Starting phenix.real_space_refine on Tue Dec 31 00:34:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9c86_45298/12_2024/9c86_45298.cif Found real_map, /net/cci-nas-00/data/ceres_data/9c86_45298/12_2024/9c86_45298.map 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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9c86_45298/12_2024/9c86_45298.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9c86_45298/12_2024/9c86_45298.map" model { file = "/net/cci-nas-00/data/ceres_data/9c86_45298/12_2024/9c86_45298.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9c86_45298/12_2024/9c86_45298.cif" } 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= 0.001 sd= 0.036 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 S 67 5.16 5 C 9177 2.51 5 N 2503 2.21 5 O 2749 1.98 5 H 44 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 14540 Number of models: 1 Model: "" Number of chains: 5 Chain: "C" Number of atoms: 3544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 483, 3544 Classifications: {'peptide': 483} Incomplete info: {'truncation_to_alanine': 48} Link IDs: {'PTRANS': 22, 'TRANS': 460} Unresolved non-hydrogen bonds: 175 Unresolved non-hydrogen angles: 212 Unresolved non-hydrogen dihedrals: 140 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 11, 'ASN:plan1': 1, 'HIS:plan': 1, 'GLU:plan': 10, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 126 Chain: "D" Number of atoms: 3570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 483, 3570 Classifications: {'peptide': 483} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'PTRANS': 22, 'TRANS': 460} Unresolved non-hydrogen bonds: 148 Unresolved non-hydrogen angles: 178 Unresolved non-hydrogen dihedrals: 118 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 12, 'ARG:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 9} Unresolved non-hydrogen planarities: 105 Chain: "A" Number of atoms: 3713 Number of conformers: 1 Conformer: "" Number of residues, atoms: 492, 3713 Classifications: {'peptide': 492} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 23, 'TRANS': 468} Unresolved non-hydrogen bonds: 73 Unresolved non-hydrogen angles: 86 Unresolved non-hydrogen dihedrals: 60 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 7, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 40 Chain: "B" Number of atoms: 3689 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 483, 3631 Classifications: {'peptide': 483} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 22, 'TRANS': 460} Unresolved non-hydrogen bonds: 98 Unresolved non-hydrogen angles: 118 Unresolved non-hydrogen dihedrals: 78 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 7, 'ASN:plan1': 1, 'ARG:plan': 2, 'ASP:plan': 8} Unresolved non-hydrogen planarities: 65 Conformer: "B" Number of residues, atoms: 483, 3631 Classifications: {'peptide': 483} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 22, 'TRANS': 460} Unresolved non-hydrogen bonds: 98 Unresolved non-hydrogen angles: 118 Unresolved non-hydrogen dihedrals: 78 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 7, 'ASN:plan1': 1, 'ARG:plan': 2, 'ASP:plan': 8} Unresolved non-hydrogen planarities: 65 bond proxies already assigned to first conformer: 3664 Conformer: "C" Number of residues, atoms: 480, 3605 Classifications: {'peptide': 480} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 22, 'TRANS': 457} Unresolved chain links: 2 Unresolved chain link angles: 6 Unresolved chain link dihedrals: 6 Unresolved non-hydrogen bonds: 98 Unresolved non-hydrogen angles: 119 Unresolved non-hydrogen dihedrals: 76 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 7, 'ASN:plan1': 1, 'ARG:plan': 2, 'ASP:plan': 8} Unresolved non-hydrogen planarities: 65 bond proxies already assigned to first conformer: 3664 Chain: "B" Number of atoms: 24 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 1, 8 Classifications: {'peptide': 1} Modifications used: {'NH1NOTPRO': 1} Conformer: "B" Number of residues, atoms: 1, 8 Classifications: {'peptide': 1} Modifications used: {'NH1NOTPRO': 1} Conformer: "C" Number of residues, atoms: 1, 8 Classifications: {'peptide': 1} Modifications used: {'NH1NOTPRO': 1} Residues with excluded nonbonded symmetry interactions: 5 residue: pdb=" N ALYS B 374 " occ=0.26 ... (54 atoms not shown) pdb=" HZ1CLYS B 374 " occ=0.09 residue: pdb=" N AMET B 375 " occ=0.69 ... (8 atoms not shown) pdb=" CB BMET B 375 " occ=0.31 residue: pdb=" N AASP B 376 " occ=0.69 ... (14 atoms not shown) pdb=" OD2BASP B 376 " occ=0.31 residue: pdb=" N AGLU B 377 " occ=0.69 ... (16 atoms not shown) pdb=" OE2BGLU B 377 " occ=0.31 residue: pdb=" N AGLY B 601 " occ=0.26 ... (22 atoms not shown) pdb=" HA3CGLY B 601 " occ=0.09 Time building chain proxies: 12.09, per 1000 atoms: 0.83 Number of scatterers: 14540 At special positions: 0 Unit cell: (99.91, 98.88, 129.78, 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 67 16.00 O 2749 8.00 N 2503 7.00 C 9177 6.00 H 44 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.74 Conformation dependent library (CDL) restraints added in 2.7 seconds 3878 Ramachandran restraints generated. 1939 Oldfield, 0 Emsley, 1939 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3568 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 15 sheets defined 42.5% alpha, 17.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.85 Creating SS restraints... Processing helix chain 'C' and resid 88 through 99 Processing helix chain 'C' and resid 115 through 131 removed outlier: 3.514A pdb=" N ALA C 119 " --> pdb=" O SER C 115 " (cutoff:3.500A) Processing helix chain 'C' and resid 145 through 159 removed outlier: 4.053A pdb=" N GLN C 149 " --> pdb=" O HIS C 145 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N GLU C 150 " --> pdb=" O LYS C 146 " (cutoff:3.500A) Processing helix chain 'C' and resid 177 through 192 Processing helix chain 'C' and resid 201 through 215 Processing helix chain 'C' and resid 220 through 226 removed outlier: 3.749A pdb=" N VAL C 224 " --> pdb=" O PRO C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 247 removed outlier: 3.715A pdb=" N GLU C 232 " --> pdb=" O PRO C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 257 through 271 Processing helix chain 'C' and resid 279 through 285 Processing helix chain 'C' and resid 286 through 292 removed outlier: 4.379A pdb=" N HIS C 289 " --> pdb=" O ASP C 286 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N TRP C 291 " --> pdb=" O SER C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 301 removed outlier: 3.577A pdb=" N PHE C 301 " --> pdb=" O LYS C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 312 through 323 Processing helix chain 'C' and resid 337 through 342 Processing helix chain 'C' and resid 343 through 345 No H-bonds generated for 'chain 'C' and resid 343 through 345' Processing helix chain 'C' and resid 347 through 351 Processing helix chain 'C' and resid 360 through 370 Processing helix chain 'C' and resid 376 through 385 Processing helix chain 'C' and resid 385 through 392 Processing helix chain 'C' and resid 475 through 487 removed outlier: 5.682A pdb=" N ARG C 481 " --> pdb=" O PHE C 477 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ILE C 482 " --> pdb=" O VAL C 478 " (cutoff:3.500A) Processing helix chain 'D' and resid 88 through 99 Processing helix chain 'D' and resid 115 through 131 Processing helix chain 'D' and resid 145 through 160 removed outlier: 4.114A pdb=" N GLN D 149 " --> pdb=" O HIS D 145 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N GLU D 150 " --> pdb=" O LYS D 146 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLY D 160 " --> pdb=" O VAL D 156 " (cutoff:3.500A) Processing helix chain 'D' and resid 177 through 192 Processing helix chain 'D' and resid 201 through 216 removed outlier: 3.538A pdb=" N ILE D 205 " --> pdb=" O ASN D 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 220 through 226 removed outlier: 3.576A pdb=" N VAL D 224 " --> pdb=" O PRO D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 228 through 247 removed outlier: 3.721A pdb=" N GLU D 232 " --> pdb=" O PRO D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 257 through 270 Processing helix chain 'D' and resid 279 through 285 Processing helix chain 'D' and resid 286 through 292 removed outlier: 4.337A pdb=" N HIS D 289 " --> pdb=" O ASP D 286 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N TRP D 291 " --> pdb=" O SER D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 294 through 300 Processing helix chain 'D' and resid 312 through 324 Processing helix chain 'D' and resid 337 through 342 Processing helix chain 'D' and resid 343 through 345 No H-bonds generated for 'chain 'D' and resid 343 through 345' Processing helix chain 'D' and resid 347 through 351 Processing helix chain 'D' and resid 360 through 369 Processing helix chain 'D' and resid 376 through 385 Processing helix chain 'D' and resid 385 through 392 removed outlier: 3.980A pdb=" N VAL D 391 " --> pdb=" O ASN D 387 " (cutoff:3.500A) Processing helix chain 'D' and resid 475 through 488 removed outlier: 5.593A pdb=" N ARG D 481 " --> pdb=" O PHE D 477 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N ILE D 482 " --> pdb=" O VAL D 478 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LEU D 488 " --> pdb=" O ALA D 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 99 Processing helix chain 'A' and resid 115 through 131 Processing helix chain 'A' and resid 145 through 160 removed outlier: 4.099A pdb=" N GLN A 149 " --> pdb=" O HIS A 145 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N GLU A 150 " --> pdb=" O LYS A 146 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLY A 160 " --> pdb=" O VAL A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 192 Processing helix chain 'A' and resid 201 through 216 Processing helix chain 'A' and resid 220 through 226 removed outlier: 3.807A pdb=" N VAL A 224 " --> pdb=" O PRO A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 247 removed outlier: 3.559A pdb=" N GLU A 232 " --> pdb=" O PRO A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 271 Processing helix chain 'A' and resid 279 through 285 Processing helix chain 'A' and resid 286 through 290 removed outlier: 4.297A pdb=" N HIS A 289 " --> pdb=" O ASP A 286 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N TYR A 290 " --> pdb=" O GLY A 287 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 286 through 290' Processing helix chain 'A' and resid 294 through 300 Processing helix chain 'A' and resid 312 through 324 Processing helix chain 'A' and resid 337 through 342 Processing helix chain 'A' and resid 343 through 345 No H-bonds generated for 'chain 'A' and resid 343 through 345' Processing helix chain 'A' and resid 347 through 351 Processing helix chain 'A' and resid 360 through 370 Processing helix chain 'A' and resid 376 through 385 Processing helix chain 'A' and resid 385 through 392 Processing helix chain 'A' and resid 475 through 488 removed outlier: 5.114A pdb=" N ARG A 481 " --> pdb=" O PHE A 477 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N ILE A 482 " --> pdb=" O VAL A 478 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LEU A 488 " --> pdb=" O ALA A 484 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 98 removed outlier: 3.784A pdb=" N THR B 93 " --> pdb=" O PHE B 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 131 Processing helix chain 'B' and resid 145 through 159 removed outlier: 3.998A pdb=" N GLN B 149 " --> pdb=" O HIS B 145 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N GLU B 150 " --> pdb=" O LYS B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 192 Processing helix chain 'B' and resid 201 through 216 Processing helix chain 'B' and resid 220 through 227 removed outlier: 3.802A pdb=" N VAL B 224 " --> pdb=" O PRO B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 247 removed outlier: 3.874A pdb=" N GLU B 232 " --> pdb=" O PRO B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 257 through 270 Processing helix chain 'B' and resid 279 through 285 removed outlier: 3.666A pdb=" N THR B 285 " --> pdb=" O ALA B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 292 removed outlier: 4.355A pdb=" N HIS B 289 " --> pdb=" O ASP B 286 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N TRP B 291 " --> pdb=" O SER B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 300 Processing helix chain 'B' and resid 312 through 323 Processing helix chain 'B' and resid 337 through 342 Processing helix chain 'B' and resid 343 through 345 No H-bonds generated for 'chain 'B' and resid 343 through 345' Processing helix chain 'B' and resid 347 through 351 Processing helix chain 'B' and resid 360 through 370 Processing helix chain 'B' and resid 378 through 385 Processing helix chain 'B' and resid 385 through 392 removed outlier: 3.620A pdb=" N ALA B 389 " --> pdb=" O SER B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 488 removed outlier: 5.486A pdb=" N ARG B 481 " --> pdb=" O PHE B 477 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ILE B 482 " --> pdb=" O VAL B 478 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU B 488 " --> pdb=" O ALA B 484 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 41 through 46 removed outlier: 5.470A pdb=" N ILE C 42 " --> pdb=" O GLU C 38 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N GLU C 38 " --> pdb=" O ILE C 42 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N PHE C 31 " --> pdb=" O LYS C 23 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N LYS C 23 " --> pdb=" O PHE C 31 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N ALA C 33 " --> pdb=" O GLY C 21 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N GLY C 21 " --> pdb=" O ALA C 33 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LYS C 56 " --> pdb=" O ARG C 16 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 65 through 67 removed outlier: 3.619A pdb=" N VAL C 445 " --> pdb=" O ILE C 411 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N VAL C 446 " --> pdb=" O VAL C 453 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 69 through 74 removed outlier: 5.552A pdb=" N GLY C 69 " --> pdb=" O THR C 101 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N HIS C 73 " --> pdb=" O ILE C 105 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N HIS C 107 " --> pdb=" O HIS C 73 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ASP C 134 " --> pdb=" O THR C 102 " (cutoff:3.500A) removed outlier: 5.807A pdb=" N SER C 163 " --> pdb=" O LEU C 137 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N TYR C 167 " --> pdb=" O ILE C 141 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N PHE C 164 " --> pdb=" O ILE C 194 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 417 through 420 removed outlier: 4.124A pdb=" N MET C 437 " --> pdb=" O ILE C 420 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 41 through 46 removed outlier: 5.081A pdb=" N ILE D 42 " --> pdb=" O GLU D 38 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N GLU D 38 " --> pdb=" O ILE D 42 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N PHE D 31 " --> pdb=" O LYS D 23 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N LYS D 23 " --> pdb=" O PHE D 31 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N ALA D 33 " --> pdb=" O GLY D 21 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N GLY D 21 " --> pdb=" O ALA D 33 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N LYS D 56 " --> pdb=" O ARG D 16 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 41 through 46 removed outlier: 5.081A pdb=" N ILE D 42 " --> pdb=" O GLU D 38 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N GLU D 38 " --> pdb=" O ILE D 42 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N PHE D 31 " --> pdb=" O LYS D 23 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N LYS D 23 " --> pdb=" O PHE D 31 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N ALA D 33 " --> pdb=" O GLY D 21 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N GLY D 21 " --> pdb=" O ALA D 33 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N VAL D 65 " --> pdb=" O GLY D 21 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N LYS D 23 " --> pdb=" O VAL D 65 " (cutoff:3.500A) removed outlier: 8.379A pdb=" N VAL D 25 " --> pdb=" O PRO D 67 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N VAL D 445 " --> pdb=" O ILE D 411 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N VAL D 446 " --> pdb=" O VAL D 453 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 69 through 74 removed outlier: 6.389A pdb=" N GLY D 69 " --> pdb=" O MET D 103 " (cutoff:3.500A) removed outlier: 7.976A pdb=" N ILE D 105 " --> pdb=" O GLY D 69 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N ASP D 71 " --> pdb=" O ILE D 105 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N HIS D 107 " --> pdb=" O ASP D 71 " (cutoff:3.500A) removed outlier: 9.857A pdb=" N HIS D 73 " --> pdb=" O HIS D 107 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N THR D 102 " --> pdb=" O ASP D 134 " (cutoff:3.500A) removed outlier: 8.556A pdb=" N SER D 136 " --> pdb=" O THR D 102 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ILE D 104 " --> pdb=" O SER D 136 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N HIS D 138 " --> pdb=" O ILE D 104 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N ASP D 106 " --> pdb=" O HIS D 138 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N ASP D 140 " --> pdb=" O ASP D 106 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N VAL D 108 " --> pdb=" O ASP D 140 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N SER D 163 " --> pdb=" O LEU D 137 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N TYR D 167 " --> pdb=" O ILE D 141 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N PHE D 164 " --> pdb=" O GLN D 196 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N HIS D 198 " --> pdb=" O PHE D 164 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N VAL D 166 " --> pdb=" O HIS D 198 " (cutoff:3.500A) removed outlier: 8.498A pdb=" N GLU D 277 " --> pdb=" O LEU D 250 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N VAL D 252 " --> pdb=" O GLU D 277 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 79 through 80 Processing sheet with id=AA9, first strand: chain 'D' and resid 417 through 419 Processing sheet with id=AB1, first strand: chain 'A' and resid 41 through 46 removed outlier: 5.424A pdb=" N ILE A 42 " --> pdb=" O GLU A 38 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N GLU A 38 " --> pdb=" O ILE A 42 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLN A 44 " --> pdb=" O TYR A 36 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N TYR A 36 " --> pdb=" O GLN A 44 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N PHE A 31 " --> pdb=" O LYS A 23 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N LYS A 23 " --> pdb=" O PHE A 31 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N ALA A 33 " --> pdb=" O GLY A 21 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N GLY A 21 " --> pdb=" O ALA A 33 " (cutoff:3.500A) removed outlier: 9.417A pdb=" N LEU A 17 " --> pdb=" O THR A 57 " (cutoff:3.500A) removed outlier: 10.644A pdb=" N GLU A 59 " --> pdb=" O LEU A 17 " (cutoff:3.500A) removed outlier: 8.793A pdb=" N ILE A 19 " --> pdb=" O GLU A 59 " (cutoff:3.500A) removed outlier: 8.617A pdb=" N HIS A 61 " --> pdb=" O ILE A 19 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N GLY A 21 " --> pdb=" O HIS A 61 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ARG A 63 " --> pdb=" O GLY A 21 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N MET A 64 " --> pdb=" O TRP A 412 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL A 445 " --> pdb=" O ILE A 411 " (cutoff:3.500A) removed outlier: 8.715A pdb=" N LEU A 444 " --> pdb=" O GLU A 455 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N GLU A 455 " --> pdb=" O LEU A 444 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N VAL A 446 " --> pdb=" O VAL A 453 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 69 through 74 removed outlier: 5.371A pdb=" N GLY A 69 " --> pdb=" O THR A 101 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N HIS A 73 " --> pdb=" O ILE A 105 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N HIS A 107 " --> pdb=" O HIS A 73 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ASP A 134 " --> pdb=" O THR A 102 " (cutoff:3.500A) removed outlier: 5.615A pdb=" N SER A 163 " --> pdb=" O LEU A 137 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N TYR A 167 " --> pdb=" O ILE A 141 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N PHE A 164 " --> pdb=" O GLN A 196 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N HIS A 198 " --> pdb=" O PHE A 164 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N VAL A 166 " --> pdb=" O HIS A 198 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ALA A 195 " --> pdb=" O TYR A 251 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N THR A 253 " --> pdb=" O ALA A 195 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N VAL A 197 " --> pdb=" O THR A 253 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 42 through 46 removed outlier: 5.413A pdb=" N ILE B 42 " --> pdb=" O GLU B 38 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N GLU B 38 " --> pdb=" O ILE B 42 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA B 33 " --> pdb=" O GLY B 22 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N GLY B 22 " --> pdb=" O ALA B 33 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N ILE B 35 " --> pdb=" O LYS B 20 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N LYS B 20 " --> pdb=" O ILE B 35 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N MET B 37 " --> pdb=" O LEU B 18 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N LEU B 18 " --> pdb=" O MET B 37 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LYS B 56 " --> pdb=" O ARG B 16 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LYS B 20 " --> pdb=" O ILE B 58 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 42 through 46 removed outlier: 5.413A pdb=" N ILE B 42 " --> pdb=" O GLU B 38 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N GLU B 38 " --> pdb=" O ILE B 42 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA B 33 " --> pdb=" O GLY B 22 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N GLY B 22 " --> pdb=" O ALA B 33 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N ILE B 35 " --> pdb=" O LYS B 20 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N LYS B 20 " --> pdb=" O ILE B 35 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N MET B 37 " --> pdb=" O LEU B 18 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N LEU B 18 " --> pdb=" O MET B 37 " (cutoff:3.500A) removed outlier: 8.138A pdb=" N VAL B 65 " --> pdb=" O GLY B 21 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N LYS B 23 " --> pdb=" O VAL B 65 " (cutoff:3.500A) removed outlier: 8.938A pdb=" N VAL B 25 " --> pdb=" O PRO B 67 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N MET B 64 " --> pdb=" O TRP B 412 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N VAL B 445 " --> pdb=" O ILE B 411 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N VAL B 446 " --> pdb=" O VAL B 453 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 69 through 74 removed outlier: 5.038A pdb=" N GLY B 69 " --> pdb=" O THR B 101 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N HIS B 73 " --> pdb=" O ILE B 105 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N HIS B 107 " --> pdb=" O HIS B 73 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ASP B 134 " --> pdb=" O THR B 102 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N SER B 163 " --> pdb=" O LEU B 137 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N TYR B 167 " --> pdb=" O ILE B 141 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL B 166 " --> pdb=" O GLN B 196 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N ALA B 195 " --> pdb=" O TYR B 251 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N THR B 253 " --> pdb=" O ALA B 195 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N VAL B 197 " --> pdb=" O THR B 253 " (cutoff:3.500A) removed outlier: 8.880A pdb=" N GLU B 277 " --> pdb=" O LEU B 250 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N VAL B 252 " --> pdb=" O GLU B 277 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 417 through 419 649 hydrogen bonds defined for protein. 1863 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: 5.30 Time building geometry restraints manager: 4.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.00 - 1.16: 44 1.16 - 1.32: 2635 1.32 - 1.49: 5778 1.49 - 1.65: 6275 1.65 - 1.81: 110 Bond restraints: 14842 Sorted by residual: bond pdb=" N CGLY B 601 " pdb=" H CGLY B 601 " ideal model delta sigma weight residual 0.860 1.004 -0.144 2.00e-02 2.50e+03 5.16e+01 bond pdb=" N BGLY B 601 " pdb=" H BGLY B 601 " ideal model delta sigma weight residual 0.860 1.003 -0.143 2.00e-02 2.50e+03 5.14e+01 bond pdb=" N AGLY B 601 " pdb=" H AGLY B 601 " ideal model delta sigma weight residual 0.860 1.003 -0.143 2.00e-02 2.50e+03 5.11e+01 bond pdb=" N ALYS B 374 " pdb=" H ALYS B 374 " ideal model delta sigma weight residual 0.860 1.003 -0.143 2.00e-02 2.50e+03 5.10e+01 bond pdb=" N BLYS B 374 " pdb=" H BLYS B 374 " ideal model delta sigma weight residual 0.860 1.003 -0.143 2.00e-02 2.50e+03 5.09e+01 ... (remaining 14837 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.83: 20228 4.83 - 9.66: 5 9.66 - 14.49: 6 14.49 - 19.32: 2 19.32 - 24.15: 3 Bond angle restraints: 20244 Sorted by residual: angle pdb=" O GLY B 373 " pdb=" C GLY B 373 " pdb=" N ALYS B 374 " ideal model delta sigma weight residual 122.35 98.20 24.15 1.33e+00 5.65e-01 3.30e+02 angle pdb=" CA GLY B 373 " pdb=" C GLY B 373 " pdb=" N ALYS B 374 " ideal model delta sigma weight residual 118.36 140.87 -22.51 1.35e+00 5.49e-01 2.78e+02 angle pdb=" C GLY B 373 " pdb=" N ALYS B 374 " pdb=" CA ALYS B 374 " ideal model delta sigma weight residual 121.81 138.62 -16.81 1.83e+00 2.99e-01 8.44e+01 angle pdb=" C GLY B 373 " pdb=" N ALYS B 374 " pdb=" H ALYS B 374 " ideal model delta sigma weight residual 124.24 104.42 19.83 3.00e+00 1.11e-01 4.37e+01 angle pdb=" C GLY B 373 " pdb=" N BLYS B 374 " pdb=" H BLYS B 374 " ideal model delta sigma weight residual 124.80 106.98 17.82 3.00e+00 1.11e-01 3.53e+01 ... (remaining 20239 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 7600 17.90 - 35.79: 882 35.79 - 53.69: 246 53.69 - 71.58: 39 71.58 - 89.48: 15 Dihedral angle restraints: 8782 sinusoidal: 3223 harmonic: 5559 Sorted by residual: dihedral pdb=" CA SER A 304 " pdb=" C SER A 304 " pdb=" N PRO A 305 " pdb=" CA PRO A 305 " ideal model delta harmonic sigma weight residual 180.00 155.83 24.17 0 5.00e+00 4.00e-02 2.34e+01 dihedral pdb=" CA SER B 304 " pdb=" C SER B 304 " pdb=" N PRO B 305 " pdb=" CA PRO B 305 " ideal model delta harmonic sigma weight residual 180.00 158.47 21.53 0 5.00e+00 4.00e-02 1.85e+01 dihedral pdb=" CA SER D 304 " pdb=" C SER D 304 " pdb=" N PRO D 305 " pdb=" CA PRO D 305 " ideal model delta harmonic sigma weight residual 180.00 159.27 20.73 0 5.00e+00 4.00e-02 1.72e+01 ... (remaining 8779 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1416 0.028 - 0.056: 561 0.056 - 0.084: 164 0.084 - 0.112: 151 0.112 - 0.140: 38 Chirality restraints: 2330 Sorted by residual: chirality pdb=" CA ILE B 35 " pdb=" N ILE B 35 " pdb=" C ILE B 35 " pdb=" CB ILE B 35 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.92e-01 chirality pdb=" CA ILE C 351 " pdb=" N ILE C 351 " pdb=" C ILE C 351 " pdb=" CB ILE C 351 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.47e-01 chirality pdb=" CA ILE D 45 " pdb=" N ILE D 45 " pdb=" C ILE D 45 " pdb=" CB ILE D 45 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.18e-01 ... (remaining 2327 not shown) Planarity restraints: 2616 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY B 373 " 0.082 2.00e-02 2.50e+03 1.49e-01 2.23e+02 pdb=" N BLYS B 374 " -0.258 2.00e-02 2.50e+03 pdb=" CA BLYS B 374 " 0.076 2.00e-02 2.50e+03 pdb=" H BLYS B 374 " 0.100 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY B 373 " 0.054 2.00e-02 2.50e+03 8.53e-02 7.28e+01 pdb=" N ALYS B 374 " -0.148 2.00e-02 2.50e+03 pdb=" CA ALYS B 374 " 0.048 2.00e-02 2.50e+03 pdb=" H ALYS B 374 " 0.045 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER D 304 " 0.049 5.00e-02 4.00e+02 7.35e-02 8.65e+00 pdb=" N PRO D 305 " -0.127 5.00e-02 4.00e+02 pdb=" CA PRO D 305 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO D 305 " 0.040 5.00e-02 4.00e+02 ... (remaining 2613 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.48: 209 2.48 - 3.01: 9265 3.01 - 3.54: 18790 3.54 - 4.07: 27400 4.07 - 4.60: 42671 Nonbonded interactions: 98335 Sorted by model distance: nonbonded pdb=" O ALA B 193 " pdb=" OH TYR B 479 " model vdw 1.947 2.800 nonbonded pdb=" O PHE D 89 " pdb=" OG1 THR D 93 " model vdw 1.949 2.800 nonbonded pdb=" OG SER C 163 " pdb=" OE1 GLN C 196 " model vdw 1.967 2.800 nonbonded pdb=" O LYS C 368 " pdb=" OG1 THR C 372 " model vdw 1.977 2.800 nonbonded pdb=" OG1 THR D 462 " pdb=" OG SER D 465 " model vdw 1.986 2.800 ... (remaining 98330 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and ((resid 15 through 16 and (name N or name CA or name C or name O \ or name CB )) or resid 17 through 26 or (resid 27 and (name N or name CA or name \ C or name O or name CB )) or resid 28 through 33 or (resid 34 and (name N or na \ me CA or name C or name O or name CB )) or resid 35 through 38 or (resid 39 and \ (name N or name CA or name C or name O or name CB )) or resid 40 through 42 or ( \ resid 43 through 44 and (name N or name CA or name C or name O or name CB )) or \ resid 45 through 49 or (resid 50 and (name N or name CA or name C or name O or n \ ame CB )) or resid 51 through 55 or (resid 56 and (name N or name CA or name C o \ r name O or name CB )) or resid 57 through 58 or (resid 59 through 60 and (name \ N or name CA or name C or name O or name CB )) or resid 61 through 76 or (resid \ 77 and (name N or name CA or name C or name O or name CB )) or resid 78 through \ 79 or (resid 80 through 81 and (name N or name CA or name C or name O or name CB \ )) or resid 82 through 110 or (resid 111 and (name N or name CA or name C or na \ me O or name CB )) or resid 112 through 129 or (resid 130 and (name N or name CA \ or name C or name O or name CB )) or resid 131 through 149 or (resid 150 throug \ h 151 and (name N or name CA or name C or name O or name CB )) or resid 152 or ( \ resid 153 through 154 and (name N or name CA or name C or name O or name CB )) o \ r resid 155 through 171 or (resid 172 and (name N or name CA or name C or name O \ or name CB )) or resid 173 through 182 or (resid 183 and (name N or name CA or \ name C or name O or name CB )) or resid 184 through 189 or (resid 190 and (name \ N or name CA or name C or name O or name CB )) or resid 191 through 202 or (resi \ d 203 and (name N or name CA or name C or name O or name CB )) or resid 204 thro \ ugh 209 or (resid 210 and (name N or name CA or name C or name O or name CB )) o \ r resid 211 through 213 or (resid 214 and (name N or name CA or name C or name O \ or name CB )) or resid 215 through 261 or (resid 262 and (name N or name CA or \ name C or name O or name CB )) or resid 263 through 345 or (resid 346 and (name \ N or name CA or name C or name O or name CB )) or resid 347 through 352 or (resi \ d 353 and (name N or name CA or name C or name O or name CB )) or resid 354 thro \ ugh 373 or resid 378 or (resid 379 and (name N or name CA or name C or name O or \ name CB )) or resid 380 through 396 or (resid 397 through 398 and (name N or na \ me CA or name C or name O or name CB )) or resid 399 or (resid 400 and (name N o \ r name CA or name C or name O or name CB )) or resid 401 or (resid 402 through 4 \ 03 and (name N or name CA or name C or name O or name CB )) or resid 404 through \ 405 or (resid 406 through 408 and (name N or name CA or name C or name O or nam \ e CB )) or resid 409 through 412 or (resid 413 and (name N or name CA or name C \ or name O or name CB )) or resid 414 or (resid 415 and (name N or name CA or nam \ e C or name O or name CB )) or resid 416 through 425 or (resid 426 and (name N o \ r name CA or name C or name O or name CB )) or resid 427 through 446 or (resid 4 \ 47 and (name N or name CA or name C or name O or name CB )) or resid 448 or (res \ id 449 and (name N or name CA or name C or name O or name CB )) or resid 450 thr \ ough 454 or (resid 455 through 456 and (name N or name CA or name C or name O or \ name CB )) or resid 457 or (resid 458 and (name N or name CA or name C or name \ O or name CB )) or resid 459 or (resid 460 and (name N or name CA or name C or n \ ame O or name CB )) or resid 461 through 462 or (resid 463 and (name N or name C \ A or name C or name O or name CB )) or resid 464 through 466 or (resid 467 and ( \ name N or name CA or name C or name O or name CB )) or resid 468 through 475 or \ (resid 476 and (name N or name CA or name C or name O or name CB )) or resid 477 \ through 486 or (resid 487 and (name N or name CA or name C or name O or name CB \ )) or resid 488 through 491 or (resid 492 and (name N or name CA or name C or n \ ame O or name CB )) or resid 493 through 497)) selection = (chain 'B' and ((resid 15 through 16 and (name N or name CA or name C or name O \ or name CB )) or resid 17 through 26 or (resid 27 and (name N or name CA or name \ C or name O or name CB )) or resid 28 through 43 or (resid 44 and (name N or na \ me CA or name C or name O or name CB )) or resid 45 through 46 or (resid 47 thro \ ugh 48 and (name N or name CA or name C or name O or name CB )) or resid 49 thro \ ugh 55 or (resid 56 and (name N or name CA or name C or name O or name CB )) or \ resid 57 through 76 or (resid 77 and (name N or name CA or name C or name O or n \ ame CB )) or resid 78 through 79 or (resid 80 through 81 and (name N or name CA \ or name C or name O or name CB )) or resid 82 through 110 or (resid 111 and (nam \ e N or name CA or name C or name O or name CB )) or resid 112 through 128 or (re \ sid 129 through 130 and (name N or name CA or name C or name O or name CB )) or \ resid 131 through 150 or (resid 151 and (name N or name CA or name C or name O o \ r name CB )) or resid 152 or (resid 153 through 154 and (name N or name CA or na \ me C or name O or name CB )) or resid 155 through 157 or (resid 158 and (name N \ or name CA or name C or name O or name CB )) or resid 159 through 171 or (resid \ 172 and (name N or name CA or name C or name O or name CB )) or resid 173 throug \ h 182 or (resid 183 and (name N or name CA or name C or name O or name CB )) or \ resid 184 through 189 or (resid 190 and (name N or name CA or name C or name O o \ r name CB )) or resid 191 through 202 or (resid 203 and (name N or name CA or na \ me C or name O or name CB )) or resid 204 through 209 or (resid 210 and (name N \ or name CA or name C or name O or name CB )) or resid 211 through 261 or (resid \ 262 and (name N or name CA or name C or name O or name CB )) or resid 263 throug \ h 345 or (resid 346 and (name N or name CA or name C or name O or name CB )) or \ resid 347 through 352 or (resid 353 and (name N or name CA or name C or name O o \ r name CB )) or resid 354 through 373 or resid 378 or (resid 379 and (name N or \ name CA or name C or name O or name CB )) or resid 380 through 396 or (resid 397 \ through 398 and (name N or name CA or name C or name O or name CB )) or resid 3 \ 99 or (resid 400 and (name N or name CA or name C or name O or name CB )) or res \ id 401 or (resid 402 through 403 and (name N or name CA or name C or name O or n \ ame CB )) or resid 404 through 412 or (resid 413 and (name N or name CA or name \ C or name O or name CB )) or resid 414 through 417 or (resid 418 and (name N or \ name CA or name C or name O or name CB )) or resid 419 through 422 or (resid 423 \ and (name N or name CA or name C or name O or name CB )) or resid 424 through 4 \ 25 or (resid 426 and (name N or name CA or name C or name O or name CB )) or res \ id 427 through 429 or (resid 430 and (name N or name CA or name C or name O or n \ ame CB )) or resid 431 through 448 or (resid 449 and (name N or name CA or name \ C or name O or name CB )) or resid 450 through 457 or (resid 458 and (name N or \ name CA or name C or name O or name CB )) or resid 459 or (resid 460 and (name N \ or name CA or name C or name O or name CB )) or resid 461 through 462 or (resid \ 463 and (name N or name CA or name C or name O or name CB )) or resid 464 throu \ gh 466 or (resid 467 and (name N or name CA or name C or name O or name CB )) or \ resid 468 through 475 or (resid 476 and (name N or name CA or name C or name O \ or name CB )) or resid 477 through 497)) selection = (chain 'C' and (resid 15 through 26 or (resid 27 and (name N or name CA or name \ C or name O or name CB )) or resid 28 through 33 or (resid 34 and (name N or nam \ e CA or name C or name O or name CB )) or resid 35 through 37 or (resid 38 throu \ gh 39 and (name N or name CA or name C or name O or name CB )) or resid 40 throu \ gh 42 or (resid 43 through 44 and (name N or name CA or name C or name O or name \ CB )) or resid 45 through 46 or (resid 47 through 48 and (name N or name CA or \ name C or name O or name CB )) or resid 49 through 79 or (resid 80 through 81 an \ d (name N or name CA or name C or name O or name CB )) or resid 82 through 149 o \ r (resid 150 through 151 and (name N or name CA or name C or name O or name CB ) \ ) or resid 152 or (resid 153 through 154 and (name N or name CA or name C or nam \ e O or name CB )) or resid 155 through 157 or (resid 158 and (name N or name CA \ or name C or name O or name CB )) or resid 159 through 261 or (resid 262 and (na \ me N or name CA or name C or name O or name CB )) or resid 263 through 373 or re \ sid 378 through 446 or (resid 447 and (name N or name CA or name C or name O or \ name CB )) or resid 448 through 450 or (resid 451 and (name N or name CA or name \ C or name O or name CB )) or resid 452 through 475 or (resid 476 and (name N or \ name CA or name C or name O or name CB )) or resid 477 through 486 or (resid 48 \ 7 and (name N or name CA or name C or name O or name CB )) or resid 488 through \ 497)) selection = (chain 'D' and ((resid 15 through 16 and (name N or name CA or name C or name O \ or name CB )) or resid 17 through 33 or (resid 34 and (name N or name CA or name \ C or name O or name CB )) or resid 35 through 55 or (resid 56 and (name N or na \ me CA or name C or name O or name CB )) or resid 57 through 58 or (resid 59 thro \ ugh 60 and (name N or name CA or name C or name O or name CB )) or resid 61 thro \ ugh 76 or (resid 77 and (name N or name CA or name C or name O or name CB )) or \ resid 78 through 124 or (resid 125 and (name N or name CA or name C or name O or \ name CB )) or resid 126 through 157 or (resid 158 and (name N or name CA or nam \ e C or name O or name CB )) or resid 159 through 182 or (resid 183 and (name N o \ r name CA or name C or name O or name CB )) or resid 184 through 189 or (resid 1 \ 90 and (name N or name CA or name C or name O or name CB )) or resid 191 through \ 202 or (resid 203 and (name N or name CA or name C or name O or name CB )) or r \ esid 204 through 209 or (resid 210 and (name N or name CA or name C or name O or \ name CB )) or resid 211 through 345 or (resid 346 and (name N or name CA or nam \ e C or name O or name CB )) or resid 347 through 352 or (resid 353 and (name N o \ r name CA or name C or name O or name CB )) or resid 354 through 373 or resid 37 \ 8 or (resid 379 and (name N or name CA or name C or name O or name CB )) or resi \ d 380 through 397 or (resid 398 and (name N or name CA or name C or name O or na \ me CB )) or resid 399 or (resid 400 and (name N or name CA or name C or name O o \ r name CB )) or resid 401 or (resid 402 through 403 and (name N or name CA or na \ me C or name O or name CB )) or resid 404 through 405 or (resid 406 through 408 \ and (name N or name CA or name C or name O or name CB )) or resid 409 through 41 \ 2 or (resid 413 and (name N or name CA or name C or name O or name CB )) or resi \ d 414 through 425 or (resid 426 and (name N or name CA or name C or name O or na \ me CB )) or resid 427 through 446 or (resid 447 and (name N or name CA or name C \ or name O or name CB )) or resid 448 through 459 or (resid 460 and (name N or n \ ame CA or name C or name O or name CB )) or resid 461 through 466 or (resid 467 \ and (name N or name CA or name C or name O or name CB )) or resid 468 through 48 \ 6 or (resid 487 and (name N or name CA or name C or name O or name CB )) or resi \ d 488 through 497)) } 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=0.09 max=1.00 mean=0.99 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: 0.330 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: 0.410 Extract box with map and model: 0.510 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 39.220 Find NCS groups from input model: 0.890 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:14.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7058 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 : 0.004 0.060 14798 Z= 0.242 Angle : 0.593 24.149 20149 Z= 0.359 Chirality : 0.042 0.140 2330 Planarity : 0.004 0.074 2614 Dihedral : 16.828 89.476 5206 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 43.20 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.76 % Favored : 95.19 % Rotamer: Outliers : 4.30 % Allowed : 30.31 % Favored : 65.39 % 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: 0.38 (0.20), residues: 1939 helix: 1.46 (0.19), residues: 743 sheet: -1.26 (0.34), residues: 224 loop : -0.25 (0.21), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 295 HIS 0.004 0.001 HIS B 223 PHE 0.019 0.001 PHE C 380 TYR 0.013 0.001 TYR D 479 ARG 0.006 0.000 ARG A 440 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3878 Ramachandran restraints generated. 1939 Oldfield, 0 Emsley, 1939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3878 Ramachandran restraints generated. 1939 Oldfield, 0 Emsley, 1939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 374 is missing expected H atoms. Skipping. Residue LYS 374 is missing expected H atoms. Skipping. Residue LYS 374 is missing expected H atoms. Skipping. Evaluate side-chains 255 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 193 time to evaluate : 1.643 Fit side-chains revert: symmetry clash outliers start: 62 outliers final: 51 residues processed: 246 average time/residue: 0.8600 time to fit residues: 244.5221 Evaluate side-chains 240 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 189 time to evaluate : 1.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 179 SER Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 239 SER Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 280 THR Chi-restraints excluded: chain C residue 308 SER Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 383 VAL Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 84 THR Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 142 THR Chi-restraints excluded: chain D residue 148 ILE Chi-restraints excluded: chain D residue 181 ILE Chi-restraints excluded: chain D residue 203 ASP Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain D residue 376 ASP Chi-restraints excluded: chain D residue 409 LEU Chi-restraints excluded: chain D residue 439 CYS Chi-restraints excluded: chain D residue 465 SER Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 64 MET Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 78 MET Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 203 ASP Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 308 SER Chi-restraints excluded: chain A residue 376 ASP Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 385 SER Chi-restraints excluded: chain A residue 416 SER Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 465 SER Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain B residue 24 ILE Chi-restraints excluded: chain B residue 30 SER Chi-restraints excluded: chain B residue 181 ILE Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 405 SER Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 465 SER Chi-restraints excluded: chain B residue 491 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 162 optimal weight: 4.9990 chunk 146 optimal weight: 0.2980 chunk 81 optimal weight: 8.9990 chunk 49 optimal weight: 3.9990 chunk 98 optimal weight: 0.1980 chunk 78 optimal weight: 5.9990 chunk 151 optimal weight: 1.9990 chunk 58 optimal weight: 7.9990 chunk 91 optimal weight: 9.9990 chunk 112 optimal weight: 6.9990 chunk 175 optimal weight: 0.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 73 HIS ** D 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 425 HIS A 266 GLN B 201 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7042 moved from start: 0.0831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 14798 Z= 0.196 Angle : 0.468 4.842 20149 Z= 0.252 Chirality : 0.042 0.151 2330 Planarity : 0.004 0.061 2614 Dihedral : 5.393 50.215 2135 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 38.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 5.11 % Allowed : 27.49 % Favored : 67.41 % 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: 0.44 (0.20), residues: 1939 helix: 1.64 (0.19), residues: 749 sheet: -1.27 (0.33), residues: 252 loop : -0.29 (0.22), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 295 HIS 0.003 0.001 HIS C 138 PHE 0.015 0.001 PHE C 380 TYR 0.011 0.001 TYR D 479 ARG 0.003 0.000 ARG D 238 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3878 Ramachandran restraints generated. 1939 Oldfield, 0 Emsley, 1939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3878 Ramachandran restraints generated. 1939 Oldfield, 0 Emsley, 1939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 374 is missing expected H atoms. Skipping. Residue LYS 374 is missing expected H atoms. Skipping. Residue LYS 374 is missing expected H atoms. Skipping. Evaluate side-chains 283 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 209 time to evaluate : 1.571 Fit side-chains revert: symmetry clash REVERT: D 406 ASP cc_start: 0.7626 (OUTLIER) cc_final: 0.7154 (t0) REVERT: D 440 ARG cc_start: 0.6892 (OUTLIER) cc_final: 0.6371 (ttm-80) REVERT: A 66 ILE cc_start: 0.6677 (OUTLIER) cc_final: 0.6222 (pt) REVERT: A 89 PHE cc_start: 0.7900 (OUTLIER) cc_final: 0.6822 (t80) REVERT: A 315 ASP cc_start: 0.7174 (m-30) cc_final: 0.6869 (m-30) REVERT: B 47 GLU cc_start: 0.7509 (OUTLIER) cc_final: 0.7098 (mm-30) REVERT: B 208 GLU cc_start: 0.7610 (tp30) cc_final: 0.7152 (mm-30) outliers start: 74 outliers final: 40 residues processed: 255 average time/residue: 0.9021 time to fit residues: 263.6905 Evaluate side-chains 246 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 201 time to evaluate : 1.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 35 ILE Chi-restraints excluded: chain C residue 181 ILE Chi-restraints excluded: chain C residue 188 ILE Chi-restraints excluded: chain C residue 274 VAL Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 312 THR Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 409 LEU Chi-restraints excluded: chain C residue 439 CYS Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain D residue 37 MET Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 142 THR Chi-restraints excluded: chain D residue 181 ILE Chi-restraints excluded: chain D residue 203 ASP Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 376 ASP Chi-restraints excluded: chain D residue 385 SER Chi-restraints excluded: chain D residue 406 ASP Chi-restraints excluded: chain D residue 440 ARG Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 31 PHE Chi-restraints excluded: chain A residue 37 MET Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 66 ILE Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 89 PHE Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 282 SER Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 385 SER Chi-restraints excluded: chain A residue 440 ARG Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 47 GLU Chi-restraints excluded: chain B residue 179 SER Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 491 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 97 optimal weight: 4.9990 chunk 54 optimal weight: 4.9990 chunk 145 optimal weight: 9.9990 chunk 119 optimal weight: 0.9980 chunk 48 optimal weight: 20.0000 chunk 175 optimal weight: 5.9990 chunk 189 optimal weight: 7.9990 chunk 156 optimal weight: 8.9990 chunk 174 optimal weight: 2.9990 chunk 59 optimal weight: 10.0000 chunk 140 optimal weight: 3.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 266 GLN ** D 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 73 HIS ** D 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 237 ASN ** D 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 107 HIS B 247 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7118 moved from start: 0.1117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 14798 Z= 0.411 Angle : 0.582 8.214 20149 Z= 0.313 Chirality : 0.046 0.154 2330 Planarity : 0.004 0.058 2614 Dihedral : 5.358 47.235 2088 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 41.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 6.72 % Allowed : 26.48 % Favored : 66.80 % 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: -0.14 (0.19), residues: 1939 helix: 1.03 (0.19), residues: 749 sheet: -1.42 (0.34), residues: 223 loop : -0.59 (0.21), residues: 967 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 412 HIS 0.005 0.001 HIS B 73 PHE 0.025 0.002 PHE C 380 TYR 0.019 0.002 TYR D 479 ARG 0.005 0.001 ARG D 238 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3878 Ramachandran restraints generated. 1939 Oldfield, 0 Emsley, 1939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3878 Ramachandran restraints generated. 1939 Oldfield, 0 Emsley, 1939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 374 is missing expected H atoms. Skipping. Residue LYS 374 is missing expected H atoms. Skipping. Residue LYS 374 is missing expected H atoms. Skipping. Evaluate side-chains 296 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 199 time to evaluate : 1.651 Fit side-chains revert: symmetry clash REVERT: C 266 GLN cc_start: 0.7880 (OUTLIER) cc_final: 0.6751 (mp-120) REVERT: C 476 ASP cc_start: 0.7239 (m-30) cc_final: 0.6960 (t0) REVERT: D 200 GLU cc_start: 0.8465 (OUTLIER) cc_final: 0.8232 (tt0) REVERT: D 256 MET cc_start: 0.8031 (mmt) cc_final: 0.6751 (mmt) REVERT: D 310 ASP cc_start: 0.7558 (t0) cc_final: 0.7174 (t0) REVERT: D 387 ASN cc_start: 0.8642 (OUTLIER) cc_final: 0.8438 (t160) REVERT: D 406 ASP cc_start: 0.7989 (OUTLIER) cc_final: 0.7597 (t0) REVERT: D 440 ARG cc_start: 0.6993 (OUTLIER) cc_final: 0.6562 (ttm-80) REVERT: A 89 PHE cc_start: 0.7838 (OUTLIER) cc_final: 0.6747 (t80) REVERT: A 315 ASP cc_start: 0.7224 (m-30) cc_final: 0.6958 (m-30) REVERT: B 47 GLU cc_start: 0.7317 (OUTLIER) cc_final: 0.7070 (mm-30) REVERT: B 221 GLU cc_start: 0.8333 (OUTLIER) cc_final: 0.7856 (pt0) REVERT: B 351 ILE cc_start: 0.8146 (OUTLIER) cc_final: 0.7621 (tp) REVERT: B 420 ILE cc_start: 0.6412 (mm) cc_final: 0.6166 (mt) outliers start: 97 outliers final: 61 residues processed: 260 average time/residue: 0.8897 time to fit residues: 266.1862 Evaluate side-chains 260 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 190 time to evaluate : 1.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 35 ILE Chi-restraints excluded: chain C residue 181 ILE Chi-restraints excluded: chain C residue 188 ILE Chi-restraints excluded: chain C residue 266 GLN Chi-restraints excluded: chain C residue 274 VAL Chi-restraints excluded: chain C residue 280 THR Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 312 THR Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 383 VAL Chi-restraints excluded: chain C residue 409 LEU Chi-restraints excluded: chain C residue 439 CYS Chi-restraints excluded: chain C residue 448 SER Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 142 THR Chi-restraints excluded: chain D residue 148 ILE Chi-restraints excluded: chain D residue 181 ILE Chi-restraints excluded: chain D residue 191 ILE Chi-restraints excluded: chain D residue 200 GLU Chi-restraints excluded: chain D residue 203 ASP Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain D residue 285 THR Chi-restraints excluded: chain D residue 303 THR Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 365 ILE Chi-restraints excluded: chain D residue 376 ASP Chi-restraints excluded: chain D residue 383 VAL Chi-restraints excluded: chain D residue 385 SER Chi-restraints excluded: chain D residue 387 ASN Chi-restraints excluded: chain D residue 403 VAL Chi-restraints excluded: chain D residue 406 ASP Chi-restraints excluded: chain D residue 440 ARG Chi-restraints excluded: chain D residue 461 VAL Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 31 PHE Chi-restraints excluded: chain A residue 35 ILE Chi-restraints excluded: chain A residue 37 MET Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 89 PHE Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 203 ASP Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 282 SER Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 385 SER Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 433 ILE Chi-restraints excluded: chain A residue 440 ARG Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 47 GLU Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 221 GLU Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 351 ILE Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 437 MET Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 491 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 173 optimal weight: 7.9990 chunk 132 optimal weight: 1.9990 chunk 91 optimal weight: 9.9990 chunk 19 optimal weight: 4.9990 chunk 83 optimal weight: 4.9990 chunk 117 optimal weight: 0.7980 chunk 176 optimal weight: 4.9990 chunk 186 optimal weight: 4.9990 chunk 92 optimal weight: 0.7980 chunk 167 optimal weight: 0.9980 chunk 50 optimal weight: 0.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 266 GLN ** C 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 247 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7041 moved from start: 0.1211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 14798 Z= 0.163 Angle : 0.440 6.410 20149 Z= 0.234 Chirality : 0.042 0.161 2330 Planarity : 0.003 0.052 2614 Dihedral : 4.670 48.842 2088 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 40.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 4.57 % Allowed : 28.76 % Favored : 66.67 % 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: 0.28 (0.20), residues: 1939 helix: 1.48 (0.19), residues: 761 sheet: -1.93 (0.39), residues: 182 loop : -0.36 (0.21), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 295 HIS 0.003 0.001 HIS B 107 PHE 0.011 0.001 PHE C 380 TYR 0.017 0.001 TYR C 135 ARG 0.003 0.000 ARG D 238 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3878 Ramachandran restraints generated. 1939 Oldfield, 0 Emsley, 1939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3878 Ramachandran restraints generated. 1939 Oldfield, 0 Emsley, 1939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 374 is missing expected H atoms. Skipping. Residue LYS 374 is missing expected H atoms. Skipping. Residue LYS 374 is missing expected H atoms. Skipping. Evaluate side-chains 274 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 209 time to evaluate : 1.661 Fit side-chains revert: symmetry clash REVERT: C 266 GLN cc_start: 0.7916 (OUTLIER) cc_final: 0.6870 (mp-120) REVERT: C 476 ASP cc_start: 0.7147 (m-30) cc_final: 0.6909 (t0) REVERT: D 200 GLU cc_start: 0.8318 (OUTLIER) cc_final: 0.8076 (tt0) REVERT: D 310 ASP cc_start: 0.7369 (t0) cc_final: 0.6994 (t0) REVERT: D 387 ASN cc_start: 0.8551 (OUTLIER) cc_final: 0.7860 (t0) REVERT: D 440 ARG cc_start: 0.7014 (OUTLIER) cc_final: 0.6772 (ttp-110) REVERT: A 89 PHE cc_start: 0.7828 (OUTLIER) cc_final: 0.6860 (t80) REVERT: A 315 ASP cc_start: 0.7181 (m-30) cc_final: 0.6882 (m-30) REVERT: B 32 TYR cc_start: 0.7610 (m-80) cc_final: 0.7399 (m-80) REVERT: B 77 GLN cc_start: 0.7344 (OUTLIER) cc_final: 0.6934 (mt0) REVERT: B 251 TYR cc_start: 0.8644 (t80) cc_final: 0.8092 (t80) REVERT: B 351 ILE cc_start: 0.8058 (OUTLIER) cc_final: 0.7536 (tp) REVERT: B 420 ILE cc_start: 0.6372 (mm) cc_final: 0.6137 (mt) REVERT: B 472 LYS cc_start: 0.8127 (mmmm) cc_final: 0.7785 (mptm) outliers start: 65 outliers final: 39 residues processed: 250 average time/residue: 0.8775 time to fit residues: 251.2279 Evaluate side-chains 242 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 196 time to evaluate : 1.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 181 ILE Chi-restraints excluded: chain C residue 266 GLN Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 409 LEU Chi-restraints excluded: chain C residue 439 CYS Chi-restraints excluded: chain D residue 30 SER Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 142 THR Chi-restraints excluded: chain D residue 148 ILE Chi-restraints excluded: chain D residue 181 ILE Chi-restraints excluded: chain D residue 200 GLU Chi-restraints excluded: chain D residue 203 ASP Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain D residue 303 THR Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 385 SER Chi-restraints excluded: chain D residue 387 ASN Chi-restraints excluded: chain D residue 440 ARG Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 37 MET Chi-restraints excluded: chain A residue 89 PHE Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 203 ASP Chi-restraints excluded: chain A residue 282 SER Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 385 SER Chi-restraints excluded: chain A residue 433 ILE Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 77 GLN Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 179 SER Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 335 THR Chi-restraints excluded: chain B residue 351 ILE Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 437 MET Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 491 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 155 optimal weight: 9.9990 chunk 105 optimal weight: 0.0270 chunk 2 optimal weight: 9.9990 chunk 138 optimal weight: 7.9990 chunk 76 optimal weight: 6.9990 chunk 159 optimal weight: 0.6980 chunk 128 optimal weight: 4.9990 chunk 0 optimal weight: 9.9990 chunk 95 optimal weight: 8.9990 chunk 167 optimal weight: 4.9990 chunk 47 optimal weight: 8.9990 overall best weight: 3.5444 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 266 GLN ** C 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 247 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7121 moved from start: 0.1346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 14798 Z= 0.395 Angle : 0.572 9.060 20149 Z= 0.306 Chirality : 0.046 0.151 2330 Planarity : 0.004 0.055 2614 Dihedral : 5.173 54.847 2082 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 42.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 7.19 % Allowed : 26.34 % Favored : 66.47 % 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: -0.22 (0.19), residues: 1939 helix: 1.02 (0.19), residues: 755 sheet: -1.48 (0.34), residues: 224 loop : -0.71 (0.21), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 412 HIS 0.006 0.001 HIS B 107 PHE 0.027 0.002 PHE C 380 TYR 0.018 0.002 TYR D 479 ARG 0.004 0.000 ARG C 238 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3878 Ramachandran restraints generated. 1939 Oldfield, 0 Emsley, 1939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3878 Ramachandran restraints generated. 1939 Oldfield, 0 Emsley, 1939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 374 is missing expected H atoms. Skipping. Residue LYS 374 is missing expected H atoms. Skipping. Residue LYS 374 is missing expected H atoms. Skipping. Evaluate side-chains 312 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 208 time to evaluate : 1.944 Fit side-chains revert: symmetry clash REVERT: C 64 MET cc_start: 0.7289 (ptp) cc_final: 0.7062 (ptp) REVERT: C 266 GLN cc_start: 0.7945 (OUTLIER) cc_final: 0.7056 (mp-120) REVERT: C 476 ASP cc_start: 0.7299 (m-30) cc_final: 0.6981 (t0) REVERT: D 89 PHE cc_start: 0.7627 (OUTLIER) cc_final: 0.6794 (t80) REVERT: D 256 MET cc_start: 0.8060 (mmt) cc_final: 0.6621 (mmt) REVERT: D 310 ASP cc_start: 0.7543 (t0) cc_final: 0.7108 (t0) REVERT: D 406 ASP cc_start: 0.7941 (OUTLIER) cc_final: 0.7589 (t0) REVERT: D 440 ARG cc_start: 0.7035 (OUTLIER) cc_final: 0.6589 (ttm-80) REVERT: A 45 ILE cc_start: 0.6864 (mm) cc_final: 0.6645 (mt) REVERT: A 89 PHE cc_start: 0.7867 (OUTLIER) cc_final: 0.6929 (t80) REVERT: A 315 ASP cc_start: 0.7227 (m-30) cc_final: 0.6960 (m-30) REVERT: B 221 GLU cc_start: 0.8317 (OUTLIER) cc_final: 0.7807 (pt0) REVERT: B 351 ILE cc_start: 0.8150 (OUTLIER) cc_final: 0.7645 (tp) REVERT: B 420 ILE cc_start: 0.6525 (mm) cc_final: 0.6279 (mt) REVERT: B 430 GLU cc_start: 0.8223 (OUTLIER) cc_final: 0.7967 (pm20) REVERT: B 472 LYS cc_start: 0.8198 (mmmm) cc_final: 0.7833 (mptm) outliers start: 104 outliers final: 71 residues processed: 274 average time/residue: 0.8755 time to fit residues: 276.2758 Evaluate side-chains 277 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 198 time to evaluate : 1.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 181 ILE Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 266 GLN Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 274 VAL Chi-restraints excluded: chain C residue 280 THR Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 312 THR Chi-restraints excluded: chain C residue 383 VAL Chi-restraints excluded: chain C residue 409 LEU Chi-restraints excluded: chain C residue 410 VAL Chi-restraints excluded: chain C residue 439 CYS Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain D residue 30 SER Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 89 PHE Chi-restraints excluded: chain D residue 136 SER Chi-restraints excluded: chain D residue 142 THR Chi-restraints excluded: chain D residue 148 ILE Chi-restraints excluded: chain D residue 181 ILE Chi-restraints excluded: chain D residue 203 ASP Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain D residue 285 THR Chi-restraints excluded: chain D residue 303 THR Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 365 ILE Chi-restraints excluded: chain D residue 376 ASP Chi-restraints excluded: chain D residue 385 SER Chi-restraints excluded: chain D residue 403 VAL Chi-restraints excluded: chain D residue 406 ASP Chi-restraints excluded: chain D residue 440 ARG Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain D residue 461 VAL Chi-restraints excluded: chain D residue 467 ARG Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 31 PHE Chi-restraints excluded: chain A residue 37 MET Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 64 MET Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 78 MET Chi-restraints excluded: chain A residue 89 PHE Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 203 ASP Chi-restraints excluded: chain A residue 282 SER Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 308 SER Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 385 SER Chi-restraints excluded: chain A residue 433 ILE Chi-restraints excluded: chain A residue 440 ARG Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 480 LYS Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 45 ILE Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 179 SER Chi-restraints excluded: chain B residue 221 GLU Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 335 THR Chi-restraints excluded: chain B residue 351 ILE Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 430 GLU Chi-restraints excluded: chain B residue 437 MET Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 491 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 62 optimal weight: 0.9990 chunk 168 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 109 optimal weight: 4.9990 chunk 46 optimal weight: 0.9980 chunk 186 optimal weight: 8.9990 chunk 155 optimal weight: 3.9990 chunk 86 optimal weight: 7.9990 chunk 15 optimal weight: 0.6980 chunk 61 optimal weight: 0.9980 chunk 98 optimal weight: 0.0470 overall best weight: 0.7478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 266 GLN ** C 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 247 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7028 moved from start: 0.1437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 14798 Z= 0.130 Angle : 0.426 5.953 20149 Z= 0.226 Chirality : 0.041 0.156 2330 Planarity : 0.003 0.046 2614 Dihedral : 4.424 51.898 2082 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 40.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 4.44 % Allowed : 29.50 % Favored : 66.06 % 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: 0.31 (0.20), residues: 1939 helix: 1.61 (0.19), residues: 761 sheet: -2.21 (0.39), residues: 176 loop : -0.38 (0.21), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 295 HIS 0.002 0.001 HIS B 107 PHE 0.012 0.001 PHE B 120 TYR 0.017 0.001 TYR C 135 ARG 0.002 0.000 ARG A 440 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3878 Ramachandran restraints generated. 1939 Oldfield, 0 Emsley, 1939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3878 Ramachandran restraints generated. 1939 Oldfield, 0 Emsley, 1939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 374 is missing expected H atoms. Skipping. Residue LYS 374 is missing expected H atoms. Skipping. Residue LYS 374 is missing expected H atoms. Skipping. Evaluate side-chains 276 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 213 time to evaluate : 2.707 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 476 ASP cc_start: 0.7259 (m-30) cc_final: 0.6967 (t0) REVERT: D 89 PHE cc_start: 0.7559 (OUTLIER) cc_final: 0.6736 (t80) REVERT: D 256 MET cc_start: 0.7768 (OUTLIER) cc_final: 0.6469 (mmt) REVERT: D 310 ASP cc_start: 0.7359 (t0) cc_final: 0.6952 (t0) REVERT: D 387 ASN cc_start: 0.8550 (OUTLIER) cc_final: 0.7879 (t0) REVERT: D 440 ARG cc_start: 0.6998 (OUTLIER) cc_final: 0.6727 (ttp-110) REVERT: A 64 MET cc_start: 0.6472 (OUTLIER) cc_final: 0.6165 (mtp) REVERT: A 315 ASP cc_start: 0.7173 (m-30) cc_final: 0.6866 (m-30) REVERT: B 275 TYR cc_start: 0.8457 (m-80) cc_final: 0.7902 (m-80) REVERT: B 351 ILE cc_start: 0.8049 (OUTLIER) cc_final: 0.7525 (tp) REVERT: B 418 LYS cc_start: 0.7203 (ptpp) cc_final: 0.6440 (mttp) REVERT: B 420 ILE cc_start: 0.6464 (mm) cc_final: 0.6203 (mt) REVERT: B 472 LYS cc_start: 0.8071 (mmmm) cc_final: 0.7764 (mptm) outliers start: 63 outliers final: 41 residues processed: 254 average time/residue: 0.9328 time to fit residues: 271.8784 Evaluate side-chains 252 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 205 time to evaluate : 1.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 171 LYS Chi-restraints excluded: chain C residue 181 ILE Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 274 VAL Chi-restraints excluded: chain C residue 280 THR Chi-restraints excluded: chain C residue 409 LEU Chi-restraints excluded: chain C residue 439 CYS Chi-restraints excluded: chain C residue 448 SER Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 89 PHE Chi-restraints excluded: chain D residue 136 SER Chi-restraints excluded: chain D residue 148 ILE Chi-restraints excluded: chain D residue 203 ASP Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain D residue 256 MET Chi-restraints excluded: chain D residue 303 THR Chi-restraints excluded: chain D residue 387 ASN Chi-restraints excluded: chain D residue 440 ARG Chi-restraints excluded: chain D residue 461 VAL Chi-restraints excluded: chain A residue 37 MET Chi-restraints excluded: chain A residue 64 MET Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 78 MET Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 203 ASP Chi-restraints excluded: chain A residue 282 SER Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 385 SER Chi-restraints excluded: chain A residue 440 ARG Chi-restraints excluded: chain A residue 480 LYS Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 179 SER Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 335 THR Chi-restraints excluded: chain B residue 351 ILE Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 437 MET Chi-restraints excluded: chain B residue 491 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 180 optimal weight: 8.9990 chunk 21 optimal weight: 6.9990 chunk 106 optimal weight: 5.9990 chunk 136 optimal weight: 9.9990 chunk 105 optimal weight: 6.9990 chunk 157 optimal weight: 9.9990 chunk 104 optimal weight: 8.9990 chunk 186 optimal weight: 8.9990 chunk 116 optimal weight: 10.0000 chunk 113 optimal weight: 4.9990 chunk 85 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: ** D 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 245 GLN B 247 ASN ** B 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7174 moved from start: 0.1635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.081 14798 Z= 0.647 Angle : 0.725 11.472 20149 Z= 0.390 Chirality : 0.052 0.227 2330 Planarity : 0.005 0.057 2614 Dihedral : 5.486 49.732 2077 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 46.25 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.76 % Favored : 92.14 % Rotamer: Outliers : 7.39 % Allowed : 26.95 % Favored : 65.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.78 (0.19), residues: 1939 helix: 0.38 (0.18), residues: 773 sheet: -1.67 (0.34), residues: 220 loop : -0.91 (0.21), residues: 946 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 412 HIS 0.010 0.002 HIS B 107 PHE 0.042 0.003 PHE B 477 TYR 0.023 0.003 TYR C 251 ARG 0.007 0.001 ARG C 238 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3878 Ramachandran restraints generated. 1939 Oldfield, 0 Emsley, 1939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3878 Ramachandran restraints generated. 1939 Oldfield, 0 Emsley, 1939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 374 is missing expected H atoms. Skipping. Residue LYS 374 is missing expected H atoms. Skipping. Residue LYS 374 is missing expected H atoms. Skipping. Evaluate side-chains 313 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 206 time to evaluate : 1.613 Fit side-chains revert: symmetry clash REVERT: C 266 GLN cc_start: 0.7867 (OUTLIER) cc_final: 0.6670 (mp-120) REVERT: C 476 ASP cc_start: 0.7361 (m-30) cc_final: 0.7049 (t0) REVERT: D 78 MET cc_start: 0.8813 (OUTLIER) cc_final: 0.7870 (ttp) REVERT: D 256 MET cc_start: 0.8157 (OUTLIER) cc_final: 0.7880 (mpt) REVERT: D 310 ASP cc_start: 0.7704 (t0) cc_final: 0.7308 (t0) REVERT: D 406 ASP cc_start: 0.7852 (OUTLIER) cc_final: 0.7478 (t0) REVERT: D 440 ARG cc_start: 0.7016 (OUTLIER) cc_final: 0.6613 (ttm-80) REVERT: A 315 ASP cc_start: 0.7345 (m-30) cc_final: 0.7074 (m-30) REVERT: B 221 GLU cc_start: 0.8332 (OUTLIER) cc_final: 0.7894 (pt0) REVERT: B 351 ILE cc_start: 0.8139 (OUTLIER) cc_final: 0.7619 (tp) REVERT: B 418 LYS cc_start: 0.7290 (ptpp) cc_final: 0.6548 (mttp) outliers start: 107 outliers final: 73 residues processed: 276 average time/residue: 0.8462 time to fit residues: 268.8551 Evaluate side-chains 280 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 200 time to evaluate : 1.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 181 ILE Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 266 GLN Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 274 VAL Chi-restraints excluded: chain C residue 280 THR Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 383 VAL Chi-restraints excluded: chain C residue 391 VAL Chi-restraints excluded: chain C residue 409 LEU Chi-restraints excluded: chain C residue 433 ILE Chi-restraints excluded: chain C residue 439 CYS Chi-restraints excluded: chain C residue 448 SER Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain D residue 30 SER Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 78 MET Chi-restraints excluded: chain D residue 89 PHE Chi-restraints excluded: chain D residue 136 SER Chi-restraints excluded: chain D residue 142 THR Chi-restraints excluded: chain D residue 148 ILE Chi-restraints excluded: chain D residue 181 ILE Chi-restraints excluded: chain D residue 191 ILE Chi-restraints excluded: chain D residue 203 ASP Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain D residue 256 MET Chi-restraints excluded: chain D residue 285 THR Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 376 ASP Chi-restraints excluded: chain D residue 383 VAL Chi-restraints excluded: chain D residue 385 SER Chi-restraints excluded: chain D residue 403 VAL Chi-restraints excluded: chain D residue 406 ASP Chi-restraints excluded: chain D residue 440 ARG Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain D residue 461 VAL Chi-restraints excluded: chain A residue 31 PHE Chi-restraints excluded: chain A residue 37 MET Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 64 MET Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 78 MET Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 282 SER Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 308 SER Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 365 ILE Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 385 SER Chi-restraints excluded: chain A residue 433 ILE Chi-restraints excluded: chain A residue 440 ARG Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 480 LYS Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 45 ILE Chi-restraints excluded: chain B residue 221 GLU Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 323 CYS Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 335 THR Chi-restraints excluded: chain B residue 351 ILE Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 437 MET Chi-restraints excluded: chain B residue 491 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 115 optimal weight: 0.9980 chunk 74 optimal weight: 1.9990 chunk 111 optimal weight: 0.9990 chunk 56 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 118 optimal weight: 1.9990 chunk 126 optimal weight: 0.7980 chunk 91 optimal weight: 10.0000 chunk 17 optimal weight: 1.9990 chunk 146 optimal weight: 0.8980 chunk 169 optimal weight: 0.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 247 ASN B 426 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7054 moved from start: 0.1557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 14798 Z= 0.151 Angle : 0.451 7.465 20149 Z= 0.240 Chirality : 0.042 0.157 2330 Planarity : 0.003 0.045 2614 Dihedral : 4.581 48.335 2077 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 41.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 4.30 % Allowed : 30.31 % Favored : 65.39 % 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: -0.00 (0.20), residues: 1939 helix: 1.31 (0.19), residues: 761 sheet: -2.16 (0.38), residues: 176 loop : -0.58 (0.20), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 295 HIS 0.003 0.001 HIS C 223 PHE 0.012 0.001 PHE B 120 TYR 0.018 0.001 TYR C 135 ARG 0.002 0.000 ARG A 440 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3878 Ramachandran restraints generated. 1939 Oldfield, 0 Emsley, 1939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3878 Ramachandran restraints generated. 1939 Oldfield, 0 Emsley, 1939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 374 is missing expected H atoms. Skipping. Residue LYS 374 is missing expected H atoms. Skipping. Residue LYS 374 is missing expected H atoms. Skipping. Evaluate side-chains 269 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 208 time to evaluate : 1.688 Fit side-chains revert: symmetry clash REVERT: C 64 MET cc_start: 0.7600 (ptp) cc_final: 0.7326 (mtt) REVERT: D 89 PHE cc_start: 0.7633 (OUTLIER) cc_final: 0.6671 (t80) REVERT: D 310 ASP cc_start: 0.7470 (t0) cc_final: 0.7080 (t0) REVERT: D 387 ASN cc_start: 0.8542 (t0) cc_final: 0.7941 (t0) REVERT: A 315 ASP cc_start: 0.7131 (m-30) cc_final: 0.6855 (m-30) REVERT: B 251 TYR cc_start: 0.8674 (t80) cc_final: 0.8293 (t80) REVERT: B 275 TYR cc_start: 0.8521 (m-80) cc_final: 0.8000 (m-80) REVERT: B 351 ILE cc_start: 0.8085 (OUTLIER) cc_final: 0.7620 (tp) REVERT: B 418 LYS cc_start: 0.7200 (ptpp) cc_final: 0.6456 (mttp) REVERT: B 420 ILE cc_start: 0.6508 (mm) cc_final: 0.6236 (mt) REVERT: B 425 HIS cc_start: 0.6089 (p90) cc_final: 0.5872 (p90) REVERT: B 472 LYS cc_start: 0.8107 (mmmm) cc_final: 0.7726 (mptm) outliers start: 61 outliers final: 45 residues processed: 249 average time/residue: 0.9162 time to fit residues: 260.6554 Evaluate side-chains 247 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 200 time to evaluate : 1.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 181 ILE Chi-restraints excluded: chain C residue 274 VAL Chi-restraints excluded: chain C residue 280 THR Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 409 LEU Chi-restraints excluded: chain C residue 439 CYS Chi-restraints excluded: chain C residue 448 SER Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain D residue 30 SER Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 89 PHE Chi-restraints excluded: chain D residue 136 SER Chi-restraints excluded: chain D residue 148 ILE Chi-restraints excluded: chain D residue 203 ASP Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 365 ILE Chi-restraints excluded: chain D residue 385 SER Chi-restraints excluded: chain D residue 461 VAL Chi-restraints excluded: chain A residue 37 MET Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 78 MET Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 282 SER Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 385 SER Chi-restraints excluded: chain A residue 440 ARG Chi-restraints excluded: chain A residue 480 LYS Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain B residue 45 ILE Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 335 THR Chi-restraints excluded: chain B residue 351 ILE Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 491 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 178 optimal weight: 4.9990 chunk 162 optimal weight: 5.9990 chunk 173 optimal weight: 9.9990 chunk 104 optimal weight: 9.9990 chunk 75 optimal weight: 7.9990 chunk 136 optimal weight: 9.9990 chunk 53 optimal weight: 8.9990 chunk 156 optimal weight: 2.9990 chunk 163 optimal weight: 10.0000 chunk 172 optimal weight: 5.9990 chunk 113 optimal weight: 3.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 266 GLN ** D 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 159 HIS B 247 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7156 moved from start: 0.1683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.069 14798 Z= 0.522 Angle : 0.651 11.634 20149 Z= 0.349 Chirality : 0.049 0.195 2330 Planarity : 0.005 0.054 2614 Dihedral : 5.317 51.569 2077 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 45.76 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.97 % Favored : 91.98 % Rotamer: Outliers : 5.38 % Allowed : 29.44 % Favored : 65.19 % 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: -0.66 (0.19), residues: 1939 helix: 0.56 (0.18), residues: 773 sheet: -1.76 (0.34), residues: 222 loop : -0.88 (0.21), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 412 HIS 0.009 0.001 HIS B 107 PHE 0.032 0.002 PHE B 477 TYR 0.022 0.003 TYR D 479 ARG 0.005 0.001 ARG C 238 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3878 Ramachandran restraints generated. 1939 Oldfield, 0 Emsley, 1939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3878 Ramachandran restraints generated. 1939 Oldfield, 0 Emsley, 1939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 374 is missing expected H atoms. Skipping. Residue LYS 374 is missing expected H atoms. Skipping. Residue LYS 374 is missing expected H atoms. Skipping. Evaluate side-chains 273 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 196 time to evaluate : 1.467 Fit side-chains revert: symmetry clash REVERT: D 89 PHE cc_start: 0.7737 (OUTLIER) cc_final: 0.6601 (t80) REVERT: D 256 MET cc_start: 0.8172 (mmt) cc_final: 0.7837 (mpt) REVERT: D 310 ASP cc_start: 0.7674 (t0) cc_final: 0.7279 (t0) REVERT: D 406 ASP cc_start: 0.7690 (OUTLIER) cc_final: 0.7362 (t0) REVERT: A 315 ASP cc_start: 0.7276 (m-30) cc_final: 0.6988 (m-30) REVERT: A 427 SER cc_start: 0.8648 (m) cc_final: 0.8324 (p) REVERT: B 351 ILE cc_start: 0.8170 (OUTLIER) cc_final: 0.7596 (tp) REVERT: B 418 LYS cc_start: 0.7234 (ptpp) cc_final: 0.6484 (mttp) REVERT: B 472 LYS cc_start: 0.8162 (mmmm) cc_final: 0.7829 (mptt) outliers start: 77 outliers final: 58 residues processed: 248 average time/residue: 0.9361 time to fit residues: 265.2959 Evaluate side-chains 258 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 197 time to evaluate : 1.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 181 ILE Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 266 GLN Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 274 VAL Chi-restraints excluded: chain C residue 280 THR Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 391 VAL Chi-restraints excluded: chain C residue 409 LEU Chi-restraints excluded: chain C residue 439 CYS Chi-restraints excluded: chain C residue 448 SER Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain D residue 30 SER Chi-restraints excluded: chain D residue 63 ARG Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 89 PHE Chi-restraints excluded: chain D residue 136 SER Chi-restraints excluded: chain D residue 142 THR Chi-restraints excluded: chain D residue 148 ILE Chi-restraints excluded: chain D residue 181 ILE Chi-restraints excluded: chain D residue 203 ASP Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain D residue 285 THR Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 365 ILE Chi-restraints excluded: chain D residue 385 SER Chi-restraints excluded: chain D residue 406 ASP Chi-restraints excluded: chain D residue 461 VAL Chi-restraints excluded: chain A residue 31 PHE Chi-restraints excluded: chain A residue 37 MET Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 78 MET Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 282 SER Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 385 SER Chi-restraints excluded: chain A residue 433 ILE Chi-restraints excluded: chain A residue 440 ARG Chi-restraints excluded: chain A residue 480 LYS Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain B residue 45 ILE Chi-restraints excluded: chain B residue 181 ILE Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 335 THR Chi-restraints excluded: chain B residue 351 ILE Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 437 MET Chi-restraints excluded: chain B residue 491 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 183 optimal weight: 0.9980 chunk 111 optimal weight: 0.7980 chunk 86 optimal weight: 2.9990 chunk 127 optimal weight: 0.9980 chunk 192 optimal weight: 2.9990 chunk 176 optimal weight: 2.9990 chunk 153 optimal weight: 7.9990 chunk 15 optimal weight: 3.9990 chunk 118 optimal weight: 1.9990 chunk 93 optimal weight: 0.6980 chunk 121 optimal weight: 3.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 61 HIS ** D 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 247 ASN ** B 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 426 ASN ** B 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7138 moved from start: 0.1691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.117 14798 Z= 0.325 Angle : 0.832 59.200 20149 Z= 0.471 Chirality : 0.045 0.157 2330 Planarity : 0.005 0.053 2614 Dihedral : 5.313 51.597 2077 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 47.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.76 % Favored : 92.24 % Rotamer: Outliers : 4.70 % Allowed : 30.24 % Favored : 65.05 % Cbeta Deviations : 0.06 % 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: -0.71 (0.19), residues: 1939 helix: 0.52 (0.18), residues: 773 sheet: -1.79 (0.34), residues: 222 loop : -0.91 (0.21), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 126 HIS 0.008 0.001 HIS B 107 PHE 0.027 0.002 PHE B 477 TYR 0.021 0.002 TYR D 479 ARG 0.003 0.000 ARG C 238 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3878 Ramachandran restraints generated. 1939 Oldfield, 0 Emsley, 1939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3878 Ramachandran restraints generated. 1939 Oldfield, 0 Emsley, 1939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 374 is missing expected H atoms. Skipping. Residue LYS 374 is missing expected H atoms. Skipping. Residue LYS 374 is missing expected H atoms. Skipping. Evaluate side-chains 266 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 199 time to evaluate : 1.546 Fit side-chains revert: symmetry clash REVERT: D 89 PHE cc_start: 0.7657 (OUTLIER) cc_final: 0.6513 (t80) REVERT: D 310 ASP cc_start: 0.7695 (t0) cc_final: 0.7300 (t0) REVERT: D 406 ASP cc_start: 0.7665 (OUTLIER) cc_final: 0.7293 (t0) REVERT: A 315 ASP cc_start: 0.7254 (m-30) cc_final: 0.6969 (m-30) REVERT: A 427 SER cc_start: 0.8642 (m) cc_final: 0.8321 (p) REVERT: B 351 ILE cc_start: 0.8179 (OUTLIER) cc_final: 0.7602 (tp) REVERT: B 418 LYS cc_start: 0.7226 (ptpp) cc_final: 0.6487 (mttp) REVERT: B 420 ILE cc_start: 0.6658 (mm) cc_final: 0.6375 (mt) REVERT: B 472 LYS cc_start: 0.8145 (mmmm) cc_final: 0.7813 (mptt) outliers start: 67 outliers final: 60 residues processed: 244 average time/residue: 0.9369 time to fit residues: 261.3985 Evaluate side-chains 262 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 199 time to evaluate : 1.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 181 ILE Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 274 VAL Chi-restraints excluded: chain C residue 280 THR Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 391 VAL Chi-restraints excluded: chain C residue 409 LEU Chi-restraints excluded: chain C residue 410 VAL Chi-restraints excluded: chain C residue 439 CYS Chi-restraints excluded: chain C residue 448 SER Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain D residue 30 SER Chi-restraints excluded: chain D residue 63 ARG Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 89 PHE Chi-restraints excluded: chain D residue 136 SER Chi-restraints excluded: chain D residue 142 THR Chi-restraints excluded: chain D residue 148 ILE Chi-restraints excluded: chain D residue 181 ILE Chi-restraints excluded: chain D residue 203 ASP Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain D residue 303 THR Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 365 ILE Chi-restraints excluded: chain D residue 385 SER Chi-restraints excluded: chain D residue 406 ASP Chi-restraints excluded: chain D residue 461 VAL Chi-restraints excluded: chain D residue 467 ARG Chi-restraints excluded: chain A residue 37 MET Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 78 MET Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 282 SER Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 385 SER Chi-restraints excluded: chain A residue 433 ILE Chi-restraints excluded: chain A residue 440 ARG Chi-restraints excluded: chain A residue 480 LYS Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain B residue 19 ILE Chi-restraints excluded: chain B residue 45 ILE Chi-restraints excluded: chain B residue 181 ILE Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 335 THR Chi-restraints excluded: chain B residue 351 ILE Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 437 MET Chi-restraints excluded: chain B residue 469 ILE Chi-restraints excluded: chain B residue 491 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 163 optimal weight: 7.9990 chunk 46 optimal weight: 2.9990 chunk 141 optimal weight: 4.9990 chunk 22 optimal weight: 1.9990 chunk 42 optimal weight: 6.9990 chunk 153 optimal weight: 6.9990 chunk 64 optimal weight: 0.6980 chunk 157 optimal weight: 4.9990 chunk 19 optimal weight: 0.8980 chunk 28 optimal weight: 8.9990 chunk 134 optimal weight: 3.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 247 ASN ** B 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 426 ASN ** B 432 ASN ** 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 = 0.4382 r_free = 0.4382 target = 0.189523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.158286 restraints weight = 32193.359| |-----------------------------------------------------------------------------| r_work (start): 0.3987 rms_B_bonded: 3.74 r_work: 0.3795 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.3795 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3804 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3804 r_free = 0.3804 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3804 r_free = 0.3804 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3804 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7022 moved from start: 0.1696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.117 14798 Z= 0.325 Angle : 0.832 59.200 20149 Z= 0.471 Chirality : 0.045 0.157 2330 Planarity : 0.005 0.053 2614 Dihedral : 5.313 51.597 2077 Min Nonbonded Distance : 1.332 Molprobity Statistics. All-atom Clashscore : 47.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.76 % Favored : 92.24 % Rotamer: Outliers : 4.44 % Allowed : 30.51 % Favored : 65.05 % Cbeta Deviations : 0.06 % 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: -0.71 (0.19), residues: 1939 helix: 0.52 (0.18), residues: 773 sheet: -1.79 (0.34), residues: 222 loop : -0.91 (0.21), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 126 HIS 0.008 0.001 HIS B 107 PHE 0.027 0.002 PHE B 477 TYR 0.021 0.002 TYR D 479 ARG 0.003 0.000 ARG C 238 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4728.27 seconds wall clock time: 87 minutes 6.45 seconds (5226.45 seconds total)