Starting phenix.real_space_refine on Sun Aug 24 17:31:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6w1x_21516/08_2025/6w1x_21516.cif Found real_map, /net/cci-nas-00/data/ceres_data/6w1x_21516/08_2025/6w1x_21516.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6w1x_21516/08_2025/6w1x_21516.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6w1x_21516/08_2025/6w1x_21516.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6w1x_21516/08_2025/6w1x_21516.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6w1x_21516/08_2025/6w1x_21516.map" } resolution = 3.9 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= 0.005 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 59 5.49 5 S 15 5.16 5 C 13426 2.51 5 N 3976 2.21 5 O 4259 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 37 residue(s): 0.01s 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: 21735 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 1817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 314, 1817 Classifications: {'peptide': 314} Incomplete info: {'truncation_to_alanine': 187} Link IDs: {'PTRANS': 23, 'TRANS': 290} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 711 Unresolved non-hydrogen angles: 907 Unresolved non-hydrogen dihedrals: 582 Unresolved non-hydrogen chiralities: 54 Planarities with less than four sites: {'GLN:plan1': 18, 'HIS:plan': 8, 'ASP:plan': 12, 'ARG:plan': 24, 'ASN:plan1': 11, 'GLU:plan': 20, 'PHE:plan': 6, 'TYR:plan': 1, 'TRP:plan': 5} Unresolved non-hydrogen planarities: 469 Chain: "B" Number of atoms: 2129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 304, 2129 Classifications: {'peptide': 304} Incomplete info: {'truncation_to_alanine': 70} Link IDs: {'PTRANS': 22, 'TRANS': 281} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 275 Unresolved non-hydrogen angles: 346 Unresolved non-hydrogen dihedrals: 223 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'ASP:plan': 8, 'GLU:plan': 10, 'ARG:plan': 14, 'ASN:plan1': 5, 'TRP:plan': 2, 'PHE:plan': 2, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 187 Chain: "C" Number of atoms: 2111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 2111 Classifications: {'peptide': 290} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 10, 'TRANS': 279} Chain breaks: 2 Unresolved non-hydrogen bonds: 139 Unresolved non-hydrogen angles: 170 Unresolved non-hydrogen dihedrals: 108 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 3, 'ARG:plan': 6, 'ASP:plan': 10, 'GLU:plan': 7, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 103 Chain: "D" Number of atoms: 2498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2498 Classifications: {'peptide': 328} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 12, 'TRANS': 315} Chain breaks: 1 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "E" Number of atoms: 2499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 329, 2499 Classifications: {'peptide': 329} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 12, 'TRANS': 316} Chain breaks: 1 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 37 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 4, 'ARG:plan': 1, 'GLU:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 32 Chain: "F" Number of atoms: 2528 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2528 Classifications: {'peptide': 335} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 12, 'TRANS': 322} Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 6, 'ARG:plan': 1, 'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 31 Chain: "G" Number of atoms: 2488 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2488 Classifications: {'peptide': 326} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 12, 'TRANS': 313} Chain breaks: 1 Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 4, 'ARG:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 25 Chain: "H" Number of atoms: 2502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2502 Classifications: {'peptide': 333} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 12, 'TRANS': 320} Unresolved non-hydrogen bonds: 78 Unresolved non-hydrogen angles: 93 Unresolved non-hydrogen dihedrals: 65 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 4, 'ASP:plan': 5, 'HIS:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 44 Chain: "M" Number of atoms: 1272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 1272 Classifications: {'RNA': 60} Modifications used: {'5*END': 1, 'rna2p_pur': 7, 'rna2p_pyr': 11, 'rna3p_pur': 22, 'rna3p_pyr': 19} Link IDs: {'rna2p': 17, 'rna3p': 42} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "L" Number of atoms: 920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 920 Classifications: {'peptide': 187} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 159} Link IDs: {'PTRANS': 15, 'TRANS': 171} Unresolved chain link angles: 15 Unresolved non-hydrogen bonds: 631 Unresolved non-hydrogen angles: 805 Unresolved non-hydrogen dihedrals: 531 Unresolved non-hydrogen chiralities: 47 Planarities with less than four sites: {'ASP:plan': 12, 'HIS:plan': 8, 'TYR:plan': 3, 'ARG:plan': 24, 'GLU:plan': 11, 'PHE:plan': 10, 'GLN:plan1': 9, 'TRP:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 378 Chain: "I" Number of atoms: 489 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 489 Classifications: {'peptide': 64} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'TRANS': 63} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "J" Number of atoms: 482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 482 Classifications: {'peptide': 64} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'TRANS': 63} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 30 Planarities with less than four sites: {'GLU:plan': 4, 'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 25 Time building chain proxies: 4.43, per 1000 atoms: 0.20 Number of scatterers: 21735 At special positions: 0 Unit cell: (118.45, 142.6, 149.5, 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 15 16.00 P 59 15.00 O 4259 8.00 N 3976 7.00 C 13426 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: 1.77 Conformation dependent library (CDL) restraints added in 975.5 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 5676 Ramachandran restraints generated. 2838 Oldfield, 0 Emsley, 2838 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5342 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 41 sheets defined 34.1% alpha, 16.6% beta 0 base pairs and 13 stacking pairs defined. Time for finding SS restraints: 2.76 Creating SS restraints... Processing helix chain 'A' and resid 72 through 74 No H-bonds generated for 'chain 'A' and resid 72 through 74' Processing helix chain 'A' and resid 172 through 176 removed outlier: 3.892A pdb=" N LYS A 176 " --> pdb=" O SER A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 211 Processing helix chain 'A' and resid 212 through 225 removed outlier: 3.530A pdb=" N ALA A 218 " --> pdb=" O ALA A 214 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N SER A 223 " --> pdb=" O ARG A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 251 Processing helix chain 'A' and resid 269 through 273 removed outlier: 4.333A pdb=" N GLN A 273 " --> pdb=" O PRO A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 305 removed outlier: 3.515A pdb=" N THR A 303 " --> pdb=" O ARG A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 308 No H-bonds generated for 'chain 'A' and resid 306 through 308' Processing helix chain 'A' and resid 312 through 316 removed outlier: 4.199A pdb=" N LEU A 316 " --> pdb=" O HIS A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 342 removed outlier: 3.520A pdb=" N ARG A 321 " --> pdb=" O ALA A 317 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N ALA A 323 " --> pdb=" O ARG A 319 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ALA A 327 " --> pdb=" O ALA A 323 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLN A 328 " --> pdb=" O GLN A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 361 removed outlier: 3.861A pdb=" N HIS A 356 " --> pdb=" O GLY A 352 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N ALA A 358 " --> pdb=" O GLN A 354 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N GLU A 359 " --> pdb=" O LEU A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 381 removed outlier: 3.768A pdb=" N ARG A 377 " --> pdb=" O THR A 373 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLY A 381 " --> pdb=" O ARG A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 399 removed outlier: 4.196A pdb=" N ASN A 389 " --> pdb=" O ALA A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 407 removed outlier: 4.018A pdb=" N GLY A 407 " --> pdb=" O GLN A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 434 removed outlier: 3.778A pdb=" N ALA A 412 " --> pdb=" O SER A 408 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLU A 432 " --> pdb=" O ILE A 428 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ARG A 433 " --> pdb=" O LEU A 429 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ASP A 434 " --> pdb=" O GLU A 430 " (cutoff:3.500A) Processing helix chain 'B' and resid 33 through 53 removed outlier: 4.077A pdb=" N PHE B 37 " --> pdb=" O SER B 33 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N ILE B 50 " --> pdb=" O ARG B 46 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N SER B 51 " --> pdb=" O ARG B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 121 Processing helix chain 'B' and resid 122 through 137 Processing helix chain 'B' and resid 165 through 181 Processing helix chain 'B' and resid 190 through 200 Processing helix chain 'B' and resid 206 through 215 removed outlier: 3.906A pdb=" N LEU B 210 " --> pdb=" O GLU B 206 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 301 Processing helix chain 'B' and resid 318 through 322 Processing helix chain 'C' and resid 48 through 55 removed outlier: 3.940A pdb=" N ASP C 53 " --> pdb=" O ALA C 50 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N SER C 55 " --> pdb=" O ARG C 52 " (cutoff:3.500A) Processing helix chain 'C' and resid 130 through 148 removed outlier: 3.536A pdb=" N ARG C 134 " --> pdb=" O ASP C 130 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 163 Processing helix chain 'C' and resid 208 through 224 Processing helix chain 'C' and resid 275 through 284 removed outlier: 3.977A pdb=" N ALA C 282 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 306 removed outlier: 3.662A pdb=" N SER C 306 " --> pdb=" O PRO C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 322 through 333 Processing helix chain 'C' and resid 338 through 352 Processing helix chain 'D' and resid 48 through 52 Processing helix chain 'D' and resid 82 through 92 removed outlier: 3.942A pdb=" N LEU D 86 " --> pdb=" O ASP D 82 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ILE D 90 " --> pdb=" O LEU D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 130 through 148 removed outlier: 3.546A pdb=" N ARG D 134 " --> pdb=" O ASP D 130 " (cutoff:3.500A) Processing helix chain 'D' and resid 150 through 163 Processing helix chain 'D' and resid 208 through 224 Processing helix chain 'D' and resid 275 through 284 removed outlier: 3.930A pdb=" N ALA D 282 " --> pdb=" O LYS D 278 " (cutoff:3.500A) Processing helix chain 'D' and resid 302 through 306 removed outlier: 3.615A pdb=" N SER D 306 " --> pdb=" O PRO D 303 " (cutoff:3.500A) Processing helix chain 'D' and resid 322 through 333 Processing helix chain 'D' and resid 338 through 352 Processing helix chain 'E' and resid 49 through 54 removed outlier: 4.014A pdb=" N ASP E 53 " --> pdb=" O ALA E 50 " (cutoff:3.500A) Processing helix chain 'E' and resid 82 through 92 removed outlier: 3.935A pdb=" N LEU E 86 " --> pdb=" O ASP E 82 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N SER E 92 " --> pdb=" O ALA E 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 130 through 148 removed outlier: 3.576A pdb=" N ARG E 134 " --> pdb=" O ASP E 130 " (cutoff:3.500A) Processing helix chain 'E' and resid 150 through 163 Processing helix chain 'E' and resid 208 through 224 Processing helix chain 'E' and resid 275 through 284 removed outlier: 3.822A pdb=" N ALA E 282 " --> pdb=" O LYS E 278 " (cutoff:3.500A) Processing helix chain 'E' and resid 302 through 306 removed outlier: 3.872A pdb=" N SER E 306 " --> pdb=" O PRO E 303 " (cutoff:3.500A) Processing helix chain 'E' and resid 322 through 333 Processing helix chain 'E' and resid 338 through 352 Processing helix chain 'F' and resid 49 through 54 removed outlier: 4.008A pdb=" N ASP F 53 " --> pdb=" O ALA F 50 " (cutoff:3.500A) Processing helix chain 'F' and resid 84 through 92 removed outlier: 3.638A pdb=" N SER F 92 " --> pdb=" O ALA F 88 " (cutoff:3.500A) Processing helix chain 'F' and resid 130 through 148 removed outlier: 3.541A pdb=" N ARG F 134 " --> pdb=" O ASP F 130 " (cutoff:3.500A) Processing helix chain 'F' and resid 150 through 163 Processing helix chain 'F' and resid 208 through 224 Processing helix chain 'F' and resid 275 through 284 removed outlier: 3.840A pdb=" N ALA F 282 " --> pdb=" O LYS F 278 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ARG F 284 " --> pdb=" O GLY F 280 " (cutoff:3.500A) Processing helix chain 'F' and resid 302 through 306 removed outlier: 3.591A pdb=" N SER F 306 " --> pdb=" O PRO F 303 " (cutoff:3.500A) Processing helix chain 'F' and resid 322 through 333 Processing helix chain 'F' and resid 338 through 352 Processing helix chain 'G' and resid 49 through 54 removed outlier: 4.003A pdb=" N ASP G 53 " --> pdb=" O ALA G 50 " (cutoff:3.500A) Processing helix chain 'G' and resid 82 through 92 removed outlier: 3.590A pdb=" N SER G 92 " --> pdb=" O ALA G 88 " (cutoff:3.500A) Processing helix chain 'G' and resid 130 through 148 removed outlier: 3.583A pdb=" N ARG G 134 " --> pdb=" O ASP G 130 " (cutoff:3.500A) Processing helix chain 'G' and resid 150 through 163 Processing helix chain 'G' and resid 208 through 224 Processing helix chain 'G' and resid 275 through 284 removed outlier: 3.965A pdb=" N ALA G 282 " --> pdb=" O LYS G 278 " (cutoff:3.500A) Processing helix chain 'G' and resid 302 through 306 removed outlier: 3.746A pdb=" N SER G 306 " --> pdb=" O PRO G 303 " (cutoff:3.500A) Processing helix chain 'G' and resid 322 through 333 Processing helix chain 'G' and resid 338 through 352 Processing helix chain 'H' and resid 48 through 53 removed outlier: 4.408A pdb=" N ASP H 53 " --> pdb=" O TRP H 49 " (cutoff:3.500A) Processing helix chain 'H' and resid 82 through 92 removed outlier: 3.520A pdb=" N SER H 92 " --> pdb=" O ALA H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 130 through 148 removed outlier: 3.571A pdb=" N ARG H 134 " --> pdb=" O ASP H 130 " (cutoff:3.500A) Processing helix chain 'H' and resid 150 through 163 Processing helix chain 'H' and resid 208 through 224 Processing helix chain 'H' and resid 275 through 284 removed outlier: 3.586A pdb=" N ALA H 282 " --> pdb=" O LYS H 278 " (cutoff:3.500A) Processing helix chain 'H' and resid 302 through 306 removed outlier: 3.736A pdb=" N SER H 306 " --> pdb=" O PRO H 303 " (cutoff:3.500A) Processing helix chain 'H' and resid 322 through 333 Processing helix chain 'H' and resid 338 through 352 Processing helix chain 'L' and resid 16 through 34 removed outlier: 3.606A pdb=" N ALA L 34 " --> pdb=" O GLN L 30 " (cutoff:3.500A) Processing helix chain 'L' and resid 63 through 73 Processing helix chain 'L' and resid 78 through 81 removed outlier: 4.400A pdb=" N ASP L 81 " --> pdb=" O GLY L 78 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 78 through 81' Processing helix chain 'L' and resid 108 through 121 removed outlier: 3.699A pdb=" N ARG L 119 " --> pdb=" O ARG L 115 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N HIS L 120 " --> pdb=" O LEU L 116 " (cutoff:3.500A) Processing helix chain 'L' and resid 123 through 131 Processing helix chain 'L' and resid 132 through 136 removed outlier: 3.581A pdb=" N VAL L 135 " --> pdb=" O PRO L 132 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ALA L 136 " --> pdb=" O ASP L 133 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 132 through 136' Processing helix chain 'I' and resid 26 through 37 removed outlier: 3.584A pdb=" N ALA I 30 " --> pdb=" O SER I 26 " (cutoff:3.500A) Processing helix chain 'J' and resid 26 through 38 Processing sheet with id=AA1, first strand: chain 'A' and resid 69 through 70 removed outlier: 3.852A pdb=" N VAL B 187 " --> pdb=" O GLU B 288 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 69 through 70 removed outlier: 7.079A pdb=" N LEU B 283 " --> pdb=" O ALA B 253 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N TRP B 247 " --> pdb=" O TRP B 289 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 178 through 181 removed outlier: 8.841A pdb=" N ARG B 278 " --> pdb=" O TYR A 187 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N LEU A 189 " --> pdb=" O ARG B 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 239 through 240 removed outlier: 3.908A pdb=" N ALA A 239 " --> pdb=" O LEU A 264 " (cutoff:3.500A) removed outlier: 8.428A pdb=" N TRP B 29 " --> pdb=" O TRP A 263 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N LEU A 265 " --> pdb=" O TRP B 29 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 138 through 139 removed outlier: 4.019A pdb=" N SER B 143 " --> pdb=" O GLN B 18 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N SER B 16 " --> pdb=" O LEU B 145 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ALA B 157 " --> pdb=" O LEU B 11 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 138 through 139 removed outlier: 4.019A pdb=" N SER B 143 " --> pdb=" O GLN B 18 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N SER B 16 " --> pdb=" O LEU B 145 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N SER B 108 " --> pdb=" O CYS B 63 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N CYS B 63 " --> pdb=" O SER B 108 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N LEU B 110 " --> pdb=" O ILE B 61 " (cutoff:3.500A) removed outlier: 5.800A pdb=" N ILE B 61 " --> pdb=" O LEU B 110 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N GLY B 112 " --> pdb=" O VAL B 59 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N VAL B 59 " --> pdb=" O GLY B 112 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 70 through 71 Processing sheet with id=AA8, first strand: chain 'B' and resid 219 through 220 Processing sheet with id=AA9, first strand: chain 'B' and resid 306 through 307 Processing sheet with id=AB1, first strand: chain 'C' and resid 127 through 128 removed outlier: 3.731A pdb=" N ALA C 127 " --> pdb=" O ALA C 32 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ALA C 32 " --> pdb=" O ALA C 127 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 193 through 196 removed outlier: 4.417A pdb=" N VAL C 228 " --> pdb=" O VAL C 118 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N ALA C 272 " --> pdb=" O MET C 44 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 184 through 185 Processing sheet with id=AB4, first strand: chain 'C' and resid 248 through 249 removed outlier: 3.896A pdb=" N THR C 264 " --> pdb=" O GLU C 249 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 127 through 128 removed outlier: 3.654A pdb=" N ALA D 127 " --> pdb=" O ALA D 32 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ALA D 32 " --> pdb=" O ALA D 127 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 193 through 196 removed outlier: 3.798A pdb=" N ALA D 42 " --> pdb=" O ILE D 274 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE D 274 " --> pdb=" O ALA D 42 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N ALA D 272 " --> pdb=" O MET D 44 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 64 through 70 removed outlier: 4.603A pdb=" N ALA D 101 " --> pdb=" O VAL D 244 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 184 through 185 Processing sheet with id=AB9, first strand: chain 'D' and resid 248 through 249 removed outlier: 4.521A pdb=" N THR D 264 " --> pdb=" O GLU D 249 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 127 through 128 removed outlier: 3.772A pdb=" N ALA E 127 " --> pdb=" O ALA E 32 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA E 32 " --> pdb=" O ALA E 127 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU E 31 " --> pdb=" O PHE E 355 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 193 through 196 removed outlier: 3.530A pdb=" N VAL E 179 " --> pdb=" O PHE E 195 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N VAL E 228 " --> pdb=" O VAL E 118 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ALA E 42 " --> pdb=" O ILE E 274 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N MET E 44 " --> pdb=" O ALA E 272 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N ALA E 272 " --> pdb=" O MET E 44 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 64 through 69 removed outlier: 3.549A pdb=" N LYS E 66 " --> pdb=" O VAL E 98 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N VAL E 98 " --> pdb=" O LYS E 66 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLN E 96 " --> pdb=" O VAL E 68 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N ALA E 101 " --> pdb=" O VAL E 244 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 248 through 249 removed outlier: 4.626A pdb=" N THR E 264 " --> pdb=" O GLU E 249 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 127 through 128 removed outlier: 3.846A pdb=" N ALA F 127 " --> pdb=" O ALA F 32 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA F 32 " --> pdb=" O ALA F 127 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 193 through 196 removed outlier: 4.535A pdb=" N VAL F 228 " --> pdb=" O VAL F 118 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ALA F 42 " --> pdb=" O ILE F 274 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE F 274 " --> pdb=" O ALA F 42 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N MET F 44 " --> pdb=" O ALA F 272 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N ALA F 272 " --> pdb=" O MET F 44 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 64 through 70 removed outlier: 4.456A pdb=" N ALA F 101 " --> pdb=" O VAL F 244 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 248 through 249 removed outlier: 4.023A pdb=" N THR F 264 " --> pdb=" O GLU F 249 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 127 through 128 removed outlier: 3.658A pdb=" N ALA G 127 " --> pdb=" O ALA G 32 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA G 32 " --> pdb=" O ALA G 127 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU G 31 " --> pdb=" O PHE G 355 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 193 through 196 removed outlier: 4.538A pdb=" N VAL G 228 " --> pdb=" O VAL G 118 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N THR G 115 " --> pdb=" O ASP G 41 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N ASP G 41 " --> pdb=" O THR G 115 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ARG G 117 " --> pdb=" O PRO G 39 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ALA G 42 " --> pdb=" O ILE G 274 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 64 through 69 removed outlier: 3.545A pdb=" N LYS G 66 " --> pdb=" O VAL G 98 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N VAL G 98 " --> pdb=" O LYS G 66 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N ALA G 101 " --> pdb=" O VAL G 244 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 184 through 185 Processing sheet with id=AD4, first strand: chain 'G' and resid 248 through 249 removed outlier: 4.322A pdb=" N THR G 264 " --> pdb=" O GLU G 249 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 127 through 128 removed outlier: 3.812A pdb=" N ALA H 127 " --> pdb=" O ALA H 32 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ALA H 32 " --> pdb=" O ALA H 127 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU H 31 " --> pdb=" O PHE H 355 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'H' and resid 43 through 47 removed outlier: 3.615A pdb=" N VAL H 179 " --> pdb=" O PHE H 195 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'H' and resid 64 through 70 removed outlier: 3.572A pdb=" N VAL H 68 " --> pdb=" O GLN H 96 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLN H 96 " --> pdb=" O VAL H 68 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N ALA H 101 " --> pdb=" O VAL H 244 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'H' and resid 267 through 268 Processing sheet with id=AD9, first strand: chain 'L' and resid 41 through 43 removed outlier: 3.769A pdb=" N GLY L 41 " --> pdb=" O HIS L 61 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'L' and resid 97 through 98 removed outlier: 3.642A pdb=" N ARG L 98 " --> pdb=" O VAL L 184 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'L' and resid 100 through 101 Processing sheet with id=AE3, first strand: chain 'L' and resid 145 through 148 removed outlier: 4.862A pdb=" N SER L 148 " --> pdb=" O GLN L 153 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N GLN L 153 " --> pdb=" O SER L 148 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'I' and resid 20 through 21 removed outlier: 6.354A pdb=" N SER I 49 " --> pdb=" O TRP I 54 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N TRP I 54 " --> pdb=" O SER I 49 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'J' and resid 20 through 21 removed outlier: 3.638A pdb=" N VAL J 10 " --> pdb=" O VAL J 44 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N SER J 49 " --> pdb=" O TRP J 54 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N TRP J 54 " --> pdb=" O SER J 49 " (cutoff:3.500A) 914 hydrogen bonds defined for protein. 2481 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 13 stacking parallelities Total time for adding SS restraints: 4.12 Time building geometry restraints manager: 2.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3615 1.31 - 1.43: 6004 1.43 - 1.56: 12503 1.56 - 1.69: 118 1.69 - 1.81: 22 Bond restraints: 22262 Sorted by residual: bond pdb=" C ASN E 94 " pdb=" O ASN E 94 " ideal model delta sigma weight residual 1.234 1.180 0.054 1.19e-02 7.06e+03 2.04e+01 bond pdb=" C ALA F 273 " pdb=" O ALA F 273 " ideal model delta sigma weight residual 1.234 1.186 0.048 1.10e-02 8.26e+03 1.92e+01 bond pdb=" C ALA E 273 " pdb=" O ALA E 273 " ideal model delta sigma weight residual 1.234 1.186 0.048 1.10e-02 8.26e+03 1.92e+01 bond pdb=" C ALA D 273 " pdb=" O ALA D 273 " ideal model delta sigma weight residual 1.234 1.189 0.046 1.10e-02 8.26e+03 1.72e+01 bond pdb=" CA SER D 247 " pdb=" CB SER D 247 " ideal model delta sigma weight residual 1.527 1.471 0.056 1.38e-02 5.25e+03 1.65e+01 ... (remaining 22257 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.83: 28812 1.83 - 3.66: 1746 3.66 - 5.49: 103 5.49 - 7.32: 10 7.32 - 9.15: 2 Bond angle restraints: 30673 Sorted by residual: angle pdb=" C4' G M 15 " pdb=" C3' G M 15 " pdb=" O3' G M 15 " ideal model delta sigma weight residual 113.00 122.15 -9.15 1.50e+00 4.44e-01 3.72e+01 angle pdb=" C3' A M 12 " pdb=" C2' A M 12 " pdb=" O2' A M 12 " ideal model delta sigma weight residual 110.70 118.30 -7.60 1.50e+00 4.44e-01 2.57e+01 angle pdb=" C4' C M 13 " pdb=" C3' C M 13 " pdb=" O3' C M 13 " ideal model delta sigma weight residual 109.40 116.40 -7.00 1.50e+00 4.44e-01 2.18e+01 angle pdb=" C4' U M 35 " pdb=" C3' U M 35 " pdb=" O3' U M 35 " ideal model delta sigma weight residual 113.00 119.77 -6.77 1.50e+00 4.44e-01 2.04e+01 angle pdb=" O3' C M 11 " pdb=" C3' C M 11 " pdb=" C2' C M 11 " ideal model delta sigma weight residual 113.70 107.07 6.63 1.50e+00 4.44e-01 1.96e+01 ... (remaining 30668 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.88: 13037 30.88 - 61.75: 202 61.75 - 92.63: 61 92.63 - 123.50: 5 123.50 - 154.38: 1 Dihedral angle restraints: 13306 sinusoidal: 5044 harmonic: 8262 Sorted by residual: dihedral pdb=" O4' U M 27 " pdb=" C1' U M 27 " pdb=" N1 U M 27 " pdb=" C2 U M 27 " ideal model delta sinusoidal sigma weight residual 200.00 80.50 119.50 1 1.50e+01 4.44e-03 6.37e+01 dihedral pdb=" O4' U M 35 " pdb=" C1' U M 35 " pdb=" N1 U M 35 " pdb=" C2 U M 35 " ideal model delta sinusoidal sigma weight residual -160.00 -63.30 -96.70 1 1.50e+01 4.44e-03 4.76e+01 dihedral pdb=" O4' C M 29 " pdb=" C1' C M 29 " pdb=" N1 C M 29 " pdb=" C2 C M 29 " ideal model delta sinusoidal sigma weight residual -160.00 -63.51 -96.49 1 1.50e+01 4.44e-03 4.75e+01 ... (remaining 13303 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.095: 2808 0.095 - 0.190: 692 0.190 - 0.285: 68 0.285 - 0.380: 19 0.380 - 0.475: 9 Chirality restraints: 3596 Sorted by residual: chirality pdb=" C2' A M 8 " pdb=" C3' A M 8 " pdb=" O2' A M 8 " pdb=" C1' A M 8 " both_signs ideal model delta sigma weight residual False -2.52 -2.04 -0.47 2.00e-01 2.50e+01 5.64e+00 chirality pdb=" C2' G M 60 " pdb=" C3' G M 60 " pdb=" O2' G M 60 " pdb=" C1' G M 60 " both_signs ideal model delta sigma weight residual False -2.52 -2.05 -0.47 2.00e-01 2.50e+01 5.49e+00 chirality pdb=" C2' C M 44 " pdb=" C3' C M 44 " pdb=" O2' C M 44 " pdb=" C1' C M 44 " both_signs ideal model delta sigma weight residual False -2.52 -2.07 -0.45 2.00e-01 2.50e+01 5.09e+00 ... (remaining 3593 not shown) Planarity restraints: 3843 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' C M 13 " -0.046 2.00e-02 2.50e+03 2.49e-02 1.39e+01 pdb=" N1 C M 13 " 0.046 2.00e-02 2.50e+03 pdb=" C2 C M 13 " -0.003 2.00e-02 2.50e+03 pdb=" O2 C M 13 " 0.002 2.00e-02 2.50e+03 pdb=" N3 C M 13 " 0.016 2.00e-02 2.50e+03 pdb=" C4 C M 13 " -0.000 2.00e-02 2.50e+03 pdb=" N4 C M 13 " -0.030 2.00e-02 2.50e+03 pdb=" C5 C M 13 " 0.011 2.00e-02 2.50e+03 pdb=" C6 C M 13 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU J 27 " 0.012 2.00e-02 2.50e+03 2.46e-02 6.04e+00 pdb=" C LEU J 27 " -0.043 2.00e-02 2.50e+03 pdb=" O LEU J 27 " 0.016 2.00e-02 2.50e+03 pdb=" N THR J 28 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY E 356 " -0.012 2.00e-02 2.50e+03 2.35e-02 5.51e+00 pdb=" C GLY E 356 " 0.041 2.00e-02 2.50e+03 pdb=" O GLY E 356 " -0.015 2.00e-02 2.50e+03 pdb=" N GLU E 357 " -0.014 2.00e-02 2.50e+03 ... (remaining 3840 not shown) Histogram of nonbonded interaction distances: 1.88 - 2.48: 113 2.48 - 3.09: 16263 3.09 - 3.69: 31440 3.69 - 4.30: 43851 4.30 - 4.90: 74897 Nonbonded interactions: 166564 Sorted by model distance: nonbonded pdb=" OG SER B 25 " pdb=" OG1 THR B 28 " model vdw 1.879 3.040 nonbonded pdb=" OG1 THR I 24 " pdb=" OG SER I 29 " model vdw 1.976 3.040 nonbonded pdb=" OH TYR A 179 " pdb=" OD2 ASP B 272 " model vdw 2.070 3.040 nonbonded pdb=" O2' G M 18 " pdb=" O4' G M 19 " model vdw 2.071 3.040 nonbonded pdb=" O2' G M 30 " pdb=" O4' C M 31 " model vdw 2.077 3.040 ... (remaining 166559 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 'C' and (resid 25 through 33 or (resid 34 and (name N or name CA or name \ C or name O or name CB )) or resid 35 through 190 or (resid 191 through 192 and \ (name N or name CA or name C or name O or name CB )) or resid 193 through 226 or \ (resid 227 and (name N or name CA or name C or name O or name CB )) or resid 22 \ 8 through 285 or (resid 286 and (name N or name CA or name C or name O or name C \ B )) or resid 287 through 295 or (resid 296 and (name N or name CA or name C or \ name O or name CB )) or resid 297 through 303 or (resid 304 and (name N or name \ CA or name C or name O or name CB )) or resid 305 through 356 or (resid 357 and \ (name N or name CA or name C or name O or name CB )))) selection = (chain 'D' and (resid 25 through 50 or (resid 51 through 57 and (name N or name \ CA or name C or name O or name CB )) or resid 58 through 63 or (resid 64 and (na \ me N or name CA or name C or name O or name CB )) or resid 65 through 66 or resi \ d 98 through 104 or (resid 105 through 107 and (name N or name CA or name C or n \ ame O or name CB )) or resid 108 through 145 or (resid 146 through 147 and (name \ N or name CA or name C or name O or name CB )) or resid 148 through 151 or (res \ id 152 and (name N or name CA or name C or name O or name CB )) or resid 153 thr \ ough 168 or (resid 169 and (name N or name CA or name C or name O or name CB )) \ or resid 170 through 174 or (resid 175 through 176 and (name N or name CA or nam \ e C or name O or name CB )) or resid 177 through 184 or (resid 185 through 186 a \ nd (name N or name CA or name C or name O or name CB )) or resid 187 or (resid 1 \ 88 and (name N or name CA or name C or name O or name CB )) or resid 189 through \ 190 or (resid 191 through 192 and (name N or name CA or name C or name O or nam \ e CB )) or resid 193 through 195 or (resid 196 through 199 and (name N or name C \ A or name C or name O or name CB )) or resid 200 through 201 or (resid 202 throu \ gh 204 and (name N or name CA or name C or name O or name CB )) or resid 205 or \ (resid 206 through 207 and (name N or name CA or name C or name O or name CB )) \ or resid 208 through 209 or (resid 210 and (name N or name CA or name C or name \ O or name CB )) or resid 211 through 226 or (resid 227 and (name N or name CA or \ name C or name O or name CB )) or resid 228 through 239 or (resid 240 and (name \ N or name CA or name C or name O or name CB )) or resid 241 through 249 or (res \ id 250 and (name N or name CA or name C or name O or name CB )) or resid 263 thr \ ough 268 or (resid 269 through 273 and (name N or name CA or name C or name O or \ name CB )) or resid 274 through 303 or (resid 304 and (name N or name CA or nam \ e C or name O or name CB )) or resid 305 through 311 or (resid 312 through 313 a \ nd (name N or name CA or name C or name O or name CB )) or resid 314 through 317 \ or (resid 318 and (name N or name CA or name C or name O or name CB )) or resid \ 319 or (resid 320 through 322 and (name N or name CA or name C or name O or nam \ e CB )) or resid 323 through 339 or (resid 340 and (name N or name CA or name C \ or name O or name CB )) or resid 341 through 356 or (resid 357 and (name N or na \ me CA or name C or name O or name CB )))) selection = (chain 'E' and (resid 25 through 33 or (resid 34 and (name N or name CA or name \ C or name O or name CB )) or resid 35 through 50 or (resid 51 through 57 and (na \ me N or name CA or name C or name O or name CB )) or resid 58 through 63 or (res \ id 64 and (name N or name CA or name C or name O or name CB )) or resid 65 throu \ gh 66 or resid 98 through 104 or (resid 105 through 107 and (name N or name CA o \ r name C or name O or name CB )) or resid 108 through 145 or (resid 146 through \ 147 and (name N or name CA or name C or name O or name CB )) or resid 148 throug \ h 151 or (resid 152 and (name N or name CA or name C or name O or name CB )) or \ resid 153 through 168 or (resid 169 and (name N or name CA or name C or name O o \ r name CB )) or resid 170 through 174 or (resid 175 through 176 and (name N or n \ ame CA or name C or name O or name CB )) or resid 177 through 184 or (resid 185 \ through 186 and (name N or name CA or name C or name O or name CB )) or resid 18 \ 7 or (resid 188 and (name N or name CA or name C or name O or name CB )) or resi \ d 189 through 190 or (resid 191 through 192 and (name N or name CA or name C or \ name O or name CB )) or resid 193 through 195 or (resid 196 through 199 and (nam \ e N or name CA or name C or name O or name CB )) or resid 200 through 201 or (re \ sid 202 through 204 and (name N or name CA or name C or name O or name CB )) or \ resid 205 or (resid 206 through 207 and (name N or name CA or name C or name O o \ r name CB )) or resid 208 through 209 or (resid 210 and (name N or name CA or na \ me C or name O or name CB )) or resid 211 through 226 or (resid 227 and (name N \ or name CA or name C or name O or name CB )) or resid 228 through 239 or (resid \ 240 and (name N or name CA or name C or name O or name CB )) or resid 241 throug \ h 249 or (resid 250 and (name N or name CA or name C or name O or name CB )) or \ resid 263 through 268 or (resid 269 through 273 and (name N or name CA or name C \ or name O or name CB )) or resid 274 through 311 or (resid 312 through 313 and \ (name N or name CA or name C or name O or name CB )) or resid 314 through 317 or \ (resid 318 and (name N or name CA or name C or name O or name CB )) or resid 31 \ 9 or (resid 320 through 322 and (name N or name CA or name C or name O or name C \ B )) or resid 323 through 339 or (resid 340 and (name N or name CA or name C or \ name O or name CB )) or resid 341 through 357)) selection = (chain 'F' and (resid 25 through 33 or (resid 34 and (name N or name CA or name \ C or name O or name CB )) or resid 35 through 50 or (resid 51 through 57 and (na \ me N or name CA or name C or name O or name CB )) or resid 58 through 63 or (res \ id 64 and (name N or name CA or name C or name O or name CB )) or resid 65 throu \ gh 66 or resid 98 through 104 or (resid 105 through 107 and (name N or name CA o \ r name C or name O or name CB )) or resid 108 through 145 or (resid 146 through \ 147 and (name N or name CA or name C or name O or name CB )) or resid 148 throug \ h 151 or (resid 152 and (name N or name CA or name C or name O or name CB )) or \ resid 153 through 168 or (resid 169 and (name N or name CA or name C or name O o \ r name CB )) or resid 170 through 174 or (resid 175 through 176 and (name N or n \ ame CA or name C or name O or name CB )) or resid 177 through 184 or (resid 185 \ through 186 and (name N or name CA or name C or name O or name CB )) or resid 18 \ 7 or (resid 188 and (name N or name CA or name C or name O or name CB )) or resi \ d 189 through 190 or (resid 191 through 192 and (name N or name CA or name C or \ name O or name CB )) or resid 193 through 195 or (resid 196 through 199 and (nam \ e N or name CA or name C or name O or name CB )) or resid 200 through 201 or (re \ sid 202 through 204 and (name N or name CA or name C or name O or name CB )) or \ resid 205 or (resid 206 through 207 and (name N or name CA or name C or name O o \ r name CB )) or resid 208 through 209 or (resid 210 and (name N or name CA or na \ me C or name O or name CB )) or resid 211 through 226 or (resid 227 and (name N \ or name CA or name C or name O or name CB )) or resid 228 through 239 or (resid \ 240 and (name N or name CA or name C or name O or name CB )) or resid 241 throug \ h 249 or (resid 250 and (name N or name CA or name C or name O or name CB )) or \ resid 263 through 268 or (resid 269 through 273 and (name N or name CA or name C \ or name O or name CB )) or resid 274 through 295 or (resid 296 and (name N or n \ ame CA or name C or name O or name CB )) or resid 297 through 303 or (resid 304 \ and (name N or name CA or name C or name O or name CB )) or resid 305 through 31 \ 1 or (resid 312 through 313 and (name N or name CA or name C or name O or name C \ B )) or resid 314 through 317 or (resid 318 and (name N or name CA or name C or \ name O or name CB )) or resid 319 or (resid 320 through 322 and (name N or name \ CA or name C or name O or name CB )) or resid 323 through 339 or (resid 340 and \ (name N or name CA or name C or name O or name CB )) or resid 341 through 356 or \ (resid 357 and (name N or name CA or name C or name O or name CB )))) selection = (chain 'G' and (resid 25 through 33 or (resid 34 and (name N or name CA or name \ C or name O or name CB )) or resid 35 through 50 or (resid 51 through 57 and (na \ me N or name CA or name C or name O or name CB )) or resid 58 through 63 or (res \ id 64 and (name N or name CA or name C or name O or name CB )) or resid 65 throu \ gh 66 or resid 98 through 104 or (resid 105 through 107 and (name N or name CA o \ r name C or name O or name CB )) or resid 108 through 145 or (resid 146 through \ 147 and (name N or name CA or name C or name O or name CB )) or resid 148 throug \ h 151 or (resid 152 and (name N or name CA or name C or name O or name CB )) or \ resid 153 through 168 or (resid 169 and (name N or name CA or name C or name O o \ r name CB )) or resid 170 through 174 or (resid 175 through 176 and (name N or n \ ame CA or name C or name O or name CB )) or resid 177 through 184 or (resid 185 \ through 186 and (name N or name CA or name C or name O or name CB )) or resid 18 \ 7 through 190 or (resid 191 through 192 and (name N or name CA or name C or name \ O or name CB )) or resid 193 through 195 or (resid 196 through 199 and (name N \ or name CA or name C or name O or name CB )) or resid 200 through 201 or (resid \ 202 through 204 and (name N or name CA or name C or name O or name CB )) or resi \ d 205 or (resid 206 through 207 and (name N or name CA or name C or name O or na \ me CB )) or resid 208 through 209 or (resid 210 and (name N or name CA or name C \ or name O or name CB )) or resid 211 through 226 or (resid 227 and (name N or n \ ame CA or name C or name O or name CB )) or resid 228 through 239 or (resid 240 \ and (name N or name CA or name C or name O or name CB )) or resid 241 through 24 \ 9 or (resid 250 and (name N or name CA or name C or name O or name CB )) or resi \ d 263 through 268 or (resid 269 through 273 and (name N or name CA or name C or \ name O or name CB )) or resid 274 through 285 or (resid 286 and (name N or name \ CA or name C or name O or name CB )) or resid 287 through 295 or (resid 296 and \ (name N or name CA or name C or name O or name CB )) or resid 297 through 303 or \ (resid 304 and (name N or name CA or name C or name O or name CB )) or resid 30 \ 5 through 311 or (resid 312 through 313 and (name N or name CA or name C or name \ O or name CB )) or resid 314 through 317 or (resid 318 and (name N or name CA o \ r name C or name O or name CB )) or resid 319 or (resid 320 through 322 and (nam \ e N or name CA or name C or name O or name CB )) or resid 323 through 339 or (re \ sid 340 and (name N or name CA or name C or name O or name CB )) or resid 341 th \ rough 356 or (resid 357 and (name N or name CA or name C or name O or name CB )) \ )) selection = (chain 'H' and (resid 25 through 33 or (resid 34 and (name N or name CA or name \ C or name O or name CB )) or resid 35 through 50 or (resid 51 through 57 and (na \ me N or name CA or name C or name O or name CB )) or resid 58 through 63 or (res \ id 64 and (name N or name CA or name C or name O or name CB )) or resid 65 throu \ gh 66 or resid 98 through 104 or (resid 105 through 107 and (name N or name CA o \ r name C or name O or name CB )) or resid 108 through 145 or (resid 146 through \ 147 and (name N or name CA or name C or name O or name CB )) or resid 148 throug \ h 151 or (resid 152 and (name N or name CA or name C or name O or name CB )) or \ resid 153 through 168 or (resid 169 and (name N or name CA or name C or name O o \ r name CB )) or resid 170 through 174 or (resid 175 through 176 and (name N or n \ ame CA or name C or name O or name CB )) or resid 177 through 184 or (resid 185 \ through 186 and (name N or name CA or name C or name O or name CB )) or resid 18 \ 7 or (resid 188 and (name N or name CA or name C or name O or name CB )) or resi \ d 189 through 195 or (resid 196 through 199 and (name N or name CA or name C or \ name O or name CB )) or resid 200 through 201 or (resid 202 through 204 and (nam \ e N or name CA or name C or name O or name CB )) or resid 205 or (resid 206 thro \ ugh 207 and (name N or name CA or name C or name O or name CB )) or resid 208 th \ rough 209 or (resid 210 and (name N or name CA or name C or name O or name CB )) \ or resid 211 through 239 or (resid 240 and (name N or name CA or name C or name \ O or name CB )) or resid 241 through 249 or (resid 250 and (name N or name CA o \ r name C or name O or name CB )) or resid 263 through 268 or (resid 269 through \ 273 and (name N or name CA or name C or name O or name CB )) or resid 274 throug \ h 303 or (resid 304 and (name N or name CA or name C or name O or name CB )) or \ resid 305 through 311 or (resid 312 through 313 and (name N or name CA or name C \ or name O or name CB )) or resid 314 through 317 or (resid 318 and (name N or n \ ame CA or name C or name O or name CB )) or resid 319 through 320 or (resid 321 \ through 322 and (name N or name CA or name C or name O or name CB )) or resid 32 \ 3 through 339 or (resid 340 and (name N or name CA or name C or name O or name C \ B )) or resid 341 through 356 or (resid 357 and (name N or name CA or name C or \ name O or name CB )))) } ncs_group { reference = (chain 'I' and (resid 3 through 17 or (resid 18 and (name N or name CA or name C \ or name O or name CB )) or resid 19 through 36 or (resid 37 and (name N or name \ CA or name C or name O or name CB )) or resid 38 through 52 or (resid 53 and (n \ ame N or name CA or name C or name O or name CB )) or resid 54 through 58 or (re \ sid 59 through 60 and (name N or name CA or name C or name O or name CB )) or re \ sid 61 through 66)) selection = (chain 'J' and (resid 3 through 31 or (resid 32 and (name N or name CA or name C \ or name O or name CB )) or resid 33 through 47 or (resid 48 and (name N or name \ CA or name C or name O or name CB )) or resid 49 through 66)) } 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: 0.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 21.130 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7084 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 : 0.011 0.061 22262 Z= 0.793 Angle : 0.989 9.148 30673 Z= 0.742 Chirality : 0.084 0.475 3596 Planarity : 0.006 0.027 3843 Dihedral : 11.587 154.380 7964 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Rotamer: Outliers : 0.06 % Allowed : 1.45 % Favored : 98.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.99 (0.14), residues: 2838 helix: 1.24 (0.18), residues: 845 sheet: -0.99 (0.21), residues: 459 loop : -1.70 (0.13), residues: 1534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG D 113 TYR 0.022 0.004 TYR G 324 PHE 0.018 0.003 PHE B 284 TRP 0.016 0.003 TRP G 168 HIS 0.014 0.002 HIS B 196 Details of bonding type rmsd covalent geometry : bond 0.01121 (22262) covalent geometry : angle 0.98850 (30673) hydrogen bonds : bond 0.18165 ( 904) hydrogen bonds : angle 6.70903 ( 2481) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5676 Ramachandran restraints generated. 2838 Oldfield, 0 Emsley, 2838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5676 Ramachandran restraints generated. 2838 Oldfield, 0 Emsley, 2838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 842 residues out of total 2331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 841 time to evaluate : 0.780 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 199 VAL cc_start: 0.9196 (t) cc_final: 0.8932 (p) REVERT: A 201 HIS cc_start: 0.7824 (t70) cc_final: 0.7446 (t70) REVERT: A 208 GLU cc_start: 0.6078 (tp30) cc_final: 0.5733 (tp30) REVERT: A 241 GLN cc_start: 0.7370 (tt0) cc_final: 0.6517 (pm20) REVERT: B 10 LEU cc_start: 0.8129 (tp) cc_final: 0.7877 (tp) REVERT: B 63 CYS cc_start: 0.7410 (t) cc_final: 0.6615 (p) REVERT: B 82 ASN cc_start: 0.8438 (m-40) cc_final: 0.7564 (m-40) REVERT: B 106 GLU cc_start: 0.7818 (tt0) cc_final: 0.7519 (tt0) REVERT: B 130 VAL cc_start: 0.8793 (t) cc_final: 0.8589 (p) REVERT: B 195 GLN cc_start: 0.8600 (tt0) cc_final: 0.8296 (tt0) REVERT: B 196 HIS cc_start: 0.8076 (m90) cc_final: 0.7721 (m-70) REVERT: C 231 GLU cc_start: 0.7873 (tt0) cc_final: 0.7628 (tt0) REVERT: D 99 ASP cc_start: 0.8321 (m-30) cc_final: 0.7261 (m-30) REVERT: D 175 GLU cc_start: 0.7749 (mt-10) cc_final: 0.7440 (tm-30) REVERT: E 44 MET cc_start: 0.8708 (mtm) cc_final: 0.8321 (mtt) REVERT: E 99 ASP cc_start: 0.8309 (m-30) cc_final: 0.7933 (m-30) REVERT: E 210 GLU cc_start: 0.6843 (mm-30) cc_final: 0.6549 (mm-30) REVERT: F 99 ASP cc_start: 0.7317 (m-30) cc_final: 0.6814 (m-30) REVERT: G 109 THR cc_start: 0.8177 (m) cc_final: 0.7968 (p) REVERT: G 135 ASP cc_start: 0.7601 (m-30) cc_final: 0.7291 (m-30) REVERT: H 343 HIS cc_start: 0.7232 (m170) cc_final: 0.6758 (m90) REVERT: J 28 THR cc_start: 0.7867 (p) cc_final: 0.7593 (t) REVERT: J 32 ARG cc_start: 0.8509 (ptp90) cc_final: 0.8085 (ptp90) outliers start: 1 outliers final: 0 residues processed: 841 average time/residue: 0.1674 time to fit residues: 205.7442 Evaluate side-chains 422 residues out of total 2331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 422 time to evaluate : 0.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 8.9990 chunk 20 optimal weight: 8.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 0.0000 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 6.9990 chunk 244 optimal weight: 0.8980 chunk 183 optimal weight: 0.1980 chunk 111 optimal weight: 0.9990 overall best weight: 1.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 86 ASN B 121 HIS B 256 ASN ** D 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 310 GLN F 74 ASN ** F 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 343 HIS F 348 ASN ** G 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 148 GLN G 281 ASN G 310 GLN ** G 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 102 ASN H 329 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.148183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.122835 restraints weight = 39536.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.123199 restraints weight = 27517.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.124656 restraints weight = 22454.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.125595 restraints weight = 16025.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.126024 restraints weight = 14184.525| |-----------------------------------------------------------------------------| r_work (final): 0.3682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7471 moved from start: 0.3719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 22262 Z= 0.127 Angle : 0.593 11.967 30673 Z= 0.301 Chirality : 0.041 0.242 3596 Planarity : 0.004 0.046 3843 Dihedral : 13.575 122.603 4022 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 3.97 % Allowed : 15.55 % Favored : 80.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.03 (0.15), residues: 2838 helix: 2.12 (0.18), residues: 859 sheet: -0.71 (0.21), residues: 483 loop : -1.09 (0.14), residues: 1496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 210 TYR 0.022 0.002 TYR I 57 PHE 0.026 0.002 PHE F 166 TRP 0.019 0.001 TRP J 54 HIS 0.008 0.001 HIS F 343 Details of bonding type rmsd covalent geometry : bond 0.00275 (22262) covalent geometry : angle 0.59303 (30673) hydrogen bonds : bond 0.03096 ( 904) hydrogen bonds : angle 4.61609 ( 2481) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5676 Ramachandran restraints generated. 2838 Oldfield, 0 Emsley, 2838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5676 Ramachandran restraints generated. 2838 Oldfield, 0 Emsley, 2838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 557 residues out of total 2331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 486 time to evaluate : 0.574 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: A 208 GLU cc_start: 0.6252 (tp30) cc_final: 0.5939 (tp30) REVERT: A 241 GLN cc_start: 0.7437 (tt0) cc_final: 0.6481 (pm20) REVERT: A 266 PRO cc_start: 0.7957 (Cg_endo) cc_final: 0.7747 (Cg_exo) REVERT: B 67 GLU cc_start: 0.7878 (pm20) cc_final: 0.7651 (pm20) REVERT: B 129 GLN cc_start: 0.7445 (mm110) cc_final: 0.6660 (tm-30) REVERT: B 131 GLN cc_start: 0.7723 (tt0) cc_final: 0.7412 (tt0) REVERT: B 194 GLN cc_start: 0.7982 (mm110) cc_final: 0.7280 (mm-40) REVERT: B 196 HIS cc_start: 0.8391 (m90) cc_final: 0.7723 (m170) REVERT: B 302 LEU cc_start: 0.8913 (mt) cc_final: 0.8671 (mt) REVERT: E 25 LEU cc_start: 0.8484 (tp) cc_final: 0.8037 (tt) REVERT: E 161 LEU cc_start: 0.8996 (OUTLIER) cc_final: 0.8685 (mp) REVERT: E 334 ASP cc_start: 0.7358 (t70) cc_final: 0.7127 (t0) REVERT: F 238 ILE cc_start: 0.9418 (mm) cc_final: 0.9008 (tt) REVERT: G 178 GLU cc_start: 0.7787 (tm-30) cc_final: 0.7425 (tm-30) REVERT: G 240 ASP cc_start: 0.7243 (t0) cc_final: 0.7004 (t0) REVERT: H 243 GLU cc_start: 0.6514 (OUTLIER) cc_final: 0.6275 (tt0) REVERT: H 249 GLU cc_start: 0.7172 (tt0) cc_final: 0.6898 (tt0) REVERT: H 302 GLU cc_start: 0.6777 (mm-30) cc_final: 0.6321 (mm-30) REVERT: I 9 GLU cc_start: 0.7863 (mt-10) cc_final: 0.7097 (mm-30) REVERT: J 28 THR cc_start: 0.9087 (p) cc_final: 0.8319 (t) REVERT: J 32 ARG cc_start: 0.8426 (ptp90) cc_final: 0.7949 (ptp90) outliers start: 71 outliers final: 39 residues processed: 528 average time/residue: 0.1566 time to fit residues: 124.9074 Evaluate side-chains 398 residues out of total 2331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 357 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 SER Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 263 TRP Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 256 ASN Chi-restraints excluded: chain B residue 314 TYR Chi-restraints excluded: chain B residue 316 TRP Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 270 ASP Chi-restraints excluded: chain D residue 334 ASP Chi-restraints excluded: chain E residue 106 ASP Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain E residue 243 GLU Chi-restraints excluded: chain E residue 247 SER Chi-restraints excluded: chain E residue 279 ILE Chi-restraints excluded: chain E residue 299 ILE Chi-restraints excluded: chain F residue 189 VAL Chi-restraints excluded: chain F residue 264 THR Chi-restraints excluded: chain F residue 299 ILE Chi-restraints excluded: chain G residue 62 THR Chi-restraints excluded: chain G residue 217 LEU Chi-restraints excluded: chain G residue 250 LEU Chi-restraints excluded: chain G residue 276 SER Chi-restraints excluded: chain G residue 349 LEU Chi-restraints excluded: chain H residue 34 GLU Chi-restraints excluded: chain H residue 137 LEU Chi-restraints excluded: chain H residue 202 LEU Chi-restraints excluded: chain H residue 232 VAL Chi-restraints excluded: chain H residue 240 ASP Chi-restraints excluded: chain H residue 243 GLU Chi-restraints excluded: chain I residue 10 VAL Chi-restraints excluded: chain I residue 44 VAL Chi-restraints excluded: chain I residue 49 SER Chi-restraints excluded: chain J residue 22 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 81 optimal weight: 0.0020 chunk 190 optimal weight: 3.9990 chunk 287 optimal weight: 9.9990 chunk 237 optimal weight: 20.0000 chunk 92 optimal weight: 9.9990 chunk 20 optimal weight: 7.9990 chunk 211 optimal weight: 7.9990 chunk 250 optimal weight: 7.9990 chunk 148 optimal weight: 9.9990 chunk 272 optimal weight: 50.0000 chunk 88 optimal weight: 7.9990 overall best weight: 5.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 HIS A 188 HIS ** A 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 172 ASN C 242 GLN D 242 GLN ** D 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 91 GLN E 146 ASN E 186 GLN E 242 GLN ** F 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 148 GLN ** F 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 281 ASN ** G 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 242 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.126012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.098431 restraints weight = 40945.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.099192 restraints weight = 36240.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.100037 restraints weight = 29393.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.100244 restraints weight = 22153.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.100574 restraints weight = 19890.051| |-----------------------------------------------------------------------------| r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.6031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.068 22262 Z= 0.308 Angle : 0.747 12.431 30673 Z= 0.390 Chirality : 0.046 0.235 3596 Planarity : 0.005 0.059 3843 Dihedral : 13.806 117.511 4022 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 5.26 % Allowed : 15.38 % Favored : 79.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.51 (0.15), residues: 2838 helix: 1.60 (0.18), residues: 852 sheet: -0.98 (0.21), residues: 473 loop : -1.30 (0.14), residues: 1513 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 169 TYR 0.024 0.002 TYR F 290 PHE 0.025 0.003 PHE E 166 TRP 0.027 0.002 TRP F 58 HIS 0.009 0.002 HIS D 343 Details of bonding type rmsd covalent geometry : bond 0.00680 (22262) covalent geometry : angle 0.74726 (30673) hydrogen bonds : bond 0.04026 ( 904) hydrogen bonds : angle 5.02109 ( 2481) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5676 Ramachandran restraints generated. 2838 Oldfield, 0 Emsley, 2838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5676 Ramachandran restraints generated. 2838 Oldfield, 0 Emsley, 2838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 458 residues out of total 2331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 364 time to evaluate : 0.818 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 GLU cc_start: 0.6102 (tp30) cc_final: 0.5856 (tp30) REVERT: B 67 GLU cc_start: 0.8122 (pm20) cc_final: 0.7907 (pm20) REVERT: B 196 HIS cc_start: 0.8674 (m90) cc_final: 0.7960 (m-70) REVERT: C 161 LEU cc_start: 0.9204 (mp) cc_final: 0.8976 (mp) REVERT: C 354 VAL cc_start: 0.8532 (t) cc_final: 0.8309 (p) REVERT: D 38 ASP cc_start: 0.8038 (t0) cc_final: 0.7720 (p0) REVERT: E 161 LEU cc_start: 0.9440 (OUTLIER) cc_final: 0.9035 (mp) REVERT: E 186 GLN cc_start: 0.7517 (OUTLIER) cc_final: 0.7072 (tm130) REVERT: E 261 LYS cc_start: 0.8740 (ttmt) cc_final: 0.8471 (ttmt) REVERT: E 334 ASP cc_start: 0.8160 (t70) cc_final: 0.7896 (t70) REVERT: F 354 VAL cc_start: 0.9255 (t) cc_final: 0.9029 (p) REVERT: G 276 SER cc_start: 0.9166 (OUTLIER) cc_final: 0.8559 (t) REVERT: H 35 ARG cc_start: 0.8719 (OUTLIER) cc_final: 0.8499 (tmm-80) REVERT: J 5 TYR cc_start: 0.7008 (m-10) cc_final: 0.6577 (m-10) REVERT: J 28 THR cc_start: 0.9173 (p) cc_final: 0.8594 (p) REVERT: J 32 ARG cc_start: 0.8468 (ptp90) cc_final: 0.8215 (ptp90) outliers start: 94 outliers final: 59 residues processed: 421 average time/residue: 0.1535 time to fit residues: 99.6212 Evaluate side-chains 361 residues out of total 2331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 298 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 SER Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 263 TRP Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain B residue 306 HIS Chi-restraints excluded: chain B residue 314 TYR Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 200 ILE Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain C residue 304 TYR Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 350 ILE Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 334 ASP Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain E residue 186 GLN Chi-restraints excluded: chain E residue 189 VAL Chi-restraints excluded: chain E residue 196 ASP Chi-restraints excluded: chain E residue 227 HIS Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain E residue 279 ILE Chi-restraints excluded: chain E residue 299 ILE Chi-restraints excluded: chain F residue 89 SER Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 189 VAL Chi-restraints excluded: chain F residue 227 HIS Chi-restraints excluded: chain F residue 230 LEU Chi-restraints excluded: chain F residue 264 THR Chi-restraints excluded: chain F residue 279 ILE Chi-restraints excluded: chain F residue 299 ILE Chi-restraints excluded: chain F residue 308 THR Chi-restraints excluded: chain G residue 40 SER Chi-restraints excluded: chain G residue 62 THR Chi-restraints excluded: chain G residue 250 LEU Chi-restraints excluded: chain G residue 276 SER Chi-restraints excluded: chain G residue 312 LYS Chi-restraints excluded: chain G residue 328 ASP Chi-restraints excluded: chain G residue 349 LEU Chi-restraints excluded: chain H residue 34 GLU Chi-restraints excluded: chain H residue 35 ARG Chi-restraints excluded: chain H residue 92 SER Chi-restraints excluded: chain H residue 95 LEU Chi-restraints excluded: chain H residue 202 LEU Chi-restraints excluded: chain H residue 238 ILE Chi-restraints excluded: chain H residue 240 ASP Chi-restraints excluded: chain H residue 247 SER Chi-restraints excluded: chain H residue 253 ASP Chi-restraints excluded: chain H residue 264 THR Chi-restraints excluded: chain H residue 349 LEU Chi-restraints excluded: chain I residue 4 THR Chi-restraints excluded: chain I residue 10 VAL Chi-restraints excluded: chain I residue 27 LEU Chi-restraints excluded: chain I residue 44 VAL Chi-restraints excluded: chain J residue 12 ASN Chi-restraints excluded: chain J residue 22 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 18 optimal weight: 20.0000 chunk 224 optimal weight: 0.9990 chunk 115 optimal weight: 1.9990 chunk 116 optimal weight: 1.9990 chunk 15 optimal weight: 7.9990 chunk 0 optimal weight: 50.0000 chunk 177 optimal weight: 7.9990 chunk 222 optimal weight: 4.9990 chunk 228 optimal weight: 5.9990 chunk 74 optimal weight: 0.0050 chunk 108 optimal weight: 7.9990 overall best weight: 2.0002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 262 ASN ** B 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 256 ASN B 282 ASN B 305 HIS C 139 GLN D 74 ASN ** D 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 146 ASN ** F 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 183 HIS ** F 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 348 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.127751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.099670 restraints weight = 40211.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.099248 restraints weight = 33279.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.100505 restraints weight = 26122.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.100826 restraints weight = 19927.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.101067 restraints weight = 18911.132| |-----------------------------------------------------------------------------| r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.6186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 22262 Z= 0.139 Angle : 0.569 9.552 30673 Z= 0.293 Chirality : 0.040 0.170 3596 Planarity : 0.004 0.043 3843 Dihedral : 13.567 115.742 4022 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 4.08 % Allowed : 17.34 % Favored : 78.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.23 (0.15), residues: 2838 helix: 1.98 (0.18), residues: 849 sheet: -0.94 (0.21), residues: 478 loop : -1.16 (0.15), residues: 1511 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 194 TYR 0.017 0.001 TYR I 57 PHE 0.018 0.002 PHE E 166 TRP 0.014 0.001 TRP E 193 HIS 0.004 0.001 HIS G 159 Details of bonding type rmsd covalent geometry : bond 0.00305 (22262) covalent geometry : angle 0.56866 (30673) hydrogen bonds : bond 0.03000 ( 904) hydrogen bonds : angle 4.57200 ( 2481) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5676 Ramachandran restraints generated. 2838 Oldfield, 0 Emsley, 2838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5676 Ramachandran restraints generated. 2838 Oldfield, 0 Emsley, 2838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 2331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 333 time to evaluate : 0.694 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 GLU cc_start: 0.6268 (tp30) cc_final: 0.6044 (tp30) REVERT: B 78 THR cc_start: 0.7621 (m) cc_final: 0.7269 (p) REVERT: B 196 HIS cc_start: 0.8697 (m90) cc_final: 0.7923 (m-70) REVERT: B 255 TYR cc_start: 0.7283 (m-80) cc_final: 0.6907 (m-80) REVERT: C 34 GLU cc_start: 0.7923 (mm-30) cc_final: 0.7615 (mm-30) REVERT: C 161 LEU cc_start: 0.9186 (mp) cc_final: 0.8964 (mp) REVERT: C 354 VAL cc_start: 0.8475 (t) cc_final: 0.8199 (p) REVERT: D 38 ASP cc_start: 0.7895 (t0) cc_final: 0.7621 (p0) REVERT: E 161 LEU cc_start: 0.9316 (OUTLIER) cc_final: 0.8990 (mp) REVERT: E 186 GLN cc_start: 0.7440 (tm-30) cc_final: 0.7152 (tm-30) REVERT: E 334 ASP cc_start: 0.8102 (t70) cc_final: 0.7731 (t0) REVERT: H 95 LEU cc_start: 0.8156 (OUTLIER) cc_final: 0.7735 (mm) REVERT: H 343 HIS cc_start: 0.7638 (m170) cc_final: 0.7354 (m90) REVERT: J 28 THR cc_start: 0.9097 (p) cc_final: 0.8132 (t) REVERT: J 32 ARG cc_start: 0.8601 (ptp90) cc_final: 0.8270 (ptp90) outliers start: 73 outliers final: 52 residues processed: 382 average time/residue: 0.1426 time to fit residues: 85.4532 Evaluate side-chains 351 residues out of total 2331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 297 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 SER Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 263 TRP Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 198 GLU Chi-restraints excluded: chain B residue 256 ASN Chi-restraints excluded: chain B residue 306 HIS Chi-restraints excluded: chain B residue 314 TYR Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 126 SER Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 243 GLU Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain D residue 43 LEU Chi-restraints excluded: chain D residue 105 SER Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain D residue 334 ASP Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 105 SER Chi-restraints excluded: chain E residue 106 ASP Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain E residue 189 VAL Chi-restraints excluded: chain E residue 227 HIS Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain E residue 299 ILE Chi-restraints excluded: chain E residue 302 GLU Chi-restraints excluded: chain F residue 189 VAL Chi-restraints excluded: chain F residue 227 HIS Chi-restraints excluded: chain F residue 264 THR Chi-restraints excluded: chain F residue 279 ILE Chi-restraints excluded: chain F residue 299 ILE Chi-restraints excluded: chain F residue 308 THR Chi-restraints excluded: chain F residue 318 LYS Chi-restraints excluded: chain G residue 250 LEU Chi-restraints excluded: chain G residue 276 SER Chi-restraints excluded: chain G residue 299 ILE Chi-restraints excluded: chain G residue 349 LEU Chi-restraints excluded: chain H residue 34 GLU Chi-restraints excluded: chain H residue 92 SER Chi-restraints excluded: chain H residue 95 LEU Chi-restraints excluded: chain H residue 202 LEU Chi-restraints excluded: chain H residue 240 ASP Chi-restraints excluded: chain H residue 327 LEU Chi-restraints excluded: chain I residue 10 VAL Chi-restraints excluded: chain I residue 13 ILE Chi-restraints excluded: chain I residue 27 LEU Chi-restraints excluded: chain I residue 44 VAL Chi-restraints excluded: chain J residue 22 VAL Chi-restraints excluded: chain J residue 27 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 214 optimal weight: 6.9990 chunk 151 optimal weight: 10.0000 chunk 227 optimal weight: 10.0000 chunk 182 optimal weight: 0.9980 chunk 46 optimal weight: 30.0000 chunk 33 optimal weight: 9.9990 chunk 172 optimal weight: 6.9990 chunk 281 optimal weight: 7.9990 chunk 16 optimal weight: 50.0000 chunk 283 optimal weight: 10.0000 chunk 249 optimal weight: 10.0000 overall best weight: 6.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 203 HIS ** B 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 172 ASN B 282 ASN B 305 HIS C 139 GLN D 74 ASN D 342 GLN E 96 GLN ** F 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.120089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.092749 restraints weight = 40961.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.093037 restraints weight = 36242.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.093989 restraints weight = 27982.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.094516 restraints weight = 21907.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.094738 restraints weight = 20764.999| |-----------------------------------------------------------------------------| r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.7137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.079 22262 Z= 0.336 Angle : 0.733 9.444 30673 Z= 0.383 Chirality : 0.045 0.238 3596 Planarity : 0.005 0.047 3843 Dihedral : 13.889 118.431 4022 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 5.26 % Allowed : 18.01 % Favored : 76.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.73 (0.15), residues: 2838 helix: 1.44 (0.18), residues: 849 sheet: -1.14 (0.23), residues: 438 loop : -1.43 (0.14), residues: 1551 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG H 169 TYR 0.023 0.002 TYR F 290 PHE 0.025 0.003 PHE F 166 TRP 0.025 0.002 TRP F 49 HIS 0.008 0.002 HIS G 275 Details of bonding type rmsd covalent geometry : bond 0.00742 (22262) covalent geometry : angle 0.73312 (30673) hydrogen bonds : bond 0.03967 ( 904) hydrogen bonds : angle 5.05953 ( 2481) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5676 Ramachandran restraints generated. 2838 Oldfield, 0 Emsley, 2838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5676 Ramachandran restraints generated. 2838 Oldfield, 0 Emsley, 2838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 2331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 297 time to evaluate : 0.770 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 196 HIS cc_start: 0.8673 (m90) cc_final: 0.8438 (m90) REVERT: B 258 LEU cc_start: 0.8047 (OUTLIER) cc_final: 0.7778 (tt) REVERT: B 288 GLU cc_start: 0.8079 (tm-30) cc_final: 0.7663 (tm-30) REVERT: C 38 ASP cc_start: 0.8521 (t0) cc_final: 0.8205 (m-30) REVERT: E 161 LEU cc_start: 0.9446 (OUTLIER) cc_final: 0.9083 (mp) REVERT: E 186 GLN cc_start: 0.7557 (mm-40) cc_final: 0.7090 (tm-30) REVERT: E 334 ASP cc_start: 0.8391 (t70) cc_final: 0.8052 (t70) REVERT: F 320 LYS cc_start: 0.8378 (mmtt) cc_final: 0.8145 (ttpt) REVERT: F 333 ARG cc_start: 0.8226 (mpt180) cc_final: 0.7933 (mpt180) REVERT: G 276 SER cc_start: 0.9278 (OUTLIER) cc_final: 0.8642 (t) REVERT: I 22 VAL cc_start: 0.8639 (m) cc_final: 0.8373 (p) REVERT: J 28 THR cc_start: 0.9115 (p) cc_final: 0.8806 (t) REVERT: J 32 ARG cc_start: 0.8614 (ptp90) cc_final: 0.8279 (ptp-110) outliers start: 94 outliers final: 68 residues processed: 361 average time/residue: 0.1368 time to fit residues: 78.8118 Evaluate side-chains 347 residues out of total 2331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 276 time to evaluate : 0.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 185 SER Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 263 TRP Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 198 GLU Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 251 ILE Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 306 HIS Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 126 SER Chi-restraints excluded: chain C residue 200 ILE Chi-restraints excluded: chain C residue 243 GLU Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain D residue 105 SER Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain D residue 334 ASP Chi-restraints excluded: chain E residue 105 SER Chi-restraints excluded: chain E residue 106 ASP Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain E residue 189 VAL Chi-restraints excluded: chain E residue 196 ASP Chi-restraints excluded: chain E residue 227 HIS Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain E residue 299 ILE Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 90 ILE Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 189 VAL Chi-restraints excluded: chain F residue 204 ASP Chi-restraints excluded: chain F residue 208 ASP Chi-restraints excluded: chain F residue 230 LEU Chi-restraints excluded: chain F residue 264 THR Chi-restraints excluded: chain F residue 279 ILE Chi-restraints excluded: chain F residue 299 ILE Chi-restraints excluded: chain F residue 308 THR Chi-restraints excluded: chain F residue 354 VAL Chi-restraints excluded: chain G residue 40 SER Chi-restraints excluded: chain G residue 62 THR Chi-restraints excluded: chain G residue 72 ILE Chi-restraints excluded: chain G residue 105 SER Chi-restraints excluded: chain G residue 250 LEU Chi-restraints excluded: chain G residue 276 SER Chi-restraints excluded: chain G residue 296 LEU Chi-restraints excluded: chain G residue 299 ILE Chi-restraints excluded: chain G residue 312 LYS Chi-restraints excluded: chain G residue 349 LEU Chi-restraints excluded: chain H residue 34 GLU Chi-restraints excluded: chain H residue 92 SER Chi-restraints excluded: chain H residue 202 LEU Chi-restraints excluded: chain H residue 238 ILE Chi-restraints excluded: chain H residue 240 ASP Chi-restraints excluded: chain H residue 247 SER Chi-restraints excluded: chain H residue 264 THR Chi-restraints excluded: chain H residue 327 LEU Chi-restraints excluded: chain I residue 4 THR Chi-restraints excluded: chain I residue 10 VAL Chi-restraints excluded: chain I residue 13 ILE Chi-restraints excluded: chain I residue 27 LEU Chi-restraints excluded: chain I residue 44 VAL Chi-restraints excluded: chain J residue 12 ASN Chi-restraints excluded: chain J residue 22 VAL Chi-restraints excluded: chain J residue 27 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 183 optimal weight: 2.9990 chunk 204 optimal weight: 3.9990 chunk 21 optimal weight: 8.9990 chunk 44 optimal weight: 8.9990 chunk 61 optimal weight: 5.9990 chunk 77 optimal weight: 2.9990 chunk 268 optimal weight: 8.9990 chunk 30 optimal weight: 40.0000 chunk 57 optimal weight: 20.0000 chunk 149 optimal weight: 6.9990 chunk 110 optimal weight: 0.9980 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 282 ASN B 305 HIS ** E 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 159 HIS F 319 GLN ** G 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.122245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.094522 restraints weight = 40661.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.093463 restraints weight = 32969.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.094769 restraints weight = 27077.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.095140 restraints weight = 20423.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.095299 restraints weight = 19483.761| |-----------------------------------------------------------------------------| r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.7223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 22262 Z= 0.194 Angle : 0.605 9.459 30673 Z= 0.315 Chirality : 0.041 0.202 3596 Planarity : 0.004 0.042 3843 Dihedral : 13.750 117.657 4022 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 3.97 % Allowed : 19.91 % Favored : 76.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.54 (0.15), residues: 2838 helix: 1.69 (0.18), residues: 844 sheet: -1.09 (0.23), residues: 435 loop : -1.34 (0.14), residues: 1559 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 169 TYR 0.015 0.002 TYR G 266 PHE 0.018 0.002 PHE F 166 TRP 0.016 0.001 TRP H 168 HIS 0.005 0.001 HIS G 227 Details of bonding type rmsd covalent geometry : bond 0.00433 (22262) covalent geometry : angle 0.60503 (30673) hydrogen bonds : bond 0.03242 ( 904) hydrogen bonds : angle 4.78996 ( 2481) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5676 Ramachandran restraints generated. 2838 Oldfield, 0 Emsley, 2838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5676 Ramachandran restraints generated. 2838 Oldfield, 0 Emsley, 2838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 2331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 304 time to evaluate : 0.747 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 192 LEU cc_start: 0.9021 (mt) cc_final: 0.8760 (mt) REVERT: B 196 HIS cc_start: 0.8679 (m90) cc_final: 0.7993 (m90) REVERT: B 255 TYR cc_start: 0.7979 (m-80) cc_final: 0.7529 (m-80) REVERT: B 288 GLU cc_start: 0.7946 (tm-30) cc_final: 0.7508 (tm-30) REVERT: C 38 ASP cc_start: 0.8433 (t0) cc_final: 0.7956 (t0) REVERT: D 99 ASP cc_start: 0.8185 (m-30) cc_final: 0.7780 (m-30) REVERT: E 161 LEU cc_start: 0.9371 (OUTLIER) cc_final: 0.9013 (mp) REVERT: E 186 GLN cc_start: 0.7454 (mm-40) cc_final: 0.7010 (tm-30) REVERT: E 334 ASP cc_start: 0.8335 (t70) cc_final: 0.7962 (t70) REVERT: F 34 GLU cc_start: 0.8153 (OUTLIER) cc_final: 0.7944 (mt-10) REVERT: F 91 GLN cc_start: 0.8108 (mt0) cc_final: 0.7878 (mp10) REVERT: F 333 ARG cc_start: 0.8147 (mpt180) cc_final: 0.7696 (mpt180) REVERT: I 22 VAL cc_start: 0.8662 (m) cc_final: 0.8401 (p) REVERT: J 28 THR cc_start: 0.9108 (p) cc_final: 0.8294 (t) REVERT: J 32 ARG cc_start: 0.8642 (ptp90) cc_final: 0.8240 (ptp90) outliers start: 71 outliers final: 61 residues processed: 350 average time/residue: 0.1248 time to fit residues: 70.0533 Evaluate side-chains 345 residues out of total 2331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 282 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 185 SER Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 263 TRP Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 198 GLU Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 306 HIS Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 126 SER Chi-restraints excluded: chain C residue 200 ILE Chi-restraints excluded: chain C residue 243 GLU Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 350 ILE Chi-restraints excluded: chain D residue 43 LEU Chi-restraints excluded: chain D residue 105 SER Chi-restraints excluded: chain D residue 106 ASP Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 105 SER Chi-restraints excluded: chain E residue 106 ASP Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain E residue 189 VAL Chi-restraints excluded: chain E residue 202 LEU Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain E residue 299 ILE Chi-restraints excluded: chain F residue 34 GLU Chi-restraints excluded: chain F residue 189 VAL Chi-restraints excluded: chain F residue 227 HIS Chi-restraints excluded: chain F residue 230 LEU Chi-restraints excluded: chain F residue 264 THR Chi-restraints excluded: chain F residue 279 ILE Chi-restraints excluded: chain F residue 299 ILE Chi-restraints excluded: chain F residue 308 THR Chi-restraints excluded: chain F residue 354 VAL Chi-restraints excluded: chain G residue 40 SER Chi-restraints excluded: chain G residue 62 THR Chi-restraints excluded: chain G residue 238 ILE Chi-restraints excluded: chain G residue 250 LEU Chi-restraints excluded: chain G residue 276 SER Chi-restraints excluded: chain G residue 299 ILE Chi-restraints excluded: chain G residue 349 LEU Chi-restraints excluded: chain H residue 34 GLU Chi-restraints excluded: chain H residue 92 SER Chi-restraints excluded: chain H residue 202 LEU Chi-restraints excluded: chain H residue 240 ASP Chi-restraints excluded: chain H residue 264 THR Chi-restraints excluded: chain H residue 321 LEU Chi-restraints excluded: chain H residue 327 LEU Chi-restraints excluded: chain I residue 4 THR Chi-restraints excluded: chain I residue 10 VAL Chi-restraints excluded: chain I residue 13 ILE Chi-restraints excluded: chain I residue 27 LEU Chi-restraints excluded: chain I residue 44 VAL Chi-restraints excluded: chain J residue 12 ASN Chi-restraints excluded: chain J residue 22 VAL Chi-restraints excluded: chain J residue 27 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 131 optimal weight: 7.9990 chunk 154 optimal weight: 9.9990 chunk 49 optimal weight: 7.9990 chunk 253 optimal weight: 9.9990 chunk 123 optimal weight: 4.9990 chunk 271 optimal weight: 7.9990 chunk 197 optimal weight: 10.0000 chunk 87 optimal weight: 0.8980 chunk 169 optimal weight: 10.0000 chunk 74 optimal weight: 20.0000 chunk 99 optimal weight: 5.9990 overall best weight: 5.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 172 ASN ** B 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 282 ASN B 305 HIS ** E 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.119197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.091559 restraints weight = 41135.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.091563 restraints weight = 34527.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.092675 restraints weight = 26048.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.092978 restraints weight = 19660.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.093148 restraints weight = 18394.902| |-----------------------------------------------------------------------------| r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.7638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 22262 Z= 0.290 Angle : 0.687 9.484 30673 Z= 0.359 Chirality : 0.044 0.246 3596 Planarity : 0.005 0.043 3843 Dihedral : 13.939 117.899 4022 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer: Outliers : 4.42 % Allowed : 20.19 % Favored : 75.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.77 (0.15), residues: 2838 helix: 1.43 (0.18), residues: 847 sheet: -1.20 (0.23), residues: 428 loop : -1.46 (0.14), residues: 1563 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 169 TYR 0.019 0.002 TYR F 290 PHE 0.021 0.002 PHE F 166 TRP 0.020 0.002 TRP F 49 HIS 0.007 0.002 HIS G 227 Details of bonding type rmsd covalent geometry : bond 0.00645 (22262) covalent geometry : angle 0.68681 (30673) hydrogen bonds : bond 0.03736 ( 904) hydrogen bonds : angle 5.00673 ( 2481) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5676 Ramachandran restraints generated. 2838 Oldfield, 0 Emsley, 2838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5676 Ramachandran restraints generated. 2838 Oldfield, 0 Emsley, 2838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 2331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 281 time to evaluate : 0.740 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 192 LEU cc_start: 0.9115 (mt) cc_final: 0.8868 (mt) REVERT: B 196 HIS cc_start: 0.8613 (m90) cc_final: 0.8002 (m90) REVERT: C 38 ASP cc_start: 0.8410 (t0) cc_final: 0.8006 (t0) REVERT: C 249 GLU cc_start: 0.7876 (mt-10) cc_final: 0.7478 (mt-10) REVERT: E 186 GLN cc_start: 0.7596 (mm-40) cc_final: 0.7062 (tm-30) REVERT: E 334 ASP cc_start: 0.8369 (t70) cc_final: 0.8040 (t70) REVERT: F 34 GLU cc_start: 0.8214 (OUTLIER) cc_final: 0.7811 (mt-10) REVERT: F 91 GLN cc_start: 0.8180 (mt0) cc_final: 0.7914 (mp10) REVERT: F 333 ARG cc_start: 0.8044 (mpt180) cc_final: 0.7558 (mpt180) REVERT: G 206 LYS cc_start: 0.8365 (mmtt) cc_final: 0.7957 (mmtp) REVERT: H 206 LYS cc_start: 0.7856 (mmtt) cc_final: 0.7616 (mmtt) REVERT: I 22 VAL cc_start: 0.8804 (m) cc_final: 0.8586 (p) REVERT: J 32 ARG cc_start: 0.8623 (ptp90) cc_final: 0.8286 (ptp-110) outliers start: 79 outliers final: 66 residues processed: 338 average time/residue: 0.1278 time to fit residues: 68.3813 Evaluate side-chains 340 residues out of total 2331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 273 time to evaluate : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 185 SER Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 263 TRP Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 198 GLU Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 306 HIS Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 126 SER Chi-restraints excluded: chain C residue 200 ILE Chi-restraints excluded: chain C residue 243 GLU Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain D residue 43 LEU Chi-restraints excluded: chain D residue 105 SER Chi-restraints excluded: chain D residue 106 ASP Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain D residue 334 ASP Chi-restraints excluded: chain D residue 350 ILE Chi-restraints excluded: chain E residue 105 SER Chi-restraints excluded: chain E residue 106 ASP Chi-restraints excluded: chain E residue 189 VAL Chi-restraints excluded: chain E residue 202 LEU Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain E residue 299 ILE Chi-restraints excluded: chain F residue 34 GLU Chi-restraints excluded: chain F residue 189 VAL Chi-restraints excluded: chain F residue 230 LEU Chi-restraints excluded: chain F residue 238 ILE Chi-restraints excluded: chain F residue 264 THR Chi-restraints excluded: chain F residue 279 ILE Chi-restraints excluded: chain F residue 299 ILE Chi-restraints excluded: chain F residue 308 THR Chi-restraints excluded: chain F residue 354 VAL Chi-restraints excluded: chain G residue 40 SER Chi-restraints excluded: chain G residue 62 THR Chi-restraints excluded: chain G residue 72 ILE Chi-restraints excluded: chain G residue 210 GLU Chi-restraints excluded: chain G residue 238 ILE Chi-restraints excluded: chain G residue 250 LEU Chi-restraints excluded: chain G residue 276 SER Chi-restraints excluded: chain G residue 299 ILE Chi-restraints excluded: chain G residue 312 LYS Chi-restraints excluded: chain G residue 349 LEU Chi-restraints excluded: chain H residue 34 GLU Chi-restraints excluded: chain H residue 61 VAL Chi-restraints excluded: chain H residue 92 SER Chi-restraints excluded: chain H residue 202 LEU Chi-restraints excluded: chain H residue 240 ASP Chi-restraints excluded: chain H residue 264 THR Chi-restraints excluded: chain H residue 321 LEU Chi-restraints excluded: chain H residue 327 LEU Chi-restraints excluded: chain I residue 4 THR Chi-restraints excluded: chain I residue 10 VAL Chi-restraints excluded: chain I residue 13 ILE Chi-restraints excluded: chain I residue 27 LEU Chi-restraints excluded: chain I residue 44 VAL Chi-restraints excluded: chain J residue 12 ASN Chi-restraints excluded: chain J residue 22 VAL Chi-restraints excluded: chain J residue 27 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 191 optimal weight: 0.9980 chunk 138 optimal weight: 2.9990 chunk 278 optimal weight: 10.0000 chunk 108 optimal weight: 7.9990 chunk 20 optimal weight: 9.9990 chunk 109 optimal weight: 1.9990 chunk 129 optimal weight: 2.9990 chunk 215 optimal weight: 6.9990 chunk 272 optimal weight: 50.0000 chunk 65 optimal weight: 5.9990 chunk 43 optimal weight: 10.0000 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 256 ASN B 282 ASN ** E 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 38 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.121490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.092782 restraints weight = 40928.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.094167 restraints weight = 32956.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.094855 restraints weight = 24577.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.095313 restraints weight = 18761.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.095464 restraints weight = 17575.388| |-----------------------------------------------------------------------------| r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.7635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 22262 Z= 0.180 Angle : 0.602 9.676 30673 Z= 0.312 Chirality : 0.041 0.219 3596 Planarity : 0.004 0.043 3843 Dihedral : 13.780 115.822 4022 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 3.97 % Allowed : 21.53 % Favored : 74.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.59 (0.15), residues: 2838 helix: 1.59 (0.18), residues: 850 sheet: -1.06 (0.23), residues: 432 loop : -1.36 (0.14), residues: 1556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 169 TYR 0.014 0.002 TYR G 266 PHE 0.017 0.002 PHE F 166 TRP 0.012 0.001 TRP H 168 HIS 0.006 0.001 HIS C 159 Details of bonding type rmsd covalent geometry : bond 0.00399 (22262) covalent geometry : angle 0.60186 (30673) hydrogen bonds : bond 0.03230 ( 904) hydrogen bonds : angle 4.78753 ( 2481) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5676 Ramachandran restraints generated. 2838 Oldfield, 0 Emsley, 2838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5676 Ramachandran restraints generated. 2838 Oldfield, 0 Emsley, 2838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 2331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 289 time to evaluate : 0.585 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 194 PHE cc_start: 0.8512 (t80) cc_final: 0.8106 (t80) REVERT: A 207 ARG cc_start: 0.7810 (tmm-80) cc_final: 0.7358 (ptm-80) REVERT: B 192 LEU cc_start: 0.9057 (mt) cc_final: 0.8845 (mt) REVERT: B 196 HIS cc_start: 0.8676 (m90) cc_final: 0.8042 (m90) REVERT: C 38 ASP cc_start: 0.8356 (t0) cc_final: 0.7937 (t0) REVERT: D 99 ASP cc_start: 0.8101 (m-30) cc_final: 0.7736 (m-30) REVERT: E 161 LEU cc_start: 0.9393 (OUTLIER) cc_final: 0.9036 (mp) REVERT: E 186 GLN cc_start: 0.7477 (mm-40) cc_final: 0.7018 (tm-30) REVERT: E 334 ASP cc_start: 0.8351 (t70) cc_final: 0.7989 (t70) REVERT: F 34 GLU cc_start: 0.8200 (OUTLIER) cc_final: 0.7740 (mt-10) REVERT: F 91 GLN cc_start: 0.8165 (mt0) cc_final: 0.7868 (mp10) REVERT: G 206 LYS cc_start: 0.8355 (mmtt) cc_final: 0.8011 (mmtp) REVERT: I 22 VAL cc_start: 0.8742 (m) cc_final: 0.8525 (p) REVERT: J 32 ARG cc_start: 0.8570 (ptp90) cc_final: 0.8251 (mtm110) REVERT: J 38 GLN cc_start: 0.8954 (tp-100) cc_final: 0.8504 (tm-30) outliers start: 71 outliers final: 60 residues processed: 336 average time/residue: 0.1270 time to fit residues: 68.5905 Evaluate side-chains 338 residues out of total 2331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 276 time to evaluate : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 185 SER Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 263 TRP Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 114 HIS Chi-restraints excluded: chain B residue 121 HIS Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 256 ASN Chi-restraints excluded: chain B residue 306 HIS Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 126 SER Chi-restraints excluded: chain C residue 200 ILE Chi-restraints excluded: chain C residue 243 GLU Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain D residue 43 LEU Chi-restraints excluded: chain D residue 105 SER Chi-restraints excluded: chain D residue 106 ASP Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 350 ILE Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 105 SER Chi-restraints excluded: chain E residue 106 ASP Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain E residue 189 VAL Chi-restraints excluded: chain E residue 202 LEU Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain F residue 34 GLU Chi-restraints excluded: chain F residue 189 VAL Chi-restraints excluded: chain F residue 230 LEU Chi-restraints excluded: chain F residue 264 THR Chi-restraints excluded: chain F residue 279 ILE Chi-restraints excluded: chain F residue 299 ILE Chi-restraints excluded: chain F residue 308 THR Chi-restraints excluded: chain F residue 318 LYS Chi-restraints excluded: chain F residue 349 LEU Chi-restraints excluded: chain F residue 354 VAL Chi-restraints excluded: chain G residue 40 SER Chi-restraints excluded: chain G residue 62 THR Chi-restraints excluded: chain G residue 67 SER Chi-restraints excluded: chain G residue 238 ILE Chi-restraints excluded: chain G residue 250 LEU Chi-restraints excluded: chain G residue 276 SER Chi-restraints excluded: chain G residue 299 ILE Chi-restraints excluded: chain G residue 349 LEU Chi-restraints excluded: chain H residue 34 GLU Chi-restraints excluded: chain H residue 92 SER Chi-restraints excluded: chain H residue 202 LEU Chi-restraints excluded: chain H residue 240 ASP Chi-restraints excluded: chain H residue 321 LEU Chi-restraints excluded: chain H residue 327 LEU Chi-restraints excluded: chain I residue 10 VAL Chi-restraints excluded: chain I residue 13 ILE Chi-restraints excluded: chain I residue 44 VAL Chi-restraints excluded: chain J residue 12 ASN Chi-restraints excluded: chain J residue 22 VAL Chi-restraints excluded: chain J residue 27 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 285 optimal weight: 9.9990 chunk 218 optimal weight: 7.9990 chunk 235 optimal weight: 20.0000 chunk 227 optimal weight: 0.9980 chunk 129 optimal weight: 9.9990 chunk 179 optimal weight: 2.9990 chunk 175 optimal weight: 0.0470 chunk 191 optimal weight: 0.7980 chunk 34 optimal weight: 5.9990 chunk 7 optimal weight: 20.0000 chunk 73 optimal weight: 10.0000 overall best weight: 2.1682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS B 256 ASN ** C 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.122879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.095231 restraints weight = 40847.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.094431 restraints weight = 32609.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.095694 restraints weight = 26059.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.096002 restraints weight = 19737.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.096233 restraints weight = 18653.079| |-----------------------------------------------------------------------------| r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.7644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 22262 Z= 0.143 Angle : 0.582 9.720 30673 Z= 0.300 Chirality : 0.040 0.196 3596 Planarity : 0.004 0.044 3843 Dihedral : 13.630 113.380 4022 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 3.41 % Allowed : 22.15 % Favored : 74.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.45 (0.15), residues: 2838 helix: 1.75 (0.18), residues: 844 sheet: -0.94 (0.23), residues: 440 loop : -1.30 (0.15), residues: 1554 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 128 TYR 0.017 0.002 TYR B 255 PHE 0.015 0.002 PHE F 166 TRP 0.011 0.001 TRP H 168 HIS 0.005 0.001 HIS C 159 Details of bonding type rmsd covalent geometry : bond 0.00319 (22262) covalent geometry : angle 0.58168 (30673) hydrogen bonds : bond 0.03027 ( 904) hydrogen bonds : angle 4.65585 ( 2481) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5676 Ramachandran restraints generated. 2838 Oldfield, 0 Emsley, 2838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5676 Ramachandran restraints generated. 2838 Oldfield, 0 Emsley, 2838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 2331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 299 time to evaluate : 0.626 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 207 ARG cc_start: 0.7833 (tmm-80) cc_final: 0.7443 (ptm-80) REVERT: B 196 HIS cc_start: 0.8713 (m90) cc_final: 0.8084 (m90) REVERT: C 34 GLU cc_start: 0.8018 (mm-30) cc_final: 0.7695 (tp30) REVERT: C 38 ASP cc_start: 0.8310 (t0) cc_final: 0.7905 (t0) REVERT: C 249 GLU cc_start: 0.7764 (mt-10) cc_final: 0.7339 (mt-10) REVERT: D 99 ASP cc_start: 0.8099 (m-30) cc_final: 0.7755 (m-30) REVERT: E 161 LEU cc_start: 0.9383 (OUTLIER) cc_final: 0.9050 (mp) REVERT: E 186 GLN cc_start: 0.7431 (mm-40) cc_final: 0.6972 (tm-30) REVERT: E 334 ASP cc_start: 0.8328 (t70) cc_final: 0.7874 (t0) REVERT: F 34 GLU cc_start: 0.8252 (OUTLIER) cc_final: 0.7752 (mt-10) REVERT: G 206 LYS cc_start: 0.8291 (mmtt) cc_final: 0.8065 (mmtm) REVERT: I 22 VAL cc_start: 0.8736 (m) cc_final: 0.8464 (p) REVERT: J 32 ARG cc_start: 0.8608 (ptp90) cc_final: 0.8302 (mtm110) outliers start: 61 outliers final: 52 residues processed: 343 average time/residue: 0.1277 time to fit residues: 70.0343 Evaluate side-chains 336 residues out of total 2331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 282 time to evaluate : 0.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 263 TRP Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 114 HIS Chi-restraints excluded: chain B residue 121 HIS Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 256 ASN Chi-restraints excluded: chain B residue 306 HIS Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 159 HIS Chi-restraints excluded: chain C residue 200 ILE Chi-restraints excluded: chain C residue 243 GLU Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain D residue 43 LEU Chi-restraints excluded: chain D residue 105 SER Chi-restraints excluded: chain D residue 106 ASP Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 350 ILE Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 105 SER Chi-restraints excluded: chain E residue 106 ASP Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain E residue 189 VAL Chi-restraints excluded: chain E residue 202 LEU Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain F residue 34 GLU Chi-restraints excluded: chain F residue 189 VAL Chi-restraints excluded: chain F residue 230 LEU Chi-restraints excluded: chain F residue 238 ILE Chi-restraints excluded: chain F residue 264 THR Chi-restraints excluded: chain F residue 279 ILE Chi-restraints excluded: chain F residue 299 ILE Chi-restraints excluded: chain F residue 308 THR Chi-restraints excluded: chain F residue 354 VAL Chi-restraints excluded: chain G residue 62 THR Chi-restraints excluded: chain G residue 250 LEU Chi-restraints excluded: chain G residue 299 ILE Chi-restraints excluded: chain G residue 349 LEU Chi-restraints excluded: chain H residue 34 GLU Chi-restraints excluded: chain H residue 202 LEU Chi-restraints excluded: chain H residue 240 ASP Chi-restraints excluded: chain H residue 264 THR Chi-restraints excluded: chain H residue 321 LEU Chi-restraints excluded: chain H residue 327 LEU Chi-restraints excluded: chain I residue 10 VAL Chi-restraints excluded: chain I residue 44 VAL Chi-restraints excluded: chain J residue 22 VAL Chi-restraints excluded: chain J residue 27 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 190 optimal weight: 0.0570 chunk 118 optimal weight: 10.0000 chunk 39 optimal weight: 20.0000 chunk 129 optimal weight: 8.9990 chunk 184 optimal weight: 7.9990 chunk 18 optimal weight: 20.0000 chunk 277 optimal weight: 10.0000 chunk 30 optimal weight: 6.9990 chunk 65 optimal weight: 6.9990 chunk 15 optimal weight: 0.9980 chunk 90 optimal weight: 0.0170 overall best weight: 3.0140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 256 ASN B 282 ASN ** C 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 348 ASN ** H 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 348 ASN J 38 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.121561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.094992 restraints weight = 40963.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.095527 restraints weight = 41455.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.096374 restraints weight = 29546.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.096627 restraints weight = 22250.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.096881 restraints weight = 20695.105| |-----------------------------------------------------------------------------| r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.7740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 22262 Z= 0.177 Angle : 0.610 15.051 30673 Z= 0.314 Chirality : 0.041 0.201 3596 Planarity : 0.004 0.047 3843 Dihedral : 13.607 113.351 4022 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 3.24 % Allowed : 22.76 % Favored : 73.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.44 (0.15), residues: 2838 helix: 1.74 (0.18), residues: 843 sheet: -0.97 (0.24), residues: 433 loop : -1.28 (0.15), residues: 1562 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG H 185 TYR 0.018 0.002 TYR J 57 PHE 0.016 0.002 PHE F 166 TRP 0.011 0.001 TRP F 49 HIS 0.008 0.001 HIS H 343 Details of bonding type rmsd covalent geometry : bond 0.00394 (22262) covalent geometry : angle 0.60996 (30673) hydrogen bonds : bond 0.03161 ( 904) hydrogen bonds : angle 4.67534 ( 2481) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5676 Ramachandran restraints generated. 2838 Oldfield, 0 Emsley, 2838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5676 Ramachandran restraints generated. 2838 Oldfield, 0 Emsley, 2838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 2331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 287 time to evaluate : 0.466 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 194 PHE cc_start: 0.8369 (t80) cc_final: 0.8136 (t80) REVERT: A 207 ARG cc_start: 0.7751 (tmm-80) cc_final: 0.7384 (ptm-80) REVERT: B 192 LEU cc_start: 0.8922 (mt) cc_final: 0.8698 (mt) REVERT: B 196 HIS cc_start: 0.8457 (m90) cc_final: 0.7962 (m90) REVERT: C 38 ASP cc_start: 0.8328 (t0) cc_final: 0.8040 (t0) REVERT: C 249 GLU cc_start: 0.7695 (mt-10) cc_final: 0.7248 (mt-10) REVERT: D 99 ASP cc_start: 0.8140 (m-30) cc_final: 0.7836 (m-30) REVERT: E 161 LEU cc_start: 0.9385 (OUTLIER) cc_final: 0.9038 (mp) REVERT: E 186 GLN cc_start: 0.7456 (mm-40) cc_final: 0.6992 (tm-30) REVERT: E 334 ASP cc_start: 0.8375 (t70) cc_final: 0.7942 (t70) REVERT: F 34 GLU cc_start: 0.8276 (OUTLIER) cc_final: 0.7795 (mt-10) REVERT: I 22 VAL cc_start: 0.8734 (m) cc_final: 0.8517 (p) REVERT: J 32 ARG cc_start: 0.8531 (ptp90) cc_final: 0.8196 (mtm110) outliers start: 58 outliers final: 55 residues processed: 327 average time/residue: 0.1198 time to fit residues: 63.3185 Evaluate side-chains 337 residues out of total 2331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 280 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 263 TRP Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 114 HIS Chi-restraints excluded: chain B residue 121 HIS Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 306 HIS Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 159 HIS Chi-restraints excluded: chain C residue 200 ILE Chi-restraints excluded: chain C residue 243 GLU Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain D residue 43 LEU Chi-restraints excluded: chain D residue 105 SER Chi-restraints excluded: chain D residue 106 ASP Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 350 ILE Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 105 SER Chi-restraints excluded: chain E residue 106 ASP Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain E residue 189 VAL Chi-restraints excluded: chain E residue 202 LEU Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain F residue 34 GLU Chi-restraints excluded: chain F residue 189 VAL Chi-restraints excluded: chain F residue 230 LEU Chi-restraints excluded: chain F residue 238 ILE Chi-restraints excluded: chain F residue 264 THR Chi-restraints excluded: chain F residue 279 ILE Chi-restraints excluded: chain F residue 299 ILE Chi-restraints excluded: chain F residue 308 THR Chi-restraints excluded: chain F residue 349 LEU Chi-restraints excluded: chain F residue 354 VAL Chi-restraints excluded: chain G residue 62 THR Chi-restraints excluded: chain G residue 67 SER Chi-restraints excluded: chain G residue 250 LEU Chi-restraints excluded: chain G residue 299 ILE Chi-restraints excluded: chain G residue 349 LEU Chi-restraints excluded: chain H residue 34 GLU Chi-restraints excluded: chain H residue 202 LEU Chi-restraints excluded: chain H residue 240 ASP Chi-restraints excluded: chain H residue 264 THR Chi-restraints excluded: chain H residue 321 LEU Chi-restraints excluded: chain H residue 327 LEU Chi-restraints excluded: chain I residue 10 VAL Chi-restraints excluded: chain I residue 13 ILE Chi-restraints excluded: chain I residue 44 VAL Chi-restraints excluded: chain J residue 22 VAL Chi-restraints excluded: chain J residue 27 LEU Chi-restraints excluded: chain J residue 43 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 225 optimal weight: 5.9990 chunk 261 optimal weight: 50.0000 chunk 84 optimal weight: 0.9990 chunk 29 optimal weight: 0.0270 chunk 82 optimal weight: 2.9990 chunk 139 optimal weight: 3.9990 chunk 124 optimal weight: 2.9990 chunk 191 optimal weight: 0.9990 chunk 281 optimal weight: 4.9990 chunk 209 optimal weight: 7.9990 chunk 164 optimal weight: 0.9990 overall best weight: 1.2046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 282 ASN ** C 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 94 ASN ** G 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 38 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.124961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.097513 restraints weight = 40593.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.097666 restraints weight = 33333.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.098858 restraints weight = 24288.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.099182 restraints weight = 18718.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.099305 restraints weight = 17351.885| |-----------------------------------------------------------------------------| r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.7679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 22262 Z= 0.113 Angle : 0.584 14.852 30673 Z= 0.295 Chirality : 0.040 0.258 3596 Planarity : 0.004 0.049 3843 Dihedral : 13.438 111.049 4022 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 3.02 % Allowed : 22.99 % Favored : 73.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.27 (0.16), residues: 2838 helix: 1.89 (0.18), residues: 844 sheet: -0.84 (0.24), residues: 432 loop : -1.19 (0.15), residues: 1562 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 185 TYR 0.016 0.001 TYR H 304 PHE 0.012 0.001 PHE H 355 TRP 0.010 0.001 TRP G 168 HIS 0.007 0.001 HIS H 343 Details of bonding type rmsd covalent geometry : bond 0.00251 (22262) covalent geometry : angle 0.58375 (30673) hydrogen bonds : bond 0.02795 ( 904) hydrogen bonds : angle 4.49064 ( 2481) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2988.76 seconds wall clock time: 52 minutes 37.56 seconds (3157.56 seconds total)