Starting phenix.real_space_refine on Thu Aug 8 02:31:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w1x_21516/08_2024/6w1x_21516.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w1x_21516/08_2024/6w1x_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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w1x_21516/08_2024/6w1x_21516.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w1x_21516/08_2024/6w1x_21516.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w1x_21516/08_2024/6w1x_21516.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w1x_21516/08_2024/6w1x_21516.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.005 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 Residue "A PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 243": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 321": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 314": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 314": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/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, 'TYR:plan': 1, 'ASN:plan1': 11, 'TRP:plan': 5, 'ASP:plan': 12, 'PHE:plan': 6, 'GLU:plan': 20, 'ARG:plan': 24} 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: {'GLN:plan1': 2, 'ASN:plan1': 5, 'TRP:plan': 2, 'ASP:plan': 8, 'PHE:plan': 2, 'GLU:plan': 10, 'ARG:plan': 14} 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, 'GLU:plan': 7, 'ARG:plan': 6, 'ASN:plan1': 1, 'ASP:plan': 10} 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, 'ARG:plan': 1, 'ASP:plan': 3} 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: {'TYR:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 4} 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: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 6} 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: {'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 4} 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: {'GLU:plan': 1, 'HIS:plan': 1, 'ARG:plan': 4, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 44 Chain: "M" Number of atoms: 1272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 1272 Classifications: {'RNA': 60} Modifications used: {'5*END': 1, 'rna2p_pur': 7, 'rna2p_pyr': 11, 'rna3p_pur': 22, 'rna3p_pyr': 19} Link IDs: {'rna2p': 17, 'rna3p': 42} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "L" Number of atoms: 920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 920 Classifications: {'peptide': 187} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 159} Link IDs: {'PTRANS': 15, 'TRANS': 171} Unresolved chain link angles: 15 Unresolved non-hydrogen bonds: 631 Unresolved non-hydrogen angles: 805 Unresolved non-hydrogen dihedrals: 531 Unresolved non-hydrogen chiralities: 47 Planarities with less than four sites: {'GLN:plan1': 9, 'ASP:plan': 12, 'TYR:plan': 3, 'ASN:plan1': 1, 'TRP:plan': 2, 'HIS:plan': 8, 'PHE:plan': 10, 'GLU:plan': 11, 'ARG:plan': 24} 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: 11.41, per 1000 atoms: 0.52 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 8.21 Conformation dependent library (CDL) restraints added in 3.8 seconds 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: 7.10 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: 7.12 Time building geometry restraints manager: 8.84 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: 98.82 - 105.95: 805 105.95 - 113.08: 12147 113.08 - 120.20: 9235 120.20 - 127.33: 8186 127.33 - 134.46: 300 Bond angle restraints: 30673 Sorted by residual: angle pdb=" C4' G M 15 " pdb=" C3' G M 15 " pdb=" O3' G M 15 " ideal model delta sigma weight residual 113.00 122.15 -9.15 1.50e+00 4.44e-01 3.72e+01 angle pdb=" C3' A M 12 " pdb=" C2' A M 12 " pdb=" O2' A M 12 " ideal model delta sigma weight residual 110.70 118.30 -7.60 1.50e+00 4.44e-01 2.57e+01 angle pdb=" C4' C M 13 " pdb=" C3' C M 13 " pdb=" O3' C M 13 " ideal model delta sigma weight residual 109.40 116.40 -7.00 1.50e+00 4.44e-01 2.18e+01 angle pdb=" C4' U M 35 " pdb=" C3' U M 35 " pdb=" O3' U M 35 " ideal model delta sigma weight residual 113.00 119.77 -6.77 1.50e+00 4.44e-01 2.04e+01 angle pdb=" O3' C M 11 " pdb=" C3' C M 11 " pdb=" C2' C M 11 " ideal model delta sigma weight residual 113.70 107.07 6.63 1.50e+00 4.44e-01 1.96e+01 ... (remaining 30668 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.88: 13037 30.88 - 61.75: 202 61.75 - 92.63: 61 92.63 - 123.50: 5 123.50 - 154.38: 1 Dihedral angle restraints: 13306 sinusoidal: 5044 harmonic: 8262 Sorted by residual: dihedral pdb=" O4' U M 27 " pdb=" C1' U M 27 " pdb=" N1 U M 27 " pdb=" C2 U M 27 " ideal model delta sinusoidal sigma weight residual 200.00 80.50 119.50 1 1.50e+01 4.44e-03 6.37e+01 dihedral pdb=" O4' U M 35 " pdb=" C1' U M 35 " pdb=" N1 U M 35 " pdb=" C2 U M 35 " ideal model delta sinusoidal sigma weight residual -160.00 -63.30 -96.70 1 1.50e+01 4.44e-03 4.76e+01 dihedral pdb=" O4' C M 29 " pdb=" C1' C M 29 " pdb=" N1 C M 29 " pdb=" C2 C M 29 " ideal model delta sinusoidal sigma weight residual -160.00 -63.51 -96.49 1 1.50e+01 4.44e-03 4.75e+01 ... (remaining 13303 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.095: 2808 0.095 - 0.190: 692 0.190 - 0.285: 68 0.285 - 0.380: 19 0.380 - 0.475: 9 Chirality restraints: 3596 Sorted by residual: chirality pdb=" C2' A M 8 " pdb=" C3' A M 8 " pdb=" O2' A M 8 " pdb=" C1' A M 8 " both_signs ideal model delta sigma weight residual False -2.52 -2.04 -0.47 2.00e-01 2.50e+01 5.64e+00 chirality pdb=" C2' G M 60 " pdb=" C3' G M 60 " pdb=" O2' G M 60 " pdb=" C1' G M 60 " both_signs ideal model delta sigma weight residual False -2.52 -2.05 -0.47 2.00e-01 2.50e+01 5.49e+00 chirality pdb=" C2' C M 44 " pdb=" C3' C M 44 " pdb=" O2' C M 44 " pdb=" C1' C M 44 " both_signs ideal model delta sigma weight residual False -2.52 -2.07 -0.45 2.00e-01 2.50e+01 5.09e+00 ... (remaining 3593 not shown) Planarity restraints: 3843 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' C M 13 " -0.046 2.00e-02 2.50e+03 2.49e-02 1.39e+01 pdb=" N1 C M 13 " 0.046 2.00e-02 2.50e+03 pdb=" C2 C M 13 " -0.003 2.00e-02 2.50e+03 pdb=" O2 C M 13 " 0.002 2.00e-02 2.50e+03 pdb=" N3 C M 13 " 0.016 2.00e-02 2.50e+03 pdb=" C4 C M 13 " -0.000 2.00e-02 2.50e+03 pdb=" N4 C M 13 " -0.030 2.00e-02 2.50e+03 pdb=" C5 C M 13 " 0.011 2.00e-02 2.50e+03 pdb=" C6 C M 13 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU J 27 " 0.012 2.00e-02 2.50e+03 2.46e-02 6.04e+00 pdb=" C LEU J 27 " -0.043 2.00e-02 2.50e+03 pdb=" O LEU J 27 " 0.016 2.00e-02 2.50e+03 pdb=" N THR J 28 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY E 356 " -0.012 2.00e-02 2.50e+03 2.35e-02 5.51e+00 pdb=" C GLY E 356 " 0.041 2.00e-02 2.50e+03 pdb=" O GLY E 356 " -0.015 2.00e-02 2.50e+03 pdb=" N GLU E 357 " -0.014 2.00e-02 2.50e+03 ... (remaining 3840 not shown) Histogram of nonbonded interaction distances: 1.88 - 2.48: 113 2.48 - 3.09: 16263 3.09 - 3.69: 31440 3.69 - 4.30: 43851 4.30 - 4.90: 74897 Nonbonded interactions: 166564 Sorted by model distance: nonbonded pdb=" OG SER B 25 " pdb=" OG1 THR B 28 " model vdw 1.879 3.040 nonbonded pdb=" OG1 THR I 24 " pdb=" OG SER I 29 " model vdw 1.976 3.040 nonbonded pdb=" OH TYR A 179 " pdb=" OD2 ASP B 272 " model vdw 2.070 3.040 nonbonded pdb=" O2' G M 18 " pdb=" O4' G M 19 " model vdw 2.071 3.040 nonbonded pdb=" O2' G M 30 " pdb=" O4' C M 31 " model vdw 2.077 3.040 ... (remaining 166559 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'C' and (resid 25 through 33 or (resid 34 and (name N or name CA or name \ C or name O or name CB )) or resid 35 through 190 or (resid 191 through 192 and \ (name N or name CA or name C or name O or name CB )) or resid 193 through 226 or \ (resid 227 and (name N or name CA or name C or name O or name CB )) or resid 22 \ 8 through 285 or (resid 286 and (name N or name CA or name C or name O or name C \ B )) or resid 287 through 295 or (resid 296 and (name N or name CA or name C or \ name O or name CB )) or resid 297 through 303 or (resid 304 and (name N or name \ CA or name C or name O or name CB )) or resid 305 through 356 or (resid 357 and \ (name N or name CA or name C or name O or name CB )))) selection = (chain 'D' and (resid 25 through 50 or (resid 51 through 57 and (name N or name \ CA or name C or name O or name CB )) or resid 58 through 63 or (resid 64 and (na \ me N or name CA or name C or name O or name CB )) or resid 65 through 66 or resi \ d 98 through 104 or (resid 105 through 107 and (name N or name CA or name C or n \ ame O or name CB )) or resid 108 through 145 or (resid 146 through 147 and (name \ N or name CA or name C or name O or name CB )) or resid 148 through 151 or (res \ id 152 and (name N or name CA or name C or name O or name CB )) or resid 153 thr \ ough 168 or (resid 169 and (name N or name CA or name C or name O or name CB )) \ or resid 170 through 174 or (resid 175 through 176 and (name N or name CA or nam \ e C or name O or name CB )) or resid 177 through 184 or (resid 185 through 186 a \ nd (name N or name CA or name C or name O or name CB )) or resid 187 or (resid 1 \ 88 and (name N or name CA or name C or name O or name CB )) or resid 189 through \ 190 or (resid 191 through 192 and (name N or name CA or name C or name O or nam \ e CB )) or resid 193 through 195 or (resid 196 through 199 and (name N or name C \ A or name C or name O or name CB )) or resid 200 through 201 or (resid 202 throu \ gh 204 and (name N or name CA or name C or name O or name CB )) or resid 205 or \ (resid 206 through 207 and (name N or name CA or name C or name O or name CB )) \ or resid 208 through 209 or (resid 210 and (name N or name CA or name C or name \ O or name CB )) or resid 211 through 226 or (resid 227 and (name N or name CA or \ name C or name O or name CB )) or resid 228 through 239 or (resid 240 and (name \ N or name CA or name C or name O or name CB )) or resid 241 through 249 or (res \ id 250 and (name N or name CA or name C or name O or name CB )) or resid 263 thr \ ough 268 or (resid 269 through 273 and (name N or name CA or name C or name O or \ name CB )) or resid 274 through 303 or (resid 304 and (name N or name CA or nam \ e C or name O or name CB )) or resid 305 through 311 or (resid 312 through 313 a \ nd (name N or name CA or name C or name O or name CB )) or resid 314 through 317 \ or (resid 318 and (name N or name CA or name C or name O or name CB )) or resid \ 319 or (resid 320 through 322 and (name N or name CA or name C or name O or nam \ e CB )) or resid 323 through 339 or (resid 340 and (name N or name CA or name C \ or name O or name CB )) or resid 341 through 356 or (resid 357 and (name N or na \ me CA or name C or name O or name CB )))) selection = (chain 'E' and (resid 25 through 33 or (resid 34 and (name N or name CA or name \ C or name O or name CB )) or resid 35 through 50 or (resid 51 through 57 and (na \ me N or name CA or name C or name O or name CB )) or resid 58 through 63 or (res \ id 64 and (name N or name CA or name C or name O or name CB )) or resid 65 throu \ gh 66 or resid 98 through 104 or (resid 105 through 107 and (name N or name CA o \ r name C or name O or name CB )) or resid 108 through 145 or (resid 146 through \ 147 and (name N or name CA or name C or name O or name CB )) or resid 148 throug \ h 151 or (resid 152 and (name N or name CA or name C or name O or name CB )) or \ resid 153 through 168 or (resid 169 and (name N or name CA or name C or name O o \ r name CB )) or resid 170 through 174 or (resid 175 through 176 and (name N or n \ ame CA or name C or name O or name CB )) or resid 177 through 184 or (resid 185 \ through 186 and (name N or name CA or name C or name O or name CB )) or resid 18 \ 7 or (resid 188 and (name N or name CA or name C or name O or name CB )) or resi \ d 189 through 190 or (resid 191 through 192 and (name N or name CA or name C or \ name O or name CB )) or resid 193 through 195 or (resid 196 through 199 and (nam \ e N or name CA or name C or name O or name CB )) or resid 200 through 201 or (re \ sid 202 through 204 and (name N or name CA or name C or name O or name CB )) or \ resid 205 or (resid 206 through 207 and (name N or name CA or name C or name O o \ r name CB )) or resid 208 through 209 or (resid 210 and (name N or name CA or na \ me C or name O or name CB )) or resid 211 through 226 or (resid 227 and (name N \ or name CA or name C or name O or name CB )) or resid 228 through 239 or (resid \ 240 and (name N or name CA or name C or name O or name CB )) or resid 241 throug \ h 249 or (resid 250 and (name N or name CA or name C or name O or name CB )) or \ resid 263 through 268 or (resid 269 through 273 and (name N or name CA or name C \ or name O or name CB )) or resid 274 through 311 or (resid 312 through 313 and \ (name N or name CA or name C or name O or name CB )) or resid 314 through 317 or \ (resid 318 and (name N or name CA or name C or name O or name CB )) or resid 31 \ 9 or (resid 320 through 322 and (name N or name CA or name C or name O or name C \ B )) or resid 323 through 339 or (resid 340 and (name N or name CA or name C or \ name O or name CB )) or resid 341 through 357)) selection = (chain 'F' and (resid 25 through 33 or (resid 34 and (name N or name CA or name \ C or name O or name CB )) or resid 35 through 50 or (resid 51 through 57 and (na \ me N or name CA or name C or name O or name CB )) or resid 58 through 63 or (res \ id 64 and (name N or name CA or name C or name O or name CB )) or resid 65 throu \ gh 66 or resid 98 through 104 or (resid 105 through 107 and (name N or name CA o \ r name C or name O or name CB )) or resid 108 through 145 or (resid 146 through \ 147 and (name N or name CA or name C or name O or name CB )) or resid 148 throug \ h 151 or (resid 152 and (name N or name CA or name C or name O or name CB )) or \ resid 153 through 168 or (resid 169 and (name N or name CA or name C or name O o \ r name CB )) or resid 170 through 174 or (resid 175 through 176 and (name N or n \ ame CA or name C or name O or name CB )) or resid 177 through 184 or (resid 185 \ through 186 and (name N or name CA or name C or name O or name CB )) or resid 18 \ 7 or (resid 188 and (name N or name CA or name C or name O or name CB )) or resi \ d 189 through 190 or (resid 191 through 192 and (name N or name CA or name C or \ name O or name CB )) or resid 193 through 195 or (resid 196 through 199 and (nam \ e N or name CA or name C or name O or name CB )) or resid 200 through 201 or (re \ sid 202 through 204 and (name N or name CA or name C or name O or name CB )) or \ resid 205 or (resid 206 through 207 and (name N or name CA or name C or name O o \ r name CB )) or resid 208 through 209 or (resid 210 and (name N or name CA or na \ me C or name O or name CB )) or resid 211 through 226 or (resid 227 and (name N \ or name CA or name C or name O or name CB )) or resid 228 through 239 or (resid \ 240 and (name N or name CA or name C or name O or name CB )) or resid 241 throug \ h 249 or (resid 250 and (name N or name CA or name C or name O or name CB )) or \ resid 263 through 268 or (resid 269 through 273 and (name N or name CA or name C \ or name O or name CB )) or resid 274 through 295 or (resid 296 and (name N or n \ ame CA or name C or name O or name CB )) or resid 297 through 303 or (resid 304 \ and (name N or name CA or name C or name O or name CB )) or resid 305 through 31 \ 1 or (resid 312 through 313 and (name N or name CA or name C or name O or name C \ B )) or resid 314 through 317 or (resid 318 and (name N or name CA or name C or \ name O or name CB )) or resid 319 or (resid 320 through 322 and (name N or name \ CA or name C or name O or name CB )) or resid 323 through 339 or (resid 340 and \ (name N or name CA or name C or name O or name CB )) or resid 341 through 356 or \ (resid 357 and (name N or name CA or name C or name O or name CB )))) selection = (chain 'G' and (resid 25 through 33 or (resid 34 and (name N or name CA or name \ C or name O or name CB )) or resid 35 through 50 or (resid 51 through 57 and (na \ me N or name CA or name C or name O or name CB )) or resid 58 through 63 or (res \ id 64 and (name N or name CA or name C or name O or name CB )) or resid 65 throu \ gh 66 or resid 98 through 104 or (resid 105 through 107 and (name N or name CA o \ r name C or name O or name CB )) or resid 108 through 145 or (resid 146 through \ 147 and (name N or name CA or name C or name O or name CB )) or resid 148 throug \ h 151 or (resid 152 and (name N or name CA or name C or name O or name CB )) or \ resid 153 through 168 or (resid 169 and (name N or name CA or name C or name O o \ r name CB )) or resid 170 through 174 or (resid 175 through 176 and (name N or n \ ame CA or name C or name O or name CB )) or resid 177 through 184 or (resid 185 \ through 186 and (name N or name CA or name C or name O or name CB )) or resid 18 \ 7 through 190 or (resid 191 through 192 and (name N or name CA or name C or name \ O or name CB )) or resid 193 through 195 or (resid 196 through 199 and (name N \ or name CA or name C or name O or name CB )) or resid 200 through 201 or (resid \ 202 through 204 and (name N or name CA or name C or name O or name CB )) or resi \ d 205 or (resid 206 through 207 and (name N or name CA or name C or name O or na \ me CB )) or resid 208 through 209 or (resid 210 and (name N or name CA or name C \ or name O or name CB )) or resid 211 through 226 or (resid 227 and (name N or n \ ame CA or name C or name O or name CB )) or resid 228 through 239 or (resid 240 \ and (name N or name CA or name C or name O or name CB )) or resid 241 through 24 \ 9 or (resid 250 and (name N or name CA or name C or name O or name CB )) or resi \ d 263 through 268 or (resid 269 through 273 and (name N or name CA or name C or \ name O or name CB )) or resid 274 through 285 or (resid 286 and (name N or name \ CA or name C or name O or name CB )) or resid 287 through 295 or (resid 296 and \ (name N or name CA or name C or name O or name CB )) or resid 297 through 303 or \ (resid 304 and (name N or name CA or name C or name O or name CB )) or resid 30 \ 5 through 311 or (resid 312 through 313 and (name N or name CA or name C or name \ O or name CB )) or resid 314 through 317 or (resid 318 and (name N or name CA o \ r name C or name O or name CB )) or resid 319 or (resid 320 through 322 and (nam \ e N or name CA or name C or name O or name CB )) or resid 323 through 339 or (re \ sid 340 and (name N or name CA or name C or name O or name CB )) or resid 341 th \ rough 356 or (resid 357 and (name N or name CA or name C or name O or name CB )) \ )) selection = (chain 'H' and (resid 25 through 33 or (resid 34 and (name N or name CA or name \ C or name O or name CB )) or resid 35 through 50 or (resid 51 through 57 and (na \ me N or name CA or name C or name O or name CB )) or resid 58 through 63 or (res \ id 64 and (name N or name CA or name C or name O or name CB )) or resid 65 throu \ gh 66 or resid 98 through 104 or (resid 105 through 107 and (name N or name CA o \ r name C or name O or name CB )) or resid 108 through 145 or (resid 146 through \ 147 and (name N or name CA or name C or name O or name CB )) or resid 148 throug \ h 151 or (resid 152 and (name N or name CA or name C or name O or name CB )) or \ resid 153 through 168 or (resid 169 and (name N or name CA or name C or name O o \ r name CB )) or resid 170 through 174 or (resid 175 through 176 and (name N or n \ ame CA or name C or name O or name CB )) or resid 177 through 184 or (resid 185 \ through 186 and (name N or name CA or name C or name O or name CB )) or resid 18 \ 7 or (resid 188 and (name N or name CA or name C or name O or name CB )) or resi \ d 189 through 195 or (resid 196 through 199 and (name N or name CA or name C or \ name O or name CB )) or resid 200 through 201 or (resid 202 through 204 and (nam \ e N or name CA or name C or name O or name CB )) or resid 205 or (resid 206 thro \ ugh 207 and (name N or name CA or name C or name O or name CB )) or resid 208 th \ rough 209 or (resid 210 and (name N or name CA or name C or name O or name CB )) \ or resid 211 through 239 or (resid 240 and (name N or name CA or name C or name \ O or name CB )) or resid 241 through 249 or (resid 250 and (name N or name CA o \ r name C or name O or name CB )) or resid 263 through 268 or (resid 269 through \ 273 and (name N or name CA or name C or name O or name CB )) or resid 274 throug \ h 303 or (resid 304 and (name N or name CA or name C or name O or name CB )) or \ resid 305 through 311 or (resid 312 through 313 and (name N or name CA or name C \ or name O or name CB )) or resid 314 through 317 or (resid 318 and (name N or n \ ame CA or name C or name O or name CB )) or resid 319 through 320 or (resid 321 \ through 322 and (name N or name CA or name C or name O or name CB )) or resid 32 \ 3 through 339 or (resid 340 and (name N or name CA or name C or name O or name C \ B )) or resid 341 through 356 or (resid 357 and (name N or name CA or name C or \ name O or name CB )))) } ncs_group { reference = (chain 'I' and (resid 3 through 17 or (resid 18 and (name N or name CA or name C \ or name O or name CB )) or resid 19 through 36 or (resid 37 and (name N or name \ CA or name C or name O or name CB )) or resid 38 through 52 or (resid 53 and (n \ ame N or name CA or name C or name O or name CB )) or resid 54 through 58 or (re \ sid 59 through 60 and (name N or name CA or name C or name O or name CB )) or re \ sid 61 through 66)) selection = (chain 'J' and (resid 3 through 31 or (resid 32 and (name N or name CA or name C \ or name O or name CB )) or resid 33 through 47 or (resid 48 and (name N or name \ CA or name C or name O or name CB )) or resid 49 through 66)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.760 Check model and map are aligned: 0.140 Set scattering table: 0.170 Process input model: 60.360 Find NCS groups from input model: 1.160 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7084 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.061 22262 Z= 0.755 Angle : 0.989 9.148 30673 Z= 0.742 Chirality : 0.084 0.475 3596 Planarity : 0.006 0.027 3843 Dihedral : 11.587 154.380 7964 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 4.63 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.016 0.003 TRP G 168 HIS 0.014 0.002 HIS B 196 PHE 0.018 0.003 PHE B 284 TYR 0.022 0.004 TYR G 324 ARG 0.022 0.001 ARG D 113 *********************** 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 fitting. rotamer outliers: 1 poor density : 841 time to evaluate : 2.258 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: 0.8936 (p) REVERT: A 201 HIS cc_start: 0.7824 (t70) cc_final: 0.7442 (t70) REVERT: A 208 GLU cc_start: 0.6078 (tp30) cc_final: 0.5735 (tp30) REVERT: A 241 GLN cc_start: 0.7370 (tt0) cc_final: 0.6506 (pm20) REVERT: B 10 LEU cc_start: 0.8129 (tp) cc_final: 0.7875 (tp) REVERT: B 63 CYS cc_start: 0.7410 (t) cc_final: 0.6623 (p) REVERT: B 106 GLU cc_start: 0.7818 (tt0) cc_final: 0.7504 (tt0) REVERT: B 130 VAL cc_start: 0.8793 (t) cc_final: 0.8590 (p) REVERT: B 195 GLN cc_start: 0.8600 (tt0) cc_final: 0.8297 (tt0) REVERT: B 196 HIS cc_start: 0.8076 (m90) cc_final: 0.7724 (m-70) REVERT: C 231 GLU cc_start: 0.7873 (tt0) cc_final: 0.7627 (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: 0.7438 (tm-30) REVERT: D 324 TYR cc_start: 0.6736 (m-10) cc_final: 0.6302 (m-10) REVERT: E 44 MET cc_start: 0.8708 (mtm) cc_final: 0.8316 (mtt) REVERT: E 99 ASP cc_start: 0.8309 (m-30) cc_final: 0.7909 (m-30) REVERT: E 210 GLU cc_start: 0.6843 (mm-30) cc_final: 0.6550 (mm-30) REVERT: F 99 ASP cc_start: 0.7317 (m-30) cc_final: 0.6817 (m-30) REVERT: G 109 THR cc_start: 0.8177 (m) cc_final: 0.7967 (p) REVERT: G 135 ASP cc_start: 0.7601 (m-30) cc_final: 0.7289 (m-30) REVERT: H 264 THR cc_start: 0.8014 (p) cc_final: 0.7684 (p) 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: 0.7591 (t) REVERT: J 32 ARG cc_start: 0.8509 (ptp90) cc_final: 0.8087 (ptp90) outliers start: 1 outliers final: 0 residues processed: 841 average time/residue: 0.3894 time to fit residues: 474.1026 Evaluate side-chains 420 residues out of total 2331 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 420 time to evaluate : 2.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 243 optimal weight: 0.9980 chunk 218 optimal weight: 0.9990 chunk 121 optimal weight: 2.9990 chunk 74 optimal weight: 9.9990 chunk 147 optimal weight: 0.8980 chunk 116 optimal weight: 4.9990 chunk 225 optimal weight: 9.9990 chunk 87 optimal weight: 5.9990 chunk 137 optimal weight: 0.8980 chunk 168 optimal weight: 4.9990 chunk 261 optimal weight: 0.0000 overall best weight: 0.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 121 HIS B 129 GLN B 256 ASN C 242 GLN ** D 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 74 ASN ** F 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 348 ASN ** G 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 148 GLN G 281 ASN G 310 GLN H 102 ASN H 329 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7443 moved from start: 0.3618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 22262 Z= 0.178 Angle : 0.591 12.309 30673 Z= 0.299 Chirality : 0.041 0.247 3596 Planarity : 0.004 0.048 3843 Dihedral : 13.555 124.280 4022 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 3.80 % Allowed : 15.44 % Favored : 80.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.15), residues: 2838 helix: 2.18 (0.18), residues: 858 sheet: -0.65 (0.21), residues: 466 loop : -1.09 (0.14), residues: 1514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP J 54 HIS 0.008 0.001 HIS G 343 PHE 0.026 0.002 PHE F 166 TYR 0.021 0.002 TYR I 57 ARG 0.010 0.001 ARG A 210 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5676 Ramachandran restraints generated. 2838 Oldfield, 0 Emsley, 2838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5676 Ramachandran restraints generated. 2838 Oldfield, 0 Emsley, 2838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 557 residues out of total 2331 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 489 time to evaluate : 2.300 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: A 208 GLU cc_start: 0.6293 (tp30) cc_final: 0.5963 (tp30) REVERT: A 241 GLN cc_start: 0.7522 (tt0) cc_final: 0.6603 (pm20) REVERT: A 266 PRO cc_start: 0.7817 (Cg_endo) cc_final: 0.7609 (Cg_exo) REVERT: B 67 GLU cc_start: 0.7776 (pm20) cc_final: 0.7569 (pm20) REVERT: B 129 GLN cc_start: 0.7642 (mm110) cc_final: 0.6857 (tm-30) REVERT: B 131 GLN cc_start: 0.7714 (tt0) cc_final: 0.7383 (tt0) REVERT: B 194 GLN cc_start: 0.7872 (mm110) cc_final: 0.7178 (mm-40) REVERT: B 196 HIS cc_start: 0.8272 (m90) cc_final: 0.7624 (m-70) REVERT: B 302 LEU cc_start: 0.8887 (mt) cc_final: 0.8681 (mt) REVERT: C 161 LEU cc_start: 0.9287 (mp) cc_final: 0.9079 (mp) REVERT: C 334 ASP cc_start: 0.8019 (t0) cc_final: 0.7793 (t0) REVERT: E 161 LEU cc_start: 0.8863 (OUTLIER) cc_final: 0.8582 (mp) REVERT: E 334 ASP cc_start: 0.7448 (t70) cc_final: 0.7212 (t0) REVERT: F 238 ILE cc_start: 0.9438 (mm) cc_final: 0.9020 (tt) REVERT: G 178 GLU cc_start: 0.7828 (tm-30) cc_final: 0.7455 (tm-30) REVERT: G 240 ASP cc_start: 0.7335 (t0) cc_final: 0.7012 (t0) REVERT: H 243 GLU cc_start: 0.6425 (OUTLIER) cc_final: 0.6162 (tt0) REVERT: H 249 GLU cc_start: 0.7635 (pt0) cc_final: 0.7231 (pt0) REVERT: H 302 GLU cc_start: 0.6755 (mm-30) cc_final: 0.6317 (mm-30) REVERT: I 9 GLU cc_start: 0.7545 (mt-10) cc_final: 0.6770 (mm-30) REVERT: I 60 ASP cc_start: 0.6769 (t0) cc_final: 0.6547 (t0) REVERT: J 32 ARG cc_start: 0.8359 (ptp90) cc_final: 0.7816 (ptp90) REVERT: J 63 ARG cc_start: 0.7994 (ttm-80) cc_final: 0.7583 (mtp85) outliers start: 68 outliers final: 37 residues processed: 526 average time/residue: 0.3499 time to fit residues: 277.7893 Evaluate side-chains 409 residues out of total 2331 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 370 time to evaluate : 2.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 SER Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 263 TRP Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 256 ASN Chi-restraints excluded: chain B residue 314 TYR Chi-restraints excluded: chain B residue 316 TRP Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 270 ASP Chi-restraints excluded: chain D residue 334 ASP Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain E residue 243 GLU Chi-restraints excluded: chain E residue 247 SER Chi-restraints excluded: chain E residue 279 ILE Chi-restraints excluded: chain E residue 299 ILE Chi-restraints excluded: chain F residue 189 VAL Chi-restraints excluded: chain F residue 264 THR Chi-restraints excluded: chain F residue 299 ILE Chi-restraints excluded: chain G residue 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 55 SER 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 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 145 optimal weight: 6.9990 chunk 81 optimal weight: 0.0670 chunk 217 optimal weight: 0.0470 chunk 178 optimal weight: 7.9990 chunk 72 optimal weight: 0.7980 chunk 262 optimal weight: 50.0000 chunk 283 optimal weight: 9.9990 chunk 233 optimal weight: 6.9990 chunk 259 optimal weight: 0.7980 chunk 89 optimal weight: 10.0000 chunk 210 optimal weight: 5.9990 overall best weight: 1.5418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 86 ASN ** B 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 256 ASN E 91 GLN E 96 GLN E 186 GLN ** F 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 183 HIS G 242 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.4554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 22262 Z= 0.189 Angle : 0.555 11.904 30673 Z= 0.281 Chirality : 0.040 0.206 3596 Planarity : 0.004 0.038 3843 Dihedral : 13.539 111.568 4022 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 3.75 % Allowed : 16.11 % Favored : 80.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.15), residues: 2838 helix: 2.24 (0.18), residues: 856 sheet: -0.53 (0.21), residues: 482 loop : -0.98 (0.15), residues: 1500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP E 193 HIS 0.013 0.001 HIS G 343 PHE 0.018 0.002 PHE F 166 TYR 0.022 0.001 TYR I 57 ARG 0.006 0.001 ARG H 185 *********************** 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 466 residues out of total 2331 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 399 time to evaluate : 2.545 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 200 HIS cc_start: 0.7884 (t-90) cc_final: 0.7495 (m-70) REVERT: A 208 GLU cc_start: 0.6415 (tp30) cc_final: 0.6160 (tp30) REVERT: A 232 PHE cc_start: 0.7498 (p90) cc_final: 0.7227 (p90) REVERT: A 241 GLN cc_start: 0.7762 (tt0) cc_final: 0.6845 (pm20) REVERT: B 106 GLU cc_start: 0.7939 (tt0) cc_final: 0.7719 (tt0) REVERT: B 196 HIS cc_start: 0.8553 (m90) cc_final: 0.7819 (m-70) REVERT: C 161 LEU cc_start: 0.9220 (OUTLIER) cc_final: 0.9014 (mp) REVERT: C 334 ASP cc_start: 0.8023 (t0) cc_final: 0.7747 (t0) REVERT: D 99 ASP cc_start: 0.8513 (m-30) cc_final: 0.8274 (m-30) REVERT: E 25 LEU cc_start: 0.8603 (tp) cc_final: 0.8177 (tt) REVERT: E 99 ASP cc_start: 0.8300 (m-30) cc_final: 0.8058 (m-30) REVERT: E 161 LEU cc_start: 0.9152 (OUTLIER) cc_final: 0.8748 (mp) REVERT: E 278 LYS cc_start: 0.8986 (tppt) cc_final: 0.8777 (tppp) REVERT: E 334 ASP cc_start: 0.7551 (t70) cc_final: 0.7154 (t0) REVERT: F 238 ILE cc_start: 0.9473 (mm) cc_final: 0.9130 (tt) REVERT: F 290 TYR cc_start: 0.5534 (m-10) cc_final: 0.5280 (m-10) REVERT: G 240 ASP cc_start: 0.7539 (t0) cc_final: 0.7312 (t0) REVERT: H 302 GLU cc_start: 0.6750 (mm-30) cc_final: 0.6532 (mm-30) REVERT: J 32 ARG cc_start: 0.8301 (ptp90) cc_final: 0.8047 (ptp90) outliers start: 67 outliers final: 37 residues processed: 438 average time/residue: 0.3306 time to fit residues: 224.5747 Evaluate side-chains 386 residues out of total 2331 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 347 time to evaluate : 2.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 SER Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 263 TRP Chi-restraints excluded: chain B residue 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 306 HIS Chi-restraints excluded: chain B residue 314 TYR Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain C residue 290 TYR Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 334 ASP Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain E residue 186 GLN Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain E residue 243 GLU Chi-restraints excluded: chain F residue 89 SER Chi-restraints excluded: chain F residue 189 VAL Chi-restraints excluded: chain F residue 227 HIS Chi-restraints excluded: chain F residue 264 THR Chi-restraints excluded: chain F residue 279 ILE Chi-restraints excluded: chain F residue 308 THR Chi-restraints excluded: chain G residue 217 LEU Chi-restraints excluded: chain G residue 250 LEU 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 76 LEU Chi-restraints excluded: chain H residue 202 LEU Chi-restraints excluded: chain I residue 10 VAL Chi-restraints excluded: chain I residue 22 VAL Chi-restraints excluded: chain I residue 27 LEU Chi-restraints excluded: chain I residue 44 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 258 optimal weight: 40.0000 chunk 196 optimal weight: 10.0000 chunk 135 optimal weight: 9.9990 chunk 29 optimal weight: 50.0000 chunk 125 optimal weight: 10.0000 chunk 175 optimal weight: 6.9990 chunk 262 optimal weight: 50.0000 chunk 278 optimal weight: 3.9990 chunk 137 optimal weight: 6.9990 chunk 249 optimal weight: 10.0000 chunk 75 optimal weight: 5.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS ** A 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 86 ASN B 172 ASN ** B 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 282 ASN C 139 GLN D 74 ASN D 160 ASN D 242 GLN ** D 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 186 GLN E 242 GLN ** F 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 148 GLN F 281 ASN ** G 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 319 GLN ** H 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.6837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.097 22262 Z= 0.540 Angle : 0.798 11.748 30673 Z= 0.419 Chirality : 0.048 0.263 3596 Planarity : 0.006 0.061 3843 Dihedral : 13.942 120.075 4022 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.40 % Favored : 95.56 % Rotamer: Outliers : 5.03 % Allowed : 16.44 % Favored : 78.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.15), residues: 2838 helix: 1.38 (0.17), residues: 847 sheet: -1.00 (0.22), residues: 454 loop : -1.36 (0.14), residues: 1537 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP F 49 HIS 0.011 0.002 HIS G 275 PHE 0.028 0.003 PHE F 166 TYR 0.024 0.002 TYR F 290 ARG 0.018 0.001 ARG D 169 *********************** 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 429 residues out of total 2331 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 339 time to evaluate : 2.285 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 GLU cc_start: 0.6394 (tp30) cc_final: 0.6129 (tp30) REVERT: B 67 GLU cc_start: 0.8103 (pm20) cc_final: 0.7804 (pm20) REVERT: B 196 HIS cc_start: 0.8607 (m90) cc_final: 0.8165 (m90) REVERT: B 198 GLU cc_start: 0.8056 (mp0) cc_final: 0.7775 (mp0) REVERT: B 258 LEU cc_start: 0.8272 (tt) cc_final: 0.8043 (tt) REVERT: C 216 GLU cc_start: 0.8122 (tm-30) cc_final: 0.7869 (tm-30) REVERT: C 334 ASP cc_start: 0.8528 (t0) cc_final: 0.8320 (t0) REVERT: D 38 ASP cc_start: 0.8015 (t0) cc_final: 0.7684 (p0) REVERT: E 109 THR cc_start: 0.9108 (OUTLIER) cc_final: 0.8897 (m) REVERT: E 161 LEU cc_start: 0.9416 (OUTLIER) cc_final: 0.9046 (mp) REVERT: E 186 GLN cc_start: 0.7354 (OUTLIER) cc_final: 0.6926 (tm-30) REVERT: E 278 LYS cc_start: 0.9156 (tppt) cc_final: 0.8736 (tppp) REVERT: E 334 ASP cc_start: 0.8469 (t70) cc_final: 0.8195 (t70) REVERT: G 276 SER cc_start: 0.9095 (OUTLIER) cc_final: 0.8613 (t) REVERT: G 354 VAL cc_start: 0.9236 (t) cc_final: 0.9017 (p) REVERT: H 245 PHE cc_start: 0.8851 (m-80) cc_final: 0.8542 (m-80) REVERT: H 355 PHE cc_start: 0.8269 (m-10) cc_final: 0.7874 (m-80) REVERT: J 32 ARG cc_start: 0.8381 (ptp90) cc_final: 0.8105 (ptp90) outliers start: 90 outliers final: 61 residues processed: 400 average time/residue: 0.3266 time to fit residues: 201.3586 Evaluate side-chains 353 residues out of total 2331 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 288 time to evaluate : 2.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 SER Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 263 TRP Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 145 LEU 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 43 LEU Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 200 ILE Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain C residue 304 TYR Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 350 ILE Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain D residue 334 ASP Chi-restraints excluded: chain E residue 40 SER Chi-restraints excluded: chain E residue 109 THR Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain E residue 186 GLN Chi-restraints excluded: chain E residue 189 VAL Chi-restraints excluded: chain E residue 196 ASP Chi-restraints excluded: chain E residue 227 HIS Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain E residue 312 LYS Chi-restraints excluded: chain F residue 91 GLN Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 189 VAL Chi-restraints excluded: chain F residue 214 LEU 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 65 GLU 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 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 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 25 THR Chi-restraints excluded: chain I residue 27 LEU Chi-restraints excluded: chain I residue 44 VAL Chi-restraints excluded: chain I residue 49 SER 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 231 optimal weight: 10.0000 chunk 158 optimal weight: 0.9990 chunk 4 optimal weight: 0.0770 chunk 207 optimal weight: 5.9990 chunk 114 optimal weight: 0.9990 chunk 237 optimal weight: 9.9990 chunk 192 optimal weight: 9.9990 chunk 0 optimal weight: 50.0000 chunk 142 optimal weight: 3.9990 chunk 249 optimal weight: 6.9990 chunk 70 optimal weight: 4.9990 overall best weight: 2.2146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 256 ASN B 282 ASN B 305 HIS D 160 ASN ** D 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 94 ASN ** 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 146 ASN G 227 HIS ** H 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 348 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.6811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 22262 Z= 0.217 Angle : 0.582 9.852 30673 Z= 0.301 Chirality : 0.041 0.194 3596 Planarity : 0.004 0.045 3843 Dihedral : 13.627 118.755 4022 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 3.36 % Allowed : 19.57 % Favored : 77.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.15), residues: 2838 helix: 1.82 (0.18), residues: 843 sheet: -0.88 (0.22), residues: 456 loop : -1.21 (0.14), residues: 1539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP H 168 HIS 0.005 0.001 HIS G 159 PHE 0.018 0.002 PHE E 166 TYR 0.025 0.002 TYR I 57 ARG 0.010 0.001 ARG E 194 *********************** 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 404 residues out of total 2331 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 344 time to evaluate : 2.303 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 243 PHE cc_start: 0.7884 (m-80) cc_final: 0.7392 (m-80) REVERT: B 196 HIS cc_start: 0.8596 (m90) cc_final: 0.8340 (m90) REVERT: B 198 GLU cc_start: 0.7872 (mp0) cc_final: 0.7634 (mp0) REVERT: B 258 LEU cc_start: 0.8199 (tt) cc_final: 0.7962 (tt) REVERT: C 38 ASP cc_start: 0.8794 (t0) cc_final: 0.8299 (t0) REVERT: C 216 GLU cc_start: 0.8081 (tm-30) cc_final: 0.7767 (tm-30) REVERT: C 238 ILE cc_start: 0.8579 (OUTLIER) cc_final: 0.8318 (tt) REVERT: E 74 ASN cc_start: 0.8200 (p0) cc_final: 0.7867 (p0) REVERT: E 161 LEU cc_start: 0.9256 (OUTLIER) cc_final: 0.8907 (mp) REVERT: E 186 GLN cc_start: 0.7434 (mm-40) cc_final: 0.6879 (tm-30) REVERT: E 334 ASP cc_start: 0.8392 (t70) cc_final: 0.8065 (t70) REVERT: G 320 LYS cc_start: 0.8027 (mmtt) cc_final: 0.7688 (mmmm) REVERT: G 324 TYR cc_start: 0.8737 (m-10) cc_final: 0.8461 (m-10) outliers start: 60 outliers final: 39 residues processed: 379 average time/residue: 0.3105 time to fit residues: 186.6857 Evaluate side-chains 340 residues out of total 2331 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 299 time to evaluate : 2.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 SER Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 263 TRP Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 145 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 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 189 VAL Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain E residue 189 VAL Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain F residue 189 VAL Chi-restraints excluded: chain F residue 227 HIS Chi-restraints excluded: chain F residue 264 THR Chi-restraints excluded: chain F residue 279 ILE Chi-restraints excluded: chain F residue 299 ILE Chi-restraints excluded: chain F residue 308 THR Chi-restraints excluded: chain F residue 354 VAL Chi-restraints excluded: chain G residue 40 SER 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 202 LEU Chi-restraints excluded: chain H residue 327 LEU Chi-restraints excluded: chain I residue 10 VAL Chi-restraints excluded: chain I residue 44 VAL Chi-restraints excluded: chain J residue 22 VAL Chi-restraints excluded: chain J residue 27 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 93 optimal weight: 8.9990 chunk 250 optimal weight: 0.9990 chunk 55 optimal weight: 9.9990 chunk 163 optimal weight: 7.9990 chunk 68 optimal weight: 3.9990 chunk 278 optimal weight: 7.9990 chunk 231 optimal weight: 5.9990 chunk 129 optimal weight: 9.9990 chunk 23 optimal weight: 20.0000 chunk 92 optimal weight: 9.9990 chunk 146 optimal weight: 0.9980 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 HIS B 172 ASN B 256 ASN B 282 ASN B 305 HIS D 342 GLN ** F 94 ASN ** 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 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.7133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 22262 Z= 0.327 Angle : 0.628 9.527 30673 Z= 0.326 Chirality : 0.042 0.208 3596 Planarity : 0.004 0.045 3843 Dihedral : 13.658 117.864 4022 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 3.64 % Allowed : 20.25 % Favored : 76.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.15), residues: 2838 helix: 1.77 (0.18), residues: 845 sheet: -0.97 (0.23), residues: 436 loop : -1.30 (0.14), residues: 1557 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP H 168 HIS 0.005 0.001 HIS D 343 PHE 0.021 0.002 PHE F 166 TYR 0.028 0.002 TYR I 57 ARG 0.013 0.001 ARG D 169 *********************** 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 374 residues out of total 2331 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 309 time to evaluate : 2.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 GLU cc_start: 0.6610 (tp30) cc_final: 0.6364 (tp30) REVERT: B 196 HIS cc_start: 0.8557 (m90) cc_final: 0.7885 (m90) REVERT: B 198 GLU cc_start: 0.7886 (mp0) cc_final: 0.7637 (mp0) REVERT: B 258 LEU cc_start: 0.8135 (OUTLIER) cc_final: 0.7934 (tt) REVERT: C 34 GLU cc_start: 0.7842 (mm-30) cc_final: 0.7614 (mm-30) REVERT: C 38 ASP cc_start: 0.8541 (t0) cc_final: 0.8237 (t0) REVERT: C 216 GLU cc_start: 0.8101 (tm-30) cc_final: 0.7699 (tm-30) REVERT: E 161 LEU cc_start: 0.9328 (OUTLIER) cc_final: 0.8927 (mp) REVERT: E 186 GLN cc_start: 0.7535 (mm-40) cc_final: 0.7067 (tm-30) REVERT: E 334 ASP cc_start: 0.8462 (t70) cc_final: 0.8111 (t70) REVERT: G 231 GLU cc_start: 0.7917 (tt0) cc_final: 0.7565 (tt0) outliers start: 65 outliers final: 50 residues processed: 348 average time/residue: 0.3395 time to fit residues: 186.5798 Evaluate side-chains 331 residues out of total 2331 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 279 time to evaluate : 2.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 185 SER Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 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 216 LEU Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 305 HIS Chi-restraints excluded: chain B residue 306 HIS Chi-restraints excluded: chain C residue 110 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 354 VAL Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain E residue 189 VAL Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain E residue 299 ILE Chi-restraints excluded: chain F residue 189 VAL Chi-restraints excluded: chain F residue 227 HIS Chi-restraints excluded: chain F residue 230 LEU Chi-restraints excluded: chain F residue 264 THR Chi-restraints excluded: chain F residue 279 ILE Chi-restraints excluded: chain F residue 299 ILE Chi-restraints excluded: chain F residue 308 THR Chi-restraints excluded: chain F residue 354 VAL Chi-restraints excluded: chain G residue 40 SER Chi-restraints excluded: chain G residue 72 ILE Chi-restraints excluded: chain G residue 276 SER Chi-restraints excluded: chain G residue 299 ILE Chi-restraints excluded: chain G residue 349 LEU Chi-restraints excluded: chain H residue 34 GLU Chi-restraints excluded: chain H residue 92 SER Chi-restraints excluded: chain H residue 202 LEU Chi-restraints excluded: chain H residue 240 ASP Chi-restraints excluded: chain H residue 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 Chi-restraints excluded: chain J residue 44 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 268 optimal weight: 40.0000 chunk 31 optimal weight: 30.0000 chunk 158 optimal weight: 5.9990 chunk 203 optimal weight: 0.8980 chunk 157 optimal weight: 5.9990 chunk 234 optimal weight: 9.9990 chunk 155 optimal weight: 3.9990 chunk 277 optimal weight: 0.9980 chunk 173 optimal weight: 5.9990 chunk 169 optimal weight: 9.9990 chunk 128 optimal weight: 10.0000 overall best weight: 3.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 256 ASN B 282 ASN B 305 HIS ** E 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 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** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.7298 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: