Starting phenix.real_space_refine on Wed Mar 20 19:23:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tax_25789/03_2024/7tax_25789.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tax_25789/03_2024/7tax_25789.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tax_25789/03_2024/7tax_25789.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tax_25789/03_2024/7tax_25789.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tax_25789/03_2024/7tax_25789.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tax_25789/03_2024/7tax_25789.pdb" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.027 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 459 atoms to isotropic. 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 98 5.49 5 S 33 5.16 5 C 17215 2.51 5 N 5054 2.21 5 O 5455 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 99": "OE1" <-> "OE2" Residue "A PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 421": "OE1" <-> "OE2" Residue "B GLU 67": "OE1" <-> "OE2" Residue "B GLU 99": "OE1" <-> "OE2" Residue "B GLU 106": "OE1" <-> "OE2" Residue "B GLU 198": "OE1" <-> "OE2" Residue "B PHE 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 222": "OE1" <-> "OE2" Residue "B GLU 274": "OE1" <-> "OE2" Residue "D GLU 34": "OE1" <-> "OE2" Residue "D GLU 231": "OE1" <-> "OE2" Residue "E PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 34": "OE1" <-> "OE2" Residue "F GLU 57": "OE1" <-> "OE2" Residue "F GLU 65": "OE1" <-> "OE2" Residue "F GLU 175": "OE1" <-> "OE2" Residue "F GLU 178": "OE1" <-> "OE2" Residue "F GLU 231": "OE1" <-> "OE2" Residue "F GLU 357": "OE1" <-> "OE2" Residue "G GLU 210": "OE1" <-> "OE2" Residue "H GLU 231": "OE1" <-> "OE2" Residue "J GLU 96": "OE1" <-> "OE2" Residue "J GLU 157": "OE1" <-> "OE2" Residue "J PHE 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 54": "OE1" <-> "OE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 27855 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 3145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3145 Classifications: {'peptide': 427} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 79} Link IDs: {'PTRANS': 24, 'TRANS': 402} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 291 Unresolved non-hydrogen angles: 369 Unresolved non-hydrogen dihedrals: 235 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLN:plan1': 9, 'ASP:plan': 11, 'TYR:plan': 1, 'ASN:plan1': 3, 'TRP:plan': 1, 'HIS:plan': 3, 'PHE:plan': 1, 'GLU:plan': 9, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 196 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: "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: {'PTRANS': 15, '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: {'PTRANS': 15, '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: "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: "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: "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: 2592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2592 Classifications: {'peptide': 335} Link IDs: {'PTRANS': 12, 'TRANS': 322} 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: "J" Number of atoms: 1766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1766 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 16, 'TRANS': 211} Chain: "K" Number of atoms: 1766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1766 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 16, 'TRANS': 211} 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: "Y" Number of atoms: 390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 390 Classifications: {'DNA': 19} Link IDs: {'rna3p': 18} Chain: "X" Number of atoms: 389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 389 Classifications: {'DNA': 19} Link IDs: {'rna3p': 18} Time building chain proxies: 15.37, per 1000 atoms: 0.55 Number of scatterers: 27855 At special positions: 0 Unit cell: (130.2, 178.5, 152.25, 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 33 16.00 P 98 15.00 O 5455 8.00 N 5054 7.00 C 17215 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 10.74 Conformation dependent library (CDL) restraints added in 4.6 seconds 6644 Ramachandran restraints generated. 3322 Oldfield, 0 Emsley, 3322 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6226 Finding SS restraints... Secondary structure from input PDB file: 102 helices and 55 sheets defined 35.1% alpha, 21.0% beta 18 base pairs and 57 stacking pairs defined. Time for finding SS restraints: 9.47 Creating SS restraints... Processing helix chain 'A' and resid 9 through 33 removed outlier: 3.518A pdb=" N LEU A 13 " --> pdb=" O THR A 9 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 45 removed outlier: 3.508A pdb=" N THR A 42 " --> pdb=" O ASP A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 61 removed outlier: 3.743A pdb=" N LEU A 53 " --> pdb=" O ARG A 49 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLY A 61 " --> pdb=" O ALA A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 100 removed outlier: 3.667A pdb=" N GLU A 99 " --> pdb=" O GLY A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 122 Processing helix chain 'A' and resid 129 through 136 removed outlier: 3.808A pdb=" N TRP A 133 " --> pdb=" O ASN A 129 " (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 195 through 212 Processing helix chain 'A' and resid 212 through 224 Processing helix chain 'A' and resid 247 through 251 Processing helix chain 'A' and resid 253 through 258 Processing helix chain 'A' and resid 285 through 290 Processing helix chain 'A' and resid 294 through 309 removed outlier: 4.018A pdb=" N ALA A 309 " --> pdb=" O GLN A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 341 Processing helix chain 'A' and resid 346 through 350 removed outlier: 3.551A pdb=" N ALA A 349 " --> pdb=" O GLY A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 364 removed outlier: 4.021A pdb=" N LEU A 361 " --> pdb=" O ASP A 357 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N TRP A 362 " --> pdb=" O ALA A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 371 removed outlier: 4.176A pdb=" N THR A 370 " --> pdb=" O LEU A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 383 Processing helix chain 'A' and resid 385 through 398 removed outlier: 3.934A pdb=" N ASN A 389 " --> pdb=" O ALA A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 408 Processing helix chain 'A' and resid 409 through 431 removed outlier: 3.904A pdb=" N ASP A 431 " --> pdb=" O GLU A 427 " (cutoff:3.500A) Processing helix chain 'B' and resid 33 through 48 removed outlier: 3.801A pdb=" N PHE B 37 " --> pdb=" O SER B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 121 Processing helix chain 'B' and resid 122 through 135 Processing helix chain 'B' and resid 165 through 180 Processing helix chain 'B' and resid 189 through 204 Processing helix chain 'B' and resid 208 through 216 Processing helix chain 'B' and resid 291 through 295 removed outlier: 3.638A pdb=" N VAL B 295 " --> pdb=" O PRO B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 302 removed outlier: 3.586A pdb=" N LEU B 301 " --> pdb=" O LEU B 298 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU B 302 " --> pdb=" O SER B 299 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 36 removed outlier: 3.773A pdb=" N LEU C 20 " --> pdb=" O PRO C 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 63 through 73 Processing helix chain 'C' and resid 74 through 77 Processing helix chain 'C' and resid 108 through 121 removed outlier: 3.949A 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 'D' and resid 51 through 55 Processing helix chain 'D' and resid 130 through 148 Processing helix chain 'D' and resid 151 through 163 Processing helix chain 'D' and resid 208 through 224 Processing helix chain 'D' and resid 275 through 284 Processing helix chain 'D' and resid 302 through 304 No H-bonds generated for 'chain 'D' and resid 302 through 304' Processing helix chain 'D' and resid 322 through 332 removed outlier: 3.547A pdb=" N LEU D 326 " --> pdb=" O ASP D 322 " (cutoff:3.500A) Processing helix chain 'D' and resid 338 through 352 Processing helix chain 'E' and resid 51 through 58 removed outlier: 5.265A pdb=" N GLN E 56 " --> pdb=" O ASP E 53 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N GLU E 57 " --> pdb=" O ALA E 54 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N TRP E 58 " --> pdb=" O SER E 55 " (cutoff:3.500A) Processing helix chain 'E' and resid 82 through 92 removed outlier: 3.549A 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 208 through 223 Processing helix chain 'E' and resid 275 through 284 Processing helix chain 'E' and resid 302 through 304 No H-bonds generated for 'chain 'E' and resid 302 through 304' Processing helix chain 'E' and resid 322 through 332 Processing helix chain 'E' and resid 338 through 352 Processing helix chain 'F' and resid 51 through 58 removed outlier: 3.555A pdb=" N SER F 55 " --> pdb=" O ARG F 52 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N GLN F 56 " --> pdb=" O ASP F 53 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N GLU F 57 " --> pdb=" O ALA F 54 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 92 Processing helix chain 'F' and resid 130 through 148 Processing helix chain 'F' and resid 151 through 163 Processing helix chain 'F' and resid 208 through 223 Processing helix chain 'F' and resid 275 through 284 Processing helix chain 'F' and resid 302 through 304 No H-bonds generated for 'chain 'F' and resid 302 through 304' Processing helix chain 'F' and resid 316 through 320 Processing helix chain 'F' and resid 322 through 332 Processing helix chain 'F' and resid 338 through 352 Processing helix chain 'G' and resid 82 through 92 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 293 through 297 removed outlier: 3.673A pdb=" N LEU G 296 " --> pdb=" O GLU G 293 " (cutoff:3.500A) Processing helix chain 'G' and resid 302 through 304 No H-bonds generated for 'chain 'G' and resid 302 through 304' Processing helix chain 'G' and resid 322 through 332 Processing helix chain 'G' and resid 338 through 352 Processing helix chain 'H' and resid 82 through 92 removed outlier: 3.629A pdb=" N SER H 92 " --> pdb=" O ALA H 88 " (cutoff:3.500A) 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 302 through 304 No H-bonds generated for 'chain 'H' and resid 302 through 304' Processing helix chain 'H' and resid 322 through 332 Processing helix chain 'H' and resid 338 through 352 Processing helix chain 'I' and resid 82 through 91 Processing helix chain 'I' and resid 130 through 148 Processing helix chain 'I' and resid 150 through 163 Processing helix chain 'I' and resid 164 through 172 removed outlier: 6.503A pdb=" N ARG I 169 " --> pdb=" O PHE I 166 " (cutoff:3.500A) Processing helix chain 'I' and resid 208 through 224 Processing helix chain 'I' and resid 275 through 284 Processing helix chain 'I' and resid 302 through 304 No H-bonds generated for 'chain 'I' and resid 302 through 304' Processing helix chain 'I' and resid 322 through 332 Processing helix chain 'I' and resid 338 through 352 Processing helix chain 'J' and resid 47 through 70 removed outlier: 3.519A pdb=" N PHE J 55 " --> pdb=" O VAL J 51 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N ASP J 57 " --> pdb=" O ASP J 53 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N ILE J 58 " --> pdb=" O GLU J 54 " (cutoff:3.500A) Processing helix chain 'J' and resid 124 through 136 Processing helix chain 'J' and resid 140 through 147 Processing helix chain 'J' and resid 163 through 168 Processing helix chain 'J' and resid 180 through 188 Processing helix chain 'J' and resid 191 through 197 Processing helix chain 'J' and resid 211 through 222 Processing helix chain 'K' and resid 47 through 70 removed outlier: 3.515A pdb=" N ASP K 53 " --> pdb=" O SER K 49 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N ASP K 57 " --> pdb=" O ASP K 53 " (cutoff:3.500A) removed outlier: 5.578A pdb=" N ILE K 58 " --> pdb=" O GLU K 54 " (cutoff:3.500A) Processing helix chain 'K' and resid 124 through 136 Processing helix chain 'K' and resid 140 through 147 Processing helix chain 'K' and resid 163 through 168 Processing helix chain 'K' and resid 180 through 189 Processing helix chain 'K' and resid 191 through 199 Processing helix chain 'K' and resid 211 through 222 Processing sheet with id=AA1, first strand: chain 'A' and resid 64 through 66 Processing sheet with id=AA2, first strand: chain 'A' and resid 94 through 95 Processing sheet with id=AA3, first strand: chain 'A' and resid 191 through 192 removed outlier: 6.423A pdb=" N ALA A 191 " --> pdb=" O VAL B 280 " (cutoff:3.500A) removed outlier: 8.458A pdb=" N ASN B 282 " --> pdb=" O ALA A 191 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N PHE B 279 " --> pdb=" O ALA B 257 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N ALA B 257 " --> pdb=" O PHE B 279 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N GLU B 281 " --> pdb=" O TYR B 255 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N TYR B 255 " --> pdb=" O GLU B 281 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N LEU B 283 " --> pdb=" O ALA B 253 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N ALA B 253 " --> pdb=" O TRP B 316 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 180 through 182 removed outlier: 4.351A pdb=" N GLY A 186 " --> pdb=" O LEU A 182 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 232 through 233 Processing sheet with id=AA6, first strand: chain 'A' and resid 239 through 240 removed outlier: 4.541A pdb=" N PHE B 81 " --> pdb=" O ILE A 240 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 265 through 267 removed outlier: 5.727A pdb=" N LEU A 265 " --> pdb=" O TRP B 29 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 54 through 61 removed outlier: 3.852A pdb=" N VAL B 59 " --> pdb=" O LEU B 110 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N LEU B 110 " --> pdb=" O VAL B 59 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N ILE B 61 " --> pdb=" O SER B 108 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N SER B 108 " --> pdb=" O ILE B 61 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N ALA B 103 " --> pdb=" O ASN B 19 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASN B 19 " --> pdb=" O ALA B 103 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N LEU B 109 " --> pdb=" O PRO B 13 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N LEU B 111 " --> pdb=" O LEU B 11 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N LEU B 11 " --> pdb=" O LEU B 111 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N VAL B 113 " --> pdb=" O LEU B 9 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N LEU B 9 " --> pdb=" O VAL B 113 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N SER B 16 " --> pdb=" O LEU B 145 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 65 through 68 removed outlier: 4.898A pdb=" N ALA B 103 " --> pdb=" O ASN B 19 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASN B 19 " --> pdb=" O ALA B 103 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N LEU B 109 " --> pdb=" O PRO B 13 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N LEU B 111 " --> pdb=" O LEU B 11 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N LEU B 11 " --> pdb=" O LEU B 111 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N VAL B 113 " --> pdb=" O LEU B 9 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N LEU B 9 " --> pdb=" O VAL B 113 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA B 157 " --> pdb=" O LEU B 11 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 41 through 43 Processing sheet with id=AB2, first strand: chain 'C' and resid 97 through 98 Processing sheet with id=AB3, first strand: chain 'C' and resid 100 through 102 Processing sheet with id=AB4, first strand: chain 'D' and resid 31 through 33 removed outlier: 3.838A pdb=" N PHE D 355 " --> pdb=" O LEU D 31 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 38 through 39 Processing sheet with id=AB6, first strand: chain 'D' and resid 38 through 39 removed outlier: 3.969A pdb=" N VAL D 228 " --> pdb=" O VAL D 118 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N LEU D 229 " --> pdb=" O ILE D 184 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N VAL D 177 " --> pdb=" O ASP D 196 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N ASP D 196 " --> pdb=" O VAL D 177 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N VAL D 179 " --> pdb=" O ARG D 194 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N ARG D 194 " --> pdb=" O VAL D 179 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N ILE D 181 " --> pdb=" O ALA D 192 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N ALA D 192 " --> pdb=" O ILE D 181 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N HIS D 183 " --> pdb=" O ALA D 190 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 42 through 43 Processing sheet with id=AB8, first strand: chain 'D' and resid 64 through 66 Processing sheet with id=AB9, first strand: chain 'D' and resid 248 through 249 removed outlier: 3.764A pdb=" N THR D 264 " --> pdb=" O GLU D 249 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 285 through 287 Processing sheet with id=AC2, first strand: chain 'D' and resid 306 through 307 Processing sheet with id=AC3, first strand: chain 'E' and resid 127 through 128 removed outlier: 3.804A pdb=" N PHE E 355 " --> pdb=" O LEU E 31 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 38 through 39 removed outlier: 4.185A pdb=" N VAL E 228 " --> pdb=" O VAL E 118 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N LEU E 229 " --> pdb=" O ILE E 184 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ALA E 176 " --> pdb=" O ARG E 237 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N VAL E 177 " --> pdb=" O ASP E 196 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N ASP E 196 " --> pdb=" O VAL E 177 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N VAL E 179 " --> pdb=" O ARG E 194 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N ARG E 194 " --> pdb=" O VAL E 179 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ILE E 181 " --> pdb=" O ALA E 192 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N ALA E 192 " --> pdb=" O ILE E 181 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N HIS E 183 " --> pdb=" O ALA E 190 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 38 through 39 Processing sheet with id=AC6, first strand: chain 'E' and resid 63 through 70 removed outlier: 3.627A pdb=" N GLY E 70 " --> pdb=" O ASN E 94 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ASN E 94 " --> pdb=" O GLY E 70 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N ALA E 101 " --> pdb=" O VAL E 244 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 285 through 287 Processing sheet with id=AC8, first strand: chain 'E' and resid 306 through 307 removed outlier: 3.723A pdb=" N LYS E 312 " --> pdb=" O VAL E 307 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 127 through 128 Processing sheet with id=AD1, first strand: chain 'F' and resid 38 through 39 removed outlier: 3.530A pdb=" N VAL F 118 " --> pdb=" O VAL F 228 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N VAL F 228 " --> pdb=" O VAL F 118 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N LEU F 229 " --> pdb=" O ILE F 184 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ALA F 176 " --> pdb=" O ARG F 237 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N VAL F 177 " --> pdb=" O ASP F 196 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N ASP F 196 " --> pdb=" O VAL F 177 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N VAL F 179 " --> pdb=" O ARG F 194 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N ARG F 194 " --> pdb=" O VAL F 179 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ILE F 181 " --> pdb=" O ALA F 192 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N ALA F 192 " --> pdb=" O ILE F 181 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N HIS F 183 " --> pdb=" O ALA F 190 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 38 through 39 Processing sheet with id=AD3, first strand: chain 'F' and resid 63 through 70 removed outlier: 3.519A pdb=" N GLN F 96 " --> pdb=" O VAL F 68 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLY F 70 " --> pdb=" O ASN F 94 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ASN F 94 " --> pdb=" O GLY F 70 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N ALA F 101 " --> pdb=" O VAL F 244 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 285 through 287 Processing sheet with id=AD5, first strand: chain 'F' and resid 306 through 307 removed outlier: 3.695A pdb=" N LYS F 312 " --> pdb=" O VAL F 307 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'G' and resid 31 through 33 Processing sheet with id=AD7, first strand: chain 'G' and resid 38 through 39 removed outlier: 4.210A pdb=" N VAL G 228 " --> pdb=" O VAL G 118 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N LEU G 229 " --> pdb=" O ILE G 184 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N VAL G 177 " --> pdb=" O ASP G 196 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N ASP G 196 " --> pdb=" O VAL G 177 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N VAL G 179 " --> pdb=" O ARG G 194 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N ARG G 194 " --> pdb=" O VAL G 179 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ILE G 181 " --> pdb=" O ALA G 192 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N ALA G 192 " --> pdb=" O ILE G 181 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N HIS G 183 " --> pdb=" O ALA G 190 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 38 through 39 Processing sheet with id=AD9, first strand: chain 'G' and resid 63 through 70 removed outlier: 3.585A pdb=" N GLY G 70 " --> pdb=" O ASN G 94 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N ALA G 101 " --> pdb=" O VAL G 244 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'G' and resid 285 through 287 Processing sheet with id=AE2, first strand: chain 'G' and resid 306 through 307 Processing sheet with id=AE3, first strand: chain 'H' and resid 127 through 128 removed outlier: 3.692A pdb=" N PHE H 355 " --> pdb=" O LEU H 31 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'H' and resid 188 through 196 removed outlier: 5.000A pdb=" N VAL H 189 " --> pdb=" O ARG H 185 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N ARG H 185 " --> pdb=" O VAL H 189 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ARG H 191 " --> pdb=" O HIS H 183 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N LEU H 229 " --> pdb=" O ILE H 184 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N VAL H 228 " --> pdb=" O VAL H 118 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'H' and resid 63 through 70 removed outlier: 3.763A pdb=" N ASN H 94 " --> pdb=" O GLY H 70 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N ALA H 101 " --> pdb=" O VAL H 244 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'H' and resid 63 through 70 removed outlier: 3.763A pdb=" N ASN H 94 " --> pdb=" O GLY H 70 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N SER H 262 " --> pdb=" O LEU H 95 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N THR H 97 " --> pdb=" O SER H 262 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N THR H 264 " --> pdb=" O THR H 97 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ASP H 99 " --> pdb=" O THR H 264 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N THR H 264 " --> pdb=" O GLU H 249 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'H' and resid 285 through 287 Processing sheet with id=AE8, first strand: chain 'H' and resid 306 through 307 removed outlier: 3.754A pdb=" N LYS H 312 " --> pdb=" O VAL H 307 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'I' and resid 127 through 128 removed outlier: 3.511A pdb=" N ALA I 127 " --> pdb=" O ALA I 32 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'I' and resid 38 through 39 removed outlier: 4.282A pdb=" N LEU I 229 " --> pdb=" O ILE I 184 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ARG I 191 " --> pdb=" O HIS I 183 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'I' and resid 38 through 39 Processing sheet with id=AF3, first strand: chain 'I' and resid 63 through 70 removed outlier: 3.964A pdb=" N ASN I 94 " --> pdb=" O GLY I 70 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'I' and resid 243 through 244 removed outlier: 4.560A pdb=" N ALA I 101 " --> pdb=" O VAL I 244 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ALA J 38 " --> pdb=" O LEU J 30 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N TYR J 32 " --> pdb=" O GLU J 36 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N GLU J 36 " --> pdb=" O TYR J 32 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'I' and resid 285 through 287 Processing sheet with id=AF6, first strand: chain 'I' and resid 306 through 307 removed outlier: 3.700A pdb=" N LYS I 312 " --> pdb=" O VAL I 307 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'J' and resid 85 through 90 removed outlier: 5.232A pdb=" N LEU J 119 " --> pdb=" O THR J 113 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N SER J 99 " --> pdb=" O GLY J 120 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'K' and resid 4 through 6 removed outlier: 6.256A pdb=" N HIS K 26 " --> pdb=" O THR K 41 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N THR K 41 " --> pdb=" O HIS K 26 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N TRP K 28 " --> pdb=" O ILE K 39 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N ILE K 39 " --> pdb=" O TRP K 28 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N LEU K 30 " --> pdb=" O MET K 37 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'K' and resid 85 through 91 Processing sheet with id=AG1, first strand: chain 'K' and resid 99 through 100 1159 hydrogen bonds defined for protein. 3156 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 43 hydrogen bonds 82 hydrogen bond angles 0 basepair planarities 18 basepair parallelities 57 stacking parallelities Total time for adding SS restraints: 11.41 Time building geometry restraints manager: 11.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 4483 1.30 - 1.43: 7939 1.43 - 1.56: 15980 1.56 - 1.68: 195 1.68 - 1.81: 52 Bond restraints: 28649 Sorted by residual: bond pdb=" CA ALA G 271 " pdb=" C ALA G 271 " ideal model delta sigma weight residual 1.521 1.455 0.066 1.19e-02 7.06e+03 3.06e+01 bond pdb=" C HIS G 159 " pdb=" O HIS G 159 " ideal model delta sigma weight residual 1.237 1.175 0.061 1.19e-02 7.06e+03 2.66e+01 bond pdb=" CA HIS G 159 " pdb=" C HIS G 159 " ideal model delta sigma weight residual 1.524 1.471 0.052 1.29e-02 6.01e+03 1.63e+01 bond pdb=" CA ARG G 269 " pdb=" C ARG G 269 " ideal model delta sigma weight residual 1.530 1.474 0.055 1.44e-02 4.82e+03 1.48e+01 bond pdb=" C ALA G 158 " pdb=" O ALA G 158 " ideal model delta sigma weight residual 1.236 1.189 0.048 1.25e-02 6.40e+03 1.45e+01 ... (remaining 28644 not shown) Histogram of bond angle deviations from ideal: 100.33 - 107.08: 1432 107.08 - 113.84: 15913 113.84 - 120.59: 11134 120.59 - 127.34: 10433 127.34 - 134.09: 474 Bond angle restraints: 39386 Sorted by residual: angle pdb=" N LEU G 161 " pdb=" CA LEU G 161 " pdb=" C LEU G 161 " ideal model delta sigma weight residual 114.04 102.35 11.69 1.24e+00 6.50e-01 8.89e+01 angle pdb=" O SER G 267 " pdb=" C SER G 267 " pdb=" N VAL G 268 " ideal model delta sigma weight residual 123.33 130.37 -7.04 1.21e+00 6.83e-01 3.39e+01 angle pdb=" C LEU G 161 " pdb=" N ALA G 162 " pdb=" CA ALA G 162 " ideal model delta sigma weight residual 120.68 111.67 9.01 1.70e+00 3.46e-01 2.81e+01 angle pdb=" N ILE D 286 " pdb=" CA ILE D 286 " pdb=" C ILE D 286 " ideal model delta sigma weight residual 113.20 108.23 4.97 9.60e-01 1.09e+00 2.68e+01 angle pdb=" CA SER G 267 " pdb=" C SER G 267 " pdb=" N VAL G 268 " ideal model delta sigma weight residual 116.01 108.52 7.49 1.51e+00 4.39e-01 2.46e+01 ... (remaining 39381 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.90: 16614 35.90 - 71.81: 474 71.81 - 107.71: 45 107.71 - 143.62: 1 143.62 - 179.52: 5 Dihedral angle restraints: 17139 sinusoidal: 7493 harmonic: 9646 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 55.78 144.22 1 1.50e+01 4.44e-03 7.73e+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 57.83 142.17 1 1.50e+01 4.44e-03 7.64e+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 232.00 52.48 179.52 1 1.70e+01 3.46e-03 6.64e+01 ... (remaining 17136 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 3645 0.051 - 0.103: 635 0.103 - 0.154: 140 0.154 - 0.205: 10 0.205 - 0.257: 2 Chirality restraints: 4432 Sorted by residual: chirality pdb=" CA ASP G 270 " pdb=" N ASP G 270 " pdb=" C ASP G 270 " pdb=" CB ASP G 270 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.65e+00 chirality pdb=" CB THR B 318 " pdb=" CA THR B 318 " pdb=" OG1 THR B 318 " pdb=" CG2 THR B 318 " both_signs ideal model delta sigma weight residual False 2.55 2.30 0.25 2.00e-01 2.50e+01 1.61e+00 chirality pdb=" CB THR A 301 " pdb=" CA THR A 301 " pdb=" OG1 THR A 301 " pdb=" CG2 THR A 301 " both_signs ideal model delta sigma weight residual False 2.55 2.35 0.20 2.00e-01 2.50e+01 9.74e-01 ... (remaining 4429 not shown) Planarity restraints: 4823 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A 71 " 0.051 5.00e-02 4.00e+02 7.71e-02 9.50e+00 pdb=" N PRO A 72 " -0.133 5.00e-02 4.00e+02 pdb=" CA PRO A 72 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO A 72 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA SER G 267 " 0.013 2.00e-02 2.50e+03 2.95e-02 8.72e+00 pdb=" C SER G 267 " -0.051 2.00e-02 2.50e+03 pdb=" O SER G 267 " 0.020 2.00e-02 2.50e+03 pdb=" N VAL G 268 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP A 364 " -0.048 5.00e-02 4.00e+02 7.36e-02 8.67e+00 pdb=" N PRO A 365 " 0.127 5.00e-02 4.00e+02 pdb=" CA PRO A 365 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 365 " -0.041 5.00e-02 4.00e+02 ... (remaining 4820 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 4673 2.77 - 3.30: 25724 3.30 - 3.83: 48928 3.83 - 4.37: 59225 4.37 - 4.90: 98107 Nonbonded interactions: 236657 Sorted by model distance: nonbonded pdb=" OH TYR A 179 " pdb=" OD2 ASP B 272 " model vdw 2.236 2.440 nonbonded pdb=" O VAL K 170 " pdb=" OG1 THR K 177 " model vdw 2.243 2.440 nonbonded pdb=" O GLY J 172 " pdb=" OG SER J 175 " model vdw 2.256 2.440 nonbonded pdb=" OH TYR F 324 " pdb=" O SER G 73 " model vdw 2.263 2.440 nonbonded pdb=" OH TYR H 324 " pdb=" O SER I 73 " model vdw 2.268 2.440 ... (remaining 236652 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model 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)) } ncs_group { reference = chain 'J' selection = chain 'K' } 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: 1.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.150 Construct map_model_manager: 0.020 Extract box with map and model: 8.330 Check model and map are aligned: 0.410 Set scattering table: 0.240 Process input model: 79.480 Find NCS groups from input model: 1.740 Set up NCS constraints: 0.170 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 105.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5452 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 : 0.003 0.066 28649 Z= 0.207 Angle : 0.668 11.694 39386 Z= 0.369 Chirality : 0.042 0.257 4432 Planarity : 0.005 0.077 4823 Dihedral : 16.218 179.523 10913 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.13), residues: 3322 helix: -0.02 (0.14), residues: 1078 sheet: 0.76 (0.21), residues: 540 loop : -1.58 (0.14), residues: 1704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP G 49 HIS 0.009 0.001 HIS K 25 PHE 0.023 0.001 PHE A 16 TYR 0.039 0.002 TYR G 304 ARG 0.009 0.001 ARG E 191 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6644 Ramachandran restraints generated. 3322 Oldfield, 0 Emsley, 3322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6644 Ramachandran restraints generated. 3322 Oldfield, 0 Emsley, 3322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 866 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 866 time to evaluate : 2.750 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 300 LEU cc_start: 0.6915 (mm) cc_final: 0.6585 (mt) REVERT: B 121 HIS cc_start: 0.5778 (m90) cc_final: 0.5506 (m-70) REVERT: D 276 SER cc_start: 0.6267 (m) cc_final: 0.6012 (t) REVERT: J 28 TRP cc_start: 0.5319 (m100) cc_final: 0.4436 (m100) outliers start: 0 outliers final: 4 residues processed: 866 average time/residue: 1.1244 time to fit residues: 1159.9359 Evaluate side-chains 514 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 510 time to evaluate : 3.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 ASP Chi-restraints excluded: chain B residue 215 ASP Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain F residue 106 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 283 optimal weight: 2.9990 chunk 254 optimal weight: 0.6980 chunk 141 optimal weight: 3.9990 chunk 86 optimal weight: 20.0000 chunk 171 optimal weight: 2.9990 chunk 136 optimal weight: 1.9990 chunk 263 optimal weight: 0.7980 chunk 101 optimal weight: 2.9990 chunk 160 optimal weight: 0.9980 chunk 196 optimal weight: 0.9990 chunk 305 optimal weight: 0.5980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 GLN A 129 ASN ** A 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 253 GLN ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 328 GLN ** A 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 21 ASN B 89 ASN B 104 HIS B 168 GLN B 293 HIS C 19 GLN D 170 ASN D 281 ASN E 91 GLN ** E 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 186 GLN F 242 GLN ** G 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 96 GLN H 242 GLN ** H 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 94 ASN I 146 ASN I 281 ASN J 26 HIS ** K 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6788 moved from start: 0.4556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 28649 Z= 0.280 Angle : 0.720 9.175 39386 Z= 0.374 Chirality : 0.044 0.359 4432 Planarity : 0.006 0.063 4823 Dihedral : 16.256 179.498 5032 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 4.10 % Allowed : 15.49 % Favored : 80.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.14), residues: 3322 helix: 0.57 (0.15), residues: 1056 sheet: 0.68 (0.20), residues: 576 loop : -1.37 (0.15), residues: 1690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP D 289 HIS 0.010 0.002 HIS A 172 PHE 0.039 0.003 PHE A 16 TYR 0.033 0.003 TYR F 266 ARG 0.031 0.001 ARG A 306 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6644 Ramachandran restraints generated. 3322 Oldfield, 0 Emsley, 3322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6644 Ramachandran restraints generated. 3322 Oldfield, 0 Emsley, 3322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 690 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 583 time to evaluate : 2.394 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 300 LEU cc_start: 0.7588 (mm) cc_final: 0.7383 (mt) REVERT: B 138 ARG cc_start: 0.6394 (OUTLIER) cc_final: 0.5756 (mmt-90) REVERT: B 259 SER cc_start: 0.4858 (t) cc_final: 0.4613 (p) REVERT: D 34 GLU cc_start: 0.6837 (OUTLIER) cc_final: 0.6534 (tt0) REVERT: D 299 ILE cc_start: 0.7923 (pp) cc_final: 0.7567 (pp) REVERT: H 41 ASP cc_start: 0.6528 (m-30) cc_final: 0.6327 (m-30) REVERT: I 113 ARG cc_start: 0.6893 (OUTLIER) cc_final: 0.6296 (ttm-80) REVERT: J 28 TRP cc_start: 0.6483 (m100) cc_final: 0.6186 (m100) REVERT: K 88 ARG cc_start: 0.6555 (OUTLIER) cc_final: 0.6197 (pmm-80) outliers start: 107 outliers final: 29 residues processed: 654 average time/residue: 1.0871 time to fit residues: 852.3384 Evaluate side-chains 438 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 405 time to evaluate : 2.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 THR Chi-restraints excluded: chain A residue 74 HIS Chi-restraints excluded: chain A residue 76 ASP Chi-restraints excluded: chain A residue 177 GLN Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 425 PHE Chi-restraints excluded: chain A residue 431 ASP Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 138 ARG Chi-restraints excluded: chain B residue 220 ASN Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain D residue 34 GLU Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain E residue 29 SER Chi-restraints excluded: chain E residue 140 THR Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 233 VAL Chi-restraints excluded: chain G residue 67 SER Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 124 THR Chi-restraints excluded: chain I residue 113 ARG Chi-restraints excluded: chain I residue 118 VAL Chi-restraints excluded: chain I residue 143 THR Chi-restraints excluded: chain I residue 334 ASP Chi-restraints excluded: chain J residue 48 SER Chi-restraints excluded: chain J residue 198 TYR Chi-restraints excluded: chain K residue 88 ARG Chi-restraints excluded: chain K residue 151 VAL Chi-restraints excluded: chain K residue 170 VAL Chi-restraints excluded: chain K residue 177 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 169 optimal weight: 1.9990 chunk 94 optimal weight: 0.0060 chunk 253 optimal weight: 2.9990 chunk 207 optimal weight: 0.8980 chunk 84 optimal weight: 9.9990 chunk 305 optimal weight: 2.9990 chunk 330 optimal weight: 3.9990 chunk 272 optimal weight: 3.9990 chunk 303 optimal weight: 2.9990 chunk 104 optimal weight: 0.0470 chunk 245 optimal weight: 0.6980 overall best weight: 0.7296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 GLN A 81 ASN ** A 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 255 ASN A 324 GLN B 18 GLN B 21 ASN B 194 GLN D 170 ASN D 183 HIS E 102 ASN ** E 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 139 GLN F 160 ASN F 242 GLN F 343 HIS ** G 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 319 GLN H 96 GLN H 163 ASN ** I 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 27 GLN ** J 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7238 moved from start: 0.6091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 28649 Z= 0.218 Angle : 0.631 12.713 39386 Z= 0.321 Chirality : 0.041 0.209 4432 Planarity : 0.005 0.062 4823 Dihedral : 15.907 178.335 5026 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 4.26 % Allowed : 20.13 % Favored : 75.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.14), residues: 3322 helix: 0.89 (0.15), residues: 1057 sheet: 0.89 (0.21), residues: 543 loop : -1.29 (0.14), residues: 1722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP H 193 HIS 0.009 0.001 HIS B 305 PHE 0.020 0.002 PHE A 20 TYR 0.028 0.002 TYR D 133 ARG 0.012 0.001 ARG E 64 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6644 Ramachandran restraints generated. 3322 Oldfield, 0 Emsley, 3322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6644 Ramachandran restraints generated. 3322 Oldfield, 0 Emsley, 3322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 511 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 400 time to evaluate : 3.115 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 256 ASN cc_start: 0.5501 (t0) cc_final: 0.5277 (m-40) REVERT: A 281 MET cc_start: 0.4528 (tpt) cc_final: 0.4182 (tpt) REVERT: G 319 GLN cc_start: 0.4997 (OUTLIER) cc_final: 0.4744 (pt0) REVERT: H 96 GLN cc_start: 0.7541 (OUTLIER) cc_final: 0.6860 (pm20) outliers start: 111 outliers final: 32 residues processed: 467 average time/residue: 1.1602 time to fit residues: 646.2413 Evaluate side-chains 360 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 326 time to evaluate : 2.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 291 PHE Chi-restraints excluded: chain A residue 431 ASP Chi-restraints excluded: chain B residue 16 SER Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 195 GLN Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 294 ASP Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 233 VAL Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain F residue 140 THR Chi-restraints excluded: chain G residue 97 THR Chi-restraints excluded: chain G residue 203 ARG Chi-restraints excluded: chain G residue 319 GLN Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 74 ASN Chi-restraints excluded: chain H residue 96 GLN Chi-restraints excluded: chain H residue 267 SER Chi-restraints excluded: chain I residue 37 LEU Chi-restraints excluded: chain I residue 112 VAL Chi-restraints excluded: chain I residue 118 VAL Chi-restraints excluded: chain I residue 189 VAL Chi-restraints excluded: chain J residue 56 SER Chi-restraints excluded: chain J residue 197 LYS Chi-restraints excluded: chain J residue 202 ASP Chi-restraints excluded: chain K residue 57 ASP Chi-restraints excluded: chain K residue 123 VAL Chi-restraints excluded: chain K residue 151 VAL Chi-restraints excluded: chain K residue 170 VAL Chi-restraints excluded: chain K residue 218 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 302 optimal weight: 0.9980 chunk 229 optimal weight: 2.9990 chunk 158 optimal weight: 0.7980 chunk 33 optimal weight: 0.9980 chunk 145 optimal weight: 2.9990 chunk 205 optimal weight: 0.0970 chunk 306 optimal weight: 9.9990 chunk 324 optimal weight: 0.9990 chunk 160 optimal weight: 1.9990 chunk 290 optimal weight: 0.9990 chunk 87 optimal weight: 20.0000 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 26 GLN A 81 ASN ** A 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 253 GLN ** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 82 ASN B 282 ASN D 170 ASN D 343 HIS E 102 ASN E 146 ASN ** E 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 242 GLN F 248 GLN F 310 GLN ** G 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 310 GLN ** G 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 343 HIS ** I 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 19 HIS ** K 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 216 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7501 moved from start: 0.7299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 28649 Z= 0.224 Angle : 0.616 10.030 39386 Z= 0.313 Chirality : 0.041 0.451 4432 Planarity : 0.004 0.062 4823 Dihedral : 15.852 178.608 5024 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 4.72 % Allowed : 20.63 % Favored : 74.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.14), residues: 3322 helix: 1.07 (0.16), residues: 1068 sheet: 0.86 (0.21), residues: 566 loop : -1.32 (0.14), residues: 1688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 228 HIS 0.009 0.001 HIS A 283 PHE 0.024 0.002 PHE A 425 TYR 0.013 0.002 TYR G 290 ARG 0.014 0.001 ARG E 64 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6644 Ramachandran restraints generated. 3322 Oldfield, 0 Emsley, 3322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6644 Ramachandran restraints generated. 3322 Oldfield, 0 Emsley, 3322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 513 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 390 time to evaluate : 3.116 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 281 MET cc_start: 0.4581 (tpt) cc_final: 0.4019 (tpt) REVERT: D 329 ASN cc_start: 0.7208 (p0) cc_final: 0.6918 (p0) REVERT: E 37 LEU cc_start: 0.8309 (OUTLIER) cc_final: 0.7976 (mp) REVERT: I 249 GLU cc_start: 0.7454 (OUTLIER) cc_final: 0.7030 (mt-10) REVERT: J 57 ASP cc_start: 0.6943 (t70) cc_final: 0.6498 (t70) REVERT: K 151 VAL cc_start: 0.7884 (OUTLIER) cc_final: 0.7664 (p) REVERT: K 155 ASP cc_start: 0.5108 (p0) cc_final: 0.4413 (p0) outliers start: 123 outliers final: 34 residues processed: 464 average time/residue: 1.1499 time to fit residues: 635.9448 Evaluate side-chains 373 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 336 time to evaluate : 2.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 THR Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 308 THR Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 56 GLN Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 233 VAL Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 130 ASP Chi-restraints excluded: chain G residue 97 THR Chi-restraints excluded: chain G residue 203 ARG Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 31 LEU Chi-restraints excluded: chain H residue 43 LEU Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 214 LEU Chi-restraints excluded: chain H residue 290 TYR Chi-restraints excluded: chain I residue 37 LEU Chi-restraints excluded: chain I residue 115 THR Chi-restraints excluded: chain I residue 118 VAL Chi-restraints excluded: chain I residue 189 VAL Chi-restraints excluded: chain I residue 249 GLU Chi-restraints excluded: chain J residue 49 SER Chi-restraints excluded: chain J residue 152 LEU Chi-restraints excluded: chain K residue 111 LEU Chi-restraints excluded: chain K residue 123 VAL Chi-restraints excluded: chain K residue 151 VAL Chi-restraints excluded: chain K residue 218 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 270 optimal weight: 3.9990 chunk 184 optimal weight: 0.8980 chunk 4 optimal weight: 10.0000 chunk 241 optimal weight: 1.9990 chunk 134 optimal weight: 4.9990 chunk 277 optimal weight: 1.9990 chunk 224 optimal weight: 3.9990 chunk 0 optimal weight: 30.0000 chunk 165 optimal weight: 0.8980 chunk 291 optimal weight: 4.9990 chunk 81 optimal weight: 3.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 HIS ** A 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 253 GLN ** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 ASN ** B 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 170 ASN D 348 ASN E 102 ASN E 146 ASN ** F 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 260 GLN ** G 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 348 ASN ** H 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 216 HIS ** K 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.9595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 28649 Z= 0.383 Angle : 0.727 11.099 39386 Z= 0.375 Chirality : 0.046 0.219 4432 Planarity : 0.005 0.087 4823 Dihedral : 16.101 179.446 5024 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 13.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 4.68 % Allowed : 22.28 % Favored : 73.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.14), residues: 3322 helix: 0.67 (0.15), residues: 1066 sheet: 0.67 (0.21), residues: 531 loop : -1.32 (0.14), residues: 1725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B 247 HIS 0.015 0.001 HIS A 283 PHE 0.029 0.002 PHE A 425 TYR 0.024 0.002 TYR D 133 ARG 0.020 0.001 ARG C 102 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6644 Ramachandran restraints generated. 3322 Oldfield, 0 Emsley, 3322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6644 Ramachandran restraints generated. 3322 Oldfield, 0 Emsley, 3322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 444 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 322 time to evaluate : 2.680 Fit side-chains revert: symmetry clash REVERT: A 281 MET cc_start: 0.5147 (tpt) cc_final: 0.4850 (mmp) REVERT: A 331 ASP cc_start: 0.5997 (m-30) cc_final: 0.5791 (m-30) REVERT: A 347 TRP cc_start: 0.7742 (p-90) cc_final: 0.7542 (p-90) REVERT: B 106 GLU cc_start: 0.8053 (OUTLIER) cc_final: 0.7836 (tt0) REVERT: D 170 ASN cc_start: 0.8164 (m-40) cc_final: 0.7956 (m110) REVERT: D 299 ILE cc_start: 0.8314 (OUTLIER) cc_final: 0.8094 (pt) REVERT: D 324 TYR cc_start: 0.8136 (m-10) cc_final: 0.7932 (m-80) REVERT: E 153 LEU cc_start: 0.8366 (OUTLIER) cc_final: 0.8160 (mt) REVERT: E 172 VAL cc_start: 0.8287 (OUTLIER) cc_final: 0.8008 (t) REVERT: F 81 ARG cc_start: 0.8195 (OUTLIER) cc_final: 0.6940 (mpp80) REVERT: J 46 TYR cc_start: 0.8685 (m-10) cc_final: 0.8445 (m-10) REVERT: K 54 GLU cc_start: 0.5214 (tm-30) cc_final: 0.4933 (tm-30) outliers start: 122 outliers final: 35 residues processed: 415 average time/residue: 1.2927 time to fit residues: 627.0632 Evaluate side-chains 303 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 263 time to evaluate : 2.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 ASP Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 230 HIS Chi-restraints excluded: chain A residue 330 CYS Chi-restraints excluded: chain A residue 413 GLN Chi-restraints excluded: chain B residue 106 GLU Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 299 ILE Chi-restraints excluded: chain D residue 308 THR Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 29 SER Chi-restraints excluded: chain E residue 56 GLN Chi-restraints excluded: chain E residue 148 GLN Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 233 VAL Chi-restraints excluded: chain E residue 264 THR Chi-restraints excluded: chain F residue 81 ARG Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain G residue 97 THR Chi-restraints excluded: chain G residue 351 ARG Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 43 LEU Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 81 ARG Chi-restraints excluded: chain H residue 128 CYS Chi-restraints excluded: chain H residue 296 LEU Chi-restraints excluded: chain H residue 318 LYS Chi-restraints excluded: chain I residue 143 THR Chi-restraints excluded: chain I residue 189 VAL Chi-restraints excluded: chain I residue 326 LEU Chi-restraints excluded: chain J residue 6 ILE Chi-restraints excluded: chain J residue 73 ASP Chi-restraints excluded: chain J residue 152 LEU Chi-restraints excluded: chain J residue 202 ASP Chi-restraints excluded: chain K residue 4 ILE Chi-restraints excluded: chain K residue 57 ASP Chi-restraints excluded: chain K residue 123 VAL Chi-restraints excluded: chain K residue 151 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 109 optimal weight: 0.5980 chunk 292 optimal weight: 0.1980 chunk 64 optimal weight: 6.9990 chunk 190 optimal weight: 0.6980 chunk 80 optimal weight: 5.9990 chunk 325 optimal weight: 0.0050 chunk 269 optimal weight: 4.9990 chunk 150 optimal weight: 0.0670 chunk 27 optimal weight: 8.9990 chunk 107 optimal weight: 0.7980 chunk 170 optimal weight: 1.9990 overall best weight: 0.3132 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 253 GLN ** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 324 GLN A 416 GLN B 220 ASN ** B 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 160 ASN ** G 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 348 ASN ** I 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 183 HIS J 27 GLN ** J 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 208 GLN J 216 HIS ** K 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 154 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.9657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.103 28649 Z= 0.175 Angle : 0.598 10.929 39386 Z= 0.303 Chirality : 0.040 0.194 4432 Planarity : 0.004 0.084 4823 Dihedral : 15.854 178.219 5024 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 2.72 % Allowed : 25.12 % Favored : 72.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.14), residues: 3322 helix: 1.19 (0.16), residues: 1070 sheet: 0.71 (0.21), residues: 569 loop : -1.34 (0.14), residues: 1683 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 414 HIS 0.009 0.001 HIS H 159 PHE 0.032 0.001 PHE A 291 TYR 0.023 0.001 TYR D 133 ARG 0.017 0.001 ARG E 64 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6644 Ramachandran restraints generated. 3322 Oldfield, 0 Emsley, 3322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6644 Ramachandran restraints generated. 3322 Oldfield, 0 Emsley, 3322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 317 time to evaluate : 3.098 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 240 ILE cc_start: 0.8403 (mm) cc_final: 0.8190 (mm) REVERT: A 281 MET cc_start: 0.5142 (tpt) cc_final: 0.4858 (mmp) REVERT: A 347 TRP cc_start: 0.7629 (p-90) cc_final: 0.7408 (p-90) REVERT: B 310 ASP cc_start: 0.7482 (m-30) cc_final: 0.7268 (m-30) REVERT: C 117 MET cc_start: 0.2600 (ttp) cc_final: 0.2026 (mpt) REVERT: G 216 GLU cc_start: 0.7329 (OUTLIER) cc_final: 0.6925 (mt-10) REVERT: J 46 TYR cc_start: 0.8567 (OUTLIER) cc_final: 0.8346 (m-10) REVERT: J 167 LEU cc_start: 0.8352 (mm) cc_final: 0.8121 (mt) REVERT: K 54 GLU cc_start: 0.5217 (tm-30) cc_final: 0.5003 (tm-30) outliers start: 71 outliers final: 23 residues processed: 369 average time/residue: 1.2546 time to fit residues: 546.0793 Evaluate side-chains 286 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 261 time to evaluate : 2.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 THR Chi-restraints excluded: chain A residue 76 ASP Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 233 VAL Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain G residue 97 THR Chi-restraints excluded: chain G residue 216 GLU Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 31 LEU Chi-restraints excluded: chain I residue 27 THR Chi-restraints excluded: chain I residue 96 GLN Chi-restraints excluded: chain I residue 189 VAL Chi-restraints excluded: chain J residue 6 ILE Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 73 ASP Chi-restraints excluded: chain J residue 125 LEU Chi-restraints excluded: chain J residue 152 LEU Chi-restraints excluded: chain K residue 57 ASP Chi-restraints excluded: chain K residue 89 VAL Chi-restraints excluded: chain K residue 123 VAL Chi-restraints excluded: chain K residue 151 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 313 optimal weight: 0.9980 chunk 36 optimal weight: 40.0000 chunk 185 optimal weight: 2.9990 chunk 237 optimal weight: 0.8980 chunk 183 optimal weight: 2.9990 chunk 273 optimal weight: 0.6980 chunk 181 optimal weight: 0.8980 chunk 323 optimal weight: 0.0010 chunk 202 optimal weight: 0.9980 chunk 197 optimal weight: 0.2980 chunk 149 optimal weight: 2.9990 overall best weight: 0.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 256 ASN ** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 324 GLN B 19 ASN ** B 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 ASN ** B 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 293 HIS D 348 ASN ** E 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 160 ASN G 248 GLN ** G 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 310 GLN ** I 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 242 GLN J 27 GLN J 154 HIS ** K 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.9795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 28649 Z= 0.179 Angle : 0.583 9.591 39386 Z= 0.295 Chirality : 0.040 0.187 4432 Planarity : 0.004 0.059 4823 Dihedral : 15.740 177.401 5024 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 2.72 % Allowed : 25.12 % Favored : 72.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.14), residues: 3322 helix: 1.33 (0.16), residues: 1070 sheet: 0.74 (0.21), residues: 580 loop : -1.31 (0.15), residues: 1672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 414 HIS 0.006 0.001 HIS A 283 PHE 0.029 0.001 PHE A 291 TYR 0.024 0.001 TYR D 133 ARG 0.014 0.001 ARG E 64 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6644 Ramachandran restraints generated. 3322 Oldfield, 0 Emsley, 3322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6644 Ramachandran restraints generated. 3322 Oldfield, 0 Emsley, 3322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 272 time to evaluate : 2.689 Fit side-chains REVERT: A 281 MET cc_start: 0.5207 (tpt) cc_final: 0.4974 (mmp) REVERT: A 347 TRP cc_start: 0.7641 (p-90) cc_final: 0.7404 (p-90) REVERT: C 117 MET cc_start: 0.2805 (ttp) cc_final: 0.2201 (mpt) REVERT: G 216 GLU cc_start: 0.7331 (OUTLIER) cc_final: 0.6909 (mt-10) REVERT: J 167 LEU cc_start: 0.8521 (mm) cc_final: 0.8292 (mt) REVERT: K 155 ASP cc_start: 0.6399 (p0) cc_final: 0.5631 (p0) outliers start: 71 outliers final: 26 residues processed: 324 average time/residue: 1.2745 time to fit residues: 490.2874 Evaluate side-chains 280 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 253 time to evaluate : 2.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 56 GLN Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 233 VAL Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain G residue 97 THR Chi-restraints excluded: chain G residue 216 GLU Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 31 LEU Chi-restraints excluded: chain H residue 102 ASN Chi-restraints excluded: chain I residue 27 THR Chi-restraints excluded: chain I residue 96 GLN Chi-restraints excluded: chain I residue 189 VAL Chi-restraints excluded: chain J residue 6 ILE Chi-restraints excluded: chain J residue 73 ASP Chi-restraints excluded: chain J residue 94 LEU Chi-restraints excluded: chain J residue 125 LEU Chi-restraints excluded: chain J residue 152 LEU Chi-restraints excluded: chain K residue 89 VAL Chi-restraints excluded: chain K residue 123 VAL Chi-restraints excluded: chain K residue 124 THR Chi-restraints excluded: chain K residue 151 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 200 optimal weight: 4.9990 chunk 129 optimal weight: 3.9990 chunk 193 optimal weight: 0.4980 chunk 97 optimal weight: 0.6980 chunk 63 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 205 optimal weight: 3.9990 chunk 220 optimal weight: 3.9990 chunk 160 optimal weight: 0.7980 chunk 30 optimal weight: 7.9990 chunk 254 optimal weight: 3.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 256 ASN ** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 ASN ** B 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 170 ASN ** E 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 27 GLN ** J 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 1.0052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 28649 Z= 0.219 Angle : 0.602 9.959 39386 Z= 0.306 Chirality : 0.041 0.254 4432 Planarity : 0.004 0.061 4823 Dihedral : 15.751 178.619 5024 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 2.15 % Allowed : 25.65 % Favored : 72.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.14), residues: 3322 helix: 1.28 (0.16), residues: 1075 sheet: 0.69 (0.21), residues: 561 loop : -1.30 (0.15), residues: 1686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP A 414 HIS 0.011 0.001 HIS A 283 PHE 0.035 0.002 PHE A 291 TYR 0.025 0.002 TYR D 133 ARG 0.011 0.001 ARG E 69 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6644 Ramachandran restraints generated. 3322 Oldfield, 0 Emsley, 3322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6644 Ramachandran restraints generated. 3322 Oldfield, 0 Emsley, 3322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 288 time to evaluate : 2.755 Fit side-chains revert: symmetry clash REVERT: B 294 ARG cc_start: 0.7217 (mpt180) cc_final: 0.6976 (mmt180) REVERT: G 216 GLU cc_start: 0.7317 (OUTLIER) cc_final: 0.6895 (mt-10) REVERT: J 167 LEU cc_start: 0.8519 (mm) cc_final: 0.8273 (mt) outliers start: 56 outliers final: 33 residues processed: 331 average time/residue: 1.2345 time to fit residues: 484.0338 Evaluate side-chains 283 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 249 time to evaluate : 2.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain C residue 81 ASP Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 56 GLN Chi-restraints excluded: chain E residue 148 GLN Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 233 VAL Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain G residue 35 ARG Chi-restraints excluded: chain G residue 43 LEU Chi-restraints excluded: chain G residue 97 THR Chi-restraints excluded: chain G residue 216 GLU Chi-restraints excluded: chain G residue 299 ILE Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 31 LEU Chi-restraints excluded: chain H residue 102 ASN Chi-restraints excluded: chain I residue 27 THR Chi-restraints excluded: chain I residue 96 GLN Chi-restraints excluded: chain I residue 189 VAL Chi-restraints excluded: chain J residue 6 ILE Chi-restraints excluded: chain J residue 73 ASP Chi-restraints excluded: chain J residue 94 LEU Chi-restraints excluded: chain J residue 125 LEU Chi-restraints excluded: chain J residue 152 LEU Chi-restraints excluded: chain J residue 206 ASN Chi-restraints excluded: chain K residue 89 VAL Chi-restraints excluded: chain K residue 123 VAL Chi-restraints excluded: chain K residue 124 THR Chi-restraints excluded: chain K residue 151 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 294 optimal weight: 1.9990 chunk 310 optimal weight: 0.3980 chunk 283 optimal weight: 0.7980 chunk 301 optimal weight: 0.0020 chunk 181 optimal weight: 0.7980 chunk 131 optimal weight: 0.6980 chunk 236 optimal weight: 0.7980 chunk 92 optimal weight: 0.0370 chunk 272 optimal weight: 3.9990 chunk 285 optimal weight: 3.9990 chunk 300 optimal weight: 0.0010 overall best weight: 0.2272 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 HIS ** A 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 256 ASN ** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 69 GLN B 220 ASN ** B 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 160 ASN G 94 ASN G 96 GLN ** G 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 27 GLN ** J 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 1.0135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 28649 Z= 0.157 Angle : 0.587 11.698 39386 Z= 0.294 Chirality : 0.040 0.278 4432 Planarity : 0.004 0.054 4823 Dihedral : 15.660 177.214 5024 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 1.92 % Allowed : 26.30 % Favored : 71.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.14), residues: 3322 helix: 1.40 (0.16), residues: 1075 sheet: 0.77 (0.21), residues: 589 loop : -1.30 (0.15), residues: 1658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP A 414 HIS 0.006 0.001 HIS A 283 PHE 0.035 0.001 PHE A 291 TYR 0.024 0.001 TYR D 133 ARG 0.009 0.000 ARG D 269 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6644 Ramachandran restraints generated. 3322 Oldfield, 0 Emsley, 3322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6644 Ramachandran restraints generated. 3322 Oldfield, 0 Emsley, 3322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 285 time to evaluate : 2.911 Fit side-chains revert: symmetry clash REVERT: A 281 MET cc_start: 0.5421 (mmp) cc_final: 0.5096 (mmp) REVERT: B 69 GLN cc_start: 0.7824 (OUTLIER) cc_final: 0.6702 (mp-120) REVERT: B 294 ARG cc_start: 0.7361 (mpt180) cc_final: 0.7148 (mmt180) REVERT: G 216 GLU cc_start: 0.7304 (OUTLIER) cc_final: 0.6878 (mt-10) REVERT: G 242 GLN cc_start: 0.8559 (mm-40) cc_final: 0.8346 (mm110) REVERT: J 167 LEU cc_start: 0.8424 (mm) cc_final: 0.8198 (mt) outliers start: 50 outliers final: 30 residues processed: 322 average time/residue: 1.2194 time to fit residues: 468.9093 Evaluate side-chains 286 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 254 time to evaluate : 2.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 69 GLN Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain C residue 81 ASP Chi-restraints excluded: chain D residue 135 ASP Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain E residue 29 SER Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 233 VAL Chi-restraints excluded: chain F residue 96 GLN Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain G residue 97 THR Chi-restraints excluded: chain G residue 216 GLU Chi-restraints excluded: chain G residue 299 ILE Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 31 LEU Chi-restraints excluded: chain H residue 102 ASN Chi-restraints excluded: chain I residue 27 THR Chi-restraints excluded: chain I residue 138 LEU Chi-restraints excluded: chain I residue 189 VAL Chi-restraints excluded: chain J residue 6 ILE Chi-restraints excluded: chain J residue 73 ASP Chi-restraints excluded: chain J residue 152 LEU Chi-restraints excluded: chain J residue 206 ASN Chi-restraints excluded: chain K residue 89 VAL Chi-restraints excluded: chain K residue 123 VAL Chi-restraints excluded: chain K residue 124 THR Chi-restraints excluded: chain K residue 151 VAL Chi-restraints excluded: chain K residue 195 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 198 optimal weight: 2.9990 chunk 319 optimal weight: 8.9990 chunk 194 optimal weight: 2.9990 chunk 151 optimal weight: 1.9990 chunk 221 optimal weight: 0.0770 chunk 334 optimal weight: 7.9990 chunk 308 optimal weight: 7.9990 chunk 266 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 205 optimal weight: 3.9990 chunk 163 optimal weight: 0.8980 overall best weight: 1.3944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 256 ASN B 64 HIS B 121 HIS B 220 ASN ** B 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 91 GLN E 248 GLN ** F 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 160 ASN ** F 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 96 GLN G 102 ASN ** G 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 1.0356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 28649 Z= 0.275 Angle : 0.647 12.108 39386 Z= 0.325 Chirality : 0.043 0.291 4432 Planarity : 0.004 0.048 4823 Dihedral : 15.785 178.574 5024 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 12.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 1.76 % Allowed : 26.80 % Favored : 71.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.14), residues: 3322 helix: 1.23 (0.16), residues: 1075 sheet: 0.84 (0.21), residues: 564 loop : -1.32 (0.15), residues: 1683 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP B 247 HIS 0.013 0.001 HIS A 283 PHE 0.028 0.002 PHE A 291 TYR 0.025 0.002 TYR D 133 ARG 0.009 0.001 ARG K 52 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6644 Ramachandran restraints generated. 3322 Oldfield, 0 Emsley, 3322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6644 Ramachandran restraints generated. 3322 Oldfield, 0 Emsley, 3322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 256 time to evaluate : 2.879 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 281 MET cc_start: 0.5688 (mmp) cc_final: 0.5477 (mmp) REVERT: B 69 GLN cc_start: 0.7861 (OUTLIER) cc_final: 0.7269 (mp10) REVERT: B 294 ARG cc_start: 0.7421 (mpt180) cc_final: 0.7089 (mmt180) REVERT: J 167 LEU cc_start: 0.8532 (mm) cc_final: 0.8295 (mt) outliers start: 46 outliers final: 27 residues processed: 294 average time/residue: 1.2008 time to fit residues: 420.5023 Evaluate side-chains 271 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 243 time to evaluate : 3.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 69 GLN Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 233 VAL Chi-restraints excluded: chain F residue 63 VAL Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain G residue 43 LEU Chi-restraints excluded: chain G residue 96 GLN Chi-restraints excluded: chain G residue 97 THR Chi-restraints excluded: chain G residue 106 ASP Chi-restraints excluded: chain G residue 299 ILE Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 31 LEU Chi-restraints excluded: chain H residue 102 ASN Chi-restraints excluded: chain I residue 27 THR Chi-restraints excluded: chain I residue 138 LEU Chi-restraints excluded: chain I residue 189 VAL Chi-restraints excluded: chain J residue 6 ILE Chi-restraints excluded: chain J residue 152 LEU Chi-restraints excluded: chain J residue 206 ASN Chi-restraints excluded: chain K residue 123 VAL Chi-restraints excluded: chain K residue 124 THR Chi-restraints excluded: chain K residue 151 VAL Chi-restraints excluded: chain K residue 188 LEU Chi-restraints excluded: chain K residue 195 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 211 optimal weight: 0.8980 chunk 283 optimal weight: 0.9980 chunk 81 optimal weight: 7.9990 chunk 245 optimal weight: 0.1980 chunk 39 optimal weight: 30.0000 chunk 74 optimal weight: 10.0000 chunk 266 optimal weight: 0.2980 chunk 111 optimal weight: 2.9990 chunk 274 optimal weight: 0.9990 chunk 33 optimal weight: 6.9990 chunk 49 optimal weight: 1.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 256 ASN B 69 GLN B 220 ASN ** B 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 160 ASN ** F 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 96 GLN ** G 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.143813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.090984 restraints weight = 53343.294| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 2.72 r_work: 0.3050 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2919 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2925 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2925 r_free = 0.2925 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2925 r_free = 0.2925 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2925 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 1.0487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 28649 Z= 0.187 Angle : 0.609 12.032 39386 Z= 0.303 Chirality : 0.041 0.290 4432 Planarity : 0.004 0.047 4823 Dihedral : 15.694 177.938 5024 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 1.65 % Allowed : 27.19 % Favored : 71.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.14), residues: 3322 helix: 1.36 (0.16), residues: 1076 sheet: 0.99 (0.21), residues: 552 loop : -1.32 (0.15), residues: 1694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP A 414 HIS 0.013 0.001 HIS A 283 PHE 0.028 0.001 PHE A 291 TYR 0.024 0.001 TYR D 133 ARG 0.014 0.001 ARG A 306 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10507.23 seconds wall clock time: 186 minutes 19.59 seconds (11179.59 seconds total)