Starting phenix.real_space_refine on Mon Sep 30 01:06:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jzx_22583/09_2024/7jzx_22583.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jzx_22583/09_2024/7jzx_22583.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jzx_22583/09_2024/7jzx_22583.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jzx_22583/09_2024/7jzx_22583.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jzx_22583/09_2024/7jzx_22583.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jzx_22583/09_2024/7jzx_22583.cif" } resolution = 3.4 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= 0.001 sd= 0.006 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 60 5.49 5 S 26 5.16 5 C 14832 2.51 5 N 4354 2.21 5 O 4676 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 119 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 23948 Number of models: 1 Model: "" Number of chains: 11 Chain: "C" Number of atoms: 1448 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 187, 1445 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 171} Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 54 Conformer: "B" Number of residues, atoms: 187, 1445 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 171} Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 54 bond proxies already assigned to first conformer: 1480 Chain: "B" Number of atoms: 2411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2411 Classifications: {'peptide': 306} Link IDs: {'PTRANS': 24, 'TRANS': 281} Chain breaks: 1 Chain: "E" Number of atoms: 2592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2592 Classifications: {'peptide': 335} Link IDs: {'PTRANS': 12, 'TRANS': 322} Chain: "D" Number of atoms: 2307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2307 Classifications: {'peptide': 298} Link IDs: {'PTRANS': 10, 'TRANS': 287} Chain breaks: 2 Chain: "F" Number of atoms: 2592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2592 Classifications: {'peptide': 335} Link IDs: {'PTRANS': 12, 'TRANS': 322} Chain: "G" Number of atoms: 2592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2592 Classifications: {'peptide': 335} Link IDs: {'PTRANS': 12, 'TRANS': 322} Chain: "H" Number of atoms: 2554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2554 Classifications: {'peptide': 330} Link IDs: {'PTRANS': 12, 'TRANS': 317} Chain breaks: 1 Chain: "I" Number of atoms: 2592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2592 Classifications: {'peptide': 335} Link IDs: {'PTRANS': 12, 'TRANS': 322} Chain: "A" Number of atoms: 3079 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3079 Classifications: {'peptide': 427} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 96} Link IDs: {'PTRANS': 24, 'TRANS': 402} Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 366 Unresolved non-hydrogen angles: 470 Unresolved non-hydrogen dihedrals: 306 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'GLN:plan1': 9, 'ASP:plan': 11, 'TYR:plan': 1, 'ASN:plan1': 3, 'TRP:plan': 3, 'HIS:plan': 5, 'PHE:plan': 2, 'GLU:plan': 9, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 240 Chain: "M" Number of atoms: 1273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 1273 Classifications: {'DNA': 1, 'RNA': 60} Modifications used: {'5*END': 1, 'rna2p_pur': 11, 'rna2p_pyr': 17, 'rna3p_pur': 17, 'rna3p_pyr': 14} Link IDs: {'rna2p': 28, 'rna3p': 32} Unresolved chain link angles: 2 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {' C:plan': 1, ' C:plan2': 1} Unresolved non-hydrogen planarities: 11 Chain: "J" Number of atoms: 508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 508 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 2, 'TRANS': 63} Time building chain proxies: 13.75, per 1000 atoms: 0.57 Number of scatterers: 23948 At special positions: 0 Unit cell: (133.35, 157.5, 148.05, 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 26 16.00 P 60 15.00 O 4676 8.00 N 4354 7.00 C 14832 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.59 Conformation dependent library (CDL) restraints added in 2.8 seconds 5854 Ramachandran restraints generated. 2927 Oldfield, 0 Emsley, 2927 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5496 Finding SS restraints... Secondary structure from input PDB file: 79 helices and 52 sheets defined 32.6% alpha, 21.8% beta 6 base pairs and 27 stacking pairs defined. Time for finding SS restraints: 7.28 Creating SS restraints... Processing helix chain 'C' and resid 16 through 36 Processing helix chain 'C' and resid 63 through 71 Processing helix chain 'C' and resid 73 through 77 removed outlier: 3.628A pdb=" N LEU C 76 " --> pdb=" O ARG C 73 " (cutoff:3.500A) Processing helix chain 'C' and resid 108 through 121 removed outlier: 3.700A pdb=" N LEU C 112 " --> pdb=" O ASN C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 131 Processing helix chain 'C' and resid 132 through 136 removed outlier: 3.583A pdb=" N VAL C 135 " --> pdb=" O PRO C 132 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ALA C 136 " --> pdb=" O ASP C 133 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 132 through 136' Processing helix chain 'B' and resid 33 through 48 removed outlier: 4.011A pdb=" N PHE B 37 " --> pdb=" O SER B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 135 Processing helix chain 'B' and resid 165 through 178 Processing helix chain 'B' and resid 189 through 204 removed outlier: 3.866A pdb=" N LEU B 193 " --> pdb=" O ARG B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 218 Processing helix chain 'B' and resid 291 through 295 removed outlier: 3.938A pdb=" N VAL B 295 " --> pdb=" O PRO B 292 " (cutoff:3.500A) Processing helix chain 'E' and resid 51 through 55 removed outlier: 3.608A pdb=" N SER E 55 " --> pdb=" O ARG E 52 " (cutoff:3.500A) Processing helix chain 'E' and resid 82 through 92 removed outlier: 3.705A pdb=" N SER E 92 " --> pdb=" O ALA E 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 130 through 148 Processing helix chain 'E' and resid 151 through 163 Processing helix chain 'E' and resid 209 through 223 Processing helix chain 'E' and resid 275 through 284 removed outlier: 3.568A pdb=" N ILE E 279 " --> pdb=" O HIS E 275 " (cutoff:3.500A) Processing helix chain 'E' and resid 293 through 297 removed outlier: 3.855A pdb=" N LEU E 296 " --> pdb=" O GLU E 293 " (cutoff:3.500A) Processing helix chain 'E' and resid 322 through 331 Processing helix chain 'E' and resid 338 through 352 Processing helix chain 'D' and resid 130 through 148 Processing helix chain 'D' and resid 152 through 163 Processing helix chain 'D' and resid 208 through 223 removed outlier: 3.605A pdb=" N ASP D 212 " --> pdb=" O ASP D 208 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ALA D 213 " --> pdb=" O ALA D 209 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 284 Processing helix chain 'D' and resid 322 through 331 Processing helix chain 'D' and resid 338 through 352 Processing helix chain 'F' and resid 51 through 55 Processing helix chain 'F' and resid 82 through 92 removed outlier: 3.671A pdb=" N SER F 92 " --> pdb=" O ALA F 88 " (cutoff:3.500A) Processing helix chain 'F' and resid 130 through 148 Processing helix chain 'F' and resid 151 through 163 Processing helix chain 'F' and resid 209 through 223 Processing helix chain 'F' and resid 275 through 284 Processing helix chain 'F' and resid 322 through 332 Processing helix chain 'F' and resid 338 through 352 Processing helix chain 'G' and resid 51 through 55 Processing helix chain 'G' and resid 82 through 92 removed outlier: 3.648A pdb=" N SER G 92 " --> pdb=" O ALA G 88 " (cutoff:3.500A) Processing helix chain 'G' and resid 130 through 148 Processing helix chain 'G' and resid 151 through 163 Processing helix chain 'G' and resid 208 through 223 Processing helix chain 'G' and resid 275 through 284 Processing helix chain 'G' and resid 322 through 332 removed outlier: 3.599A pdb=" N LEU G 326 " --> pdb=" O ASP G 322 " (cutoff:3.500A) Processing helix chain 'G' and resid 338 through 352 Processing helix chain 'H' and resid 82 through 92 Processing helix chain 'H' and resid 130 through 148 Processing helix chain 'H' and resid 151 through 163 Processing helix chain 'H' and resid 208 through 223 Processing helix chain 'H' and resid 275 through 284 Processing helix chain 'H' and resid 322 through 331 Processing helix chain 'H' and resid 338 through 352 Processing helix chain 'I' and resid 51 through 55 removed outlier: 3.531A pdb=" N SER I 55 " --> pdb=" O ARG I 52 " (cutoff:3.500A) Processing helix chain 'I' and resid 82 through 90 Processing helix chain 'I' and resid 130 through 148 Processing helix chain 'I' and resid 152 through 163 Processing helix chain 'I' and resid 208 through 224 Processing helix chain 'I' and resid 275 through 284 Processing helix chain 'I' and resid 322 through 332 Processing helix chain 'I' and resid 338 through 352 Processing helix chain 'A' and resid 9 through 31 removed outlier: 3.650A pdb=" N LEU A 13 " --> pdb=" O THR A 9 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 47 removed outlier: 4.172A pdb=" N THR A 42 " --> pdb=" O ASP A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 60 removed outlier: 3.533A pdb=" N ALA A 54 " --> pdb=" O GLU A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 122 removed outlier: 4.010A pdb=" N PHE A 118 " --> pdb=" O ALA A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 136 removed outlier: 3.753A pdb=" N GLU A 136 " --> pdb=" O ASN A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 161 Processing helix chain 'A' and resid 162 through 164 No H-bonds generated for 'chain 'A' and resid 162 through 164' Processing helix chain 'A' and resid 196 through 212 Processing helix chain 'A' and resid 212 through 224 removed outlier: 3.909A pdb=" N ALA A 218 " --> pdb=" O ALA A 214 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N SER A 223 " --> pdb=" O ARG A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 251 removed outlier: 3.582A pdb=" N ASN A 250 " --> pdb=" O LYS A 247 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ILE A 251 " --> pdb=" O PRO A 248 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 247 through 251' Processing helix chain 'A' and resid 253 through 258 removed outlier: 4.013A pdb=" N GLU A 257 " --> pdb=" O GLN A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 289 Processing helix chain 'A' and resid 294 through 306 removed outlier: 3.618A pdb=" N THR A 303 " --> pdb=" O ARG A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 344 removed outlier: 4.517A pdb=" N ALA A 317 " --> pdb=" O HIS A 313 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLU A 344 " --> pdb=" O LEU A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 349 Processing helix chain 'A' and resid 376 through 381 removed outlier: 3.967A pdb=" N GLY A 381 " --> pdb=" O ARG A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 399 removed outlier: 3.739A pdb=" N ARG A 390 " --> pdb=" O GLU A 386 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ASN A 393 " --> pdb=" O ASN A 389 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N TRP A 394 " --> pdb=" O ARG A 390 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU A 395 " --> pdb=" O PHE A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 407 Processing helix chain 'A' and resid 409 through 431 removed outlier: 4.040A pdb=" N ASP A 431 " --> pdb=" O GLU A 427 " (cutoff:3.500A) Processing helix chain 'J' and resid 44 through 52 Processing helix chain 'J' and resid 59 through 70 removed outlier: 4.306A pdb=" N GLU J 63 " --> pdb=" O ALA J 59 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLN J 70 " --> pdb=" O ALA J 66 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 41 through 43 Processing sheet with id=AA2, first strand: chain 'C' and resid 41 through 43 Processing sheet with id=AA3, first strand: chain 'C' and resid 97 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 100 through 102 Processing sheet with id=AA5, first strand: chain 'B' and resid 55 through 57 removed outlier: 5.335A pdb=" N LEU B 105 " --> pdb=" O GLN B 18 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N GLN B 18 " --> pdb=" O LEU B 105 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N VAL B 107 " --> pdb=" O SER B 16 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N SER B 16 " --> pdb=" O VAL B 107 " (cutoff:3.500A) removed outlier: 8.186A pdb=" N LEU B 109 " --> pdb=" O ARG B 14 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N ARG B 14 " --> pdb=" O LEU B 109 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N LEU B 111 " --> pdb=" O LEU B 12 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N LEU B 12 " --> pdb=" O LEU B 111 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N VAL B 113 " --> pdb=" O LEU B 10 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N LEU B 10 " --> pdb=" O VAL B 113 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N SER B 16 " --> pdb=" O LEU B 145 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 65 through 68 removed outlier: 5.335A pdb=" N LEU B 105 " --> pdb=" O GLN B 18 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N GLN B 18 " --> pdb=" O LEU B 105 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N VAL B 107 " --> pdb=" O SER B 16 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N SER B 16 " --> pdb=" O VAL B 107 " (cutoff:3.500A) removed outlier: 8.186A pdb=" N LEU B 109 " --> pdb=" O ARG B 14 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N ARG B 14 " --> pdb=" O LEU B 109 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N LEU B 111 " --> pdb=" O LEU B 12 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N LEU B 12 " --> pdb=" O LEU B 111 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N VAL B 113 " --> pdb=" O LEU B 10 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N LEU B 10 " --> pdb=" O VAL B 113 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ALA B 157 " --> pdb=" O LEU B 11 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 28 through 30 removed outlier: 5.953A pdb=" N TRP B 29 " --> pdb=" O SER A 267 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 70 through 71 Processing sheet with id=AA9, first strand: chain 'B' and resid 185 through 188 removed outlier: 7.545A pdb=" N PHE B 279 " --> pdb=" O ALA B 257 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N ALA B 257 " --> pdb=" O PHE B 279 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N GLU B 281 " --> pdb=" O TYR B 255 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N TYR B 255 " --> pdb=" O GLU B 281 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N LEU B 283 " --> pdb=" O ALA B 253 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N TRP B 247 " --> pdb=" O TRP B 289 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 185 through 188 Processing sheet with id=AB2, first strand: chain 'B' and resid 221 through 222 Processing sheet with id=AB3, first strand: chain 'B' and resid 304 through 306 Processing sheet with id=AB4, first strand: chain 'E' and resid 127 through 128 Processing sheet with id=AB5, first strand: chain 'E' and resid 38 through 39 removed outlier: 4.325A pdb=" N VAL E 228 " --> pdb=" O VAL E 118 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N LEU E 229 " --> pdb=" O ILE E 184 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 189 through 192 removed outlier: 6.790A pdb=" N HIS E 183 " --> pdb=" O ALA E 190 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N ALA E 192 " --> pdb=" O ILE E 181 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N ILE E 181 " --> pdb=" O ALA E 192 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N LEU E 229 " --> pdb=" O ILE E 184 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N VAL E 228 " --> pdb=" O VAL E 118 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 64 through 70 removed outlier: 3.579A pdb=" N ASN E 94 " --> pdb=" O GLY E 70 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 248 through 249 removed outlier: 4.399A pdb=" N THR E 264 " --> pdb=" O GLU E 249 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 285 through 287 Processing sheet with id=AC1, first strand: chain 'D' and resid 127 through 128 Processing sheet with id=AC2, first strand: chain 'D' and resid 38 through 39 removed outlier: 4.163A pdb=" N VAL D 228 " --> pdb=" O VAL D 118 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ARG D 191 " --> pdb=" O HIS D 183 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 38 through 39 Processing sheet with id=AC4, first strand: chain 'D' and resid 64 through 66 Processing sheet with id=AC5, first strand: chain 'D' and resid 248 through 249 removed outlier: 4.541A pdb=" N THR D 264 " --> pdb=" O GLU D 249 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 285 through 287 Processing sheet with id=AC7, first strand: chain 'D' and resid 306 through 307 Processing sheet with id=AC8, first strand: chain 'F' and resid 31 through 33 Processing sheet with id=AC9, first strand: chain 'F' and resid 38 through 39 removed outlier: 4.074A pdb=" N VAL F 228 " --> pdb=" O VAL F 118 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N LEU F 229 " --> pdb=" O ILE F 184 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 189 through 192 removed outlier: 6.808A pdb=" N HIS F 183 " --> pdb=" O ALA F 190 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N ALA F 192 " --> pdb=" O ILE F 181 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ILE F 181 " --> pdb=" O ALA F 192 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N LEU F 229 " --> pdb=" O ILE F 184 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N VAL F 228 " --> pdb=" O VAL F 118 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 64 through 70 removed outlier: 3.511A pdb=" N GLY F 70 " --> pdb=" O ASN F 94 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ASN F 94 " --> pdb=" O GLY F 70 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N ALA F 101 " --> pdb=" O VAL F 244 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 306 through 307 Processing sheet with id=AD4, first strand: chain 'G' and resid 127 through 128 removed outlier: 3.534A pdb=" N ALA G 127 " --> pdb=" O ALA G 32 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'G' and resid 38 through 39 removed outlier: 4.126A pdb=" N VAL G 228 " --> pdb=" O VAL G 118 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N LEU G 229 " --> pdb=" O ILE G 184 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N VAL G 177 " --> pdb=" O ASP G 196 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N ASP G 196 " --> pdb=" O VAL G 177 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N VAL G 179 " --> pdb=" O ARG G 194 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N ARG G 194 " --> pdb=" O VAL G 179 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ILE G 181 " --> pdb=" O ALA G 192 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N ALA G 192 " --> pdb=" O ILE G 181 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N HIS G 183 " --> pdb=" O ALA G 190 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'G' and resid 38 through 39 Processing sheet with id=AD7, first strand: chain 'G' and resid 64 through 70 removed outlier: 4.395A pdb=" N ALA G 101 " --> pdb=" O VAL G 244 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 306 through 307 Processing sheet with id=AD9, first strand: chain 'H' and resid 127 through 128 Processing sheet with id=AE1, first strand: chain 'H' and resid 38 through 39 removed outlier: 4.068A pdb=" N VAL H 228 " --> pdb=" O VAL H 118 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N LEU H 229 " --> pdb=" O ILE H 184 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'H' and resid 189 through 192 removed outlier: 6.712A pdb=" N HIS H 183 " --> pdb=" O ALA H 190 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N ALA H 192 " --> pdb=" O ILE H 181 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ILE H 181 " --> pdb=" O ALA H 192 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N LEU H 229 " --> pdb=" O ILE H 184 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N VAL H 228 " --> pdb=" O VAL H 118 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'H' and resid 64 through 70 removed outlier: 3.754A pdb=" N ASN H 94 " --> pdb=" O GLY H 70 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N ALA H 101 " --> pdb=" O VAL H 244 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'H' and resid 248 through 249 removed outlier: 4.662A pdb=" N THR H 264 " --> pdb=" O GLU H 249 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'H' and resid 306 through 307 removed outlier: 3.670A pdb=" N LYS H 312 " --> pdb=" O VAL H 307 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'I' and resid 127 through 128 Processing sheet with id=AE7, first strand: chain 'I' and resid 38 through 39 removed outlier: 4.429A pdb=" N LEU I 229 " --> pdb=" O ILE I 184 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ARG I 191 " --> pdb=" O HIS I 183 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'I' and resid 38 through 39 Processing sheet with id=AE9, first strand: chain 'I' and resid 63 through 70 removed outlier: 3.641A pdb=" N ASN I 94 " --> pdb=" O GLY I 70 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N ALA I 101 " --> pdb=" O VAL I 244 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'I' and resid 63 through 70 removed outlier: 3.641A pdb=" N ASN I 94 " --> pdb=" O GLY I 70 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N LYS I 261 " --> pdb=" O LEU I 95 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N THR I 97 " --> pdb=" O LYS I 261 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LYS I 263 " --> pdb=" O THR I 97 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'I' and resid 285 through 287 Processing sheet with id=AF3, first strand: chain 'I' and resid 306 through 307 removed outlier: 3.561A pdb=" N LYS I 312 " --> pdb=" O VAL I 307 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'A' and resid 63 through 65 Processing sheet with id=AF5, first strand: chain 'A' and resid 68 through 69 Processing sheet with id=AF6, first strand: chain 'A' and resid 180 through 181 Processing sheet with id=AF7, first strand: chain 'J' and resid 20 through 25 removed outlier: 4.206A pdb=" N PHE J 35 " --> pdb=" O VAL J 79 " (cutoff:3.500A) 1038 hydrogen bonds defined for protein. 2868 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 16 hydrogen bonds 28 hydrogen bond angles 0 basepair planarities 6 basepair parallelities 27 stacking parallelities Total time for adding SS restraints: 7.74 Time building geometry restraints manager: 6.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 5557 1.33 - 1.45: 5414 1.45 - 1.57: 13418 1.57 - 1.69: 120 1.69 - 1.81: 40 Bond restraints: 24549 Sorted by residual: bond pdb=" O3' A M 36 " pdb=" P C M 37 " ideal model delta sigma weight residual 1.607 1.672 -0.065 1.50e-02 4.44e+03 1.89e+01 bond pdb=" C LEU B 181 " pdb=" N PRO B 182 " ideal model delta sigma weight residual 1.337 1.379 -0.042 9.80e-03 1.04e+04 1.83e+01 bond pdb=" N ARG H 185 " pdb=" CA ARG H 185 " ideal model delta sigma weight residual 1.457 1.491 -0.034 1.29e-02 6.01e+03 6.92e+00 bond pdb=" N LEU B 301 " pdb=" CA LEU B 301 " ideal model delta sigma weight residual 1.462 1.500 -0.039 1.48e-02 4.57e+03 6.82e+00 bond pdb=" N ASP I 135 " pdb=" CA ASP I 135 " ideal model delta sigma weight residual 1.459 1.490 -0.031 1.23e-02 6.61e+03 6.28e+00 ... (remaining 24544 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.16: 32419 2.16 - 4.32: 1056 4.32 - 6.48: 116 6.48 - 8.64: 36 8.64 - 10.79: 3 Bond angle restraints: 33630 Sorted by residual: angle pdb=" C GLN A 124 " pdb=" N TYR A 125 " pdb=" CA TYR A 125 " ideal model delta sigma weight residual 120.79 128.74 -7.95 1.39e+00 5.18e-01 3.27e+01 angle pdb=" C LYS G 77 " pdb=" N THR G 78 " pdb=" CA THR G 78 " ideal model delta sigma weight residual 121.54 132.33 -10.79 1.91e+00 2.74e-01 3.19e+01 angle pdb=" C LYS E 77 " pdb=" N THR E 78 " pdb=" CA THR E 78 " ideal model delta sigma weight residual 121.54 130.74 -9.20 1.91e+00 2.74e-01 2.32e+01 angle pdb=" C ARG I 185 " pdb=" N GLN I 186 " pdb=" CA GLN I 186 " ideal model delta sigma weight residual 120.82 128.04 -7.22 1.50e+00 4.44e-01 2.32e+01 angle pdb=" C LYS H 77 " pdb=" N THR H 78 " pdb=" CA THR H 78 " ideal model delta sigma weight residual 121.54 129.95 -8.41 1.91e+00 2.74e-01 1.94e+01 ... (remaining 33625 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.96: 14349 35.96 - 71.92: 423 71.92 - 107.88: 43 107.88 - 143.84: 2 143.84 - 179.80: 5 Dihedral angle restraints: 14822 sinusoidal: 6316 harmonic: 8506 Sorted by residual: dihedral pdb=" O4' U M 33 " pdb=" C1' U M 33 " pdb=" N1 U M 33 " pdb=" C2 U M 33 " ideal model delta sinusoidal sigma weight residual 200.00 56.03 143.97 1 1.50e+01 4.44e-03 7.72e+01 dihedral pdb=" O4' U M 21 " pdb=" C1' U M 21 " pdb=" N1 U M 21 " pdb=" C2 U M 21 " ideal model delta sinusoidal sigma weight residual 200.00 70.81 129.19 1 1.50e+01 4.44e-03 6.96e+01 dihedral pdb=" O4' C M 20 " pdb=" C1' C M 20 " pdb=" N1 C M 20 " pdb=" C2 C M 20 " ideal model delta sinusoidal sigma weight residual -128.00 51.80 -179.80 1 1.70e+01 3.46e-03 6.64e+01 ... (remaining 14819 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 2631 0.048 - 0.096: 893 0.096 - 0.144: 228 0.144 - 0.192: 42 0.192 - 0.241: 4 Chirality restraints: 3798 Sorted by residual: chirality pdb=" C1' U M 33 " pdb=" O4' U M 33 " pdb=" C2' U M 33 " pdb=" N1 U M 33 " both_signs ideal model delta sigma weight residual False 2.47 2.23 0.24 2.00e-01 2.50e+01 1.45e+00 chirality pdb=" CA LEU B 181 " pdb=" N LEU B 181 " pdb=" C LEU B 181 " pdb=" CB LEU B 181 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.12e+00 chirality pdb=" CB ILE J 23 " pdb=" CA ILE J 23 " pdb=" CG1 ILE J 23 " pdb=" CG2 ILE J 23 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.20 2.00e-01 2.50e+01 1.04e+00 ... (remaining 3795 not shown) Planarity restraints: 4221 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A 71 " 0.048 5.00e-02 4.00e+02 7.24e-02 8.38e+00 pdb=" N PRO A 72 " -0.125 5.00e-02 4.00e+02 pdb=" CA PRO A 72 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO A 72 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER B 291 " -0.047 5.00e-02 4.00e+02 7.09e-02 8.04e+00 pdb=" N PRO B 292 " 0.123 5.00e-02 4.00e+02 pdb=" CA PRO B 292 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO B 292 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER B 25 " -0.045 5.00e-02 4.00e+02 6.70e-02 7.19e+00 pdb=" N PRO B 26 " 0.116 5.00e-02 4.00e+02 pdb=" CA PRO B 26 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO B 26 " -0.037 5.00e-02 4.00e+02 ... (remaining 4218 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 5107 2.77 - 3.30: 21176 3.30 - 3.84: 41098 3.84 - 4.37: 49237 4.37 - 4.90: 84009 Nonbonded interactions: 200627 Sorted by model distance: nonbonded pdb=" OH TYR G 324 " pdb=" O SER H 73 " model vdw 2.239 3.040 nonbonded pdb=" OG SER E 29 " pdb=" OD1 ASN E 129 " model vdw 2.260 3.040 nonbonded pdb=" OH TYR H 324 " pdb=" O SER I 73 " model vdw 2.266 3.040 nonbonded pdb=" O ARG I 69 " pdb=" O2' C M 13 " model vdw 2.278 3.040 nonbonded pdb=" OH TYR F 324 " pdb=" O SER G 73 " model vdw 2.285 3.040 ... (remaining 200622 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 'D' selection = (chain 'E' and (resid 24 through 68 or resid 96 through 250 or resid 261 through \ 358)) selection = (chain 'F' and (resid 24 through 68 or resid 96 through 250 or resid 261 through \ 358)) selection = (chain 'G' and (resid 24 through 68 or resid 96 through 250 or resid 261 through \ 358)) selection = (chain 'H' and (resid 24 through 68 or resid 96 through 250 or resid 261 through \ 358)) selection = (chain 'I' and (resid 24 through 68 or resid 96 through 250 or resid 261 through \ 358)) } 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=0.37 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.910 Check model and map are aligned: 0.160 Set scattering table: 0.190 Process input model: 54.050 Find NCS groups from input model: 0.840 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: 0.000 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 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 : 0.009 0.076 24549 Z= 0.572 Angle : 0.916 10.795 33630 Z= 0.514 Chirality : 0.051 0.241 3798 Planarity : 0.006 0.072 4221 Dihedral : 17.055 179.805 9326 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.01 % Favored : 92.99 % Rotamer: Outliers : 0.40 % Allowed : 7.51 % Favored : 92.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % 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: -3.94 (0.12), residues: 2927 helix: -2.81 (0.11), residues: 905 sheet: -1.73 (0.21), residues: 495 loop : -2.82 (0.13), residues: 1527 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP I 49 HIS 0.007 0.002 HIS B 42 PHE 0.022 0.003 PHE G 166 TYR 0.017 0.003 TYR E 304 ARG 0.014 0.001 ARG G 169 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5854 Ramachandran restraints generated. 2927 Oldfield, 0 Emsley, 2927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5854 Ramachandran restraints generated. 2927 Oldfield, 0 Emsley, 2927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 2385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 184 time to evaluate : 2.661 Fit side-chains REVERT: C 19 GLN cc_start: 0.7841 (tt0) cc_final: 0.7565 (mt0) REVERT: C 110 GLU cc_start: 0.7623 (mp0) cc_final: 0.7184 (pm20) REVERT: B 244 LYS cc_start: 0.8488 (mtmt) cc_final: 0.8231 (mtmm) REVERT: I 257 LYS cc_start: 0.7844 (mmmt) cc_final: 0.7637 (tptt) REVERT: A 228 TRP cc_start: 0.8689 (t-100) cc_final: 0.8469 (t-100) REVERT: A 299 ARG cc_start: 0.8001 (tmm160) cc_final: 0.7788 (tmm160) REVERT: J 44 ASP cc_start: 0.8331 (t0) cc_final: 0.8046 (t0) outliers start: 9 outliers final: 0 residues processed: 190 average time/residue: 0.4890 time to fit residues: 132.7596 Evaluate side-chains 136 residues out of total 2385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 136 time to evaluate : 2.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 249 optimal weight: 8.9990 chunk 224 optimal weight: 0.9990 chunk 124 optimal weight: 0.7980 chunk 76 optimal weight: 4.9990 chunk 151 optimal weight: 0.9980 chunk 119 optimal weight: 0.9980 chunk 232 optimal weight: 3.9990 chunk 89 optimal weight: 3.9990 chunk 141 optimal weight: 6.9990 chunk 172 optimal weight: 4.9990 chunk 268 optimal weight: 5.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 19 GLN C 84 GLN C 165 GLN B 293 HIS ** E 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 159 HIS E 348 ASN D 102 ASN D 146 ASN ** F 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 129 ASN G 51 GLN G 260 GLN ** H 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 183 HIS I 342 GLN ** A 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 335 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.1195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 24549 Z= 0.239 Angle : 0.570 12.351 33630 Z= 0.303 Chirality : 0.040 0.197 3798 Planarity : 0.004 0.060 4221 Dihedral : 15.414 178.535 4162 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 1.19 % Allowed : 10.33 % Favored : 88.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % 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: -2.41 (0.14), residues: 2927 helix: -0.68 (0.15), residues: 923 sheet: -1.07 (0.23), residues: 430 loop : -2.39 (0.14), residues: 1574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 394 HIS 0.006 0.001 HIS B 305 PHE 0.012 0.001 PHE E 166 TYR 0.017 0.002 TYR I 304 ARG 0.007 0.000 ARG C 73 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5854 Ramachandran restraints generated. 2927 Oldfield, 0 Emsley, 2927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5854 Ramachandran restraints generated. 2927 Oldfield, 0 Emsley, 2927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 2385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 156 time to evaluate : 2.398 Fit side-chains REVERT: C 19 GLN cc_start: 0.7972 (tt0) cc_final: 0.7608 (tt0) REVERT: C 35 GLN cc_start: 0.8351 (tp40) cc_final: 0.7875 (tp40) REVERT: B 137 MET cc_start: 0.8869 (mtp) cc_final: 0.8512 (mtp) REVERT: B 244 LYS cc_start: 0.8353 (mtmt) cc_final: 0.8115 (mtmm) REVERT: B 314 TYR cc_start: 0.8246 (m-80) cc_final: 0.8021 (m-80) REVERT: D 318 LYS cc_start: 0.8761 (tttm) cc_final: 0.8533 (tttp) REVERT: F 307 VAL cc_start: 0.9050 (OUTLIER) cc_final: 0.8839 (m) REVERT: I 216 GLU cc_start: 0.7477 (OUTLIER) cc_final: 0.7073 (mt-10) REVERT: I 257 LYS cc_start: 0.7846 (mmmt) cc_final: 0.7642 (tptt) REVERT: A 228 TRP cc_start: 0.8648 (t-100) cc_final: 0.8428 (t-100) REVERT: J 44 ASP cc_start: 0.8143 (t0) cc_final: 0.7698 (t0) REVERT: J 61 VAL cc_start: 0.8414 (t) cc_final: 0.8205 (t) outliers start: 27 outliers final: 11 residues processed: 177 average time/residue: 0.4150 time to fit residues: 109.5670 Evaluate side-chains 159 residues out of total 2385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 146 time to evaluate : 2.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain E residue 250 LEU Chi-restraints excluded: chain E residue 268 VAL Chi-restraints excluded: chain D residue 44 MET Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain F residue 307 VAL Chi-restraints excluded: chain G residue 147 ASP Chi-restraints excluded: chain I residue 216 GLU Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain J residue 41 GLN Chi-restraints excluded: chain J residue 58 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 149 optimal weight: 0.9980 chunk 83 optimal weight: 9.9990 chunk 223 optimal weight: 3.9990 chunk 183 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 chunk 269 optimal weight: 30.0000 chunk 290 optimal weight: 0.0770 chunk 239 optimal weight: 3.9990 chunk 267 optimal weight: 3.9990 chunk 91 optimal weight: 4.9990 chunk 216 optimal weight: 1.9990 overall best weight: 2.0144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 29 HIS ** C 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 19 ASN E 91 GLN E 129 ASN D 102 ASN D 348 ASN ** F 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 260 GLN ** H 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 74 HIS A 335 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.1479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 24549 Z= 0.283 Angle : 0.556 11.476 33630 Z= 0.292 Chirality : 0.040 0.188 3798 Planarity : 0.004 0.061 4221 Dihedral : 15.249 178.329 4162 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 1.49 % Allowed : 12.21 % Favored : 86.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % 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: -1.71 (0.15), residues: 2927 helix: 0.30 (0.17), residues: 922 sheet: -0.87 (0.23), residues: 461 loop : -2.20 (0.14), residues: 1544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 394 HIS 0.006 0.001 HIS B 42 PHE 0.012 0.001 PHE E 166 TYR 0.016 0.002 TYR H 290 ARG 0.006 0.000 ARG C 160 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5854 Ramachandran restraints generated. 2927 Oldfield, 0 Emsley, 2927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5854 Ramachandran restraints generated. 2927 Oldfield, 0 Emsley, 2927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 2385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 150 time to evaluate : 2.566 Fit side-chains REVERT: C 19 GLN cc_start: 0.7914 (tt0) cc_final: 0.7535 (mt0) REVERT: C 35 GLN cc_start: 0.8423 (tp40) cc_final: 0.7888 (tp40) REVERT: B 76 LYS cc_start: 0.8778 (mttp) cc_final: 0.8491 (mttp) REVERT: B 137 MET cc_start: 0.8968 (mtp) cc_final: 0.8654 (mtp) REVERT: D 318 LYS cc_start: 0.8742 (tttm) cc_final: 0.8537 (tttp) REVERT: F 307 VAL cc_start: 0.9061 (OUTLIER) cc_final: 0.8839 (m) REVERT: I 90 ILE cc_start: 0.8921 (pt) cc_final: 0.8638 (mt) REVERT: I 216 GLU cc_start: 0.7420 (OUTLIER) cc_final: 0.7032 (mt-10) REVERT: A 228 TRP cc_start: 0.8611 (t-100) cc_final: 0.8382 (t-100) REVERT: J 36 TYR cc_start: 0.8502 (m-80) cc_final: 0.8208 (m-80) REVERT: J 44 ASP cc_start: 0.8199 (t0) cc_final: 0.7735 (t0) outliers start: 34 outliers final: 17 residues processed: 171 average time/residue: 0.3995 time to fit residues: 104.6652 Evaluate side-chains 161 residues out of total 2385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 142 time to evaluate : 2.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain E residue 146 ASN Chi-restraints excluded: chain E residue 250 LEU Chi-restraints excluded: chain E residue 268 VAL Chi-restraints excluded: chain E residue 348 ASN Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 304 TYR Chi-restraints excluded: chain F residue 307 VAL Chi-restraints excluded: chain G residue 147 ASP Chi-restraints excluded: chain G residue 264 THR Chi-restraints excluded: chain I residue 216 GLU Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain J residue 23 ILE Chi-restraints excluded: chain J residue 41 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 266 optimal weight: 2.9990 chunk 202 optimal weight: 4.9990 chunk 139 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 128 optimal weight: 2.9990 chunk 180 optimal weight: 8.9990 chunk 270 optimal weight: 8.9990 chunk 286 optimal weight: 6.9990 chunk 141 optimal weight: 0.7980 chunk 256 optimal weight: 20.0000 chunk 77 optimal weight: 8.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 154 HIS ** C 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 69 GLN E 51 GLN ** F 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 348 ASN ** H 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 159 HIS A 74 HIS J 65 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.1665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 24549 Z= 0.297 Angle : 0.549 11.047 33630 Z= 0.287 Chirality : 0.040 0.184 3798 Planarity : 0.004 0.064 4221 Dihedral : 15.174 179.594 4162 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 1.54 % Allowed : 14.10 % Favored : 84.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % 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: -1.38 (0.15), residues: 2927 helix: 0.73 (0.17), residues: 927 sheet: -0.80 (0.23), residues: 450 loop : -2.07 (0.15), residues: 1550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 394 HIS 0.006 0.001 HIS B 293 PHE 0.013 0.001 PHE B 152 TYR 0.016 0.002 TYR H 290 ARG 0.005 0.000 ARG C 160 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5854 Ramachandran restraints generated. 2927 Oldfield, 0 Emsley, 2927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5854 Ramachandran restraints generated. 2927 Oldfield, 0 Emsley, 2927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 2385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 147 time to evaluate : 2.730 Fit side-chains REVERT: C 19 GLN cc_start: 0.7902 (tt0) cc_final: 0.7503 (mt0) REVERT: C 35 GLN cc_start: 0.8449 (tp40) cc_final: 0.7885 (tp40) REVERT: B 137 MET cc_start: 0.8991 (mtp) cc_final: 0.8694 (mtp) REVERT: D 318 LYS cc_start: 0.8740 (tttm) cc_final: 0.8527 (tttp) REVERT: F 307 VAL cc_start: 0.9075 (OUTLIER) cc_final: 0.8851 (m) REVERT: I 90 ILE cc_start: 0.8922 (pt) cc_final: 0.8634 (mt) REVERT: I 216 GLU cc_start: 0.7520 (OUTLIER) cc_final: 0.7146 (mt-10) REVERT: A 228 TRP cc_start: 0.8657 (t-100) cc_final: 0.8451 (t-100) REVERT: J 44 ASP cc_start: 0.8239 (t0) cc_final: 0.7743 (t0) outliers start: 35 outliers final: 25 residues processed: 166 average time/residue: 0.4074 time to fit residues: 103.5271 Evaluate side-chains 170 residues out of total 2385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 143 time to evaluate : 2.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain E residue 146 ASN Chi-restraints excluded: chain E residue 250 LEU Chi-restraints excluded: chain E residue 251 ILE Chi-restraints excluded: chain E residue 268 VAL Chi-restraints excluded: chain E residue 348 ASN Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 304 TYR Chi-restraints excluded: chain F residue 304 TYR Chi-restraints excluded: chain F residue 307 VAL Chi-restraints excluded: chain G residue 147 ASP Chi-restraints excluded: chain G residue 250 LEU Chi-restraints excluded: chain G residue 264 THR Chi-restraints excluded: chain I residue 216 GLU Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 177 GLN Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain J residue 22 SER Chi-restraints excluded: chain J residue 23 ILE Chi-restraints excluded: chain J residue 25 THR Chi-restraints excluded: chain J residue 41 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 238 optimal weight: 0.1980 chunk 162 optimal weight: 1.9990 chunk 4 optimal weight: 10.0000 chunk 213 optimal weight: 0.6980 chunk 118 optimal weight: 2.9990 chunk 244 optimal weight: 0.3980 chunk 197 optimal weight: 5.9990 chunk 0 optimal weight: 9.9990 chunk 146 optimal weight: 0.7980 chunk 256 optimal weight: 2.9990 chunk 72 optimal weight: 0.8980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 129 ASN D 102 ASN ** F 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 148 GLN J 65 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.2061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 24549 Z= 0.133 Angle : 0.481 8.726 33630 Z= 0.253 Chirality : 0.038 0.160 3798 Planarity : 0.003 0.060 4221 Dihedral : 14.980 178.958 4162 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 1.58 % Allowed : 14.81 % Favored : 83.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % 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: -0.90 (0.15), residues: 2927 helix: 1.28 (0.17), residues: 924 sheet: -0.60 (0.23), residues: 464 loop : -1.86 (0.15), residues: 1539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 394 HIS 0.005 0.001 HIS B 293 PHE 0.014 0.001 PHE B 152 TYR 0.014 0.001 TYR I 290 ARG 0.005 0.000 ARG C 160 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5854 Ramachandran restraints generated. 2927 Oldfield, 0 Emsley, 2927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5854 Ramachandran restraints generated. 2927 Oldfield, 0 Emsley, 2927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 2385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 162 time to evaluate : 2.675 Fit side-chains revert: symmetry clash REVERT: C 1 MET cc_start: 0.5965 (mtp) cc_final: 0.5316 (mpp) REVERT: C 19 GLN cc_start: 0.7979 (tt0) cc_final: 0.7572 (mt0) REVERT: C 35 GLN cc_start: 0.8434 (tp40) cc_final: 0.8003 (tt0) REVERT: B 76 LYS cc_start: 0.8682 (mttp) cc_final: 0.8336 (mttt) REVERT: E 324 TYR cc_start: 0.7961 (m-80) cc_final: 0.7184 (m-80) REVERT: I 251 ILE cc_start: 0.8908 (mt) cc_final: 0.8688 (mt) REVERT: J 44 ASP cc_start: 0.8263 (t0) cc_final: 0.7784 (t0) outliers start: 36 outliers final: 24 residues processed: 186 average time/residue: 0.4208 time to fit residues: 117.3324 Evaluate side-chains 169 residues out of total 2385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 145 time to evaluate : 2.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 165 GLN Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain E residue 250 LEU Chi-restraints excluded: chain E residue 304 TYR Chi-restraints excluded: chain E residue 348 ASN Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 304 TYR Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain F residue 304 TYR Chi-restraints excluded: chain G residue 264 THR Chi-restraints excluded: chain H residue 44 MET Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain J residue 22 SER Chi-restraints excluded: chain J residue 41 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 96 optimal weight: 6.9990 chunk 257 optimal weight: 10.0000 chunk 56 optimal weight: 5.9990 chunk 167 optimal weight: 5.9990 chunk 70 optimal weight: 0.5980 chunk 286 optimal weight: 7.9990 chunk 237 optimal weight: 5.9990 chunk 132 optimal weight: 4.9990 chunk 23 optimal weight: 0.9980 chunk 94 optimal weight: 7.9990 chunk 150 optimal weight: 0.9980 overall best weight: 2.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 159 HIS H 281 ASN ** I 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.1921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 24549 Z= 0.354 Angle : 0.554 10.843 33630 Z= 0.287 Chirality : 0.041 0.170 3798 Planarity : 0.004 0.066 4221 Dihedral : 15.045 179.572 4162 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 2.02 % Allowed : 15.47 % Favored : 82.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % 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: -0.93 (0.15), residues: 2927 helix: 1.25 (0.17), residues: 926 sheet: -0.49 (0.24), residues: 442 loop : -1.91 (0.15), residues: 1559 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP G 49 HIS 0.005 0.001 HIS B 305 PHE 0.016 0.001 PHE H 114 TYR 0.017 0.002 TYR H 290 ARG 0.004 0.000 ARG B 268 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5854 Ramachandran restraints generated. 2927 Oldfield, 0 Emsley, 2927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5854 Ramachandran restraints generated. 2927 Oldfield, 0 Emsley, 2927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 2385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 145 time to evaluate : 2.806 Fit side-chains REVERT: C 1 MET cc_start: 0.5955 (mtp) cc_final: 0.5303 (mpp) REVERT: C 19 GLN cc_start: 0.7932 (tt0) cc_final: 0.7517 (mt0) REVERT: C 35 GLN cc_start: 0.8466 (tp40) cc_final: 0.8213 (tt0) REVERT: B 76 LYS cc_start: 0.8818 (mttp) cc_final: 0.8451 (mttt) REVERT: B 158 GLU cc_start: 0.7518 (OUTLIER) cc_final: 0.7114 (tt0) REVERT: E 324 TYR cc_start: 0.8254 (m-80) cc_final: 0.7432 (m-80) REVERT: H 251 ILE cc_start: 0.8977 (OUTLIER) cc_final: 0.8635 (mp) REVERT: I 90 ILE cc_start: 0.8906 (pt) cc_final: 0.8583 (mt) REVERT: J 44 ASP cc_start: 0.8277 (t0) cc_final: 0.7785 (t0) outliers start: 46 outliers final: 32 residues processed: 176 average time/residue: 0.4315 time to fit residues: 115.3837 Evaluate side-chains 176 residues out of total 2385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 142 time to evaluate : 2.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 165 GLN Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 158 GLU Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 300 ASP Chi-restraints excluded: chain E residue 146 ASN Chi-restraints excluded: chain E residue 250 LEU Chi-restraints excluded: chain E residue 251 ILE Chi-restraints excluded: chain E residue 348 ASN Chi-restraints excluded: chain E residue 354 VAL Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 304 TYR Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain F residue 304 TYR Chi-restraints excluded: chain G residue 264 THR Chi-restraints excluded: chain G residue 340 GLU Chi-restraints excluded: chain H residue 44 MET Chi-restraints excluded: chain H residue 90 ILE Chi-restraints excluded: chain H residue 251 ILE Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 177 GLN Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain J residue 25 THR Chi-restraints excluded: chain J residue 37 VAL Chi-restraints excluded: chain J residue 41 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 276 optimal weight: 20.0000 chunk 32 optimal weight: 0.2980 chunk 163 optimal weight: 0.9990 chunk 209 optimal weight: 6.9990 chunk 162 optimal weight: 0.8980 chunk 241 optimal weight: 0.6980 chunk 159 optimal weight: 0.6980 chunk 285 optimal weight: 6.9990 chunk 178 optimal weight: 3.9990 chunk 173 optimal weight: 2.9990 chunk 131 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 69 GLN ** F 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.2158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 24549 Z= 0.147 Angle : 0.485 8.462 33630 Z= 0.254 Chirality : 0.038 0.160 3798 Planarity : 0.003 0.062 4221 Dihedral : 14.937 178.562 4162 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 1.85 % Allowed : 15.60 % Favored : 82.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % 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: -0.69 (0.16), residues: 2927 helix: 1.52 (0.17), residues: 925 sheet: -0.38 (0.24), residues: 451 loop : -1.81 (0.15), residues: 1551 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 263 HIS 0.005 0.001 HIS B 293 PHE 0.012 0.001 PHE B 152 TYR 0.014 0.001 TYR H 290 ARG 0.006 0.000 ARG B 268 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5854 Ramachandran restraints generated. 2927 Oldfield, 0 Emsley, 2927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5854 Ramachandran restraints generated. 2927 Oldfield, 0 Emsley, 2927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 2385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 150 time to evaluate : 2.561 Fit side-chains revert: symmetry clash REVERT: C 1 MET cc_start: 0.5744 (mtp) cc_final: 0.5261 (mpp) REVERT: C 19 GLN cc_start: 0.7914 (tt0) cc_final: 0.7498 (mt0) REVERT: C 35 GLN cc_start: 0.8343 (tp40) cc_final: 0.8141 (tt0) REVERT: B 76 LYS cc_start: 0.8783 (mttp) cc_final: 0.8435 (mttt) REVERT: B 244 LYS cc_start: 0.8572 (OUTLIER) cc_final: 0.8302 (ttmm) REVERT: E 324 TYR cc_start: 0.8067 (m-80) cc_final: 0.7272 (m-80) REVERT: I 251 ILE cc_start: 0.8938 (mt) cc_final: 0.8680 (mt) REVERT: J 44 ASP cc_start: 0.8262 (t0) cc_final: 0.7784 (t0) outliers start: 42 outliers final: 30 residues processed: 180 average time/residue: 0.4010 time to fit residues: 111.3243 Evaluate side-chains 179 residues out of total 2385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 148 time to evaluate : 2.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 165 GLN Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 244 LYS Chi-restraints excluded: chain E residue 250 LEU Chi-restraints excluded: chain E residue 348 ASN Chi-restraints excluded: chain E residue 354 VAL Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 304 TYR Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain F residue 304 TYR Chi-restraints excluded: chain G residue 264 THR Chi-restraints excluded: chain G residue 340 GLU Chi-restraints excluded: chain H residue 44 MET Chi-restraints excluded: chain H residue 90 ILE Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 177 GLN Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain J residue 22 SER Chi-restraints excluded: chain J residue 25 THR Chi-restraints excluded: chain J residue 41 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 176 optimal weight: 8.9990 chunk 113 optimal weight: 5.9990 chunk 170 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 56 optimal weight: 0.2980 chunk 55 optimal weight: 2.9990 chunk 181 optimal weight: 10.0000 chunk 194 optimal weight: 5.9990 chunk 141 optimal weight: 0.0060 chunk 26 optimal weight: 5.9990 chunk 224 optimal weight: 1.9990 overall best weight: 1.6602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 3 HIS ** C 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 102 ASN ** F 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 65 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.2127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 24549 Z= 0.241 Angle : 0.514 12.266 33630 Z= 0.267 Chirality : 0.039 0.161 3798 Planarity : 0.003 0.063 4221 Dihedral : 14.922 179.693 4162 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 1.93 % Allowed : 15.86 % Favored : 82.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % 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: -0.69 (0.16), residues: 2927 helix: 1.53 (0.17), residues: 925 sheet: -0.44 (0.24), residues: 458 loop : -1.80 (0.15), residues: 1544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 49 HIS 0.005 0.001 HIS B 42 PHE 0.012 0.001 PHE H 114 TYR 0.015 0.001 TYR H 290 ARG 0.005 0.000 ARG B 268 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5854 Ramachandran restraints generated. 2927 Oldfield, 0 Emsley, 2927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5854 Ramachandran restraints generated. 2927 Oldfield, 0 Emsley, 2927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 2385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 148 time to evaluate : 2.763 Fit side-chains REVERT: C 1 MET cc_start: 0.5715 (mtp) cc_final: 0.5270 (mpp) REVERT: C 19 GLN cc_start: 0.7928 (tt0) cc_final: 0.7501 (mt0) REVERT: C 35 GLN cc_start: 0.8350 (tp40) cc_final: 0.8140 (tt0) REVERT: B 76 LYS cc_start: 0.8798 (mttp) cc_final: 0.8425 (mttt) REVERT: B 244 LYS cc_start: 0.8583 (OUTLIER) cc_final: 0.8280 (ttmm) REVERT: E 318 LYS cc_start: 0.8211 (mmmt) cc_final: 0.7834 (mmtt) REVERT: E 324 TYR cc_start: 0.8182 (m-80) cc_final: 0.7263 (m-80) REVERT: I 90 ILE cc_start: 0.8881 (pt) cc_final: 0.8613 (mt) REVERT: J 44 ASP cc_start: 0.8261 (t0) cc_final: 0.7763 (t0) outliers start: 44 outliers final: 35 residues processed: 175 average time/residue: 0.4128 time to fit residues: 108.9308 Evaluate side-chains 184 residues out of total 2385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 148 time to evaluate : 2.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 165 GLN Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 244 LYS Chi-restraints excluded: chain B residue 300 ASP Chi-restraints excluded: chain E residue 146 ASN Chi-restraints excluded: chain E residue 250 LEU Chi-restraints excluded: chain E residue 348 ASN Chi-restraints excluded: chain E residue 354 VAL Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 304 TYR Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain F residue 304 TYR Chi-restraints excluded: chain G residue 264 THR Chi-restraints excluded: chain G residue 340 GLU Chi-restraints excluded: chain H residue 44 MET Chi-restraints excluded: chain H residue 90 ILE Chi-restraints excluded: chain I residue 44 MET Chi-restraints excluded: chain I residue 228 VAL Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 177 GLN Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain J residue 22 SER Chi-restraints excluded: chain J residue 25 THR Chi-restraints excluded: chain J residue 37 VAL Chi-restraints excluded: chain J residue 41 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 259 optimal weight: 0.3980 chunk 273 optimal weight: 5.9990 chunk 249 optimal weight: 5.9990 chunk 265 optimal weight: 4.9990 chunk 160 optimal weight: 6.9990 chunk 115 optimal weight: 10.0000 chunk 208 optimal weight: 5.9990 chunk 81 optimal weight: 9.9990 chunk 240 optimal weight: 0.9990 chunk 251 optimal weight: 0.9990 chunk 264 optimal weight: 5.9990 overall best weight: 2.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.2065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 24549 Z= 0.352 Angle : 0.565 11.955 33630 Z= 0.291 Chirality : 0.041 0.172 3798 Planarity : 0.004 0.066 4221 Dihedral : 14.976 178.582 4162 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 1.89 % Allowed : 15.82 % Favored : 82.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % 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: -0.84 (0.15), residues: 2927 helix: 1.37 (0.17), residues: 927 sheet: -0.60 (0.23), residues: 477 loop : -1.85 (0.15), residues: 1523 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP I 49 HIS 0.006 0.001 HIS B 305 PHE 0.014 0.001 PHE H 114 TYR 0.016 0.002 TYR H 290 ARG 0.008 0.000 ARG H 269 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5854 Ramachandran restraints generated. 2927 Oldfield, 0 Emsley, 2927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5854 Ramachandran restraints generated. 2927 Oldfield, 0 Emsley, 2927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 2385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 147 time to evaluate : 2.567 Fit side-chains REVERT: C 19 GLN cc_start: 0.7882 (tt0) cc_final: 0.7477 (mt0) REVERT: C 35 GLN cc_start: 0.8380 (tp40) cc_final: 0.8169 (tt0) REVERT: C 108 ASN cc_start: 0.6068 (t0) cc_final: 0.5807 (t0) REVERT: C 110 GLU cc_start: 0.7745 (mp0) cc_final: 0.7475 (mp0) REVERT: B 76 LYS cc_start: 0.8835 (mttp) cc_final: 0.8446 (mttt) REVERT: B 244 LYS cc_start: 0.8639 (OUTLIER) cc_final: 0.8346 (ttmm) REVERT: E 324 TYR cc_start: 0.8250 (m-80) cc_final: 0.7445 (m-80) REVERT: I 90 ILE cc_start: 0.8891 (pt) cc_final: 0.8568 (mt) REVERT: J 44 ASP cc_start: 0.8283 (t0) cc_final: 0.7781 (t0) outliers start: 43 outliers final: 38 residues processed: 173 average time/residue: 0.4126 time to fit residues: 107.7087 Evaluate side-chains 181 residues out of total 2385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 142 time to evaluate : 2.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 165 GLN Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 244 LYS Chi-restraints excluded: chain B residue 300 ASP Chi-restraints excluded: chain E residue 146 ASN Chi-restraints excluded: chain E residue 250 LEU Chi-restraints excluded: chain E residue 251 ILE Chi-restraints excluded: chain E residue 348 ASN Chi-restraints excluded: chain E residue 354 VAL Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 304 TYR Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain F residue 304 TYR Chi-restraints excluded: chain G residue 147 ASP Chi-restraints excluded: chain G residue 264 THR Chi-restraints excluded: chain G residue 340 GLU Chi-restraints excluded: chain H residue 44 MET Chi-restraints excluded: chain H residue 90 ILE Chi-restraints excluded: chain I residue 44 MET Chi-restraints excluded: chain I residue 228 VAL Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 177 GLN Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain J residue 21 THR Chi-restraints excluded: chain J residue 22 SER Chi-restraints excluded: chain J residue 25 THR Chi-restraints excluded: chain J residue 37 VAL Chi-restraints excluded: chain J residue 41 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 174 optimal weight: 0.9990 chunk 281 optimal weight: 30.0000 chunk 171 optimal weight: 4.9990 chunk 133 optimal weight: 9.9990 chunk 195 optimal weight: 0.7980 chunk 294 optimal weight: 0.8980 chunk 271 optimal weight: 3.9990 chunk 234 optimal weight: 0.8980 chunk 24 optimal weight: 3.9990 chunk 181 optimal weight: 5.9990 chunk 143 optimal weight: 4.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 3 HIS ** C 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 65 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.2162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 24549 Z= 0.230 Angle : 0.523 12.057 33630 Z= 0.271 Chirality : 0.039 0.168 3798 Planarity : 0.003 0.064 4221 Dihedral : 14.948 179.863 4162 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 1.58 % Allowed : 16.30 % Favored : 82.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % 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: -0.75 (0.16), residues: 2927 helix: 1.47 (0.17), residues: 925 sheet: -0.49 (0.23), residues: 470 loop : -1.82 (0.15), residues: 1532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 155 HIS 0.006 0.001 HIS B 42 PHE 0.010 0.001 PHE H 114 TYR 0.016 0.001 TYR H 290 ARG 0.006 0.000 ARG B 268 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5854 Ramachandran restraints generated. 2927 Oldfield, 0 Emsley, 2927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5854 Ramachandran restraints generated. 2927 Oldfield, 0 Emsley, 2927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 2385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 145 time to evaluate : 2.563 Fit side-chains revert: symmetry clash REVERT: C 19 GLN cc_start: 0.7877 (tt0) cc_final: 0.7462 (mt0) REVERT: C 108 ASN cc_start: 0.5979 (t0) cc_final: 0.5699 (t0) REVERT: C 110 GLU cc_start: 0.7735 (mp0) cc_final: 0.7456 (mp0) REVERT: B 76 LYS cc_start: 0.8798 (mttp) cc_final: 0.8411 (mttt) REVERT: B 244 LYS cc_start: 0.8602 (OUTLIER) cc_final: 0.8366 (ttmm) REVERT: E 324 TYR cc_start: 0.8192 (m-80) cc_final: 0.7326 (m-80) REVERT: I 90 ILE cc_start: 0.8889 (pt) cc_final: 0.8589 (mt) REVERT: J 44 ASP cc_start: 0.8287 (t0) cc_final: 0.7776 (t0) REVERT: J 63 GLU cc_start: 0.8278 (pt0) cc_final: 0.8068 (pm20) outliers start: 36 outliers final: 33 residues processed: 167 average time/residue: 0.3952 time to fit residues: 100.9551 Evaluate side-chains 178 residues out of total 2385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 144 time to evaluate : 2.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 165 GLN Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 244 LYS Chi-restraints excluded: chain E residue 250 LEU Chi-restraints excluded: chain E residue 251 ILE Chi-restraints excluded: chain E residue 348 ASN Chi-restraints excluded: chain E residue 354 VAL Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 304 TYR Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain F residue 304 TYR Chi-restraints excluded: chain G residue 264 THR Chi-restraints excluded: chain G residue 340 GLU Chi-restraints excluded: chain H residue 44 MET Chi-restraints excluded: chain H residue 90 ILE Chi-restraints excluded: chain I residue 44 MET Chi-restraints excluded: chain I residue 228 VAL Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 177 GLN Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain J residue 22 SER Chi-restraints excluded: chain J residue 37 VAL Chi-restraints excluded: chain J residue 41 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 186 optimal weight: 2.9990 chunk 250 optimal weight: 8.9990 chunk 71 optimal weight: 10.0000 chunk 216 optimal weight: 1.9990 chunk 34 optimal weight: 8.9990 chunk 65 optimal weight: 4.9990 chunk 235 optimal weight: 0.6980 chunk 98 optimal weight: 6.9990 chunk 241 optimal weight: 0.9990 chunk 29 optimal weight: 9.9990 chunk 43 optimal weight: 5.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.067683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.051549 restraints weight = 83896.028| |-----------------------------------------------------------------------------| r_work (start): 0.2837 rms_B_bonded: 2.79 r_work: 0.2706 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2706 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2708 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2708 r_free = 0.2708 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2708 r_free = 0.2708 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2708 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.2138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 24549 Z= 0.319 Angle : 0.552 11.960 33630 Z= 0.285 Chirality : 0.040 0.169 3798 Planarity : 0.004 0.066 4221 Dihedral : 14.963 178.673 4162 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.80 % Favored : 93.20 % Rotamer: Outliers : 1.71 % Allowed : 16.17 % Favored : 82.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % 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: -0.81 (0.16), residues: 2927 helix: 1.39 (0.17), residues: 927 sheet: -0.51 (0.23), residues: 470 loop : -1.85 (0.15), residues: 1530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 155 HIS 0.005 0.001 HIS B 42 PHE 0.014 0.001 PHE H 114 TYR 0.016 0.002 TYR H 290 ARG 0.007 0.000 ARG H 269 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4078.39 seconds wall clock time: 74 minutes 15.66 seconds (4455.66 seconds total)