Starting phenix.real_space_refine on Sun Sep 13 07:12:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6w1x_21516/09_2026/6w1x_21516.cif Found real_map, /net/cci-nas-00/data/ceres_data/6w1x_21516/09_2026/6w1x_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_21516/09_2026/6w1x_21516.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6w1x_21516/09_2026/6w1x_21516.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6w1x_21516/09_2026/6w1x_21516.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6w1x_21516/09_2026/6w1x_21516.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6w1x_21516/09_2026/6w1x_21516.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6w1x_21516/09_2026/6w1x_21516.cif" } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/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: {'RNAv2': 60} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 11, 'rna3p_pur': 22, 'rna3p_pyr': 19} Link IDs: {'rna2p': 17, 'rna3p': 42} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 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: 5.12, per 1000 atoms: 0.24 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: 1.70 Conformation dependent library (CDL) restraints added in 875.3 milliseconds 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: 2.30 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: 3.91 Time building geometry restraints manager: 2.29 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 - 1.94: 29034 1.94 - 3.88: 1495 3.88 - 5.82: 77 5.82 - 7.76: 34 7.76 - 9.70: 33 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 112.50 122.15 -9.65 2.00e+00 2.50e-01 2.33e+01 angle pdb=" C3' A M 8 " pdb=" C2' A M 8 " pdb=" O2' A M 8 " ideal model delta sigma weight residual 109.80 119.32 -9.52 2.00e+00 2.50e-01 2.26e+01 angle pdb=" C3' G M 60 " pdb=" C2' G M 60 " pdb=" O2' G M 60 " ideal model delta sigma weight residual 109.80 119.27 -9.47 2.00e+00 2.50e-01 2.24e+01 angle pdb=" C3' A M 3 " pdb=" C2' A M 3 " pdb=" O2' A M 3 " ideal model delta sigma weight residual 109.80 119.24 -9.44 2.00e+00 2.50e-01 2.23e+01 angle pdb=" O3' A M 8 " pdb=" C3' A M 8 " pdb=" C2' A M 8 " ideal model delta sigma weight residual 113.80 104.58 9.22 2.00e+00 2.50e-01 2.12e+01 ... (remaining 30668 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.88: 12864 30.88 - 61.75: 199 61.75 - 92.63: 12 92.63 - 123.50: 0 123.50 - 154.38: 1 Dihedral angle restraints: 13076 sinusoidal: 4814 harmonic: 8262 Sorted by residual: dihedral pdb=" C4' U M 2 " pdb=" C3' U M 2 " pdb=" C2' U M 2 " pdb=" C1' U M 2 " ideal model delta sinusoidal sigma weight residual 36.34 -26.81 63.16 1 3.10e+00 1.04e-01 5.48e+02 dihedral pdb=" C4' G M 32 " pdb=" C3' G M 32 " pdb=" C2' G M 32 " pdb=" C1' G M 32 " ideal model delta sinusoidal sigma weight residual 36.34 -26.63 62.97 1 3.10e+00 1.04e-01 5.45e+02 dihedral pdb=" C4' C M 31 " pdb=" C3' C M 31 " pdb=" C2' C M 31 " pdb=" C1' C M 31 " ideal model delta sinusoidal sigma weight residual 36.34 -26.40 62.74 1 3.10e+00 1.04e-01 5.41e+02 ... (remaining 13073 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.149: 3326 0.149 - 0.298: 222 0.298 - 0.448: 29 0.448 - 0.597: 3 0.597 - 0.746: 16 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 -2.79 -2.04 -0.75 2.00e-01 2.50e+01 1.39e+01 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 -2.79 -2.05 -0.74 2.00e-01 2.50e+01 1.37e+01 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 -2.79 -2.07 -0.72 2.00e-01 2.50e+01 1.30e+01 ... (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: 0.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.340 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 21.720 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.040 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:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7194 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= 0.790 Angle : 1.056 9.697 30673 Z= 0.720 Chirality : 0.100 0.746 3596 Planarity : 0.006 0.027 3843 Dihedral : 10.183 154.380 7734 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 are 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/Z covalent geometry : bond 0.01124 / 0.79 (22262) covalent geometry : angle 1.05636 / 0.72 (30673) hydrogen bonds : bond 0.18165 / 13.46 ( 904) hydrogen bonds : angle 6.70903 / 5.07 ( 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 : 0.772 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: 0.1764 time to fit residues: 218.6297 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 : 0.847 ------------------------------------------------------------------------------- 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... B 86 ASN B 121 HIS B 256 ASN C 242 GLN ** D 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 74 ASN ** F 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 310 GLN ** G 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 102 ASN H 329 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.148503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.123821 restraints weight = 39865.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.123881 restraints weight = 27442.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.125476 restraints weight = 22126.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.125957 restraints weight = 17640.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.126221 restraints weight = 15793.331| |-----------------------------------------------------------------------------| r_work (final): 0.3685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.3764 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= 0.135 Angle : 0.754 15.789 30673 Z= 0.338 Chirality : 0.057 0.802 3596 Planarity : 0.004 0.045 3843 Dihedral : 10.885 156.142 3792 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 3.91 % Allowed : 15.38 % Favored : 80.70 % 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 are not related in a simple way. whole: -0.01 (0.15), residues: 2838 helix: 2.15 (0.18), residues: 859 sheet: -0.72 (0.21), residues: 483 loop : -1.08 (0.15), 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 0.007 0.001 HIS F 343 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 (22262) covalent geometry : angle 0.75397 / 0.34 (30673) hydrogen bonds : bond 0.03117 / 2.24 ( 904) hydrogen bonds : angle 4.61968 / 3.46 ( 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 556 residues out of total 2331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 486 time to evaluate : 0.586 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: A 208 GLU cc_start: 0.6267 (tp30) cc_final: 0.5944 (tp30) REVERT: A 241 GLN cc_start: 0.7445 (tt0) cc_final: 0.6502 (pm20) REVERT: A 266 PRO cc_start: 0.7945 (Cg_endo) cc_final: 0.7731 (Cg_exo) REVERT: B 129 GLN cc_start: 0.7490 (mm110) cc_final: 0.6628 (tm-30) REVERT: B 131 GLN cc_start: 0.7795 (tt0) cc_final: 0.7503 (tt0) REVERT: B 194 GLN cc_start: 0.7972 (mm110) cc_final: 0.7270 (mm-40) REVERT: B 196 HIS cc_start: 0.8364 (m90) cc_final: 0.7717 (m170) REVERT: B 302 LEU cc_start: 0.8940 (mt) cc_final: 0.8686 (mt) REVERT: C 161 LEU cc_start: 0.9156 (mp) cc_final: 0.8949 (mp) REVERT: E 161 LEU cc_start: 0.8966 (OUTLIER) cc_final: 0.8681 (mp) REVERT: E 334 ASP cc_start: 0.7346 (t70) cc_final: 0.7095 (t0) REVERT: F 238 ILE cc_start: 0.9406 (mm) cc_final: 0.8988 (tt) REVERT: G 67 SER cc_start: 0.9243 (t) cc_final: 0.8994 (t) REVERT: G 178 GLU cc_start: 0.7847 (tm-30) cc_final: 0.7508 (tm-30) REVERT: G 240 ASP cc_start: 0.7243 (t0) cc_final: 0.6931 (t0) REVERT: G 340 GLU cc_start: 0.7877 (mm-30) cc_final: 0.7596 (mm-30) REVERT: H 243 GLU cc_start: 0.6471 (OUTLIER) cc_final: 0.6246 (tt0) REVERT: H 249 GLU cc_start: 0.7088 (tt0) cc_final: 0.6808 (tt0) REVERT: H 302 GLU cc_start: 0.6648 (mm-30) cc_final: 0.6284 (mm-30) REVERT: I 9 GLU cc_start: 0.7760 (mt-10) cc_final: 0.7024 (mm-30) REVERT: J 28 THR cc_start: 0.9088 (p) cc_final: 0.8352 (t) REVERT: J 32 ARG cc_start: 0.8421 (ptp90) cc_final: 0.7961 (ptp90) REVERT: J 63 ARG cc_start: 0.7896 (ttm-80) cc_final: 0.7533 (mtp85) outliers start: 70 outliers final: 38 residues processed: 528 average time/residue: 0.1578 time to fit residues: 126.6980 Evaluate side-chains 403 residues out of total 2331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 363 time to evaluate : 0.669 ------------------------------------------------------------------------------- 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 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 161 LEU Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain E residue 243 GLU 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 243 GLU Chi-restraints excluded: chain H residue 247 SER 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: 0.5980 chunk 190 optimal weight: 3.9990 chunk 287 optimal weight: 10.0000 chunk 237 optimal weight: 6.9990 chunk 92 optimal weight: 9.9990 chunk 20 optimal weight: 7.9990 chunk 211 optimal weight: 7.9990 chunk 250 optimal weight: 0.3980 chunk 148 optimal weight: 10.0000 chunk 272 optimal weight: 50.0000 chunk 88 optimal weight: 9.9990 overall best weight: 3.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 188 HIS ** A 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 172 ASN D 242 GLN ** D 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 91 GLN E 146 ASN E 186 GLN F 94 ASN F 148 GLN ** F 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 242 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.129935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.100894 restraints weight = 40526.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.102893 restraints weight = 32192.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.103742 restraints weight = 22293.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.103652 restraints weight = 16843.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.104220 restraints weight = 16922.026| |-----------------------------------------------------------------------------| r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.5498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 22262 Z= 0.231 Angle : 0.748 12.391 30673 Z= 0.357 Chirality : 0.054 0.697 3596 Planarity : 0.005 0.070 3843 Dihedral : 11.113 150.457 3792 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 4.87 % Allowed : 15.88 % Favored : 79.25 % 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 are not related in a simple way. whole: -0.18 (0.15), residues: 2838 helix: 1.97 (0.18), residues: 853 sheet: -0.84 (0.21), residues: 490 loop : -1.14 (0.15), residues: 1495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 169 TYR 0.022 0.002 TYR I 57 PHE 0.022 0.003 PHE E 166 TRP 0.022 0.002 TRP F 58 HIS 0.007 0.001 HIS D 343 Details of bonding type rmsd/Z covalent geometry : bond 0.00514 / 0.23 (22262) covalent geometry : angle 0.74835 / 0.36 (30673) hydrogen bonds : bond 0.03522 / 2.52 ( 904) hydrogen bonds : angle 4.72578 / 3.54 ( 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 464 residues out of total 2331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 377 time to evaluate : 0.746 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: 0.5965 (tp30) REVERT: A 222 ARG cc_start: 0.7971 (tpt-90) cc_final: 0.7744 (ttt90) REVERT: A 237 ASN cc_start: 0.8143 (t0) cc_final: 0.7936 (m110) REVERT: B 196 HIS cc_start: 0.8726 (m90) cc_final: 0.7882 (m-70) REVERT: C 161 LEU cc_start: 0.9258 (OUTLIER) cc_final: 0.9032 (mp) REVERT: C 354 VAL cc_start: 0.8512 (t) cc_final: 0.8207 (p) REVERT: D 38 ASP cc_start: 0.7872 (t0) cc_final: 0.7644 (p0) REVERT: E 25 LEU cc_start: 0.8878 (tp) cc_final: 0.8428 (tt) REVERT: E 35 ARG cc_start: 0.8600 (ptt-90) cc_final: 0.8332 (ptt-90) REVERT: E 161 LEU cc_start: 0.9388 (OUTLIER) cc_final: 0.8933 (mp) REVERT: E 334 ASP cc_start: 0.7781 (t70) cc_final: 0.7475 (t70) REVERT: F 324 TYR cc_start: 0.8351 (m-80) cc_final: 0.7840 (m-10) REVERT: F 354 VAL cc_start: 0.9280 (t) cc_final: 0.9020 (p) REVERT: G 44 MET cc_start: 0.8467 (mtt) cc_final: 0.8131 (mtt) REVERT: G 73 SER cc_start: 0.6881 (p) cc_final: 0.6590 (p) REVERT: H 245 PHE cc_start: 0.8887 (m-80) cc_final: 0.8626 (m-80) REVERT: J 5 TYR cc_start: 0.6975 (m-10) cc_final: 0.6523 (m-10) REVERT: J 28 THR cc_start: 0.9183 (p) cc_final: 0.8602 (p) REVERT: J 32 ARG cc_start: 0.8457 (ptp90) cc_final: 0.8175 (ptp90) outliers start: 87 outliers final: 53 residues processed: 433 average time/residue: 0.1537 time to fit residues: 103.7366 Evaluate side-chains 363 residues out of total 2331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 308 time to evaluate : 0.766 ------------------------------------------------------------------------------- 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 263 TRP Chi-restraints excluded: chain B residue 28 THR 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 98 VAL Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 200 ILE 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 30 VAL Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain D residue 299 ILE 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 230 LEU Chi-restraints excluded: chain E residue 279 ILE Chi-restraints excluded: chain E residue 299 ILE Chi-restraints excluded: chain F residue 94 ASN 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 308 THR Chi-restraints excluded: chain G residue 40 SER Chi-restraints excluded: chain G residue 95 LEU Chi-restraints excluded: chain G residue 250 LEU 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 92 SER Chi-restraints excluded: chain H residue 202 LEU 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 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: 10.0000 chunk 224 optimal weight: 0.6980 chunk 115 optimal weight: 5.9990 chunk 116 optimal weight: 4.9990 chunk 15 optimal weight: 6.9990 chunk 0 optimal weight: 50.0000 chunk 177 optimal weight: 8.9990 chunk 222 optimal weight: 6.9990 chunk 228 optimal weight: 9.9990 chunk 74 optimal weight: 9.9990 chunk 108 optimal weight: 8.9990 overall best weight: 5.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 203 HIS B 256 ASN D 160 ASN ** D 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 146 ASN E 242 GLN F 94 ASN ** F 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.123105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.095139 restraints weight = 40964.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.094634 restraints weight = 34000.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.095912 restraints weight = 27576.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.096227 restraints weight = 20656.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.096391 restraints weight = 19454.904| |-----------------------------------------------------------------------------| r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.6666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 22262 Z= 0.276 Angle : 0.779 11.599 30673 Z= 0.373 Chirality : 0.055 0.779 3596 Planarity : 0.005 0.047 3843 Dihedral : 11.199 150.811 3792 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 5.70 % Allowed : 16.83 % Favored : 77.46 % 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 are not related in a simple way. whole: -0.52 (0.15), residues: 2838 helix: 1.68 (0.18), residues: 845 sheet: -1.07 (0.22), residues: 462 loop : -1.31 (0.14), residues: 1531 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG F 75 TYR 0.018 0.002 TYR I 57 PHE 0.026 0.003 PHE F 166 TRP 0.020 0.002 TRP F 49 HIS 0.007 0.002 HIS F 227 Details of bonding type rmsd/Z covalent geometry : bond 0.00610 / 0.28 (22262) covalent geometry : angle 0.77866 / 0.37 (30673) hydrogen bonds : bond 0.03660 / 2.63 ( 904) hydrogen bonds : angle 4.86551 / 3.65 ( 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 430 residues out of total 2331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 328 time to evaluate : 0.808 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 222 ARG cc_start: 0.8118 (tpt-90) cc_final: 0.7907 (ttt90) REVERT: A 237 ASN cc_start: 0.8508 (t0) cc_final: 0.8070 (m-40) REVERT: A 262 ASN cc_start: 0.7481 (p0) cc_final: 0.7201 (p0) REVERT: B 21 ASN cc_start: 0.8396 (t0) cc_final: 0.8149 (t0) REVERT: B 78 THR cc_start: 0.8030 (m) cc_final: 0.7692 (p) REVERT: B 196 HIS cc_start: 0.8676 (m90) cc_final: 0.8401 (m90) REVERT: B 255 TYR cc_start: 0.7389 (m-80) cc_final: 0.7158 (m-80) REVERT: B 258 LEU cc_start: 0.8069 (tt) cc_final: 0.7790 (tt) REVERT: C 38 ASP cc_start: 0.8447 (t0) cc_final: 0.8015 (t0) REVERT: C 161 LEU cc_start: 0.9242 (OUTLIER) cc_final: 0.9032 (mp) REVERT: C 302 GLU cc_start: 0.8060 (tp30) cc_final: 0.7787 (tp30) REVERT: C 354 VAL cc_start: 0.8648 (t) cc_final: 0.8314 (p) REVERT: D 38 ASP cc_start: 0.8029 (t0) cc_final: 0.7678 (p0) REVERT: E 161 LEU cc_start: 0.9388 (OUTLIER) cc_final: 0.8982 (mp) REVERT: E 186 GLN cc_start: 0.7322 (tm-30) cc_final: 0.6670 (tm-30) REVERT: E 334 ASP cc_start: 0.8320 (t70) cc_final: 0.8020 (t70) REVERT: F 354 VAL cc_start: 0.9276 (t) cc_final: 0.9051 (p) REVERT: G 324 TYR cc_start: 0.8882 (m-10) cc_final: 0.8489 (m-80) REVERT: H 302 GLU cc_start: 0.7858 (mm-30) cc_final: 0.7596 (mm-30) REVERT: J 28 THR cc_start: 0.9151 (p) cc_final: 0.8912 (t) REVERT: J 32 ARG cc_start: 0.8621 (ptp90) cc_final: 0.8237 (mtm110) outliers start: 102 outliers final: 69 residues processed: 398 average time/residue: 0.1476 time to fit residues: 92.7143 Evaluate side-chains 365 residues out of total 2331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 294 time to evaluate : 0.668 ------------------------------------------------------------------------------- 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 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 256 ASN 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 161 LEU 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 189 VAL Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 299 ILE Chi-restraints excluded: chain D residue 334 ASP Chi-restraints excluded: chain D residue 350 ILE Chi-restraints excluded: chain E residue 68 VAL 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 279 ILE Chi-restraints excluded: chain E residue 299 ILE Chi-restraints excluded: chain E residue 302 GLU Chi-restraints excluded: chain F residue 35 ARG Chi-restraints excluded: chain F residue 90 ILE Chi-restraints excluded: chain F residue 94 ASN 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 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 72 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 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 214 optimal weight: 2.9990 chunk 151 optimal weight: 1.9990 chunk 227 optimal weight: 7.9990 chunk 182 optimal weight: 0.9990 chunk 46 optimal weight: 30.0000 chunk 33 optimal weight: 8.9990 chunk 172 optimal weight: 2.9990 chunk 281 optimal weight: 9.9990 chunk 16 optimal weight: 50.0000 chunk 283 optimal weight: 9.9990 chunk 249 optimal weight: 9.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 172 ASN ** B 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 139 GLN D 74 ASN D 160 ASN ** D 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 94 ASN ** F 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 91 GLN ** H 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 348 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.123797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.096607 restraints weight = 40578.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.095548 restraints weight = 36786.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.097049 restraints weight = 30496.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.097353 restraints weight = 22338.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.097459 restraints weight = 21366.459| |-----------------------------------------------------------------------------| r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.6924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 22262 Z= 0.196 Angle : 0.696 10.848 30673 Z= 0.331 Chirality : 0.051 0.600 3596 Planarity : 0.004 0.046 3843 Dihedral : 10.954 148.595 3792 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 4.25 % Allowed : 19.41 % Favored : 76.34 % 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 are not related in a simple way. whole: -0.45 (0.15), residues: 2838 helix: 1.74 (0.18), residues: 847 sheet: -1.05 (0.22), residues: 457 loop : -1.27 (0.14), residues: 1534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 69 TYR 0.027 0.002 TYR I 57 PHE 0.021 0.002 PHE E 166 TRP 0.020 0.001 TRP H 168 HIS 0.004 0.001 HIS B 42 Details of bonding type rmsd/Z covalent geometry : bond 0.00436 / 0.20 (22262) covalent geometry : angle 0.69642 / 0.33 (30673) hydrogen bonds : bond 0.03250 / 2.32 ( 904) hydrogen bonds : angle 4.71875 / 3.55 ( 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 389 residues out of total 2331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 313 time to evaluate : 0.802 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 GLU cc_start: 0.6757 (tp30) cc_final: 0.6532 (tp30) REVERT: A 237 ASN cc_start: 0.8460 (m-40) cc_final: 0.8001 (m-40) REVERT: A 262 ASN cc_start: 0.7484 (p0) cc_final: 0.7235 (p0) REVERT: B 78 THR cc_start: 0.7922 (m) cc_final: 0.7654 (p) REVERT: B 196 HIS cc_start: 0.8735 (m90) cc_final: 0.8028 (m170) REVERT: C 38 ASP cc_start: 0.8470 (t0) cc_final: 0.8114 (t0) REVERT: C 216 GLU cc_start: 0.7967 (tm-30) cc_final: 0.7648 (tm-30) REVERT: C 302 GLU cc_start: 0.8050 (tp30) cc_final: 0.7838 (tp30) REVERT: C 354 VAL cc_start: 0.8564 (t) cc_final: 0.8359 (p) REVERT: E 161 LEU cc_start: 0.9322 (OUTLIER) cc_final: 0.8958 (mp) REVERT: E 186 GLN cc_start: 0.7538 (mm-40) cc_final: 0.7030 (tm-30) REVERT: E 334 ASP cc_start: 0.8332 (t70) cc_final: 0.7978 (t70) REVERT: F 354 VAL cc_start: 0.9351 (t) cc_final: 0.9106 (p) REVERT: G 324 TYR cc_start: 0.8898 (m-10) cc_final: 0.8543 (m-80) REVERT: H 302 GLU cc_start: 0.7777 (mm-30) cc_final: 0.7570 (mm-30) REVERT: J 28 THR cc_start: 0.9150 (p) cc_final: 0.8313 (t) REVERT: J 32 ARG cc_start: 0.8606 (ptp90) cc_final: 0.8168 (ptp90) outliers start: 76 outliers final: 63 residues processed: 364 average time/residue: 0.1432 time to fit residues: 83.9445 Evaluate side-chains 356 residues out of total 2331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 292 time to evaluate : 0.778 ------------------------------------------------------------------------------- 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 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 198 GLU 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 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 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 C residue 350 ILE Chi-restraints excluded: chain D residue 73 SER Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain D residue 299 ILE Chi-restraints excluded: chain D residue 334 ASP Chi-restraints excluded: chain D residue 350 ILE 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 279 ILE Chi-restraints excluded: chain E residue 299 ILE Chi-restraints excluded: chain F residue 35 ARG Chi-restraints excluded: chain F residue 189 VAL Chi-restraints excluded: chain F residue 204 ASP 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 91 GLN 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 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 307 VAL 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 183 optimal weight: 1.9990 chunk 204 optimal weight: 9.9990 chunk 21 optimal weight: 20.0000 chunk 44 optimal weight: 30.0000 chunk 61 optimal weight: 4.9990 chunk 77 optimal weight: 1.9990 chunk 268 optimal weight: 30.0000 chunk 30 optimal weight: 7.9990 chunk 57 optimal weight: 20.0000 chunk 149 optimal weight: 0.8980 chunk 110 optimal weight: 9.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 139 GLN D 342 GLN ** E 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 96 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.122910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.094897 restraints weight = 40718.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.094145 restraints weight = 31111.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.095366 restraints weight = 25578.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.095779 restraints weight = 19670.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.095864 restraints weight = 18674.546| |-----------------------------------------------------------------------------| r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.7202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 22262 Z= 0.204 Angle : 0.695 11.003 30673 Z= 0.331 Chirality : 0.050 0.547 3596 Planarity : 0.004 0.049 3843 Dihedral : 10.919 147.272 3792 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 4.25 % Allowed : 19.91 % Favored : 75.84 % 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 are not related in a simple way. whole: -0.48 (0.15), residues: 2838 helix: 1.68 (0.18), residues: 854 sheet: -1.05 (0.23), residues: 453 loop : -1.29 (0.14), residues: 1531 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 185 TYR 0.029 0.002 TYR I 57 PHE 0.020 0.002 PHE F 166 TRP 0.013 0.001 TRP F 49 HIS 0.004 0.001 HIS G 227 Details of bonding type rmsd/Z covalent geometry : bond 0.00454 / 0.20 (22262) covalent geometry : angle 0.69525 / 0.33 (30673) hydrogen bonds : bond 0.03287 / 2.36 ( 904) hydrogen bonds : angle 4.71802 / 3.54 ( 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 380 residues out of total 2331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 304 time to evaluate : 0.780 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 237 ASN cc_start: 0.8424 (m-40) cc_final: 0.7947 (m-40) REVERT: A 262 ASN cc_start: 0.7637 (p0) cc_final: 0.7264 (p0) REVERT: B 78 THR cc_start: 0.7806 (m) cc_final: 0.7474 (p) REVERT: B 192 LEU cc_start: 0.9034 (mt) cc_final: 0.8793 (mt) REVERT: B 196 HIS cc_start: 0.8782 (m90) cc_final: 0.8075 (m90) REVERT: C 38 ASP cc_start: 0.8369 (t0) cc_final: 0.8143 (t0) REVERT: C 302 GLU cc_start: 0.8101 (tp30) cc_final: 0.7639 (tp30) REVERT: C 354 VAL cc_start: 0.8629 (t) cc_final: 0.8383 (p) REVERT: D 99 ASP cc_start: 0.8172 (m-30) cc_final: 0.7917 (m-30) REVERT: E 161 LEU cc_start: 0.9349 (OUTLIER) cc_final: 0.8976 (mp) REVERT: E 186 GLN cc_start: 0.7468 (mm-40) cc_final: 0.6966 (tm-30) REVERT: E 334 ASP cc_start: 0.8280 (t70) cc_final: 0.7914 (t70) REVERT: F 354 VAL cc_start: 0.9300 (t) cc_final: 0.9079 (p) REVERT: G 324 TYR cc_start: 0.8891 (m-10) cc_final: 0.8449 (m-80) REVERT: H 302 GLU cc_start: 0.7864 (mm-30) cc_final: 0.7633 (mm-30) REVERT: H 343 HIS cc_start: 0.7618 (m170) cc_final: 0.7229 (m90) REVERT: I 22 VAL cc_start: 0.8791 (m) cc_final: 0.8550 (p) REVERT: J 28 THR cc_start: 0.9120 (p) cc_final: 0.8362 (t) REVERT: J 32 ARG cc_start: 0.8618 (ptp90) cc_final: 0.8205 (ptp90) outliers start: 76 outliers final: 66 residues processed: 357 average time/residue: 0.1478 time to fit residues: 84.2783 Evaluate side-chains 356 residues out of total 2331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 289 time to evaluate : 0.798 ------------------------------------------------------------------------------- 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 106 ASP Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain D residue 299 ILE Chi-restraints excluded: chain D residue 334 ASP Chi-restraints excluded: chain D residue 350 ILE 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 279 ILE Chi-restraints excluded: chain E residue 299 ILE Chi-restraints excluded: chain F residue 35 ARG 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 72 ILE Chi-restraints excluded: chain G residue 91 GLN 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 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 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: 6.9990 chunk 154 optimal weight: 10.0000 chunk 49 optimal weight: 5.9990 chunk 253 optimal weight: 6.9990 chunk 123 optimal weight: 0.9990 chunk 271 optimal weight: 50.0000 chunk 197 optimal weight: 0.8980 chunk 87 optimal weight: 9.9990 chunk 169 optimal weight: 9.9990 chunk 74 optimal weight: 20.0000 chunk 99 optimal weight: 5.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 172 ASN B 256 ASN ** C 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 319 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.121609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.094697 restraints weight = 40922.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.093859 restraints weight = 36526.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.095162 restraints weight = 32571.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.095417 restraints weight = 23384.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.095668 restraints weight = 21007.590| |-----------------------------------------------------------------------------| r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.7494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 22262 Z= 0.230 Angle : 0.723 10.847 30673 Z= 0.344 Chirality : 0.051 0.541 3596 Planarity : 0.004 0.052 3843 Dihedral : 10.971 147.243 3792 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 4.14 % Allowed : 19.85 % Favored : 76.01 % 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 are not related in a simple way. whole: -0.58 (0.15), residues: 2838 helix: 1.63 (0.18), residues: 850 sheet: -1.03 (0.23), residues: 454 loop : -1.38 (0.14), residues: 1534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 185 TYR 0.026 0.002 TYR I 57 PHE 0.020 0.002 PHE F 166 TRP 0.015 0.002 TRP F 49 HIS 0.005 0.001 HIS A 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00513 / 0.23 (22262) covalent geometry : angle 0.72343 / 0.34 (30673) hydrogen bonds : bond 0.03404 / 2.44 ( 904) hydrogen bonds : angle 4.77888 / 3.58 ( 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 367 residues out of total 2331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 293 time to evaluate : 0.811 Fit side-chains revert: symmetry clash REVERT: A 237 ASN cc_start: 0.8402 (m-40) cc_final: 0.7957 (m-40) REVERT: A 262 ASN cc_start: 0.7905 (p0) cc_final: 0.7579 (p0) REVERT: B 78 THR cc_start: 0.7883 (m) cc_final: 0.7547 (p) REVERT: B 192 LEU cc_start: 0.9056 (mt) cc_final: 0.8850 (mt) REVERT: B 196 HIS cc_start: 0.8713 (m90) cc_final: 0.8073 (m90) REVERT: C 238 ILE cc_start: 0.8347 (OUTLIER) cc_final: 0.7902 (tp) REVERT: C 354 VAL cc_start: 0.8660 (t) cc_final: 0.8428 (p) REVERT: D 99 ASP cc_start: 0.8239 (m-30) cc_final: 0.7025 (m-30) REVERT: E 161 LEU cc_start: 0.9333 (OUTLIER) cc_final: 0.8960 (mp) REVERT: E 186 GLN cc_start: 0.7556 (OUTLIER) cc_final: 0.7044 (tm-30) REVERT: E 334 ASP cc_start: 0.8382 (t70) cc_final: 0.8020 (t70) REVERT: G 324 TYR cc_start: 0.8863 (m-10) cc_final: 0.8401 (m-80) REVERT: H 206 LYS cc_start: 0.7631 (mmtt) cc_final: 0.7352 (mmtt) REVERT: I 22 VAL cc_start: 0.8824 (m) cc_final: 0.8565 (p) REVERT: J 28 THR cc_start: 0.9108 (p) cc_final: 0.8459 (t) REVERT: J 32 ARG cc_start: 0.8610 (ptp90) cc_final: 0.8218 (ptp90) outliers start: 74 outliers final: 65 residues processed: 345 average time/residue: 0.1454 time to fit residues: 80.6132 Evaluate side-chains 346 residues out of total 2331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 278 time to evaluate : 0.844 ------------------------------------------------------------------------------- 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 143 SER Chi-restraints excluded: chain B residue 198 GLU 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 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 106 ASP Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 299 ILE Chi-restraints excluded: chain D residue 334 ASP Chi-restraints excluded: chain D residue 350 ILE Chi-restraints excluded: chain E residue 106 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 230 LEU Chi-restraints excluded: chain E residue 279 ILE Chi-restraints excluded: chain E residue 299 ILE Chi-restraints excluded: chain F residue 35 ARG 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 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 G residue 40 SER Chi-restraints excluded: chain G residue 72 ILE Chi-restraints excluded: chain G residue 91 GLN 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 78 THR 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 191 optimal weight: 6.9990 chunk 138 optimal weight: 3.9990 chunk 278 optimal weight: 9.9990 chunk 108 optimal weight: 7.9990 chunk 20 optimal weight: 6.9990 chunk 109 optimal weight: 2.9990 chunk 129 optimal weight: 7.9990 chunk 215 optimal weight: 5.9990 chunk 272 optimal weight: 50.0000 chunk 65 optimal weight: 0.0980 chunk 43 optimal weight: 7.9990 overall best weight: 4.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 172 ASN B 256 ASN ** E 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.121638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.094907 restraints weight = 41106.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.093765 restraints weight = 38901.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.095159 restraints weight = 32093.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.095483 restraints weight = 23204.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.095655 restraints weight = 21960.552| |-----------------------------------------------------------------------------| r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.7651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 22262 Z= 0.221 Angle : 0.716 10.939 30673 Z= 0.341 Chirality : 0.051 0.505 3596 Planarity : 0.004 0.050 3843 Dihedral : 10.950 147.400 3792 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 4.47 % Allowed : 20.30 % Favored : 75.22 % 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 are not related in a simple way. whole: -0.57 (0.15), residues: 2838 helix: 1.60 (0.18), residues: 850 sheet: -0.96 (0.23), residues: 449 loop : -1.38 (0.14), residues: 1539 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 169 TYR 0.024 0.002 TYR I 57 PHE 0.019 0.002 PHE F 166 TRP 0.015 0.001 TRP J 54 HIS 0.009 0.001 HIS B 42 Details of bonding type rmsd/Z covalent geometry : bond 0.00493 / 0.22 (22262) covalent geometry : angle 0.71599 / 0.34 (30673) hydrogen bonds : bond 0.03353 / 2.41 ( 904) hydrogen bonds : angle 4.81268 / 3.61 ( 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 365 residues out of total 2331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 285 time to evaluate : 0.774 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 187 TYR cc_start: 0.7644 (m-10) cc_final: 0.7370 (m-10) REVERT: A 237 ASN cc_start: 0.8405 (m-40) cc_final: 0.7924 (m-40) REVERT: A 262 ASN cc_start: 0.7935 (p0) cc_final: 0.7626 (p0) REVERT: B 78 THR cc_start: 0.7795 (m) cc_final: 0.7419 (p) REVERT: B 196 HIS cc_start: 0.8700 (m90) cc_final: 0.8080 (m90) REVERT: C 238 ILE cc_start: 0.8322 (OUTLIER) cc_final: 0.7697 (tt) REVERT: C 354 VAL cc_start: 0.8664 (t) cc_final: 0.8433 (p) REVERT: E 161 LEU cc_start: 0.9327 (OUTLIER) cc_final: 0.8977 (mp) REVERT: E 186 GLN cc_start: 0.7645 (OUTLIER) cc_final: 0.7102 (tm-30) REVERT: E 334 ASP cc_start: 0.8415 (t70) cc_final: 0.8054 (t70) REVERT: G 324 TYR cc_start: 0.8876 (m-10) cc_final: 0.8411 (m-80) REVERT: H 206 LYS cc_start: 0.7906 (mmtt) cc_final: 0.7659 (mmtt) REVERT: I 22 VAL cc_start: 0.8824 (m) cc_final: 0.8572 (p) REVERT: J 32 ARG cc_start: 0.8621 (ptp90) cc_final: 0.8310 (mtm110) REVERT: J 48 GLU cc_start: 0.7197 (tp30) cc_final: 0.6974 (tp30) outliers start: 80 outliers final: 71 residues processed: 341 average time/residue: 0.1396 time to fit residues: 76.3971 Evaluate side-chains 344 residues out of total 2331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 270 time to evaluate : 0.746 ------------------------------------------------------------------------------- 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 121 HIS 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 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 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 106 ASP Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 299 ILE Chi-restraints excluded: chain D residue 334 ASP Chi-restraints excluded: chain D residue 350 ILE Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain E residue 106 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 202 LEU 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 35 ARG 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 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 G residue 40 SER Chi-restraints excluded: chain G residue 72 ILE Chi-restraints excluded: chain G residue 91 GLN 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 78 THR Chi-restraints excluded: chain H residue 92 SER Chi-restraints excluded: chain H residue 105 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 285 optimal weight: 10.0000 chunk 218 optimal weight: 1.9990 chunk 235 optimal weight: 8.9990 chunk 227 optimal weight: 0.9990 chunk 129 optimal weight: 8.9990 chunk 179 optimal weight: 2.9990 chunk 175 optimal weight: 1.9990 chunk 191 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 7 optimal weight: 5.9990 chunk 73 optimal weight: 6.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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** ** F 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.124036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.097548 restraints weight = 40660.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.095935 restraints weight = 28926.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.096908 restraints weight = 26049.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.097291 restraints weight = 21829.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.097385 restraints weight = 20099.367| |-----------------------------------------------------------------------------| r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.7620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 22262 Z= 0.134 Angle : 0.656 11.185 30673 Z= 0.309 Chirality : 0.048 0.391 3596 Planarity : 0.004 0.051 3843 Dihedral : 10.710 144.845 3792 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 3.47 % Allowed : 21.42 % Favored : 75.11 % 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 are not related in a simple way. whole: -0.42 (0.15), residues: 2838 helix: 1.73 (0.18), residues: 849 sheet: -0.83 (0.23), residues: 447 loop : -1.31 (0.15), residues: 1542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 185 TYR 0.023 0.002 TYR I 57 PHE 0.016 0.002 PHE E 166 TRP 0.014 0.001 TRP J 54 HIS 0.004 0.001 HIS C 159 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 (22262) covalent geometry : angle 0.65567 / 0.31 (30673) hydrogen bonds : bond 0.03007 / 2.15 ( 904) hydrogen bonds : angle 4.63268 / 3.47 ( 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 367 residues out of total 2331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 305 time to evaluate : 0.963 Fit side-chains revert: symmetry clash REVERT: A 187 TYR cc_start: 0.7817 (m-10) cc_final: 0.7249 (m-10) REVERT: A 237 ASN cc_start: 0.8291 (m-40) cc_final: 0.7814 (m-40) REVERT: A 262 ASN cc_start: 0.7777 (p0) cc_final: 0.7395 (p0) REVERT: B 78 THR cc_start: 0.7604 (m) cc_final: 0.7237 (p) REVERT: B 192 LEU cc_start: 0.8881 (mt) cc_final: 0.8673 (mt) REVERT: B 196 HIS cc_start: 0.8861 (m90) cc_final: 0.8164 (m90) REVERT: C 238 ILE cc_start: 0.8356 (OUTLIER) cc_final: 0.7832 (tt) REVERT: C 354 VAL cc_start: 0.8663 (t) cc_final: 0.8412 (p) REVERT: E 161 LEU cc_start: 0.9306 (OUTLIER) cc_final: 0.8938 (mp) REVERT: E 186 GLN cc_start: 0.7448 (OUTLIER) cc_final: 0.6948 (tm-30) REVERT: E 334 ASP cc_start: 0.8327 (t70) cc_final: 0.7894 (t0) REVERT: G 324 TYR cc_start: 0.8810 (m-10) cc_final: 0.8386 (m-80) REVERT: H 206 LYS cc_start: 0.7881 (mmtt) cc_final: 0.7635 (mmtt) REVERT: H 343 HIS cc_start: 0.7563 (m170) cc_final: 0.7201 (m90) REVERT: I 22 VAL cc_start: 0.8793 (m) cc_final: 0.8534 (p) REVERT: J 32 ARG cc_start: 0.8623 (ptp90) cc_final: 0.8373 (mtm110) outliers start: 62 outliers final: 51 residues processed: 345 average time/residue: 0.1453 time to fit residues: 79.3753 Evaluate side-chains 342 residues out of total 2331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 288 time to evaluate : 0.791 ------------------------------------------------------------------------------- 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 198 GLU Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 251 ILE 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 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 106 ASP Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 299 ILE Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain E residue 106 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 202 LEU Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain E residue 299 ILE Chi-restraints excluded: chain F residue 35 ARG 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 G residue 91 GLN 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 92 SER Chi-restraints excluded: chain H residue 202 LEU Chi-restraints excluded: chain H residue 240 ASP Chi-restraints excluded: chain H residue 247 SER 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 12 ASN 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: 4.9990 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: 5.9990 chunk 30 optimal weight: 10.0000 chunk 65 optimal weight: 6.9990 chunk 15 optimal weight: 7.9990 chunk 90 optimal weight: 0.9980 overall best weight: 5.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.119648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.091772 restraints weight = 41503.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.091238 restraints weight = 34128.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.092575 restraints weight = 26604.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.092898 restraints weight = 20196.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.093017 restraints weight = 18852.703| |-----------------------------------------------------------------------------| r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.7966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 22262 Z= 0.286 Angle : 0.794 14.647 30673 Z= 0.377 Chirality : 0.054 0.492 3596 Planarity : 0.005 0.051 3843 Dihedral : 11.173 149.029 3792 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 12.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 3.69 % Allowed : 21.81 % 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 are not related in a simple way. whole: -0.67 (0.15), residues: 2838 helix: 1.44 (0.18), residues: 851 sheet: -0.94 (0.24), residues: 442 loop : -1.43 (0.14), residues: 1545 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG H 185 TYR 0.031 0.002 TYR I 57 PHE 0.023 0.002 PHE G 33 TRP 0.019 0.002 TRP F 49 HIS 0.006 0.001 HIS B 42 Details of bonding type rmsd/Z covalent geometry : bond 0.00639 / 0.29 (22262) covalent geometry : angle 0.79430 / 0.38 (30673) hydrogen bonds : bond 0.03718 / 2.67 ( 904) hydrogen bonds : angle 4.96233 / 3.72 ( 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 337 residues out of total 2331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 271 time to evaluate : 0.558 Fit side-chains revert: symmetry clash REVERT: A 207 ARG cc_start: 0.7891 (tmm-80) cc_final: 0.7437 (ptm-80) REVERT: A 237 ASN cc_start: 0.8494 (m-40) cc_final: 0.7967 (m-40) REVERT: A 262 ASN cc_start: 0.7920 (p0) cc_final: 0.7662 (p0) REVERT: B 196 HIS cc_start: 0.8629 (m90) cc_final: 0.8053 (m90) REVERT: C 238 ILE cc_start: 0.8420 (OUTLIER) cc_final: 0.7888 (tt) REVERT: E 161 LEU cc_start: 0.9374 (OUTLIER) cc_final: 0.9019 (mp) REVERT: E 186 GLN cc_start: 0.7677 (OUTLIER) cc_final: 0.7100 (tm-30) REVERT: E 334 ASP cc_start: 0.8430 (t70) cc_final: 0.8026 (t70) REVERT: I 22 VAL cc_start: 0.8870 (m) cc_final: 0.8632 (p) REVERT: J 32 ARG cc_start: 0.8602 (ptp90) cc_final: 0.8241 (ptp-110) outliers start: 66 outliers final: 58 residues processed: 320 average time/residue: 0.1387 time to fit residues: 71.7218 Evaluate side-chains 331 residues out of total 2331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 270 time to evaluate : 0.886 ------------------------------------------------------------------------------- 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 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 198 GLU Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 251 ILE 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 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 106 ASP Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 245 PHE Chi-restraints excluded: chain D residue 299 ILE Chi-restraints excluded: chain D residue 350 ILE Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 106 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 202 LEU Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain E residue 299 ILE Chi-restraints excluded: chain F residue 35 ARG Chi-restraints excluded: chain F residue 161 LEU 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 G residue 91 GLN 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 105 SER Chi-restraints excluded: chain H residue 202 LEU 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 225 optimal weight: 4.9990 chunk 261 optimal weight: 30.0000 chunk 84 optimal weight: 3.9990 chunk 29 optimal weight: 10.0000 chunk 82 optimal weight: 3.9990 chunk 139 optimal weight: 7.9990 chunk 124 optimal weight: 4.9990 chunk 191 optimal weight: 4.9990 chunk 281 optimal weight: 9.9990 chunk 209 optimal weight: 0.9990 chunk 164 optimal weight: 0.8980 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.122260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.094067 restraints weight = 41049.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.093853 restraints weight = 30584.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.095020 restraints weight = 24653.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.095396 restraints weight = 18771.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.095557 restraints weight = 17629.486| |-----------------------------------------------------------------------------| r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.7949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 22262 Z= 0.180 Angle : 0.709 14.797 30673 Z= 0.334 Chirality : 0.050 0.397 3596 Planarity : 0.004 0.071 3843 Dihedral : 10.891 147.005 3792 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 3.47 % Allowed : 21.87 % Favored : 74.66 % 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 are not related in a simple way. whole: -0.54 (0.15), residues: 2838 helix: 1.61 (0.18), residues: 844 sheet: -0.93 (0.23), residues: 452 loop : -1.34 (0.15), residues: 1542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 128 TYR 0.029 0.002 TYR I 57 PHE 0.019 0.002 PHE G 33 TRP 0.011 0.001 TRP J 54 HIS 0.008 0.001 HIS G 227 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.18 (22262) covalent geometry : angle 0.70858 / 0.33 (30673) hydrogen bonds : bond 0.03218 / 2.30 ( 904) hydrogen bonds : angle 4.78891 / 3.59 ( 2481) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3313.44 seconds wall clock time: 58 minutes 30.13 seconds (3510.13 seconds total)