0.6933 (m-80) cc_final: 0.6300 (m-10) REVERT: H 191 GLN cc_start: 0.9036 (OUTLIER) cc_final: 0.8745 (pp30) REVERT: H 206 LEU cc_start: 0.9400 (mt) cc_final: 0.8977 (mt) REVERT: H 208 ASN cc_start: 0.8666 (m110) cc_final: 0.7517 (t0) REVERT: H 261 PHE cc_start: 0.7652 (t80) cc_final: 0.7337 (t80) REVERT: H 272 ASN cc_start: 0.8558 (t0) cc_final: 0.8356 (t0) REVERT: I 22 GLU cc_start: 0.8738 (tm-30) cc_final: 0.8056 (tm-30) REVERT: I 56 MET cc_start: 0.8744 (mmm) cc_final: 0.8480 (mmm) REVERT: I 77 TRP cc_start: 0.8438 (t60) cc_final: 0.7532 (t60) REVERT: I 81 GLN cc_start: 0.8993 (OUTLIER) cc_final: 0.8530 (mp10) REVERT: I 84 GLU cc_start: 0.8558 (tp30) cc_final: 0.8145 (tp30) REVERT: I 87 GLN cc_start: 0.9096 (tt0) cc_final: 0.8568 (tm-30) REVERT: I 96 GLU cc_start: 0.8454 (OUTLIER) cc_final: 0.7925 (pm20) REVERT: I 109 THR cc_start: 0.8188 (m) cc_final: 0.7429 (p) REVERT: I 113 PHE cc_start: 0.7905 (m-10) cc_final: 0.7485 (m-10) REVERT: I 119 LYS cc_start: 0.9230 (ptmm) cc_final: 0.8872 (ptmm) REVERT: I 123 ASN cc_start: 0.8607 (m110) cc_final: 0.8189 (m110) REVERT: J 18 PHE cc_start: 0.8751 (t80) cc_final: 0.8230 (t80) REVERT: J 52 PHE cc_start: 0.8055 (m-10) cc_final: 0.7667 (m-80) REVERT: J 57 ARG cc_start: 0.8776 (mtm110) cc_final: 0.8426 (mtm-85) REVERT: J 78 GLU cc_start: 0.8930 (tp30) cc_final: 0.8424 (tp30) REVERT: J 80 ARG cc_start: 0.8382 (mtm-85) cc_final: 0.8090 (mtm-85) REVERT: J 91 ASN cc_start: 0.8592 (m-40) cc_final: 0.8087 (m-40) REVERT: J 98 GLN cc_start: 0.8537 (tt0) cc_final: 0.8231 (tp40) REVERT: J 116 ASP cc_start: 0.7220 (t0) cc_final: 0.6754 (t0) REVERT: J 120 ASN cc_start: 0.8172 (m110) cc_final: 0.7436 (m-40) REVERT: J 123 ASN cc_start: 0.8536 (m-40) cc_final: 0.8293 (m-40) REVERT: K 12 ARG cc_start: 0.8168 (mmp80) cc_final: 0.7841 (mmp80) REVERT: K 250 TYR cc_start: 0.7935 (OUTLIER) cc_final: 0.6421 (p90) REVERT: K 309 LYS cc_start: 0.8430 (tppt) cc_final: 0.8152 (ttpp) REVERT: K 436 LEU cc_start: 0.8955 (tp) cc_final: 0.8656 (tp) REVERT: K 526 GLU cc_start: 0.7412 (mm-30) cc_final: 0.6669 (tp30) REVERT: M 16 GLN cc_start: 0.7244 (mm-40) cc_final: 0.7013 (tp40) REVERT: M 54 ILE cc_start: 0.8999 (mm) cc_final: 0.8786 (mm) REVERT: M 130 GLN cc_start: 0.7523 (OUTLIER) cc_final: 0.7264 (tt0) REVERT: M 204 GLN cc_start: 0.8339 (tm-30) cc_final: 0.7958 (tm-30) REVERT: M 277 LYS cc_start: 0.7797 (mppt) cc_final: 0.7454 (mppt) REVERT: N 23 ARG cc_start: 0.7637 (OUTLIER) cc_final: 0.7339 (mtt90) REVERT: N 66 ARG cc_start: 0.8023 (mtp180) cc_final: 0.7807 (mtp85) REVERT: N 68 ASN cc_start: 0.8045 (t0) cc_final: 0.7490 (t0) REVERT: N 116 ASP cc_start: 0.6897 (p0) cc_final: 0.6649 (p0) REVERT: N 152 LEU cc_start: 0.8553 (mp) cc_final: 0.8305 (mp) REVERT: N 166 GLN cc_start: 0.8166 (pt0) cc_final: 0.7865 (pm20) REVERT: N 175 MET cc_start: 0.6536 (ttp) cc_final: 0.6299 (ttp) REVERT: L 17 LEU cc_start: 0.9033 (tt) cc_final: 0.8658 (pp) REVERT: L 40 TYR cc_start: 0.8614 (m-10) cc_final: 0.8308 (m-80) REVERT: L 52 PHE cc_start: 0.6362 (m-10) cc_final: 0.5682 (m-10) REVERT: L 76 GLN cc_start: 0.8637 (OUTLIER) cc_final: 0.8310 (mm110) REVERT: L 81 GLN cc_start: 0.8449 (OUTLIER) cc_final: 0.8211 (mm-40) outliers start: 132 outliers final: 74 residues processed: 808 average time/residue: 0.4958 time to fit residues: 627.5490 Evaluate side-chains 782 residues out of total 2762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 692 time to evaluate : 2.965 ------------------------------------------------------------------------------- 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 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 228 VAL Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 250 VAL 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 69 GLU Chi-restraints excluded: chain D residue 260 SER Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain E residue 125 VAL Chi-restraints excluded: chain E residue 134 SER 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 207 VAL Chi-restraints excluded: chain F residue 21 ASN Chi-restraints excluded: chain F residue 25 ASP Chi-restraints excluded: chain F residue 32 ILE Chi-restraints excluded: chain F residue 40 LEU Chi-restraints excluded: chain F residue 118 THR Chi-restraints excluded: chain F residue 124 GLN 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 120 ASN Chi-restraints excluded: chain G residue 124 GLU Chi-restraints excluded: chain H residue 81 HIS Chi-restraints excluded: chain H residue 132 THR Chi-restraints excluded: chain H residue 187 HIS Chi-restraints excluded: chain H residue 191 GLN Chi-restraints excluded: chain H residue 212 HIS Chi-restraints excluded: chain H residue 228 VAL Chi-restraints excluded: chain H residue 229 PHE Chi-restraints excluded: chain H residue 253 ASP Chi-restraints excluded: chain H residue 266 VAL 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 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 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 381 LEU 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 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 180 CYS Chi-restraints excluded: chain M residue 209 MET Chi-restraints excluded: chain M residue 272 ASN Chi-restraints excluded: chain M residue 276 THR Chi-restraints excluded: chain N residue 21 VAL Chi-restraints excluded: chain N residue 23 ARG 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 303 optimal weight: 0.4980 chunk 142 optimal weight: 0.0670 chunk 87 optimal weight: 0.9980 chunk 130 optimal weight: 3.9990 chunk 167 optimal weight: 5.9990 chunk 140 optimal weight: 0.9990 chunk 249 optimal weight: 0.7980 chunk 96 optimal weight: 4.9990 chunk 74 optimal weight: 2.9990 chunk 206 optimal weight: 20.0000 chunk 91 optimal weight: 0.5980 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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 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** D 83 GLN ** E 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** H 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 62 HIS ** 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 ** 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** ** L 74 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 = 0.4144 r_free = 0.4144 target = 0.154326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.117230 restraints weight = 47679.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.121746 restraints weight = 21273.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.124518 restraints weight = 12459.724| |-----------------------------------------------------------------------------| r_work (final): 0.3960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.4406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 27430 Z= 0.193 Angle : 0.805 15.029 37194 Z= 0.416 Chirality : 0.050 0.431 4023 Planarity : 0.005 0.081 4752 Dihedral : 14.385 169.480 4190 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 29.05 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.11 % Favored : 90.86 % Rotamer: Outliers : 4.64 % Allowed : 22.39 % Favored : 72.97 % 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: -2.34 (0.14), residues: 3184 helix: -0.52 (0.14), residues: 1274 sheet: -2.73 (0.24), residues: 390 loop : -2.11 (0.15), residues: 1520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP I 77 HIS 0.025 0.002 HIS C 214 PHE 0.039 0.002 PHE M 112 TYR 0.038 0.002 TYR J 106 ARG 0.012 0.001 ARG F 218 Details of bonding type rmsd hydrogen bonds : bond 0.04681 ( 1148) hydrogen bonds : angle 6.59013 ( 3315) covalent geometry : bond 0.00441 (27430) covalent geometry : angle 0.80507 (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 879 residues out of total 2762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 751 time to evaluate : 2.849 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 ASN cc_start: 0.7956 (t0) cc_final: 0.7513 (t0) REVERT: A 133 TRP cc_start: 0.7299 (t-100) cc_final: 0.6721 (t-100) REVERT: A 155 TYR cc_start: 0.8378 (m-80) cc_final: 0.8060 (m-80) REVERT: A 164 GLU cc_start: 0.8226 (tp30) cc_final: 0.7927 (tp30) REVERT: A 167 GLN cc_start: 0.8552 (tm-30) cc_final: 0.8002 (tm-30) REVERT: B 141 MET cc_start: 0.6523 (mmt) cc_final: 0.6261 (mmt) REVERT: B 201 LEU cc_start: 0.8338 (OUTLIER) cc_final: 0.8016 (mm) REVERT: C 67 ILE cc_start: 0.8368 (OUTLIER) cc_final: 0.7837 (mm) REVERT: C 103 CYS cc_start: 0.8022 (m) cc_final: 0.7808 (m) REVERT: C 110 ARG cc_start: 0.7393 (ptm160) cc_final: 0.7075 (ptm160) REVERT: C 147 ILE cc_start: 0.8263 (mt) cc_final: 0.8015 (mm) REVERT: C 243 LEU cc_start: 0.7763 (OUTLIER) cc_final: 0.7450 (mt) REVERT: C 256 GLU cc_start: 0.7250 (tm-30) cc_final: 0.6890 (tm-30) REVERT: C 271 LYS cc_start: 0.8431 (mmmt) cc_final: 0.8135 (mmmt) REVERT: D 21 ASN cc_start: 0.7375 (t0) cc_final: 0.7107 (t0) REVERT: D 35 GLN cc_start: 0.8383 (mm-40) cc_final: 0.7986 (tp40) REVERT: D 36 THR cc_start: 0.7885 (OUTLIER) cc_final: 0.7614 (p) REVERT: D 134 SER cc_start: 0.7722 (p) cc_final: 0.7026 (t) REVERT: D 227 TYR cc_start: 0.8333 (m-80) cc_final: 0.8100 (m-80) REVERT: E 79 GLU cc_start: 0.7847 (tm-30) cc_final: 0.7593 (tm-30) REVERT: E 167 MET cc_start: 0.8607 (mtm) cc_final: 0.8336 (mtp) REVERT: E 169 ARG cc_start: 0.8253 (mtp85) cc_final: 0.7943 (mtp-110) REVERT: E 184 ILE cc_start: 0.8545 (OUTLIER) cc_final: 0.8165 (mm) REVERT: E 233 ASN cc_start: 0.8009 (m-40) cc_final: 0.7764 (m-40) REVERT: E 241 ASP cc_start: 0.7107 (t70) cc_final: 0.6789 (t0) REVERT: F 25 ASP cc_start: 0.7549 (OUTLIER) cc_final: 0.6638 (t0) REVERT: F 72 ILE cc_start: 0.8158 (mm) cc_final: 0.7841 (mm) REVERT: F 172 THR cc_start: 0.7769 (m) cc_final: 0.7512 (m) REVERT: G 9 ASP cc_start: 0.7939 (t0) cc_final: 0.7694 (m-30) REVERT: G 68 PHE cc_start: 0.8087 (t80) cc_final: 0.7744 (t80) REVERT: G 71 ARG cc_start: 0.8764 (mmm160) cc_final: 0.8221 (mmm-85) REVERT: G 94 ASN cc_start: 0.8616 (p0) cc_final: 0.7991 (p0) REVERT: G 106 TYR cc_start: 0.8332 (m-80) cc_final: 0.7904 (m-80) REVERT: G 110 GLN cc_start: 0.7752 (tp-100) cc_final: 0.7420 (tp-100) REVERT: G 121 LEU cc_start: 0.8394 (mt) cc_final: 0.8087 (pp) REVERT: G 122 PHE cc_start: 0.8166 (t80) cc_final: 0.7618 (t80) REVERT: H 8 ASP cc_start: 0.6764 (p0) cc_final: 0.6234 (p0) REVERT: H 81 HIS cc_start: 0.8647 (OUTLIER) cc_final: 0.8007 (t-90) REVERT: H 102 MET cc_start: 0.8966 (mmm) cc_final: 0.8314 (mmm) REVERT: H 126 ARG cc_start: 0.7494 (ttt-90) cc_final: 0.6785 (tmt170) REVERT: H 178 TYR cc_start: 0.6751 (m-80) cc_final: 0.6297 (m-10) REVERT: H 190 LYS cc_start: 0.8677 (mttm) cc_final: 0.8358 (mttp) REVERT: H 191 GLN cc_start: 0.8819 (OUTLIER) cc_final: 0.8617 (pp30) REVERT: H 206 LEU cc_start: 0.9352 (mt) cc_final: 0.8823 (tt) REVERT: H 208 ASN cc_start: 0.8691 (m110) cc_final: 0.7656 (t0) REVERT: H 261 PHE cc_start: 0.7743 (t80) cc_final: 0.7472 (t80) REVERT: H 272 ASN cc_start: 0.8449 (t0) cc_final: 0.8129 (t0) REVERT: I 18 PHE cc_start: 0.8773 (t80) cc_final: 0.8535 (t80) REVERT: I 21 LEU cc_start: 0.8782 (mp) cc_final: 0.8517 (mp) REVERT: I 22 GLU cc_start: 0.8738 (tm-30) cc_final: 0.8216 (tm-30) REVERT: I 56 MET cc_start: 0.8726 (mmm) cc_final: 0.8433 (mmm) REVERT: I 74 GLN cc_start: 0.8721 (pt0) cc_final: 0.7753 (mt0) REVERT: I 77 TRP cc_start: 0.8377 (t60) cc_final: 0.7601 (t60) REVERT: I 80 ARG cc_start: 0.8215 (mtp180) cc_final: 0.7852 (mtp-110) REVERT: I 81 GLN cc_start: 0.8945 (OUTLIER) cc_final: 0.8401 (mp10) REVERT: I 84 GLU cc_start: 0.8524 (tp30) cc_final: 0.8105 (tp30) REVERT: I 87 GLN cc_start: 0.8993 (tt0) cc_final: 0.8437 (tm-30) REVERT: I 91 ASN cc_start: 0.8768 (t0) cc_final: 0.8275 (t0) REVERT: I 96 GLU cc_start: 0.8478 (OUTLIER) cc_final: 0.7867 (pm20) REVERT: I 109 THR cc_start: 0.8119 (m) cc_final: 0.7396 (p) REVERT: I 110 GLN cc_start: 0.8157 (tp40) cc_final: 0.7756 (tp40) REVERT: I 113 PHE cc_start: 0.7360 (m-10) cc_final: 0.7015 (m-10) REVERT: I 119 LYS cc_start: 0.9204 (ptmm) cc_final: 0.8639 (ptmm) REVERT: I 123 ASN cc_start: 0.8662 (m110) cc_final: 0.8234 (m110) REVERT: J 8 GLN cc_start: 0.8033 (tp-100) cc_final: 0.7775 (tp-100) REVERT: J 18 PHE cc_start: 0.8782 (t80) cc_final: 0.8242 (t80) REVERT: J 57 ARG cc_start: 0.8751 (mtm110) cc_final: 0.8431 (mtm-85) REVERT: J 62 HIS cc_start: 0.8137 (m90) cc_final: 0.7701 (m-70) REVERT: J 77 TRP cc_start: 0.8115 (t60) cc_final: 0.7831 (t60) REVERT: J 78 GLU cc_start: 0.8793 (tp30) cc_final: 0.8360 (tp30) REVERT: J 85 HIS cc_start: 0.8166 (m170) cc_final: 0.7790 (m170) REVERT: J 91 ASN cc_start: 0.8495 (m-40) cc_final: 0.8034 (m-40) REVERT: J 108 GLU cc_start: 0.7972 (mt-10) cc_final: 0.7742 (mt-10) REVERT: J 116 ASP cc_start: 0.7006 (t0) cc_final: 0.6648 (t0) REVERT: J 123 ASN cc_start: 0.8592 (m-40) cc_final: 0.8382 (m-40) REVERT: K 46 GLU cc_start: 0.8622 (tm-30) cc_final: 0.8347 (tm-30) REVERT: K 59 ARG cc_start: 0.8814 (mpp80) cc_final: 0.8524 (mpp80) REVERT: K 250 TYR cc_start: 0.7818 (OUTLIER) cc_final: 0.6510 (p90) REVERT: K 295 ASP cc_start: 0.8472 (t0) cc_final: 0.8135 (t0) REVERT: K 309 LYS cc_start: 0.8346 (tppt) cc_final: 0.8014 (ttpp) REVERT: K 436 LEU cc_start: 0.8980 (tp) cc_final: 0.8726 (tp) REVERT: M 16 GLN cc_start: 0.7301 (mm-40) cc_final: 0.7002 (tp40) REVERT: M 54 ILE cc_start: 0.8935 (mm) cc_final: 0.8697 (mm) REVERT: M 198 ASP cc_start: 0.7524 (m-30) cc_final: 0.7289 (m-30) REVERT: M 204 GLN cc_start: 0.8178 (tm-30) cc_final: 0.7760 (tm-30) REVERT: M 259 ARG cc_start: 0.7213 (mtm110) cc_final: 0.6882 (mtm110) REVERT: M 277 LYS cc_start: 0.7697 (mppt) cc_final: 0.7441 (mppt) REVERT: N 7 ILE cc_start: 0.8220 (mp) cc_final: 0.7802 (mm) REVERT: N 66 ARG cc_start: 0.7811 (mtp180) cc_final: 0.7508 (mtp85) REVERT: N 68 ASN cc_start: 0.8050 (t0) cc_final: 0.7618 (t0) REVERT: N 76 GLU cc_start: 0.6971 (mm-30) cc_final: 0.5742 (mm-30) REVERT: N 152 LEU cc_start: 0.8372 (mp) cc_final: 0.8159 (mp) REVERT: L 17 LEU cc_start: 0.9087 (tt) cc_final: 0.8717 (pp) REVERT: L 25 GLN cc_start: 0.8392 (OUTLIER) cc_final: 0.8117 (tt0) REVERT: L 40 TYR cc_start: 0.8604 (m-10) cc_final: 0.8277 (m-80) REVERT: L 52 PHE cc_start: 0.6224 (m-10) cc_final: 0.5397 (m-10) REVERT: L 76 GLN cc_start: 0.8652 (OUTLIER) cc_final: 0.8400 (mm110) outliers start: 128 outliers final: 69 residues processed: 825 average time/residue: 0.3917 time to fit residues: 506.9204 Evaluate side-chains 780 residues out of total 2762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 698 time to evaluate : 3.005 ------------------------------------------------------------------------------- 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 118 THR Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 32 ILE Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 109 ILE Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 133 PHE 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 C residue 279 LEU 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 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 184 ILE Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 259 ARG Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 21 ASN Chi-restraints excluded: chain F residue 25 ASP Chi-restraints excluded: chain F residue 32 ILE Chi-restraints excluded: chain F residue 67 ILE Chi-restraints excluded: chain G residue 10 ILE Chi-restraints excluded: chain G residue 17 LEU Chi-restraints excluded: chain G residue 49 ILE Chi-restraints excluded: chain G residue 81 GLN Chi-restraints excluded: chain G residue 88 ARG Chi-restraints excluded: chain G residue 95 LEU Chi-restraints excluded: chain H residue 81 HIS Chi-restraints excluded: chain H residue 100 GLN 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 58 LEU Chi-restraints excluded: chain K residue 91 TYR Chi-restraints excluded: chain K residue 250 TYR Chi-restraints excluded: chain K residue 269 VAL Chi-restraints excluded: chain K residue 306 THR Chi-restraints excluded: chain K residue 330 LEU Chi-restraints excluded: chain K residue 381 LEU Chi-restraints excluded: chain K residue 430 THR Chi-restraints excluded: chain M residue 42 THR Chi-restraints excluded: chain M residue 137 ILE Chi-restraints excluded: chain M residue 166 THR 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 25 GLN 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 81 optimal weight: 0.9980 chunk 278 optimal weight: 0.6980 chunk 128 optimal weight: 0.9990 chunk 142 optimal weight: 10.0000 chunk 76 optimal weight: 0.9980 chunk 45 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 3 optimal weight: 0.7980 chunk 247 optimal weight: 0.8980 chunk 194 optimal weight: 1.9990 chunk 258 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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** ** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 214 HIS ** 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** ** 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** ** H 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 97 GLN ** J 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 74 GLN 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 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** ** L 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 98 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.158990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.125323 restraints weight = 47130.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.129958 restraints weight = 21240.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 61)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.132896 restraints weight = 12320.227| |-----------------------------------------------------------------------------| r_work (final): 0.3962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.4700 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= 0.212 Angle : 0.810 12.324 37194 Z= 0.420 Chirality : 0.050 0.456 4023 Planarity : 0.005 0.073 4752 Dihedral : 14.342 168.917 4190 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 29.74 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.30 % Favored : 90.64 % Rotamer: Outliers : 3.95 % Allowed : 24.09 % Favored : 71.96 % 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: -2.30 (0.14), residues: 3184 helix: -0.49 (0.14), residues: 1283 sheet: -2.63 (0.25), residues: 380 loop : -2.13 (0.15), residues: 1521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP A 165 HIS 0.025 0.002 HIS C 214 PHE 0.043 0.002 PHE H 183 TYR 0.043 0.003 TYR A 125 ARG 0.008 0.001 ARG B 224 Details of bonding type rmsd hydrogen bonds : bond 0.04569 ( 1148) hydrogen bonds : angle 6.57419 ( 3315) covalent geometry : bond 0.00488 (27430) covalent geometry : angle 0.80967 (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 849 residues out of total 2762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 740 time to evaluate : 3.420 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: A 119 PHE cc_start: 0.7931 (OUTLIER) cc_final: 0.6230 (t80) REVERT: A 126 ASN cc_start: 0.8026 (t0) cc_final: 0.7599 (t0) REVERT: A 133 TRP cc_start: 0.7516 (t-100) cc_final: 0.7179 (t-100) REVERT: A 153 ASN cc_start: 0.7140 (m-40) cc_final: 0.6867 (m-40) REVERT: A 155 TYR cc_start: 0.8402 (m-80) cc_final: 0.8038 (m-80) REVERT: A 164 GLU cc_start: 0.8366 (tp30) cc_final: 0.7905 (tp30) REVERT: A 165 TRP cc_start: 0.8678 (m-10) cc_final: 0.7734 (m100) REVERT: A 167 GLN cc_start: 0.8817 (tm-30) cc_final: 0.7863 (tm-30) REVERT: A 168 TYR cc_start: 0.7424 (m-80) cc_final: 0.7088 (m-10) REVERT: A 169 GLU cc_start: 0.7746 (tt0) cc_final: 0.7478 (tp30) REVERT: A 179 GLU cc_start: 0.7828 (tm-30) cc_final: 0.7148 (tt0) REVERT: B 141 MET cc_start: 0.6515 (mmt) cc_final: 0.6282 (mmt) REVERT: B 175 TYR cc_start: 0.8310 (t80) cc_final: 0.7995 (t80) REVERT: B 183 PHE cc_start: 0.7854 (m-80) cc_final: 0.7604 (m-10) REVERT: B 259 ARG cc_start: 0.7710 (mtm110) cc_final: 0.7385 (mtp180) REVERT: C 11 PHE cc_start: 0.7768 (t80) cc_final: 0.7523 (t80) REVERT: C 48 ARG cc_start: 0.7639 (tpt90) cc_final: 0.7397 (tpt90) REVERT: C 67 ILE cc_start: 0.8421 (OUTLIER) cc_final: 0.7813 (mm) REVERT: C 91 LYS cc_start: 0.8742 (pptt) cc_final: 0.8420 (ttmt) REVERT: C 103 CYS cc_start: 0.8189 (m) cc_final: 0.7866 (m) REVERT: C 110 ARG cc_start: 0.7403 (ptm160) cc_final: 0.7062 (ptm160) REVERT: C 256 GLU cc_start: 0.7370 (tm-30) cc_final: 0.6983 (tm-30) REVERT: C 271 LYS cc_start: 0.8483 (mmmt) cc_final: 0.8162 (mmtm) REVERT: D 21 ASN cc_start: 0.7451 (t0) cc_final: 0.7131 (t0) REVERT: D 35 GLN cc_start: 0.8524 (mm-40) cc_final: 0.8054 (tp40) REVERT: D 36 THR cc_start: 0.7960 (OUTLIER) cc_final: 0.7640 (p) REVERT: D 54 ILE cc_start: 0.8409 (mm) cc_final: 0.7788 (pt) REVERT: D 245 LYS cc_start: 0.8167 (mmtp) cc_final: 0.7835 (mmtp) REVERT: E 79 GLU cc_start: 0.7851 (tm-30) cc_final: 0.7525 (tm-30) REVERT: E 141 MET cc_start: 0.7514 (tpp) cc_final: 0.6921 (tpp) REVERT: E 169 ARG cc_start: 0.8344 (mtp85) cc_final: 0.7912 (mtp-110) REVERT: E 184 ILE cc_start: 0.8646 (OUTLIER) cc_final: 0.8269 (mm) REVERT: E 233 ASN cc_start: 0.7999 (m-40) cc_final: 0.7751 (m-40) REVERT: E 241 ASP cc_start: 0.7146 (t70) cc_final: 0.6799 (t0) REVERT: F 25 ASP cc_start: 0.7112 (OUTLIER) cc_final: 0.6215 (t0) REVERT: F 72 ILE cc_start: 0.8132 (mm) cc_final: 0.7783 (mm) REVERT: F 172 THR cc_start: 0.7656 (m) cc_final: 0.7362 (m) REVERT: G 68 PHE cc_start: 0.8128 (t80) cc_final: 0.7755 (t80) REVERT: G 71 ARG cc_start: 0.8727 (mmm160) cc_final: 0.8494 (mtp85) REVERT: G 94 ASN cc_start: 0.8672 (p0) cc_final: 0.8274 (p0) REVERT: G 97 GLN cc_start: 0.8421 (tp40) cc_final: 0.8207 (tp40) REVERT: G 106 TYR cc_start: 0.8349 (m-80) cc_final: 0.7895 (m-80) REVERT: G 108 GLU cc_start: 0.8398 (mm-30) cc_final: 0.8189 (mt-10) REVERT: G 122 PHE cc_start: 0.8123 (t80) cc_final: 0.7652 (t80) REVERT: H 8 ASP cc_start: 0.6394 (p0) cc_final: 0.5111 (p0) REVERT: H 81 HIS cc_start: 0.8768 (OUTLIER) cc_final: 0.8043 (t-90) REVERT: H 102 MET cc_start: 0.9035 (mmm) cc_final: 0.8492 (mmm) REVERT: H 178 TYR cc_start: 0.6815 (m-80) cc_final: 0.6395 (m-10) REVERT: H 190 LYS cc_start: 0.8674 (mttm) cc_final: 0.8366 (mttp) REVERT: H 191 GLN cc_start: 0.8880 (OUTLIER) cc_final: 0.8658 (pp30) REVERT: H 208 ASN cc_start: 0.8678 (m110) cc_final: 0.7598 (t0) REVERT: H 261 PHE cc_start: 0.7802 (t80) cc_final: 0.7516 (t80) REVERT: I 18 PHE cc_start: 0.8730 (t80) cc_final: 0.8431 (t80) REVERT: I 22 GLU cc_start: 0.8730 (tm-30) cc_final: 0.8200 (tm-30) REVERT: I 56 MET cc_start: 0.8584 (mmm) cc_final: 0.8353 (mmm) REVERT: I 74 GLN cc_start: 0.8673 (pt0) cc_final: 0.7752 (mt0) REVERT: I 77 TRP cc_start: 0.8291 (t60) cc_final: 0.7046 (t60) REVERT: I 80 ARG cc_start: 0.8279 (mtp180) cc_final: 0.7149 (mtm-85) REVERT: I 81 GLN cc_start: 0.8841 (OUTLIER) cc_final: 0.8230 (mp10) REVERT: I 84 GLU cc_start: 0.8638 (tp30) cc_final: 0.8148 (tp30) REVERT: I 87 GLN cc_start: 0.9048 (tt0) cc_final: 0.8437 (tm-30) REVERT: I 91 ASN cc_start: 0.8830 (t0) cc_final: 0.8283 (t0) REVERT: I 96 GLU cc_start: 0.8530 (OUTLIER) cc_final: 0.7850 (pm20) REVERT: I 109 THR cc_start: 0.8142 (m) cc_final: 0.7396 (p) REVERT: I 110 GLN cc_start: 0.8028 (tp40) cc_final: 0.7725 (tp40) REVERT: I 119 LYS cc_start: 0.9189 (ptmm) cc_final: 0.8642 (ptmm) REVERT: I 123 ASN cc_start: 0.8738 (m110) cc_final: 0.8315 (m110) REVERT: J 8 GLN cc_start: 0.7991 (tp-100) cc_final: 0.7728 (tp-100) REVERT: J 18 PHE cc_start: 0.8852 (t80) cc_final: 0.8379 (t80) REVERT: J 45 SER cc_start: 0.8533 (t) cc_final: 0.7559 (p) REVERT: J 78 GLU cc_start: 0.8887 (tp30) cc_final: 0.8458 (tp30) REVERT: J 81 GLN cc_start: 0.8581 (OUTLIER) cc_final: 0.8360 (mp-120) REVERT: J 85 HIS cc_start: 0.8170 (m170) cc_final: 0.7769 (m170) REVERT: J 91 ASN cc_start: 0.8577 (m-40) cc_final: 0.8110 (m-40) REVERT: J 98 GLN cc_start: 0.8386 (OUTLIER) cc_final: 0.7761 (tp-100) REVERT: J 108 GLU cc_start: 0.8057 (mt-10) cc_final: 0.7603 (mt-10) REVERT: J 116 ASP cc_start: 0.7147 (t0) cc_final: 0.6752 (t0) REVERT: K 46 GLU cc_start: 0.8591 (tm-30) cc_final: 0.8342 (tm-30) REVERT: K 250 TYR cc_start: 0.7923 (OUTLIER) cc_final: 0.6499 (p90) REVERT: K 277 LYS cc_start: 0.9209 (tppt) cc_final: 0.8803 (mmtm) REVERT: K 281 LEU cc_start: 0.8448 (mp) cc_final: 0.8158 (mp) REVERT: K 295 ASP cc_start: 0.8614 (t0) cc_final: 0.8230 (t0) REVERT: K 309 LYS cc_start: 0.8421 (tppt) cc_final: 0.8025 (ttpp) REVERT: K 504 THR cc_start: 0.8738 (m) cc_final: 0.8307 (p) REVERT: M 54 ILE cc_start: 0.8928 (mm) cc_final: 0.8686 (mm) REVERT: M 56 MET cc_start: 0.8102 (ttm) cc_final: 0.7637 (ttm) REVERT: M 102 MET cc_start: 0.6721 (mtp) cc_final: 0.6114 (mtp) REVERT: M 175 TYR cc_start: 0.8395 (t80) cc_final: 0.8015 (t80) REVERT: M 198 ASP cc_start: 0.7942 (m-30) cc_final: 0.7474 (m-30) REVERT: M 204 GLN cc_start: 0.8290 (tm-30) cc_final: 0.7681 (tm-30) REVERT: M 221 MET cc_start: 0.7941 (mtp) cc_final: 0.7644 (ttt) REVERT: M 273 LEU cc_start: 0.8368 (tt) cc_final: 0.8125 (mt) REVERT: M 277 LYS cc_start: 0.7678 (mppt) cc_final: 0.7297 (mppt) REVERT: N 66 ARG cc_start: 0.7884 (mtp180) cc_final: 0.7572 (mtp85) REVERT: N 68 ASN cc_start: 0.8067 (t0) cc_final: 0.7827 (t0) REVERT: N 133 GLN cc_start: 0.7601 (OUTLIER) cc_final: 0.7082 (mm110) REVERT: L 17 LEU cc_start: 0.9072 (tt) cc_final: 0.8775 (pp) REVERT: L 25 GLN cc_start: 0.8438 (OUTLIER) cc_final: 0.8110 (tt0) REVERT: L 40 TYR cc_start: 0.8515 (m-10) cc_final: 0.8170 (m-80) REVERT: L 52 PHE cc_start: 0.6443 (m-10) cc_final: 0.5673 (m-10) REVERT: L 76 GLN cc_start: 0.8639 (OUTLIER) cc_final: 0.8415 (mm110) REVERT: L 96 GLU cc_start: 0.8412 (pm20) cc_final: 0.8030 (pm20) outliers start: 109 outliers final: 67 residues processed: 799 average time/residue: 0.4907 time to fit residues: 625.0837 Evaluate side-chains 770 residues out of total 2762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 688 time to evaluate : 2.815 ------------------------------------------------------------------------------- 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 160 ILE Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 209 MET Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 32 ILE Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 109 ILE Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 156 LYS Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 279 LEU Chi-restraints excluded: chain D residue 36 THR Chi-restraints excluded: chain D residue 45 CYS Chi-restraints excluded: chain D residue 69 GLU 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 143 LEU Chi-restraints excluded: chain E residue 144 GLU 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 F residue 15 VAL Chi-restraints excluded: chain F residue 21 ASN Chi-restraints excluded: chain F residue 25 ASP Chi-restraints excluded: chain F residue 32 ILE Chi-restraints excluded: chain F residue 67 ILE Chi-restraints excluded: chain G residue 17 LEU Chi-restraints excluded: chain G residue 49 ILE Chi-restraints excluded: chain G residue 81 GLN Chi-restraints excluded: chain G residue 88 ARG Chi-restraints excluded: chain G residue 95 LEU Chi-restraints excluded: chain H residue 81 HIS Chi-restraints excluded: chain H residue 100 GLN 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 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 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 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 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 272 ASN Chi-restraints excluded: chain M residue 276 THR Chi-restraints excluded: chain N residue 30 THR Chi-restraints excluded: chain N residue 37 ILE Chi-restraints excluded: chain N residue 70 VAL Chi-restraints excluded: chain N residue 133 GLN Chi-restraints excluded: chain N residue 159 LEU Chi-restraints excluded: chain N residue 192 PHE Chi-restraints excluded: chain N residue 201 VAL Chi-restraints excluded: chain L residue 25 GLN Chi-restraints excluded: chain L residue 76 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: 0.6980 chunk 260 optimal weight: 4.9990 chunk 82 optimal weight: 0.6980 chunk 187 optimal weight: 0.1980 chunk 216 optimal weight: 9.9990 chunk 251 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 chunk 238 optimal weight: 2.9990 chunk 137 optimal weight: 5.9990 chunk 316 optimal weight: 20.0000 chunk 182 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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** 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** ** D 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 75 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** ** F 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 76 GLN ** G 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 123 ASN ** H 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 97 GLN I 120 ASN ** J 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 74 GLN J 81 GLN J 98 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 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.154117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.117083 restraints weight = 47652.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.121573 restraints weight = 21380.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 62)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.124440 restraints weight = 12578.859| |-----------------------------------------------------------------------------| r_work (final): 0.3971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.4894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 27430 Z= 0.216 Angle : 0.823 11.045 37194 Z= 0.426 Chirality : 0.052 0.469 4023 Planarity : 0.005 0.061 4752 Dihedral : 14.317 168.814 4190 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 29.77 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.39 % Favored : 90.58 % Rotamer: Outliers : 3.80 % Allowed : 25.25 % Favored : 70.94 % 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: -2.32 (0.14), residues: 3184 helix: -0.53 (0.14), residues: 1271 sheet: -2.45 (0.25), residues: 392 loop : -2.16 (0.15), residues: 1521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.071 0.003 TRP J 77 HIS 0.025 0.002 HIS C 214 PHE 0.036 0.003 PHE M 13 TYR 0.049 0.003 TYR A 125 ARG 0.011 0.001 ARG E 224 Details of bonding type rmsd hydrogen bonds : bond 0.04630 ( 1148) hydrogen bonds : angle 6.53103 ( 3315) covalent geometry : bond 0.00498 (27430) covalent geometry : angle 0.82319 (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 831 residues out of total 2762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 726 time to evaluate : 3.173 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 PHE cc_start: 0.7971 (OUTLIER) cc_final: 0.6159 (t80) REVERT: A 126 ASN cc_start: 0.7862 (t0) cc_final: 0.7548 (t0) REVERT: A 153 ASN cc_start: 0.7057 (m-40) cc_final: 0.6786 (m-40) REVERT: A 155 TYR cc_start: 0.8356 (m-80) cc_final: 0.7994 (m-80) REVERT: A 164 GLU cc_start: 0.8216 (tp30) cc_final: 0.7977 (tp30) REVERT: A 165 TRP cc_start: 0.8696 (m-10) cc_final: 0.7852 (m100) REVERT: A 167 GLN cc_start: 0.8857 (tm-30) cc_final: 0.8050 (tm-30) REVERT: A 168 TYR cc_start: 0.7377 (m-80) cc_final: 0.7142 (m-10) REVERT: A 169 GLU cc_start: 0.7801 (tt0) cc_final: 0.7569 (tp30) REVERT: A 179 GLU cc_start: 0.7810 (tm-30) cc_final: 0.7267 (tt0) REVERT: B 70 LYS cc_start: 0.7347 (OUTLIER) cc_final: 0.6929 (mttp) REVERT: B 141 MET cc_start: 0.6668 (mmt) cc_final: 0.6453 (mmt) REVERT: B 175 TYR cc_start: 0.8285 (t80) cc_final: 0.7830 (t80) REVERT: B 183 PHE cc_start: 0.7924 (m-80) cc_final: 0.7583 (m-10) REVERT: B 259 ARG cc_start: 0.7635 (mtm110) cc_final: 0.7407 (mtm110) REVERT: C 11 PHE cc_start: 0.7793 (t80) cc_final: 0.7491 (t80) REVERT: C 67 ILE cc_start: 0.8373 (OUTLIER) cc_final: 0.7791 (mm) REVERT: C 91 LYS cc_start: 0.8649 (pptt) cc_final: 0.8386 (ttmt) REVERT: C 103 CYS cc_start: 0.7998 (m) cc_final: 0.7764 (m) REVERT: C 110 ARG cc_start: 0.7461 (ptm160) cc_final: 0.7183 (ptm160) REVERT: C 256 GLU cc_start: 0.7155 (tm-30) cc_final: 0.6844 (tm-30) REVERT: C 271 LYS cc_start: 0.8380 (mmmt) cc_final: 0.8119 (mmmt) REVERT: D 21 ASN cc_start: 0.7500 (t0) cc_final: 0.7165 (t0) REVERT: D 35 GLN cc_start: 0.8367 (mm-40) cc_final: 0.8029 (tp40) REVERT: D 36 THR cc_start: 0.7855 (OUTLIER) cc_final: 0.7606 (p) REVERT: D 48 ARG cc_start: 0.7156 (OUTLIER) cc_final: 0.5715 (ttm-80) REVERT: D 54 ILE cc_start: 0.8407 (mm) cc_final: 0.7834 (pt) REVERT: D 221 MET cc_start: 0.7651 (mtp) cc_final: 0.7334 (mmm) REVERT: E 17 ASP cc_start: 0.8001 (t70) cc_final: 0.7171 (t0) REVERT: E 79 GLU cc_start: 0.7840 (tm-30) cc_final: 0.7510 (tm-30) REVERT: E 167 MET cc_start: 0.8416 (mtm) cc_final: 0.8189 (mtp) REVERT: E 169 ARG cc_start: 0.8229 (mtp85) cc_final: 0.7842 (mtp-110) REVERT: E 184 ILE cc_start: 0.8563 (OUTLIER) cc_final: 0.8243 (mm) REVERT: E 221 MET cc_start: 0.7699 (mtm) cc_final: 0.7235 (mtm) REVERT: E 241 ASP cc_start: 0.7104 (t70) cc_final: 0.6770 (t0) REVERT: F 25 ASP cc_start: 0.7157 (OUTLIER) cc_final: 0.6291 (t0) REVERT: F 72 ILE cc_start: 0.8244 (mm) cc_final: 0.7910 (mm) REVERT: F 145 HIS cc_start: 0.8680 (m-70) cc_final: 0.8356 (m-70) REVERT: F 187 HIS cc_start: 0.7268 (OUTLIER) cc_final: 0.6094 (p90) REVERT: F 188 PHE cc_start: 0.8350 (m-10) cc_final: 0.8108 (m-10) REVERT: G 68 PHE cc_start: 0.8071 (t80) cc_final: 0.7720 (t80) REVERT: G 94 ASN cc_start: 0.8707 (p0) cc_final: 0.8324 (p0) REVERT: G 96 GLU cc_start: 0.8786 (pm20) cc_final: 0.8365 (pm20) REVERT: G 106 TYR cc_start: 0.8371 (m-80) cc_final: 0.7885 (m-80) REVERT: G 110 GLN cc_start: 0.7527 (tp-100) cc_final: 0.7100 (tp-100) REVERT: H 81 HIS cc_start: 0.8700 (OUTLIER) cc_final: 0.8012 (t-90) REVERT: H 102 MET cc_start: 0.8996 (mmm) cc_final: 0.8531 (mmm) REVERT: H 178 TYR cc_start: 0.6683 (m-80) cc_final: 0.6327 (m-10) REVERT: H 206 LEU cc_start: 0.8905 (mt) cc_final: 0.8632 (mt) REVERT: H 208 ASN cc_start: 0.8617 (m110) cc_final: 0.7554 (t0) REVERT: H 261 PHE cc_start: 0.7706 (t80) cc_final: 0.7500 (t80) REVERT: I 18 PHE cc_start: 0.8744 (t80) cc_final: 0.8504 (t80) REVERT: I 22 GLU cc_start: 0.8753 (tm-30) cc_final: 0.8195 (tm-30) REVERT: I 74 GLN cc_start: 0.8669 (pt0) cc_final: 0.7763 (mt0) REVERT: I 77 TRP cc_start: 0.8297 (t60) cc_final: 0.7095 (t60) REVERT: I 80 ARG cc_start: 0.8135 (mtp180) cc_final: 0.7044 (mtm-85) REVERT: I 81 GLN cc_start: 0.8743 (OUTLIER) cc_final: 0.8152 (mp10) REVERT: I 84 GLU cc_start: 0.8522 (tp30) cc_final: 0.8113 (tp30) REVERT: I 86 CYS cc_start: 0.8874 (t) cc_final: 0.8207 (p) REVERT: I 96 GLU cc_start: 0.8459 (OUTLIER) cc_final: 0.7792 (pm20) REVERT: I 108 GLU cc_start: 0.8035 (mm-30) cc_final: 0.6842 (tp30) REVERT: I 109 THR cc_start: 0.8223 (m) cc_final: 0.7494 (p) REVERT: I 119 LYS cc_start: 0.9168 (ptmm) cc_final: 0.8659 (ptmm) REVERT: I 123 ASN cc_start: 0.8773 (m110) cc_final: 0.8353 (m110) REVERT: J 8 GLN cc_start: 0.7988 (tp-100) cc_final: 0.7650 (tp-100) REVERT: J 18 PHE cc_start: 0.8889 (t80) cc_final: 0.8466 (t80) REVERT: J 45 SER cc_start: 0.8448 (t) cc_final: 0.7395 (p) REVERT: J 61 HIS cc_start: 0.8343 (t-90) cc_final: 0.7924 (t-90) REVERT: J 78 GLU cc_start: 0.8685 (tp30) cc_final: 0.8334 (tp30) REVERT: J 88 ARG cc_start: 0.7297 (OUTLIER) cc_final: 0.6942 (tmt170) REVERT: J 91 ASN cc_start: 0.8441 (m-40) cc_final: 0.7998 (m-40) REVERT: J 98 GLN cc_start: 0.8381 (OUTLIER) cc_final: 0.7930 (tp-100) REVERT: J 116 ASP cc_start: 0.6978 (t0) cc_final: 0.6515 (t0) REVERT: K 46 GLU cc_start: 0.8507 (tm-30) cc_final: 0.8266 (tm-30) REVERT: K 59 ARG cc_start: 0.8650 (mpp80) cc_final: 0.8292 (mpp80) REVERT: K 141 MET cc_start: 0.1871 (tpt) cc_final: 0.1636 (tpt) REVERT: K 250 TYR cc_start: 0.7860 (OUTLIER) cc_final: 0.6431 (p90) REVERT: K 277 LYS cc_start: 0.9086 (tppt) cc_final: 0.8817 (mmtm) REVERT: K 281 LEU cc_start: 0.8322 (mp) cc_final: 0.8079 (mp) REVERT: K 295 ASP cc_start: 0.8471 (t0) cc_final: 0.8121 (t0) REVERT: K 309 LYS cc_start: 0.8320 (tppt) cc_final: 0.8007 (ttpp) REVERT: K 428 LYS cc_start: 0.8744 (ttpt) cc_final: 0.8473 (ttpp) REVERT: K 504 THR cc_start: 0.8754 (m) cc_final: 0.8370 (p) REVERT: K 513 MET cc_start: 0.8664 (tpp) cc_final: 0.8360 (mmm) REVERT: M 56 MET cc_start: 0.8218 (ttm) cc_final: 0.7548 (ttm) REVERT: M 198 ASP cc_start: 0.7642 (m-30) cc_final: 0.7266 (m-30) REVERT: M 204 GLN cc_start: 0.8217 (tm-30) cc_final: 0.7608 (tm-30) REVERT: M 221 MET cc_start: 0.7867 (mtp) cc_final: 0.7535 (ttt) REVERT: M 263 ASP cc_start: 0.7357 (t0) cc_final: 0.7067 (t0) REVERT: M 277 LYS cc_start: 0.7621 (mppt) cc_final: 0.7375 (mppt) REVERT: N 7 ILE cc_start: 0.8321 (mp) cc_final: 0.7705 (mm) REVERT: N 66 ARG cc_start: 0.7810 (mtp180) cc_final: 0.7601 (mtp85) REVERT: N 133 GLN cc_start: 0.7607 (OUTLIER) cc_final: 0.7031 (mm110) REVERT: L 17 LEU cc_start: 0.9073 (tt) cc_final: 0.8756 (pp) REVERT: L 25 GLN cc_start: 0.8445 (OUTLIER) cc_final: 0.8196 (tt0) REVERT: L 40 TYR cc_start: 0.8466 (m-10) cc_final: 0.8083 (m-80) REVERT: L 52 PHE cc_start: 0.6455 (m-10) cc_final: 0.5733 (m-80) REVERT: L 76 GLN cc_start: 0.8550 (OUTLIER) cc_final: 0.8326 (mm110) outliers start: 105 outliers final: 68 residues processed: 787 average time/residue: 0.3865 time to fit residues: 479.3987 Evaluate side-chains 774 residues out of total 2762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 689 time to evaluate : 2.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 PHE 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 209 MET Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 32 ILE Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 109 ILE Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 156 LYS Chi-restraints excluded: chain C residue 222 ASN 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 48 ARG 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 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 184 ILE Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 21 ASN Chi-restraints excluded: chain F residue 25 ASP Chi-restraints excluded: chain F residue 32 ILE Chi-restraints excluded: chain F residue 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 G residue 95 LEU Chi-restraints excluded: chain H residue 66 PHE Chi-restraints excluded: chain H residue 81 HIS Chi-restraints excluded: chain H residue 100 GLN 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 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 58 LEU Chi-restraints excluded: chain J residue 74 GLN 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 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 273 CYS 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 166 THR Chi-restraints excluded: chain M residue 180 CYS Chi-restraints excluded: chain M residue 272 ASN Chi-restraints excluded: chain M residue 276 THR Chi-restraints excluded: chain N residue 30 THR 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 76 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: 0.7980 chunk 130 optimal weight: 9.9990 chunk 199 optimal weight: 0.5980 chunk 241 optimal weight: 0.0770 chunk 70 optimal weight: 6.9990 chunk 233 optimal weight: 5.9990 chunk 148 optimal weight: 5.9990 chunk 49 optimal weight: 7.9990 chunk 297 optimal weight: 6.9990 chunk 35 optimal weight: 0.9990 chunk 56 optimal weight: 0.8980 overall best weight: 0.6740 ------------------------------------------------------------------------------- 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** ** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 97 GLN ** J 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 85 HIS J 98 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 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 272 ASN ** 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 Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.161044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.127848 restraints weight = 47269.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.132481 restraints weight = 21209.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.135363 restraints weight = 12320.451| |-----------------------------------------------------------------------------| r_work (final): 0.3971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.5169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 27430 Z= 0.203 Angle : 0.847 14.081 37194 Z= 0.437 Chirality : 0.052 0.468 4023 Planarity : 0.006 0.081 4752 Dihedral : 14.291 166.344 4190 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 29.87 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.14 % Favored : 90.83 % Rotamer: Outliers : 3.44 % Allowed : 26.20 % Favored : 70.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (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: -2.33 (0.14), residues: 3184 helix: -0.55 (0.14), residues: 1264 sheet: -2.32 (0.25), residues: 392 loop : -2.19 (0.15), residues: 1528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.102 0.003 TRP J 77 HIS 0.026 0.002 HIS C 214 PHE 0.043 0.003 PHE D 183 TYR 0.059 0.003 TYR K 87 ARG 0.009 0.001 ARG C 280 Details of bonding type rmsd hydrogen bonds : bond 0.04592 ( 1148) hydrogen bonds : angle 6.52998 ( 3315) covalent geometry : bond 0.00471 (27430) covalent geometry : angle 0.84730 (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 829 residues out of total 2762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 734 time to evaluate : 3.029 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: 0.7885 (OUTLIER) cc_final: 0.6032 (t80) REVERT: A 125 TYR cc_start: 0.7489 (t80) cc_final: 0.7194 (t80) REVERT: A 126 ASN cc_start: 0.7670 (t0) cc_final: 0.7396 (t0) REVERT: A 153 ASN cc_start: 0.6989 (m-40) cc_final: 0.6715 (m110) REVERT: A 155 TYR cc_start: 0.8395 (m-80) cc_final: 0.7978 (m-80) REVERT: A 164 GLU cc_start: 0.8369 (tp30) cc_final: 0.7855 (tp30) REVERT: A 165 TRP cc_start: 0.8676 (m-10) cc_final: 0.8304 (m100) REVERT: A 167 GLN cc_start: 0.8813 (tm-30) cc_final: 0.7460 (tm-30) REVERT: A 168 TYR cc_start: 0.7294 (m-80) cc_final: 0.6737 (m-10) REVERT: A 179 GLU cc_start: 0.7661 (tm-30) cc_final: 0.7085 (tt0) REVERT: B 70 LYS cc_start: 0.7304 (OUTLIER) cc_final: 0.6906 (mttp) REVERT: B 83 GLN cc_start: 0.8506 (mm-40) cc_final: 0.7763 (mm-40) REVERT: B 141 MET cc_start: 0.6609 (mmt) cc_final: 0.6378 (mmt) REVERT: B 175 TYR cc_start: 0.8292 (t80) cc_final: 0.7745 (t80) REVERT: B 183 PHE cc_start: 0.7900 (m-80) cc_final: 0.7606 (m-10) REVERT: B 241 ASP cc_start: 0.7808 (t70) cc_final: 0.7174 (t0) REVERT: C 11 PHE cc_start: 0.7870 (t80) cc_final: 0.7612 (t80) REVERT: C 43 ASP cc_start: 0.8149 (p0) cc_final: 0.7912 (p0) REVERT: C 67 ILE cc_start: 0.8403 (OUTLIER) cc_final: 0.7900 (mm) REVERT: C 91 LYS cc_start: 0.8653 (pptt) cc_final: 0.8380 (ttmt) REVERT: C 256 GLU cc_start: 0.7254 (tm-30) cc_final: 0.6906 (tm-30) REVERT: C 271 LYS cc_start: 0.8463 (mmmt) cc_final: 0.8257 (mmmt) REVERT: D 35 GLN cc_start: 0.8468 (mm-40) cc_final: 0.8051 (tp40) REVERT: D 36 THR cc_start: 0.7880 (OUTLIER) cc_final: 0.7580 (p) REVERT: D 48 ARG cc_start: 0.6971 (OUTLIER) cc_final: 0.5741 (ttm-80) REVERT: D 221 MET cc_start: 0.7662 (mtp) cc_final: 0.7459 (mtp) REVERT: E 79 GLU cc_start: 0.7811 (tm-30) cc_final: 0.7433 (tm-30) REVERT: E 138 ASP cc_start: 0.7519 (m-30) cc_final: 0.6746 (m-30) REVERT: E 141 MET cc_start: 0.7361 (tpp) cc_final: 0.6871 (tpp) REVERT: E 167 MET cc_start: 0.8381 (mtm) cc_final: 0.8086 (mtp) REVERT: E 169 ARG cc_start: 0.8311 (mtp85) cc_final: 0.7944 (mtp-110) REVERT: E 177 LEU cc_start: 0.9263 (tp) cc_final: 0.9021 (mt) REVERT: E 184 ILE cc_start: 0.8696 (OUTLIER) cc_final: 0.8377 (mm) REVERT: E 221 MET cc_start: 0.7853 (mtm) cc_final: 0.7417 (mtm) REVERT: E 241 ASP cc_start: 0.7130 (t70) cc_final: 0.6811 (t0) REVERT: F 25 ASP cc_start: 0.7042 (OUTLIER) cc_final: 0.6197 (t0) REVERT: F 72 ILE cc_start: 0.8124 (mm) cc_final: 0.7775 (mm) REVERT: F 82 GLU cc_start: 0.8809 (mt-10) cc_final: 0.8585 (mt-10) REVERT: F 124 GLN cc_start: 0.8485 (OUTLIER) cc_final: 0.8230 (mt0) REVERT: F 145 HIS cc_start: 0.8573 (m-70) cc_final: 0.8288 (m-70) REVERT: F 187 HIS cc_start: 0.7277 (OUTLIER) cc_final: 0.6606 (p90) REVERT: G 68 PHE cc_start: 0.8153 (t80) cc_final: 0.7723 (t80) REVERT: G 71 ARG cc_start: 0.8693 (mtp85) cc_final: 0.8306 (mtp85) REVERT: G 94 ASN cc_start: 0.8844 (p0) cc_final: 0.8186 (p0) REVERT: G 96 GLU cc_start: 0.8810 (pm20) cc_final: 0.8035 (pm20) REVERT: G 97 GLN cc_start: 0.8484 (tp40) cc_final: 0.7992 (mt0) REVERT: G 106 TYR cc_start: 0.8491 (m-80) cc_final: 0.7958 (m-80) REVERT: G 110 GLN cc_start: 0.7393 (tp-100) cc_final: 0.7078 (tp-100) REVERT: H 6 ARG cc_start: 0.8854 (ttp80) cc_final: 0.7862 (ttt180) REVERT: H 81 HIS cc_start: 0.8709 (OUTLIER) cc_final: 0.8198 (t-90) REVERT: H 102 MET cc_start: 0.9084 (mmm) cc_final: 0.8476 (mmm) REVERT: H 178 TYR cc_start: 0.6817 (m-80) cc_final: 0.6429 (m-10) REVERT: H 208 ASN cc_start: 0.8805 (m110) cc_final: 0.7693 (t0) REVERT: H 261 PHE cc_start: 0.7755 (t80) cc_final: 0.7540 (t80) REVERT: I 22 GLU cc_start: 0.8784 (tm-30) cc_final: 0.8289 (tm-30) REVERT: I 57 ARG cc_start: 0.8580 (tpp80) cc_final: 0.8337 (tpp80) REVERT: I 74 GLN cc_start: 0.8612 (pt0) cc_final: 0.7674 (mt0) REVERT: I 77 TRP cc_start: 0.8256 (t60) cc_final: 0.7101 (t60) REVERT: I 80 ARG cc_start: 0.8250 (mtp180) cc_final: 0.7013 (mtm-85) REVERT: I 81 GLN cc_start: 0.8674 (OUTLIER) cc_final: 0.8027 (mp10) REVERT: I 84 GLU cc_start: 0.8594 (tp30) cc_final: 0.8183 (tp30) REVERT: I 86 CYS cc_start: 0.8934 (t) cc_final: 0.8213 (p) REVERT: I 96 GLU cc_start: 0.8462 (OUTLIER) cc_final: 0.7803 (pm20) REVERT: I 108 GLU cc_start: 0.8179 (OUTLIER) cc_final: 0.7029 (tp30) REVERT: I 119 LYS cc_start: 0.9079 (ptmm) cc_final: 0.8550 (ptmm) REVERT: I 123 ASN cc_start: 0.8798 (m110) cc_final: 0.8266 (m110) REVERT: J 8 GLN cc_start: 0.8099 (tp-100) cc_final: 0.7836 (tp-100) REVERT: J 18 PHE cc_start: 0.8811 (t80) cc_final: 0.8469 (t80) REVERT: J 39 ARG cc_start: 0.8074 (mtp85) cc_final: 0.7827 (mmm160) REVERT: J 57 ARG cc_start: 0.8738 (mtm110) cc_final: 0.8307 (mtm-85) REVERT: J 78 GLU cc_start: 0.8809 (tp30) cc_final: 0.8426 (tp30) REVERT: J 81 GLN cc_start: 0.8282 (mp10) cc_final: 0.7984 (mp10) REVERT: J 88 ARG cc_start: 0.7485 (OUTLIER) cc_final: 0.7142 (tmt170) REVERT: J 91 ASN cc_start: 0.8546 (m-40) cc_final: 0.8095 (m-40) REVERT: J 108 GLU cc_start: 0.8404 (mt-10) cc_final: 0.7833 (mt-10) REVERT: J 116 ASP cc_start: 0.7415 (t0) cc_final: 0.7024 (t0) REVERT: K 46 GLU cc_start: 0.8604 (tm-30) cc_final: 0.8334 (tm-30) REVERT: K 65 LYS cc_start: 0.9196 (mppt) cc_final: 0.8867 (mtmm) REVERT: K 89 LEU cc_start: 0.9325 (mt) cc_final: 0.9086 (mm) REVERT: K 141 MET cc_start: 0.1628 (tpt) cc_final: 0.1406 (tpt) REVERT: K 170 CYS cc_start: 0.9195 (m) cc_final: 0.8980 (m) REVERT: K 250 TYR cc_start: 0.7804 (OUTLIER) cc_final: 0.6318 (p90) REVERT: K 281 LEU cc_start: 0.8131 (mp) cc_final: 0.7855 (mp) REVERT: K 290 ASN cc_start: 0.8895 (m-40) cc_final: 0.8447 (t0) REVERT: K 295 ASP cc_start: 0.8562 (t0) cc_final: 0.8177 (t0) REVERT: K 309 LYS cc_start: 0.8353 (tppt) cc_final: 0.7947 (ttpp) REVERT: K 428 LYS cc_start: 0.8676 (ttpt) cc_final: 0.8363 (ttpp) REVERT: K 504 THR cc_start: 0.8641 (m) cc_final: 0.8281 (p) REVERT: K 513 MET cc_start: 0.8781 (tpp) cc_final: 0.8391 (tpp) REVERT: M 54 ILE cc_start: 0.8904 (mm) cc_final: 0.8704 (mm) REVERT: M 56 MET cc_start: 0.8169 (ttm) cc_final: 0.7391 (ttm) REVERT: M 198 ASP cc_start: 0.7836 (m-30) cc_final: 0.7303 (m-30) REVERT: M 204 GLN cc_start: 0.8178 (tm-30) cc_final: 0.7664 (tm-30) REVERT: M 221 MET cc_start: 0.7821 (mtp) cc_final: 0.7610 (ttt) REVERT: M 263 ASP cc_start: 0.7581 (t0) cc_final: 0.7202 (t0) REVERT: M 273 LEU cc_start: 0.8131 (mt) cc_final: 0.6711 (tt) REVERT: N 66 ARG cc_start: 0.7815 (mtp180) cc_final: 0.7535 (mtp85) REVERT: N 97 ASP cc_start: 0.7431 (m-30) cc_final: 0.6930 (p0) REVERT: L 17 LEU cc_start: 0.9059 (tt) cc_final: 0.8761 (pp) REVERT: L 25 GLN cc_start: 0.8502 (OUTLIER) cc_final: 0.8152 (tt0) REVERT: L 40 TYR cc_start: 0.8249 (m-10) cc_final: 0.7902 (m-80) REVERT: L 52 PHE cc_start: 0.6893 (m-10) cc_final: 0.6295 (m-80) REVERT: L 76 GLN cc_start: 0.8488 (OUTLIER) cc_final: 0.8282 (mm110) outliers start: 95 outliers final: 67 residues processed: 780 average time/residue: 0.4336 time to fit residues: 536.9818 Evaluate side-chains 772 residues out of total 2762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 688 time to evaluate : 3.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 PHE Chi-restraints excluded: chain A residue 140 ASP 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 67 ILE Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 104 SER 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 214 HIS Chi-restraints excluded: chain C residue 222 ASN 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 48 ARG 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 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 184 ILE Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 21 ASN Chi-restraints excluded: chain F residue 25 ASP Chi-restraints excluded: chain F residue 32 ILE Chi-restraints excluded: chain F residue 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 G residue 95 LEU Chi-restraints excluded: chain H residue 66 PHE Chi-restraints excluded: chain H residue 81 HIS Chi-restraints excluded: chain H residue 100 GLN 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 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 I residue 108 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 K residue 32 PHE Chi-restraints excluded: chain K residue 195 CYS Chi-restraints excluded: chain K residue 250 TYR Chi-restraints excluded: chain K residue 257 LEU Chi-restraints excluded: chain K residue 266 ILE Chi-restraints excluded: chain K residue 269 VAL Chi-restraints excluded: chain K residue 273 CYS 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 46 LEU Chi-restraints excluded: chain M residue 166 THR Chi-restraints excluded: chain M residue 180 CYS Chi-restraints excluded: chain M residue 276 THR Chi-restraints excluded: chain N residue 30 THR 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 76 GLN Chi-restraints excluded: chain L residue 81 GLN Chi-restraints excluded: chain L residue 98 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 103 optimal weight: 2.9990 chunk 52 optimal weight: 0.9990 chunk 227 optimal weight: 1.9990 chunk 299 optimal weight: 0.1980 chunk 40 optimal weight: 1.9990 chunk 115 optimal weight: 2.9990 chunk 317 optimal weight: 7.9990 chunk 42 optimal weight: 7.9990 chunk 170 optimal weight: 10.0000 chunk 262 optimal weight: 0.6980 chunk 252 optimal weight: 0.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- 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 ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 212 HIS ** 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** E 233 ASN ** F 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 97 GLN ** J 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 74 GLN J 85 HIS ** K 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 89 GLN N 137 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.160025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.127291 restraints weight = 47239.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.131824 restraints weight = 21194.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.134739 restraints weight = 12310.975| |-----------------------------------------------------------------------------| r_work (final): 0.3986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.5302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 27430 Z= 0.224 Angle : 0.876 16.895 37194 Z= 0.452 Chirality : 0.053 0.471 4023 Planarity : 0.006 0.076 4752 Dihedral : 14.266 166.567 4190 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 30.48 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.52 % Favored : 90.45 % Rotamer: Outliers : 3.70 % Allowed : 26.70 % Favored : 69.60 % 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: -2.36 (0.14), residues: 3184 helix: -0.62 (0.14), residues: 1261 sheet: -2.32 (0.26), residues: 380 loop : -2.17 (0.15), residues: 1543 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.134 0.004 TRP J 77 HIS 0.026 0.002 HIS C 214 PHE 0.042 0.003 PHE H 183 TYR 0.050 0.003 TYR K 440 ARG 0.011 0.001 ARG F 135 Details of bonding type rmsd hydrogen bonds : bond 0.04736 ( 1148) hydrogen bonds : angle 6.58598 ( 3315) covalent geometry : bond 0.00517 (27430) covalent geometry : angle 0.87613 (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 803 residues out of total 2762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 701 time to evaluate : 2.821 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 ASN cc_start: 0.6984 (m-40) cc_final: 0.6696 (m-40) REVERT: A 155 TYR cc_start: 0.8438 (m-80) cc_final: 0.8006 (m-80) REVERT: A 164 GLU cc_start: 0.8333 (tp30) cc_final: 0.7962 (tp30) REVERT: A 165 TRP cc_start: 0.8612 (m-10) cc_final: 0.8256 (m100) REVERT: A 167 GLN cc_start: 0.8859 (tm-30) cc_final: 0.7950 (tm-30) REVERT: A 168 TYR cc_start: 0.7284 (m-80) cc_final: 0.6875 (m-10) REVERT: A 178 GLU cc_start: 0.7645 (tt0) cc_final: 0.7234 (tt0) REVERT: A 179 GLU cc_start: 0.7703 (tm-30) cc_final: 0.6915 (tt0) REVERT: B 70 LYS cc_start: 0.7306 (OUTLIER) cc_final: 0.6983 (mttp) REVERT: B 83 GLN cc_start: 0.8522 (mm-40) cc_final: 0.7813 (mm-40) REVERT: B 141 MET cc_start: 0.6635 (mmt) cc_final: 0.6387 (mmt) REVERT: B 175 TYR cc_start: 0.8244 (t80) cc_final: 0.7612 (t80) REVERT: B 183 PHE cc_start: 0.7813 (m-80) cc_final: 0.7596 (m-10) REVERT: B 241 ASP cc_start: 0.7808 (t70) cc_final: 0.7198 (t0) REVERT: C 43 ASP cc_start: 0.8096 (p0) cc_final: 0.7846 (p0) REVERT: C 67 ILE cc_start: 0.8388 (OUTLIER) cc_final: 0.7878 (mm) REVERT: C 91 LYS cc_start: 0.8670 (pptt) cc_final: 0.8423 (mmmt) REVERT: C 256 GLU cc_start: 0.7241 (tm-30) cc_final: 0.6928 (tm-30) REVERT: D 35 GLN cc_start: 0.8496 (mm-40) cc_final: 0.8081 (tp40) REVERT: D 36 THR cc_start: 0.7899 (OUTLIER) cc_final: 0.7599 (p) REVERT: D 199 LEU cc_start: 0.8406 (tp) cc_final: 0.8143 (tp) REVERT: D 209 MET cc_start: 0.7434 (mmm) cc_final: 0.6963 (mmm) REVERT: D 221 MET cc_start: 0.7779 (mtp) cc_final: 0.7534 (mtp) REVERT: E 116 MET cc_start: 0.8496 (mmt) cc_final: 0.8238 (mmt) REVERT: E 138 ASP cc_start: 0.7645 (m-30) cc_final: 0.6854 (m-30) REVERT: E 141 MET cc_start: 0.7310 (tpp) cc_final: 0.6827 (tpp) REVERT: E 169 ARG cc_start: 0.8301 (mtp85) cc_final: 0.7926 (mtp-110) REVERT: E 177 LEU cc_start: 0.9273 (tp) cc_final: 0.9018 (mt) REVERT: E 184 ILE cc_start: 0.8627 (OUTLIER) cc_final: 0.8325 (mm) REVERT: E 221 MET cc_start: 0.7875 (mtm) cc_final: 0.7402 (mtm) REVERT: F 25 ASP cc_start: 0.6935 (OUTLIER) cc_final: 0.6117 (t0) REVERT: F 72 ILE cc_start: 0.8152 (mm) cc_final: 0.7820 (mm) REVERT: F 78 ASP cc_start: 0.8076 (m-30) cc_final: 0.7743 (m-30) REVERT: F 82 GLU cc_start: 0.8776 (mt-10) cc_final: 0.8552 (mt-10) REVERT: F 124 GLN cc_start: 0.8306 (OUTLIER) cc_final: 0.7981 (mt0) REVERT: F 187 HIS cc_start: 0.7355 (OUTLIER) cc_final: 0.6920 (p90) REVERT: F 188 PHE cc_start: 0.8357 (m-10) cc_final: 0.7972 (m-10) REVERT: G 16 ARG cc_start: 0.8454 (tpt-90) cc_final: 0.7509 (tpt-90) REVERT: G 55 LEU cc_start: 0.8747 (mt) cc_final: 0.8437 (mm) REVERT: G 68 PHE cc_start: 0.8126 (t80) cc_final: 0.7751 (t80) REVERT: G 85 HIS cc_start: 0.8678 (m-70) cc_final: 0.8341 (m-70) REVERT: G 98 GLN cc_start: 0.8373 (tt0) cc_final: 0.7940 (tt0) REVERT: G 106 TYR cc_start: 0.8482 (m-80) cc_final: 0.7963 (m-80) REVERT: G 124 GLU cc_start: 0.8900 (OUTLIER) cc_final: 0.8699 (pm20) REVERT: H 6 ARG cc_start: 0.8837 (ttp80) cc_final: 0.8101 (ttt180) REVERT: H 41 VAL cc_start: 0.8867 (m) cc_final: 0.8572 (p) REVERT: H 102 MET cc_start: 0.9036 (mmm) cc_final: 0.8571 (mmm) REVERT: H 178 TYR cc_start: 0.6792 (m-80) cc_final: 0.6556 (m-10) REVERT: H 190 LYS cc_start: 0.8715 (mttm) cc_final: 0.8374 (mttp) REVERT: H 208 ASN cc_start: 0.8785 (m110) cc_final: 0.7713 (t0) REVERT: I 22 GLU cc_start: 0.8698 (tm-30) cc_final: 0.8174 (tm-30) REVERT: I 57 ARG cc_start: 0.8631 (tpp80) cc_final: 0.8148 (tpp80) REVERT: I 74 GLN cc_start: 0.8589 (pt0) cc_final: 0.7636 (mt0) REVERT: I 77 TRP cc_start: 0.8135 (t60) cc_final: 0.7510 (t60) REVERT: I 80 ARG cc_start: 0.8243 (mtp180) cc_final: 0.7468 (mtp-110) REVERT: I 81 GLN cc_start: 0.8707 (OUTLIER) cc_final: 0.8043 (mp10) REVERT: I 84 GLU cc_start: 0.8542 (tp30) cc_final: 0.8189 (tp30) REVERT: I 86 CYS cc_start: 0.8905 (t) cc_final: 0.8185 (p) REVERT: I 96 GLU cc_start: 0.8452 (OUTLIER) cc_final: 0.7811 (pm20) REVERT: I 108 GLU cc_start: 0.8112 (OUTLIER) cc_final: 0.6973 (tp30) REVERT: I 119 LYS cc_start: 0.9076 (ptmm) cc_final: 0.8519 (ptmm) REVERT: I 123 ASN cc_start: 0.8758 (m110) cc_final: 0.8235 (m110) REVERT: J 8 GLN cc_start: 0.8062 (tp-100) cc_final: 0.7837 (tp-100) REVERT: J 18 PHE cc_start: 0.8891 (t80) cc_final: 0.8499 (t80) REVERT: J 39 ARG cc_start: 0.7848 (mtp85) cc_final: 0.7565 (mmm-85) REVERT: J 57 ARG cc_start: 0.8696 (mtm110) cc_final: 0.8442 (mtm-85) REVERT: J 78 GLU cc_start: 0.8691 (tp30) cc_final: 0.8393 (tp30) REVERT: J 88 ARG cc_start: 0.7536 (OUTLIER) cc_final: 0.7235 (tmt170) REVERT: J 91 ASN cc_start: 0.8557 (m-40) cc_final: 0.8138 (m-40) REVERT: J 116 ASP cc_start: 0.7260 (t0) cc_final: 0.6852 (t0) REVERT: K 46 GLU cc_start: 0.8578 (tm-30) cc_final: 0.8330 (tm-30) REVERT: K 59 ARG cc_start: 0.8729 (mpp80) cc_final: 0.8485 (mpp80) REVERT: K 89 LEU cc_start: 0.9349 (mt) cc_final: 0.9108 (mm) REVERT: K 141 MET cc_start: 0.1629 (tpt) cc_final: 0.1418 (tpt) REVERT: K 170 CYS cc_start: 0.9163 (m) cc_final: 0.8954 (m) REVERT: K 250 TYR cc_start: 0.7844 (OUTLIER) cc_final: 0.6376 (p90) REVERT: K 281 LEU cc_start: 0.8092 (mp) cc_final: 0.7829 (mp) REVERT: K 290 ASN cc_start: 0.8905 (m-40) cc_final: 0.8522 (t0) REVERT: K 295 ASP cc_start: 0.8539 (t0) cc_final: 0.8154 (t0) REVERT: K 309 LYS cc_start: 0.8292 (tppt) cc_final: 0.7864 (ttpp) REVERT: K 395 SER cc_start: 0.7546 (t) cc_final: 0.7265 (p) REVERT: K 428 LYS cc_start: 0.8694 (ttpt) cc_final: 0.8380 (ttpp) REVERT: K 482 GLN cc_start: 0.7894 (OUTLIER) cc_final: 0.7129 (tm-30) REVERT: K 504 THR cc_start: 0.8680 (m) cc_final: 0.8286 (p) REVERT: K 513 MET cc_start: 0.8706 (tpp) cc_final: 0.8414 (mmm) REVERT: M 54 ILE cc_start: 0.9022 (mm) cc_final: 0.8820 (mm) REVERT: M 56 MET cc_start: 0.8211 (ttm) cc_final: 0.7500 (ttm) REVERT: M 102 MET cc_start: 0.6137 (mtp) cc_final: 0.5911 (mtp) REVERT: M 175 TYR cc_start: 0.8460 (t80) cc_final: 0.8114 (t80) REVERT: M 183 PHE cc_start: 0.9069 (m-80) cc_final: 0.8639 (m-80) REVERT: M 196 GLU cc_start: 0.8323 (tm-30) cc_final: 0.8096 (tm-30) REVERT: M 198 ASP cc_start: 0.7751 (m-30) cc_final: 0.7272 (m-30) REVERT: M 204 GLN cc_start: 0.8215 (tm-30) cc_final: 0.7680 (tm-30) REVERT: M 221 MET cc_start: 0.8065 (mtp) cc_final: 0.7770 (ttt) REVERT: M 263 ASP cc_start: 0.7688 (t0) cc_final: 0.7301 (t0) REVERT: N 97 ASP cc_start: 0.7421 (m-30) cc_final: 0.6928 (p0) REVERT: N 137 GLN cc_start: 0.7541 (OUTLIER) cc_final: 0.7163 (tt0) REVERT: L 17 LEU cc_start: 0.9068 (tt) cc_final: 0.8791 (pp) REVERT: L 25 GLN cc_start: 0.8482 (OUTLIER) cc_final: 0.8209 (tt0) REVERT: L 40 TYR cc_start: 0.8157 (m-10) cc_final: 0.7869 (m-80) REVERT: L 52 PHE cc_start: 0.6907 (m-10) cc_final: 0.6047 (m-80) REVERT: L 56 MET cc_start: 0.8017 (mmm) cc_final: 0.6856 (tmm) outliers start: 102 outliers final: 74 residues processed: 755 average time/residue: 0.3975 time to fit residues: 471.0089 Evaluate side-chains 759 residues out of total 2762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 669 time to evaluate : 3.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 PHE Chi-restraints excluded: chain A residue 140 ASP Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 70 LYS Chi-restraints excluded: chain B residue 124 GLN 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 32 ILE Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 104 SER Chi-restraints excluded: chain C residue 109 ILE Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 214 HIS Chi-restraints excluded: chain C residue 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 69 GLU Chi-restraints excluded: chain D residue 260 SER 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 184 ILE Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 259 ARG Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 21 ASN Chi-restraints excluded: chain F residue 25 ASP Chi-restraints excluded: chain F residue 32 ILE Chi-restraints excluded: chain F residue 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 88 ARG Chi-restraints excluded: chain G residue 95 LEU Chi-restraints excluded: chain G residue 124 GLU Chi-restraints excluded: chain H residue 66 PHE Chi-restraints excluded: chain H residue 100 GLN 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 253 ASP Chi-restraints excluded: chain H residue 266 VAL Chi-restraints excluded: chain H residue 276 THR Chi-restraints excluded: chain I residue 58 LEU Chi-restraints excluded: chain I residue 66 LEU Chi-restraints excluded: chain I residue 81 GLN Chi-restraints excluded: chain I residue 96 GLU Chi-restraints excluded: chain I residue 108 GLU Chi-restraints excluded: chain J residue 58 LEU Chi-restraints excluded: chain J residue 74 GLN Chi-restraints excluded: chain J residue 88 ARG 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 273 CYS 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 482 GLN Chi-restraints excluded: chain M residue 42 THR Chi-restraints excluded: chain M residue 46 LEU Chi-restraints excluded: chain M residue 166 THR Chi-restraints excluded: chain M residue 180 CYS Chi-restraints excluded: chain M residue 276 THR Chi-restraints excluded: chain N residue 30 THR Chi-restraints excluded: chain N residue 42 LEU Chi-restraints excluded: chain N residue 70 VAL Chi-restraints excluded: chain N residue 133 GLN Chi-restraints excluded: chain N residue 137 GLN Chi-restraints excluded: chain N residue 159 LEU Chi-restraints excluded: chain N residue 192 PHE Chi-restraints excluded: chain N residue 201 VAL Chi-restraints excluded: chain L residue 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: 7.9990 chunk 110 optimal weight: 2.9990 chunk 215 optimal weight: 6.9990 chunk 236 optimal weight: 0.5980 chunk 126 optimal weight: 2.9990 chunk 151 optimal weight: 0.8980 chunk 300 optimal weight: 0.8980 chunk 119 optimal weight: 0.6980 chunk 13 optimal weight: 0.9990 chunk 171 optimal weight: 20.0000 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 58 GLN E 62 HIS ** E 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 29 ASN ** I 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 97 GLN J 74 GLN J 85 HIS ** K 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 368 ASN ** K 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 427 GLN ** K 521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 137 GLN ** L 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.161053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.128251 restraints weight = 47113.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.132854 restraints weight = 21215.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.135785 restraints weight = 12267.541| |-----------------------------------------------------------------------------| r_work (final): 0.3981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.5458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 27430 Z= 0.214 Angle : 0.873 17.525 37194 Z= 0.451 Chirality : 0.053 0.462 4023 Planarity : 0.006 0.075 4752 Dihedral : 14.231 165.910 4190 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 30.46 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.55 % Favored : 90.42 % Rotamer: Outliers : 3.66 % Allowed : 26.70 % Favored : 69.64 % 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: -0.64 (0.14), residues: 1262 sheet: -2.27 (0.26), residues: 375 loop : -2.16 (0.15), residues: 1547 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.111 0.003 TRP J 77 HIS 0.025 0.002 HIS C 214 PHE 0.040 0.003 PHE H 261 TYR 0.050 0.003 TYR K 440 ARG 0.022 0.001 ARG C 110 Details of bonding type rmsd hydrogen bonds : bond 0.04746 ( 1148) hydrogen bonds : angle 6.57076 ( 3315) covalent geometry : bond 0.00495 (27430) covalent geometry : angle 0.87255 (37194) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12178.66 seconds wall clock time: 213 minutes 51.45 seconds (12831.45 seconds total)