Starting phenix.real_space_refine on Fri Feb 16 18:42:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ual_26428/02_2024/7ual_26428_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ual_26428/02_2024/7ual_26428.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ual_26428/02_2024/7ual_26428_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ual_26428/02_2024/7ual_26428_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ual_26428/02_2024/7ual_26428_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ual_26428/02_2024/7ual_26428.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ual_26428/02_2024/7ual_26428.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ual_26428/02_2024/7ual_26428_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ual_26428/02_2024/7ual_26428_updated.pdb" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 sd= 0.100 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 28 5.49 5 S 80 5.16 5 C 10220 2.51 5 N 2788 2.21 5 O 3048 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 347": "OE1" <-> "OE2" Residue "A GLU 368": "OE1" <-> "OE2" Residue "A GLU 419": "OE1" <-> "OE2" Residue "B GLU 368": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 16164 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 484, 3929 Classifications: {'peptide': 484} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 460} Chain: "B" Number of atoms: 3929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 484, 3929 Classifications: {'peptide': 484} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 460} Chain: "C" Number of atoms: 3929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 484, 3929 Classifications: {'peptide': 484} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 460} Chain: "D" Number of atoms: 3929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 484, 3929 Classifications: {'peptide': 484} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 460} Chain: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 112 Unusual residues: {'BG6': 1, 'NAP': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 112 Unusual residues: {'BG6': 1, 'NAP': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 112 Unusual residues: {'BG6': 1, 'NAP': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 112 Unusual residues: {'BG6': 1, 'NAP': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 8.80, per 1000 atoms: 0.54 Number of scatterers: 16164 At special positions: 0 Unit cell: (133.63, 92.96, 116.2, 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 80 16.00 P 28 15.00 O 3048 8.00 N 2788 7.00 C 10220 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: 6.33 Conformation dependent library (CDL) restraints added in 3.0 seconds 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3624 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 65 helices and 9 sheets defined 36.5% alpha, 17.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.66 Creating SS restraints... Processing helix chain 'A' and resid 42 through 57 removed outlier: 5.023A pdb=" N TYR A 49 " --> pdb=" O LYS A 45 " (cutoff:3.500A) Proline residue: A 50 - end of helix Processing helix chain 'A' and resid 77 through 88 Proline residue: A 86 - end of helix Processing helix chain 'A' and resid 92 through 103 removed outlier: 4.929A pdb=" N LEU A 96 " --> pdb=" O GLU A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 126 Processing helix chain 'A' and resid 144 through 157 removed outlier: 5.070A pdb=" N GLU A 148 " --> pdb=" O THR A 145 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER A 157 " --> pdb=" O ILE A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 190 removed outlier: 3.537A pdb=" N LEU A 183 " --> pdb=" O SER A 179 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU A 190 " --> pdb=" O HIS A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 204 Processing helix chain 'A' and resid 206 through 216 removed outlier: 4.468A pdb=" N MET A 212 " --> pdb=" O VAL A 208 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N VAL A 213 " --> pdb=" O GLN A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 259 removed outlier: 3.641A pdb=" N GLU A 252 " --> pdb=" O GLY A 248 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N PHE A 253 " --> pdb=" O TYR A 249 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N ILE A 255 " --> pdb=" O ASP A 251 " (cutoff:3.500A) removed outlier: 8.986A pdb=" N ILE A 256 " --> pdb=" O GLU A 252 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N ARG A 257 " --> pdb=" O PHE A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 272 Processing helix chain 'A' and resid 281 through 294 removed outlier: 3.599A pdb=" N CYS A 294 " --> pdb=" O LYS A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 319 Processing helix chain 'A' and resid 322 through 324 No H-bonds generated for 'chain 'A' and resid 322 through 324' Processing helix chain 'A' and resid 436 through 446 Processing helix chain 'A' and resid 455 through 475 removed outlier: 4.002A pdb=" N PHE A 465 " --> pdb=" O ALA A 461 " (cutoff:3.500A) Proline residue: A 467 - end of helix Processing helix chain 'A' and resid 490 through 498 Processing helix chain 'B' and resid 42 through 57 removed outlier: 5.323A pdb=" N TYR B 49 " --> pdb=" O LYS B 45 " (cutoff:3.500A) Proline residue: B 50 - end of helix Processing helix chain 'B' and resid 77 through 88 Proline residue: B 86 - end of helix Processing helix chain 'B' and resid 92 through 103 removed outlier: 4.060A pdb=" N LYS B 95 " --> pdb=" O PRO B 92 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N LEU B 96 " --> pdb=" O GLU B 93 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N PHE B 102 " --> pdb=" O GLU B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 126 Processing helix chain 'B' and resid 144 through 157 removed outlier: 5.191A pdb=" N GLU B 148 " --> pdb=" O THR B 145 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N SER B 157 " --> pdb=" O ILE B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 188 removed outlier: 3.653A pdb=" N LEU B 183 " --> pdb=" O SER B 179 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 216 removed outlier: 4.259A pdb=" N MET B 212 " --> pdb=" O VAL B 208 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N VAL B 213 " --> pdb=" O GLN B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 259 removed outlier: 3.724A pdb=" N GLU B 252 " --> pdb=" O GLY B 248 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N PHE B 253 " --> pdb=" O TYR B 249 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N ILE B 255 " --> pdb=" O ASP B 251 " (cutoff:3.500A) removed outlier: 9.036A pdb=" N ILE B 256 " --> pdb=" O GLU B 252 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N ARG B 257 " --> pdb=" O PHE B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 272 Processing helix chain 'B' and resid 281 through 294 removed outlier: 3.683A pdb=" N CYS B 294 " --> pdb=" O LYS B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 316 through 319 removed outlier: 3.615A pdb=" N THR B 319 " --> pdb=" O GLY B 316 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 316 through 319' Processing helix chain 'B' and resid 322 through 324 No H-bonds generated for 'chain 'B' and resid 322 through 324' Processing helix chain 'B' and resid 436 through 446 Processing helix chain 'B' and resid 455 through 475 removed outlier: 3.876A pdb=" N PHE B 465 " --> pdb=" O ALA B 461 " (cutoff:3.500A) Proline residue: B 467 - end of helix Processing helix chain 'B' and resid 490 through 498 Processing helix chain 'C' and resid 42 through 57 removed outlier: 5.315A pdb=" N TYR C 49 " --> pdb=" O LYS C 45 " (cutoff:3.500A) Proline residue: C 50 - end of helix Processing helix chain 'C' and resid 77 through 87 Proline residue: C 86 - end of helix Processing helix chain 'C' and resid 92 through 103 removed outlier: 3.831A pdb=" N LYS C 95 " --> pdb=" O PRO C 92 " (cutoff:3.500A) removed outlier: 5.249A pdb=" N LEU C 96 " --> pdb=" O GLU C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 115 through 126 Processing helix chain 'C' and resid 144 through 157 removed outlier: 5.351A pdb=" N GLU C 148 " --> pdb=" O THR C 145 " (cutoff:3.500A) Processing helix chain 'C' and resid 177 through 188 removed outlier: 3.555A pdb=" N LEU C 183 " --> pdb=" O SER C 179 " (cutoff:3.500A) Processing helix chain 'C' and resid 201 through 204 Processing helix chain 'C' and resid 206 through 216 removed outlier: 4.170A pdb=" N MET C 212 " --> pdb=" O VAL C 208 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N VAL C 213 " --> pdb=" O GLN C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 247 through 253 Processing helix chain 'C' and resid 255 through 259 Processing helix chain 'C' and resid 263 through 272 Processing helix chain 'C' and resid 281 through 294 removed outlier: 3.682A pdb=" N CYS C 294 " --> pdb=" O LYS C 290 " (cutoff:3.500A) Processing helix chain 'C' and resid 300 through 302 No H-bonds generated for 'chain 'C' and resid 300 through 302' Processing helix chain 'C' and resid 316 through 319 removed outlier: 3.558A pdb=" N THR C 319 " --> pdb=" O GLY C 316 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 316 through 319' Processing helix chain 'C' and resid 436 through 446 Processing helix chain 'C' and resid 455 through 475 removed outlier: 3.759A pdb=" N PHE C 465 " --> pdb=" O ALA C 461 " (cutoff:3.500A) Proline residue: C 467 - end of helix Processing helix chain 'C' and resid 490 through 498 Processing helix chain 'D' and resid 42 through 57 removed outlier: 5.432A pdb=" N TYR D 49 " --> pdb=" O LYS D 45 " (cutoff:3.500A) Proline residue: D 50 - end of helix Processing helix chain 'D' and resid 77 through 88 Proline residue: D 86 - end of helix Processing helix chain 'D' and resid 92 through 103 removed outlier: 4.734A pdb=" N LEU D 96 " --> pdb=" O GLU D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 115 through 126 Processing helix chain 'D' and resid 144 through 157 removed outlier: 5.235A pdb=" N GLU D 148 " --> pdb=" O THR D 145 " (cutoff:3.500A) Processing helix chain 'D' and resid 177 through 188 removed outlier: 3.560A pdb=" N LEU D 183 " --> pdb=" O SER D 179 " (cutoff:3.500A) Processing helix chain 'D' and resid 201 through 203 No H-bonds generated for 'chain 'D' and resid 201 through 203' Processing helix chain 'D' and resid 206 through 216 removed outlier: 4.340A pdb=" N MET D 212 " --> pdb=" O VAL D 208 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N VAL D 213 " --> pdb=" O GLN D 209 " (cutoff:3.500A) Processing helix chain 'D' and resid 247 through 253 Processing helix chain 'D' and resid 255 through 259 Processing helix chain 'D' and resid 263 through 272 Processing helix chain 'D' and resid 281 through 294 removed outlier: 3.674A pdb=" N CYS D 294 " --> pdb=" O LYS D 290 " (cutoff:3.500A) Processing helix chain 'D' and resid 316 through 319 Processing helix chain 'D' and resid 322 through 324 No H-bonds generated for 'chain 'D' and resid 322 through 324' Processing helix chain 'D' and resid 436 through 446 Processing helix chain 'D' and resid 455 through 475 removed outlier: 3.625A pdb=" N PHE D 465 " --> pdb=" O ALA D 461 " (cutoff:3.500A) Proline residue: D 467 - end of helix Processing helix chain 'D' and resid 490 through 499 Processing sheet with id= A, first strand: chain 'A' and resid 196 through 198 removed outlier: 8.110A pdb=" N TYR A 197 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N ILE A 167 " --> pdb=" O TYR A 197 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N ARG A 136 " --> pdb=" O ARG A 166 " (cutoff:3.500A) removed outlier: 8.491A pdb=" N ILE A 168 " --> pdb=" O ARG A 136 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N PHE A 138 " --> pdb=" O ILE A 168 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ALA A 71 " --> pdb=" O VAL A 108 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 480 through 483 removed outlier: 3.555A pdb=" N GLN A 307 " --> pdb=" O ILE A 480 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N GLN A 372 " --> pdb=" O ALA A 231 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N VAL A 233 " --> pdb=" O ARG A 370 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N ARG A 370 " --> pdb=" O VAL A 233 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N LEU A 235 " --> pdb=" O GLU A 368 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N GLU A 368 " --> pdb=" O LEU A 235 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N PHE A 237 " --> pdb=" O LYS A 366 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N LYS A 366 " --> pdb=" O PHE A 237 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N VAL A 369 " --> pdb=" O ARG A 393 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N ARG A 393 " --> pdb=" O VAL A 369 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N LEU A 371 " --> pdb=" O VAL A 391 " (cutoff:3.500A) removed outlier: 5.514A pdb=" N VAL A 391 " --> pdb=" O LEU A 371 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N PHE A 373 " --> pdb=" O GLU A 389 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N GLU A 389 " --> pdb=" O PHE A 373 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 196 through 198 removed outlier: 8.094A pdb=" N TYR B 197 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ILE B 167 " --> pdb=" O TYR B 197 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N ARG B 136 " --> pdb=" O ARG B 166 " (cutoff:3.500A) removed outlier: 8.667A pdb=" N ILE B 168 " --> pdb=" O ARG B 136 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N PHE B 138 " --> pdb=" O ILE B 168 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA B 71 " --> pdb=" O VAL B 108 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 480 through 483 removed outlier: 3.594A pdb=" N GLN B 307 " --> pdb=" O ILE B 480 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N TYR B 482 " --> pdb=" O GLN B 307 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N GLN B 372 " --> pdb=" O ALA B 231 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N VAL B 233 " --> pdb=" O ARG B 370 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N ARG B 370 " --> pdb=" O VAL B 233 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N LEU B 235 " --> pdb=" O GLU B 368 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N GLU B 368 " --> pdb=" O LEU B 235 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N PHE B 237 " --> pdb=" O LYS B 366 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N LYS B 366 " --> pdb=" O PHE B 237 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N VAL B 369 " --> pdb=" O ARG B 393 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N ARG B 393 " --> pdb=" O VAL B 369 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N LEU B 371 " --> pdb=" O VAL B 391 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N VAL B 391 " --> pdb=" O LEU B 371 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N PHE B 373 " --> pdb=" O GLU B 389 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N GLU B 389 " --> pdb=" O PHE B 373 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N THR B 402 " --> pdb=" O LEU B 420 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 196 through 198 removed outlier: 8.152A pdb=" N TYR C 197 " --> pdb=" O ASN C 165 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N ILE C 167 " --> pdb=" O TYR C 197 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N ARG C 136 " --> pdb=" O ARG C 166 " (cutoff:3.500A) removed outlier: 8.561A pdb=" N ILE C 168 " --> pdb=" O ARG C 136 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N PHE C 138 " --> pdb=" O ILE C 168 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N ILE C 33 " --> pdb=" O LEU C 137 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N TYR C 139 " --> pdb=" O ILE C 33 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N ILE C 35 " --> pdb=" O TYR C 139 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ALA C 71 " --> pdb=" O VAL C 108 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 480 through 483 removed outlier: 3.596A pdb=" N GLN C 307 " --> pdb=" O ILE C 480 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N GLN C 372 " --> pdb=" O ALA C 231 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N VAL C 233 " --> pdb=" O ARG C 370 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ARG C 370 " --> pdb=" O VAL C 233 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N LEU C 235 " --> pdb=" O GLU C 368 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N GLU C 368 " --> pdb=" O LEU C 235 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N PHE C 237 " --> pdb=" O LYS C 366 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N LYS C 366 " --> pdb=" O PHE C 237 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N VAL C 369 " --> pdb=" O ARG C 393 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N ARG C 393 " --> pdb=" O VAL C 369 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N LEU C 371 " --> pdb=" O VAL C 391 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N VAL C 391 " --> pdb=" O LEU C 371 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N PHE C 373 " --> pdb=" O GLU C 389 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N GLU C 389 " --> pdb=" O PHE C 373 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA C 399 " --> pdb=" O ARG C 393 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THR C 402 " --> pdb=" O LEU C 420 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'D' and resid 135 through 140 removed outlier: 3.749A pdb=" N ALA D 71 " --> pdb=" O VAL D 108 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 167 through 169 Processing sheet with id= I, first strand: chain 'D' and resid 480 through 483 removed outlier: 6.899A pdb=" N GLN D 372 " --> pdb=" O ALA D 231 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N VAL D 233 " --> pdb=" O ARG D 370 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ARG D 370 " --> pdb=" O VAL D 233 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N LEU D 235 " --> pdb=" O GLU D 368 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N GLU D 368 " --> pdb=" O LEU D 235 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N PHE D 237 " --> pdb=" O LYS D 366 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N LYS D 366 " --> pdb=" O PHE D 237 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N VAL D 369 " --> pdb=" O ARG D 393 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N ARG D 393 " --> pdb=" O VAL D 369 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N LEU D 371 " --> pdb=" O VAL D 391 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N VAL D 391 " --> pdb=" O LEU D 371 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N PHE D 373 " --> pdb=" O GLU D 389 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N GLU D 389 " --> pdb=" O PHE D 373 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ALA D 399 " --> pdb=" O ARG D 393 " (cutoff:3.500A) 570 hydrogen bonds defined for protein. 1455 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.01 Time building geometry restraints manager: 6.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2640 1.31 - 1.43: 4580 1.43 - 1.56: 9176 1.56 - 1.69: 44 1.69 - 1.81: 132 Bond restraints: 16572 Sorted by residual: bond pdb=" C1B NAP A 602 " pdb=" C2B NAP A 602 " ideal model delta sigma weight residual 1.528 1.308 0.220 2.00e-02 2.50e+03 1.21e+02 bond pdb=" C1B NAP D 602 " pdb=" C2B NAP D 602 " ideal model delta sigma weight residual 1.528 1.308 0.220 2.00e-02 2.50e+03 1.21e+02 bond pdb=" C1B NAP C 602 " pdb=" C2B NAP C 602 " ideal model delta sigma weight residual 1.528 1.309 0.219 2.00e-02 2.50e+03 1.20e+02 bond pdb=" C1B NAP C 601 " pdb=" C2B NAP C 601 " ideal model delta sigma weight residual 1.528 1.309 0.219 2.00e-02 2.50e+03 1.20e+02 bond pdb=" C1B NAP D 601 " pdb=" C2B NAP D 601 " ideal model delta sigma weight residual 1.528 1.309 0.219 2.00e-02 2.50e+03 1.20e+02 ... (remaining 16567 not shown) Histogram of bond angle deviations from ideal: 99.13 - 106.17: 490 106.17 - 113.21: 8796 113.21 - 120.26: 6242 120.26 - 127.30: 6769 127.30 - 134.34: 203 Bond angle restraints: 22500 Sorted by residual: angle pdb=" N GLN C 133 " pdb=" CA GLN C 133 " pdb=" C GLN C 133 " ideal model delta sigma weight residual 112.87 105.78 7.09 1.20e+00 6.94e-01 3.49e+01 angle pdb=" N1A NAP B 602 " pdb=" C6A NAP B 602 " pdb=" N6A NAP B 602 " ideal model delta sigma weight residual 119.30 105.57 13.73 3.00e+00 1.11e-01 2.09e+01 angle pdb=" N1A NAP C 602 " pdb=" C6A NAP C 602 " pdb=" N6A NAP C 602 " ideal model delta sigma weight residual 119.30 105.58 13.72 3.00e+00 1.11e-01 2.09e+01 angle pdb=" N1A NAP A 602 " pdb=" C6A NAP A 602 " pdb=" N6A NAP A 602 " ideal model delta sigma weight residual 119.30 105.61 13.69 3.00e+00 1.11e-01 2.08e+01 angle pdb=" N1A NAP B 601 " pdb=" C6A NAP B 601 " pdb=" N6A NAP B 601 " ideal model delta sigma weight residual 119.30 105.61 13.69 3.00e+00 1.11e-01 2.08e+01 ... (remaining 22495 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.69: 9215 21.69 - 43.38: 780 43.38 - 65.07: 188 65.07 - 86.76: 29 86.76 - 108.45: 20 Dihedral angle restraints: 10232 sinusoidal: 4592 harmonic: 5640 Sorted by residual: dihedral pdb=" C3 BG6 A 603 " pdb=" C4 BG6 A 603 " pdb=" C5 BG6 A 603 " pdb=" O5 BG6 A 603 " ideal model delta sinusoidal sigma weight residual 52.96 -55.49 108.45 1 3.00e+01 1.11e-03 1.40e+01 dihedral pdb=" C3 BG6 B 603 " pdb=" C4 BG6 B 603 " pdb=" C5 BG6 B 603 " pdb=" O5 BG6 B 603 " ideal model delta sinusoidal sigma weight residual 52.96 -55.14 108.10 1 3.00e+01 1.11e-03 1.40e+01 dihedral pdb=" C2 BG6 D 603 " pdb=" C3 BG6 D 603 " pdb=" C4 BG6 D 603 " pdb=" C5 BG6 D 603 " ideal model delta sinusoidal sigma weight residual -52.82 54.60 -107.42 1 3.00e+01 1.11e-03 1.39e+01 ... (remaining 10229 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 2101 0.075 - 0.149: 267 0.149 - 0.223: 4 0.223 - 0.298: 8 0.298 - 0.372: 16 Chirality restraints: 2396 Sorted by residual: chirality pdb=" C2B NAP D 602 " pdb=" C1B NAP D 602 " pdb=" C3B NAP D 602 " pdb=" O2B NAP D 602 " both_signs ideal model delta sigma weight residual False -2.75 -2.38 -0.37 2.00e-01 2.50e+01 3.47e+00 chirality pdb=" C2B NAP C 602 " pdb=" C1B NAP C 602 " pdb=" C3B NAP C 602 " pdb=" O2B NAP C 602 " both_signs ideal model delta sigma weight residual False -2.75 -2.39 -0.37 2.00e-01 2.50e+01 3.36e+00 chirality pdb=" C2B NAP A 602 " pdb=" C1B NAP A 602 " pdb=" C3B NAP A 602 " pdb=" O2B NAP A 602 " both_signs ideal model delta sigma weight residual False -2.75 -2.39 -0.36 2.00e-01 2.50e+01 3.25e+00 ... (remaining 2393 not shown) Planarity restraints: 2868 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN D 311 " 0.050 5.00e-02 4.00e+02 7.56e-02 9.14e+00 pdb=" N PRO D 312 " -0.131 5.00e-02 4.00e+02 pdb=" CA PRO D 312 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO D 312 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 91 " -0.036 5.00e-02 4.00e+02 5.44e-02 4.73e+00 pdb=" N PRO B 92 " 0.094 5.00e-02 4.00e+02 pdb=" CA PRO B 92 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 92 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 91 " -0.035 5.00e-02 4.00e+02 5.26e-02 4.42e+00 pdb=" N PRO C 92 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO C 92 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO C 92 " -0.029 5.00e-02 4.00e+02 ... (remaining 2865 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1569 2.74 - 3.28: 16517 3.28 - 3.82: 28627 3.82 - 4.36: 35256 4.36 - 4.90: 58883 Nonbonded interactions: 140852 Sorted by model distance: nonbonded pdb=" OH TYR A 70 " pdb=" O GLN A 111 " model vdw 2.204 2.440 nonbonded pdb=" NH1 ARG A 215 " pdb=" O MET A 273 " model vdw 2.206 2.520 nonbonded pdb=" OH TYR D 139 " pdb=" OE1 GLU D 170 " model vdw 2.220 2.440 nonbonded pdb=" OG1 THR C 91 " pdb=" OE1 GLU C 94 " model vdw 2.221 2.440 nonbonded pdb=" NH1 ARG B 215 " pdb=" O MET B 273 " model vdw 2.235 2.520 ... (remaining 140847 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 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 2.240 Check model and map are aligned: 0.220 Set scattering table: 0.140 Process input model: 45.340 Find NCS groups from input model: 0.990 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.220 16572 Z= 0.604 Angle : 0.964 13.727 22500 Z= 0.400 Chirality : 0.055 0.372 2396 Planarity : 0.005 0.076 2868 Dihedral : 17.363 108.447 6608 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.05 % Favored : 95.80 % Rotamer: Outliers : 0.47 % Allowed : 0.77 % Favored : 98.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: -0.44 (0.20), residues: 1928 helix: 0.31 (0.21), residues: 688 sheet: -1.21 (0.28), residues: 352 loop : -0.21 (0.21), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP D 164 HIS 0.008 0.001 HIS A 124 PHE 0.012 0.001 PHE B 412 TYR 0.018 0.001 TYR D 139 ARG 0.009 0.000 ARG A 459 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 259 time to evaluate : 1.991 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: A 497 LYS cc_start: 0.8410 (ptmm) cc_final: 0.7841 (mmtm) REVERT: B 130 LEU cc_start: 0.8274 (OUTLIER) cc_final: 0.7900 (mt) REVERT: B 261 GLN cc_start: 0.8694 (tm-30) cc_final: 0.8209 (tm-30) REVERT: C 37 MET cc_start: 0.7134 (mmt) cc_final: 0.6780 (mmp) REVERT: C 483 ILE cc_start: 0.7407 (mm) cc_final: 0.7174 (pt) outliers start: 8 outliers final: 3 residues processed: 266 average time/residue: 1.2778 time to fit residues: 377.2850 Evaluate side-chains 174 residues out of total 1696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 170 time to evaluate : 1.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain C residue 132 SER Chi-restraints excluded: chain C residue 282 ASP Chi-restraints excluded: chain C residue 327 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 162 optimal weight: 0.5980 chunk 145 optimal weight: 7.9990 chunk 80 optimal weight: 7.9990 chunk 49 optimal weight: 5.9990 chunk 98 optimal weight: 6.9990 chunk 77 optimal weight: 20.0000 chunk 150 optimal weight: 3.9990 chunk 58 optimal weight: 8.9990 chunk 91 optimal weight: 6.9990 chunk 112 optimal weight: 10.0000 chunk 174 optimal weight: 0.0060 overall best weight: 3.5202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 ASN A 124 HIS A 186 HIS ** A 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 430 ASN B 64 ASN ** B 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 129 HIS D 165 ASN D 430 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.1195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 16572 Z= 0.267 Angle : 0.633 12.105 22500 Z= 0.319 Chirality : 0.045 0.141 2396 Planarity : 0.005 0.059 2868 Dihedral : 16.089 105.035 2714 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.05 % Favored : 95.90 % Rotamer: Outliers : 2.12 % Allowed : 10.85 % Favored : 87.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: -0.62 (0.20), residues: 1928 helix: -0.02 (0.21), residues: 700 sheet: -1.24 (0.27), residues: 360 loop : -0.16 (0.21), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP B 462 HIS 0.012 0.001 HIS A 201 PHE 0.011 0.001 PHE D 102 TYR 0.018 0.001 TYR D 308 ARG 0.010 0.001 ARG A 136 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 177 time to evaluate : 1.847 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 411 MET cc_start: 0.8159 (mmm) cc_final: 0.7818 (mmt) REVERT: B 108 VAL cc_start: 0.8286 (t) cc_final: 0.7997 (m) REVERT: B 130 LEU cc_start: 0.8404 (OUTLIER) cc_final: 0.8039 (mt) REVERT: B 159 MET cc_start: 0.6487 (mmt) cc_final: 0.6059 (tpt) REVERT: C 411 MET cc_start: 0.7727 (tpp) cc_final: 0.7492 (mmt) REVERT: C 456 ASP cc_start: 0.8091 (m-30) cc_final: 0.7888 (m-30) REVERT: D 411 MET cc_start: 0.8037 (tpp) cc_final: 0.7490 (mpp) REVERT: D 456 ASP cc_start: 0.7749 (OUTLIER) cc_final: 0.7381 (p0) outliers start: 36 outliers final: 15 residues processed: 192 average time/residue: 1.2554 time to fit residues: 268.6414 Evaluate side-chains 173 residues out of total 1696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 156 time to evaluate : 1.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 HIS Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 296 SER Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain C residue 129 HIS Chi-restraints excluded: chain C residue 147 TYR Chi-restraints excluded: chain C residue 282 ASP Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 327 THR Chi-restraints excluded: chain D residue 113 ASP Chi-restraints excluded: chain D residue 159 MET Chi-restraints excluded: chain D residue 382 HIS Chi-restraints excluded: chain D residue 404 MET Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain D residue 456 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 96 optimal weight: 10.0000 chunk 54 optimal weight: 9.9990 chunk 145 optimal weight: 6.9990 chunk 118 optimal weight: 3.9990 chunk 48 optimal weight: 10.0000 chunk 174 optimal weight: 30.0000 chunk 188 optimal weight: 6.9990 chunk 155 optimal weight: 8.9990 chunk 173 optimal weight: 5.9990 chunk 59 optimal weight: 5.9990 chunk 140 optimal weight: 5.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 HIS ** A 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 430 ASN ** B 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 470 HIS C 129 HIS ** C 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 430 ASN ** D 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.1753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 16572 Z= 0.379 Angle : 0.662 9.624 22500 Z= 0.335 Chirality : 0.046 0.140 2396 Planarity : 0.005 0.052 2868 Dihedral : 15.755 108.467 2713 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 13.01 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.46 % Favored : 95.49 % Rotamer: Outliers : 2.24 % Allowed : 13.50 % Favored : 84.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: -0.82 (0.19), residues: 1928 helix: -0.14 (0.20), residues: 692 sheet: -1.31 (0.26), residues: 388 loop : -0.28 (0.21), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP B 462 HIS 0.010 0.001 HIS A 201 PHE 0.013 0.002 PHE A 88 TYR 0.026 0.002 TYR D 308 ARG 0.009 0.001 ARG D 459 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 166 time to evaluate : 1.820 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 MET cc_start: 0.7634 (mmt) cc_final: 0.7368 (tpt) REVERT: A 281 SER cc_start: 0.7879 (m) cc_final: 0.7417 (m) REVERT: A 419 GLU cc_start: 0.7990 (pm20) cc_final: 0.7774 (pm20) REVERT: B 108 VAL cc_start: 0.8372 (t) cc_final: 0.8080 (m) REVERT: B 130 LEU cc_start: 0.8629 (OUTLIER) cc_final: 0.8232 (mt) REVERT: B 154 ILE cc_start: 0.8437 (tt) cc_final: 0.8090 (tp) REVERT: B 159 MET cc_start: 0.6701 (mmt) cc_final: 0.6359 (tpt) REVERT: D 382 HIS cc_start: 0.8139 (OUTLIER) cc_final: 0.7547 (m-70) REVERT: D 456 ASP cc_start: 0.7882 (OUTLIER) cc_final: 0.7366 (p0) outliers start: 38 outliers final: 17 residues processed: 188 average time/residue: 1.2477 time to fit residues: 261.2555 Evaluate side-chains 175 residues out of total 1696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 155 time to evaluate : 1.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 GLN Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 296 SER Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain C residue 147 TYR Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 327 THR Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain D residue 119 GLN Chi-restraints excluded: chain D residue 147 TYR Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 159 MET Chi-restraints excluded: chain D residue 258 ASP Chi-restraints excluded: chain D residue 315 GLU Chi-restraints excluded: chain D residue 382 HIS Chi-restraints excluded: chain D residue 404 MET Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain D residue 456 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 172 optimal weight: 6.9990 chunk 131 optimal weight: 10.0000 chunk 90 optimal weight: 9.9990 chunk 19 optimal weight: 10.0000 chunk 83 optimal weight: 1.9990 chunk 117 optimal weight: 0.4980 chunk 175 optimal weight: 10.0000 chunk 185 optimal weight: 8.9990 chunk 91 optimal weight: 0.0670 chunk 166 optimal weight: 6.9990 chunk 50 optimal weight: 7.9990 overall best weight: 3.3124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 430 ASN ** B 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 129 HIS ** D 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.1889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 16572 Z= 0.254 Angle : 0.609 8.704 22500 Z= 0.306 Chirality : 0.044 0.140 2396 Planarity : 0.004 0.048 2868 Dihedral : 15.258 107.611 2711 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.10 % Favored : 95.85 % Rotamer: Outliers : 2.30 % Allowed : 14.74 % Favored : 82.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: -0.73 (0.19), residues: 1928 helix: -0.08 (0.21), residues: 692 sheet: -1.22 (0.25), residues: 408 loop : -0.22 (0.22), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP B 462 HIS 0.010 0.001 HIS A 201 PHE 0.011 0.001 PHE D 413 TYR 0.020 0.001 TYR A 482 ARG 0.008 0.000 ARG D 459 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 173 time to evaluate : 1.718 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 281 SER cc_start: 0.7863 (m) cc_final: 0.7416 (m) REVERT: A 368 GLU cc_start: 0.7498 (tt0) cc_final: 0.6856 (pt0) REVERT: A 419 GLU cc_start: 0.7934 (pm20) cc_final: 0.7618 (pm20) REVERT: B 108 VAL cc_start: 0.8285 (t) cc_final: 0.7992 (m) REVERT: B 130 LEU cc_start: 0.8644 (OUTLIER) cc_final: 0.8239 (mt) REVERT: B 159 MET cc_start: 0.6670 (mmt) cc_final: 0.6328 (tpt) REVERT: B 456 ASP cc_start: 0.8090 (OUTLIER) cc_final: 0.7834 (p0) REVERT: C 459 ARG cc_start: 0.7826 (mtp-110) cc_final: 0.7330 (mtp85) REVERT: D 456 ASP cc_start: 0.7730 (OUTLIER) cc_final: 0.7294 (p0) outliers start: 39 outliers final: 24 residues processed: 195 average time/residue: 1.2033 time to fit residues: 262.4952 Evaluate side-chains 183 residues out of total 1696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 156 time to evaluate : 1.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 GLN Chi-restraints excluded: chain A residue 301 ASN Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 456 ASP Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 296 SER Chi-restraints excluded: chain B residue 456 ASP Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain C residue 129 HIS Chi-restraints excluded: chain C residue 147 TYR Chi-restraints excluded: chain C residue 327 THR Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain C residue 456 ASP Chi-restraints excluded: chain D residue 119 GLN Chi-restraints excluded: chain D residue 147 TYR Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 159 MET Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 258 ASP Chi-restraints excluded: chain D residue 282 ASP Chi-restraints excluded: chain D residue 315 GLU Chi-restraints excluded: chain D residue 345 GLU Chi-restraints excluded: chain D residue 439 ARG Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain D residue 456 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 154 optimal weight: 20.0000 chunk 105 optimal weight: 20.0000 chunk 2 optimal weight: 1.9990 chunk 138 optimal weight: 10.0000 chunk 76 optimal weight: 10.0000 chunk 158 optimal weight: 6.9990 chunk 128 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 94 optimal weight: 10.0000 chunk 166 optimal weight: 7.9990 chunk 46 optimal weight: 2.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 430 ASN ** B 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 129 HIS ** C 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 430 ASN ** D 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.2098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 16572 Z= 0.328 Angle : 0.642 9.708 22500 Z= 0.322 Chirality : 0.045 0.142 2396 Planarity : 0.005 0.049 2868 Dihedral : 15.139 109.023 2711 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 13.48 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.67 % Favored : 95.28 % Rotamer: Outliers : 3.12 % Allowed : 15.62 % Favored : 81.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.19), residues: 1928 helix: -0.14 (0.21), residues: 692 sheet: -1.30 (0.25), residues: 408 loop : -0.24 (0.22), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP B 462 HIS 0.013 0.001 HIS C 129 PHE 0.011 0.001 PHE A 88 TYR 0.023 0.002 TYR D 308 ARG 0.010 0.000 ARG B 459 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 168 time to evaluate : 1.981 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 281 SER cc_start: 0.7907 (m) cc_final: 0.7446 (m) REVERT: B 108 VAL cc_start: 0.8329 (t) cc_final: 0.8038 (m) REVERT: B 130 LEU cc_start: 0.8769 (OUTLIER) cc_final: 0.8411 (mt) REVERT: B 159 MET cc_start: 0.6803 (OUTLIER) cc_final: 0.6456 (tpt) REVERT: B 419 GLU cc_start: 0.8167 (pm20) cc_final: 0.7948 (pm20) REVERT: B 456 ASP cc_start: 0.8112 (OUTLIER) cc_final: 0.7845 (p0) REVERT: C 214 LEU cc_start: 0.9103 (OUTLIER) cc_final: 0.8869 (mp) REVERT: D 411 MET cc_start: 0.8048 (tpp) cc_final: 0.7619 (mpp) REVERT: D 456 ASP cc_start: 0.7783 (OUTLIER) cc_final: 0.7333 (p0) outliers start: 53 outliers final: 26 residues processed: 199 average time/residue: 1.1977 time to fit residues: 266.4588 Evaluate side-chains 191 residues out of total 1696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 160 time to evaluate : 1.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 GLN Chi-restraints excluded: chain A residue 301 ASN Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 456 ASP Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 147 TYR Chi-restraints excluded: chain B residue 159 MET Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 296 SER Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 456 ASP Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain C residue 147 TYR Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain C residue 327 THR Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 119 GLN Chi-restraints excluded: chain D residue 147 TYR Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 159 MET Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 258 ASP Chi-restraints excluded: chain D residue 262 ASN Chi-restraints excluded: chain D residue 282 ASP Chi-restraints excluded: chain D residue 315 GLU Chi-restraints excluded: chain D residue 345 GLU Chi-restraints excluded: chain D residue 439 ARG Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain D residue 456 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 62 optimal weight: 5.9990 chunk 167 optimal weight: 0.9990 chunk 36 optimal weight: 6.9990 chunk 108 optimal weight: 8.9990 chunk 45 optimal weight: 9.9990 chunk 185 optimal weight: 0.9980 chunk 154 optimal weight: 20.0000 chunk 86 optimal weight: 3.9990 chunk 15 optimal weight: 6.9990 chunk 61 optimal weight: 6.9990 chunk 97 optimal weight: 10.0000 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 430 ASN ** B 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 374 HIS ** D 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.2208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 16572 Z= 0.277 Angle : 0.618 8.524 22500 Z= 0.311 Chirality : 0.044 0.138 2396 Planarity : 0.004 0.052 2868 Dihedral : 14.882 108.715 2711 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 12.98 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.25 % Favored : 95.70 % Rotamer: Outliers : 2.48 % Allowed : 16.10 % Favored : 81.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: -0.77 (0.19), residues: 1928 helix: -0.09 (0.21), residues: 692 sheet: -1.32 (0.25), residues: 408 loop : -0.21 (0.22), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.001 TRP B 462 HIS 0.011 0.001 HIS A 186 PHE 0.015 0.001 PHE D 413 TYR 0.020 0.001 TYR D 308 ARG 0.012 0.000 ARG D 459 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 169 time to evaluate : 1.834 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 281 SER cc_start: 0.7899 (m) cc_final: 0.7444 (m) REVERT: A 330 ARG cc_start: 0.7382 (mmm160) cc_final: 0.7150 (mmp80) REVERT: B 108 VAL cc_start: 0.8325 (t) cc_final: 0.8041 (m) REVERT: B 130 LEU cc_start: 0.8783 (mt) cc_final: 0.8444 (mt) REVERT: B 419 GLU cc_start: 0.8154 (pm20) cc_final: 0.7936 (pm20) REVERT: B 456 ASP cc_start: 0.8085 (OUTLIER) cc_final: 0.7837 (p0) REVERT: C 125 MET cc_start: 0.5964 (tpt) cc_final: 0.5694 (tpt) REVERT: C 214 LEU cc_start: 0.9072 (OUTLIER) cc_final: 0.8835 (mp) REVERT: C 411 MET cc_start: 0.7858 (tpp) cc_final: 0.7574 (mmt) REVERT: D 287 GLU cc_start: 0.8177 (OUTLIER) cc_final: 0.7815 (mp0) REVERT: D 456 ASP cc_start: 0.7727 (OUTLIER) cc_final: 0.7318 (p0) outliers start: 42 outliers final: 25 residues processed: 194 average time/residue: 1.1938 time to fit residues: 258.7427 Evaluate side-chains 190 residues out of total 1696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 161 time to evaluate : 1.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 GLN Chi-restraints excluded: chain A residue 301 ASN Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 456 ASP Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain B residue 147 TYR Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 296 SER Chi-restraints excluded: chain B residue 456 ASP Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain C residue 147 TYR Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain C residue 282 ASP Chi-restraints excluded: chain C residue 327 THR Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 119 GLN Chi-restraints excluded: chain D residue 147 TYR Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 159 MET Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 258 ASP Chi-restraints excluded: chain D residue 262 ASN Chi-restraints excluded: chain D residue 282 ASP Chi-restraints excluded: chain D residue 287 GLU Chi-restraints excluded: chain D residue 345 GLU Chi-restraints excluded: chain D residue 439 ARG Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain D residue 456 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 179 optimal weight: 9.9990 chunk 20 optimal weight: 7.9990 chunk 105 optimal weight: 8.9990 chunk 135 optimal weight: 7.9990 chunk 156 optimal weight: 5.9990 chunk 103 optimal weight: 9.9990 chunk 185 optimal weight: 9.9990 chunk 115 optimal weight: 3.9990 chunk 112 optimal weight: 7.9990 chunk 85 optimal weight: 6.9990 chunk 114 optimal weight: 4.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 430 ASN B 126 ASN ** B 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.2428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 16572 Z= 0.394 Angle : 0.678 9.971 22500 Z= 0.343 Chirality : 0.046 0.146 2396 Planarity : 0.005 0.060 2868 Dihedral : 15.021 110.285 2709 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 14.08 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.82 % Favored : 95.12 % Rotamer: Outliers : 2.71 % Allowed : 16.75 % Favored : 80.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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 (0.19), residues: 1928 helix: -0.37 (0.20), residues: 720 sheet: -1.42 (0.25), residues: 408 loop : -0.23 (0.22), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.002 TRP B 462 HIS 0.014 0.001 HIS A 186 PHE 0.015 0.002 PHE A 88 TYR 0.026 0.002 TYR D 308 ARG 0.012 0.000 ARG B 459 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 166 time to evaluate : 2.028 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 108 VAL cc_start: 0.8416 (t) cc_final: 0.8130 (m) REVERT: B 130 LEU cc_start: 0.8857 (mt) cc_final: 0.8490 (mt) REVERT: B 159 MET cc_start: 0.6992 (mmt) cc_final: 0.6620 (tpt) REVERT: B 297 GLU cc_start: 0.7105 (pp20) cc_final: 0.6854 (pp20) REVERT: B 456 ASP cc_start: 0.8111 (OUTLIER) cc_final: 0.7866 (p0) REVERT: C 125 MET cc_start: 0.6023 (tpt) cc_final: 0.5689 (tpt) REVERT: C 214 LEU cc_start: 0.9087 (OUTLIER) cc_final: 0.8833 (mp) REVERT: D 411 MET cc_start: 0.8097 (tpp) cc_final: 0.7721 (mpp) outliers start: 46 outliers final: 29 residues processed: 194 average time/residue: 1.1931 time to fit residues: 259.1338 Evaluate side-chains 182 residues out of total 1696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 151 time to evaluate : 1.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 GLN Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 456 ASP Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain B residue 147 TYR Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 296 SER Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 456 ASP Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 147 TYR Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain C residue 327 THR Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 119 GLN Chi-restraints excluded: chain D residue 147 TYR Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 159 MET Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 262 ASN Chi-restraints excluded: chain D residue 282 ASP Chi-restraints excluded: chain D residue 345 GLU Chi-restraints excluded: chain D residue 439 ARG Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain D residue 456 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 73 optimal weight: 8.9990 chunk 110 optimal weight: 5.9990 chunk 55 optimal weight: 7.9990 chunk 36 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 chunk 117 optimal weight: 5.9990 chunk 126 optimal weight: 7.9990 chunk 91 optimal weight: 0.7980 chunk 17 optimal weight: 2.9990 chunk 145 optimal weight: 8.9990 chunk 168 optimal weight: 6.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 430 ASN ** B 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.2443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 16572 Z= 0.279 Angle : 0.635 9.299 22500 Z= 0.321 Chirality : 0.045 0.157 2396 Planarity : 0.005 0.061 2868 Dihedral : 14.741 109.358 2709 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 13.32 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.15 % Favored : 95.80 % Rotamer: Outliers : 2.71 % Allowed : 17.04 % Favored : 80.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: -0.95 (0.19), residues: 1928 helix: -0.36 (0.20), residues: 728 sheet: -1.38 (0.25), residues: 408 loop : -0.19 (0.22), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.074 0.002 TRP B 462 HIS 0.011 0.001 HIS A 186 PHE 0.014 0.001 PHE D 413 TYR 0.021 0.001 TYR C 118 ARG 0.013 0.000 ARG B 459 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 165 time to evaluate : 1.848 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 330 ARG cc_start: 0.7457 (mmm160) cc_final: 0.7154 (mmp80) REVERT: B 108 VAL cc_start: 0.8367 (t) cc_final: 0.8085 (m) REVERT: B 130 LEU cc_start: 0.8827 (mt) cc_final: 0.8474 (mt) REVERT: B 297 GLU cc_start: 0.7114 (pp20) cc_final: 0.6909 (pp20) REVERT: B 456 ASP cc_start: 0.8100 (OUTLIER) cc_final: 0.7844 (p0) REVERT: C 125 MET cc_start: 0.5942 (tpt) cc_final: 0.5669 (tpt) REVERT: C 214 LEU cc_start: 0.9089 (OUTLIER) cc_final: 0.8848 (mp) REVERT: D 287 GLU cc_start: 0.8168 (OUTLIER) cc_final: 0.7827 (mp0) REVERT: D 456 ASP cc_start: 0.7703 (OUTLIER) cc_final: 0.7286 (p0) outliers start: 46 outliers final: 30 residues processed: 199 average time/residue: 1.2116 time to fit residues: 269.4989 Evaluate side-chains 186 residues out of total 1696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 152 time to evaluate : 1.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 GLN Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 456 ASP Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain B residue 147 TYR Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 296 SER Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 456 ASP Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 147 TYR Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain C residue 282 ASP Chi-restraints excluded: chain C residue 327 THR Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain C residue 456 ASP Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 119 GLN Chi-restraints excluded: chain D residue 147 TYR Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 159 MET Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 262 ASN Chi-restraints excluded: chain D residue 282 ASP Chi-restraints excluded: chain D residue 287 GLU Chi-restraints excluded: chain D residue 345 GLU Chi-restraints excluded: chain D residue 439 ARG Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain D residue 456 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 177 optimal weight: 5.9990 chunk 161 optimal weight: 8.9990 chunk 172 optimal weight: 7.9990 chunk 103 optimal weight: 10.0000 chunk 75 optimal weight: 1.9990 chunk 135 optimal weight: 1.9990 chunk 52 optimal weight: 20.0000 chunk 155 optimal weight: 3.9990 chunk 163 optimal weight: 5.9990 chunk 171 optimal weight: 8.9990 chunk 113 optimal weight: 7.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 430 ASN ** B 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.2507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 16572 Z= 0.296 Angle : 0.659 11.495 22500 Z= 0.330 Chirality : 0.045 0.162 2396 Planarity : 0.005 0.069 2868 Dihedral : 14.649 109.762 2709 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 13.45 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.67 % Favored : 95.28 % Rotamer: Outliers : 2.42 % Allowed : 17.69 % Favored : 79.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: -0.96 (0.19), residues: 1928 helix: -0.38 (0.20), residues: 728 sheet: -1.37 (0.25), residues: 408 loop : -0.18 (0.22), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.090 0.002 TRP B 462 HIS 0.013 0.001 HIS A 186 PHE 0.010 0.001 PHE D 337 TYR 0.021 0.002 TYR D 308 ARG 0.013 0.000 ARG B 459 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 160 time to evaluate : 2.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 108 VAL cc_start: 0.8376 (t) cc_final: 0.8098 (m) REVERT: B 130 LEU cc_start: 0.8845 (mt) cc_final: 0.8502 (mt) REVERT: B 159 MET cc_start: 0.6889 (mmt) cc_final: 0.6538 (tpt) REVERT: B 297 GLU cc_start: 0.7110 (pp20) cc_final: 0.6894 (pp20) REVERT: B 456 ASP cc_start: 0.8093 (OUTLIER) cc_final: 0.7845 (p0) REVERT: C 125 MET cc_start: 0.6012 (tpt) cc_final: 0.5774 (tpt) REVERT: C 159 MET cc_start: 0.6195 (OUTLIER) cc_final: 0.5730 (tpt) REVERT: C 214 LEU cc_start: 0.9078 (OUTLIER) cc_final: 0.8832 (mp) REVERT: C 411 MET cc_start: 0.7798 (tpp) cc_final: 0.7535 (mmp) REVERT: D 287 GLU cc_start: 0.8172 (OUTLIER) cc_final: 0.7810 (mp0) REVERT: D 456 ASP cc_start: 0.7685 (OUTLIER) cc_final: 0.7264 (p0) outliers start: 41 outliers final: 29 residues processed: 189 average time/residue: 1.2573 time to fit residues: 265.8191 Evaluate side-chains 187 residues out of total 1696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 153 time to evaluate : 1.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 GLN Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 301 ASN Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 456 ASP Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain B residue 147 TYR Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 296 SER Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 456 ASP Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 147 TYR Chi-restraints excluded: chain C residue 159 MET Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain C residue 327 THR Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain C residue 456 ASP Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 119 GLN Chi-restraints excluded: chain D residue 147 TYR Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 159 MET Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 262 ASN Chi-restraints excluded: chain D residue 282 ASP Chi-restraints excluded: chain D residue 287 GLU Chi-restraints excluded: chain D residue 439 ARG Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain D residue 456 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 182 optimal weight: 6.9990 chunk 111 optimal weight: 6.9990 chunk 86 optimal weight: 0.3980 chunk 126 optimal weight: 7.9990 chunk 191 optimal weight: 0.4980 chunk 176 optimal weight: 8.9990 chunk 152 optimal weight: 8.9990 chunk 15 optimal weight: 7.9990 chunk 117 optimal weight: 4.9990 chunk 93 optimal weight: 0.8980 chunk 120 optimal weight: 3.9990 overall best weight: 2.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 430 ASN ** B 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 470 HIS ** C 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.2476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 16572 Z= 0.216 Angle : 0.629 11.242 22500 Z= 0.316 Chirality : 0.044 0.154 2396 Planarity : 0.004 0.068 2868 Dihedral : 14.344 108.998 2709 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.84 % Favored : 96.11 % Rotamer: Outliers : 1.95 % Allowed : 18.75 % Favored : 79.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: -0.80 (0.20), residues: 1928 helix: -0.19 (0.21), residues: 704 sheet: -1.29 (0.25), residues: 408 loop : -0.17 (0.22), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.077 0.002 TRP B 462 HIS 0.014 0.001 HIS A 186 PHE 0.014 0.001 PHE D 413 TYR 0.022 0.001 TYR C 118 ARG 0.014 0.000 ARG B 459 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 167 time to evaluate : 1.951 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 281 SER cc_start: 0.7875 (m) cc_final: 0.7417 (m) REVERT: A 330 ARG cc_start: 0.7444 (mmm160) cc_final: 0.7099 (mmp80) REVERT: B 108 VAL cc_start: 0.8310 (t) cc_final: 0.8055 (m) REVERT: B 130 LEU cc_start: 0.8832 (mt) cc_final: 0.8484 (mt) REVERT: B 297 GLU cc_start: 0.7092 (pp20) cc_final: 0.6828 (pp20) REVERT: B 456 ASP cc_start: 0.8052 (OUTLIER) cc_final: 0.7822 (p0) REVERT: C 125 MET cc_start: 0.5949 (tpt) cc_final: 0.5715 (tpt) REVERT: C 159 MET cc_start: 0.6080 (OUTLIER) cc_final: 0.5655 (tpp) REVERT: D 287 GLU cc_start: 0.8121 (OUTLIER) cc_final: 0.7791 (mp0) outliers start: 33 outliers final: 26 residues processed: 187 average time/residue: 1.2646 time to fit residues: 264.3696 Evaluate side-chains 185 residues out of total 1696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 156 time to evaluate : 1.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 GLN Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 301 ASN Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 456 ASP Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain B residue 147 TYR Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 456 ASP Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 147 TYR Chi-restraints excluded: chain C residue 159 MET Chi-restraints excluded: chain C residue 327 THR Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 119 GLN Chi-restraints excluded: chain D residue 147 TYR Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 262 ASN Chi-restraints excluded: chain D residue 282 ASP Chi-restraints excluded: chain D residue 287 GLU Chi-restraints excluded: chain D residue 315 GLU Chi-restraints excluded: chain D residue 439 ARG Chi-restraints excluded: chain D residue 453 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 162 optimal weight: 0.9980 chunk 46 optimal weight: 8.9990 chunk 140 optimal weight: 5.9990 chunk 22 optimal weight: 2.9990 chunk 42 optimal weight: 10.0000 chunk 152 optimal weight: 30.0000 chunk 63 optimal weight: 8.9990 chunk 156 optimal weight: 0.7980 chunk 19 optimal weight: 2.9990 chunk 28 optimal weight: 0.3980 chunk 133 optimal weight: 4.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 430 ASN ** B 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 470 HIS ** C 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.144442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.119804 restraints weight = 26034.405| |-----------------------------------------------------------------------------| r_work (start): 0.3826 rms_B_bonded: 2.69 r_work: 0.3746 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.2490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 16572 Z= 0.192 Angle : 0.622 11.246 22500 Z= 0.312 Chirality : 0.044 0.272 2396 Planarity : 0.004 0.058 2868 Dihedral : 14.109 108.754 2709 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 12.60 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.84 % Favored : 96.11 % Rotamer: Outliers : 1.71 % Allowed : 19.10 % Favored : 79.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: -0.73 (0.20), residues: 1928 helix: -0.17 (0.21), residues: 704 sheet: -1.23 (0.25), residues: 408 loop : -0.12 (0.22), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.067 0.002 TRP B 462 HIS 0.008 0.001 HIS A 201 PHE 0.009 0.001 PHE D 101 TYR 0.023 0.001 TYR C 70 ARG 0.013 0.000 ARG D 459 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4887.58 seconds wall clock time: 88 minutes 36.69 seconds (5316.69 seconds total)