Starting phenix.real_space_refine on Tue Dec 31 01:44:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7rgd_24448/12_2024/7rgd_24448_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rgd_24448/12_2024/7rgd_24448.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7rgd_24448/12_2024/7rgd_24448.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rgd_24448/12_2024/7rgd_24448.map" model { file = "/net/cci-nas-00/data/ceres_data/7rgd_24448/12_2024/7rgd_24448_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rgd_24448/12_2024/7rgd_24448_trim.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.305 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: 6 Type Number sf(0) Gaussians P 96 5.49 5 S 200 5.16 5 C 20272 2.51 5 N 5568 2.21 5 O 6448 1.98 5 H 31840 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 306 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 64424 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 7891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 519, 7891 Classifications: {'peptide': 519} Link IDs: {'PTRANS': 18, 'TRANS': 500} Chain breaks: 2 Chain: "B" Number of atoms: 7891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 519, 7891 Classifications: {'peptide': 519} Link IDs: {'PTRANS': 18, 'TRANS': 500} Chain breaks: 2 Chain: "C" Number of atoms: 7891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 519, 7891 Classifications: {'peptide': 519} Link IDs: {'PTRANS': 18, 'TRANS': 500} Chain breaks: 2 Chain: "D" Number of atoms: 7891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 519, 7891 Classifications: {'peptide': 519} Link IDs: {'PTRANS': 18, 'TRANS': 500} Chain breaks: 2 Chain: "E" Number of atoms: 7891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 519, 7891 Classifications: {'peptide': 519} Link IDs: {'PTRANS': 18, 'TRANS': 500} Chain breaks: 2 Chain: "F" Number of atoms: 7891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 519, 7891 Classifications: {'peptide': 519} Link IDs: {'PTRANS': 18, 'TRANS': 500} Chain breaks: 2 Chain: "G" Number of atoms: 7891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 519, 7891 Classifications: {'peptide': 519} Link IDs: {'PTRANS': 18, 'TRANS': 500} Chain breaks: 2 Chain: "H" Number of atoms: 7891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 519, 7891 Classifications: {'peptide': 519} Link IDs: {'PTRANS': 18, 'TRANS': 500} Chain breaks: 2 Chain: "A" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 162 Unusual residues: {'ATP': 1, 'GTP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 4} Modifications used: {'rna3p': 1} Link IDs: {None: 4} Chain: "B" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 162 Unusual residues: {'ATP': 1, 'GTP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 4} Modifications used: {'rna3p': 1} Link IDs: {None: 4} Chain: "C" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 162 Unusual residues: {'ATP': 1, 'GTP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 4} Modifications used: {'rna3p': 1} Link IDs: {None: 4} Chain: "D" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 162 Unusual residues: {'ATP': 1, 'GTP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 4} Modifications used: {'rna3p': 1} Link IDs: {None: 4} Chain: "E" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 162 Unusual residues: {'ATP': 1, 'GTP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 4} Modifications used: {'rna3p': 1} Link IDs: {None: 4} Chain: "F" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 162 Unusual residues: {'ATP': 1, 'GTP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 4} Modifications used: {'rna3p': 1} Link IDs: {None: 4} Chain: "G" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 162 Unusual residues: {'ATP': 1, 'GTP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 4} Modifications used: {'rna3p': 1} Link IDs: {None: 4} Chain: "H" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 162 Unusual residues: {'ATP': 1, 'GTP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 4} Modifications used: {'rna3p': 1} Link IDs: {None: 4} Time building chain proxies: 23.13, per 1000 atoms: 0.36 Number of scatterers: 64424 At special positions: 0 Unit cell: (172.815, 172.815, 135.723, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 200 16.00 P 96 15.00 O 6448 8.00 N 5568 7.00 C 20272 6.00 H 31840 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=0, symmetry=0 Time building additional restraints: 12.47 Conformation dependent library (CDL) restraints added in 4.2 seconds 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7456 Finding SS restraints... Secondary structure from input PDB file: 177 helices and 48 sheets defined 42.3% alpha, 10.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.10 Creating SS restraints... Processing helix chain 'A' and resid -18 through -7 Processing helix chain 'A' and resid 2 through 7 removed outlier: 3.573A pdb=" N ILE A 6 " --> pdb=" O ALA A 2 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N SER A 7 " --> pdb=" O ASP A 3 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2 through 7' Processing helix chain 'A' and resid 19 through 26 removed outlier: 3.833A pdb=" N SER A 26 " --> pdb=" O GLN A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 31 through 33 No H-bonds generated for 'chain 'A' and resid 31 through 33' Processing helix chain 'A' and resid 75 through 85 Processing helix chain 'A' and resid 96 through 110 Processing helix chain 'A' and resid 126 through 137 removed outlier: 3.528A pdb=" N VAL A 130 " --> pdb=" O THR A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 163 removed outlier: 3.953A pdb=" N ASP A 162 " --> pdb=" O THR A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 178 Processing helix chain 'A' and resid 193 through 205 removed outlier: 3.529A pdb=" N LYS A 205 " --> pdb=" O LEU A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 233 Processing helix chain 'A' and resid 254 through 266 removed outlier: 4.281A pdb=" N TYR A 258 " --> pdb=" O GLU A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 294 Processing helix chain 'A' and resid 306 through 317 removed outlier: 3.955A pdb=" N ASN A 312 " --> pdb=" O ALA A 308 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU A 313 " --> pdb=" O GLN A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 338 Processing helix chain 'A' and resid 342 through 355 Processing helix chain 'A' and resid 356 through 358 No H-bonds generated for 'chain 'A' and resid 356 through 358' Processing helix chain 'A' and resid 369 through 379 Processing helix chain 'A' and resid 452 through 472 Proline residue: A 458 - end of helix Processing helix chain 'A' and resid 475 through 485 Processing helix chain 'A' and resid 494 through 501 Processing helix chain 'B' and resid -18 through -7 Processing helix chain 'B' and resid 2 through 7 removed outlier: 3.665A pdb=" N SER B 7 " --> pdb=" O ASP B 3 " (cutoff:3.500A) Processing helix chain 'B' and resid 19 through 26 removed outlier: 3.867A pdb=" N SER B 26 " --> pdb=" O GLN B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 33 No H-bonds generated for 'chain 'B' and resid 31 through 33' Processing helix chain 'B' and resid 45 through 49 Processing helix chain 'B' and resid 75 through 85 Processing helix chain 'B' and resid 96 through 110 removed outlier: 3.509A pdb=" N PHE B 110 " --> pdb=" O LYS B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 126 through 137 removed outlier: 3.840A pdb=" N VAL B 130 " --> pdb=" O THR B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 163 removed outlier: 3.603A pdb=" N ASP B 162 " --> pdb=" O THR B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 178 Processing helix chain 'B' and resid 183 through 185 No H-bonds generated for 'chain 'B' and resid 183 through 185' Processing helix chain 'B' and resid 193 through 205 Processing helix chain 'B' and resid 224 through 233 Processing helix chain 'B' and resid 254 through 266 removed outlier: 4.271A pdb=" N TYR B 258 " --> pdb=" O GLU B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 294 Processing helix chain 'B' and resid 306 through 317 removed outlier: 3.981A pdb=" N ASN B 312 " --> pdb=" O ALA B 308 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU B 313 " --> pdb=" O GLN B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 338 Processing helix chain 'B' and resid 342 through 355 Processing helix chain 'B' and resid 356 through 358 No H-bonds generated for 'chain 'B' and resid 356 through 358' Processing helix chain 'B' and resid 369 through 379 Processing helix chain 'B' and resid 452 through 472 Proline residue: B 458 - end of helix Processing helix chain 'B' and resid 475 through 485 Processing helix chain 'B' and resid 494 through 502 removed outlier: 3.549A pdb=" N GLY B 502 " --> pdb=" O GLN B 498 " (cutoff:3.500A) Processing helix chain 'C' and resid -18 through -7 Processing helix chain 'C' and resid 2 through 7 Processing helix chain 'C' and resid 19 through 26 removed outlier: 3.895A pdb=" N SER C 26 " --> pdb=" O GLN C 22 " (cutoff:3.500A) Processing helix chain 'C' and resid 31 through 33 No H-bonds generated for 'chain 'C' and resid 31 through 33' Processing helix chain 'C' and resid 45 through 49 removed outlier: 3.515A pdb=" N VAL C 49 " --> pdb=" O ALA C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 75 through 85 Processing helix chain 'C' and resid 96 through 110 Processing helix chain 'C' and resid 126 through 137 Processing helix chain 'C' and resid 159 through 163 removed outlier: 3.587A pdb=" N ASP C 162 " --> pdb=" O THR C 159 " (cutoff:3.500A) Processing helix chain 'C' and resid 174 through 178 Processing helix chain 'C' and resid 183 through 185 No H-bonds generated for 'chain 'C' and resid 183 through 185' Processing helix chain 'C' and resid 193 through 205 Processing helix chain 'C' and resid 224 through 233 Processing helix chain 'C' and resid 255 through 266 removed outlier: 3.638A pdb=" N ARG C 259 " --> pdb=" O ASP C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 294 Processing helix chain 'C' and resid 306 through 317 removed outlier: 3.987A pdb=" N ASN C 312 " --> pdb=" O ALA C 308 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU C 313 " --> pdb=" O GLN C 309 " (cutoff:3.500A) Processing helix chain 'C' and resid 332 through 338 Processing helix chain 'C' and resid 342 through 355 Processing helix chain 'C' and resid 356 through 358 No H-bonds generated for 'chain 'C' and resid 356 through 358' Processing helix chain 'C' and resid 369 through 379 Processing helix chain 'C' and resid 452 through 472 Proline residue: C 458 - end of helix Processing helix chain 'C' and resid 475 through 485 Processing helix chain 'C' and resid 494 through 502 Processing helix chain 'D' and resid -18 through -7 Processing helix chain 'D' and resid 2 through 7 removed outlier: 3.583A pdb=" N ILE D 6 " --> pdb=" O ALA D 2 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N SER D 7 " --> pdb=" O ASP D 3 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 2 through 7' Processing helix chain 'D' and resid 19 through 26 removed outlier: 3.889A pdb=" N SER D 26 " --> pdb=" O GLN D 22 " (cutoff:3.500A) Processing helix chain 'D' and resid 31 through 33 No H-bonds generated for 'chain 'D' and resid 31 through 33' Processing helix chain 'D' and resid 75 through 85 Processing helix chain 'D' and resid 96 through 110 Processing helix chain 'D' and resid 126 through 138 removed outlier: 3.513A pdb=" N VAL D 130 " --> pdb=" O THR D 126 " (cutoff:3.500A) Processing helix chain 'D' and resid 159 through 164 Processing helix chain 'D' and resid 174 through 178 Processing helix chain 'D' and resid 183 through 185 No H-bonds generated for 'chain 'D' and resid 183 through 185' Processing helix chain 'D' and resid 193 through 205 Processing helix chain 'D' and resid 224 through 233 Processing helix chain 'D' and resid 255 through 266 removed outlier: 3.630A pdb=" N ARG D 259 " --> pdb=" O ASP D 255 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 294 Processing helix chain 'D' and resid 306 through 317 removed outlier: 3.980A pdb=" N ASN D 312 " --> pdb=" O ALA D 308 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU D 313 " --> pdb=" O GLN D 309 " (cutoff:3.500A) Processing helix chain 'D' and resid 332 through 338 Processing helix chain 'D' and resid 342 through 355 Processing helix chain 'D' and resid 369 through 379 Processing helix chain 'D' and resid 452 through 472 Proline residue: D 458 - end of helix Processing helix chain 'D' and resid 475 through 485 Processing helix chain 'D' and resid 494 through 501 Processing helix chain 'E' and resid -18 through -7 Processing helix chain 'E' and resid 2 through 7 removed outlier: 3.681A pdb=" N SER E 7 " --> pdb=" O ASP E 3 " (cutoff:3.500A) Processing helix chain 'E' and resid 19 through 26 removed outlier: 3.889A pdb=" N SER E 26 " --> pdb=" O GLN E 22 " (cutoff:3.500A) Processing helix chain 'E' and resid 31 through 33 No H-bonds generated for 'chain 'E' and resid 31 through 33' Processing helix chain 'E' and resid 45 through 49 removed outlier: 3.565A pdb=" N VAL E 49 " --> pdb=" O ALA E 46 " (cutoff:3.500A) Processing helix chain 'E' and resid 75 through 85 Processing helix chain 'E' and resid 96 through 110 Processing helix chain 'E' and resid 126 through 137 Processing helix chain 'E' and resid 174 through 178 Processing helix chain 'E' and resid 183 through 185 No H-bonds generated for 'chain 'E' and resid 183 through 185' Processing helix chain 'E' and resid 193 through 205 removed outlier: 3.584A pdb=" N LYS E 205 " --> pdb=" O LEU E 201 " (cutoff:3.500A) Processing helix chain 'E' and resid 224 through 233 Processing helix chain 'E' and resid 255 through 266 removed outlier: 3.621A pdb=" N ARG E 259 " --> pdb=" O ASP E 255 " (cutoff:3.500A) Processing helix chain 'E' and resid 280 through 294 Processing helix chain 'E' and resid 306 through 317 removed outlier: 4.035A pdb=" N ASN E 312 " --> pdb=" O ALA E 308 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU E 313 " --> pdb=" O GLN E 309 " (cutoff:3.500A) Processing helix chain 'E' and resid 332 through 338 Processing helix chain 'E' and resid 342 through 355 Processing helix chain 'E' and resid 356 through 358 No H-bonds generated for 'chain 'E' and resid 356 through 358' Processing helix chain 'E' and resid 369 through 379 Processing helix chain 'E' and resid 452 through 472 Proline residue: E 458 - end of helix Processing helix chain 'E' and resid 475 through 485 Processing helix chain 'E' and resid 494 through 502 Processing helix chain 'F' and resid -18 through -7 Processing helix chain 'F' and resid 2 through 7 removed outlier: 3.535A pdb=" N ILE F 6 " --> pdb=" O ALA F 2 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N SER F 7 " --> pdb=" O ASP F 3 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 2 through 7' Processing helix chain 'F' and resid 19 through 26 removed outlier: 3.834A pdb=" N SER F 26 " --> pdb=" O GLN F 22 " (cutoff:3.500A) Processing helix chain 'F' and resid 31 through 33 No H-bonds generated for 'chain 'F' and resid 31 through 33' Processing helix chain 'F' and resid 45 through 49 Processing helix chain 'F' and resid 75 through 85 Processing helix chain 'F' and resid 96 through 110 Processing helix chain 'F' and resid 126 through 137 removed outlier: 3.834A pdb=" N VAL F 130 " --> pdb=" O THR F 126 " (cutoff:3.500A) Processing helix chain 'F' and resid 159 through 163 Processing helix chain 'F' and resid 174 through 178 Processing helix chain 'F' and resid 193 through 205 removed outlier: 3.560A pdb=" N LYS F 205 " --> pdb=" O LEU F 201 " (cutoff:3.500A) Processing helix chain 'F' and resid 224 through 233 Processing helix chain 'F' and resid 255 through 266 removed outlier: 3.642A pdb=" N ARG F 259 " --> pdb=" O ASP F 255 " (cutoff:3.500A) Processing helix chain 'F' and resid 280 through 294 Processing helix chain 'F' and resid 306 through 317 removed outlier: 3.987A pdb=" N ASN F 312 " --> pdb=" O ALA F 308 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU F 313 " --> pdb=" O GLN F 309 " (cutoff:3.500A) Processing helix chain 'F' and resid 332 through 338 Processing helix chain 'F' and resid 342 through 355 Processing helix chain 'F' and resid 356 through 358 No H-bonds generated for 'chain 'F' and resid 356 through 358' Processing helix chain 'F' and resid 369 through 379 Processing helix chain 'F' and resid 452 through 472 Proline residue: F 458 - end of helix Processing helix chain 'F' and resid 475 through 485 Processing helix chain 'F' and resid 494 through 502 Processing helix chain 'G' and resid -18 through -7 Processing helix chain 'G' and resid 2 through 7 removed outlier: 3.654A pdb=" N SER G 7 " --> pdb=" O ASP G 3 " (cutoff:3.500A) Processing helix chain 'G' and resid 19 through 26 removed outlier: 3.907A pdb=" N SER G 26 " --> pdb=" O GLN G 22 " (cutoff:3.500A) Processing helix chain 'G' and resid 31 through 33 No H-bonds generated for 'chain 'G' and resid 31 through 33' Processing helix chain 'G' and resid 45 through 49 removed outlier: 3.524A pdb=" N VAL G 49 " --> pdb=" O ALA G 46 " (cutoff:3.500A) Processing helix chain 'G' and resid 75 through 85 Processing helix chain 'G' and resid 96 through 110 Processing helix chain 'G' and resid 126 through 138 Processing helix chain 'G' and resid 159 through 164 removed outlier: 3.582A pdb=" N ILE G 163 " --> pdb=" O THR G 159 " (cutoff:3.500A) Processing helix chain 'G' and resid 174 through 178 Processing helix chain 'G' and resid 183 through 185 No H-bonds generated for 'chain 'G' and resid 183 through 185' Processing helix chain 'G' and resid 193 through 205 removed outlier: 3.582A pdb=" N LYS G 205 " --> pdb=" O LEU G 201 " (cutoff:3.500A) Processing helix chain 'G' and resid 224 through 233 Processing helix chain 'G' and resid 255 through 266 removed outlier: 3.626A pdb=" N ARG G 259 " --> pdb=" O ASP G 255 " (cutoff:3.500A) Processing helix chain 'G' and resid 280 through 294 Processing helix chain 'G' and resid 306 through 317 removed outlier: 4.018A pdb=" N ASN G 312 " --> pdb=" O ALA G 308 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU G 313 " --> pdb=" O GLN G 309 " (cutoff:3.500A) Processing helix chain 'G' and resid 332 through 337 Processing helix chain 'G' and resid 342 through 355 Processing helix chain 'G' and resid 356 through 358 No H-bonds generated for 'chain 'G' and resid 356 through 358' Processing helix chain 'G' and resid 369 through 379 Processing helix chain 'G' and resid 452 through 472 Proline residue: G 458 - end of helix Processing helix chain 'G' and resid 475 through 485 Processing helix chain 'G' and resid 494 through 501 Processing helix chain 'H' and resid -18 through -7 Processing helix chain 'H' and resid 2 through 7 removed outlier: 3.592A pdb=" N ILE H 6 " --> pdb=" O ALA H 2 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N SER H 7 " --> pdb=" O ASP H 3 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 2 through 7' Processing helix chain 'H' and resid 19 through 26 removed outlier: 3.812A pdb=" N SER H 26 " --> pdb=" O GLN H 22 " (cutoff:3.500A) Processing helix chain 'H' and resid 31 through 33 No H-bonds generated for 'chain 'H' and resid 31 through 33' Processing helix chain 'H' and resid 75 through 85 Processing helix chain 'H' and resid 96 through 110 Processing helix chain 'H' and resid 126 through 137 Processing helix chain 'H' and resid 160 through 164 Processing helix chain 'H' and resid 174 through 178 Processing helix chain 'H' and resid 183 through 185 No H-bonds generated for 'chain 'H' and resid 183 through 185' Processing helix chain 'H' and resid 193 through 205 removed outlier: 3.572A pdb=" N LYS H 205 " --> pdb=" O LEU H 201 " (cutoff:3.500A) Processing helix chain 'H' and resid 224 through 233 Processing helix chain 'H' and resid 255 through 266 removed outlier: 3.624A pdb=" N ARG H 259 " --> pdb=" O ASP H 255 " (cutoff:3.500A) Processing helix chain 'H' and resid 280 through 294 Processing helix chain 'H' and resid 306 through 317 removed outlier: 4.001A pdb=" N ASN H 312 " --> pdb=" O ALA H 308 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU H 313 " --> pdb=" O GLN H 309 " (cutoff:3.500A) Processing helix chain 'H' and resid 332 through 338 Processing helix chain 'H' and resid 342 through 355 Processing helix chain 'H' and resid 356 through 358 No H-bonds generated for 'chain 'H' and resid 356 through 358' Processing helix chain 'H' and resid 369 through 379 Processing helix chain 'H' and resid 452 through 472 Proline residue: H 458 - end of helix Processing helix chain 'H' and resid 475 through 485 Processing helix chain 'H' and resid 494 through 502 Processing sheet with id=AA1, first strand: chain 'A' and resid 35 through 37 Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 54 Processing sheet with id=AA3, first strand: chain 'A' and resid 65 through 67 removed outlier: 6.567A pdb=" N ALA A 248 " --> pdb=" O VAL A 272 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N ILE A 271 " --> pdb=" O ILE A 300 " (cutoff:3.500A) removed outlier: 7.922A pdb=" N GLY A 302 " --> pdb=" O ILE A 271 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N LEU A 273 " --> pdb=" O GLY A 302 " (cutoff:3.500A) removed outlier: 8.254A pdb=" N VAL A 304 " --> pdb=" O LEU A 273 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N ILE A 361 " --> pdb=" O THR A 383 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N MET A 385 " --> pdb=" O ILE A 361 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N ALA A 363 " --> pdb=" O MET A 385 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ILE A 66 " --> pdb=" O MET A 386 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 142 through 145 Processing sheet with id=AA5, first strand: chain 'A' and resid 188 through 189 removed outlier: 6.282A pdb=" N ALA A 188 " --> pdb=" O VAL A 212 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 408 through 411 Processing sheet with id=AA7, first strand: chain 'B' and resid 35 through 37 Processing sheet with id=AA8, first strand: chain 'B' and resid 53 through 54 Processing sheet with id=AA9, first strand: chain 'B' and resid 65 through 67 removed outlier: 6.589A pdb=" N ALA B 248 " --> pdb=" O VAL B 272 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ILE B 271 " --> pdb=" O ILE B 300 " (cutoff:3.500A) removed outlier: 7.832A pdb=" N GLY B 302 " --> pdb=" O ILE B 271 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLY B 320 " --> pdb=" O VAL B 299 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ASN B 303 " --> pdb=" O ARG B 322 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N ILE B 361 " --> pdb=" O THR B 383 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N MET B 385 " --> pdb=" O ILE B 361 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N ALA B 363 " --> pdb=" O MET B 385 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ILE B 66 " --> pdb=" O MET B 386 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 142 through 145 Processing sheet with id=AB2, first strand: chain 'B' and resid 188 through 189 removed outlier: 6.385A pdb=" N ALA B 188 " --> pdb=" O VAL B 212 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 409 through 411 Processing sheet with id=AB4, first strand: chain 'C' and resid 35 through 37 Processing sheet with id=AB5, first strand: chain 'C' and resid 53 through 54 Processing sheet with id=AB6, first strand: chain 'C' and resid 65 through 67 removed outlier: 6.523A pdb=" N ALA C 248 " --> pdb=" O VAL C 272 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ILE C 271 " --> pdb=" O ILE C 300 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N GLY C 302 " --> pdb=" O ILE C 271 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLY C 320 " --> pdb=" O VAL C 299 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N ASN C 303 " --> pdb=" O ARG C 322 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N ILE C 361 " --> pdb=" O THR C 383 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N MET C 385 " --> pdb=" O ILE C 361 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N ALA C 363 " --> pdb=" O MET C 385 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 142 through 145 removed outlier: 6.732A pdb=" N ILE C 142 " --> pdb=" O ILE C 157 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N ILE C 157 " --> pdb=" O ILE C 142 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N ILE C 144 " --> pdb=" O VAL C 155 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 188 through 189 Processing sheet with id=AB9, first strand: chain 'C' and resid 409 through 410 Processing sheet with id=AC1, first strand: chain 'D' and resid 35 through 37 Processing sheet with id=AC2, first strand: chain 'D' and resid 53 through 54 Processing sheet with id=AC3, first strand: chain 'D' and resid 65 through 67 removed outlier: 6.662A pdb=" N ALA D 248 " --> pdb=" O VAL D 272 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ILE D 271 " --> pdb=" O ILE D 300 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N GLY D 302 " --> pdb=" O ILE D 271 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N ASN D 303 " --> pdb=" O ARG D 322 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ILE D 361 " --> pdb=" O THR D 383 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N MET D 385 " --> pdb=" O ILE D 361 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N ALA D 363 " --> pdb=" O MET D 385 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 142 through 145 removed outlier: 6.730A pdb=" N ILE D 142 " --> pdb=" O ILE D 157 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N ILE D 157 " --> pdb=" O ILE D 142 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N ILE D 144 " --> pdb=" O VAL D 155 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 188 through 189 removed outlier: 6.366A pdb=" N ALA D 188 " --> pdb=" O VAL D 212 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 409 through 411 removed outlier: 3.828A pdb=" N TYR D 411 " --> pdb=" O GLY D 445 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 35 through 37 Processing sheet with id=AC8, first strand: chain 'E' and resid 53 through 54 Processing sheet with id=AC9, first strand: chain 'E' and resid 65 through 67 removed outlier: 6.432A pdb=" N ALA E 248 " --> pdb=" O VAL E 272 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N ILE E 271 " --> pdb=" O ILE E 300 " (cutoff:3.500A) removed outlier: 8.002A pdb=" N GLY E 302 " --> pdb=" O ILE E 271 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N LEU E 273 " --> pdb=" O GLY E 302 " (cutoff:3.500A) removed outlier: 8.545A pdb=" N VAL E 304 " --> pdb=" O LEU E 273 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLY E 320 " --> pdb=" O VAL E 299 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ASN E 303 " --> pdb=" O ARG E 322 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N ILE E 361 " --> pdb=" O THR E 383 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N MET E 385 " --> pdb=" O ILE E 361 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N ALA E 363 " --> pdb=" O MET E 385 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N ILE E 66 " --> pdb=" O MET E 386 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 142 through 145 Processing sheet with id=AD2, first strand: chain 'E' and resid 188 through 189 removed outlier: 6.368A pdb=" N ALA E 188 " --> pdb=" O VAL E 212 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 409 through 411 Processing sheet with id=AD4, first strand: chain 'F' and resid 35 through 37 Processing sheet with id=AD5, first strand: chain 'F' and resid 53 through 54 Processing sheet with id=AD6, first strand: chain 'F' and resid 65 through 67 removed outlier: 6.557A pdb=" N ALA F 248 " --> pdb=" O VAL F 272 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N ILE F 271 " --> pdb=" O ILE F 300 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N GLY F 302 " --> pdb=" O ILE F 271 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N ASN F 303 " --> pdb=" O ARG F 322 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N ILE F 361 " --> pdb=" O THR F 383 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N MET F 385 " --> pdb=" O ILE F 361 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N ALA F 363 " --> pdb=" O MET F 385 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'F' and resid 142 through 145 Processing sheet with id=AD8, first strand: chain 'F' and resid 188 through 189 removed outlier: 6.281A pdb=" N ALA F 188 " --> pdb=" O VAL F 212 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'F' and resid 408 through 411 removed outlier: 3.744A pdb=" N TYR F 411 " --> pdb=" O GLY F 445 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'G' and resid 35 through 37 Processing sheet with id=AE2, first strand: chain 'G' and resid 53 through 54 Processing sheet with id=AE3, first strand: chain 'G' and resid 65 through 67 removed outlier: 6.382A pdb=" N GLY G 89 " --> pdb=" O GLY G 247 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N ALA G 249 " --> pdb=" O GLY G 89 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N ILE G 91 " --> pdb=" O ALA G 249 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N ALA G 248 " --> pdb=" O VAL G 272 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N GLY G 302 " --> pdb=" O LEU G 273 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLY G 320 " --> pdb=" O VAL G 299 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N ASN G 303 " --> pdb=" O ARG G 322 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N ILE G 361 " --> pdb=" O THR G 383 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N MET G 385 " --> pdb=" O ILE G 361 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N ALA G 363 " --> pdb=" O MET G 385 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ILE G 66 " --> pdb=" O MET G 386 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'G' and resid 142 through 145 removed outlier: 6.727A pdb=" N ILE G 142 " --> pdb=" O ILE G 157 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N ILE G 157 " --> pdb=" O ILE G 142 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N ILE G 144 " --> pdb=" O VAL G 155 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'G' and resid 188 through 189 removed outlier: 6.335A pdb=" N ALA G 188 " --> pdb=" O VAL G 212 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'G' and resid 409 through 411 removed outlier: 3.762A pdb=" N TYR G 411 " --> pdb=" O GLY G 445 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'H' and resid 35 through 37 Processing sheet with id=AE8, first strand: chain 'H' and resid 53 through 54 Processing sheet with id=AE9, first strand: chain 'H' and resid 65 through 67 removed outlier: 6.579A pdb=" N ALA H 248 " --> pdb=" O VAL H 272 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N ILE H 271 " --> pdb=" O ILE H 300 " (cutoff:3.500A) removed outlier: 7.927A pdb=" N GLY H 302 " --> pdb=" O ILE H 271 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLY H 320 " --> pdb=" O VAL H 299 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N ASN H 303 " --> pdb=" O ARG H 322 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N ILE H 361 " --> pdb=" O THR H 383 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N MET H 385 " --> pdb=" O ILE H 361 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N ALA H 363 " --> pdb=" O MET H 385 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N ILE H 66 " --> pdb=" O MET H 386 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'H' and resid 141 through 145 removed outlier: 6.684A pdb=" N ILE H 142 " --> pdb=" O ILE H 157 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N ILE H 157 " --> pdb=" O ILE H 142 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N ILE H 144 " --> pdb=" O VAL H 155 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'H' and resid 188 through 189 Processing sheet with id=AF3, first strand: chain 'H' and resid 408 through 411 removed outlier: 3.825A pdb=" N TYR H 411 " --> pdb=" O GLY H 445 " (cutoff:3.500A) 1230 hydrogen bonds defined for protein. 3450 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: 26.02 Time building geometry restraints manager: 15.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.70 - 0.93: 2 0.93 - 1.16: 31782 1.16 - 1.39: 11329 1.39 - 1.62: 21551 1.62 - 1.85: 344 Bond restraints: 65008 Sorted by residual: bond pdb=" CZ PHE C 511 " pdb=" HZ PHE C 511 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.71e+01 bond pdb=" NH2 ARG F 322 " pdb="HH21 ARG F 322 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.71e+01 bond pdb=" N LEU G 227 " pdb=" H LEU G 227 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.71e+01 bond pdb=" NE2 GLN D 454 " pdb="HE21 GLN D 454 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.71e+01 bond pdb=" NH1 ARG E 105 " pdb="HH12 ARG E 105 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.71e+01 ... (remaining 65003 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.90: 108637 3.90 - 7.81: 8383 7.81 - 11.71: 393 11.71 - 15.61: 37 15.61 - 19.52: 14 Bond angle restraints: 117464 Sorted by residual: angle pdb=" PB ATP B 603 " pdb=" O3B ATP B 603 " pdb=" PG ATP B 603 " ideal model delta sigma weight residual 139.87 121.76 18.11 1.00e+00 1.00e+00 3.28e+02 angle pdb=" PB ATP G 603 " pdb=" O3B ATP G 603 " pdb=" PG ATP G 603 " ideal model delta sigma weight residual 139.87 122.27 17.60 1.00e+00 1.00e+00 3.10e+02 angle pdb=" PB ATP C 603 " pdb=" O3B ATP C 603 " pdb=" PG ATP C 603 " ideal model delta sigma weight residual 139.87 122.66 17.21 1.00e+00 1.00e+00 2.96e+02 angle pdb=" PB ATP D 603 " pdb=" O3B ATP D 603 " pdb=" PG ATP D 603 " ideal model delta sigma weight residual 139.87 122.72 17.15 1.00e+00 1.00e+00 2.94e+02 angle pdb=" PB ATP H 603 " pdb=" O3B ATP H 603 " pdb=" PG ATP H 603 " ideal model delta sigma weight residual 139.87 123.83 16.04 1.00e+00 1.00e+00 2.57e+02 ... (remaining 117459 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.00: 28886 35.00 - 70.00: 1713 70.00 - 105.00: 94 105.00 - 140.00: 34 140.00 - 175.00: 25 Dihedral angle restraints: 30752 sinusoidal: 17520 harmonic: 13232 Sorted by residual: dihedral pdb=" O5' GTP D 602 " pdb=" O3A GTP D 602 " pdb=" PA GTP D 602 " pdb=" PB GTP D 602 " ideal model delta sinusoidal sigma weight residual 274.12 99.13 175.00 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" O5' GTP G 602 " pdb=" O3A GTP G 602 " pdb=" PA GTP G 602 " pdb=" PB GTP G 602 " ideal model delta sinusoidal sigma weight residual 274.12 99.20 174.92 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" C8 GTP G 602 " pdb=" C1' GTP G 602 " pdb=" N9 GTP G 602 " pdb=" O4' GTP G 602 " ideal model delta sinusoidal sigma weight residual 104.59 -68.23 172.82 1 2.00e+01 2.50e-03 4.78e+01 ... (remaining 30749 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.112: 4024 0.112 - 0.224: 999 0.224 - 0.336: 138 0.336 - 0.449: 22 0.449 - 0.561: 9 Chirality restraints: 5192 Sorted by residual: chirality pdb=" CA THR F 515 " pdb=" N THR F 515 " pdb=" C THR F 515 " pdb=" CB THR F 515 " both_signs ideal model delta sigma weight residual False 2.53 1.97 0.56 2.00e-01 2.50e+01 7.86e+00 chirality pdb=" CA PHE G 401 " pdb=" N PHE G 401 " pdb=" C PHE G 401 " pdb=" CB PHE G 401 " both_signs ideal model delta sigma weight residual False 2.51 2.00 0.51 2.00e-01 2.50e+01 6.42e+00 chirality pdb=" CA PHE D 401 " pdb=" N PHE D 401 " pdb=" C PHE D 401 " pdb=" CB PHE D 401 " both_signs ideal model delta sigma weight residual False 2.51 2.02 0.49 2.00e-01 2.50e+01 6.05e+00 ... (remaining 5189 not shown) Planarity restraints: 9544 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' IMP D 604 " 0.150 2.00e-02 2.50e+03 8.60e-02 1.85e+02 pdb=" C2 IMP D 604 " -0.097 2.00e-02 2.50e+03 pdb=" C4 IMP D 604 " -0.023 2.00e-02 2.50e+03 pdb=" C5 IMP D 604 " 0.009 2.00e-02 2.50e+03 pdb=" C6 IMP D 604 " 0.125 2.00e-02 2.50e+03 pdb=" C8 IMP D 604 " -0.080 2.00e-02 2.50e+03 pdb=" N1 IMP D 604 " 0.078 2.00e-02 2.50e+03 pdb=" N3 IMP D 604 " -0.092 2.00e-02 2.50e+03 pdb=" N7 IMP D 604 " -0.070 2.00e-02 2.50e+03 pdb=" N9 IMP D 604 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' IMP H 604 " 0.138 2.00e-02 2.50e+03 8.29e-02 1.72e+02 pdb=" C2 IMP H 604 " -0.097 2.00e-02 2.50e+03 pdb=" C4 IMP H 604 " -0.019 2.00e-02 2.50e+03 pdb=" C5 IMP H 604 " 0.004 2.00e-02 2.50e+03 pdb=" C6 IMP H 604 " 0.123 2.00e-02 2.50e+03 pdb=" C8 IMP H 604 " -0.069 2.00e-02 2.50e+03 pdb=" N1 IMP H 604 " 0.079 2.00e-02 2.50e+03 pdb=" N3 IMP H 604 " -0.089 2.00e-02 2.50e+03 pdb=" N7 IMP H 604 " -0.077 2.00e-02 2.50e+03 pdb=" N9 IMP H 604 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' IMP C 604 " -0.135 2.00e-02 2.50e+03 8.19e-02 1.67e+02 pdb=" C2 IMP C 604 " 0.097 2.00e-02 2.50e+03 pdb=" C4 IMP C 604 " 0.012 2.00e-02 2.50e+03 pdb=" C5 IMP C 604 " -0.007 2.00e-02 2.50e+03 pdb=" C6 IMP C 604 " -0.117 2.00e-02 2.50e+03 pdb=" C8 IMP C 604 " 0.072 2.00e-02 2.50e+03 pdb=" N1 IMP C 604 " -0.080 2.00e-02 2.50e+03 pdb=" N3 IMP C 604 " 0.091 2.00e-02 2.50e+03 pdb=" N7 IMP C 604 " 0.075 2.00e-02 2.50e+03 pdb=" N9 IMP C 604 " -0.008 2.00e-02 2.50e+03 ... (remaining 9541 not shown) Histogram of nonbonded interaction distances: 1.42 - 2.05: 2165 2.05 - 2.69: 87836 2.69 - 3.33: 198375 3.33 - 3.96: 265018 3.96 - 4.60: 396088 Nonbonded interactions: 949482 Sorted by model distance: nonbonded pdb=" HB2 MET B 1 " pdb=" HE3 MET B 1 " model vdw 1.417 2.440 nonbonded pdb=" H SER B 122 " pdb=" HD2 HIS B 125 " model vdw 1.433 2.100 nonbonded pdb=" HA3 GLY F 156 " pdb=" HE2 MET F 179 " model vdw 1.454 2.440 nonbonded pdb=" H SER F 122 " pdb=" HD2 HIS F 125 " model vdw 1.463 2.100 nonbonded pdb=" H SER E 140 " pdb=" HG SER E 140 " model vdw 1.466 2.100 ... (remaining 949477 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.270 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: 0.840 Extract box with map and model: 1.840 Check model and map are aligned: 0.360 Set scattering table: 0.430 Process input model: 105.380 Find NCS groups from input model: 2.070 Set up NCS constraints: 0.260 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: 0.020 Load rotamer database and sin/cos tables:11.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 126.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 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 : 0.013 0.102 33168 Z= 0.848 Angle : 1.999 19.516 45072 Z= 1.277 Chirality : 0.100 0.561 5192 Planarity : 0.014 0.128 5560 Dihedral : 19.225 174.998 12728 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.32 % Allowed : 6.60 % Favored : 93.08 % Rotamer: Outliers : 3.19 % Allowed : 7.91 % Favored : 88.90 % Cbeta Deviations : 0.43 % 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: -1.64 (0.12), residues: 4104 helix: -1.04 (0.11), residues: 1528 sheet: -0.51 (0.25), residues: 392 loop : -1.16 (0.12), residues: 2184 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.021 0.004 HIS C 504 PHE 0.083 0.014 PHE B 44 TYR 0.118 0.020 TYR B 348 ARG 0.009 0.001 ARG C 480 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 921 residues out of total 3352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 814 time to evaluate : 4.293 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 GLU cc_start: 0.7758 (mm-30) cc_final: 0.7403 (mm-30) REVERT: A 106 LYS cc_start: 0.8611 (mtpt) cc_final: 0.8408 (mtpm) REVERT: A 131 LEU cc_start: 0.8074 (mp) cc_final: 0.7725 (mm) REVERT: A 228 LYS cc_start: 0.8358 (mtmt) cc_final: 0.8069 (mtmt) REVERT: A 315 ASP cc_start: 0.7540 (m-30) cc_final: 0.7220 (m-30) REVERT: A 337 MET cc_start: 0.7482 (mmm) cc_final: 0.6906 (mmp) REVERT: A 454 GLN cc_start: 0.7929 (mt0) cc_final: 0.7718 (mt0) REVERT: A 509 TYR cc_start: 0.6917 (OUTLIER) cc_final: 0.6444 (t80) REVERT: B 103 GLU cc_start: 0.7787 (mm-30) cc_final: 0.7526 (mm-30) REVERT: B 106 LYS cc_start: 0.8532 (mtpt) cc_final: 0.8232 (mtpm) REVERT: B 131 LEU cc_start: 0.7873 (mp) cc_final: 0.7531 (mm) REVERT: B 179 MET cc_start: 0.8017 (ptt) cc_final: 0.7654 (ptm) REVERT: B 195 LYS cc_start: 0.7763 (ttpp) cc_final: 0.7507 (ttmm) REVERT: B 228 LYS cc_start: 0.8323 (mtmt) cc_final: 0.8088 (mtmt) REVERT: B 281 VAL cc_start: 0.9096 (p) cc_final: 0.8776 (m) REVERT: B 454 GLN cc_start: 0.8003 (mt0) cc_final: 0.7800 (mt0) REVERT: B 509 TYR cc_start: 0.7073 (OUTLIER) cc_final: 0.6391 (t80) REVERT: C 103 GLU cc_start: 0.7753 (mm-30) cc_final: 0.7429 (mm-30) REVERT: C 106 LYS cc_start: 0.8553 (mtpt) cc_final: 0.8350 (mtpm) REVERT: C 129 ASP cc_start: 0.7643 (m-30) cc_final: 0.7166 (m-30) REVERT: C 131 LEU cc_start: 0.7890 (mp) cc_final: 0.7554 (mm) REVERT: C 196 GLU cc_start: 0.7405 (mt-10) cc_final: 0.6961 (mt-10) REVERT: C 228 LYS cc_start: 0.8326 (mtmt) cc_final: 0.8077 (mtmt) REVERT: C 281 VAL cc_start: 0.9177 (p) cc_final: 0.8839 (m) REVERT: C 368 GLN cc_start: 0.8104 (mt0) cc_final: 0.7894 (mt0) REVERT: C 410 LYS cc_start: 0.7066 (tttt) cc_final: 0.6863 (ttmm) REVERT: C 509 TYR cc_start: 0.6924 (OUTLIER) cc_final: 0.6404 (t80) REVERT: D 103 GLU cc_start: 0.7730 (mm-30) cc_final: 0.7443 (mm-30) REVERT: D 105 ARG cc_start: 0.7751 (ttm110) cc_final: 0.7500 (ttm110) REVERT: D 106 LYS cc_start: 0.8581 (mtpt) cc_final: 0.8352 (mtpm) REVERT: D 131 LEU cc_start: 0.8017 (mp) cc_final: 0.7747 (mm) REVERT: D 195 LYS cc_start: 0.7861 (ttpp) cc_final: 0.7593 (ttmm) REVERT: D 228 LYS cc_start: 0.8346 (mtmt) cc_final: 0.8088 (mtmt) REVERT: D 281 VAL cc_start: 0.9155 (p) cc_final: 0.8813 (m) REVERT: D 315 ASP cc_start: 0.7550 (m-30) cc_final: 0.7240 (m-30) REVERT: D 368 GLN cc_start: 0.8066 (mt0) cc_final: 0.7865 (mt0) REVERT: D 509 TYR cc_start: 0.6881 (OUTLIER) cc_final: 0.5853 (t80) REVERT: D 515 THR cc_start: 0.7494 (OUTLIER) cc_final: 0.7272 (t) REVERT: E 71 ASP cc_start: 0.8082 (p0) cc_final: 0.7842 (p0) REVERT: E 103 GLU cc_start: 0.7750 (mm-30) cc_final: 0.7411 (mm-30) REVERT: E 106 LYS cc_start: 0.8493 (mtpt) cc_final: 0.8287 (mtpm) REVERT: E 129 ASP cc_start: 0.7599 (m-30) cc_final: 0.7346 (m-30) REVERT: E 131 LEU cc_start: 0.8114 (mp) cc_final: 0.7751 (mm) REVERT: E 195 LYS cc_start: 0.7782 (ttpp) cc_final: 0.7557 (ttmm) REVERT: E 335 GLU cc_start: 0.7010 (mp0) cc_final: 0.6806 (mp0) REVERT: E 410 LYS cc_start: 0.6967 (ttpt) cc_final: 0.6709 (ttpp) REVERT: E 474 ARG cc_start: 0.7296 (mtp85) cc_final: 0.6990 (mtt90) REVERT: E 509 TYR cc_start: 0.6983 (OUTLIER) cc_final: 0.6143 (t80) REVERT: E 515 THR cc_start: 0.7373 (OUTLIER) cc_final: 0.7138 (t) REVERT: F 103 GLU cc_start: 0.7761 (mm-30) cc_final: 0.7432 (mm-30) REVERT: F 105 ARG cc_start: 0.7681 (ttm110) cc_final: 0.7440 (ttm110) REVERT: F 106 LYS cc_start: 0.8502 (mtpt) cc_final: 0.8281 (mtpm) REVERT: F 131 LEU cc_start: 0.7772 (mp) cc_final: 0.7442 (mm) REVERT: F 195 LYS cc_start: 0.7777 (ttpp) cc_final: 0.7501 (ttmm) REVERT: F 228 LYS cc_start: 0.8360 (mtmt) cc_final: 0.8118 (mtmt) REVERT: F 281 VAL cc_start: 0.9199 (p) cc_final: 0.8855 (m) REVERT: F 368 GLN cc_start: 0.8003 (mt0) cc_final: 0.7789 (mt0) REVERT: F 474 ARG cc_start: 0.7533 (ttm-80) cc_final: 0.7208 (ttt90) REVERT: F 509 TYR cc_start: 0.6991 (OUTLIER) cc_final: 0.6361 (t80) REVERT: G 70 MET cc_start: 0.9012 (mtm) cc_final: 0.8797 (mtp) REVERT: G 103 GLU cc_start: 0.7720 (mm-30) cc_final: 0.7382 (mm-30) REVERT: G 106 LYS cc_start: 0.8553 (mtpt) cc_final: 0.8301 (mtpp) REVERT: G 131 LEU cc_start: 0.8077 (mp) cc_final: 0.7800 (mm) REVERT: G 195 LYS cc_start: 0.7948 (ttpp) cc_final: 0.7673 (ttmm) REVERT: G 196 GLU cc_start: 0.7318 (mt-10) cc_final: 0.6979 (mt-10) REVERT: G 243 GLN cc_start: 0.8909 (mt0) cc_final: 0.8392 (mt0) REVERT: G 322 ARG cc_start: 0.9077 (OUTLIER) cc_final: 0.7325 (ttm170) REVERT: G 410 LYS cc_start: 0.7054 (tttt) cc_final: 0.6836 (ttpp) REVERT: G 509 TYR cc_start: 0.6972 (OUTLIER) cc_final: 0.6162 (t80) REVERT: G 515 THR cc_start: 0.7159 (OUTLIER) cc_final: 0.6834 (t) REVERT: H 103 GLU cc_start: 0.7794 (mm-30) cc_final: 0.7485 (mm-30) REVERT: H 106 LYS cc_start: 0.8573 (mtpt) cc_final: 0.8349 (mtpm) REVERT: H 160 SER cc_start: 0.8435 (t) cc_final: 0.8184 (m) REVERT: H 195 LYS cc_start: 0.7956 (ttpp) cc_final: 0.7670 (ttmm) REVERT: H 281 VAL cc_start: 0.9102 (p) cc_final: 0.8821 (m) REVERT: H 337 MET cc_start: 0.7412 (mmm) cc_final: 0.7211 (mpp) REVERT: H 368 GLN cc_start: 0.8130 (mt0) cc_final: 0.7909 (mt0) REVERT: H 509 TYR cc_start: 0.6836 (OUTLIER) cc_final: 0.5910 (t80) REVERT: H 515 THR cc_start: 0.7285 (OUTLIER) cc_final: 0.7018 (t) outliers start: 107 outliers final: 54 residues processed: 897 average time/residue: 2.3282 time to fit residues: 2525.5187 Evaluate side-chains 727 residues out of total 3352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 660 time to evaluate : 3.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 117 ASP Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 509 TYR Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 117 ASP Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 322 ARG Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 457 VAL Chi-restraints excluded: chain B residue 509 TYR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 322 ARG Chi-restraints excluded: chain C residue 457 VAL Chi-restraints excluded: chain C residue 509 TYR Chi-restraints excluded: chain C residue 512 LEU Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 117 ASP Chi-restraints excluded: chain D residue 225 THR Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 322 ARG Chi-restraints excluded: chain D residue 408 LEU Chi-restraints excluded: chain D residue 457 VAL Chi-restraints excluded: chain D residue 509 TYR Chi-restraints excluded: chain D residue 511 PHE Chi-restraints excluded: chain D residue 515 THR Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 117 ASP Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain E residue 214 ASP Chi-restraints excluded: chain E residue 408 LEU Chi-restraints excluded: chain E residue 457 VAL Chi-restraints excluded: chain E residue 509 TYR Chi-restraints excluded: chain E residue 515 THR Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 117 ASP Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 225 THR Chi-restraints excluded: chain F residue 272 VAL Chi-restraints excluded: chain F residue 322 ARG Chi-restraints excluded: chain F residue 335 GLU Chi-restraints excluded: chain F residue 457 VAL Chi-restraints excluded: chain F residue 509 TYR Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 117 ASP Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain G residue 272 VAL Chi-restraints excluded: chain G residue 277 GLN Chi-restraints excluded: chain G residue 322 ARG Chi-restraints excluded: chain G residue 330 ILE Chi-restraints excluded: chain G residue 509 TYR Chi-restraints excluded: chain G residue 515 THR Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 272 VAL Chi-restraints excluded: chain H residue 322 ARG Chi-restraints excluded: chain H residue 333 THR Chi-restraints excluded: chain H residue 420 MET Chi-restraints excluded: chain H residue 457 VAL Chi-restraints excluded: chain H residue 509 TYR Chi-restraints excluded: chain H residue 511 PHE Chi-restraints excluded: chain H residue 515 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 344 optimal weight: 0.8980 chunk 309 optimal weight: 0.9980 chunk 171 optimal weight: 3.9990 chunk 105 optimal weight: 0.9990 chunk 208 optimal weight: 0.7980 chunk 165 optimal weight: 0.9990 chunk 319 optimal weight: 0.9990 chunk 123 optimal weight: 1.9990 chunk 194 optimal weight: 1.9990 chunk 238 optimal weight: 0.9980 chunk 370 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: A 93 HIS A 94 ASN A 100 GLN A 198 ASN A 312 ASN B 94 ASN ** B 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 HIS B 198 ASN B 312 ASN C -20 HIS C 94 ASN C 100 GLN C 125 HIS ** C 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 303 ASN C 312 ASN D -20 HIS D 94 ASN D 100 GLN D 125 HIS D 198 ASN D 303 ASN D 312 ASN E -20 HIS E 93 HIS E 94 ASN E 100 GLN E 125 HIS E 198 ASN E 230 ASN ** E 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 303 ASN E 312 ASN F -20 HIS F 100 GLN F 230 ASN F 283 GLN F 303 ASN F 312 ASN F 507 HIS G -20 HIS G 94 ASN G 198 ASN ** G 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 312 ASN G 454 GLN H 100 GLN H 198 ASN H 283 GLN H 303 ASN H 312 ASN Total number of N/Q/H flips: 48 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.2602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 33168 Z= 0.241 Angle : 0.687 7.708 45072 Z= 0.353 Chirality : 0.045 0.182 5192 Planarity : 0.005 0.076 5560 Dihedral : 19.920 178.889 5561 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 3.19 % Allowed : 14.47 % Favored : 82.34 % 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: -0.53 (0.13), residues: 4104 helix: 0.71 (0.13), residues: 1512 sheet: -1.42 (0.31), residues: 264 loop : -0.92 (0.12), residues: 2328 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS F 92 PHE 0.019 0.002 PHE C 24 TYR 0.015 0.001 TYR A 509 ARG 0.009 0.001 ARG F 203 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 784 residues out of total 3352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 677 time to evaluate : 3.731 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 GLN cc_start: 0.7570 (tm-30) cc_final: 0.7352 (tm-30) REVERT: A 103 GLU cc_start: 0.7704 (mm-30) cc_final: 0.7414 (mm-30) REVERT: A 179 MET cc_start: 0.8083 (ptm) cc_final: 0.7501 (ptm) REVERT: A 195 LYS cc_start: 0.7832 (OUTLIER) cc_final: 0.7520 (ttmm) REVERT: A 228 LYS cc_start: 0.8290 (mtmt) cc_final: 0.7986 (mtmt) REVERT: A 277 GLN cc_start: 0.8942 (OUTLIER) cc_final: 0.7231 (tm-30) REVERT: A 296 HIS cc_start: 0.7647 (OUTLIER) cc_final: 0.7193 (p-80) REVERT: A 509 TYR cc_start: 0.6820 (OUTLIER) cc_final: 0.6502 (t80) REVERT: B 58 LYS cc_start: 0.8316 (mttt) cc_final: 0.8060 (mttp) REVERT: B 75 GLU cc_start: 0.7695 (OUTLIER) cc_final: 0.7347 (mt-10) REVERT: B 103 GLU cc_start: 0.7736 (mm-30) cc_final: 0.7394 (mm-30) REVERT: B 106 LYS cc_start: 0.8538 (mtpt) cc_final: 0.8283 (ttmm) REVERT: B 228 LYS cc_start: 0.8244 (mtmt) cc_final: 0.7975 (mtmt) REVERT: B 277 GLN cc_start: 0.8986 (OUTLIER) cc_final: 0.7401 (tm-30) REVERT: B 509 TYR cc_start: 0.6886 (OUTLIER) cc_final: 0.6338 (t80) REVERT: C 75 GLU cc_start: 0.7620 (OUTLIER) cc_final: 0.7295 (mt-10) REVERT: C 103 GLU cc_start: 0.7761 (mm-30) cc_final: 0.7461 (mm-30) REVERT: C 129 ASP cc_start: 0.7843 (m-30) cc_final: 0.7332 (m-30) REVERT: C 131 LEU cc_start: 0.7682 (mp) cc_final: 0.7338 (mm) REVERT: C 196 GLU cc_start: 0.7033 (mt-10) cc_final: 0.6670 (mt-10) REVERT: C 277 GLN cc_start: 0.8788 (OUTLIER) cc_final: 0.7341 (tm-30) REVERT: C 410 LYS cc_start: 0.6958 (tttt) cc_final: 0.6697 (ttpp) REVERT: C 509 TYR cc_start: 0.6738 (OUTLIER) cc_final: 0.6313 (t80) REVERT: D 75 GLU cc_start: 0.7571 (OUTLIER) cc_final: 0.7333 (mt-10) REVERT: D 103 GLU cc_start: 0.7767 (mm-30) cc_final: 0.7422 (mm-30) REVERT: D 131 LEU cc_start: 0.7719 (mp) cc_final: 0.7495 (mm) REVERT: D 228 LYS cc_start: 0.8286 (mtmt) cc_final: 0.7944 (mtpt) REVERT: D 322 ARG cc_start: 0.9054 (OUTLIER) cc_final: 0.7371 (ttm170) REVERT: D 368 GLN cc_start: 0.8236 (mt0) cc_final: 0.8033 (mt0) REVERT: D 509 TYR cc_start: 0.6767 (OUTLIER) cc_final: 0.5829 (t80) REVERT: E 58 LYS cc_start: 0.8293 (mttt) cc_final: 0.8030 (mttp) REVERT: E 103 GLU cc_start: 0.7701 (mm-30) cc_final: 0.7470 (mm-30) REVERT: E 129 ASP cc_start: 0.7726 (m-30) cc_final: 0.7376 (m-30) REVERT: E 131 LEU cc_start: 0.7750 (mp) cc_final: 0.7360 (mm) REVERT: E 150 MET cc_start: 0.7508 (pmm) cc_final: 0.7194 (pmm) REVERT: E 277 GLN cc_start: 0.8951 (OUTLIER) cc_final: 0.7327 (tm-30) REVERT: E 335 GLU cc_start: 0.7129 (mp0) cc_final: 0.6917 (mp0) REVERT: E 410 LYS cc_start: 0.6645 (ttpt) cc_final: 0.6399 (ttpp) REVERT: E 474 ARG cc_start: 0.7366 (mtp85) cc_final: 0.6983 (mtt90) REVERT: E 509 TYR cc_start: 0.6850 (OUTLIER) cc_final: 0.6135 (t80) REVERT: F 58 LYS cc_start: 0.8290 (OUTLIER) cc_final: 0.8052 (mttp) REVERT: F 75 GLU cc_start: 0.7633 (OUTLIER) cc_final: 0.7365 (mt-10) REVERT: F 103 GLU cc_start: 0.7801 (mm-30) cc_final: 0.7483 (mm-30) REVERT: F 228 LYS cc_start: 0.8332 (mtmt) cc_final: 0.8004 (mtpt) REVERT: F 277 GLN cc_start: 0.8721 (OUTLIER) cc_final: 0.7249 (tm-30) REVERT: F 474 ARG cc_start: 0.7613 (ttm-80) cc_final: 0.7289 (ttt180) REVERT: F 509 TYR cc_start: 0.6887 (OUTLIER) cc_final: 0.6444 (t80) REVERT: G 58 LYS cc_start: 0.8292 (OUTLIER) cc_final: 0.8047 (mttp) REVERT: G 103 GLU cc_start: 0.7683 (mm-30) cc_final: 0.7404 (mm-30) REVERT: G 106 LYS cc_start: 0.8626 (mtpt) cc_final: 0.8407 (mtpt) REVERT: G 131 LEU cc_start: 0.7872 (mp) cc_final: 0.7532 (mm) REVERT: G 196 GLU cc_start: 0.7129 (mt-10) cc_final: 0.6813 (mt-10) REVERT: G 410 LYS cc_start: 0.6811 (tttt) cc_final: 0.6590 (ttpp) REVERT: G 509 TYR cc_start: 0.6824 (OUTLIER) cc_final: 0.6223 (t80) REVERT: H 71 ASP cc_start: 0.8228 (p0) cc_final: 0.8017 (p0) REVERT: H 103 GLU cc_start: 0.7731 (mm-30) cc_final: 0.7471 (mm-30) REVERT: H 131 LEU cc_start: 0.7832 (mp) cc_final: 0.7457 (mm) REVERT: H 277 GLN cc_start: 0.8984 (OUTLIER) cc_final: 0.7367 (tm-30) REVERT: H 509 TYR cc_start: 0.6735 (OUTLIER) cc_final: 0.5959 (t80) REVERT: H 515 THR cc_start: 0.7085 (OUTLIER) cc_final: 0.6845 (t) outliers start: 107 outliers final: 46 residues processed: 760 average time/residue: 2.4868 time to fit residues: 2273.7637 Evaluate side-chains 680 residues out of total 3352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 610 time to evaluate : 3.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 195 LYS Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain A residue 296 HIS Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 509 TYR Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 420 MET Chi-restraints excluded: chain B residue 509 TYR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 75 GLU Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain C residue 457 VAL Chi-restraints excluded: chain C residue 509 TYR Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain D residue 150 MET Chi-restraints excluded: chain D residue 225 THR Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 322 ARG Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain D residue 408 LEU Chi-restraints excluded: chain D residue 509 TYR Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain E residue 160 SER Chi-restraints excluded: chain E residue 162 ASP Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain E residue 408 LEU Chi-restraints excluded: chain E residue 509 TYR Chi-restraints excluded: chain F residue 58 LYS Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 75 GLU Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 225 THR Chi-restraints excluded: chain F residue 272 VAL Chi-restraints excluded: chain F residue 277 GLN Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain F residue 509 TYR Chi-restraints excluded: chain G residue 58 LYS Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain G residue 272 VAL Chi-restraints excluded: chain G residue 277 GLN Chi-restraints excluded: chain G residue 330 ILE Chi-restraints excluded: chain G residue 509 TYR Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain H residue 126 THR Chi-restraints excluded: chain H residue 272 VAL Chi-restraints excluded: chain H residue 277 GLN Chi-restraints excluded: chain H residue 333 THR Chi-restraints excluded: chain H residue 420 MET Chi-restraints excluded: chain H residue 470 ASP Chi-restraints excluded: chain H residue 509 TYR Chi-restraints excluded: chain H residue 515 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 205 optimal weight: 6.9990 chunk 114 optimal weight: 1.9990 chunk 308 optimal weight: 3.9990 chunk 252 optimal weight: 1.9990 chunk 102 optimal weight: 0.9980 chunk 371 optimal weight: 1.9990 chunk 400 optimal weight: 7.9990 chunk 330 optimal weight: 0.9980 chunk 368 optimal weight: 0.5980 chunk 126 optimal weight: 0.9980 chunk 297 optimal weight: 3.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 ASN A 454 GLN ** B 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 507 HIS C 94 ASN C 198 ASN ** C 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 94 ASN F 198 ASN G 94 ASN G 198 ASN G 303 ASN G 454 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.3126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 33168 Z= 0.213 Angle : 0.605 7.662 45072 Z= 0.306 Chirality : 0.044 0.157 5192 Planarity : 0.005 0.081 5560 Dihedral : 18.216 178.453 5507 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 2.54 % Allowed : 16.83 % Favored : 80.64 % 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: 0.05 (0.13), residues: 4104 helix: 1.35 (0.14), residues: 1520 sheet: -1.18 (0.29), residues: 320 loop : -0.68 (0.13), residues: 2264 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS F 92 PHE 0.015 0.001 PHE E 24 TYR 0.012 0.001 TYR A 509 ARG 0.010 0.001 ARG H 412 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 727 residues out of total 3352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 642 time to evaluate : 3.636 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 GLU cc_start: 0.7729 (mm-30) cc_final: 0.7449 (mm-30) REVERT: A 179 MET cc_start: 0.8051 (ptm) cc_final: 0.7499 (ptm) REVERT: A 195 LYS cc_start: 0.7843 (ttpp) cc_final: 0.7555 (ttmm) REVERT: A 196 GLU cc_start: 0.7122 (mt-10) cc_final: 0.6803 (mt-10) REVERT: A 228 LYS cc_start: 0.8266 (mtmt) cc_final: 0.7963 (mtmt) REVERT: A 277 GLN cc_start: 0.9009 (OUTLIER) cc_final: 0.7536 (tm-30) REVERT: A 296 HIS cc_start: 0.7712 (OUTLIER) cc_final: 0.7248 (p-80) REVERT: A 322 ARG cc_start: 0.8882 (OUTLIER) cc_final: 0.7157 (ttm170) REVERT: A 509 TYR cc_start: 0.6827 (OUTLIER) cc_final: 0.6508 (t80) REVERT: B 58 LYS cc_start: 0.8336 (mttt) cc_final: 0.8105 (mttp) REVERT: B 103 GLU cc_start: 0.7796 (mm-30) cc_final: 0.7472 (mm-30) REVERT: B 106 LYS cc_start: 0.8590 (mtpt) cc_final: 0.8319 (ttmm) REVERT: B 228 LYS cc_start: 0.8273 (mtmt) cc_final: 0.7996 (mtmt) REVERT: B 277 GLN cc_start: 0.9023 (OUTLIER) cc_final: 0.7728 (tm-30) REVERT: B 509 TYR cc_start: 0.6811 (OUTLIER) cc_final: 0.6185 (t80) REVERT: C 103 GLU cc_start: 0.7804 (mm-30) cc_final: 0.7481 (mm-30) REVERT: C 129 ASP cc_start: 0.7822 (m-30) cc_final: 0.7267 (m-30) REVERT: C 131 LEU cc_start: 0.7735 (mp) cc_final: 0.7360 (mm) REVERT: C 196 GLU cc_start: 0.7020 (mt-10) cc_final: 0.6701 (mt-10) REVERT: C 228 LYS cc_start: 0.8216 (mtmt) cc_final: 0.7800 (mtmt) REVERT: C 232 ASP cc_start: 0.7804 (m-30) cc_final: 0.7516 (m-30) REVERT: C 277 GLN cc_start: 0.8947 (OUTLIER) cc_final: 0.7547 (tm-30) REVERT: C 410 LYS cc_start: 0.7036 (tttt) cc_final: 0.6735 (ttpp) REVERT: C 509 TYR cc_start: 0.6762 (OUTLIER) cc_final: 0.6354 (t80) REVERT: D 103 GLU cc_start: 0.7704 (mm-30) cc_final: 0.7409 (mm-30) REVERT: D 131 LEU cc_start: 0.7726 (mp) cc_final: 0.7479 (mm) REVERT: D 228 LYS cc_start: 0.8273 (mtmt) cc_final: 0.7939 (mtpt) REVERT: D 296 HIS cc_start: 0.7635 (OUTLIER) cc_final: 0.7278 (p-80) REVERT: D 322 ARG cc_start: 0.9058 (OUTLIER) cc_final: 0.7260 (ttm170) REVERT: D 368 GLN cc_start: 0.8239 (mt0) cc_final: 0.8024 (mt0) REVERT: D 410 LYS cc_start: 0.6870 (ttmp) cc_final: 0.6445 (ttpp) REVERT: D 503 VAL cc_start: 0.8147 (t) cc_final: 0.7940 (t) REVERT: D 509 TYR cc_start: 0.6756 (OUTLIER) cc_final: 0.5882 (t80) REVERT: E 103 GLU cc_start: 0.7712 (mm-30) cc_final: 0.7462 (mm-30) REVERT: E 129 ASP cc_start: 0.7759 (m-30) cc_final: 0.7427 (m-30) REVERT: E 131 LEU cc_start: 0.7767 (mp) cc_final: 0.7349 (mm) REVERT: E 150 MET cc_start: 0.7411 (pmm) cc_final: 0.7064 (pmm) REVERT: E 228 LYS cc_start: 0.8095 (mtmt) cc_final: 0.7641 (mtpt) REVERT: E 232 ASP cc_start: 0.7786 (m-30) cc_final: 0.7491 (m-30) REVERT: E 277 GLN cc_start: 0.8976 (OUTLIER) cc_final: 0.7594 (tm-30) REVERT: E 335 GLU cc_start: 0.7368 (mp0) cc_final: 0.6994 (mp0) REVERT: E 509 TYR cc_start: 0.6771 (OUTLIER) cc_final: 0.6081 (t80) REVERT: F 103 GLU cc_start: 0.7734 (mm-30) cc_final: 0.7463 (mm-30) REVERT: F 131 LEU cc_start: 0.7725 (mp) cc_final: 0.7354 (mm) REVERT: F 228 LYS cc_start: 0.8318 (mtmt) cc_final: 0.8043 (mtmt) REVERT: F 322 ARG cc_start: 0.8841 (OUTLIER) cc_final: 0.7219 (ttm170) REVERT: F 410 LYS cc_start: 0.7365 (OUTLIER) cc_final: 0.6992 (tttt) REVERT: F 474 ARG cc_start: 0.7568 (ttm-80) cc_final: 0.7256 (ttt180) REVERT: F 509 TYR cc_start: 0.6780 (OUTLIER) cc_final: 0.6308 (t80) REVERT: G 103 GLU cc_start: 0.7757 (mm-30) cc_final: 0.7378 (mm-30) REVERT: G 131 LEU cc_start: 0.7838 (mp) cc_final: 0.7472 (mm) REVERT: G 196 GLU cc_start: 0.7186 (mt-10) cc_final: 0.6737 (mt-10) REVERT: G 296 HIS cc_start: 0.7706 (OUTLIER) cc_final: 0.7349 (p-80) REVERT: G 322 ARG cc_start: 0.9077 (OUTLIER) cc_final: 0.7418 (ttm170) REVERT: G 441 GLN cc_start: 0.8075 (mt0) cc_final: 0.7873 (mt0) REVERT: G 509 TYR cc_start: 0.6758 (OUTLIER) cc_final: 0.6081 (t80) REVERT: H 103 GLU cc_start: 0.7755 (mm-30) cc_final: 0.7456 (mm-30) REVERT: H 277 GLN cc_start: 0.8990 (OUTLIER) cc_final: 0.7491 (tm-30) REVERT: H 322 ARG cc_start: 0.9013 (OUTLIER) cc_final: 0.7193 (ttm170) REVERT: H 509 TYR cc_start: 0.6643 (OUTLIER) cc_final: 0.5824 (t80) outliers start: 85 outliers final: 33 residues processed: 708 average time/residue: 2.4916 time to fit residues: 2117.2327 Evaluate side-chains 646 residues out of total 3352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 591 time to evaluate : 3.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain A residue 296 HIS Chi-restraints excluded: chain A residue 322 ARG Chi-restraints excluded: chain A residue 509 TYR Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 117 ASP Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 322 ARG Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 420 MET Chi-restraints excluded: chain B residue 509 TYR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain C residue 509 TYR Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 225 THR Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 296 HIS Chi-restraints excluded: chain D residue 322 ARG Chi-restraints excluded: chain D residue 408 LEU Chi-restraints excluded: chain D residue 509 TYR Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain E residue 140 SER Chi-restraints excluded: chain E residue 275 SER Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain E residue 408 LEU Chi-restraints excluded: chain E residue 509 TYR Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 272 VAL Chi-restraints excluded: chain F residue 322 ARG Chi-restraints excluded: chain F residue 410 LYS Chi-restraints excluded: chain F residue 509 TYR Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain G residue 272 VAL Chi-restraints excluded: chain G residue 275 SER Chi-restraints excluded: chain G residue 277 GLN Chi-restraints excluded: chain G residue 296 HIS Chi-restraints excluded: chain G residue 322 ARG Chi-restraints excluded: chain G residue 509 TYR Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 272 VAL Chi-restraints excluded: chain H residue 277 GLN Chi-restraints excluded: chain H residue 322 ARG Chi-restraints excluded: chain H residue 330 ILE Chi-restraints excluded: chain H residue 333 THR Chi-restraints excluded: chain H residue 420 MET Chi-restraints excluded: chain H residue 509 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 366 optimal weight: 0.8980 chunk 279 optimal weight: 2.9990 chunk 192 optimal weight: 1.9990 chunk 41 optimal weight: 0.8980 chunk 177 optimal weight: 2.9990 chunk 249 optimal weight: 4.9990 chunk 372 optimal weight: 8.9990 chunk 394 optimal weight: 0.2980 chunk 194 optimal weight: 0.0770 chunk 353 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 overall best weight: 0.8340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 137 HIS ** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 303 ASN C 94 ASN ** C 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 303 ASN D 303 ASN E 303 ASN G 303 ASN H 303 ASN H 507 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.3339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 33168 Z= 0.176 Angle : 0.567 7.312 45072 Z= 0.283 Chirality : 0.043 0.150 5192 Planarity : 0.005 0.083 5560 Dihedral : 17.285 179.601 5499 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 2.24 % Allowed : 17.75 % Favored : 80.01 % 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: 0.34 (0.14), residues: 4104 helix: 1.69 (0.14), residues: 1520 sheet: -1.26 (0.29), residues: 320 loop : -0.56 (0.14), residues: 2264 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS H 507 PHE 0.013 0.001 PHE B 24 TYR 0.011 0.001 TYR C 509 ARG 0.010 0.000 ARG G 203 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 700 residues out of total 3352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 625 time to evaluate : 3.694 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 GLU cc_start: 0.7690 (mm-30) cc_final: 0.7370 (mm-30) REVERT: A 150 MET cc_start: 0.7519 (pmm) cc_final: 0.7114 (pmm) REVERT: A 179 MET cc_start: 0.8050 (ptm) cc_final: 0.7309 (ptm) REVERT: A 195 LYS cc_start: 0.7865 (ttpp) cc_final: 0.7532 (ttmm) REVERT: A 196 GLU cc_start: 0.7136 (mt-10) cc_final: 0.6837 (mt-10) REVERT: A 228 LYS cc_start: 0.8260 (mtmt) cc_final: 0.7946 (mtmt) REVERT: A 277 GLN cc_start: 0.8979 (OUTLIER) cc_final: 0.7593 (tm-30) REVERT: A 296 HIS cc_start: 0.7712 (OUTLIER) cc_final: 0.7233 (p-80) REVERT: A 322 ARG cc_start: 0.8820 (OUTLIER) cc_final: 0.7143 (ttm170) REVERT: A 509 TYR cc_start: 0.6817 (OUTLIER) cc_final: 0.6502 (t80) REVERT: B 103 GLU cc_start: 0.7797 (mm-30) cc_final: 0.7468 (mm-30) REVERT: B 106 LYS cc_start: 0.8604 (mtpt) cc_final: 0.8332 (ttmm) REVERT: B 131 LEU cc_start: 0.7783 (OUTLIER) cc_final: 0.7394 (mm) REVERT: B 196 GLU cc_start: 0.7022 (mt-10) cc_final: 0.6700 (mt-10) REVERT: B 228 LYS cc_start: 0.8265 (mtmt) cc_final: 0.7688 (mtmt) REVERT: B 232 ASP cc_start: 0.7781 (m-30) cc_final: 0.7474 (m-30) REVERT: B 277 GLN cc_start: 0.8977 (OUTLIER) cc_final: 0.7772 (tm-30) REVERT: B 333 THR cc_start: 0.8183 (OUTLIER) cc_final: 0.7955 (t) REVERT: B 410 LYS cc_start: 0.6999 (ttpp) cc_final: 0.6763 (ttpp) REVERT: B 509 TYR cc_start: 0.6688 (OUTLIER) cc_final: 0.6092 (t80) REVERT: C 103 GLU cc_start: 0.7796 (mm-30) cc_final: 0.7468 (mm-30) REVERT: C 129 ASP cc_start: 0.7849 (m-30) cc_final: 0.7310 (m-30) REVERT: C 131 LEU cc_start: 0.7766 (OUTLIER) cc_final: 0.7355 (mm) REVERT: C 196 GLU cc_start: 0.7037 (mt-10) cc_final: 0.6694 (mt-10) REVERT: C 228 LYS cc_start: 0.8209 (mtmt) cc_final: 0.7752 (mtmt) REVERT: C 232 ASP cc_start: 0.7787 (m-30) cc_final: 0.7491 (m-30) REVERT: C 277 GLN cc_start: 0.8936 (OUTLIER) cc_final: 0.7774 (tm-30) REVERT: C 322 ARG cc_start: 0.9081 (OUTLIER) cc_final: 0.7370 (ttm170) REVERT: C 410 LYS cc_start: 0.7047 (tttt) cc_final: 0.6753 (ttpp) REVERT: C 509 TYR cc_start: 0.6627 (OUTLIER) cc_final: 0.6301 (t80) REVERT: D 71 ASP cc_start: 0.8339 (p0) cc_final: 0.8129 (p0) REVERT: D 103 GLU cc_start: 0.7678 (mm-30) cc_final: 0.7384 (mm-30) REVERT: D 228 LYS cc_start: 0.8291 (mtmt) cc_final: 0.7984 (mtmt) REVERT: D 296 HIS cc_start: 0.7628 (OUTLIER) cc_final: 0.7275 (p-80) REVERT: D 410 LYS cc_start: 0.6882 (ttmp) cc_final: 0.6476 (ttpp) REVERT: E 103 GLU cc_start: 0.7702 (mm-30) cc_final: 0.7409 (mm-30) REVERT: E 129 ASP cc_start: 0.7764 (m-30) cc_final: 0.7420 (m-30) REVERT: E 131 LEU cc_start: 0.7771 (mp) cc_final: 0.7345 (mm) REVERT: E 228 LYS cc_start: 0.8160 (mtmt) cc_final: 0.7732 (mtpt) REVERT: E 232 ASP cc_start: 0.7769 (m-30) cc_final: 0.7502 (m-30) REVERT: E 277 GLN cc_start: 0.8952 (OUTLIER) cc_final: 0.7651 (tm-30) REVERT: E 322 ARG cc_start: 0.9046 (OUTLIER) cc_final: 0.7329 (ttm170) REVERT: E 335 GLU cc_start: 0.7413 (mp0) cc_final: 0.6952 (mp0) REVERT: E 410 LYS cc_start: 0.6889 (ttpp) cc_final: 0.6655 (ttpp) REVERT: F 71 ASP cc_start: 0.8469 (p0) cc_final: 0.8267 (p0) REVERT: F 103 GLU cc_start: 0.7706 (mm-30) cc_final: 0.7404 (mm-30) REVERT: F 131 LEU cc_start: 0.7748 (mp) cc_final: 0.7408 (mm) REVERT: F 228 LYS cc_start: 0.8316 (mtmt) cc_final: 0.8053 (mtmt) REVERT: F 322 ARG cc_start: 0.8810 (OUTLIER) cc_final: 0.7028 (ttm170) REVERT: F 474 ARG cc_start: 0.7589 (ttm-80) cc_final: 0.7242 (ttt180) REVERT: F 509 TYR cc_start: 0.6663 (OUTLIER) cc_final: 0.6164 (t80) REVERT: G 71 ASP cc_start: 0.8380 (p0) cc_final: 0.8158 (p0) REVERT: G 103 GLU cc_start: 0.7638 (mm-30) cc_final: 0.7361 (mm-30) REVERT: G 131 LEU cc_start: 0.7855 (mp) cc_final: 0.7517 (mm) REVERT: G 196 GLU cc_start: 0.7130 (mt-10) cc_final: 0.6730 (mt-10) REVERT: G 232 ASP cc_start: 0.7755 (m-30) cc_final: 0.7440 (m-30) REVERT: G 296 HIS cc_start: 0.7668 (OUTLIER) cc_final: 0.7313 (p-80) REVERT: H 103 GLU cc_start: 0.7736 (mm-30) cc_final: 0.7450 (mm-30) REVERT: H 160 SER cc_start: 0.8154 (m) cc_final: 0.7892 (p) REVERT: H 277 GLN cc_start: 0.8925 (OUTLIER) cc_final: 0.7553 (tm-30) REVERT: H 322 ARG cc_start: 0.9003 (OUTLIER) cc_final: 0.7187 (ttm170) REVERT: H 509 TYR cc_start: 0.6543 (OUTLIER) cc_final: 0.5605 (t80) outliers start: 75 outliers final: 35 residues processed: 682 average time/residue: 2.5253 time to fit residues: 2089.3776 Evaluate side-chains 640 residues out of total 3352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 584 time to evaluate : 3.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain A residue 296 HIS Chi-restraints excluded: chain A residue 322 ARG Chi-restraints excluded: chain A residue 509 TYR Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 322 ARG Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 420 MET Chi-restraints excluded: chain B residue 509 TYR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain C residue 322 ARG Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain C residue 509 TYR Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 117 ASP Chi-restraints excluded: chain D residue 225 THR Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 296 HIS Chi-restraints excluded: chain D residue 408 LEU Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain E residue 322 ARG Chi-restraints excluded: chain E residue 408 LEU Chi-restraints excluded: chain E residue 455 LYS Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 272 VAL Chi-restraints excluded: chain F residue 322 ARG Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain F residue 410 LYS Chi-restraints excluded: chain F residue 509 TYR Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain G residue 277 GLN Chi-restraints excluded: chain G residue 296 HIS Chi-restraints excluded: chain G residue 330 ILE Chi-restraints excluded: chain G residue 408 LEU Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 126 THR Chi-restraints excluded: chain H residue 272 VAL Chi-restraints excluded: chain H residue 277 GLN Chi-restraints excluded: chain H residue 322 ARG Chi-restraints excluded: chain H residue 333 THR Chi-restraints excluded: chain H residue 420 MET Chi-restraints excluded: chain H residue 509 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 328 optimal weight: 2.9990 chunk 223 optimal weight: 5.9990 chunk 5 optimal weight: 2.9990 chunk 293 optimal weight: 2.9990 chunk 162 optimal weight: 2.9990 chunk 336 optimal weight: 1.9990 chunk 272 optimal weight: 4.9990 chunk 0 optimal weight: 3.9990 chunk 201 optimal weight: 1.9990 chunk 353 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 100 GLN ** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 441 GLN D 441 GLN E 230 ASN F 441 GLN H 507 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.3465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 33168 Z= 0.416 Angle : 0.659 8.792 45072 Z= 0.335 Chirality : 0.047 0.186 5192 Planarity : 0.006 0.093 5560 Dihedral : 17.117 177.292 5488 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 3.10 % Allowed : 17.69 % Favored : 79.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.03 (0.13), residues: 4104 helix: 1.21 (0.14), residues: 1520 sheet: -1.16 (0.27), residues: 336 loop : -0.68 (0.14), residues: 2248 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS G 372 PHE 0.022 0.002 PHE F 24 TYR 0.013 0.002 TYR E 348 ARG 0.010 0.001 ARG F 203 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 732 residues out of total 3352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 628 time to evaluate : 3.696 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 GLU cc_start: 0.7749 (mm-30) cc_final: 0.7428 (mm-30) REVERT: A 131 LEU cc_start: 0.7913 (mt) cc_final: 0.7660 (mm) REVERT: A 179 MET cc_start: 0.8035 (ptm) cc_final: 0.7449 (ptm) REVERT: A 195 LYS cc_start: 0.7879 (ttpp) cc_final: 0.7511 (ttmm) REVERT: A 196 GLU cc_start: 0.7181 (mt-10) cc_final: 0.6806 (mt-10) REVERT: A 228 LYS cc_start: 0.8286 (mtmt) cc_final: 0.7993 (mtmt) REVERT: A 277 GLN cc_start: 0.9047 (OUTLIER) cc_final: 0.7719 (tm-30) REVERT: A 322 ARG cc_start: 0.9006 (OUTLIER) cc_final: 0.7319 (ttm170) REVERT: A 509 TYR cc_start: 0.6953 (OUTLIER) cc_final: 0.6587 (t80) REVERT: B 103 GLU cc_start: 0.7824 (mm-30) cc_final: 0.7467 (mm-30) REVERT: B 106 LYS cc_start: 0.8660 (mtpt) cc_final: 0.8352 (ttmm) REVERT: B 117 ASP cc_start: 0.8462 (t70) cc_final: 0.8254 (t0) REVERT: B 131 LEU cc_start: 0.7838 (OUTLIER) cc_final: 0.7424 (mm) REVERT: B 196 GLU cc_start: 0.7168 (mt-10) cc_final: 0.6777 (mt-10) REVERT: B 228 LYS cc_start: 0.8299 (mtmt) cc_final: 0.8031 (mtmt) REVERT: B 277 GLN cc_start: 0.9048 (OUTLIER) cc_final: 0.7923 (tm-30) REVERT: B 333 THR cc_start: 0.8321 (OUTLIER) cc_final: 0.8094 (t) REVERT: B 509 TYR cc_start: 0.6815 (OUTLIER) cc_final: 0.6344 (t80) REVERT: C 103 GLU cc_start: 0.7826 (mm-30) cc_final: 0.7520 (mm-30) REVERT: C 129 ASP cc_start: 0.7930 (m-30) cc_final: 0.7356 (m-30) REVERT: C 131 LEU cc_start: 0.7782 (OUTLIER) cc_final: 0.7414 (mm) REVERT: C 196 GLU cc_start: 0.7095 (mt-10) cc_final: 0.6763 (mt-10) REVERT: C 277 GLN cc_start: 0.9022 (OUTLIER) cc_final: 0.7855 (tm-30) REVERT: C 410 LYS cc_start: 0.7169 (tttt) cc_final: 0.6855 (ttpp) REVERT: C 509 TYR cc_start: 0.6799 (OUTLIER) cc_final: 0.6461 (t80) REVERT: D 103 GLU cc_start: 0.7739 (mm-30) cc_final: 0.7475 (mm-30) REVERT: D 117 ASP cc_start: 0.8490 (t0) cc_final: 0.8257 (t0) REVERT: D 131 LEU cc_start: 0.7847 (OUTLIER) cc_final: 0.7586 (mm) REVERT: D 196 GLU cc_start: 0.7140 (mt-10) cc_final: 0.6826 (mt-10) REVERT: D 228 LYS cc_start: 0.8314 (mtmt) cc_final: 0.8019 (mtmt) REVERT: D 277 GLN cc_start: 0.8940 (OUTLIER) cc_final: 0.7326 (tm-30) REVERT: D 296 HIS cc_start: 0.7730 (OUTLIER) cc_final: 0.7400 (p-80) REVERT: D 410 LYS cc_start: 0.7081 (ttmp) cc_final: 0.6606 (ttpp) REVERT: D 509 TYR cc_start: 0.6763 (OUTLIER) cc_final: 0.6231 (t80) REVERT: E 103 GLU cc_start: 0.7778 (mm-30) cc_final: 0.7514 (mm-30) REVERT: E 129 ASP cc_start: 0.7846 (m-30) cc_final: 0.7454 (m-30) REVERT: E 131 LEU cc_start: 0.7802 (mp) cc_final: 0.7332 (mm) REVERT: E 277 GLN cc_start: 0.9044 (OUTLIER) cc_final: 0.7826 (tm-30) REVERT: E 509 TYR cc_start: 0.6778 (OUTLIER) cc_final: 0.6336 (t80) REVERT: F 103 GLU cc_start: 0.7756 (mm-30) cc_final: 0.7481 (mm-30) REVERT: F 131 LEU cc_start: 0.7867 (OUTLIER) cc_final: 0.7469 (mm) REVERT: F 228 LYS cc_start: 0.8326 (mtmt) cc_final: 0.8053 (mtmt) REVERT: F 277 GLN cc_start: 0.8912 (OUTLIER) cc_final: 0.7570 (tm-30) REVERT: F 322 ARG cc_start: 0.9007 (OUTLIER) cc_final: 0.7393 (ttm170) REVERT: F 474 ARG cc_start: 0.7640 (ttm-80) cc_final: 0.7350 (ttt180) REVERT: F 509 TYR cc_start: 0.6846 (OUTLIER) cc_final: 0.6509 (t80) REVERT: G 71 ASP cc_start: 0.8438 (p0) cc_final: 0.8210 (p0) REVERT: G 103 GLU cc_start: 0.7704 (mm-30) cc_final: 0.7453 (mm-30) REVERT: G 131 LEU cc_start: 0.7855 (mp) cc_final: 0.7459 (mm) REVERT: G 196 GLU cc_start: 0.7191 (mt-10) cc_final: 0.6795 (mt-10) REVERT: G 296 HIS cc_start: 0.7773 (OUTLIER) cc_final: 0.7389 (p-80) REVERT: G 509 TYR cc_start: 0.6833 (OUTLIER) cc_final: 0.6347 (t80) REVERT: H 103 GLU cc_start: 0.7814 (mm-30) cc_final: 0.7512 (mm-30) REVERT: H 131 LEU cc_start: 0.7918 (mp) cc_final: 0.7510 (mm) REVERT: H 196 GLU cc_start: 0.7077 (mt-10) cc_final: 0.6701 (mt-10) REVERT: H 322 ARG cc_start: 0.9117 (OUTLIER) cc_final: 0.7484 (ttm170) REVERT: H 509 TYR cc_start: 0.6756 (OUTLIER) cc_final: 0.5946 (t80) outliers start: 104 outliers final: 53 residues processed: 711 average time/residue: 2.4634 time to fit residues: 2100.6495 Evaluate side-chains 684 residues out of total 3352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 607 time to evaluate : 3.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain A residue 322 ARG Chi-restraints excluded: chain A residue 410 LYS Chi-restraints excluded: chain A residue 509 TYR Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 322 ARG Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 420 MET Chi-restraints excluded: chain B residue 509 TYR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain C residue 322 ARG Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain C residue 474 ARG Chi-restraints excluded: chain C residue 509 TYR Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 225 THR Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain D residue 296 HIS Chi-restraints excluded: chain D residue 322 ARG Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain D residue 408 LEU Chi-restraints excluded: chain D residue 474 ARG Chi-restraints excluded: chain D residue 509 TYR Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain E residue 160 SER Chi-restraints excluded: chain E residue 275 SER Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain E residue 322 ARG Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain E residue 408 LEU Chi-restraints excluded: chain E residue 455 LYS Chi-restraints excluded: chain E residue 509 TYR Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 117 ASP Chi-restraints excluded: chain F residue 131 LEU Chi-restraints excluded: chain F residue 140 SER Chi-restraints excluded: chain F residue 272 VAL Chi-restraints excluded: chain F residue 277 GLN Chi-restraints excluded: chain F residue 322 ARG Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain F residue 455 LYS Chi-restraints excluded: chain F residue 509 TYR Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain G residue 275 SER Chi-restraints excluded: chain G residue 277 GLN Chi-restraints excluded: chain G residue 296 HIS Chi-restraints excluded: chain G residue 322 ARG Chi-restraints excluded: chain G residue 330 ILE Chi-restraints excluded: chain G residue 455 LYS Chi-restraints excluded: chain G residue 509 TYR Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 126 THR Chi-restraints excluded: chain H residue 272 VAL Chi-restraints excluded: chain H residue 277 GLN Chi-restraints excluded: chain H residue 322 ARG Chi-restraints excluded: chain H residue 330 ILE Chi-restraints excluded: chain H residue 333 THR Chi-restraints excluded: chain H residue 420 MET Chi-restraints excluded: chain H residue 509 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 132 optimal weight: 2.9990 chunk 355 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 231 optimal weight: 0.9980 chunk 97 optimal weight: 0.8980 chunk 394 optimal weight: 0.4980 chunk 327 optimal weight: 0.9990 chunk 182 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 130 optimal weight: 0.9990 chunk 207 optimal weight: 0.5980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 202 GLN ** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 303 ASN B 454 GLN ** C 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 303 ASN D 303 ASN E 303 ASN G -20 HIS ** G 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 303 ASN H 303 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.3642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 33168 Z= 0.173 Angle : 0.571 7.828 45072 Z= 0.283 Chirality : 0.043 0.149 5192 Planarity : 0.005 0.098 5560 Dihedral : 16.214 179.411 5488 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 2.24 % Allowed : 18.74 % Favored : 79.03 % 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: 0.34 (0.14), residues: 4104 helix: 1.65 (0.14), residues: 1520 sheet: -0.94 (0.29), residues: 344 loop : -0.57 (0.14), residues: 2240 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS B 92 PHE 0.009 0.001 PHE C 24 TYR 0.012 0.001 TYR C 509 ARG 0.014 0.001 ARG A 203 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 701 residues out of total 3352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 626 time to evaluate : 3.808 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 GLU cc_start: 0.7666 (mm-30) cc_final: 0.7365 (mm-30) REVERT: A 131 LEU cc_start: 0.7901 (mt) cc_final: 0.7655 (mm) REVERT: A 195 LYS cc_start: 0.7818 (ttpp) cc_final: 0.7512 (ttmm) REVERT: A 196 GLU cc_start: 0.7104 (mt-10) cc_final: 0.6711 (mt-10) REVERT: A 228 LYS cc_start: 0.8231 (mtmt) cc_final: 0.7957 (mtmt) REVERT: A 277 GLN cc_start: 0.8949 (OUTLIER) cc_final: 0.7794 (tm-30) REVERT: A 296 HIS cc_start: 0.7746 (OUTLIER) cc_final: 0.7317 (p-80) REVERT: A 322 ARG cc_start: 0.8879 (OUTLIER) cc_final: 0.7217 (ttm170) REVERT: A 337 MET cc_start: 0.7252 (mmm) cc_final: 0.6605 (mmp) REVERT: A 509 TYR cc_start: 0.6811 (OUTLIER) cc_final: 0.6589 (t80) REVERT: B 103 GLU cc_start: 0.7801 (mm-30) cc_final: 0.7481 (mm-30) REVERT: B 106 LYS cc_start: 0.8612 (mtpt) cc_final: 0.8320 (ttmm) REVERT: B 117 ASP cc_start: 0.8413 (t70) cc_final: 0.8203 (t0) REVERT: B 131 LEU cc_start: 0.7792 (OUTLIER) cc_final: 0.7403 (mm) REVERT: B 196 GLU cc_start: 0.7058 (mt-10) cc_final: 0.6688 (mt-10) REVERT: B 228 LYS cc_start: 0.8262 (mtmt) cc_final: 0.8002 (mtmt) REVERT: B 243 GLN cc_start: 0.8848 (mt0) cc_final: 0.8600 (mt0) REVERT: B 277 GLN cc_start: 0.8949 (OUTLIER) cc_final: 0.7901 (tm-30) REVERT: B 333 THR cc_start: 0.8237 (OUTLIER) cc_final: 0.8005 (t) REVERT: B 441 GLN cc_start: 0.8131 (mt0) cc_final: 0.7830 (mt0) REVERT: B 509 TYR cc_start: 0.6678 (OUTLIER) cc_final: 0.6212 (t80) REVERT: C 103 GLU cc_start: 0.7806 (mm-30) cc_final: 0.7504 (mm-30) REVERT: C 129 ASP cc_start: 0.7873 (m-30) cc_final: 0.7356 (m-30) REVERT: C 131 LEU cc_start: 0.7792 (OUTLIER) cc_final: 0.7361 (mm) REVERT: C 196 GLU cc_start: 0.7049 (mt-10) cc_final: 0.6677 (mt-10) REVERT: C 232 ASP cc_start: 0.7841 (m-30) cc_final: 0.7544 (m-30) REVERT: C 277 GLN cc_start: 0.8921 (OUTLIER) cc_final: 0.7867 (tm-30) REVERT: C 410 LYS cc_start: 0.7013 (tttt) cc_final: 0.6739 (ttpp) REVERT: C 509 TYR cc_start: 0.6657 (OUTLIER) cc_final: 0.6392 (t80) REVERT: D 103 GLU cc_start: 0.7687 (mm-30) cc_final: 0.7377 (mm-30) REVERT: D 117 ASP cc_start: 0.8451 (t0) cc_final: 0.8240 (t0) REVERT: D 131 LEU cc_start: 0.7824 (OUTLIER) cc_final: 0.7618 (mm) REVERT: D 196 GLU cc_start: 0.7065 (mt-10) cc_final: 0.6738 (mt-10) REVERT: D 228 LYS cc_start: 0.8327 (mtmt) cc_final: 0.8021 (mtmt) REVERT: D 277 GLN cc_start: 0.8851 (OUTLIER) cc_final: 0.7243 (tm-30) REVERT: D 296 HIS cc_start: 0.7686 (OUTLIER) cc_final: 0.7364 (p-80) REVERT: D 337 MET cc_start: 0.7326 (mmm) cc_final: 0.6734 (mmp) REVERT: D 410 LYS cc_start: 0.6946 (ttmp) cc_final: 0.6504 (ttpp) REVERT: E 103 GLU cc_start: 0.7682 (mm-30) cc_final: 0.7393 (mm-30) REVERT: E 129 ASP cc_start: 0.7887 (m-30) cc_final: 0.7487 (m-30) REVERT: E 131 LEU cc_start: 0.7863 (mp) cc_final: 0.7449 (mm) REVERT: E 160 SER cc_start: 0.8235 (m) cc_final: 0.7810 (p) REVERT: E 232 ASP cc_start: 0.7823 (m-30) cc_final: 0.7533 (m-30) REVERT: E 243 GLN cc_start: 0.8830 (mt0) cc_final: 0.8609 (mt0) REVERT: E 277 GLN cc_start: 0.8949 (OUTLIER) cc_final: 0.7798 (tm-30) REVERT: E 509 TYR cc_start: 0.6625 (OUTLIER) cc_final: 0.6096 (t80) REVERT: F 103 GLU cc_start: 0.7688 (mm-30) cc_final: 0.7381 (mm-30) REVERT: F 131 LEU cc_start: 0.7830 (OUTLIER) cc_final: 0.7469 (mm) REVERT: F 162 ASP cc_start: 0.7921 (m-30) cc_final: 0.7395 (m-30) REVERT: F 228 LYS cc_start: 0.8332 (mtmt) cc_final: 0.8058 (mtmt) REVERT: F 322 ARG cc_start: 0.8853 (OUTLIER) cc_final: 0.7167 (ttm170) REVERT: F 333 THR cc_start: 0.8102 (OUTLIER) cc_final: 0.7871 (t) REVERT: F 474 ARG cc_start: 0.7579 (ttm-80) cc_final: 0.7215 (ttt180) REVERT: F 509 TYR cc_start: 0.6686 (OUTLIER) cc_final: 0.6306 (t80) REVERT: G 103 GLU cc_start: 0.7652 (mm-30) cc_final: 0.7363 (mm-30) REVERT: G 131 LEU cc_start: 0.7840 (mp) cc_final: 0.7487 (mm) REVERT: G 134 LYS cc_start: 0.7188 (OUTLIER) cc_final: 0.6374 (tptt) REVERT: G 196 GLU cc_start: 0.7164 (mt-10) cc_final: 0.6793 (mt-10) REVERT: G 277 GLN cc_start: 0.8978 (OUTLIER) cc_final: 0.7545 (tm-30) REVERT: G 296 HIS cc_start: 0.7738 (OUTLIER) cc_final: 0.7360 (p-80) REVERT: G 509 TYR cc_start: 0.6637 (OUTLIER) cc_final: 0.6098 (t80) REVERT: H 103 GLU cc_start: 0.7740 (mm-30) cc_final: 0.7457 (mm-30) REVERT: H 129 ASP cc_start: 0.7805 (m-30) cc_final: 0.7601 (m-30) REVERT: H 131 LEU cc_start: 0.7898 (mp) cc_final: 0.7500 (mm) REVERT: H 196 GLU cc_start: 0.7054 (mt-10) cc_final: 0.6757 (mt-10) REVERT: H 277 GLN cc_start: 0.8907 (OUTLIER) cc_final: 0.7612 (tm-30) REVERT: H 322 ARG cc_start: 0.9050 (OUTLIER) cc_final: 0.7310 (ttm170) REVERT: H 509 TYR cc_start: 0.6564 (OUTLIER) cc_final: 0.5532 (t80) outliers start: 75 outliers final: 35 residues processed: 680 average time/residue: 2.5193 time to fit residues: 2069.9722 Evaluate side-chains 660 residues out of total 3352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 598 time to evaluate : 3.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain A residue 296 HIS Chi-restraints excluded: chain A residue 322 ARG Chi-restraints excluded: chain A residue 410 LYS Chi-restraints excluded: chain A residue 509 TYR Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 420 MET Chi-restraints excluded: chain B residue 455 LYS Chi-restraints excluded: chain B residue 509 TYR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain C residue 509 TYR Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 225 THR Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain D residue 296 HIS Chi-restraints excluded: chain D residue 322 ARG Chi-restraints excluded: chain D residue 408 LEU Chi-restraints excluded: chain D residue 455 LYS Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain E residue 408 LEU Chi-restraints excluded: chain E residue 455 LYS Chi-restraints excluded: chain E residue 509 TYR Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 131 LEU Chi-restraints excluded: chain F residue 272 VAL Chi-restraints excluded: chain F residue 322 ARG Chi-restraints excluded: chain F residue 333 THR Chi-restraints excluded: chain F residue 455 LYS Chi-restraints excluded: chain F residue 509 TYR Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain G residue 134 LYS Chi-restraints excluded: chain G residue 225 THR Chi-restraints excluded: chain G residue 277 GLN Chi-restraints excluded: chain G residue 296 HIS Chi-restraints excluded: chain G residue 408 LEU Chi-restraints excluded: chain G residue 455 LYS Chi-restraints excluded: chain G residue 509 TYR Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 126 THR Chi-restraints excluded: chain H residue 272 VAL Chi-restraints excluded: chain H residue 277 GLN Chi-restraints excluded: chain H residue 322 ARG Chi-restraints excluded: chain H residue 333 THR Chi-restraints excluded: chain H residue 420 MET Chi-restraints excluded: chain H residue 509 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 380 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 224 optimal weight: 0.7980 chunk 288 optimal weight: 1.9990 chunk 223 optimal weight: 0.9980 chunk 332 optimal weight: 2.9990 chunk 220 optimal weight: 0.5980 chunk 393 optimal weight: 1.9990 chunk 246 optimal weight: 3.9990 chunk 239 optimal weight: 1.9990 chunk 181 optimal weight: 2.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 303 ASN E 303 ASN ** G 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 303 ASN H 303 ASN H 507 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.3721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 33168 Z= 0.232 Angle : 0.578 7.994 45072 Z= 0.288 Chirality : 0.043 0.153 5192 Planarity : 0.005 0.107 5560 Dihedral : 15.901 178.491 5488 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 2.48 % Allowed : 18.71 % Favored : 78.82 % 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: 0.36 (0.14), residues: 4104 helix: 1.66 (0.14), residues: 1520 sheet: -1.04 (0.28), residues: 328 loop : -0.53 (0.14), residues: 2256 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 466 PHE 0.013 0.001 PHE F 24 TYR 0.011 0.001 TYR C 509 ARG 0.013 0.001 ARG C 203 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 699 residues out of total 3352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 616 time to evaluate : 3.661 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 GLU cc_start: 0.7678 (mm-30) cc_final: 0.7370 (mm-30) REVERT: A 131 LEU cc_start: 0.7896 (mt) cc_final: 0.7659 (mm) REVERT: A 195 LYS cc_start: 0.7843 (ttpp) cc_final: 0.7514 (ttmm) REVERT: A 196 GLU cc_start: 0.7107 (mt-10) cc_final: 0.6697 (mt-10) REVERT: A 228 LYS cc_start: 0.8229 (mtmt) cc_final: 0.7963 (mtmt) REVERT: A 243 GLN cc_start: 0.8840 (mt0) cc_final: 0.8529 (mt0) REVERT: A 277 GLN cc_start: 0.8975 (OUTLIER) cc_final: 0.7786 (tm-30) REVERT: A 296 HIS cc_start: 0.7755 (OUTLIER) cc_final: 0.7323 (p-80) REVERT: A 322 ARG cc_start: 0.8922 (OUTLIER) cc_final: 0.7201 (ttm170) REVERT: A 410 LYS cc_start: 0.7463 (OUTLIER) cc_final: 0.7160 (ttmp) REVERT: A 509 TYR cc_start: 0.6855 (OUTLIER) cc_final: 0.6625 (t80) REVERT: B 103 GLU cc_start: 0.7821 (mm-30) cc_final: 0.7489 (mm-30) REVERT: B 106 LYS cc_start: 0.8640 (mtpt) cc_final: 0.8337 (ttmm) REVERT: B 131 LEU cc_start: 0.7817 (OUTLIER) cc_final: 0.7414 (mm) REVERT: B 196 GLU cc_start: 0.7096 (mt-10) cc_final: 0.6795 (mt-10) REVERT: B 203 ARG cc_start: 0.7658 (mtm110) cc_final: 0.7440 (mtm110) REVERT: B 228 LYS cc_start: 0.8254 (mtmt) cc_final: 0.7994 (mtmt) REVERT: B 243 GLN cc_start: 0.8845 (mt0) cc_final: 0.8524 (mt0) REVERT: B 277 GLN cc_start: 0.8977 (OUTLIER) cc_final: 0.7873 (tm-30) REVERT: B 441 GLN cc_start: 0.8086 (mt0) cc_final: 0.7847 (mt0) REVERT: B 509 TYR cc_start: 0.6649 (OUTLIER) cc_final: 0.6177 (t80) REVERT: C 103 GLU cc_start: 0.7837 (mm-30) cc_final: 0.7507 (mm-30) REVERT: C 129 ASP cc_start: 0.7924 (m-30) cc_final: 0.7353 (m-30) REVERT: C 131 LEU cc_start: 0.7797 (OUTLIER) cc_final: 0.7435 (mm) REVERT: C 196 GLU cc_start: 0.7059 (mt-10) cc_final: 0.6702 (mt-10) REVERT: C 277 GLN cc_start: 0.8983 (OUTLIER) cc_final: 0.7885 (tm-30) REVERT: C 410 LYS cc_start: 0.7024 (tttt) cc_final: 0.6763 (ttpp) REVERT: C 509 TYR cc_start: 0.6677 (OUTLIER) cc_final: 0.6369 (t80) REVERT: D 103 GLU cc_start: 0.7706 (mm-30) cc_final: 0.7389 (mm-30) REVERT: D 131 LEU cc_start: 0.7855 (mm) cc_final: 0.7629 (mm) REVERT: D 196 GLU cc_start: 0.7096 (mt-10) cc_final: 0.6759 (mt-10) REVERT: D 228 LYS cc_start: 0.8310 (mtmt) cc_final: 0.8019 (mtmt) REVERT: D 277 GLN cc_start: 0.8877 (OUTLIER) cc_final: 0.7181 (tm-30) REVERT: D 296 HIS cc_start: 0.7698 (OUTLIER) cc_final: 0.7368 (p-80) REVERT: D 322 ARG cc_start: 0.9020 (OUTLIER) cc_final: 0.7290 (ttm170) REVERT: D 337 MET cc_start: 0.7352 (mmm) cc_final: 0.6817 (mmp) REVERT: D 410 LYS cc_start: 0.7012 (ttmp) cc_final: 0.6635 (ttpp) REVERT: D 509 TYR cc_start: 0.6572 (OUTLIER) cc_final: 0.5964 (t80) REVERT: E 103 GLU cc_start: 0.7705 (mm-30) cc_final: 0.7407 (mm-30) REVERT: E 129 ASP cc_start: 0.7929 (m-30) cc_final: 0.7533 (m-30) REVERT: E 131 LEU cc_start: 0.7778 (mp) cc_final: 0.7349 (mm) REVERT: E 160 SER cc_start: 0.8225 (m) cc_final: 0.7861 (p) REVERT: E 232 ASP cc_start: 0.7828 (m-30) cc_final: 0.7541 (m-30) REVERT: E 243 GLN cc_start: 0.8842 (mt0) cc_final: 0.8612 (mt0) REVERT: E 277 GLN cc_start: 0.8986 (OUTLIER) cc_final: 0.7795 (tm-30) REVERT: E 368 GLN cc_start: 0.8329 (mt0) cc_final: 0.8116 (mt0) REVERT: E 509 TYR cc_start: 0.6631 (OUTLIER) cc_final: 0.6134 (t80) REVERT: F 103 GLU cc_start: 0.7689 (mm-30) cc_final: 0.7381 (mm-30) REVERT: F 131 LEU cc_start: 0.7853 (OUTLIER) cc_final: 0.7475 (mm) REVERT: F 162 ASP cc_start: 0.7890 (m-30) cc_final: 0.7349 (m-30) REVERT: F 228 LYS cc_start: 0.8340 (mtmt) cc_final: 0.8063 (mtmt) REVERT: F 277 GLN cc_start: 0.8824 (OUTLIER) cc_final: 0.7555 (tm-30) REVERT: F 322 ARG cc_start: 0.8950 (OUTLIER) cc_final: 0.7269 (ttm170) REVERT: F 474 ARG cc_start: 0.7606 (ttm-80) cc_final: 0.7303 (ttt90) REVERT: F 509 TYR cc_start: 0.6632 (OUTLIER) cc_final: 0.6301 (t80) REVERT: G 103 GLU cc_start: 0.7666 (mm-30) cc_final: 0.7373 (mm-30) REVERT: G 131 LEU cc_start: 0.7855 (mp) cc_final: 0.7479 (mm) REVERT: G 196 GLU cc_start: 0.7172 (mt-10) cc_final: 0.6810 (mt-10) REVERT: G 296 HIS cc_start: 0.7767 (OUTLIER) cc_final: 0.7373 (p-80) REVERT: G 509 TYR cc_start: 0.6637 (OUTLIER) cc_final: 0.6108 (t80) REVERT: H 103 GLU cc_start: 0.7762 (mm-30) cc_final: 0.7469 (mm-30) REVERT: H 131 LEU cc_start: 0.7907 (mp) cc_final: 0.7507 (mm) REVERT: H 196 GLU cc_start: 0.7077 (mt-10) cc_final: 0.6785 (mt-10) REVERT: H 243 GLN cc_start: 0.8835 (mt0) cc_final: 0.8571 (mt0) REVERT: H 277 GLN cc_start: 0.8962 (OUTLIER) cc_final: 0.7540 (tm-30) REVERT: H 322 ARG cc_start: 0.9068 (OUTLIER) cc_final: 0.7424 (ttm170) REVERT: H 337 MET cc_start: 0.7330 (mmm) cc_final: 0.6812 (mmp) outliers start: 83 outliers final: 38 residues processed: 675 average time/residue: 2.4986 time to fit residues: 2036.6046 Evaluate side-chains 659 residues out of total 3352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 596 time to evaluate : 3.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain A residue 296 HIS Chi-restraints excluded: chain A residue 322 ARG Chi-restraints excluded: chain A residue 410 LYS Chi-restraints excluded: chain A residue 509 TYR Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 322 ARG Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 420 MET Chi-restraints excluded: chain B residue 509 TYR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain C residue 474 ARG Chi-restraints excluded: chain C residue 509 TYR Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 225 THR Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain D residue 296 HIS Chi-restraints excluded: chain D residue 322 ARG Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain D residue 408 LEU Chi-restraints excluded: chain D residue 455 LYS Chi-restraints excluded: chain D residue 509 TYR Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain E residue 140 SER Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain E residue 408 LEU Chi-restraints excluded: chain E residue 455 LYS Chi-restraints excluded: chain E residue 509 TYR Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 131 LEU Chi-restraints excluded: chain F residue 272 VAL Chi-restraints excluded: chain F residue 277 GLN Chi-restraints excluded: chain F residue 322 ARG Chi-restraints excluded: chain F residue 455 LYS Chi-restraints excluded: chain F residue 509 TYR Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain G residue 225 THR Chi-restraints excluded: chain G residue 277 GLN Chi-restraints excluded: chain G residue 296 HIS Chi-restraints excluded: chain G residue 408 LEU Chi-restraints excluded: chain G residue 455 LYS Chi-restraints excluded: chain G residue 509 TYR Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 126 THR Chi-restraints excluded: chain H residue 272 VAL Chi-restraints excluded: chain H residue 277 GLN Chi-restraints excluded: chain H residue 322 ARG Chi-restraints excluded: chain H residue 333 THR Chi-restraints excluded: chain H residue 420 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 243 optimal weight: 1.9990 chunk 157 optimal weight: 2.9990 chunk 234 optimal weight: 2.9990 chunk 118 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 76 optimal weight: 0.9990 chunk 250 optimal weight: 2.9990 chunk 267 optimal weight: 1.9990 chunk 194 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 309 optimal weight: 0.9980 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B -15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 507 HIS ** C 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 303 ASN E 303 ASN G 94 ASN ** G 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 507 HIS H 303 ASN H 507 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.3781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 33168 Z= 0.269 Angle : 0.591 8.007 45072 Z= 0.295 Chirality : 0.044 0.168 5192 Planarity : 0.005 0.106 5560 Dihedral : 15.748 177.520 5486 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 2.60 % Allowed : 19.06 % Favored : 78.34 % 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 (0.14), residues: 4104 helix: 1.60 (0.14), residues: 1520 sheet: -0.99 (0.28), residues: 328 loop : -0.56 (0.14), residues: 2256 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.011 0.001 HIS G -20 PHE 0.014 0.001 PHE A 24 TYR 0.011 0.001 TYR C 509 ARG 0.015 0.001 ARG F 203 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 692 residues out of total 3352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 605 time to evaluate : 3.676 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 GLU cc_start: 0.7693 (mm-30) cc_final: 0.7388 (mm-30) REVERT: A 131 LEU cc_start: 0.7898 (mt) cc_final: 0.7639 (mm) REVERT: A 179 MET cc_start: 0.8059 (ptm) cc_final: 0.7460 (ptm) REVERT: A 195 LYS cc_start: 0.7838 (ttpp) cc_final: 0.7481 (ttmm) REVERT: A 196 GLU cc_start: 0.7149 (mt-10) cc_final: 0.6760 (mt-10) REVERT: A 228 LYS cc_start: 0.8240 (mtmt) cc_final: 0.7606 (mtmt) REVERT: A 232 ASP cc_start: 0.7771 (m-30) cc_final: 0.7424 (m-30) REVERT: A 277 GLN cc_start: 0.8988 (OUTLIER) cc_final: 0.7797 (tm-30) REVERT: A 296 HIS cc_start: 0.7699 (OUTLIER) cc_final: 0.7280 (p-80) REVERT: A 322 ARG cc_start: 0.8934 (OUTLIER) cc_final: 0.7279 (ttm170) REVERT: A 337 MET cc_start: 0.7267 (mmm) cc_final: 0.7064 (mmt) REVERT: A 410 LYS cc_start: 0.7467 (OUTLIER) cc_final: 0.7154 (ttmp) REVERT: A 509 TYR cc_start: 0.6877 (OUTLIER) cc_final: 0.6618 (t80) REVERT: B 103 GLU cc_start: 0.7827 (mm-30) cc_final: 0.7494 (mm-30) REVERT: B 106 LYS cc_start: 0.8645 (mtpt) cc_final: 0.8332 (ttmm) REVERT: B 131 LEU cc_start: 0.7821 (OUTLIER) cc_final: 0.7412 (mm) REVERT: B 196 GLU cc_start: 0.7108 (mt-10) cc_final: 0.6812 (mt-10) REVERT: B 203 ARG cc_start: 0.7662 (mtm110) cc_final: 0.7376 (mtm110) REVERT: B 228 LYS cc_start: 0.8251 (mtmt) cc_final: 0.7633 (mtmt) REVERT: B 232 ASP cc_start: 0.7826 (m-30) cc_final: 0.7470 (m-30) REVERT: B 277 GLN cc_start: 0.8984 (OUTLIER) cc_final: 0.7878 (tm-30) REVERT: B 333 THR cc_start: 0.8284 (OUTLIER) cc_final: 0.8059 (t) REVERT: B 337 MET cc_start: 0.7167 (mmm) cc_final: 0.6640 (mmp) REVERT: B 441 GLN cc_start: 0.8044 (mt0) cc_final: 0.7731 (mt0) REVERT: B 509 TYR cc_start: 0.6667 (OUTLIER) cc_final: 0.6274 (t80) REVERT: C 103 GLU cc_start: 0.7776 (mm-30) cc_final: 0.7485 (mm-30) REVERT: C 129 ASP cc_start: 0.7914 (m-30) cc_final: 0.7369 (m-30) REVERT: C 131 LEU cc_start: 0.7917 (OUTLIER) cc_final: 0.7493 (mm) REVERT: C 196 GLU cc_start: 0.7077 (mt-10) cc_final: 0.6723 (mt-10) REVERT: C 277 GLN cc_start: 0.8990 (OUTLIER) cc_final: 0.7801 (tm-30) REVERT: C 337 MET cc_start: 0.7266 (mpt) cc_final: 0.6782 (mpm) REVERT: C 410 LYS cc_start: 0.6987 (tttt) cc_final: 0.6727 (ttpp) REVERT: C 509 TYR cc_start: 0.6689 (OUTLIER) cc_final: 0.6443 (t80) REVERT: D 103 GLU cc_start: 0.7719 (mm-30) cc_final: 0.7408 (mm-30) REVERT: D 131 LEU cc_start: 0.7863 (OUTLIER) cc_final: 0.7638 (mm) REVERT: D 196 GLU cc_start: 0.7107 (mt-10) cc_final: 0.6772 (mt-10) REVERT: D 228 LYS cc_start: 0.8309 (mtmt) cc_final: 0.7666 (mtmt) REVERT: D 232 ASP cc_start: 0.7821 (m-30) cc_final: 0.7486 (m-30) REVERT: D 277 GLN cc_start: 0.8901 (OUTLIER) cc_final: 0.7217 (tm-30) REVERT: D 296 HIS cc_start: 0.7702 (OUTLIER) cc_final: 0.7378 (p-80) REVERT: D 322 ARG cc_start: 0.9041 (OUTLIER) cc_final: 0.7298 (ttm170) REVERT: D 410 LYS cc_start: 0.7058 (ttmp) cc_final: 0.6670 (ttpp) REVERT: D 509 TYR cc_start: 0.6583 (OUTLIER) cc_final: 0.5969 (t80) REVERT: E 103 GLU cc_start: 0.7721 (mm-30) cc_final: 0.7429 (mm-30) REVERT: E 126 THR cc_start: 0.7479 (OUTLIER) cc_final: 0.7237 (p) REVERT: E 131 LEU cc_start: 0.7818 (mp) cc_final: 0.7367 (mm) REVERT: E 160 SER cc_start: 0.8210 (m) cc_final: 0.7874 (p) REVERT: E 232 ASP cc_start: 0.7829 (m-30) cc_final: 0.7533 (m-30) REVERT: E 243 GLN cc_start: 0.8881 (mt0) cc_final: 0.8642 (mt0) REVERT: E 277 GLN cc_start: 0.8999 (OUTLIER) cc_final: 0.7818 (tm-30) REVERT: E 509 TYR cc_start: 0.6624 (OUTLIER) cc_final: 0.6194 (t80) REVERT: F 103 GLU cc_start: 0.7697 (mm-30) cc_final: 0.7401 (mm-30) REVERT: F 131 LEU cc_start: 0.7845 (OUTLIER) cc_final: 0.7470 (mm) REVERT: F 228 LYS cc_start: 0.8344 (mtmt) cc_final: 0.8059 (mtmt) REVERT: F 277 GLN cc_start: 0.8824 (OUTLIER) cc_final: 0.7587 (tm-30) REVERT: F 322 ARG cc_start: 0.9002 (OUTLIER) cc_final: 0.7326 (ttm170) REVERT: F 474 ARG cc_start: 0.7610 (ttm-80) cc_final: 0.7306 (ttt180) REVERT: F 509 TYR cc_start: 0.6648 (OUTLIER) cc_final: 0.6326 (t80) REVERT: G 103 GLU cc_start: 0.7684 (mm-30) cc_final: 0.7393 (mm-30) REVERT: G 131 LEU cc_start: 0.7868 (mp) cc_final: 0.7478 (mm) REVERT: G 196 GLU cc_start: 0.7166 (mt-10) cc_final: 0.6810 (mt-10) REVERT: G 296 HIS cc_start: 0.7784 (OUTLIER) cc_final: 0.7396 (p-80) REVERT: G 509 TYR cc_start: 0.6659 (OUTLIER) cc_final: 0.6119 (t80) REVERT: H 103 GLU cc_start: 0.7778 (mm-30) cc_final: 0.7445 (mm-30) REVERT: H 131 LEU cc_start: 0.7911 (mp) cc_final: 0.7495 (mm) REVERT: H 196 GLU cc_start: 0.7118 (mt-10) cc_final: 0.6836 (mt-10) REVERT: H 232 ASP cc_start: 0.7770 (m-30) cc_final: 0.7429 (m-30) REVERT: H 277 GLN cc_start: 0.8966 (OUTLIER) cc_final: 0.7555 (tm-30) REVERT: H 322 ARG cc_start: 0.9109 (OUTLIER) cc_final: 0.7439 (ttm170) REVERT: H 455 LYS cc_start: 0.8348 (OUTLIER) cc_final: 0.8128 (tppt) outliers start: 87 outliers final: 40 residues processed: 668 average time/residue: 2.6307 time to fit residues: 2151.0514 Evaluate side-chains 662 residues out of total 3352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 593 time to evaluate : 3.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain A residue 296 HIS Chi-restraints excluded: chain A residue 322 ARG Chi-restraints excluded: chain A residue 410 LYS Chi-restraints excluded: chain A residue 509 TYR Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 322 ARG Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 420 MET Chi-restraints excluded: chain B residue 509 TYR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain C residue 474 ARG Chi-restraints excluded: chain C residue 509 TYR Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 225 THR Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain D residue 296 HIS Chi-restraints excluded: chain D residue 322 ARG Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain D residue 408 LEU Chi-restraints excluded: chain D residue 455 LYS Chi-restraints excluded: chain D residue 509 TYR Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 75 GLU Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain E residue 140 SER Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain E residue 322 ARG Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain E residue 408 LEU Chi-restraints excluded: chain E residue 455 LYS Chi-restraints excluded: chain E residue 509 TYR Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 131 LEU Chi-restraints excluded: chain F residue 272 VAL Chi-restraints excluded: chain F residue 277 GLN Chi-restraints excluded: chain F residue 322 ARG Chi-restraints excluded: chain F residue 455 LYS Chi-restraints excluded: chain F residue 509 TYR Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain G residue 225 THR Chi-restraints excluded: chain G residue 277 GLN Chi-restraints excluded: chain G residue 296 HIS Chi-restraints excluded: chain G residue 408 LEU Chi-restraints excluded: chain G residue 509 TYR Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 126 THR Chi-restraints excluded: chain H residue 272 VAL Chi-restraints excluded: chain H residue 277 GLN Chi-restraints excluded: chain H residue 322 ARG Chi-restraints excluded: chain H residue 330 ILE Chi-restraints excluded: chain H residue 420 MET Chi-restraints excluded: chain H residue 455 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 357 optimal weight: 3.9990 chunk 376 optimal weight: 5.9990 chunk 343 optimal weight: 0.5980 chunk 366 optimal weight: 2.9990 chunk 220 optimal weight: 2.9990 chunk 159 optimal weight: 1.9990 chunk 287 optimal weight: 1.9990 chunk 112 optimal weight: 2.9990 chunk 331 optimal weight: 0.9990 chunk 346 optimal weight: 1.9990 chunk 365 optimal weight: 0.5980 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 202 GLN ** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 507 HIS ** C 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 303 ASN ** G 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 303 ASN G 507 HIS H 303 ASN H 507 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.3843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 33168 Z= 0.221 Angle : 0.576 8.047 45072 Z= 0.286 Chirality : 0.043 0.161 5192 Planarity : 0.005 0.077 5560 Dihedral : 15.486 179.893 5485 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 2.36 % Allowed : 19.45 % Favored : 78.19 % 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: 0.41 (0.14), residues: 4104 helix: 1.70 (0.14), residues: 1520 sheet: -0.97 (0.28), residues: 328 loop : -0.51 (0.14), residues: 2256 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.001 HIS G -20 PHE 0.011 0.001 PHE E 24 TYR 0.011 0.001 TYR C 509 ARG 0.012 0.001 ARG C 203 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 685 residues out of total 3352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 606 time to evaluate : 3.697 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 GLU cc_start: 0.7679 (mm-30) cc_final: 0.7374 (mm-30) REVERT: A 131 LEU cc_start: 0.7911 (mt) cc_final: 0.7681 (mm) REVERT: A 195 LYS cc_start: 0.7797 (ttpp) cc_final: 0.7500 (ttmm) REVERT: A 196 GLU cc_start: 0.7085 (mt-10) cc_final: 0.6698 (mt-10) REVERT: A 228 LYS cc_start: 0.8229 (mtmt) cc_final: 0.7615 (mtmt) REVERT: A 232 ASP cc_start: 0.7744 (m-30) cc_final: 0.7410 (m-30) REVERT: A 277 GLN cc_start: 0.8964 (OUTLIER) cc_final: 0.7735 (tm-30) REVERT: A 296 HIS cc_start: 0.7688 (OUTLIER) cc_final: 0.7263 (p-80) REVERT: A 322 ARG cc_start: 0.8914 (OUTLIER) cc_final: 0.7186 (ttm170) REVERT: A 410 LYS cc_start: 0.7461 (OUTLIER) cc_final: 0.7142 (ttmp) REVERT: A 509 TYR cc_start: 0.6831 (OUTLIER) cc_final: 0.6576 (t80) REVERT: B 103 GLU cc_start: 0.7818 (mm-30) cc_final: 0.7493 (mm-30) REVERT: B 106 LYS cc_start: 0.8642 (mtpt) cc_final: 0.8332 (ttmm) REVERT: B 131 LEU cc_start: 0.7809 (OUTLIER) cc_final: 0.7405 (mm) REVERT: B 196 GLU cc_start: 0.7096 (mt-10) cc_final: 0.6755 (mt-10) REVERT: B 203 ARG cc_start: 0.7680 (mtm110) cc_final: 0.7395 (mtm110) REVERT: B 228 LYS cc_start: 0.8251 (mtmt) cc_final: 0.7992 (mtmt) REVERT: B 243 GLN cc_start: 0.8833 (mt0) cc_final: 0.8580 (mt0) REVERT: B 277 GLN cc_start: 0.8957 (OUTLIER) cc_final: 0.7935 (tm-30) REVERT: B 333 THR cc_start: 0.8250 (OUTLIER) cc_final: 0.7996 (t) REVERT: B 441 GLN cc_start: 0.8047 (mt0) cc_final: 0.7718 (mt0) REVERT: B 509 TYR cc_start: 0.6610 (OUTLIER) cc_final: 0.6179 (t80) REVERT: C 103 GLU cc_start: 0.7719 (mm-30) cc_final: 0.7433 (mm-30) REVERT: C 129 ASP cc_start: 0.7896 (m-30) cc_final: 0.7359 (m-30) REVERT: C 131 LEU cc_start: 0.7920 (OUTLIER) cc_final: 0.7491 (mm) REVERT: C 196 GLU cc_start: 0.7077 (mt-10) cc_final: 0.6723 (mt-10) REVERT: C 277 GLN cc_start: 0.8963 (OUTLIER) cc_final: 0.7848 (tm-30) REVERT: C 410 LYS cc_start: 0.6927 (tttt) cc_final: 0.6684 (ttpp) REVERT: C 509 TYR cc_start: 0.6613 (OUTLIER) cc_final: 0.6403 (t80) REVERT: D 103 GLU cc_start: 0.7705 (mm-30) cc_final: 0.7399 (mm-30) REVERT: D 131 LEU cc_start: 0.7870 (OUTLIER) cc_final: 0.7645 (mm) REVERT: D 196 GLU cc_start: 0.7102 (mt-10) cc_final: 0.6770 (mt-10) REVERT: D 228 LYS cc_start: 0.8290 (mtmt) cc_final: 0.8016 (mtmt) REVERT: D 277 GLN cc_start: 0.8876 (OUTLIER) cc_final: 0.7257 (tm-30) REVERT: D 296 HIS cc_start: 0.7702 (OUTLIER) cc_final: 0.7378 (p-80) REVERT: D 322 ARG cc_start: 0.9007 (OUTLIER) cc_final: 0.7298 (ttm170) REVERT: D 410 LYS cc_start: 0.7024 (ttmp) cc_final: 0.6656 (ttpp) REVERT: D 509 TYR cc_start: 0.6560 (OUTLIER) cc_final: 0.5991 (t80) REVERT: E 103 GLU cc_start: 0.7710 (mm-30) cc_final: 0.7416 (mm-30) REVERT: E 129 ASP cc_start: 0.8025 (m-30) cc_final: 0.7609 (m-30) REVERT: E 131 LEU cc_start: 0.7894 (mp) cc_final: 0.7487 (mm) REVERT: E 160 SER cc_start: 0.8219 (m) cc_final: 0.7902 (p) REVERT: E 232 ASP cc_start: 0.7802 (m-30) cc_final: 0.7515 (m-30) REVERT: E 243 GLN cc_start: 0.8890 (mt0) cc_final: 0.8655 (mt0) REVERT: E 277 GLN cc_start: 0.8982 (OUTLIER) cc_final: 0.7858 (tm-30) REVERT: E 509 TYR cc_start: 0.6605 (OUTLIER) cc_final: 0.6147 (t80) REVERT: F 103 GLU cc_start: 0.7665 (mm-30) cc_final: 0.7361 (mm-30) REVERT: F 131 LEU cc_start: 0.7839 (OUTLIER) cc_final: 0.7461 (mm) REVERT: F 162 ASP cc_start: 0.7934 (m-30) cc_final: 0.7439 (m-30) REVERT: F 203 ARG cc_start: 0.7733 (mtm110) cc_final: 0.7521 (mtm110) REVERT: F 228 LYS cc_start: 0.8350 (mtmt) cc_final: 0.8066 (mtmt) REVERT: F 277 GLN cc_start: 0.8813 (OUTLIER) cc_final: 0.7539 (tm-30) REVERT: F 322 ARG cc_start: 0.8968 (OUTLIER) cc_final: 0.7286 (ttm170) REVERT: F 333 THR cc_start: 0.8104 (OUTLIER) cc_final: 0.7882 (t) REVERT: F 474 ARG cc_start: 0.7606 (ttm-80) cc_final: 0.7302 (ttt180) REVERT: F 509 TYR cc_start: 0.6610 (OUTLIER) cc_final: 0.6261 (t80) REVERT: G 103 GLU cc_start: 0.7671 (mm-30) cc_final: 0.7381 (mm-30) REVERT: G 131 LEU cc_start: 0.7868 (mp) cc_final: 0.7519 (mm) REVERT: G 196 GLU cc_start: 0.7156 (mt-10) cc_final: 0.6751 (mt-10) REVERT: G 296 HIS cc_start: 0.7773 (OUTLIER) cc_final: 0.7435 (p-80) REVERT: G 410 LYS cc_start: 0.6782 (tttt) cc_final: 0.6548 (ttpm) REVERT: G 509 TYR cc_start: 0.6626 (OUTLIER) cc_final: 0.6063 (t80) REVERT: H 103 GLU cc_start: 0.7703 (mm-30) cc_final: 0.7449 (mm-30) REVERT: H 131 LEU cc_start: 0.7923 (mp) cc_final: 0.7499 (mm) REVERT: H 196 GLU cc_start: 0.7084 (mt-10) cc_final: 0.6769 (mt-10) REVERT: H 277 GLN cc_start: 0.8931 (OUTLIER) cc_final: 0.7544 (tm-30) REVERT: H 322 ARG cc_start: 0.9097 (OUTLIER) cc_final: 0.7412 (ttm170) REVERT: H 455 LYS cc_start: 0.8376 (OUTLIER) cc_final: 0.8151 (tppt) outliers start: 79 outliers final: 40 residues processed: 662 average time/residue: 2.5012 time to fit residues: 1997.3609 Evaluate side-chains 662 residues out of total 3352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 593 time to evaluate : 3.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain A residue 296 HIS Chi-restraints excluded: chain A residue 322 ARG Chi-restraints excluded: chain A residue 410 LYS Chi-restraints excluded: chain A residue 509 TYR Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 117 ASP Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 255 ASP Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 322 ARG Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 420 MET Chi-restraints excluded: chain B residue 455 LYS Chi-restraints excluded: chain B residue 509 TYR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain C residue 509 TYR Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 225 THR Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain D residue 296 HIS Chi-restraints excluded: chain D residue 322 ARG Chi-restraints excluded: chain D residue 408 LEU Chi-restraints excluded: chain D residue 455 LYS Chi-restraints excluded: chain D residue 509 TYR Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain E residue 140 SER Chi-restraints excluded: chain E residue 225 THR Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain E residue 408 LEU Chi-restraints excluded: chain E residue 455 LYS Chi-restraints excluded: chain E residue 509 TYR Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 131 LEU Chi-restraints excluded: chain F residue 140 SER Chi-restraints excluded: chain F residue 272 VAL Chi-restraints excluded: chain F residue 277 GLN Chi-restraints excluded: chain F residue 322 ARG Chi-restraints excluded: chain F residue 333 THR Chi-restraints excluded: chain F residue 455 LYS Chi-restraints excluded: chain F residue 509 TYR Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain G residue 225 THR Chi-restraints excluded: chain G residue 275 SER Chi-restraints excluded: chain G residue 277 GLN Chi-restraints excluded: chain G residue 296 HIS Chi-restraints excluded: chain G residue 408 LEU Chi-restraints excluded: chain G residue 509 TYR Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 126 THR Chi-restraints excluded: chain H residue 272 VAL Chi-restraints excluded: chain H residue 277 GLN Chi-restraints excluded: chain H residue 322 ARG Chi-restraints excluded: chain H residue 420 MET Chi-restraints excluded: chain H residue 455 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 240 optimal weight: 1.9990 chunk 387 optimal weight: 1.9990 chunk 236 optimal weight: 0.9990 chunk 183 optimal weight: 2.9990 chunk 269 optimal weight: 3.9990 chunk 406 optimal weight: 1.9990 chunk 374 optimal weight: 0.4980 chunk 323 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 250 optimal weight: 0.5980 chunk 198 optimal weight: 4.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 507 HIS ** C 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 303 ASN E 303 ASN ** G -20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 303 ASN G 507 HIS H 303 ASN H 507 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.3873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 33168 Z= 0.222 Angle : 0.580 8.050 45072 Z= 0.288 Chirality : 0.043 0.163 5192 Planarity : 0.005 0.117 5560 Dihedral : 15.419 179.779 5484 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 2.03 % Allowed : 20.02 % Favored : 77.95 % 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: 0.42 (0.14), residues: 4104 helix: 1.72 (0.14), residues: 1520 sheet: -0.98 (0.28), residues: 336 loop : -0.51 (0.14), residues: 2248 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.012 0.001 HIS G -20 PHE 0.012 0.001 PHE G 24 TYR 0.011 0.001 TYR A 509 ARG 0.018 0.001 ARG E 203 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 663 residues out of total 3352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 595 time to evaluate : 3.679 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 GLU cc_start: 0.7679 (mm-30) cc_final: 0.7375 (mm-30) REVERT: A 131 LEU cc_start: 0.7912 (mt) cc_final: 0.7678 (mm) REVERT: A 179 MET cc_start: 0.8068 (ptm) cc_final: 0.7510 (ptt) REVERT: A 195 LYS cc_start: 0.7824 (ttpp) cc_final: 0.7500 (ttmm) REVERT: A 196 GLU cc_start: 0.7090 (mt-10) cc_final: 0.6696 (mt-10) REVERT: A 228 LYS cc_start: 0.8253 (mtmt) cc_final: 0.7632 (mtmt) REVERT: A 232 ASP cc_start: 0.7751 (m-30) cc_final: 0.7415 (m-30) REVERT: A 277 GLN cc_start: 0.8957 (OUTLIER) cc_final: 0.7739 (tm-30) REVERT: A 296 HIS cc_start: 0.7685 (OUTLIER) cc_final: 0.7258 (p-80) REVERT: A 322 ARG cc_start: 0.8913 (OUTLIER) cc_final: 0.7181 (ttm170) REVERT: A 509 TYR cc_start: 0.6832 (OUTLIER) cc_final: 0.6572 (t80) REVERT: B 103 GLU cc_start: 0.7820 (mm-30) cc_final: 0.7497 (mm-30) REVERT: B 106 LYS cc_start: 0.8643 (mtpt) cc_final: 0.8331 (ttmm) REVERT: B 131 LEU cc_start: 0.7810 (OUTLIER) cc_final: 0.7406 (mm) REVERT: B 196 GLU cc_start: 0.7104 (mt-10) cc_final: 0.6761 (mt-10) REVERT: B 203 ARG cc_start: 0.7678 (mtm110) cc_final: 0.7388 (mtm110) REVERT: B 228 LYS cc_start: 0.8262 (mtmt) cc_final: 0.8007 (mtmt) REVERT: B 243 GLN cc_start: 0.8834 (mt0) cc_final: 0.8582 (mt0) REVERT: B 277 GLN cc_start: 0.8958 (OUTLIER) cc_final: 0.7937 (tm-30) REVERT: B 337 MET cc_start: 0.6944 (mmt) cc_final: 0.6688 (mpm) REVERT: B 441 GLN cc_start: 0.7997 (mt0) cc_final: 0.7689 (mt0) REVERT: B 509 TYR cc_start: 0.6601 (OUTLIER) cc_final: 0.6114 (t80) REVERT: C 103 GLU cc_start: 0.7718 (mm-30) cc_final: 0.7431 (mm-30) REVERT: C 129 ASP cc_start: 0.7904 (m-30) cc_final: 0.7363 (m-30) REVERT: C 131 LEU cc_start: 0.7918 (OUTLIER) cc_final: 0.7490 (mm) REVERT: C 196 GLU cc_start: 0.7120 (mt-10) cc_final: 0.6768 (mt-10) REVERT: C 277 GLN cc_start: 0.8964 (OUTLIER) cc_final: 0.7856 (tm-30) REVERT: C 337 MET cc_start: 0.7290 (mpt) cc_final: 0.6794 (mpm) REVERT: C 410 LYS cc_start: 0.6918 (tttt) cc_final: 0.6660 (ttpp) REVERT: C 509 TYR cc_start: 0.6586 (OUTLIER) cc_final: 0.6379 (t80) REVERT: D 103 GLU cc_start: 0.7706 (mm-30) cc_final: 0.7397 (mm-30) REVERT: D 131 LEU cc_start: 0.7872 (OUTLIER) cc_final: 0.7645 (mm) REVERT: D 196 GLU cc_start: 0.7104 (mt-10) cc_final: 0.6770 (mt-10) REVERT: D 228 LYS cc_start: 0.8287 (mtmt) cc_final: 0.8014 (mtmt) REVERT: D 277 GLN cc_start: 0.8879 (OUTLIER) cc_final: 0.7256 (tm-30) REVERT: D 296 HIS cc_start: 0.7705 (OUTLIER) cc_final: 0.7381 (p-80) REVERT: D 322 ARG cc_start: 0.9018 (OUTLIER) cc_final: 0.7286 (ttm170) REVERT: D 410 LYS cc_start: 0.7026 (ttmp) cc_final: 0.6656 (ttpp) REVERT: D 509 TYR cc_start: 0.6558 (OUTLIER) cc_final: 0.5987 (t80) REVERT: E 103 GLU cc_start: 0.7712 (mm-30) cc_final: 0.7418 (mm-30) REVERT: E 129 ASP cc_start: 0.8010 (m-30) cc_final: 0.7616 (m-30) REVERT: E 131 LEU cc_start: 0.7892 (mp) cc_final: 0.7456 (mm) REVERT: E 160 SER cc_start: 0.8206 (m) cc_final: 0.7903 (p) REVERT: E 232 ASP cc_start: 0.7803 (m-30) cc_final: 0.7519 (m-30) REVERT: E 243 GLN cc_start: 0.8891 (mt0) cc_final: 0.8656 (mt0) REVERT: E 277 GLN cc_start: 0.8977 (OUTLIER) cc_final: 0.7860 (tm-30) REVERT: E 509 TYR cc_start: 0.6627 (OUTLIER) cc_final: 0.6166 (t80) REVERT: F 103 GLU cc_start: 0.7663 (mm-30) cc_final: 0.7352 (mm-30) REVERT: F 131 LEU cc_start: 0.7838 (OUTLIER) cc_final: 0.7463 (mm) REVERT: F 162 ASP cc_start: 0.7927 (m-30) cc_final: 0.7425 (m-30) REVERT: F 203 ARG cc_start: 0.7736 (mtm110) cc_final: 0.7504 (mtm110) REVERT: F 228 LYS cc_start: 0.8350 (mtmt) cc_final: 0.8066 (mtmt) REVERT: F 277 GLN cc_start: 0.8812 (OUTLIER) cc_final: 0.7539 (tm-30) REVERT: F 322 ARG cc_start: 0.8972 (OUTLIER) cc_final: 0.7291 (ttm170) REVERT: F 333 THR cc_start: 0.8103 (OUTLIER) cc_final: 0.7885 (t) REVERT: F 474 ARG cc_start: 0.7608 (ttm-80) cc_final: 0.7299 (ttt180) REVERT: F 509 TYR cc_start: 0.6623 (OUTLIER) cc_final: 0.6298 (t80) REVERT: G 103 GLU cc_start: 0.7672 (mm-30) cc_final: 0.7383 (mm-30) REVERT: G 131 LEU cc_start: 0.7873 (mp) cc_final: 0.7494 (mm) REVERT: G 196 GLU cc_start: 0.7160 (mt-10) cc_final: 0.6755 (mt-10) REVERT: G 296 HIS cc_start: 0.7774 (OUTLIER) cc_final: 0.7435 (p-80) REVERT: G 336 VAL cc_start: 0.8496 (t) cc_final: 0.8195 (t) REVERT: G 410 LYS cc_start: 0.6774 (tttt) cc_final: 0.6549 (ttpm) REVERT: G 509 TYR cc_start: 0.6593 (OUTLIER) cc_final: 0.6034 (t80) REVERT: H 103 GLU cc_start: 0.7702 (mm-30) cc_final: 0.7454 (mm-30) REVERT: H 131 LEU cc_start: 0.7896 (mp) cc_final: 0.7467 (mm) REVERT: H 196 GLU cc_start: 0.7110 (mt-10) cc_final: 0.6797 (mt-10) REVERT: H 277 GLN cc_start: 0.8927 (OUTLIER) cc_final: 0.7547 (tm-30) REVERT: H 322 ARG cc_start: 0.9097 (OUTLIER) cc_final: 0.7412 (ttm170) REVERT: H 455 LYS cc_start: 0.8376 (OUTLIER) cc_final: 0.8154 (tppt) outliers start: 68 outliers final: 36 residues processed: 644 average time/residue: 2.5015 time to fit residues: 1934.8767 Evaluate side-chains 655 residues out of total 3352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 592 time to evaluate : 3.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain A residue 296 HIS Chi-restraints excluded: chain A residue 322 ARG Chi-restraints excluded: chain A residue 410 LYS Chi-restraints excluded: chain A residue 509 TYR Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 322 ARG Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 420 MET Chi-restraints excluded: chain B residue 455 LYS Chi-restraints excluded: chain B residue 509 TYR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain C residue 509 TYR Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 225 THR Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain D residue 296 HIS Chi-restraints excluded: chain D residue 322 ARG Chi-restraints excluded: chain D residue 408 LEU Chi-restraints excluded: chain D residue 455 LYS Chi-restraints excluded: chain D residue 509 TYR Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain E residue 140 SER Chi-restraints excluded: chain E residue 225 THR Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain E residue 408 LEU Chi-restraints excluded: chain E residue 455 LYS Chi-restraints excluded: chain E residue 509 TYR Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 131 LEU Chi-restraints excluded: chain F residue 272 VAL Chi-restraints excluded: chain F residue 277 GLN Chi-restraints excluded: chain F residue 322 ARG Chi-restraints excluded: chain F residue 333 THR Chi-restraints excluded: chain F residue 455 LYS Chi-restraints excluded: chain F residue 509 TYR Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain G residue 225 THR Chi-restraints excluded: chain G residue 275 SER Chi-restraints excluded: chain G residue 277 GLN Chi-restraints excluded: chain G residue 296 HIS Chi-restraints excluded: chain G residue 408 LEU Chi-restraints excluded: chain G residue 509 TYR Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 126 THR Chi-restraints excluded: chain H residue 272 VAL Chi-restraints excluded: chain H residue 277 GLN Chi-restraints excluded: chain H residue 322 ARG Chi-restraints excluded: chain H residue 420 MET Chi-restraints excluded: chain H residue 455 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 257 optimal weight: 1.9990 chunk 344 optimal weight: 2.9990 chunk 99 optimal weight: 0.9990 chunk 298 optimal weight: 7.9990 chunk 47 optimal weight: 1.9990 chunk 89 optimal weight: 3.9990 chunk 324 optimal weight: 0.0970 chunk 135 optimal weight: 1.9990 chunk 332 optimal weight: 0.6980 chunk 41 optimal weight: 0.0170 chunk 59 optimal weight: 0.8980 overall best weight: 0.5418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 230 ASN ** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 507 HIS ** C 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 303 ASN E 303 ASN ** G 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 303 ASN G 507 HIS H 303 ASN H 507 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.142119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.104944 restraints weight = 102336.409| |-----------------------------------------------------------------------------| r_work (start): 0.2984 rms_B_bonded: 1.77 r_work: 0.2843 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2712 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.3986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 33168 Z= 0.149 Angle : 0.549 8.169 45072 Z= 0.270 Chirality : 0.042 0.161 5192 Planarity : 0.005 0.079 5560 Dihedral : 14.958 179.684 5482 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 1.58 % Allowed : 20.58 % Favored : 77.83 % 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: 0.65 (0.14), residues: 4104 helix: 1.98 (0.14), residues: 1520 sheet: -1.03 (0.31), residues: 288 loop : -0.43 (0.14), residues: 2296 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.012 0.001 HIS B -20 PHE 0.009 0.001 PHE A 90 TYR 0.010 0.001 TYR A 509 ARG 0.010 0.000 ARG F 203 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 26890.37 seconds wall clock time: 459 minutes 12.69 seconds (27552.69 seconds total)