Starting phenix.real_space_refine on Mon Aug 25 08:22:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g9t_29878/08_2025/8g9t_29878.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g9t_29878/08_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_29878/08_2025/8g9t_29878.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g9t_29878/08_2025/8g9t_29878.map" model { file = "/net/cci-nas-00/data/ceres_data/8g9t_29878/08_2025/8g9t_29878.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g9t_29878/08_2025/8g9t_29878.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.060 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 43 5.49 5 S 110 5.16 5 C 16729 2.51 5 N 4769 2.21 5 O 5153 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 224 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 26804 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 583 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 1, 'TRANS': 68} Chain: "B" Number of atoms: 2206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2206 Classifications: {'peptide': 275} Link IDs: {'PTRANS': 8, 'TRANS': 266} Chain breaks: 1 Chain: "C" Number of atoms: 2241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2241 Classifications: {'peptide': 280} Link IDs: {'PTRANS': 8, 'TRANS': 271} Chain breaks: 1 Chain: "D" Number of atoms: 2214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 2214 Classifications: {'peptide': 276} Link IDs: {'PTRANS': 8, 'TRANS': 267} Chain breaks: 1 Chain: "E" Number of atoms: 2225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 2225 Classifications: {'peptide': 278} Link IDs: {'PTRANS': 8, 'TRANS': 269} Chain breaks: 1 Chain: "F" Number of atoms: 2097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2097 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 8, 'TRANS': 252} Chain breaks: 1 Chain: "G" Number of atoms: 1007 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 1007 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 4, 'TRANS': 119} Chain: "H" Number of atoms: 1955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1955 Classifications: {'peptide': 242} Link IDs: {'PTRANS': 5, 'TRANS': 236} Chain breaks: 2 Chain: "I" Number of atoms: 1007 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 1007 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 4, 'TRANS': 119} Chain: "J" Number of atoms: 1007 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 1007 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 4, 'TRANS': 119} Chain: "K" Number of atoms: 4559 Number of conformers: 1 Conformer: "" Number of residues, atoms: 582, 4559 Classifications: {'peptide': 582} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 1, 'PTRANS': 21, 'TRANS': 559} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "M" Number of atoms: 2101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 2101 Classifications: {'peptide': 263} Link IDs: {'PTRANS': 8, 'TRANS': 254} Chain breaks: 1 Chain: "N" Number of atoms: 1674 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1674 Classifications: {'peptide': 205} Link IDs: {'PTRANS': 11, 'TRANS': 193} Chain: "O" Number of atoms: 921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 921 Classifications: {'RNA': 43} Modifications used: {'rna2p_pur': 10, 'rna2p_pyr': 13, 'rna3p_pur': 14, 'rna3p_pyr': 6} Link IDs: {'rna2p': 22, 'rna3p': 20} Chain: "L" Number of atoms: 1007 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 1007 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 4, 'TRANS': 119} Time building chain proxies: 6.37, per 1000 atoms: 0.24 Number of scatterers: 26804 At special positions: 0 Unit cell: (108.697, 116.142, 203.993, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 110 16.00 P 43 15.00 O 5153 8.00 N 4769 7.00 C 16729 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.57 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 715.3 nanoseconds 6368 Ramachandran restraints generated. 3184 Oldfield, 0 Emsley, 3184 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5976 Finding SS restraints... Secondary structure from input PDB file: 114 helices and 41 sheets defined 43.3% alpha, 15.0% beta 0 base pairs and 12 stacking pairs defined. Time for finding SS restraints: 3.58 Creating SS restraints... Processing helix chain 'A' and resid 135 through 147 Processing helix chain 'A' and resid 161 through 163 No H-bonds generated for 'chain 'A' and resid 161 through 163' Processing helix chain 'A' and resid 164 through 169 removed outlier: 3.722A pdb=" N TYR A 168 " --> pdb=" O GLU A 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 58 removed outlier: 3.537A pdb=" N LEU B 46 " --> pdb=" O THR B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 82 Processing helix chain 'B' and resid 83 through 88 removed outlier: 3.536A pdb=" N GLY B 88 " --> pdb=" O GLU B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 106 Processing helix chain 'B' and resid 106 through 112 Processing helix chain 'B' and resid 185 through 193 removed outlier: 3.505A pdb=" N GLN B 191 " --> pdb=" O HIS B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 209 Processing helix chain 'B' and resid 210 through 213 Processing helix chain 'B' and resid 239 through 247 removed outlier: 3.554A pdb=" N ILE B 247 " --> pdb=" O LEU B 243 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 262 No H-bonds generated for 'chain 'B' and resid 260 through 262' Processing helix chain 'B' and resid 272 through 276 removed outlier: 4.297A pdb=" N GLU B 275 " --> pdb=" O ASN B 272 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 58 Processing helix chain 'C' and resid 72 through 81 Processing helix chain 'C' and resid 92 through 106 removed outlier: 4.033A pdb=" N GLU C 96 " --> pdb=" O GLY C 92 " (cutoff:3.500A) Processing helix chain 'C' and resid 106 through 113 Processing helix chain 'C' and resid 185 through 193 removed outlier: 4.578A pdb=" N GLN C 191 " --> pdb=" O HIS C 187 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N THR C 192 " --> pdb=" O PHE C 188 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 209 Processing helix chain 'C' and resid 239 through 246 removed outlier: 3.514A pdb=" N LEU C 243 " --> pdb=" O PRO C 239 " (cutoff:3.500A) Processing helix chain 'D' and resid 42 through 58 removed outlier: 4.032A pdb=" N LYS D 49 " --> pdb=" O CYS D 45 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 83 removed outlier: 4.515A pdb=" N ALA D 80 " --> pdb=" O LEU D 76 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLN D 83 " --> pdb=" O GLU D 79 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 88 removed outlier: 4.123A pdb=" N GLY D 88 " --> pdb=" O GLU D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 106 removed outlier: 3.940A pdb=" N THR D 95 " --> pdb=" O LYS D 91 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N GLU D 96 " --> pdb=" O GLY D 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 106 through 112 Processing helix chain 'D' and resid 185 through 190 Processing helix chain 'D' and resid 195 through 213 removed outlier: 5.397A pdb=" N PHE D 210 " --> pdb=" O LEU D 206 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N ASP D 211 " --> pdb=" O VAL D 207 " (cutoff:3.500A) Processing helix chain 'D' and resid 239 through 246 Processing helix chain 'E' and resid 42 through 58 Processing helix chain 'E' and resid 72 through 82 Processing helix chain 'E' and resid 90 through 106 removed outlier: 4.336A pdb=" N THR E 95 " --> pdb=" O LYS E 91 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N GLU E 96 " --> pdb=" O GLY E 92 " (cutoff:3.500A) Processing helix chain 'E' and resid 106 through 112 Processing helix chain 'E' and resid 185 through 193 Processing helix chain 'E' and resid 195 through 210 removed outlier: 4.489A pdb=" N PHE E 210 " --> pdb=" O LEU E 206 " (cutoff:3.500A) Processing helix chain 'E' and resid 211 through 213 No H-bonds generated for 'chain 'E' and resid 211 through 213' Processing helix chain 'E' and resid 239 through 247 Processing helix chain 'E' and resid 260 through 262 No H-bonds generated for 'chain 'E' and resid 260 through 262' Processing helix chain 'E' and resid 272 through 276 Processing helix chain 'F' and resid 42 through 58 removed outlier: 3.609A pdb=" N LEU F 46 " --> pdb=" O THR F 42 " (cutoff:3.500A) Processing helix chain 'F' and resid 72 through 82 Processing helix chain 'F' and resid 93 through 106 Processing helix chain 'F' and resid 106 through 112 removed outlier: 3.609A pdb=" N ARG F 110 " --> pdb=" O TYR F 106 " (cutoff:3.500A) Processing helix chain 'F' and resid 185 through 190 Processing helix chain 'F' and resid 195 through 209 Processing helix chain 'F' and resid 239 through 247 Processing helix chain 'F' and resid 260 through 262 No H-bonds generated for 'chain 'F' and resid 260 through 262' Processing helix chain 'F' and resid 272 through 276 removed outlier: 4.455A pdb=" N GLU F 275 " --> pdb=" O ASN F 272 " (cutoff:3.500A) Processing helix chain 'G' and resid 9 through 29 Processing helix chain 'G' and resid 35 through 47 removed outlier: 6.547A pdb=" N GLY G 42 " --> pdb=" O ASP G 38 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N SER G 43 " --> pdb=" O ARG G 39 " (cutoff:3.500A) Processing helix chain 'G' and resid 47 through 66 removed outlier: 4.071A pdb=" N VAL G 51 " --> pdb=" O THR G 47 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N THR G 54 " --> pdb=" O ALA G 50 " (cutoff:3.500A) Proline residue: G 60 - end of helix Processing helix chain 'G' and resid 68 through 86 removed outlier: 3.532A pdb=" N ALA G 72 " --> pdb=" O PHE G 68 " (cutoff:3.500A) Processing helix chain 'G' and resid 94 through 114 Processing helix chain 'G' and resid 116 through 124 removed outlier: 3.759A pdb=" N ASN G 120 " --> pdb=" O ASP G 116 " (cutoff:3.500A) Processing helix chain 'H' and resid 42 through 58 Processing helix chain 'H' and resid 72 through 82 Processing helix chain 'H' and resid 91 through 106 Processing helix chain 'H' and resid 106 through 112 Processing helix chain 'H' and resid 185 through 193 Processing helix chain 'H' and resid 195 through 209 Processing helix chain 'H' and resid 210 through 214 Processing helix chain 'H' and resid 239 through 246 Processing helix chain 'H' and resid 260 through 262 No H-bonds generated for 'chain 'H' and resid 260 through 262' Processing helix chain 'H' and resid 272 through 276 removed outlier: 4.177A pdb=" N THR H 276 " --> pdb=" O LEU H 273 " (cutoff:3.500A) Processing helix chain 'I' and resid 9 through 29 Processing helix chain 'I' and resid 35 through 47 removed outlier: 6.546A pdb=" N GLY I 42 " --> pdb=" O ASP I 38 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N SER I 43 " --> pdb=" O ARG I 39 " (cutoff:3.500A) Processing helix chain 'I' and resid 47 through 66 removed outlier: 4.071A pdb=" N VAL I 51 " --> pdb=" O THR I 47 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N THR I 54 " --> pdb=" O ALA I 50 " (cutoff:3.500A) Proline residue: I 60 - end of helix Processing helix chain 'I' and resid 68 through 86 removed outlier: 3.531A pdb=" N ALA I 72 " --> pdb=" O PHE I 68 " (cutoff:3.500A) Processing helix chain 'I' and resid 94 through 114 Processing helix chain 'I' and resid 116 through 124 removed outlier: 3.759A pdb=" N ASN I 120 " --> pdb=" O ASP I 116 " (cutoff:3.500A) Processing helix chain 'J' and resid 9 through 29 Processing helix chain 'J' and resid 35 through 47 removed outlier: 6.547A pdb=" N GLY J 42 " --> pdb=" O ASP J 38 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N SER J 43 " --> pdb=" O ARG J 39 " (cutoff:3.500A) Processing helix chain 'J' and resid 47 through 66 removed outlier: 4.071A pdb=" N VAL J 51 " --> pdb=" O THR J 47 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N THR J 54 " --> pdb=" O ALA J 50 " (cutoff:3.500A) Proline residue: J 60 - end of helix Processing helix chain 'J' and resid 68 through 86 removed outlier: 3.530A pdb=" N ALA J 72 " --> pdb=" O PHE J 68 " (cutoff:3.500A) Processing helix chain 'J' and resid 94 through 114 Processing helix chain 'J' and resid 116 through 124 removed outlier: 3.759A pdb=" N ASN J 120 " --> pdb=" O ASP J 116 " (cutoff:3.500A) Processing helix chain 'K' and resid 2 through 16 Processing helix chain 'K' and resid 73 through 77 Processing helix chain 'K' and resid 84 through 89 Processing helix chain 'K' and resid 97 through 118 Processing helix chain 'K' and resid 121 through 133 Processing helix chain 'K' and resid 134 through 144 removed outlier: 4.009A pdb=" N VAL K 140 " --> pdb=" O GLU K 136 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N GLN K 142 " --> pdb=" O SER K 138 " (cutoff:3.500A) Processing helix chain 'K' and resid 172 through 190 Processing helix chain 'K' and resid 243 through 260 Processing helix chain 'K' and resid 282 through 290 removed outlier: 4.501A pdb=" N SER K 287 " --> pdb=" O GLU K 283 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N MET K 288 " --> pdb=" O SER K 284 " (cutoff:3.500A) Processing helix chain 'K' and resid 299 through 302 Processing helix chain 'K' and resid 303 through 311 Processing helix chain 'K' and resid 347 through 361 Processing helix chain 'K' and resid 376 through 384 Processing helix chain 'K' and resid 397 through 408 Processing helix chain 'K' and resid 412 through 427 Processing helix chain 'K' and resid 430 through 447 Processing helix chain 'K' and resid 468 through 486 removed outlier: 4.103A pdb=" N LEU K 474 " --> pdb=" O VAL K 470 " (cutoff:3.500A) Processing helix chain 'K' and resid 493 through 504 removed outlier: 7.152A pdb=" N GLY K 499 " --> pdb=" O ASP K 495 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N SER K 500 " --> pdb=" O ARG K 496 " (cutoff:3.500A) Processing helix chain 'K' and resid 504 through 522 removed outlier: 3.683A pdb=" N VAL K 508 " --> pdb=" O THR K 504 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N THR K 511 " --> pdb=" O ALA K 507 " (cutoff:3.500A) Proline residue: K 517 - end of helix removed outlier: 3.640A pdb=" N LYS K 522 " --> pdb=" O HIS K 518 " (cutoff:3.500A) Processing helix chain 'K' and resid 525 through 543 removed outlier: 3.646A pdb=" N HIS K 542 " --> pdb=" O GLN K 538 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N CYS K 543 " --> pdb=" O ILE K 539 " (cutoff:3.500A) Processing helix chain 'K' and resid 551 through 571 Processing helix chain 'K' and resid 573 through 582 Processing helix chain 'M' and resid 42 through 58 Processing helix chain 'M' and resid 96 through 106 Processing helix chain 'M' and resid 106 through 113 removed outlier: 3.648A pdb=" N ARG M 110 " --> pdb=" O TYR M 106 " (cutoff:3.500A) Processing helix chain 'M' and resid 185 through 192 Processing helix chain 'M' and resid 195 through 213 removed outlier: 5.635A pdb=" N PHE M 210 " --> pdb=" O LEU M 206 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N ASP M 211 " --> pdb=" O VAL M 207 " (cutoff:3.500A) Processing helix chain 'M' and resid 239 through 246 Processing helix chain 'M' and resid 260 through 262 No H-bonds generated for 'chain 'M' and resid 260 through 262' Processing helix chain 'M' and resid 271 through 276 removed outlier: 3.933A pdb=" N GLU M 274 " --> pdb=" O LYS M 271 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N THR M 276 " --> pdb=" O LEU M 273 " (cutoff:3.500A) Processing helix chain 'N' and resid 30 through 42 Processing helix chain 'N' and resid 117 through 131 Processing helix chain 'L' and resid 9 through 29 Processing helix chain 'L' and resid 35 through 47 removed outlier: 6.546A pdb=" N GLY L 42 " --> pdb=" O ASP L 38 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N SER L 43 " --> pdb=" O ARG L 39 " (cutoff:3.500A) Processing helix chain 'L' and resid 47 through 66 removed outlier: 4.071A pdb=" N VAL L 51 " --> pdb=" O THR L 47 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N THR L 54 " --> pdb=" O ALA L 50 " (cutoff:3.500A) Proline residue: L 60 - end of helix Processing helix chain 'L' and resid 68 through 86 removed outlier: 3.531A pdb=" N ALA L 72 " --> pdb=" O PHE L 68 " (cutoff:3.500A) Processing helix chain 'L' and resid 94 through 114 Processing helix chain 'L' and resid 116 through 124 removed outlier: 3.759A pdb=" N ASN L 120 " --> pdb=" O ASP L 116 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 156 through 159 Processing sheet with id=AA2, first strand: chain 'B' and resid 40 through 41 Processing sheet with id=AA3, first strand: chain 'B' and resid 40 through 41 removed outlier: 5.749A pdb=" N ARG B 6 " --> pdb=" O GLU B 230 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N GLU B 230 " --> pdb=" O ARG B 6 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ASP B 8 " --> pdb=" O VAL B 228 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N VAL B 228 " --> pdb=" O ASP B 8 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N VAL B 10 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N LEU B 226 " --> pdb=" O VAL B 10 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N LEU B 12 " --> pdb=" O ARG B 224 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N GLN B 220 " --> pdb=" O GLN B 16 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU B 278 " --> pdb=" O GLU B 230 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 114 through 115 Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 149 Processing sheet with id=AA6, first strand: chain 'B' and resid 248 through 251 Processing sheet with id=AA7, first strand: chain 'C' and resid 31 through 32 removed outlier: 3.811A pdb=" N ARG C 31 " --> pdb=" O LEU C 40 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N GLY C 39 " --> pdb=" O SER C 136 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 31 through 32 removed outlier: 3.811A pdb=" N ARG C 31 " --> pdb=" O LEU C 40 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N GLY C 39 " --> pdb=" O SER C 136 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ASP C 14 " --> pdb=" O ALA C 223 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N ALA C 223 " --> pdb=" O ASP C 14 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 145 through 147 removed outlier: 3.741A pdb=" N HIS C 145 " --> pdb=" O LYS C 170 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 247 through 251 Processing sheet with id=AB2, first strand: chain 'D' and resid 32 through 33 removed outlier: 4.820A pdb=" N GLY D 39 " --> pdb=" O SER D 136 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 32 through 33 removed outlier: 4.820A pdb=" N GLY D 39 " --> pdb=" O SER D 136 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N GLY D 176 " --> pdb=" O VAL D 15 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N VAL D 15 " --> pdb=" O GLY D 176 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N ARG D 6 " --> pdb=" O GLU D 230 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N GLU D 230 " --> pdb=" O ARG D 6 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ASP D 8 " --> pdb=" O VAL D 228 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N VAL D 228 " --> pdb=" O ASP D 8 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N VAL D 10 " --> pdb=" O LEU D 226 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N LEU D 226 " --> pdb=" O VAL D 10 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N LEU D 12 " --> pdb=" O ARG D 224 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 145 through 147 removed outlier: 3.728A pdb=" N HIS D 145 " --> pdb=" O LYS D 170 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 247 through 251 Processing sheet with id=AB6, first strand: chain 'E' and resid 129 through 131 Processing sheet with id=AB7, first strand: chain 'E' and resid 40 through 41 Processing sheet with id=AB8, first strand: chain 'E' and resid 22 through 23 removed outlier: 3.548A pdb=" N LEU E 29 " --> pdb=" O ASP E 23 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 114 through 115 Processing sheet with id=AC1, first strand: chain 'E' and resid 145 through 147 removed outlier: 3.826A pdb=" N HIS E 145 " --> pdb=" O LYS E 170 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 248 through 251 removed outlier: 3.776A pdb=" N GLN E 248 " --> pdb=" O SER E 267 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 40 through 41 removed outlier: 3.789A pdb=" N ARG F 135 " --> pdb=" O ARG F 179 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 40 through 41 removed outlier: 3.789A pdb=" N ARG F 135 " --> pdb=" O ARG F 179 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N ASP F 8 " --> pdb=" O VAL F 228 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N VAL F 228 " --> pdb=" O ASP F 8 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N VAL F 10 " --> pdb=" O LEU F 226 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N LEU F 226 " --> pdb=" O VAL F 10 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N LEU F 12 " --> pdb=" O ARG F 224 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 17 through 18 Processing sheet with id=AC6, first strand: chain 'F' and resid 114 through 115 Processing sheet with id=AC7, first strand: chain 'F' and resid 248 through 251 Processing sheet with id=AC8, first strand: chain 'H' and resid 32 through 33 removed outlier: 4.862A pdb=" N GLY H 39 " --> pdb=" O SER H 136 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'H' and resid 32 through 33 removed outlier: 4.862A pdb=" N GLY H 39 " --> pdb=" O SER H 136 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'H' and resid 114 through 115 removed outlier: 3.784A pdb=" N VAL H 125 " --> pdb=" O ALA H 114 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 247 through 251 Processing sheet with id=AD3, first strand: chain 'K' and resid 25 through 26 Processing sheet with id=AD4, first strand: chain 'K' and resid 29 through 30 removed outlier: 3.607A pdb=" N ILE K 30 " --> pdb=" O ARG K 59 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ARG K 59 " --> pdb=" O ILE K 30 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'K' and resid 44 through 47 Processing sheet with id=AD6, first strand: chain 'K' and resid 324 through 325 Processing sheet with id=AD7, first strand: chain 'K' and resid 330 through 333 Processing sheet with id=AD8, first strand: chain 'M' and resid 40 through 41 removed outlier: 3.955A pdb=" N ARG M 135 " --> pdb=" O ARG M 179 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLY M 176 " --> pdb=" O VAL M 15 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ASP M 14 " --> pdb=" O ALA M 223 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N ALA M 223 " --> pdb=" O ASP M 14 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'M' and resid 114 through 115 Processing sheet with id=AE1, first strand: chain 'M' and resid 143 through 147 removed outlier: 4.273A pdb=" N HIS M 145 " --> pdb=" O LYS M 170 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'M' and resid 247 through 251 Processing sheet with id=AE3, first strand: chain 'N' and resid 23 through 24 removed outlier: 6.957A pdb=" N ARG N 23 " --> pdb=" O MET N 93 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N LEU N 95 " --> pdb=" O ARG N 23 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ASP N 10 " --> pdb=" O ASP N 97 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ALA N 99 " --> pdb=" O SER N 8 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N SER N 8 " --> pdb=" O ALA N 99 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N ARG N 101 " --> pdb=" O GLU N 6 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N GLU N 6 " --> pdb=" O ARG N 101 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N HIS N 103 " --> pdb=" O ILE N 4 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ILE N 4 " --> pdb=" O HIS N 103 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ILE N 4 " --> pdb=" O LEU N 152 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'N' and resid 62 through 70 removed outlier: 7.119A pdb=" N ALA N 99 " --> pdb=" O ILE N 56 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N ILE N 56 " --> pdb=" O ALA N 99 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N ARG N 101 " --> pdb=" O ILE N 54 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N ILE N 54 " --> pdb=" O ARG N 101 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N HIS N 103 " --> pdb=" O LEU N 52 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'N' and resid 170 through 171 1175 hydrogen bonds defined for protein. 3315 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 12 stacking parallelities Total time for adding SS restraints: 5.09 Time building geometry restraints manager: 3.21 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: 1.100 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: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 27.040 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.460 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.57 (0.13), residues: 3184 helix: -1.85 (0.13), residues: 1236 sheet: -2.69 (0.24), residues: 384 loop : -2.71 (0.14), residues: 1564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.047 0.002 ARG D 48 TYR 0.042 0.005 TYR C 7 PHE 0.072 0.004 PHE B 183 TRP 0.053 0.006 TRP L 77 HIS 0.029 0.003 HIS C 214 Details of bonding type rmsd covalent geometry : bond 0.01318 (27430) covalent geometry : angle 1.32558 (37194) hydrogen bonds : bond 0.18718 ( 1148) hydrogen bonds : angle 9.00116 ( 3315) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6368 Ramachandran restraints generated. 3184 Oldfield, 0 Emsley, 3184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6368 Ramachandran restraints generated. 3184 Oldfield, 0 Emsley, 3184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 904 residues out of total 2762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 832 time to evaluate : 0.805 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 144 ASP cc_start: 0.8403 (m-30) cc_final: 0.8145 (m-30) REVERT: B 82 GLU cc_start: 0.7780 (tm-30) cc_final: 0.7333 (tm-30) REVERT: B 183 PHE cc_start: 0.8049 (m-10) cc_final: 0.7321 (m-10) REVERT: B 263 ASP cc_start: 0.8035 (m-30) cc_final: 0.7777 (m-30) REVERT: C 4 GLU cc_start: 0.7791 (tp30) cc_final: 0.7554 (tp30) REVERT: C 25 ASP cc_start: 0.7711 (m-30) cc_final: 0.7319 (m-30) REVERT: C 72 ILE cc_start: 0.8824 (mm) cc_final: 0.8589 (mm) REVERT: C 75 ASN cc_start: 0.8433 (m110) cc_final: 0.7985 (m-40) REVERT: C 156 LYS cc_start: 0.8526 (ttpp) cc_final: 0.8292 (tttm) REVERT: C 209 MET cc_start: 0.6932 (ptm) cc_final: 0.6680 (ptm) REVERT: D 263 ASP cc_start: 0.8616 (m-30) cc_final: 0.8265 (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: 0.8625 (mtp) REVERT: E 171 PHE cc_start: 0.8656 (m-80) cc_final: 0.8223 (m-80) REVERT: E 204 GLN cc_start: 0.8084 (tm130) cc_final: 0.7519 (tm-30) REVERT: E 233 ASN cc_start: 0.8215 (m-40) cc_final: 0.7918 (m-40) REVERT: E 241 ASP cc_start: 0.7245 (t70) cc_final: 0.6700 (t0) REVERT: F 40 LEU cc_start: 0.7679 (tp) cc_final: 0.7310 (tp) REVERT: F 72 ILE cc_start: 0.8290 (mm) cc_final: 0.6734 (mm) REVERT: F 108 ASP cc_start: 0.7638 (t0) cc_final: 0.7358 (t0) REVERT: F 137 ILE cc_start: 0.9459 (mm) cc_final: 0.9139 (mm) REVERT: F 141 MET cc_start: 0.8235 (ttm) cc_final: 0.7861 (ttt) REVERT: F 144 GLU cc_start: 0.7449 (pp20) cc_final: 0.7226 (pp20) REVERT: F 170 LYS cc_start: 0.7766 (ttmm) cc_final: 0.7555 (ttmt) REVERT: G 10 ILE cc_start: 0.8936 (OUTLIER) cc_final: 0.8735 (tp) REVERT: G 17 LEU cc_start: 0.8994 (tt) cc_final: 0.8787 (tt) REVERT: G 56 MET cc_start: 0.9012 (mmm) cc_final: 0.8738 (tmm) REVERT: G 77 TRP cc_start: 0.7854 (t60) cc_final: 0.7060 (t60) REVERT: G 105 TYR cc_start: 0.8764 (t80) cc_final: 0.7703 (t80) REVERT: G 108 GLU cc_start: 0.8156 (mm-30) cc_final: 0.7873 (mm-30) REVERT: G 111 PHE cc_start: 0.8128 (t80) cc_final: 0.7805 (t80) REVERT: G 122 PHE cc_start: 0.7259 (t80) cc_final: 0.6987 (t80) REVERT: H 11 PHE cc_start: 0.7956 (t80) cc_final: 0.7399 (t80) REVERT: H 55 GLN cc_start: 0.9201 (mm110) cc_final: 0.8994 (mm-40) REVERT: H 58 GLN cc_start: 0.8822 (tp-100) cc_final: 0.8170 (tp-100) REVERT: H 96 GLU cc_start: 0.8388 (tp30) cc_final: 0.7963 (tp30) REVERT: H 100 GLN cc_start: 0.7660 (mp-120) cc_final: 0.6897 (mm110) REVERT: H 102 MET cc_start: 0.8794 (mmp) cc_final: 0.8139 (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: 0.8508 (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: 0.8288 (tppt) REVERT: I 84 GLU cc_start: 0.8228 (OUTLIER) cc_final: 0.7738 (tp30) REVERT: I 108 GLU cc_start: 0.8755 (mm-30) cc_final: 0.8430 (mm-30) REVERT: I 110 GLN cc_start: 0.8437 (tp40) cc_final: 0.8028 (tp40) REVERT: I 121 LEU cc_start: 0.8026 (OUTLIER) cc_final: 0.7717 (tp) REVERT: J 9 ASP cc_start: 0.8414 (t0) cc_final: 0.8106 (t0) REVERT: J 27 GLU cc_start: 0.8197 (mt-10) cc_final: 0.7896 (mt-10) REVERT: J 52 PHE cc_start: 0.8134 (m-10) cc_final: 0.7158 (m-80) REVERT: J 56 MET cc_start: 0.8807 (mmm) cc_final: 0.8168 (tmm) REVERT: J 71 ARG cc_start: 0.8025 (OUTLIER) cc_final: 0.6830 (tpp80) REVERT: J 77 TRP cc_start: 0.7756 (t60) cc_final: 0.7535 (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: 0.7339 (m-40) REVERT: K 16 SER cc_start: 0.7730 (t) cc_final: 0.7494 (p) REVERT: K 23 GLU cc_start: 0.6976 (tm-30) cc_final: 0.6574 (tm-30) REVERT: K 61 PHE cc_start: 0.8251 (m-10) cc_final: 0.8010 (m-10) REVERT: K 156 ASN cc_start: 0.8008 (m110) cc_final: 0.7634 (m110) REVERT: K 508 VAL cc_start: 0.8542 (m) cc_final: 0.8207 (p) REVERT: M 16 GLN cc_start: 0.7734 (mm-40) cc_final: 0.7529 (mm-40) REVERT: M 35 GLN cc_start: 0.8108 (mp10) cc_final: 0.7861 (mp10) REVERT: M 221 MET cc_start: 0.8568 (ttt) cc_final: 0.8040 (ttt) REVERT: M 263 ASP cc_start: 0.8076 (m-30) cc_final: 0.7619 (m-30) REVERT: M 277 LYS cc_start: 0.8104 (mppt) cc_final: 0.7888 (mppt) REVERT: N 68 ASN cc_start: 0.7796 (t0) cc_final: 0.7591 (t0) REVERT: N 93 MET cc_start: 0.7439 (ttp) cc_final: 0.7178 (ttp) REVERT: L 17 LEU cc_start: 0.9424 (tt) cc_final: 0.9074 (tt) REVERT: L 103 ILE cc_start: 0.7827 (tt) cc_final: 0.6517 (tt) REVERT: L 107 HIS cc_start: 0.7386 (m90) cc_final: 0.6552 (m90) outliers start: 72 outliers final: 21 residues processed: 865 average time/residue: 0.1801 time to fit residues: 245.5822 Evaluate side-chains 662 residues out of total 2762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 635 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 10 ILE Chi-restraints excluded: chain G residue 13 VAL Chi-restraints excluded: chain G residue 58 LEU Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 124 GLU Chi-restraints excluded: chain I residue 5 ARG Chi-restraints excluded: chain I residue 8 GLN Chi-restraints excluded: chain I residue 13 VAL Chi-restraints excluded: chain I residue 23 LYS Chi-restraints excluded: chain I residue 58 LEU Chi-restraints excluded: chain I residue 76 GLN Chi-restraints excluded: chain I residue 84 GLU Chi-restraints excluded: chain I residue 109 THR Chi-restraints excluded: chain I residue 121 LEU Chi-restraints excluded: chain I residue 124 GLU Chi-restraints excluded: chain J residue 5 ARG Chi-restraints excluded: chain J residue 10 ILE Chi-restraints excluded: chain J residue 71 ARG Chi-restraints excluded: chain J residue 73 VAL Chi-restraints excluded: chain J residue 109 THR Chi-restraints excluded: chain J residue 119 LYS Chi-restraints excluded: chain J residue 124 GLU Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 71 ARG Chi-restraints excluded: chain L residue 76 GLN Chi-restraints excluded: chain L residue 109 THR Chi-restraints excluded: chain L residue 119 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 197 optimal weight: 0.5980 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 0.7980 chunk 261 optimal weight: 0.7980 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 0.0170 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 0.8980 chunk 183 optimal weight: 0.6980 chunk 298 optimal weight: 0.7980 overall best weight: 0.5818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 62 HIS ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 130 GLN ** E 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 63 HIS F 233 ASN ** G 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 97 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 ** 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 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 L 91 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.153469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.120446 restraints weight = 46978.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 67)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.124955 restraints weight = 20844.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.127805 restraints weight = 12070.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 60)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.129641 restraints weight = 8393.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 63)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.130806 restraints weight = 6598.567| |-----------------------------------------------------------------------------| r_work (final): 0.3934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.2407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.091 27430 Z= 0.248 Angle : 0.929 15.614 37194 Z= 0.484 Chirality : 0.052 0.323 4023 Planarity : 0.007 0.118 4752 Dihedral : 15.298 178.105 4257 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 36.52 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.30 % Favored : 90.64 % Rotamer: Outliers : 3.08 % Allowed : 13.70 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.77 (0.14), residues: 3184 helix: -0.96 (0.13), residues: 1258 sheet: -2.55 (0.24), residues: 366 loop : -2.40 (0.14), residues: 1560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 224 TYR 0.033 0.003 TYR L 106 PHE 0.033 0.003 PHE B 183 TRP 0.044 0.003 TRP I 77 HIS 0.018 0.002 HIS C 214 Details of bonding type rmsd covalent geometry : bond 0.00562 (27430) covalent geometry : angle 0.92885 (37194) hydrogen bonds : bond 0.06164 ( 1148) hydrogen bonds : angle 7.29760 ( 3315) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6368 Ramachandran restraints generated. 3184 Oldfield, 0 Emsley, 3184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6368 Ramachandran restraints generated. 3184 Oldfield, 0 Emsley, 3184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 939 residues out of total 2762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 854 time to evaluate : 0.913 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: 0.8099 (t0) cc_final: 0.7512 (t0) REVERT: A 144 ASP cc_start: 0.8514 (m-30) cc_final: 0.8252 (m-30) REVERT: A 165 TRP cc_start: 0.8561 (m-10) cc_final: 0.8324 (m100) REVERT: A 167 GLN cc_start: 0.8243 (tm-30) cc_final: 0.7029 (tm-30) REVERT: A 168 TYR cc_start: 0.7586 (m-80) cc_final: 0.6910 (m-80) REVERT: B 40 LEU cc_start: 0.9014 (mt) cc_final: 0.8777 (mt) REVERT: B 141 MET cc_start: 0.7120 (mmt) cc_final: 0.6766 (mmt) REVERT: B 175 TYR cc_start: 0.8631 (t80) cc_final: 0.8070 (t80) REVERT: B 183 PHE cc_start: 0.8090 (m-10) cc_final: 0.6992 (m-10) REVERT: C 4 GLU cc_start: 0.7693 (tp30) cc_final: 0.7439 (tp30) REVERT: C 72 ILE cc_start: 0.8812 (mm) cc_final: 0.8418 (mm) REVERT: C 75 ASN cc_start: 0.8373 (m110) cc_final: 0.8043 (m-40) REVERT: C 124 GLN cc_start: 0.7643 (mt0) cc_final: 0.7086 (mt0) REVERT: C 156 LYS cc_start: 0.8710 (ttpp) cc_final: 0.8476 (tttm) REVERT: C 175 TYR cc_start: 0.9166 (t80) cc_final: 0.8845 (t80) REVERT: C 191 GLN cc_start: 0.8251 (tt0) cc_final: 0.7975 (tt0) REVERT: C 209 MET cc_start: 0.7202 (ptm) cc_final: 0.7000 (ttp) REVERT: C 220 GLN cc_start: 0.7816 (tm-30) cc_final: 0.6838 (tm-30) REVERT: C 226 LEU cc_start: 0.8679 (tp) cc_final: 0.8452 (tp) REVERT: D 116 MET cc_start: 0.8867 (mmt) cc_final: 0.8527 (mmm) REVERT: D 244 PHE cc_start: 0.9032 (m-10) cc_final: 0.8698 (m-10) REVERT: D 260 SER cc_start: 0.9096 (p) cc_final: 0.8828 (t) REVERT: E 56 MET cc_start: 0.7872 (mtm) cc_final: 0.7626 (mtm) REVERT: E 79 GLU cc_start: 0.7523 (tm-30) cc_final: 0.6962 (tm-30) REVERT: E 184 ILE cc_start: 0.8738 (mm) cc_final: 0.8479 (mm) REVERT: E 204 GLN cc_start: 0.7685 (tm130) cc_final: 0.7232 (tm-30) REVERT: E 221 MET cc_start: 0.8418 (mtm) cc_final: 0.8040 (mtm) REVERT: E 226 LEU cc_start: 0.8785 (tp) cc_final: 0.8358 (tp) REVERT: E 233 ASN cc_start: 0.8244 (m-40) cc_final: 0.7880 (m-40) REVERT: E 241 ASP cc_start: 0.7158 (t70) cc_final: 0.6665 (t0) REVERT: F 19 ASN cc_start: 0.7267 (t0) cc_final: 0.7064 (t0) REVERT: F 72 ILE cc_start: 0.8279 (mm) cc_final: 0.7946 (mm) REVERT: F 108 ASP cc_start: 0.7662 (t0) cc_final: 0.7327 (t0) REVERT: F 124 GLN cc_start: 0.8240 (mt0) cc_final: 0.8024 (mt0) REVERT: F 141 MET cc_start: 0.8375 (ttm) cc_final: 0.7775 (ttt) REVERT: G 16 ARG cc_start: 0.8657 (ttt180) cc_final: 0.8428 (tpt-90) REVERT: G 40 TYR cc_start: 0.8050 (m-80) cc_final: 0.7768 (m-80) REVERT: G 68 PHE cc_start: 0.7258 (t80) cc_final: 0.6851 (t80) REVERT: G 77 TRP cc_start: 0.8105 (t60) cc_final: 0.7392 (t60) REVERT: G 88 ARG cc_start: 0.8069 (OUTLIER) cc_final: 0.7144 (ttp80) REVERT: G 97 GLN cc_start: 0.8436 (tt0) cc_final: 0.7888 (mm-40) REVERT: G 105 TYR cc_start: 0.8364 (t80) cc_final: 0.8107 (t80) REVERT: G 107 HIS cc_start: 0.8519 (m90) cc_final: 0.8305 (m90) REVERT: G 121 LEU cc_start: 0.8231 (mt) cc_final: 0.7909 (mt) REVERT: G 122 PHE cc_start: 0.7578 (t80) cc_final: 0.7094 (t80) REVERT: H 11 PHE cc_start: 0.7584 (t80) cc_final: 0.7189 (t80) REVERT: H 126 ARG cc_start: 0.7024 (ttt-90) cc_final: 0.6442 (tmt170) REVERT: H 178 TYR cc_start: 0.6923 (m-80) cc_final: 0.6544 (m-80) REVERT: H 181 HIS cc_start: 0.7939 (m-70) cc_final: 0.7679 (m-70) REVERT: H 206 LEU cc_start: 0.9394 (mt) cc_final: 0.8950 (mt) REVERT: H 246 ARG cc_start: 0.7233 (mmt90) cc_final: 0.6609 (mmm-85) REVERT: H 261 PHE cc_start: 0.7408 (t80) cc_final: 0.7012 (t80) REVERT: H 272 ASN cc_start: 0.8888 (OUTLIER) cc_final: 0.8464 (t0) REVERT: I 22 GLU cc_start: 0.8713 (tm-30) cc_final: 0.8019 (tm-30) REVERT: I 23 LYS cc_start: 0.8788 (tppt) cc_final: 0.8266 (tppt) REVERT: I 76 GLN cc_start: 0.8397 (mp10) cc_final: 0.7966 (mm-40) REVERT: I 84 GLU cc_start: 0.8462 (tp30) cc_final: 0.8179 (tp30) REVERT: I 87 GLN cc_start: 0.9149 (tt0) cc_final: 0.8614 (tm-30) REVERT: I 94 ASN cc_start: 0.8098 (p0) cc_final: 0.7329 (p0) REVERT: I 113 PHE cc_start: 0.8205 (m-80) cc_final: 0.7953 (m-80) REVERT: I 121 LEU cc_start: 0.8224 (OUTLIER) cc_final: 0.7918 (tp) REVERT: J 18 PHE cc_start: 0.8812 (t80) cc_final: 0.8264 (t80) REVERT: J 23 LYS cc_start: 0.8736 (mmmt) cc_final: 0.8107 (tppp) REVERT: J 52 PHE cc_start: 0.8101 (m-10) cc_final: 0.7469 (m-80) REVERT: J 61 HIS cc_start: 0.8320 (t70) cc_final: 0.7959 (t-90) REVERT: J 65 LYS cc_start: 0.9034 (mttp) cc_final: 0.8622 (mmtm) REVERT: J 97 GLN cc_start: 0.8158 (mm-40) cc_final: 0.7394 (mm-40) REVERT: J 98 GLN cc_start: 0.8745 (tt0) cc_final: 0.8504 (tt0) REVERT: J 100 LEU cc_start: 0.8841 (OUTLIER) cc_final: 0.8525 (mt) REVERT: J 105 TYR cc_start: 0.8901 (t80) cc_final: 0.8445 (t80) REVERT: J 116 ASP cc_start: 0.7230 (t0) cc_final: 0.6984 (t0) REVERT: J 120 ASN cc_start: 0.8149 (m110) cc_final: 0.7724 (m-40) REVERT: K 16 SER cc_start: 0.7925 (t) cc_final: 0.7325 (p) REVERT: K 82 TRP cc_start: 0.8614 (p-90) cc_final: 0.8058 (p-90) REVERT: K 156 ASN cc_start: 0.7929 (m110) cc_final: 0.7560 (m-40) REVERT: K 285 LEU cc_start: 0.9307 (mt) cc_final: 0.9047 (mp) REVERT: K 309 LYS cc_start: 0.8568 (tppt) cc_final: 0.8357 (ttmm) REVERT: K 403 ASP cc_start: 0.7355 (OUTLIER) cc_final: 0.6561 (t70) REVERT: K 565 GLU cc_start: 0.7444 (mm-30) cc_final: 0.6108 (mm-30) REVERT: M 16 GLN cc_start: 0.7272 (mm-40) cc_final: 0.7048 (tp40) REVERT: M 21 ASN cc_start: 0.8087 (p0) cc_final: 0.7719 (p0) REVERT: M 55 GLN cc_start: 0.8698 (tt0) cc_final: 0.8436 (tt0) REVERT: M 102 MET cc_start: 0.5880 (mtt) cc_final: 0.5558 (mtp) REVERT: M 130 GLN cc_start: 0.7245 (OUTLIER) cc_final: 0.6753 (tt0) REVERT: M 198 ASP cc_start: 0.7578 (m-30) cc_final: 0.7020 (m-30) REVERT: M 204 GLN cc_start: 0.8419 (tm-30) cc_final: 0.8132 (tm-30) REVERT: M 212 HIS cc_start: 0.6911 (m-70) cc_final: 0.6331 (m-70) REVERT: M 221 MET cc_start: 0.8443 (ttt) cc_final: 0.7800 (ttt) REVERT: M 263 ASP cc_start: 0.7703 (m-30) cc_final: 0.7409 (m-30) REVERT: N 7 ILE cc_start: 0.8655 (mt) cc_final: 0.8434 (mm) REVERT: N 26 TYR cc_start: 0.8573 (m-80) cc_final: 0.8094 (m-80) REVERT: N 56 ILE cc_start: 0.8728 (mm) cc_final: 0.8514 (mm) REVERT: N 63 THR cc_start: 0.8825 (t) cc_final: 0.8430 (p) REVERT: N 68 ASN cc_start: 0.7729 (t0) cc_final: 0.7518 (t0) REVERT: N 76 GLU cc_start: 0.6760 (mm-30) cc_final: 0.6154 (mm-30) REVERT: N 100 TYR cc_start: 0.8405 (m-80) cc_final: 0.7782 (m-80) REVERT: L 17 LEU cc_start: 0.9366 (tt) cc_final: 0.8995 (tt) REVERT: L 40 TYR cc_start: 0.8619 (m-10) cc_final: 0.8360 (m-10) REVERT: L 56 MET cc_start: 0.7933 (mmm) cc_final: 0.7588 (mmm) REVERT: L 103 ILE cc_start: 0.8393 (tt) cc_final: 0.8085 (tt) REVERT: L 107 HIS cc_start: 0.7438 (m90) cc_final: 0.7006 (m90) outliers start: 85 outliers final: 38 residues processed: 882 average time/residue: 0.1634 time to fit residues: 228.5108 Evaluate side-chains 750 residues out of total 2762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 706 time to evaluate : 1.061 ------------------------------------------------------------------------------- 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 E residue 207 VAL 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 132 THR 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 120 ASN 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 64 optimal weight: 0.9980 chunk 125 optimal weight: 7.9990 chunk 221 optimal weight: 3.9990 chunk 134 optimal weight: 0.8980 chunk 321 optimal weight: 8.9990 chunk 311 optimal weight: 9.9990 chunk 131 optimal weight: 4.9990 chunk 82 optimal weight: 2.9990 chunk 116 optimal weight: 5.9990 chunk 119 optimal weight: 0.7980 chunk 17 optimal weight: 0.5980 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 ASN ** B 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 21 ASN C 55 GLN C 62 HIS ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 52 ASN E 63 HIS ** E 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 97 GLN ** G 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 100 GLN ** H 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 33 ASN ** I 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 8 GLN J 62 HIS ** 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 187 HIS ** 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 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.151149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.118507 restraints weight = 47028.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.122916 restraints weight = 20889.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.125763 restraints weight = 12063.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.127483 restraints weight = 8322.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.128645 restraints weight = 6572.679| |-----------------------------------------------------------------------------| r_work (final): 0.3913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.3132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.083 27430 Z= 0.262 Angle : 0.863 11.735 37194 Z= 0.450 Chirality : 0.051 0.331 4023 Planarity : 0.006 0.071 4752 Dihedral : 14.831 174.458 4197 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 32.63 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.45 % Favored : 90.52 % Rotamer: Outliers : 3.91 % Allowed : 18.08 % Favored : 78.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.64 (0.14), residues: 3184 helix: -0.77 (0.14), residues: 1278 sheet: -2.82 (0.24), residues: 403 loop : -2.29 (0.15), residues: 1503 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 224 TYR 0.037 0.003 TYR K 440 PHE 0.037 0.003 PHE G 111 TRP 0.051 0.003 TRP I 77 HIS 0.024 0.002 HIS C 214 Details of bonding type rmsd covalent geometry : bond 0.00593 (27430) covalent geometry : angle 0.86324 (37194) hydrogen bonds : bond 0.05420 ( 1148) hydrogen bonds : angle 6.92333 ( 3315) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6368 Ramachandran restraints generated. 3184 Oldfield, 0 Emsley, 3184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6368 Ramachandran restraints generated. 3184 Oldfield, 0 Emsley, 3184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 873 residues out of total 2762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 765 time to evaluate : 0.794 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 PHE cc_start: 0.8357 (OUTLIER) cc_final: 0.5985 (t80) REVERT: A 126 ASN cc_start: 0.8359 (t0) cc_final: 0.7472 (t0) REVERT: A 144 ASP cc_start: 0.8591 (m-30) cc_final: 0.8323 (m-30) REVERT: A 155 TYR cc_start: 0.8690 (m-80) cc_final: 0.8469 (m-80) REVERT: A 165 TRP cc_start: 0.8559 (m-10) cc_final: 0.8318 (m100) REVERT: A 167 GLN cc_start: 0.8485 (tm-30) cc_final: 0.7815 (tm-30) REVERT: A 168 TYR cc_start: 0.7711 (m-80) cc_final: 0.7477 (m-80) REVERT: B 91 LYS cc_start: 0.8219 (mtpt) cc_final: 0.8004 (mtpt) REVERT: B 175 TYR cc_start: 0.8631 (t80) cc_final: 0.8063 (t80) REVERT: B 183 PHE cc_start: 0.8412 (m-80) cc_final: 0.7470 (m-10) REVERT: C 4 GLU cc_start: 0.7453 (tp30) cc_final: 0.7086 (tp30) REVERT: C 156 LYS cc_start: 0.8733 (ttpp) cc_final: 0.8513 (tttm) REVERT: C 220 GLN cc_start: 0.7909 (tm-30) cc_final: 0.6697 (tm-30) REVERT: C 226 LEU cc_start: 0.8177 (tp) cc_final: 0.7795 (tp) REVERT: C 279 LEU cc_start: 0.8351 (OUTLIER) cc_final: 0.8121 (tp) REVERT: D 36 THR cc_start: 0.8111 (OUTLIER) cc_final: 0.7720 (p) REVERT: D 102 MET cc_start: 0.8076 (mmt) cc_final: 0.7835 (mmt) REVERT: D 244 PHE cc_start: 0.8996 (m-10) cc_final: 0.8642 (m-10) REVERT: E 79 GLU cc_start: 0.7686 (tm-30) cc_final: 0.7176 (tm-30) REVERT: E 101 TYR cc_start: 0.7859 (t80) cc_final: 0.7638 (t80) REVERT: E 184 ILE cc_start: 0.8766 (mm) cc_final: 0.8556 (mm) REVERT: E 204 GLN cc_start: 0.7730 (tm130) cc_final: 0.7070 (tm-30) REVERT: E 221 MET cc_start: 0.8456 (mtm) cc_final: 0.8163 (mtm) REVERT: E 226 LEU cc_start: 0.8887 (tp) cc_final: 0.8460 (tp) REVERT: E 233 ASN cc_start: 0.8287 (m-40) cc_final: 0.7905 (m-40) REVERT: E 241 ASP cc_start: 0.7070 (t70) cc_final: 0.6559 (t0) REVERT: F 66 PHE cc_start: 0.8755 (t80) cc_final: 0.8520 (t80) REVERT: F 72 ILE cc_start: 0.8307 (mm) cc_final: 0.7967 (mm) REVERT: F 108 ASP cc_start: 0.7771 (t0) cc_final: 0.7317 (t0) REVERT: F 145 HIS cc_start: 0.8676 (m170) cc_final: 0.8228 (m170) REVERT: F 172 THR cc_start: 0.8030 (m) cc_final: 0.7109 (p) REVERT: G 25 GLN cc_start: 0.8677 (OUTLIER) cc_final: 0.8426 (pt0) REVERT: G 58 LEU cc_start: 0.8198 (tp) cc_final: 0.7768 (tp) REVERT: G 68 PHE cc_start: 0.7642 (t80) cc_final: 0.7423 (t80) REVERT: G 71 ARG cc_start: 0.8395 (mmm160) cc_final: 0.7900 (mmm-85) REVERT: G 77 TRP cc_start: 0.8156 (t60) cc_final: 0.7405 (t60) REVERT: G 88 ARG cc_start: 0.8064 (OUTLIER) cc_final: 0.7143 (ttp80) REVERT: G 96 GLU cc_start: 0.8949 (pm20) cc_final: 0.8609 (pm20) REVERT: G 98 GLN cc_start: 0.7937 (tt0) cc_final: 0.7685 (tm-30) REVERT: G 105 TYR cc_start: 0.8519 (t80) cc_final: 0.8275 (t80) REVERT: G 110 GLN cc_start: 0.7757 (tp-100) cc_final: 0.7341 (tp-100) REVERT: G 111 PHE cc_start: 0.8199 (t80) cc_final: 0.7733 (t80) REVERT: G 122 PHE cc_start: 0.7770 (t80) cc_final: 0.7213 (t80) REVERT: H 11 PHE cc_start: 0.7609 (t80) cc_final: 0.7047 (t80) REVERT: H 81 HIS cc_start: 0.8401 (OUTLIER) cc_final: 0.7820 (t-90) REVERT: H 102 MET cc_start: 0.8794 (mmm) cc_final: 0.7832 (mmm) REVERT: H 126 ARG cc_start: 0.7258 (ttt-90) cc_final: 0.6913 (ttt-90) REVERT: H 178 TYR cc_start: 0.7102 (m-80) cc_final: 0.6345 (m-10) REVERT: H 181 HIS cc_start: 0.8019 (m-70) cc_final: 0.7494 (m-70) REVERT: H 261 PHE cc_start: 0.7593 (t80) cc_final: 0.7250 (t80) REVERT: I 18 PHE cc_start: 0.8831 (t80) cc_final: 0.8591 (t80) REVERT: I 21 LEU cc_start: 0.8896 (mp) cc_final: 0.8671 (mp) REVERT: I 22 GLU cc_start: 0.8777 (tm-30) cc_final: 0.7971 (tm-30) REVERT: I 23 LYS cc_start: 0.8839 (tppt) cc_final: 0.8258 (tppt) REVERT: I 71 ARG cc_start: 0.8871 (mmm160) cc_final: 0.8610 (mmm160) REVERT: I 77 TRP cc_start: 0.8172 (t60) cc_final: 0.7593 (t60) REVERT: I 81 GLN cc_start: 0.8979 (OUTLIER) cc_final: 0.8495 (mp10) REVERT: I 82 ILE cc_start: 0.8435 (mm) cc_final: 0.8213 (mm) REVERT: I 84 GLU cc_start: 0.8444 (tp30) cc_final: 0.8082 (tp30) REVERT: I 87 GLN cc_start: 0.9112 (tt0) cc_final: 0.8615 (tm-30) REVERT: I 88 ARG cc_start: 0.7687 (ttp80) cc_final: 0.6859 (tmm-80) REVERT: I 113 PHE cc_start: 0.8226 (m-80) cc_final: 0.7801 (m-80) REVERT: I 123 ASN cc_start: 0.8566 (m110) cc_final: 0.8270 (m-40) REVERT: J 18 PHE cc_start: 0.8759 (t80) cc_final: 0.8090 (t80) REVERT: J 23 LYS cc_start: 0.8840 (mmmt) cc_final: 0.8560 (tppp) REVERT: J 52 PHE cc_start: 0.8067 (m-10) cc_final: 0.7499 (m-80) REVERT: J 61 HIS cc_start: 0.8348 (t70) cc_final: 0.7547 (t-90) REVERT: J 65 LYS cc_start: 0.9207 (mttp) cc_final: 0.8875 (mttp) REVERT: J 78 GLU cc_start: 0.8983 (tp30) cc_final: 0.8410 (tp30) REVERT: J 80 ARG cc_start: 0.8195 (mtm-85) cc_final: 0.7706 (mmm-85) REVERT: J 91 ASN cc_start: 0.8509 (m-40) cc_final: 0.7984 (m-40) REVERT: J 105 TYR cc_start: 0.8916 (t80) cc_final: 0.8425 (t80) REVERT: J 115 LYS cc_start: 0.5433 (mmtt) cc_final: 0.5111 (mmtt) REVERT: J 116 ASP cc_start: 0.7316 (t0) cc_final: 0.6941 (t0) REVERT: J 120 ASN cc_start: 0.8125 (m110) cc_final: 0.7392 (m-40) REVERT: K 82 TRP cc_start: 0.8566 (p-90) cc_final: 0.8003 (p-90) REVERT: K 156 ASN cc_start: 0.7917 (m110) cc_final: 0.7465 (m-40) REVERT: K 250 TYR cc_start: 0.7976 (OUTLIER) cc_final: 0.6680 (p90) REVERT: K 285 LEU cc_start: 0.9292 (mt) cc_final: 0.9049 (mp) REVERT: K 288 MET cc_start: 0.7791 (mtm) cc_final: 0.7511 (ptp) REVERT: K 309 LYS cc_start: 0.8584 (tppt) cc_final: 0.8364 (ttmm) REVERT: K 436 LEU cc_start: 0.8943 (mt) cc_final: 0.8490 (tp) REVERT: M 16 GLN cc_start: 0.7194 (mm-40) cc_final: 0.6933 (tp40) REVERT: M 102 MET cc_start: 0.5921 (mtt) cc_final: 0.5637 (mtt) REVERT: M 147 ILE cc_start: 0.9119 (pt) cc_final: 0.8872 (mt) REVERT: M 204 GLN cc_start: 0.8460 (tm-30) cc_final: 0.8183 (tm-30) REVERT: M 209 MET cc_start: 0.8019 (ttp) cc_final: 0.7665 (ttp) REVERT: M 221 MET cc_start: 0.8379 (ttt) cc_final: 0.7922 (ttt) REVERT: M 233 ASN cc_start: 0.7238 (OUTLIER) cc_final: 0.7031 (t0) REVERT: M 277 LYS cc_start: 0.7939 (mppt) cc_final: 0.7517 (mppt) REVERT: N 26 TYR cc_start: 0.8588 (m-80) cc_final: 0.7903 (m-80) REVERT: N 63 THR cc_start: 0.8974 (t) cc_final: 0.8507 (p) REVERT: N 68 ASN cc_start: 0.7768 (t0) cc_final: 0.7453 (t0) REVERT: N 146 PRO cc_start: 0.9172 (Cg_endo) cc_final: 0.8931 (Cg_exo) REVERT: L 17 LEU cc_start: 0.9399 (tt) cc_final: 0.8697 (pp) REVERT: L 40 TYR cc_start: 0.8557 (m-10) cc_final: 0.8059 (m-80) REVERT: L 76 GLN cc_start: 0.8823 (mp10) cc_final: 0.8510 (mm110) REVERT: L 96 GLU cc_start: 0.8242 (pm20) cc_final: 0.7939 (pm20) REVERT: L 98 GLN cc_start: 0.7754 (tt0) cc_final: 0.7527 (pt0) REVERT: L 103 ILE cc_start: 0.8398 (tt) cc_final: 0.7942 (tt) REVERT: L 107 HIS cc_start: 0.6603 (m90) cc_final: 0.5956 (m90) outliers start: 108 outliers final: 57 residues processed: 815 average time/residue: 0.1654 time to fit residues: 212.1722 Evaluate side-chains 748 residues out of total 2762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 682 time to evaluate : 1.029 ------------------------------------------------------------------------------- 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 A residue 176 SER Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain C residue 109 ILE Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 279 LEU 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 E residue 52 ASN Chi-restraints excluded: chain E residue 109 ILE Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 203 TRP Chi-restraints excluded: chain F residue 21 ASN Chi-restraints excluded: chain F residue 32 ILE Chi-restraints excluded: chain F residue 40 LEU Chi-restraints excluded: chain G residue 10 ILE Chi-restraints excluded: chain G residue 13 VAL Chi-restraints excluded: chain G residue 25 GLN Chi-restraints excluded: chain G residue 49 ILE Chi-restraints excluded: chain G residue 88 ARG Chi-restraints excluded: chain G residue 95 LEU Chi-restraints excluded: chain H residue 81 HIS Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain H residue 132 THR Chi-restraints excluded: chain H residue 229 PHE Chi-restraints excluded: chain H residue 253 ASP Chi-restraints excluded: chain H residue 276 THR Chi-restraints excluded: chain I residue 13 VAL Chi-restraints excluded: chain I residue 20 VAL Chi-restraints excluded: chain I residue 25 GLN Chi-restraints excluded: chain I residue 81 GLN Chi-restraints excluded: chain K residue 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 458 MET Chi-restraints excluded: chain K residue 481 ILE Chi-restraints excluded: chain M residue 42 THR Chi-restraints excluded: chain M residue 46 LEU Chi-restraints excluded: chain M residue 125 VAL Chi-restraints excluded: chain M residue 180 CYS Chi-restraints excluded: chain M residue 233 ASN 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 107 optimal weight: 0.9980 chunk 301 optimal weight: 2.9990 chunk 170 optimal weight: 0.9990 chunk 79 optimal weight: 0.6980 chunk 139 optimal weight: 10.0000 chunk 182 optimal weight: 1.9990 chunk 186 optimal weight: 0.9980 chunk 236 optimal weight: 0.9990 chunk 209 optimal weight: 7.9990 chunk 169 optimal weight: 0.9980 chunk 259 optimal weight: 2.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 ASN ** B 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 124 GLN ** C 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 25 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 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 55 GLN ** H 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 97 GLN J 8 GLN ** J 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 74 GLN J 123 ASN ** K 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 383 ASN ** K 407 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 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 98 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.153047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.119733 restraints weight = 46672.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.124253 restraints weight = 20908.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 60)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.127165 restraints weight = 12156.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.128985 restraints weight = 8431.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.130061 restraints weight = 6660.364| |-----------------------------------------------------------------------------| r_work (final): 0.3940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 0.3656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 27430 Z= 0.223 Angle : 0.812 12.404 37194 Z= 0.425 Chirality : 0.050 0.305 4023 Planarity : 0.006 0.089 4752 Dihedral : 14.656 172.707 4195 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 31.47 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.98 % Favored : 90.99 % Rotamer: Outliers : 4.24 % Allowed : 20.22 % Favored : 75.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.52 (0.14), residues: 3184 helix: -0.67 (0.14), residues: 1282 sheet: -2.78 (0.24), residues: 377 loop : -2.24 (0.15), residues: 1525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 280 TYR 0.039 0.003 TYR J 106 PHE 0.033 0.003 PHE G 111 TRP 0.047 0.003 TRP J 77 HIS 0.025 0.002 HIS C 214 Details of bonding type rmsd covalent geometry : bond 0.00501 (27430) covalent geometry : angle 0.81219 (37194) hydrogen bonds : bond 0.05006 ( 1148) hydrogen bonds : angle 6.76646 ( 3315) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6368 Ramachandran restraints generated. 3184 Oldfield, 0 Emsley, 3184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6368 Ramachandran restraints generated. 3184 Oldfield, 0 Emsley, 3184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 872 residues out of total 2762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 755 time to evaluate : 0.970 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 119 PHE cc_start: 0.8257 (OUTLIER) cc_final: 0.6345 (t80) REVERT: A 126 ASN cc_start: 0.8289 (t0) cc_final: 0.7444 (t0) REVERT: A 155 TYR cc_start: 0.8537 (m-80) cc_final: 0.8248 (m-80) REVERT: A 164 GLU cc_start: 0.8187 (tp30) cc_final: 0.7744 (tp30) REVERT: A 165 TRP cc_start: 0.8530 (m-10) cc_final: 0.8236 (m100) REVERT: A 167 GLN cc_start: 0.8544 (tm-30) cc_final: 0.7677 (tm-30) REVERT: A 168 TYR cc_start: 0.7463 (m-80) cc_final: 0.7207 (m-80) REVERT: B 69 GLU cc_start: 0.6697 (tm-30) cc_final: 0.6341 (tm-30) REVERT: B 83 GLN cc_start: 0.8654 (mm-40) cc_final: 0.8448 (mm-40) REVERT: B 141 MET cc_start: 0.6848 (mmt) cc_final: 0.6415 (mmt) REVERT: B 175 TYR cc_start: 0.8576 (t80) cc_final: 0.8121 (t80) REVERT: B 183 PHE cc_start: 0.8299 (m-80) cc_final: 0.7751 (m-10) REVERT: C 67 ILE cc_start: 0.8417 (OUTLIER) cc_final: 0.7996 (mm) REVERT: C 110 ARG cc_start: 0.7572 (ptm160) cc_final: 0.6821 (ptm160) REVERT: C 146 SER cc_start: 0.8335 (t) cc_final: 0.8003 (t) REVERT: C 220 GLN cc_start: 0.7823 (tm-30) cc_final: 0.6516 (tm-30) REVERT: C 226 LEU cc_start: 0.8096 (tp) cc_final: 0.7753 (tp) REVERT: C 256 GLU cc_start: 0.7521 (tm-30) cc_final: 0.7272 (tm-30) REVERT: D 35 GLN cc_start: 0.8467 (mm-40) cc_final: 0.8109 (tp-100) REVERT: D 36 THR cc_start: 0.7986 (OUTLIER) cc_final: 0.7660 (p) REVERT: D 102 MET cc_start: 0.8045 (mmt) cc_final: 0.7783 (mmt) REVERT: E 17 ASP cc_start: 0.8392 (t70) cc_final: 0.7470 (t0) REVERT: E 79 GLU cc_start: 0.7683 (tm-30) cc_final: 0.7099 (tm-30) REVERT: E 101 TYR cc_start: 0.8010 (t80) cc_final: 0.7803 (t80) REVERT: E 116 MET cc_start: 0.8078 (mmt) cc_final: 0.7802 (mmt) REVERT: E 167 MET cc_start: 0.8789 (mtm) cc_final: 0.8531 (mtp) REVERT: E 184 ILE cc_start: 0.8844 (mm) cc_final: 0.8624 (mm) REVERT: E 204 GLN cc_start: 0.7726 (tm130) cc_final: 0.7038 (tm-30) REVERT: E 221 MET cc_start: 0.8322 (OUTLIER) cc_final: 0.7539 (mtm) REVERT: E 226 LEU cc_start: 0.8762 (tp) cc_final: 0.8473 (tp) REVERT: E 233 ASN cc_start: 0.8190 (m-40) cc_final: 0.7831 (m-40) REVERT: E 241 ASP cc_start: 0.7039 (t70) cc_final: 0.6630 (t0) REVERT: F 72 ILE cc_start: 0.8315 (mm) cc_final: 0.7963 (mm) REVERT: F 145 HIS cc_start: 0.8676 (m170) cc_final: 0.8454 (m170) REVERT: F 221 MET cc_start: 0.7341 (mtm) cc_final: 0.7139 (mtm) REVERT: G 8 GLN cc_start: 0.8433 (mm110) cc_final: 0.8210 (mm-40) REVERT: G 17 LEU cc_start: 0.9145 (OUTLIER) cc_final: 0.8671 (pp) REVERT: G 25 GLN cc_start: 0.8429 (OUTLIER) cc_final: 0.8113 (pt0) REVERT: G 68 PHE cc_start: 0.7619 (t80) cc_final: 0.7399 (t80) REVERT: G 71 ARG cc_start: 0.8554 (mmm160) cc_final: 0.8129 (mmm-85) REVERT: G 77 TRP cc_start: 0.8256 (t60) cc_final: 0.8003 (t60) REVERT: G 88 ARG cc_start: 0.8033 (OUTLIER) cc_final: 0.7070 (ttp80) REVERT: G 110 GLN cc_start: 0.7558 (tp-100) cc_final: 0.7180 (tp-100) REVERT: G 111 PHE cc_start: 0.8173 (t80) cc_final: 0.7973 (t80) REVERT: G 122 PHE cc_start: 0.8120 (t80) cc_final: 0.7487 (t80) REVERT: H 11 PHE cc_start: 0.7555 (t80) cc_final: 0.6902 (t80) REVERT: H 86 VAL cc_start: 0.8411 (OUTLIER) cc_final: 0.6397 (p) REVERT: H 96 GLU cc_start: 0.8857 (tp30) cc_final: 0.8653 (tp30) REVERT: H 102 MET cc_start: 0.8827 (mmm) cc_final: 0.8034 (mmm) REVERT: H 126 ARG cc_start: 0.7326 (ttt-90) cc_final: 0.7124 (ttt-90) REVERT: H 178 TYR cc_start: 0.7059 (m-80) cc_final: 0.6334 (m-10) REVERT: H 206 LEU cc_start: 0.9406 (mt) cc_final: 0.8985 (mt) REVERT: H 261 PHE cc_start: 0.7609 (t80) cc_final: 0.7267 (t80) REVERT: I 18 PHE cc_start: 0.8795 (t80) cc_final: 0.8573 (t80) REVERT: I 22 GLU cc_start: 0.8855 (tm-30) cc_final: 0.8195 (tm-30) REVERT: I 23 LYS cc_start: 0.8891 (tppt) cc_final: 0.8564 (tppt) REVERT: I 71 ARG cc_start: 0.8831 (mmm160) cc_final: 0.8574 (mmm160) REVERT: I 77 TRP cc_start: 0.8433 (t60) cc_final: 0.7435 (t60) REVERT: I 81 GLN cc_start: 0.8997 (OUTLIER) cc_final: 0.8198 (mp10) REVERT: I 84 GLU cc_start: 0.8467 (tp30) cc_final: 0.7920 (tp30) REVERT: I 87 GLN cc_start: 0.9100 (tt0) cc_final: 0.8631 (tm-30) REVERT: I 119 LYS cc_start: 0.9290 (ptmm) cc_final: 0.8790 (ptmm) REVERT: I 123 ASN cc_start: 0.8568 (m110) cc_final: 0.8174 (m110) REVERT: J 18 PHE cc_start: 0.8744 (t80) cc_final: 0.8147 (t80) REVERT: J 52 PHE cc_start: 0.8042 (m-10) cc_final: 0.7609 (m-80) REVERT: J 61 HIS cc_start: 0.8219 (t70) cc_final: 0.7673 (t-90) REVERT: J 78 GLU cc_start: 0.8906 (tp30) cc_final: 0.8416 (tp30) REVERT: J 91 ASN cc_start: 0.8535 (m-40) cc_final: 0.7981 (m-40) REVERT: J 98 GLN cc_start: 0.8545 (tt0) cc_final: 0.8185 (tp40) REVERT: J 115 LYS cc_start: 0.5389 (mmtt) cc_final: 0.5089 (mmtt) REVERT: K 59 ARG cc_start: 0.8961 (mpp80) cc_final: 0.8757 (mpp80) REVERT: K 250 TYR cc_start: 0.7899 (OUTLIER) cc_final: 0.6574 (p90) REVERT: K 281 LEU cc_start: 0.8456 (mp) cc_final: 0.8086 (mp) REVERT: K 526 GLU cc_start: 0.7568 (mm-30) cc_final: 0.6735 (tp30) REVERT: M 16 GLN cc_start: 0.7102 (mm-40) cc_final: 0.6891 (tp40) REVERT: M 54 ILE cc_start: 0.8997 (mm) cc_final: 0.8794 (mm) REVERT: M 130 GLN cc_start: 0.7275 (OUTLIER) cc_final: 0.6923 (tt0) REVERT: M 175 TYR cc_start: 0.8486 (t80) cc_final: 0.8251 (t80) REVERT: M 204 GLN cc_start: 0.8297 (tm-30) cc_final: 0.7955 (tm-30) REVERT: M 221 MET cc_start: 0.8228 (ttt) cc_final: 0.7959 (ttt) REVERT: M 277 LYS cc_start: 0.7854 (mppt) cc_final: 0.7364 (mppt) REVERT: N 26 TYR cc_start: 0.8432 (m-80) cc_final: 0.7563 (m-80) REVERT: N 63 THR cc_start: 0.8980 (t) cc_final: 0.8531 (p) REVERT: N 68 ASN cc_start: 0.7611 (t0) cc_final: 0.7185 (t0) REVERT: N 89 GLN cc_start: 0.8402 (OUTLIER) cc_final: 0.7948 (mt0) REVERT: N 152 LEU cc_start: 0.8594 (mp) cc_final: 0.8281 (mp) REVERT: N 171 MET cc_start: 0.7184 (mtm) cc_final: 0.6518 (mtm) REVERT: L 17 LEU cc_start: 0.8985 (tt) cc_final: 0.8631 (pp) REVERT: L 24 ILE cc_start: 0.8875 (mt) cc_final: 0.8635 (mp) REVERT: L 35 THR cc_start: 0.8635 (OUTLIER) cc_final: 0.8402 (t) REVERT: L 40 TYR cc_start: 0.8683 (m-10) cc_final: 0.8314 (m-80) REVERT: L 76 GLN cc_start: 0.8819 (OUTLIER) cc_final: 0.8501 (mm110) REVERT: L 96 GLU cc_start: 0.8178 (pm20) cc_final: 0.7899 (pm20) REVERT: L 98 GLN cc_start: 0.7910 (OUTLIER) cc_final: 0.7683 (pt0) outliers start: 117 outliers final: 58 residues processed: 818 average time/residue: 0.1628 time to fit residues: 212.4958 Evaluate side-chains 760 residues out of total 2762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 687 time to evaluate : 0.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 PHE Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 109 ILE Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 133 PHE Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain D residue 36 THR Chi-restraints excluded: chain D residue 44 VAL 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 201 LEU Chi-restraints excluded: chain E residue 207 VAL Chi-restraints excluded: chain E residue 221 MET Chi-restraints excluded: chain F residue 21 ASN Chi-restraints excluded: chain F residue 32 ILE Chi-restraints excluded: chain F residue 40 LEU Chi-restraints excluded: chain F residue 67 ILE Chi-restraints excluded: chain F residue 124 GLN Chi-restraints excluded: chain F residue 187 HIS Chi-restraints excluded: chain G residue 10 ILE Chi-restraints excluded: chain G residue 17 LEU Chi-restraints excluded: chain G residue 25 GLN 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 124 GLU Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain H residue 132 THR Chi-restraints excluded: chain H residue 228 VAL Chi-restraints excluded: chain H residue 229 PHE Chi-restraints excluded: chain H residue 253 ASP Chi-restraints excluded: chain H residue 266 VAL Chi-restraints excluded: chain H residue 276 THR Chi-restraints excluded: chain I residue 13 VAL Chi-restraints excluded: chain I residue 25 GLN Chi-restraints excluded: chain I residue 81 GLN Chi-restraints excluded: chain J residue 25 GLN 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 330 LEU Chi-restraints excluded: chain K residue 383 ASN Chi-restraints excluded: chain K residue 403 ASP Chi-restraints excluded: chain K residue 478 LEU Chi-restraints excluded: chain M residue 42 THR Chi-restraints excluded: chain M residue 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 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 89 GLN Chi-restraints excluded: chain N residue 133 GLN Chi-restraints excluded: chain N residue 159 LEU Chi-restraints excluded: chain N residue 192 PHE Chi-restraints excluded: chain N residue 201 VAL Chi-restraints excluded: chain L residue 35 THR Chi-restraints excluded: chain L residue 76 GLN Chi-restraints excluded: chain L residue 81 GLN Chi-restraints excluded: chain L residue 84 GLU Chi-restraints excluded: chain L residue 98 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 69 optimal weight: 0.7980 chunk 243 optimal weight: 0.5980 chunk 218 optimal weight: 0.4980 chunk 253 optimal weight: 1.9990 chunk 260 optimal weight: 3.9990 chunk 64 optimal weight: 0.0040 chunk 149 optimal weight: 1.9990 chunk 183 optimal weight: 0.5980 chunk 294 optimal weight: 2.9990 chunk 266 optimal weight: 0.6980 chunk 279 optimal weight: 2.9990 overall best weight: 0.4792 ------------------------------------------------------------------------------- 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 ** B 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 58 GLN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 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** ** F 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 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 I 98 GLN J 8 GLN ** J 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 74 GLN J 85 HIS ** K 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 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 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.158283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.124511 restraints weight = 46779.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.129120 restraints weight = 21035.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.132086 restraints weight = 12249.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 61)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.133994 restraints weight = 8484.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.134946 restraints weight = 6669.950| |-----------------------------------------------------------------------------| r_work (final): 0.3975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7500 moved from start: 0.4151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 27430 Z= 0.191 Angle : 0.802 13.064 37194 Z= 0.417 Chirality : 0.049 0.290 4023 Planarity : 0.006 0.075 4752 Dihedral : 14.498 170.572 4193 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 29.34 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.79 % Favored : 91.17 % Rotamer: Outliers : 5.14 % Allowed : 20.58 % Favored : 74.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.45 (0.14), residues: 3184 helix: -0.60 (0.14), residues: 1273 sheet: -2.74 (0.24), residues: 374 loop : -2.22 (0.14), residues: 1537 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 280 TYR 0.036 0.003 TYR J 106 PHE 0.034 0.002 PHE G 111 TRP 0.066 0.003 TRP J 77 HIS 0.027 0.002 HIS C 214 Details of bonding type rmsd covalent geometry : bond 0.00432 (27430) covalent geometry : angle 0.80153 (37194) hydrogen bonds : bond 0.04766 ( 1148) hydrogen bonds : angle 6.68395 ( 3315) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6368 Ramachandran restraints generated. 3184 Oldfield, 0 Emsley, 3184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6368 Ramachandran restraints generated. 3184 Oldfield, 0 Emsley, 3184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 914 residues out of total 2762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 772 time to evaluate : 0.799 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 126 ASN cc_start: 0.8315 (t0) cc_final: 0.7352 (t0) REVERT: A 133 TRP cc_start: 0.7512 (t-100) cc_final: 0.7055 (t-100) REVERT: A 155 TYR cc_start: 0.8503 (m-80) cc_final: 0.8273 (m-80) REVERT: A 164 GLU cc_start: 0.8293 (tp30) cc_final: 0.7796 (tp30) REVERT: A 165 TRP cc_start: 0.8496 (m-10) cc_final: 0.8235 (m100) REVERT: A 167 GLN cc_start: 0.8476 (tm-30) cc_final: 0.7562 (tm-30) REVERT: A 168 TYR cc_start: 0.7442 (m-80) cc_final: 0.7019 (m-80) REVERT: B 69 GLU cc_start: 0.6479 (tm-30) cc_final: 0.6246 (tm-30) REVERT: B 141 MET cc_start: 0.6708 (mmt) cc_final: 0.6306 (mmt) REVERT: B 171 PHE cc_start: 0.8323 (m-80) cc_final: 0.8108 (m-80) REVERT: B 175 TYR cc_start: 0.8445 (t80) cc_final: 0.8082 (t80) REVERT: B 183 PHE cc_start: 0.8079 (m-80) cc_final: 0.7740 (m-80) REVERT: B 201 LEU cc_start: 0.8185 (OUTLIER) cc_final: 0.7891 (mm) REVERT: B 241 ASP cc_start: 0.7875 (t70) cc_final: 0.7346 (t0) REVERT: C 48 ARG cc_start: 0.7553 (tpt90) cc_final: 0.7277 (tpt90) REVERT: C 67 ILE cc_start: 0.8469 (OUTLIER) cc_final: 0.7798 (mm) REVERT: C 103 CYS cc_start: 0.8170 (m) cc_final: 0.7946 (m) REVERT: C 146 SER cc_start: 0.8157 (t) cc_final: 0.7864 (t) REVERT: C 220 GLN cc_start: 0.7713 (tm-30) cc_final: 0.6292 (tm-30) REVERT: C 226 LEU cc_start: 0.7998 (tp) cc_final: 0.7719 (tp) REVERT: C 243 LEU cc_start: 0.7832 (OUTLIER) cc_final: 0.7474 (mt) REVERT: D 35 GLN cc_start: 0.8529 (mm-40) cc_final: 0.8219 (tp-100) REVERT: D 36 THR cc_start: 0.8007 (OUTLIER) cc_final: 0.7662 (p) REVERT: D 227 TYR cc_start: 0.8369 (m-80) cc_final: 0.8142 (m-80) REVERT: E 17 ASP cc_start: 0.7951 (t70) cc_final: 0.6858 (t0) REVERT: E 79 GLU cc_start: 0.7686 (tm-30) cc_final: 0.7084 (tm-30) REVERT: E 116 MET cc_start: 0.8290 (mmt) cc_final: 0.7896 (mmt) REVERT: E 144 GLU cc_start: 0.7913 (mt-10) cc_final: 0.7602 (mt-10) REVERT: E 167 MET cc_start: 0.8685 (mtm) cc_final: 0.8451 (mtp) REVERT: E 184 ILE cc_start: 0.8682 (mm) cc_final: 0.8445 (mm) REVERT: E 204 GLN cc_start: 0.7711 (tm130) cc_final: 0.6908 (tm-30) REVERT: E 233 ASN cc_start: 0.8120 (m-40) cc_final: 0.7803 (m-40) REVERT: E 241 ASP cc_start: 0.7034 (t70) cc_final: 0.6717 (t0) REVERT: E 264 TYR cc_start: 0.8550 (OUTLIER) cc_final: 0.8339 (m-10) REVERT: F 25 ASP cc_start: 0.7400 (OUTLIER) cc_final: 0.7038 (t70) REVERT: F 48 ARG cc_start: 0.7183 (tpt170) cc_final: 0.6776 (tpm170) REVERT: F 72 ILE cc_start: 0.8158 (mm) cc_final: 0.7804 (mm) REVERT: F 82 GLU cc_start: 0.8700 (mt-10) cc_final: 0.8494 (mt-10) REVERT: F 145 HIS cc_start: 0.8615 (m170) cc_final: 0.8344 (m170) REVERT: F 172 THR cc_start: 0.7874 (m) cc_final: 0.7381 (m) REVERT: G 8 GLN cc_start: 0.8374 (mm110) cc_final: 0.7954 (mm-40) REVERT: G 17 LEU cc_start: 0.9168 (OUTLIER) cc_final: 0.8353 (pp) REVERT: G 25 GLN cc_start: 0.8169 (OUTLIER) cc_final: 0.7760 (pt0) REVERT: G 68 PHE cc_start: 0.7916 (t80) cc_final: 0.7619 (t80) REVERT: G 71 ARG cc_start: 0.8468 (mmm160) cc_final: 0.8096 (mmm-85) REVERT: G 88 ARG cc_start: 0.7980 (OUTLIER) cc_final: 0.6868 (ttp80) REVERT: G 96 GLU cc_start: 0.8896 (pm20) cc_final: 0.8679 (pm20) REVERT: G 122 PHE cc_start: 0.8126 (t80) cc_final: 0.7822 (t80) REVERT: H 11 PHE cc_start: 0.7533 (t80) cc_final: 0.6852 (t80) REVERT: H 81 HIS cc_start: 0.8538 (OUTLIER) cc_final: 0.7608 (t-90) REVERT: H 86 VAL cc_start: 0.7862 (OUTLIER) cc_final: 0.7191 (p) REVERT: H 102 MET cc_start: 0.8897 (mmm) cc_final: 0.8202 (mmm) REVERT: H 116 MET cc_start: 0.8680 (mtp) cc_final: 0.8474 (mtm) REVERT: H 126 ARG cc_start: 0.7245 (ttt-90) cc_final: 0.6481 (ttt-90) REVERT: H 178 TYR cc_start: 0.6918 (m-80) cc_final: 0.6315 (m-10) REVERT: H 206 LEU cc_start: 0.9396 (mt) cc_final: 0.8970 (mt) REVERT: H 208 ASN cc_start: 0.8638 (m110) cc_final: 0.7514 (t0) REVERT: H 261 PHE cc_start: 0.7564 (t80) cc_final: 0.7300 (t80) REVERT: I 18 PHE cc_start: 0.8634 (t80) cc_final: 0.8262 (t80) REVERT: I 21 LEU cc_start: 0.8802 (mp) cc_final: 0.8475 (mt) REVERT: I 22 GLU cc_start: 0.8710 (tm-30) cc_final: 0.8055 (tm-30) REVERT: I 23 LYS cc_start: 0.8864 (tppt) cc_final: 0.8567 (tppt) REVERT: I 71 ARG cc_start: 0.8670 (mmm160) cc_final: 0.8434 (mmm160) REVERT: I 77 TRP cc_start: 0.8346 (t60) cc_final: 0.7479 (t60) REVERT: I 81 GLN cc_start: 0.9014 (OUTLIER) cc_final: 0.8526 (mp10) REVERT: I 84 GLU cc_start: 0.8598 (tp30) cc_final: 0.8074 (tp30) REVERT: I 108 GLU cc_start: 0.8980 (mm-30) cc_final: 0.8657 (mm-30) REVERT: I 113 PHE cc_start: 0.7898 (m-10) cc_final: 0.7466 (m-10) REVERT: I 119 LYS cc_start: 0.9289 (ptmm) cc_final: 0.8854 (ptmm) REVERT: I 123 ASN cc_start: 0.8578 (m110) cc_final: 0.8133 (m110) REVERT: J 18 PHE cc_start: 0.8736 (t80) cc_final: 0.8189 (t80) REVERT: J 39 ARG cc_start: 0.8031 (mtp85) cc_final: 0.7767 (mmm-85) REVERT: J 52 PHE cc_start: 0.7942 (m-10) cc_final: 0.7694 (m-80) REVERT: J 78 GLU cc_start: 0.8850 (tp30) cc_final: 0.8530 (tp30) REVERT: J 91 ASN cc_start: 0.8543 (m-40) cc_final: 0.8035 (m-40) REVERT: J 98 GLN cc_start: 0.8454 (tt0) cc_final: 0.8221 (tp40) REVERT: J 115 LYS cc_start: 0.5988 (mmtt) cc_final: 0.5645 (mttt) REVERT: J 116 ASP cc_start: 0.7221 (t0) cc_final: 0.6959 (t0) REVERT: J 119 LYS cc_start: 0.8637 (ttpp) cc_final: 0.8349 (mtpp) REVERT: J 120 ASN cc_start: 0.8046 (p0) cc_final: 0.7621 (p0) REVERT: J 123 ASN cc_start: 0.7591 (m-40) cc_final: 0.7242 (m110) REVERT: K 12 ARG cc_start: 0.8119 (mmp80) cc_final: 0.7801 (mmp80) REVERT: K 82 TRP cc_start: 0.8370 (p-90) cc_final: 0.7907 (p-90) REVERT: K 250 TYR cc_start: 0.7821 (OUTLIER) cc_final: 0.6362 (p90) REVERT: K 436 LEU cc_start: 0.8980 (tp) cc_final: 0.8656 (tp) REVERT: K 504 THR cc_start: 0.8614 (m) cc_final: 0.8226 (p) REVERT: M 48 ARG cc_start: 0.8646 (tpp-160) cc_final: 0.8328 (tpp-160) REVERT: M 54 ILE cc_start: 0.8943 (mm) cc_final: 0.8707 (mm) REVERT: M 130 GLN cc_start: 0.7216 (OUTLIER) cc_final: 0.6933 (tt0) REVERT: M 147 ILE cc_start: 0.9067 (pt) cc_final: 0.8833 (mt) REVERT: M 204 GLN cc_start: 0.8215 (tm-30) cc_final: 0.7795 (tm-30) REVERT: M 212 HIS cc_start: 0.6727 (m-70) cc_final: 0.6523 (m-70) REVERT: M 277 LYS cc_start: 0.7809 (mppt) cc_final: 0.7355 (mppt) REVERT: N 26 TYR cc_start: 0.8311 (m-80) cc_final: 0.7469 (m-80) REVERT: N 68 ASN cc_start: 0.7569 (t0) cc_final: 0.7072 (t0) REVERT: N 76 GLU cc_start: 0.6979 (mm-30) cc_final: 0.6195 (mm-30) REVERT: N 89 GLN cc_start: 0.8312 (OUTLIER) cc_final: 0.8006 (mt0) REVERT: N 116 ASP cc_start: 0.6870 (p0) cc_final: 0.6664 (p0) REVERT: N 133 GLN cc_start: 0.7422 (OUTLIER) cc_final: 0.6775 (mm110) REVERT: N 152 LEU cc_start: 0.8506 (mp) cc_final: 0.8266 (mp) REVERT: N 171 MET cc_start: 0.6943 (mtm) cc_final: 0.6304 (mtm) REVERT: L 21 LEU cc_start: 0.8191 (OUTLIER) cc_final: 0.7959 (mt) REVERT: L 24 ILE cc_start: 0.8942 (mt) cc_final: 0.8700 (mp) REVERT: L 35 THR cc_start: 0.8560 (t) cc_final: 0.8356 (t) REVERT: L 40 TYR cc_start: 0.8711 (m-10) cc_final: 0.8281 (m-80) REVERT: L 56 MET cc_start: 0.7361 (mmm) cc_final: 0.6361 (tmm) REVERT: L 76 GLN cc_start: 0.8806 (OUTLIER) cc_final: 0.8500 (mm-40) REVERT: L 96 GLU cc_start: 0.8155 (pm20) cc_final: 0.7829 (pm20) outliers start: 142 outliers final: 70 residues processed: 840 average time/residue: 0.1678 time to fit residues: 220.5892 Evaluate side-chains 793 residues out of total 2762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 705 time to evaluate : 0.913 ------------------------------------------------------------------------------- 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 40 LEU Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain C residue 32 ILE Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 109 ILE Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 156 LYS Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 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 44 VAL Chi-restraints excluded: chain D residue 45 CYS Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 134 SER Chi-restraints excluded: chain E residue 143 LEU Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 207 VAL Chi-restraints excluded: chain E residue 264 TYR Chi-restraints excluded: chain F residue 21 ASN Chi-restraints excluded: chain F residue 25 ASP Chi-restraints excluded: chain F residue 32 ILE Chi-restraints excluded: chain F residue 40 LEU Chi-restraints excluded: chain F residue 124 GLN Chi-restraints excluded: chain G residue 10 ILE Chi-restraints excluded: chain G residue 17 LEU Chi-restraints excluded: chain G residue 25 GLN 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 124 GLU Chi-restraints excluded: chain H residue 81 HIS Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain H residue 132 THR Chi-restraints excluded: chain H residue 191 GLN Chi-restraints excluded: chain H residue 228 VAL Chi-restraints excluded: chain H residue 229 PHE Chi-restraints excluded: chain H residue 253 ASP Chi-restraints excluded: chain H residue 264 TYR Chi-restraints excluded: chain H residue 276 THR Chi-restraints excluded: chain I residue 13 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 25 GLN Chi-restraints excluded: chain K residue 195 CYS Chi-restraints excluded: chain K residue 250 TYR Chi-restraints excluded: chain K residue 257 LEU Chi-restraints excluded: chain K residue 269 VAL Chi-restraints excluded: chain K residue 306 THR Chi-restraints excluded: chain K residue 330 LEU Chi-restraints excluded: chain K residue 393 LEU Chi-restraints excluded: chain K residue 403 ASP Chi-restraints excluded: chain K residue 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 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 30 THR Chi-restraints excluded: chain N residue 37 ILE Chi-restraints excluded: chain N residue 70 VAL Chi-restraints excluded: chain N residue 89 GLN Chi-restraints excluded: chain N residue 133 GLN Chi-restraints excluded: chain N residue 159 LEU Chi-restraints excluded: chain N residue 192 PHE Chi-restraints excluded: chain N residue 201 VAL Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 45 SER Chi-restraints excluded: chain L residue 76 GLN Chi-restraints excluded: chain L residue 81 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 231 optimal weight: 0.0020 chunk 44 optimal weight: 0.6980 chunk 12 optimal weight: 1.9990 chunk 132 optimal weight: 1.9990 chunk 80 optimal weight: 4.9990 chunk 306 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 chunk 305 optimal weight: 7.9990 chunk 319 optimal weight: 9.9990 chunk 296 optimal weight: 0.9980 chunk 45 optimal weight: 0.7980 overall best weight: 0.8990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 16 GLN ** B 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 ASN B 181 HIS ** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 83 GLN ** E 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 6 ASN ** G 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 123 ASN ** H 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 62 HIS ** I 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 98 GLN J 8 GLN ** J 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 74 GLN ** J 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 220 GLN ** N 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 137 GLN ** N 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.157931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.124296 restraints weight = 47073.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.128876 restraints weight = 21023.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 64)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.131787 restraints weight = 12186.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 65)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.133635 restraints weight = 8474.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.134620 restraints weight = 6692.437| |-----------------------------------------------------------------------------| r_work (final): 0.3987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.4449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 27430 Z= 0.212 Angle : 0.814 11.206 37194 Z= 0.420 Chirality : 0.050 0.324 4023 Planarity : 0.006 0.077 4752 Dihedral : 14.431 170.084 4193 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 29.62 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.89 % Favored : 91.08 % Rotamer: Outliers : 5.04 % Allowed : 22.03 % Favored : 72.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.39 (0.14), residues: 3184 helix: -0.56 (0.14), residues: 1270 sheet: -2.69 (0.24), residues: 377 loop : -2.17 (0.15), residues: 1537 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 224 TYR 0.038 0.003 TYR J 106 PHE 0.037 0.003 PHE M 112 TRP 0.080 0.003 TRP J 77 HIS 0.025 0.002 HIS C 214 Details of bonding type rmsd covalent geometry : bond 0.00483 (27430) covalent geometry : angle 0.81418 (37194) hydrogen bonds : bond 0.04715 ( 1148) hydrogen bonds : angle 6.59570 ( 3315) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6368 Ramachandran restraints generated. 3184 Oldfield, 0 Emsley, 3184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6368 Ramachandran restraints generated. 3184 Oldfield, 0 Emsley, 3184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 889 residues out of total 2762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 750 time to evaluate : 0.971 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 ASN cc_start: 0.8374 (t0) cc_final: 0.7360 (t0) REVERT: A 155 TYR cc_start: 0.8493 (m-80) cc_final: 0.8249 (m-80) REVERT: A 164 GLU cc_start: 0.8295 (tp30) cc_final: 0.7958 (tp30) REVERT: A 167 GLN cc_start: 0.8561 (tm-30) cc_final: 0.7967 (tm-30) REVERT: A 168 TYR cc_start: 0.7291 (m-80) cc_final: 0.7060 (m-80) REVERT: A 169 GLU cc_start: 0.7816 (tt0) cc_final: 0.7523 (tt0) REVERT: B 69 GLU cc_start: 0.6577 (tm-30) cc_final: 0.6336 (tm-30) REVERT: B 124 GLN cc_start: 0.8396 (mp10) cc_final: 0.8157 (mp10) REVERT: B 141 MET cc_start: 0.6673 (mmt) cc_final: 0.6301 (mmt) REVERT: B 171 PHE cc_start: 0.8281 (m-80) cc_final: 0.7896 (m-80) REVERT: B 241 ASP cc_start: 0.7803 (t70) cc_final: 0.7450 (t70) REVERT: B 259 ARG cc_start: 0.7604 (mtm110) cc_final: 0.6961 (mtp-110) REVERT: C 48 ARG cc_start: 0.7661 (tpt90) cc_final: 0.7108 (tpt90) REVERT: C 67 ILE cc_start: 0.8440 (OUTLIER) cc_final: 0.7754 (mm) REVERT: C 103 CYS cc_start: 0.8398 (m) cc_final: 0.8098 (m) REVERT: C 133 PHE cc_start: 0.8211 (OUTLIER) cc_final: 0.7264 (t80) REVERT: C 138 ASP cc_start: 0.6394 (m-30) cc_final: 0.6182 (m-30) REVERT: C 146 SER cc_start: 0.8127 (t) cc_final: 0.7750 (t) REVERT: C 226 LEU cc_start: 0.8124 (tp) cc_final: 0.7857 (tp) REVERT: C 243 LEU cc_start: 0.7915 (OUTLIER) cc_final: 0.7591 (mt) REVERT: C 271 LYS cc_start: 0.8477 (mmmt) cc_final: 0.8165 (mmtm) REVERT: D 21 ASN cc_start: 0.7483 (t0) cc_final: 0.7147 (t0) REVERT: D 35 GLN cc_start: 0.8587 (mm-40) cc_final: 0.8292 (tp-100) REVERT: D 36 THR cc_start: 0.8046 (OUTLIER) cc_final: 0.7706 (p) REVERT: D 134 SER cc_start: 0.8097 (p) cc_final: 0.7190 (t) REVERT: D 227 TYR cc_start: 0.8315 (m-80) cc_final: 0.8081 (m-80) REVERT: E 17 ASP cc_start: 0.7992 (t70) cc_final: 0.6829 (t0) REVERT: E 79 GLU cc_start: 0.7782 (tm-30) cc_final: 0.7423 (tm-30) REVERT: E 116 MET cc_start: 0.8217 (mmt) cc_final: 0.7685 (mmt) REVERT: E 141 MET cc_start: 0.7430 (OUTLIER) cc_final: 0.7173 (tpp) REVERT: E 144 GLU cc_start: 0.7879 (mt-10) cc_final: 0.7615 (mt-10) REVERT: E 167 MET cc_start: 0.8644 (mtm) cc_final: 0.8347 (mtp) REVERT: E 184 ILE cc_start: 0.8766 (mm) cc_final: 0.8544 (mm) REVERT: E 204 GLN cc_start: 0.7721 (tm130) cc_final: 0.7166 (tm-30) REVERT: E 233 ASN cc_start: 0.8106 (m-40) cc_final: 0.7821 (m-40) REVERT: E 241 ASP cc_start: 0.7141 (t70) cc_final: 0.6790 (t0) REVERT: E 264 TYR cc_start: 0.8564 (OUTLIER) cc_final: 0.8313 (m-10) REVERT: F 25 ASP cc_start: 0.7413 (OUTLIER) cc_final: 0.7052 (t70) REVERT: F 35 GLN cc_start: 0.8169 (tp-100) cc_final: 0.7725 (tp40) REVERT: F 72 ILE cc_start: 0.8134 (mm) cc_final: 0.7802 (mm) REVERT: F 82 GLU cc_start: 0.8683 (mt-10) cc_final: 0.8471 (mt-10) REVERT: F 141 MET cc_start: 0.8245 (ttp) cc_final: 0.7615 (ttt) REVERT: F 145 HIS cc_start: 0.8640 (m170) cc_final: 0.8195 (m170) REVERT: F 187 HIS cc_start: 0.7519 (OUTLIER) cc_final: 0.6988 (p90) REVERT: F 209 MET cc_start: 0.6648 (tmm) cc_final: 0.6411 (tmm) REVERT: G 8 GLN cc_start: 0.8170 (mm110) cc_final: 0.7942 (mm-40) REVERT: G 25 GLN cc_start: 0.8108 (OUTLIER) cc_final: 0.7675 (pt0) REVERT: G 68 PHE cc_start: 0.7901 (t80) cc_final: 0.7617 (t80) REVERT: G 71 ARG cc_start: 0.8644 (mmm160) cc_final: 0.8340 (mmm-85) REVERT: G 88 ARG cc_start: 0.7995 (OUTLIER) cc_final: 0.6851 (ttp80) REVERT: G 96 GLU cc_start: 0.8823 (pm20) cc_final: 0.8508 (pm20) REVERT: G 110 GLN cc_start: 0.7262 (tp-100) cc_final: 0.7006 (tp-100) REVERT: G 122 PHE cc_start: 0.8098 (t80) cc_final: 0.7615 (t80) REVERT: H 81 HIS cc_start: 0.8526 (OUTLIER) cc_final: 0.7739 (t-90) REVERT: H 102 MET cc_start: 0.8967 (mmm) cc_final: 0.8292 (mmm) REVERT: H 126 ARG cc_start: 0.7484 (ttt-90) cc_final: 0.7243 (ttt-90) REVERT: H 178 TYR cc_start: 0.6865 (m-80) cc_final: 0.6451 (m-10) REVERT: H 190 LYS cc_start: 0.8654 (mttm) cc_final: 0.8330 (mttp) REVERT: H 208 ASN cc_start: 0.8720 (m110) cc_final: 0.7690 (t0) REVERT: H 261 PHE cc_start: 0.7732 (t80) cc_final: 0.7477 (t80) REVERT: I 18 PHE cc_start: 0.8598 (t80) cc_final: 0.8193 (t80) REVERT: I 21 LEU cc_start: 0.8850 (mp) cc_final: 0.8549 (mt) REVERT: I 22 GLU cc_start: 0.8738 (tm-30) cc_final: 0.8200 (tm-30) REVERT: I 23 LYS cc_start: 0.8890 (tppt) cc_final: 0.8686 (tppt) REVERT: I 27 GLU cc_start: 0.7608 (mt-10) cc_final: 0.7223 (mt-10) REVERT: I 74 GLN cc_start: 0.8807 (pt0) cc_final: 0.7762 (mt0) REVERT: I 76 GLN cc_start: 0.8035 (tp40) cc_final: 0.7686 (tp40) REVERT: I 77 TRP cc_start: 0.8391 (t60) cc_final: 0.7598 (t60) REVERT: I 81 GLN cc_start: 0.8992 (OUTLIER) cc_final: 0.8368 (mp10) REVERT: I 84 GLU cc_start: 0.8560 (tp30) cc_final: 0.8108 (tp30) REVERT: I 86 CYS cc_start: 0.8840 (t) cc_final: 0.8150 (p) REVERT: I 96 GLU cc_start: 0.8049 (OUTLIER) cc_final: 0.7748 (tp30) REVERT: I 109 THR cc_start: 0.8506 (m) cc_final: 0.8051 (t) REVERT: I 110 GLN cc_start: 0.8151 (tp40) cc_final: 0.7847 (tp40) REVERT: I 113 PHE cc_start: 0.7937 (m-10) cc_final: 0.7221 (m-10) REVERT: I 123 ASN cc_start: 0.8658 (m110) cc_final: 0.8213 (m110) REVERT: J 8 GLN cc_start: 0.7978 (tp40) cc_final: 0.7740 (tp-100) REVERT: J 18 PHE cc_start: 0.8758 (t80) cc_final: 0.8265 (t80) REVERT: J 78 GLU cc_start: 0.8824 (tp30) cc_final: 0.8590 (tp30) REVERT: J 91 ASN cc_start: 0.8581 (m-40) cc_final: 0.8113 (m-40) REVERT: J 98 GLN cc_start: 0.8439 (tt0) cc_final: 0.8204 (tp40) REVERT: J 116 ASP cc_start: 0.7031 (t0) cc_final: 0.6736 (t0) REVERT: K 12 ARG cc_start: 0.8076 (mmp80) cc_final: 0.7758 (mmp80) REVERT: K 250 TYR cc_start: 0.7829 (OUTLIER) cc_final: 0.6479 (p90) REVERT: K 295 ASP cc_start: 0.8486 (t0) cc_final: 0.8151 (t0) REVERT: K 428 LYS cc_start: 0.8692 (ttpt) cc_final: 0.8435 (ttpp) REVERT: K 436 LEU cc_start: 0.8941 (tp) cc_final: 0.8566 (tp) REVERT: K 504 THR cc_start: 0.8622 (m) cc_final: 0.8036 (p) REVERT: M 54 ILE cc_start: 0.8981 (mm) cc_final: 0.8768 (mm) REVERT: M 198 ASP cc_start: 0.7718 (m-30) cc_final: 0.7398 (m-30) REVERT: M 273 LEU cc_start: 0.8600 (tt) cc_final: 0.8333 (mt) REVERT: M 277 LYS cc_start: 0.7770 (mppt) cc_final: 0.7316 (mppt) REVERT: N 68 ASN cc_start: 0.7676 (t0) cc_final: 0.7071 (t0) REVERT: N 69 GLU cc_start: 0.7539 (OUTLIER) cc_final: 0.7241 (mt-10) REVERT: N 133 GLN cc_start: 0.7449 (OUTLIER) cc_final: 0.6763 (mm110) REVERT: N 152 LEU cc_start: 0.8386 (mp) cc_final: 0.8177 (mp) REVERT: L 24 ILE cc_start: 0.8955 (mt) cc_final: 0.8681 (mp) REVERT: L 40 TYR cc_start: 0.8584 (m-10) cc_final: 0.8298 (m-80) REVERT: L 56 MET cc_start: 0.7598 (mmm) cc_final: 0.6310 (tmm) REVERT: L 76 GLN cc_start: 0.8796 (OUTLIER) cc_final: 0.8591 (mm110) REVERT: L 96 GLU cc_start: 0.8328 (pm20) cc_final: 0.8011 (pm20) outliers start: 139 outliers final: 78 residues processed: 816 average time/residue: 0.1908 time to fit residues: 245.2074 Evaluate side-chains 788 residues out of total 2762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 693 time to evaluate : 1.166 ------------------------------------------------------------------------------- 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 176 SER Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 209 MET Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain C residue 5 LYS Chi-restraints excluded: chain C residue 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 D residue 36 THR Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 45 CYS Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 69 GLU Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 134 SER Chi-restraints excluded: chain E residue 141 MET Chi-restraints excluded: chain E residue 143 LEU Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 207 VAL Chi-restraints excluded: chain E residue 259 ARG Chi-restraints excluded: chain E residue 264 TYR Chi-restraints excluded: chain F residue 21 ASN Chi-restraints excluded: chain F residue 25 ASP Chi-restraints excluded: chain F residue 32 ILE Chi-restraints excluded: chain F residue 40 LEU Chi-restraints excluded: chain F residue 67 ILE Chi-restraints excluded: chain F residue 124 GLN Chi-restraints excluded: chain F residue 187 HIS Chi-restraints excluded: chain G residue 10 ILE Chi-restraints excluded: chain G residue 17 LEU Chi-restraints excluded: chain G residue 25 GLN 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 132 THR Chi-restraints excluded: chain H residue 187 HIS Chi-restraints excluded: chain H residue 191 GLN Chi-restraints excluded: chain H residue 228 VAL Chi-restraints excluded: chain H residue 229 PHE Chi-restraints excluded: chain H residue 253 ASP Chi-restraints excluded: chain H residue 264 TYR Chi-restraints excluded: chain H residue 266 VAL Chi-restraints excluded: chain H residue 276 THR Chi-restraints excluded: chain I residue 81 GLN Chi-restraints excluded: chain I residue 96 GLU Chi-restraints excluded: chain J residue 25 GLN Chi-restraints excluded: chain K residue 195 CYS Chi-restraints excluded: chain K residue 250 TYR Chi-restraints excluded: chain K residue 257 LEU Chi-restraints excluded: chain K residue 266 ILE Chi-restraints excluded: chain K residue 306 THR Chi-restraints excluded: chain K residue 330 LEU Chi-restraints excluded: chain K residue 393 LEU Chi-restraints excluded: chain K residue 403 ASP Chi-restraints excluded: chain K residue 430 THR Chi-restraints excluded: chain K residue 458 MET 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 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 69 GLU 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 4 ASP Chi-restraints excluded: chain L residue 76 GLN Chi-restraints excluded: chain L residue 81 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 8 optimal weight: 0.4980 chunk 20 optimal weight: 0.6980 chunk 238 optimal weight: 1.9990 chunk 150 optimal weight: 0.9980 chunk 88 optimal weight: 0.4980 chunk 44 optimal weight: 2.9990 chunk 104 optimal weight: 6.9990 chunk 97 optimal weight: 1.9990 chunk 156 optimal weight: 5.9990 chunk 123 optimal weight: 2.9990 chunk 203 optimal weight: 3.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 55 GLN ** 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** ** E 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 6 ASN ** G 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 76 GLN ** G 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 97 GLN I 98 GLN ** J 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 64 ASN ** J 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 137 GLN N 194 GLN ** L 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 98 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.158762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.126854 restraints weight = 46597.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.131239 restraints weight = 20853.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 65)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.134032 restraints weight = 12031.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 62)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.135812 restraints weight = 8282.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.136896 restraints weight = 6492.729| |-----------------------------------------------------------------------------| r_work (final): 0.4001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.4661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 27430 Z= 0.217 Angle : 0.826 12.927 37194 Z= 0.427 Chirality : 0.051 0.358 4023 Planarity : 0.006 0.071 4752 Dihedral : 14.387 169.701 4192 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 30.19 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.27 % Favored : 90.70 % Rotamer: Outliers : 4.42 % Allowed : 23.77 % Favored : 71.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.41 (0.14), residues: 3184 helix: -0.56 (0.14), residues: 1270 sheet: -2.67 (0.24), residues: 373 loop : -2.20 (0.14), residues: 1541 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG C 110 TYR 0.040 0.003 TYR B 175 PHE 0.037 0.003 PHE M 112 TRP 0.104 0.003 TRP J 77 HIS 0.021 0.002 HIS C 214 Details of bonding type rmsd covalent geometry : bond 0.00495 (27430) covalent geometry : angle 0.82634 (37194) hydrogen bonds : bond 0.04719 ( 1148) hydrogen bonds : angle 6.59068 ( 3315) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6368 Ramachandran restraints generated. 3184 Oldfield, 0 Emsley, 3184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6368 Ramachandran restraints generated. 3184 Oldfield, 0 Emsley, 3184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 868 residues out of total 2762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 746 time to evaluate : 1.145 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 ASN cc_start: 0.8406 (t0) cc_final: 0.7576 (t0) REVERT: A 155 TYR cc_start: 0.8490 (m-80) cc_final: 0.8248 (m-80) REVERT: A 164 GLU cc_start: 0.8238 (tp30) cc_final: 0.7884 (tp30) REVERT: A 167 GLN cc_start: 0.8509 (tm-30) cc_final: 0.7810 (tm-30) REVERT: A 168 TYR cc_start: 0.7388 (m-80) cc_final: 0.7056 (m-80) REVERT: A 169 GLU cc_start: 0.7825 (tt0) cc_final: 0.7424 (tt0) REVERT: A 179 GLU cc_start: 0.7934 (tm-30) cc_final: 0.7350 (tt0) REVERT: B 69 GLU cc_start: 0.6577 (tm-30) cc_final: 0.6352 (tm-30) REVERT: B 124 GLN cc_start: 0.8311 (mp10) cc_final: 0.8105 (mp10) REVERT: B 141 MET cc_start: 0.6650 (mmt) cc_final: 0.6421 (mmt) REVERT: B 175 TYR cc_start: 0.8335 (t80) cc_final: 0.8114 (t80) REVERT: B 241 ASP cc_start: 0.7766 (t70) cc_final: 0.7431 (t70) REVERT: C 67 ILE cc_start: 0.8407 (OUTLIER) cc_final: 0.7706 (mm) REVERT: C 103 CYS cc_start: 0.8237 (m) cc_final: 0.7729 (m) REVERT: C 133 PHE cc_start: 0.8221 (OUTLIER) cc_final: 0.7075 (t80) REVERT: C 226 LEU cc_start: 0.8089 (tp) cc_final: 0.7790 (tp) REVERT: C 243 LEU cc_start: 0.8189 (OUTLIER) cc_final: 0.7921 (mt) REVERT: C 271 LYS cc_start: 0.8405 (mmmt) cc_final: 0.8091 (mmtm) REVERT: D 21 ASN cc_start: 0.7491 (t0) cc_final: 0.7155 (t0) REVERT: D 35 GLN cc_start: 0.8603 (mm-40) cc_final: 0.8099 (tp40) REVERT: D 36 THR cc_start: 0.8036 (OUTLIER) cc_final: 0.7693 (p) REVERT: D 221 MET cc_start: 0.6926 (mmm) cc_final: 0.6677 (tpp) REVERT: D 227 TYR cc_start: 0.8320 (m-80) cc_final: 0.8043 (m-80) REVERT: D 259 ARG cc_start: 0.9045 (mmp80) cc_final: 0.8606 (mmt-90) REVERT: E 17 ASP cc_start: 0.7995 (t70) cc_final: 0.6804 (t0) REVERT: E 79 GLU cc_start: 0.7767 (tm-30) cc_final: 0.7304 (tm-30) REVERT: E 101 TYR cc_start: 0.7923 (t80) cc_final: 0.7668 (t80) REVERT: E 116 MET cc_start: 0.8285 (mmt) cc_final: 0.7933 (mmt) REVERT: E 144 GLU cc_start: 0.7907 (mt-10) cc_final: 0.7602 (mt-10) REVERT: E 184 ILE cc_start: 0.8794 (OUTLIER) cc_final: 0.8547 (mm) REVERT: E 204 GLN cc_start: 0.7807 (tm130) cc_final: 0.7080 (tm-30) REVERT: E 233 ASN cc_start: 0.7939 (m-40) cc_final: 0.7710 (m-40) REVERT: E 241 ASP cc_start: 0.7097 (t70) cc_final: 0.6761 (t0) REVERT: E 264 TYR cc_start: 0.8545 (OUTLIER) cc_final: 0.8316 (m-10) REVERT: F 25 ASP cc_start: 0.7466 (OUTLIER) cc_final: 0.7136 (t70) REVERT: F 72 ILE cc_start: 0.8255 (mm) cc_final: 0.7933 (mm) REVERT: F 82 GLU cc_start: 0.8639 (mt-10) cc_final: 0.8394 (mt-10) REVERT: F 141 MET cc_start: 0.8180 (ttp) cc_final: 0.7527 (ttt) REVERT: F 145 HIS cc_start: 0.8557 (m170) cc_final: 0.8104 (m170) REVERT: F 188 PHE cc_start: 0.8179 (m-10) cc_final: 0.7839 (m-10) REVERT: F 209 MET cc_start: 0.6788 (tmm) cc_final: 0.6409 (tmm) REVERT: G 25 GLN cc_start: 0.8073 (OUTLIER) cc_final: 0.7705 (pt0) REVERT: G 71 ARG cc_start: 0.8624 (mmm160) cc_final: 0.8236 (mtp85) REVERT: G 88 ARG cc_start: 0.7998 (OUTLIER) cc_final: 0.6852 (ttp80) REVERT: G 96 GLU cc_start: 0.8695 (pm20) cc_final: 0.8320 (pm20) REVERT: G 110 GLN cc_start: 0.7380 (tp-100) cc_final: 0.7013 (tp-100) REVERT: G 122 PHE cc_start: 0.8257 (t80) cc_final: 0.7822 (t80) REVERT: H 8 ASP cc_start: 0.6308 (p0) cc_final: 0.5481 (p0) REVERT: H 11 PHE cc_start: 0.7665 (t80) cc_final: 0.7389 (t80) REVERT: H 81 HIS cc_start: 0.8504 (OUTLIER) cc_final: 0.7702 (t-90) REVERT: H 102 MET cc_start: 0.8950 (mmm) cc_final: 0.8433 (mmm) REVERT: H 178 TYR cc_start: 0.6758 (m-80) cc_final: 0.6398 (m-10) REVERT: H 190 LYS cc_start: 0.8632 (mttm) cc_final: 0.8309 (mttp) REVERT: H 206 LEU cc_start: 0.9063 (mt) cc_final: 0.8821 (mt) REVERT: H 208 ASN cc_start: 0.8665 (m110) cc_final: 0.7650 (t0) REVERT: H 261 PHE cc_start: 0.7701 (t80) cc_final: 0.7455 (t80) REVERT: I 18 PHE cc_start: 0.8751 (t80) cc_final: 0.8335 (t80) REVERT: I 21 LEU cc_start: 0.8864 (mp) cc_final: 0.8646 (mt) REVERT: I 22 GLU cc_start: 0.8800 (tm-30) cc_final: 0.8264 (tm-30) REVERT: I 65 LYS cc_start: 0.8756 (mttp) cc_final: 0.8488 (mttt) REVERT: I 74 GLN cc_start: 0.8678 (pt0) cc_final: 0.7862 (mt0) REVERT: I 77 TRP cc_start: 0.8664 (t60) cc_final: 0.7744 (t60) REVERT: I 81 GLN cc_start: 0.8994 (OUTLIER) cc_final: 0.8384 (mp10) REVERT: I 84 GLU cc_start: 0.8518 (tp30) cc_final: 0.8119 (tp30) REVERT: I 96 GLU cc_start: 0.7973 (OUTLIER) cc_final: 0.7681 (tp30) REVERT: I 109 THR cc_start: 0.8416 (m) cc_final: 0.7855 (t) REVERT: I 123 ASN cc_start: 0.8644 (m110) cc_final: 0.8158 (m110) REVERT: J 8 GLN cc_start: 0.7917 (tp40) cc_final: 0.7636 (tp-100) REVERT: J 18 PHE cc_start: 0.8808 (t80) cc_final: 0.8280 (t80) REVERT: J 39 ARG cc_start: 0.7896 (mtp85) cc_final: 0.7615 (mmm-85) REVERT: J 52 PHE cc_start: 0.7834 (m-80) cc_final: 0.7559 (m-80) REVERT: J 77 TRP cc_start: 0.7575 (t60) cc_final: 0.7098 (t60) REVERT: J 80 ARG cc_start: 0.8293 (mtm-85) cc_final: 0.8088 (ttm-80) REVERT: J 88 ARG cc_start: 0.7399 (OUTLIER) cc_final: 0.7153 (tmt170) REVERT: J 91 ASN cc_start: 0.8517 (m-40) cc_final: 0.8051 (m-40) REVERT: J 98 GLN cc_start: 0.8435 (tt0) cc_final: 0.8214 (tp40) REVERT: J 116 ASP cc_start: 0.6845 (t0) cc_final: 0.6482 (t0) REVERT: K 12 ARG cc_start: 0.7998 (mmp80) cc_final: 0.7780 (mmp80) REVERT: K 46 GLU cc_start: 0.8548 (tm-30) cc_final: 0.8321 (tm-30) REVERT: K 82 TRP cc_start: 0.8410 (p-90) cc_final: 0.7932 (p-90) REVERT: K 250 TYR cc_start: 0.7849 (OUTLIER) cc_final: 0.6629 (p90) REVERT: K 281 LEU cc_start: 0.8410 (mp) cc_final: 0.8136 (mp) REVERT: K 295 ASP cc_start: 0.8367 (t0) cc_final: 0.8021 (t0) REVERT: K 428 LYS cc_start: 0.8705 (ttpt) cc_final: 0.8455 (ttpp) REVERT: M 19 ASN cc_start: 0.7982 (t0) cc_final: 0.7770 (t0) REVERT: M 54 ILE cc_start: 0.8980 (mm) cc_final: 0.8718 (mm) REVERT: M 56 MET cc_start: 0.8174 (ttm) cc_final: 0.7523 (tmm) REVERT: M 198 ASP cc_start: 0.7785 (m-30) cc_final: 0.7332 (m-30) REVERT: M 204 GLN cc_start: 0.8260 (tm-30) cc_final: 0.7757 (tm-30) REVERT: M 263 ASP cc_start: 0.7473 (m-30) cc_final: 0.7175 (m-30) REVERT: M 273 LEU cc_start: 0.8533 (tt) cc_final: 0.8322 (mt) REVERT: M 277 LYS cc_start: 0.7692 (mppt) cc_final: 0.7266 (mppt) REVERT: N 68 ASN cc_start: 0.7822 (t0) cc_final: 0.7191 (t0) REVERT: N 69 GLU cc_start: 0.7602 (OUTLIER) cc_final: 0.7121 (mt-10) REVERT: N 133 GLN cc_start: 0.7359 (OUTLIER) cc_final: 0.6797 (mm110) REVERT: N 193 TYR cc_start: 0.7424 (t80) cc_final: 0.7207 (t80) REVERT: L 24 ILE cc_start: 0.8936 (mt) cc_final: 0.8707 (mp) REVERT: L 40 TYR cc_start: 0.8573 (m-10) cc_final: 0.8255 (m-80) REVERT: L 56 MET cc_start: 0.7601 (mmm) cc_final: 0.6393 (tmm) REVERT: L 76 GLN cc_start: 0.8846 (OUTLIER) cc_final: 0.8646 (mm110) REVERT: L 96 GLU cc_start: 0.8283 (pm20) cc_final: 0.8002 (pm20) outliers start: 122 outliers final: 79 residues processed: 804 average time/residue: 0.1879 time to fit residues: 239.3559 Evaluate side-chains 775 residues out of total 2762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 679 time to evaluate : 1.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 PHE Chi-restraints excluded: chain A residue 176 SER Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 43 ASP Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 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 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 214 HIS Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain D residue 36 THR Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 45 CYS Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 125 VAL Chi-restraints excluded: chain E residue 134 SER Chi-restraints excluded: chain E residue 143 LEU Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain E residue 184 ILE Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 207 VAL Chi-restraints excluded: chain E residue 259 ARG Chi-restraints excluded: chain E residue 264 TYR Chi-restraints excluded: chain F residue 21 ASN Chi-restraints excluded: chain F residue 25 ASP Chi-restraints excluded: chain F residue 32 ILE Chi-restraints excluded: chain F residue 40 LEU Chi-restraints excluded: chain F residue 67 ILE Chi-restraints excluded: chain F residue 132 THR Chi-restraints excluded: chain G residue 10 ILE Chi-restraints excluded: chain G residue 25 GLN 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 132 THR Chi-restraints excluded: chain H residue 187 HIS Chi-restraints excluded: chain H residue 228 VAL Chi-restraints excluded: chain H residue 229 PHE Chi-restraints excluded: chain H residue 253 ASP Chi-restraints excluded: chain H residue 264 TYR 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 119 LYS Chi-restraints excluded: chain J residue 25 GLN Chi-restraints excluded: chain J residue 88 ARG 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 393 LEU Chi-restraints excluded: chain K residue 430 THR Chi-restraints excluded: chain K residue 478 LEU Chi-restraints excluded: chain K residue 536 ILE 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 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 69 GLU 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 4 ASP 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 280 optimal weight: 2.9990 chunk 3 optimal weight: 0.9990 chunk 134 optimal weight: 0.8980 chunk 178 optimal weight: 0.2980 chunk 247 optimal weight: 0.6980 chunk 318 optimal weight: 6.9990 chunk 224 optimal weight: 2.9990 chunk 171 optimal weight: 0.7980 chunk 109 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 249 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 222 ASN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 52 ASN ** E 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 6 ASN ** G 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 92 HIS ** 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 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 97 GLN I 98 GLN ** J 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 85 HIS ** K 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 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 98 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.156186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.119191 restraints weight = 47831.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.123740 restraints weight = 21417.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.126654 restraints weight = 12545.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.128506 restraints weight = 8771.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.129517 restraints weight = 6969.061| |-----------------------------------------------------------------------------| r_work (final): 0.4014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.4950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 27430 Z= 0.199 Angle : 0.839 17.685 37194 Z= 0.433 Chirality : 0.051 0.372 4023 Planarity : 0.006 0.074 4752 Dihedral : 14.334 167.588 4192 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 29.01 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.01 % Favored : 90.95 % Rotamer: Outliers : 4.42 % Allowed : 24.60 % Favored : 70.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.32 (0.14), residues: 3184 helix: -0.49 (0.14), residues: 1252 sheet: -2.56 (0.25), residues: 373 loop : -2.15 (0.14), residues: 1559 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 280 TYR 0.050 0.003 TYR K 87 PHE 0.047 0.002 PHE H 183 TRP 0.075 0.003 TRP J 77 HIS 0.021 0.002 HIS C 214 Details of bonding type rmsd covalent geometry : bond 0.00458 (27430) covalent geometry : angle 0.83872 (37194) hydrogen bonds : bond 0.04683 ( 1148) hydrogen bonds : angle 6.55166 ( 3315) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6368 Ramachandran restraints generated. 3184 Oldfield, 0 Emsley, 3184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6368 Ramachandran restraints generated. 3184 Oldfield, 0 Emsley, 3184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 869 residues out of total 2762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 747 time to evaluate : 0.863 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: A 119 PHE cc_start: 0.7948 (OUTLIER) cc_final: 0.6707 (t80) REVERT: A 126 ASN cc_start: 0.8376 (t0) cc_final: 0.7555 (t0) REVERT: A 155 TYR cc_start: 0.8418 (m-80) cc_final: 0.8214 (m-80) REVERT: A 164 GLU cc_start: 0.8154 (tp30) cc_final: 0.7635 (tp30) REVERT: A 167 GLN cc_start: 0.8415 (tm-30) cc_final: 0.7284 (tm-30) REVERT: A 168 TYR cc_start: 0.7163 (m-80) cc_final: 0.6765 (m-80) REVERT: A 169 GLU cc_start: 0.7621 (tt0) cc_final: 0.7040 (tt0) REVERT: A 179 GLU cc_start: 0.7881 (tm-30) cc_final: 0.7441 (tt0) REVERT: B 69 GLU cc_start: 0.6508 (tm-30) cc_final: 0.6273 (tm-30) REVERT: B 141 MET cc_start: 0.6560 (mmt) cc_final: 0.6333 (mmt) REVERT: B 175 TYR cc_start: 0.8275 (t80) cc_final: 0.7803 (t80) REVERT: B 241 ASP cc_start: 0.7697 (t70) cc_final: 0.7134 (t0) REVERT: B 259 ARG cc_start: 0.7545 (mtm110) cc_final: 0.7333 (mtm110) REVERT: C 67 ILE cc_start: 0.8358 (OUTLIER) cc_final: 0.7566 (mm) REVERT: C 103 CYS cc_start: 0.8022 (m) cc_final: 0.7475 (m) REVERT: C 133 PHE cc_start: 0.8122 (OUTLIER) cc_final: 0.6958 (t80) REVERT: C 271 LYS cc_start: 0.8376 (mmmt) cc_final: 0.8082 (mmmt) REVERT: D 21 ASN cc_start: 0.7462 (t0) cc_final: 0.7170 (t0) REVERT: D 35 GLN cc_start: 0.8455 (mm-40) cc_final: 0.7983 (tp40) REVERT: D 36 THR cc_start: 0.7866 (OUTLIER) cc_final: 0.7598 (p) REVERT: D 227 TYR cc_start: 0.8222 (m-80) cc_final: 0.7895 (m-80) REVERT: D 259 ARG cc_start: 0.8849 (mmp80) cc_final: 0.8385 (mmt-90) REVERT: E 17 ASP cc_start: 0.7953 (t70) cc_final: 0.6981 (t0) REVERT: E 79 GLU cc_start: 0.7825 (tm-30) cc_final: 0.7447 (tm-30) REVERT: E 101 TYR cc_start: 0.7818 (t80) cc_final: 0.7573 (t80) REVERT: E 116 MET cc_start: 0.8288 (mmt) cc_final: 0.8065 (mmt) REVERT: E 144 GLU cc_start: 0.7813 (mt-10) cc_final: 0.7610 (mt-10) REVERT: E 167 MET cc_start: 0.8372 (mtm) cc_final: 0.8156 (mtp) REVERT: E 184 ILE cc_start: 0.8795 (OUTLIER) cc_final: 0.8584 (mm) REVERT: E 204 GLN cc_start: 0.7941 (tm130) cc_final: 0.7162 (tm-30) REVERT: E 226 LEU cc_start: 0.8184 (tp) cc_final: 0.7863 (tp) REVERT: E 241 ASP cc_start: 0.7043 (t70) cc_final: 0.6743 (t0) REVERT: E 264 TYR cc_start: 0.8494 (OUTLIER) cc_final: 0.8249 (m-10) REVERT: F 25 ASP cc_start: 0.7130 (OUTLIER) cc_final: 0.6747 (t70) REVERT: F 56 MET cc_start: 0.8342 (ptm) cc_final: 0.7819 (tmm) REVERT: F 72 ILE cc_start: 0.8257 (mm) cc_final: 0.7935 (mm) REVERT: F 82 GLU cc_start: 0.8692 (mt-10) cc_final: 0.8452 (mt-10) REVERT: F 141 MET cc_start: 0.8220 (ttp) cc_final: 0.7602 (ttt) REVERT: F 145 HIS cc_start: 0.8483 (m170) cc_final: 0.7986 (m170) REVERT: F 209 MET cc_start: 0.7023 (tmm) cc_final: 0.6615 (tmm) REVERT: G 23 LYS cc_start: 0.8183 (tptt) cc_final: 0.7647 (tttt) REVERT: G 88 ARG cc_start: 0.7960 (OUTLIER) cc_final: 0.6817 (ttp80) REVERT: G 96 GLU cc_start: 0.8590 (pm20) cc_final: 0.8138 (pm20) REVERT: G 97 GLN cc_start: 0.8557 (tt0) cc_final: 0.8145 (mt0) REVERT: G 124 GLU cc_start: 0.8892 (OUTLIER) cc_final: 0.8678 (pm20) REVERT: H 11 PHE cc_start: 0.7608 (t80) cc_final: 0.7348 (t80) REVERT: H 81 HIS cc_start: 0.8498 (OUTLIER) cc_final: 0.7766 (t-90) REVERT: H 102 MET cc_start: 0.8985 (mmm) cc_final: 0.8460 (mmm) REVERT: H 137 ILE cc_start: 0.8856 (pt) cc_final: 0.8220 (pt) REVERT: H 178 TYR cc_start: 0.6735 (m-80) cc_final: 0.6356 (m-10) REVERT: H 206 LEU cc_start: 0.8823 (mt) cc_final: 0.8331 (mt) REVERT: H 208 ASN cc_start: 0.8590 (m110) cc_final: 0.7562 (t0) REVERT: H 261 PHE cc_start: 0.7706 (t80) cc_final: 0.7444 (t80) REVERT: I 18 PHE cc_start: 0.8790 (t80) cc_final: 0.8507 (t80) REVERT: I 22 GLU cc_start: 0.8785 (tm-30) cc_final: 0.8268 (tm-30) REVERT: I 65 LYS cc_start: 0.8768 (mttp) cc_final: 0.8508 (mttt) REVERT: I 77 TRP cc_start: 0.8453 (t60) cc_final: 0.7760 (t60) REVERT: I 81 GLN cc_start: 0.9066 (OUTLIER) cc_final: 0.8532 (mp10) REVERT: I 84 GLU cc_start: 0.8480 (tp30) cc_final: 0.8033 (tp30) REVERT: I 96 GLU cc_start: 0.7848 (OUTLIER) cc_final: 0.7637 (tp30) REVERT: I 109 THR cc_start: 0.8225 (m) cc_final: 0.7282 (p) REVERT: I 113 PHE cc_start: 0.7649 (m-10) cc_final: 0.6973 (m-10) REVERT: I 123 ASN cc_start: 0.8649 (m110) cc_final: 0.8179 (m110) REVERT: J 8 GLN cc_start: 0.7811 (tp40) cc_final: 0.7517 (tp-100) REVERT: J 18 PHE cc_start: 0.8817 (t80) cc_final: 0.8409 (t80) REVERT: J 39 ARG cc_start: 0.8020 (mtp85) cc_final: 0.7734 (mmm-85) REVERT: J 77 TRP cc_start: 0.7672 (t60) cc_final: 0.7370 (t60) REVERT: J 80 ARG cc_start: 0.8294 (mtm-85) cc_final: 0.7925 (tpp80) REVERT: J 91 ASN cc_start: 0.8386 (m-40) cc_final: 0.8040 (m-40) REVERT: J 116 ASP cc_start: 0.6801 (t0) cc_final: 0.6425 (t0) REVERT: K 46 GLU cc_start: 0.8506 (tm-30) cc_final: 0.8269 (tm-30) REVERT: K 250 TYR cc_start: 0.7877 (OUTLIER) cc_final: 0.6267 (p90) REVERT: K 281 LEU cc_start: 0.8277 (mp) cc_final: 0.8046 (mp) REVERT: K 295 ASP cc_start: 0.8308 (t0) cc_final: 0.7971 (t0) REVERT: K 428 LYS cc_start: 0.8652 (ttpt) cc_final: 0.8369 (ttpp) REVERT: K 460 LEU cc_start: 0.6180 (OUTLIER) cc_final: 0.5617 (tt) REVERT: K 504 THR cc_start: 0.8617 (m) cc_final: 0.8273 (p) REVERT: M 19 ASN cc_start: 0.7914 (t0) cc_final: 0.7657 (t0) REVERT: M 56 MET cc_start: 0.8132 (ttm) cc_final: 0.7795 (ttm) REVERT: M 147 ILE cc_start: 0.8951 (pt) cc_final: 0.8708 (mt) REVERT: M 183 PHE cc_start: 0.9041 (m-80) cc_final: 0.8627 (m-80) REVERT: M 198 ASP cc_start: 0.7376 (m-30) cc_final: 0.7046 (m-30) REVERT: M 204 GLN cc_start: 0.8149 (tm-30) cc_final: 0.7527 (tm-30) REVERT: M 221 MET cc_start: 0.7576 (ttt) cc_final: 0.7367 (mtp) REVERT: M 259 ARG cc_start: 0.7134 (mtm110) cc_final: 0.6793 (mtm110) REVERT: N 7 ILE cc_start: 0.8334 (mp) cc_final: 0.7806 (mm) REVERT: N 68 ASN cc_start: 0.7600 (t0) cc_final: 0.7047 (t0) REVERT: N 69 GLU cc_start: 0.7482 (OUTLIER) cc_final: 0.7208 (mt-10) REVERT: N 133 GLN cc_start: 0.7338 (OUTLIER) cc_final: 0.6818 (mm110) REVERT: N 137 GLN cc_start: 0.7202 (tp40) cc_final: 0.6523 (tt0) REVERT: L 24 ILE cc_start: 0.8946 (mt) cc_final: 0.8702 (mp) REVERT: L 25 GLN cc_start: 0.8466 (OUTLIER) cc_final: 0.8169 (tt0) REVERT: L 40 TYR cc_start: 0.8590 (m-10) cc_final: 0.8247 (m-80) REVERT: L 56 MET cc_start: 0.7650 (mmm) cc_final: 0.6272 (tmm) REVERT: L 96 GLU cc_start: 0.8264 (pm20) cc_final: 0.8010 (pm20) outliers start: 122 outliers final: 76 residues processed: 807 average time/residue: 0.1725 time to fit residues: 220.7899 Evaluate side-chains 788 residues out of total 2762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 695 time to evaluate : 1.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 PHE Chi-restraints excluded: chain A residue 176 SER Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 43 ASP Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 150 MET Chi-restraints excluded: chain B residue 187 HIS Chi-restraints excluded: chain B residue 209 MET Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain C residue 5 LYS Chi-restraints excluded: chain C residue 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 214 HIS Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain D residue 36 THR Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 45 CYS Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain E residue 50 VAL 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 184 ILE Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 207 VAL Chi-restraints excluded: chain E residue 259 ARG Chi-restraints excluded: chain E residue 264 TYR Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 21 ASN Chi-restraints excluded: chain F residue 25 ASP Chi-restraints excluded: chain F residue 32 ILE Chi-restraints excluded: chain F residue 40 LEU Chi-restraints excluded: chain F residue 273 LEU Chi-restraints excluded: chain G residue 10 ILE Chi-restraints excluded: chain G residue 17 LEU Chi-restraints excluded: chain G residue 49 ILE Chi-restraints excluded: chain G residue 81 GLN Chi-restraints excluded: chain G residue 88 ARG Chi-restraints excluded: chain G residue 95 LEU Chi-restraints excluded: chain G residue 124 GLU Chi-restraints excluded: chain H residue 66 PHE 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 229 PHE Chi-restraints excluded: chain H residue 253 ASP Chi-restraints excluded: chain H residue 266 VAL Chi-restraints excluded: chain H residue 276 THR Chi-restraints excluded: chain I residue 58 LEU Chi-restraints excluded: chain I residue 81 GLN Chi-restraints excluded: chain I residue 96 GLU Chi-restraints excluded: chain J residue 24 ILE 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 460 LEU 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 209 MET Chi-restraints excluded: chain M residue 272 ASN Chi-restraints excluded: chain M residue 276 THR Chi-restraints excluded: chain N residue 30 THR Chi-restraints excluded: chain N residue 69 GLU Chi-restraints excluded: chain N residue 94 LEU 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 4 ASP Chi-restraints excluded: chain L residue 25 GLN Chi-restraints excluded: chain L residue 81 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 0 optimal weight: 5.9990 chunk 316 optimal weight: 20.0000 chunk 229 optimal weight: 0.0970 chunk 65 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 203 optimal weight: 5.9990 chunk 172 optimal weight: 4.9990 chunk 63 optimal weight: 0.8980 chunk 16 optimal weight: 3.9990 chunk 107 optimal weight: 0.0670 chunk 56 optimal weight: 0.8980 overall best weight: 0.7918 ------------------------------------------------------------------------------- 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 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 55 GLN ** 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 16 GLN ** D 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 191 GLN E 62 HIS E 75 ASN ** E 222 ASN ** 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 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 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 97 GLN ** J 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 85 HIS J 98 GLN ** K 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 58 GLN ** 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 L 98 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.155840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.118808 restraints weight = 47611.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.123333 restraints weight = 21492.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.126223 restraints weight = 12640.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 56)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.128051 restraints weight = 8878.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.129028 restraints weight = 7070.268| |-----------------------------------------------------------------------------| r_work (final): 0.4029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.5189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 27430 Z= 0.210 Angle : 0.869 19.947 37194 Z= 0.447 Chirality : 0.052 0.480 4023 Planarity : 0.006 0.071 4752 Dihedral : 14.330 166.821 4192 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 29.45 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.11 % Favored : 90.86 % Rotamer: Outliers : 4.28 % Allowed : 25.69 % Favored : 70.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.32 (0.14), residues: 3184 helix: -0.51 (0.14), residues: 1252 sheet: -2.41 (0.25), residues: 380 loop : -2.17 (0.15), residues: 1552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 280 TYR 0.040 0.003 TYR K 440 PHE 0.051 0.003 PHE B 183 TRP 0.063 0.003 TRP J 77 HIS 0.020 0.002 HIS C 214 Details of bonding type rmsd covalent geometry : bond 0.00484 (27430) covalent geometry : angle 0.86948 (37194) hydrogen bonds : bond 0.04719 ( 1148) hydrogen bonds : angle 6.56136 ( 3315) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6368 Ramachandran restraints generated. 3184 Oldfield, 0 Emsley, 3184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6368 Ramachandran restraints generated. 3184 Oldfield, 0 Emsley, 3184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 843 residues out of total 2762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 725 time to evaluate : 0.991 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 TYR cc_start: 0.7611 (m-80) cc_final: 0.7389 (m-10) REVERT: A 126 ASN cc_start: 0.8255 (t0) cc_final: 0.7412 (t0) REVERT: A 155 TYR cc_start: 0.8409 (m-80) cc_final: 0.8188 (m-80) REVERT: A 164 GLU cc_start: 0.8162 (tp30) cc_final: 0.7800 (tp30) REVERT: A 167 GLN cc_start: 0.8385 (tm-30) cc_final: 0.7541 (tm-30) REVERT: A 168 TYR cc_start: 0.6969 (m-80) cc_final: 0.6718 (m-80) REVERT: A 169 GLU cc_start: 0.7827 (tt0) cc_final: 0.7239 (tt0) REVERT: A 179 GLU cc_start: 0.7756 (tm-30) cc_final: 0.7322 (tt0) REVERT: B 69 GLU cc_start: 0.6521 (tm-30) cc_final: 0.6275 (tm-30) REVERT: B 83 GLN cc_start: 0.8208 (mm-40) cc_final: 0.7626 (mm-40) REVERT: B 141 MET cc_start: 0.6504 (mmt) cc_final: 0.6285 (mmt) REVERT: B 175 TYR cc_start: 0.8265 (t80) cc_final: 0.7750 (t80) REVERT: B 241 ASP cc_start: 0.7604 (t70) cc_final: 0.7297 (t70) REVERT: B 259 ARG cc_start: 0.7549 (mtm110) cc_final: 0.7346 (mtm110) REVERT: C 67 ILE cc_start: 0.8359 (OUTLIER) cc_final: 0.7704 (mm) REVERT: C 70 LYS cc_start: 0.7644 (mttm) cc_final: 0.7081 (mmmt) REVERT: C 271 LYS cc_start: 0.8300 (mmmt) cc_final: 0.8090 (mmmt) REVERT: D 21 ASN cc_start: 0.7544 (t0) cc_final: 0.6797 (t0) REVERT: D 35 GLN cc_start: 0.8458 (mm-40) cc_final: 0.7994 (tp40) REVERT: D 36 THR cc_start: 0.7854 (OUTLIER) cc_final: 0.7587 (p) REVERT: D 150 MET cc_start: 0.5951 (ppp) cc_final: 0.4890 (ppp) REVERT: D 227 TYR cc_start: 0.8252 (m-80) cc_final: 0.7928 (m-80) REVERT: D 259 ARG cc_start: 0.8763 (mmp80) cc_final: 0.8308 (mmt-90) REVERT: E 62 HIS cc_start: 0.7575 (OUTLIER) cc_final: 0.7333 (t70) REVERT: E 79 GLU cc_start: 0.7852 (tm-30) cc_final: 0.7464 (tm-30) REVERT: E 101 TYR cc_start: 0.7830 (t80) cc_final: 0.7577 (t80) REVERT: E 116 MET cc_start: 0.8332 (mmt) cc_final: 0.8095 (mmp) REVERT: E 141 MET cc_start: 0.7723 (tpp) cc_final: 0.7125 (tpp) REVERT: E 144 GLU cc_start: 0.7681 (mt-10) cc_final: 0.7349 (mt-10) REVERT: E 184 ILE cc_start: 0.8664 (OUTLIER) cc_final: 0.8449 (mm) REVERT: E 204 GLN cc_start: 0.7950 (tm130) cc_final: 0.7280 (tm-30) REVERT: E 226 LEU cc_start: 0.8249 (tp) cc_final: 0.7945 (tp) REVERT: E 241 ASP cc_start: 0.7062 (t70) cc_final: 0.6710 (t0) REVERT: E 264 TYR cc_start: 0.8470 (OUTLIER) cc_final: 0.8226 (m-10) REVERT: F 25 ASP cc_start: 0.7200 (OUTLIER) cc_final: 0.6782 (t70) REVERT: F 40 LEU cc_start: 0.7824 (OUTLIER) cc_final: 0.7588 (tp) REVERT: F 72 ILE cc_start: 0.8216 (mm) cc_final: 0.7912 (mm) REVERT: F 82 GLU cc_start: 0.8777 (mt-10) cc_final: 0.8465 (mt-10) REVERT: F 124 GLN cc_start: 0.8332 (OUTLIER) cc_final: 0.8013 (mt0) REVERT: F 141 MET cc_start: 0.8217 (ttp) cc_final: 0.7498 (ttt) REVERT: F 145 HIS cc_start: 0.8461 (m170) cc_final: 0.7980 (m170) REVERT: F 209 MET cc_start: 0.6966 (tmm) cc_final: 0.6744 (tmm) REVERT: G 23 LYS cc_start: 0.8095 (tptt) cc_final: 0.7463 (tttt) REVERT: G 108 GLU cc_start: 0.8020 (mm-30) cc_final: 0.7685 (mm-30) REVERT: G 110 GLN cc_start: 0.7466 (tp-100) cc_final: 0.7173 (tp-100) REVERT: G 124 GLU cc_start: 0.8783 (OUTLIER) cc_final: 0.8573 (pm20) REVERT: H 81 HIS cc_start: 0.8503 (OUTLIER) cc_final: 0.7876 (t-90) REVERT: H 102 MET cc_start: 0.9092 (mmm) cc_final: 0.8346 (mmm) REVERT: H 137 ILE cc_start: 0.8851 (pt) cc_final: 0.8532 (mp) REVERT: H 178 TYR cc_start: 0.6828 (m-80) cc_final: 0.6449 (m-10) REVERT: H 190 LYS cc_start: 0.8700 (mttm) cc_final: 0.8346 (mttp) REVERT: H 206 LEU cc_start: 0.8878 (mt) cc_final: 0.8487 (mt) REVERT: H 208 ASN cc_start: 0.8770 (m110) cc_final: 0.7698 (t0) REVERT: H 261 PHE cc_start: 0.7845 (t80) cc_final: 0.7512 (t80) REVERT: I 16 ARG cc_start: 0.9011 (ttt-90) cc_final: 0.8350 (ttt90) REVERT: I 18 PHE cc_start: 0.8718 (t80) cc_final: 0.8509 (t80) REVERT: I 22 GLU cc_start: 0.8766 (tm-30) cc_final: 0.8281 (tm-30) REVERT: I 65 LYS cc_start: 0.8771 (mttp) cc_final: 0.8490 (mttt) REVERT: I 74 GLN cc_start: 0.8616 (pt0) cc_final: 0.8083 (mp10) REVERT: I 77 TRP cc_start: 0.8414 (t60) cc_final: 0.7789 (t60) REVERT: I 81 GLN cc_start: 0.8983 (OUTLIER) cc_final: 0.8330 (mp10) REVERT: I 84 GLU cc_start: 0.8444 (tp30) cc_final: 0.8042 (tp30) REVERT: I 109 THR cc_start: 0.8059 (m) cc_final: 0.7374 (p) REVERT: I 123 ASN cc_start: 0.8605 (m110) cc_final: 0.8112 (m110) REVERT: J 8 GLN cc_start: 0.8023 (tp40) cc_final: 0.7663 (tp-100) REVERT: J 18 PHE cc_start: 0.8869 (t80) cc_final: 0.8456 (t80) REVERT: J 25 GLN cc_start: 0.8069 (tt0) cc_final: 0.7684 (pp30) REVERT: J 39 ARG cc_start: 0.7721 (mtp85) cc_final: 0.7479 (mmm-85) REVERT: J 45 SER cc_start: 0.8521 (t) cc_final: 0.7663 (p) REVERT: J 56 MET cc_start: 0.8461 (mmm) cc_final: 0.8224 (mmm) REVERT: J 77 TRP cc_start: 0.7869 (t60) cc_final: 0.7446 (t60) REVERT: J 78 GLU cc_start: 0.8726 (tp30) cc_final: 0.8198 (tp30) REVERT: J 88 ARG cc_start: 0.7354 (OUTLIER) cc_final: 0.7154 (tmt170) REVERT: J 91 ASN cc_start: 0.8407 (m-40) cc_final: 0.8059 (m-40) REVERT: J 116 ASP cc_start: 0.6784 (t0) cc_final: 0.6406 (t0) REVERT: K 46 GLU cc_start: 0.8464 (tm-30) cc_final: 0.8261 (tm-30) REVERT: K 89 LEU cc_start: 0.9195 (mt) cc_final: 0.8946 (mt) REVERT: K 137 LYS cc_start: 0.8278 (mmmt) cc_final: 0.7261 (mmmm) REVERT: K 170 CYS cc_start: 0.9031 (m) cc_final: 0.8819 (m) REVERT: K 250 TYR cc_start: 0.7826 (OUTLIER) cc_final: 0.6479 (p90) REVERT: K 281 LEU cc_start: 0.8241 (mp) cc_final: 0.8035 (mp) REVERT: K 295 ASP cc_start: 0.8333 (t0) cc_final: 0.7979 (t0) REVERT: K 428 LYS cc_start: 0.8630 (ttpt) cc_final: 0.8329 (ttpp) REVERT: K 460 LEU cc_start: 0.6034 (OUTLIER) cc_final: 0.5621 (tt) REVERT: K 504 THR cc_start: 0.8609 (m) cc_final: 0.8285 (p) REVERT: M 19 ASN cc_start: 0.7943 (t0) cc_final: 0.7709 (t0) REVERT: M 56 MET cc_start: 0.8180 (ttm) cc_final: 0.7815 (ttm) REVERT: M 147 ILE cc_start: 0.8956 (pt) cc_final: 0.8717 (mt) REVERT: M 204 GLN cc_start: 0.8249 (OUTLIER) cc_final: 0.7652 (tm-30) REVERT: N 7 ILE cc_start: 0.8457 (mp) cc_final: 0.7865 (mm) REVERT: N 68 ASN cc_start: 0.7885 (t0) cc_final: 0.7342 (t0) REVERT: N 69 GLU cc_start: 0.7277 (OUTLIER) cc_final: 0.6956 (mt-10) REVERT: L 24 ILE cc_start: 0.8961 (mt) cc_final: 0.8702 (mp) REVERT: L 25 GLN cc_start: 0.8447 (OUTLIER) cc_final: 0.8128 (tt0) REVERT: L 40 TYR cc_start: 0.8386 (m-10) cc_final: 0.8048 (m-80) REVERT: L 56 MET cc_start: 0.7875 (mmm) cc_final: 0.6235 (tmm) REVERT: L 96 GLU cc_start: 0.8283 (pm20) cc_final: 0.8041 (pm20) outliers start: 118 outliers final: 78 residues processed: 787 average time/residue: 0.1635 time to fit residues: 204.8356 Evaluate side-chains 767 residues out of total 2762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 672 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 PHE Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 43 ASP Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 150 MET Chi-restraints excluded: chain B residue 187 HIS Chi-restraints excluded: chain B residue 209 MET Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain C residue 5 LYS Chi-restraints excluded: chain C residue 8 ASP Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 32 ILE Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 109 ILE Chi-restraints excluded: chain C residue 115 VAL 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 D residue 16 GLN Chi-restraints excluded: chain D residue 36 THR Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 45 CYS Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 56 MET Chi-restraints excluded: chain E residue 62 HIS 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 152 VAL 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 E residue 259 ARG Chi-restraints excluded: chain E residue 264 TYR Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 21 ASN Chi-restraints excluded: chain F residue 25 ASP Chi-restraints excluded: chain F residue 32 ILE Chi-restraints excluded: chain F residue 40 LEU Chi-restraints excluded: chain F residue 124 GLN Chi-restraints excluded: chain G residue 10 ILE Chi-restraints excluded: chain G residue 17 LEU Chi-restraints excluded: chain G residue 49 ILE Chi-restraints excluded: chain G residue 81 GLN Chi-restraints excluded: chain G residue 88 ARG Chi-restraints excluded: chain G residue 95 LEU Chi-restraints excluded: chain G residue 124 GLU Chi-restraints excluded: chain H residue 66 PHE 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 229 PHE Chi-restraints excluded: chain H residue 253 ASP Chi-restraints excluded: chain H residue 276 THR Chi-restraints excluded: chain I residue 58 LEU Chi-restraints excluded: chain I residue 81 GLN Chi-restraints excluded: chain I residue 124 GLU Chi-restraints excluded: chain J residue 58 LEU Chi-restraints excluded: chain J residue 88 ARG Chi-restraints excluded: chain K residue 32 PHE Chi-restraints excluded: chain K residue 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 387 ASP Chi-restraints excluded: chain K residue 393 LEU Chi-restraints excluded: chain K residue 403 ASP Chi-restraints excluded: chain K residue 460 LEU Chi-restraints excluded: chain 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 204 GLN 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 28 VAL Chi-restraints excluded: chain N residue 30 THR Chi-restraints excluded: chain N residue 69 GLU 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 4 ASP 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 82 optimal weight: 4.9990 chunk 302 optimal weight: 4.9990 chunk 18 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 141 optimal weight: 0.0970 chunk 221 optimal weight: 0.5980 chunk 263 optimal weight: 0.6980 chunk 65 optimal weight: 0.5980 chunk 239 optimal weight: 2.9990 chunk 167 optimal weight: 4.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 52 ASN ** B 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 16 GLN ** D 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 191 GLN ** E 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 233 ASN ** F 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 6 ASN ** G 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 97 GLN I 98 GLN ** J 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.161439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.128432 restraints weight = 46983.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.132982 restraints weight = 21158.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.135877 restraints weight = 12243.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 59)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.137722 restraints weight = 8477.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.138822 restraints weight = 6652.229| |-----------------------------------------------------------------------------| r_work (final): 0.4023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7469 moved from start: 0.5377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.094 27430 Z= 0.217 Angle : 0.903 20.228 37194 Z= 0.463 Chirality : 0.053 0.553 4023 Planarity : 0.006 0.079 4752 Dihedral : 14.311 166.242 4192 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 29.95 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.17 % Favored : 90.80 % Rotamer: Outliers : 3.62 % Allowed : 26.78 % Favored : 69.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.35 (0.14), residues: 3184 helix: -0.58 (0.14), residues: 1251 sheet: -2.42 (0.25), residues: 369 loop : -2.16 (0.14), residues: 1564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG F 259 TYR 0.046 0.003 TYR K 440 PHE 0.056 0.003 PHE M 53 TRP 0.059 0.003 TRP J 77 HIS 0.024 0.002 HIS C 214 Details of bonding type rmsd covalent geometry : bond 0.00505 (27430) covalent geometry : angle 0.90349 (37194) hydrogen bonds : bond 0.04893 ( 1148) hydrogen bonds : angle 6.57894 ( 3315) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6368 Ramachandran restraints generated. 3184 Oldfield, 0 Emsley, 3184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6368 Ramachandran restraints generated. 3184 Oldfield, 0 Emsley, 3184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 795 residues out of total 2762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 695 time to evaluate : 0.826 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: A 126 ASN cc_start: 0.8271 (t0) cc_final: 0.7336 (t0) REVERT: A 153 ASN cc_start: 0.6638 (m-40) cc_final: 0.6309 (m110) REVERT: A 155 TYR cc_start: 0.8474 (m-80) cc_final: 0.8212 (m-80) REVERT: A 164 GLU cc_start: 0.8294 (tp30) cc_final: 0.7913 (tp30) REVERT: A 167 GLN cc_start: 0.8289 (tm-30) cc_final: 0.7463 (tm-30) REVERT: A 168 TYR cc_start: 0.7059 (m-80) cc_final: 0.6823 (m-80) REVERT: A 169 GLU cc_start: 0.8014 (tt0) cc_final: 0.7504 (tt0) REVERT: A 178 GLU cc_start: 0.7514 (tt0) cc_final: 0.7171 (tt0) REVERT: A 179 GLU cc_start: 0.7749 (tm-30) cc_final: 0.7316 (tt0) REVERT: B 69 GLU cc_start: 0.6543 (tm-30) cc_final: 0.6276 (tm-30) REVERT: B 137 ILE cc_start: 0.8214 (mt) cc_final: 0.7830 (mt) REVERT: B 141 MET cc_start: 0.6487 (mmt) cc_final: 0.6248 (mmt) REVERT: B 175 TYR cc_start: 0.8274 (t80) cc_final: 0.7675 (t80) REVERT: B 241 ASP cc_start: 0.7662 (t70) cc_final: 0.7306 (t70) REVERT: B 259 ARG cc_start: 0.7618 (mtm110) cc_final: 0.7384 (mtm110) REVERT: C 7 TYR cc_start: 0.7079 (m-80) cc_final: 0.6035 (m-80) REVERT: C 67 ILE cc_start: 0.8364 (OUTLIER) cc_final: 0.7881 (mm) REVERT: C 70 LYS cc_start: 0.7564 (mttm) cc_final: 0.6936 (mmmt) REVERT: C 116 MET cc_start: 0.8930 (mpp) cc_final: 0.7950 (mpp) REVERT: C 230 GLU cc_start: 0.7407 (tt0) cc_final: 0.7167 (tt0) REVERT: D 16 GLN cc_start: 0.6766 (OUTLIER) cc_final: 0.6392 (mt0) REVERT: D 21 ASN cc_start: 0.7483 (t0) cc_final: 0.6695 (t0) REVERT: D 35 GLN cc_start: 0.8564 (mm-40) cc_final: 0.7954 (tp40) REVERT: D 36 THR cc_start: 0.7931 (OUTLIER) cc_final: 0.7604 (p) REVERT: D 150 MET cc_start: 0.6129 (ppp) cc_final: 0.4920 (ppp) REVERT: D 227 TYR cc_start: 0.8278 (m-80) cc_final: 0.7964 (m-80) REVERT: E 79 GLU cc_start: 0.7944 (tm-30) cc_final: 0.7554 (tm-30) REVERT: E 101 TYR cc_start: 0.8010 (t80) cc_final: 0.7772 (t80) REVERT: E 116 MET cc_start: 0.8405 (mmt) cc_final: 0.8129 (mmt) REVERT: E 138 ASP cc_start: 0.7696 (m-30) cc_final: 0.6962 (m-30) REVERT: E 141 MET cc_start: 0.7553 (tpp) cc_final: 0.6875 (tpp) REVERT: E 144 GLU cc_start: 0.7716 (mt-10) cc_final: 0.7407 (mt-10) REVERT: E 167 MET cc_start: 0.7715 (mtp) cc_final: 0.7373 (mtm) REVERT: E 169 ARG cc_start: 0.8418 (mtp85) cc_final: 0.7845 (mtp-110) REVERT: E 204 GLN cc_start: 0.7816 (tm130) cc_final: 0.7181 (tm-30) REVERT: E 226 LEU cc_start: 0.8275 (tp) cc_final: 0.7978 (tp) REVERT: E 264 TYR cc_start: 0.8343 (OUTLIER) cc_final: 0.7939 (m-10) REVERT: F 40 LEU cc_start: 0.8555 (OUTLIER) cc_final: 0.8265 (mp) REVERT: F 72 ILE cc_start: 0.8187 (mm) cc_final: 0.7843 (mm) REVERT: F 82 GLU cc_start: 0.8809 (mt-10) cc_final: 0.8489 (mt-10) REVERT: F 141 MET cc_start: 0.8163 (ttp) cc_final: 0.7539 (ttt) REVERT: F 145 HIS cc_start: 0.8553 (m170) cc_final: 0.8084 (m170) REVERT: F 209 MET cc_start: 0.6980 (tmm) cc_final: 0.6709 (tmm) REVERT: G 124 GLU cc_start: 0.8758 (OUTLIER) cc_final: 0.8515 (pm20) REVERT: H 8 ASP cc_start: 0.7833 (t0) cc_final: 0.7484 (t70) REVERT: H 102 MET cc_start: 0.8995 (mmm) cc_final: 0.8560 (mmm) REVERT: H 178 TYR cc_start: 0.6883 (m-80) cc_final: 0.6463 (m-10) REVERT: H 190 LYS cc_start: 0.8667 (mttm) cc_final: 0.8372 (mttp) REVERT: H 208 ASN cc_start: 0.8817 (m110) cc_final: 0.7738 (t0) REVERT: H 261 PHE cc_start: 0.7588 (t80) cc_final: 0.7384 (t80) REVERT: I 18 PHE cc_start: 0.8759 (t80) cc_final: 0.8448 (t80) REVERT: I 22 GLU cc_start: 0.8786 (tm-30) cc_final: 0.8289 (tm-30) REVERT: I 39 ARG cc_start: 0.7879 (ptm160) cc_final: 0.7289 (ptm160) REVERT: I 65 LYS cc_start: 0.8825 (mttp) cc_final: 0.8499 (mttt) REVERT: I 74 GLN cc_start: 0.8516 (pt0) cc_final: 0.7977 (mp10) REVERT: I 77 TRP cc_start: 0.8414 (t60) cc_final: 0.7951 (t60) REVERT: I 84 GLU cc_start: 0.8501 (tp30) cc_final: 0.8150 (tp30) REVERT: I 113 PHE cc_start: 0.7515 (m-10) cc_final: 0.6979 (m-10) REVERT: I 123 ASN cc_start: 0.8656 (m110) cc_final: 0.8162 (m110) REVERT: J 8 GLN cc_start: 0.8155 (tp40) cc_final: 0.7782 (tp-100) REVERT: J 18 PHE cc_start: 0.8735 (t80) cc_final: 0.8263 (t80) REVERT: J 39 ARG cc_start: 0.7855 (mtp85) cc_final: 0.7614 (mmm-85) REVERT: J 57 ARG cc_start: 0.8615 (mtm180) cc_final: 0.8266 (mtm-85) REVERT: J 77 TRP cc_start: 0.8102 (t60) cc_final: 0.7611 (t60) REVERT: J 88 ARG cc_start: 0.7487 (OUTLIER) cc_final: 0.7250 (tmt170) REVERT: J 91 ASN cc_start: 0.8504 (m-40) cc_final: 0.8105 (m-40) REVERT: J 116 ASP cc_start: 0.6880 (t0) cc_final: 0.6479 (t0) REVERT: K 46 GLU cc_start: 0.8526 (tm-30) cc_final: 0.8309 (tm-30) REVERT: K 89 LEU cc_start: 0.9192 (mt) cc_final: 0.8931 (mt) REVERT: K 170 CYS cc_start: 0.9032 (m) cc_final: 0.8793 (m) REVERT: K 250 TYR cc_start: 0.7776 (OUTLIER) cc_final: 0.6352 (p90) REVERT: K 281 LEU cc_start: 0.8307 (mp) cc_final: 0.8089 (mp) REVERT: K 288 MET cc_start: 0.7722 (mtm) cc_final: 0.7215 (mtm) REVERT: K 295 ASP cc_start: 0.8377 (t0) cc_final: 0.8003 (t0) REVERT: K 421 ARG cc_start: 0.8383 (ttm-80) cc_final: 0.8069 (ttm-80) REVERT: K 428 LYS cc_start: 0.8604 (ttpt) cc_final: 0.8292 (ttpp) REVERT: K 482 GLN cc_start: 0.7818 (OUTLIER) cc_final: 0.7141 (tm-30) REVERT: K 496 ARG cc_start: 0.7459 (ptt-90) cc_final: 0.7227 (tmm-80) REVERT: K 504 THR cc_start: 0.8643 (m) cc_final: 0.8289 (p) REVERT: M 56 MET cc_start: 0.8242 (ttm) cc_final: 0.7796 (ttm) REVERT: M 147 ILE cc_start: 0.9019 (pt) cc_final: 0.8801 (mt) REVERT: M 196 GLU cc_start: 0.8253 (tm-30) cc_final: 0.8029 (tm-30) REVERT: M 198 ASP cc_start: 0.7655 (m-30) cc_final: 0.7218 (m-30) REVERT: M 204 GLN cc_start: 0.8229 (OUTLIER) cc_final: 0.7765 (tm-30) REVERT: M 221 MET cc_start: 0.7920 (mtp) cc_final: 0.7446 (ttt) REVERT: N 7 ILE cc_start: 0.8397 (mp) cc_final: 0.7849 (mm) REVERT: N 25 SER cc_start: 0.8867 (m) cc_final: 0.8553 (m) REVERT: N 68 ASN cc_start: 0.7703 (t0) cc_final: 0.6965 (t0) REVERT: N 69 GLU cc_start: 0.7559 (OUTLIER) cc_final: 0.7235 (mt-10) REVERT: N 93 MET cc_start: 0.7033 (ptt) cc_final: 0.6788 (ptt) REVERT: N 97 ASP cc_start: 0.7250 (m-30) cc_final: 0.6822 (p0) REVERT: L 24 ILE cc_start: 0.9026 (mt) cc_final: 0.8799 (mp) REVERT: L 25 GLN cc_start: 0.8529 (OUTLIER) cc_final: 0.8144 (tt0) REVERT: L 40 TYR cc_start: 0.8348 (m-10) cc_final: 0.8010 (m-80) REVERT: L 56 MET cc_start: 0.8085 (mmm) cc_final: 0.6682 (tmm) REVERT: L 77 TRP cc_start: 0.8716 (t60) cc_final: 0.7974 (t60) REVERT: L 96 GLU cc_start: 0.8276 (pm20) cc_final: 0.7885 (pm20) outliers start: 100 outliers final: 71 residues processed: 749 average time/residue: 0.1658 time to fit residues: 196.3507 Evaluate side-chains 750 residues out of total 2762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 667 time to evaluate : 0.757 ------------------------------------------------------------------------------- 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 29 LEU Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 43 ASP Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 150 MET Chi-restraints excluded: chain B residue 187 HIS Chi-restraints excluded: chain B residue 209 MET Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain C residue 5 LYS Chi-restraints excluded: chain C residue 8 ASP Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 32 ILE Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain D residue 16 GLN Chi-restraints excluded: chain D residue 36 THR Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 45 CYS Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 56 MET 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 152 VAL Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 207 VAL Chi-restraints excluded: chain E residue 259 ARG Chi-restraints excluded: chain E residue 264 TYR Chi-restraints excluded: chain F residue 21 ASN Chi-restraints excluded: chain F residue 32 ILE Chi-restraints excluded: chain F residue 40 LEU Chi-restraints excluded: chain F residue 95 THR Chi-restraints excluded: chain G residue 10 ILE Chi-restraints excluded: chain G residue 17 LEU Chi-restraints excluded: chain G residue 49 ILE Chi-restraints excluded: chain G residue 81 GLN Chi-restraints excluded: chain G residue 88 ARG Chi-restraints excluded: chain G residue 95 LEU Chi-restraints excluded: chain G residue 124 GLU Chi-restraints excluded: chain H residue 66 PHE Chi-restraints excluded: chain H residue 187 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 58 LEU 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 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 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 204 GLN Chi-restraints excluded: chain M residue 272 ASN Chi-restraints excluded: chain M residue 276 THR Chi-restraints excluded: chain N residue 28 VAL Chi-restraints excluded: chain N residue 30 THR Chi-restraints excluded: chain N residue 42 LEU Chi-restraints excluded: chain N residue 69 GLU Chi-restraints excluded: chain N residue 133 GLN Chi-restraints excluded: chain N residue 159 LEU Chi-restraints excluded: chain N residue 201 VAL Chi-restraints excluded: chain L residue 25 GLN Chi-restraints excluded: chain L residue 81 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 201 optimal weight: 3.9990 chunk 269 optimal weight: 0.3980 chunk 155 optimal weight: 10.0000 chunk 128 optimal weight: 2.9990 chunk 261 optimal weight: 0.6980 chunk 185 optimal weight: 0.6980 chunk 195 optimal weight: 0.8980 chunk 55 optimal weight: 0.7980 chunk 307 optimal weight: 4.9990 chunk 158 optimal weight: 9.9990 chunk 14 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 191 GLN ** E 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 6 ASN ** G 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 123 ASN ** H 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 97 GLN ** J 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 368 ASN ** K 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 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** ** L 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.163853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.131305 restraints weight = 47114.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.135856 restraints weight = 21102.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 65)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.138710 restraints weight = 12165.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 60)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.140526 restraints weight = 8427.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.141612 restraints weight = 6621.268| |-----------------------------------------------------------------------------| r_work (final): 0.4040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7447 moved from start: 0.5588 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= 0.204 Angle : 0.890 20.872 37194 Z= 0.458 Chirality : 0.053 0.583 4023 Planarity : 0.006 0.085 4752 Dihedral : 14.287 165.523 4192 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 28.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.01 % Favored : 90.99 % Rotamer: Outliers : 3.41 % Allowed : 27.50 % Favored : 69.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.34 (0.14), residues: 3184 helix: -0.58 (0.14), residues: 1263 sheet: -2.39 (0.25), residues: 382 loop : -2.16 (0.15), residues: 1539 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG B 110 TYR 0.047 0.003 TYR G 106 PHE 0.049 0.003 PHE M 53 TRP 0.055 0.003 TRP J 77 HIS 0.024 0.002 HIS C 214 Details of bonding type rmsd covalent geometry : bond 0.00472 (27430) covalent geometry : angle 0.88975 (37194) hydrogen bonds : bond 0.04840 ( 1148) hydrogen bonds : angle 6.56151 ( 3315) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5785.02 seconds wall clock time: 100 minutes 48.63 seconds (6048.63 seconds total)