Starting phenix.real_space_refine on Tue Dec 31 11:23:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7snh_25226/12_2024/7snh_25226.cif Found real_map, /net/cci-nas-00/data/ceres_data/7snh_25226/12_2024/7snh_25226.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7snh_25226/12_2024/7snh_25226.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7snh_25226/12_2024/7snh_25226.map" model { file = "/net/cci-nas-00/data/ceres_data/7snh_25226/12_2024/7snh_25226.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7snh_25226/12_2024/7snh_25226.cif" } resolution = 2.2 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= 0.009 sd= 0.234 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 24 5.49 5 S 80 5.16 5 C 10028 2.51 5 N 2724 2.21 5 O 2972 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 15828 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3861 Number of conformers: 1 Conformer: "" Number of residues, atoms: 476, 3861 Classifications: {'peptide': 476} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 452} Chain breaks: 1 Chain: "B" Number of atoms: 3861 Number of conformers: 1 Conformer: "" Number of residues, atoms: 476, 3861 Classifications: {'peptide': 476} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 452} Chain breaks: 1 Chain: "C" Number of atoms: 3861 Number of conformers: 1 Conformer: "" Number of residues, atoms: 476, 3861 Classifications: {'peptide': 476} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 452} Chain breaks: 1 Chain: "D" Number of atoms: 3861 Number of conformers: 1 Conformer: "" Number of residues, atoms: 476, 3861 Classifications: {'peptide': 476} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 452} Chain breaks: 1 Chain: "A" Number of atoms: 96 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 96 Unusual residues: {'NAP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 96 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 96 Unusual residues: {'NAP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 96 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 96 Unusual residues: {'NAP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 96 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 96 Unusual residues: {'NAP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 8.81, per 1000 atoms: 0.56 Number of scatterers: 15828 At special positions: 0 Unit cell: (90.47, 115.37, 136.95, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 80 16.00 P 24 15.00 O 2972 8.00 N 2724 7.00 C 10028 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.04 Conformation dependent library (CDL) restraints added in 1.9 seconds 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3568 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 6 sheets defined 43.5% alpha, 17.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.82 Creating SS restraints... Processing helix chain 'A' and resid 41 through 58 removed outlier: 5.022A pdb=" N TYR A 49 " --> pdb=" O LYS A 45 " (cutoff:3.500A) Proline residue: A 50 - end of helix Processing helix chain 'A' and resid 76 through 89 Proline residue: A 86 - end of helix removed outlier: 3.635A pdb=" N LYS A 89 " --> pdb=" O GLU A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 93 No H-bonds generated for 'chain 'A' and resid 91 through 93' Processing helix chain 'A' and resid 94 through 102 Processing helix chain 'A' and resid 114 through 127 Processing helix chain 'A' and resid 143 through 145 No H-bonds generated for 'chain 'A' and resid 143 through 145' Processing helix chain 'A' and resid 146 through 158 Processing helix chain 'A' and resid 176 through 189 Processing helix chain 'A' and resid 192 through 194 No H-bonds generated for 'chain 'A' and resid 192 through 194' Processing helix chain 'A' and resid 200 through 204 Processing helix chain 'A' and resid 205 through 217 removed outlier: 4.551A pdb=" N MET A 212 " --> pdb=" O VAL A 208 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N VAL A 213 " --> pdb=" O GLN A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 252 removed outlier: 3.646A pdb=" N PHE A 250 " --> pdb=" O ARG A 246 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLU A 252 " --> pdb=" O GLY A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 259 removed outlier: 4.373A pdb=" N ARG A 257 " --> pdb=" O PHE A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 273 Processing helix chain 'A' and resid 280 through 294 removed outlier: 3.600A pdb=" N CYS A 294 " --> pdb=" O LYS A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 301 No H-bonds generated for 'chain 'A' and resid 299 through 301' Processing helix chain 'A' and resid 315 through 320 removed outlier: 4.125A pdb=" N ALA A 318 " --> pdb=" O GLU A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 447 Processing helix chain 'A' and resid 454 through 476 Proline residue: A 467 - end of helix Processing helix chain 'A' and resid 489 through 500 removed outlier: 4.045A pdb=" N ASP A 493 " --> pdb=" O PRO A 489 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 58 removed outlier: 5.023A pdb=" N TYR B 49 " --> pdb=" O LYS B 45 " (cutoff:3.500A) Proline residue: B 50 - end of helix Processing helix chain 'B' and resid 76 through 89 Proline residue: B 86 - end of helix removed outlier: 3.675A pdb=" N LYS B 89 " --> pdb=" O GLU B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 93 No H-bonds generated for 'chain 'B' and resid 91 through 93' Processing helix chain 'B' and resid 94 through 102 Processing helix chain 'B' and resid 114 through 128 Processing helix chain 'B' and resid 143 through 145 No H-bonds generated for 'chain 'B' and resid 143 through 145' Processing helix chain 'B' and resid 146 through 158 Processing helix chain 'B' and resid 176 through 189 Processing helix chain 'B' and resid 192 through 194 No H-bonds generated for 'chain 'B' and resid 192 through 194' Processing helix chain 'B' and resid 201 through 204 Processing helix chain 'B' and resid 205 through 217 removed outlier: 4.551A pdb=" N MET B 212 " --> pdb=" O VAL B 208 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N VAL B 213 " --> pdb=" O GLN B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 252 removed outlier: 3.647A pdb=" N PHE B 250 " --> pdb=" O ARG B 246 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLU B 252 " --> pdb=" O GLY B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 259 removed outlier: 4.375A pdb=" N ARG B 257 " --> pdb=" O PHE B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 273 Processing helix chain 'B' and resid 280 through 294 removed outlier: 3.599A pdb=" N CYS B 294 " --> pdb=" O LYS B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 299 through 301 No H-bonds generated for 'chain 'B' and resid 299 through 301' Processing helix chain 'B' and resid 315 through 320 removed outlier: 4.139A pdb=" N ALA B 318 " --> pdb=" O GLU B 315 " (cutoff:3.500A) Processing helix chain 'B' and resid 435 through 447 Processing helix chain 'B' and resid 454 through 476 Proline residue: B 467 - end of helix Processing helix chain 'B' and resid 489 through 500 removed outlier: 4.043A pdb=" N ASP B 493 " --> pdb=" O PRO B 489 " (cutoff:3.500A) Processing helix chain 'C' and resid 41 through 58 removed outlier: 5.025A pdb=" N TYR C 49 " --> pdb=" O LYS C 45 " (cutoff:3.500A) Proline residue: C 50 - end of helix Processing helix chain 'C' and resid 76 through 89 Proline residue: C 86 - end of helix removed outlier: 3.674A pdb=" N LYS C 89 " --> pdb=" O GLU C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 93 No H-bonds generated for 'chain 'C' and resid 91 through 93' Processing helix chain 'C' and resid 94 through 102 Processing helix chain 'C' and resid 114 through 128 Processing helix chain 'C' and resid 143 through 145 No H-bonds generated for 'chain 'C' and resid 143 through 145' Processing helix chain 'C' and resid 146 through 158 Processing helix chain 'C' and resid 176 through 189 Processing helix chain 'C' and resid 192 through 194 No H-bonds generated for 'chain 'C' and resid 192 through 194' Processing helix chain 'C' and resid 200 through 204 Processing helix chain 'C' and resid 205 through 217 removed outlier: 4.536A pdb=" N MET C 212 " --> pdb=" O VAL C 208 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N VAL C 213 " --> pdb=" O GLN C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 246 through 252 removed outlier: 3.648A pdb=" N PHE C 250 " --> pdb=" O ARG C 246 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLU C 252 " --> pdb=" O GLY C 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 259 removed outlier: 4.375A pdb=" N ARG C 257 " --> pdb=" O PHE C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 262 through 273 Processing helix chain 'C' and resid 280 through 294 removed outlier: 3.600A pdb=" N CYS C 294 " --> pdb=" O LYS C 290 " (cutoff:3.500A) Processing helix chain 'C' and resid 299 through 301 No H-bonds generated for 'chain 'C' and resid 299 through 301' Processing helix chain 'C' and resid 315 through 320 removed outlier: 4.141A pdb=" N ALA C 318 " --> pdb=" O GLU C 315 " (cutoff:3.500A) Processing helix chain 'C' and resid 435 through 447 Processing helix chain 'C' and resid 454 through 476 Proline residue: C 467 - end of helix Processing helix chain 'C' and resid 489 through 500 removed outlier: 4.042A pdb=" N ASP C 493 " --> pdb=" O PRO C 489 " (cutoff:3.500A) Processing helix chain 'D' and resid 41 through 58 removed outlier: 5.019A pdb=" N TYR D 49 " --> pdb=" O LYS D 45 " (cutoff:3.500A) Proline residue: D 50 - end of helix Processing helix chain 'D' and resid 76 through 89 Proline residue: D 86 - end of helix removed outlier: 3.678A pdb=" N LYS D 89 " --> pdb=" O GLU D 85 " (cutoff:3.500A) Processing helix chain 'D' and resid 91 through 93 No H-bonds generated for 'chain 'D' and resid 91 through 93' Processing helix chain 'D' and resid 94 through 102 Processing helix chain 'D' and resid 114 through 128 Processing helix chain 'D' and resid 143 through 145 No H-bonds generated for 'chain 'D' and resid 143 through 145' Processing helix chain 'D' and resid 146 through 158 Processing helix chain 'D' and resid 176 through 189 Processing helix chain 'D' and resid 192 through 194 No H-bonds generated for 'chain 'D' and resid 192 through 194' Processing helix chain 'D' and resid 201 through 204 Processing helix chain 'D' and resid 205 through 217 removed outlier: 4.541A pdb=" N MET D 212 " --> pdb=" O VAL D 208 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N VAL D 213 " --> pdb=" O GLN D 209 " (cutoff:3.500A) Processing helix chain 'D' and resid 246 through 252 removed outlier: 3.645A pdb=" N PHE D 250 " --> pdb=" O ARG D 246 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLU D 252 " --> pdb=" O GLY D 248 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 259 removed outlier: 4.375A pdb=" N ARG D 257 " --> pdb=" O PHE D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 262 through 273 Processing helix chain 'D' and resid 280 through 294 removed outlier: 3.602A pdb=" N CYS D 294 " --> pdb=" O LYS D 290 " (cutoff:3.500A) Processing helix chain 'D' and resid 299 through 301 No H-bonds generated for 'chain 'D' and resid 299 through 301' Processing helix chain 'D' and resid 315 through 320 removed outlier: 4.134A pdb=" N ALA D 318 " --> pdb=" O GLU D 315 " (cutoff:3.500A) Processing helix chain 'D' and resid 435 through 447 Processing helix chain 'D' and resid 454 through 476 Proline residue: D 467 - end of helix Processing helix chain 'D' and resid 489 through 500 removed outlier: 4.044A pdb=" N ASP D 493 " --> pdb=" O PRO D 489 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 105 through 109 removed outlier: 6.517A pdb=" N ARG A 136 " --> pdb=" O ARG A 166 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N ILE A 168 " --> pdb=" O ARG A 136 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N PHE A 138 " --> pdb=" O ILE A 168 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N TYR A 197 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N ILE A 167 " --> pdb=" O TYR A 197 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 480 through 483 removed outlier: 6.461A pdb=" N ALA A 367 " --> pdb=" O VAL A 394 " (cutoff:3.500A) removed outlier: 5.207A pdb=" N VAL A 400 " --> pdb=" O LEU A 422 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N VAL B 400 " --> pdb=" O LEU B 422 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N ALA B 367 " --> pdb=" O VAL B 394 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 105 through 109 removed outlier: 6.536A pdb=" N ARG B 136 " --> pdb=" O ARG B 166 " (cutoff:3.500A) removed outlier: 7.867A pdb=" N ILE B 168 " --> pdb=" O ARG B 136 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N PHE B 138 " --> pdb=" O ILE B 168 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N TYR B 197 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N ILE B 167 " --> pdb=" O TYR B 197 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N ILE B 199 " --> pdb=" O ILE B 167 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N VAL B 169 " --> pdb=" O ILE B 199 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N ARG B 198 " --> pdb=" O VAL B 453 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 105 through 109 removed outlier: 6.536A pdb=" N ARG C 136 " --> pdb=" O ARG C 166 " (cutoff:3.500A) removed outlier: 7.873A pdb=" N ILE C 168 " --> pdb=" O ARG C 136 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N PHE C 138 " --> pdb=" O ILE C 168 " (cutoff:3.500A) removed outlier: 7.982A pdb=" N TYR C 197 " --> pdb=" O ASN C 165 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N ILE C 167 " --> pdb=" O TYR C 197 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 480 through 483 removed outlier: 6.459A pdb=" N ALA C 367 " --> pdb=" O VAL C 394 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N VAL C 400 " --> pdb=" O LEU C 422 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N VAL D 400 " --> pdb=" O LEU D 422 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N ALA D 367 " --> pdb=" O VAL D 394 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 105 through 109 removed outlier: 6.529A pdb=" N ARG D 136 " --> pdb=" O ARG D 166 " (cutoff:3.500A) removed outlier: 7.873A pdb=" N ILE D 168 " --> pdb=" O ARG D 136 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N PHE D 138 " --> pdb=" O ILE D 168 " (cutoff:3.500A) removed outlier: 7.982A pdb=" N TYR D 197 " --> pdb=" O ASN D 165 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N ILE D 167 " --> pdb=" O TYR D 197 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N ILE D 199 " --> pdb=" O ILE D 167 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N VAL D 169 " --> pdb=" O ILE D 199 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N ARG D 198 " --> pdb=" O VAL D 453 " (cutoff:3.500A) 703 hydrogen bonds defined for protein. 2007 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.61 Time building geometry restraints manager: 4.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3566 1.33 - 1.45: 3622 1.45 - 1.57: 8868 1.57 - 1.69: 40 1.69 - 1.81: 132 Bond restraints: 16228 Sorted by residual: bond pdb=" O2B NAP B 602 " pdb=" P2B NAP B 602 " ideal model delta sigma weight residual 1.736 1.597 0.139 2.00e-02 2.50e+03 4.84e+01 bond pdb=" O2B NAP A 602 " pdb=" P2B NAP A 602 " ideal model delta sigma weight residual 1.736 1.597 0.139 2.00e-02 2.50e+03 4.80e+01 bond pdb=" O2B NAP D 602 " pdb=" P2B NAP D 602 " ideal model delta sigma weight residual 1.736 1.598 0.138 2.00e-02 2.50e+03 4.79e+01 bond pdb=" O2B NAP C 602 " pdb=" P2B NAP C 602 " ideal model delta sigma weight residual 1.736 1.598 0.138 2.00e-02 2.50e+03 4.79e+01 bond pdb=" O2B NAP B 601 " pdb=" P2B NAP B 601 " ideal model delta sigma weight residual 1.736 1.603 0.133 2.00e-02 2.50e+03 4.41e+01 ... (remaining 16223 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.84: 21317 1.84 - 3.69: 548 3.69 - 5.53: 119 5.53 - 7.38: 28 7.38 - 9.22: 16 Bond angle restraints: 22028 Sorted by residual: angle pdb=" N PHE C 138 " pdb=" CA PHE C 138 " pdb=" C PHE C 138 " ideal model delta sigma weight residual 108.20 113.47 -5.27 1.71e+00 3.42e-01 9.51e+00 angle pdb=" C2A NAP B 601 " pdb=" N3A NAP B 601 " pdb=" C4A NAP B 601 " ideal model delta sigma weight residual 111.82 121.04 -9.22 3.00e+00 1.11e-01 9.44e+00 angle pdb=" N PHE D 138 " pdb=" CA PHE D 138 " pdb=" C PHE D 138 " ideal model delta sigma weight residual 108.20 113.43 -5.23 1.71e+00 3.42e-01 9.35e+00 angle pdb=" C2A NAP D 601 " pdb=" N3A NAP D 601 " pdb=" C4A NAP D 601 " ideal model delta sigma weight residual 111.82 120.99 -9.17 3.00e+00 1.11e-01 9.35e+00 angle pdb=" C2A NAP A 601 " pdb=" N3A NAP A 601 " pdb=" C4A NAP A 601 " ideal model delta sigma weight residual 111.82 120.99 -9.17 3.00e+00 1.11e-01 9.33e+00 ... (remaining 22023 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 8315 17.92 - 35.84: 1111 35.84 - 53.76: 423 53.76 - 71.69: 121 71.69 - 89.61: 58 Dihedral angle restraints: 10028 sinusoidal: 4484 harmonic: 5544 Sorted by residual: dihedral pdb=" CA ARG A 348 " pdb=" C ARG A 348 " pdb=" N TRP A 349 " pdb=" CA TRP A 349 " ideal model delta harmonic sigma weight residual -180.00 -162.25 -17.75 0 5.00e+00 4.00e-02 1.26e+01 dihedral pdb=" CA ARG D 348 " pdb=" C ARG D 348 " pdb=" N TRP D 349 " pdb=" CA TRP D 349 " ideal model delta harmonic sigma weight residual -180.00 -162.29 -17.71 0 5.00e+00 4.00e-02 1.25e+01 dihedral pdb=" CA ARG C 348 " pdb=" C ARG C 348 " pdb=" N TRP C 349 " pdb=" CA TRP C 349 " ideal model delta harmonic sigma weight residual -180.00 -162.30 -17.70 0 5.00e+00 4.00e-02 1.25e+01 ... (remaining 10025 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1686 0.044 - 0.088: 466 0.088 - 0.133: 168 0.133 - 0.177: 16 0.177 - 0.221: 8 Chirality restraints: 2344 Sorted by residual: chirality pdb=" C1B NAP D 601 " pdb=" C2B NAP D 601 " pdb=" N9A NAP D 601 " pdb=" O4B NAP D 601 " both_signs ideal model delta sigma weight residual False 2.31 2.53 -0.22 2.00e-01 2.50e+01 1.22e+00 chirality pdb=" C1B NAP B 601 " pdb=" C2B NAP B 601 " pdb=" N9A NAP B 601 " pdb=" O4B NAP B 601 " both_signs ideal model delta sigma weight residual False 2.31 2.53 -0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" C1B NAP C 601 " pdb=" C2B NAP C 601 " pdb=" N9A NAP C 601 " pdb=" O4B NAP C 601 " both_signs ideal model delta sigma weight residual False 2.31 2.53 -0.22 2.00e-01 2.50e+01 1.20e+00 ... (remaining 2341 not shown) Planarity restraints: 2816 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO D 143 " 0.048 5.00e-02 4.00e+02 7.35e-02 8.64e+00 pdb=" N PRO D 144 " -0.127 5.00e-02 4.00e+02 pdb=" CA PRO D 144 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO D 144 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 143 " 0.048 5.00e-02 4.00e+02 7.30e-02 8.54e+00 pdb=" N PRO A 144 " -0.126 5.00e-02 4.00e+02 pdb=" CA PRO A 144 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 144 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO B 143 " -0.048 5.00e-02 4.00e+02 7.29e-02 8.51e+00 pdb=" N PRO B 144 " 0.126 5.00e-02 4.00e+02 pdb=" CA PRO B 144 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO B 144 " -0.040 5.00e-02 4.00e+02 ... (remaining 2813 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1669 2.75 - 3.29: 15381 3.29 - 3.83: 28851 3.83 - 4.36: 35352 4.36 - 4.90: 57211 Nonbonded interactions: 138464 Sorted by model distance: nonbonded pdb=" OH TYR B 139 " pdb=" OE2 GLU B 170 " model vdw 2.213 3.040 nonbonded pdb=" OH TYR B 202 " pdb=" NE2 GLN B 395 " model vdw 2.231 3.120 nonbonded pdb=" OH TYR D 202 " pdb=" NE2 GLN D 395 " model vdw 2.232 3.120 nonbonded pdb=" OH TYR C 202 " pdb=" NE2 GLN C 395 " model vdw 2.232 3.120 nonbonded pdb=" OH TYR A 202 " pdb=" NE2 GLN A 395 " model vdw 2.233 3.120 ... (remaining 138459 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' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.620 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 35.540 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:14.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 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 : 0.006 0.139 16228 Z= 0.413 Angle : 0.747 9.219 22028 Z= 0.347 Chirality : 0.047 0.221 2344 Planarity : 0.006 0.073 2816 Dihedral : 20.228 89.608 6460 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.32 % Allowed : 21.22 % Favored : 77.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.19), residues: 1888 helix: 0.81 (0.20), residues: 696 sheet: -0.37 (0.23), residues: 444 loop : 0.49 (0.23), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 164 HIS 0.004 0.001 HIS B 155 PHE 0.022 0.001 PHE C 88 TYR 0.020 0.002 TYR D 202 ARG 0.002 0.000 ARG C 246 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 204 time to evaluate : 1.888 Fit side-chains REVERT: B 66 PHE cc_start: 0.7894 (m-80) cc_final: 0.7677 (m-80) outliers start: 22 outliers final: 16 residues processed: 221 average time/residue: 1.4746 time to fit residues: 357.6554 Evaluate side-chains 216 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 200 time to evaluate : 1.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 TYR Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain B residue 202 TYR Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain C residue 202 TYR Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 340 VAL Chi-restraints excluded: chain D residue 202 TYR Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 298 VAL Chi-restraints excluded: chain D residue 340 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 158 optimal weight: 10.0000 chunk 142 optimal weight: 7.9990 chunk 79 optimal weight: 5.9990 chunk 48 optimal weight: 7.9990 chunk 96 optimal weight: 9.9990 chunk 76 optimal weight: 5.9990 chunk 147 optimal weight: 10.0000 chunk 57 optimal weight: 20.0000 chunk 89 optimal weight: 3.9990 chunk 109 optimal weight: 10.0000 chunk 170 optimal weight: 0.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 GLN A 185 ASN A 186 HIS B 185 ASN B 186 HIS C 185 ASN C 186 HIS D 185 ASN D 186 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.0781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 16228 Z= 0.292 Angle : 0.621 5.904 22028 Z= 0.332 Chirality : 0.047 0.146 2344 Planarity : 0.007 0.094 2816 Dihedral : 14.948 83.339 2656 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.10 % Allowed : 20.14 % Favored : 77.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.19), residues: 1888 helix: 0.67 (0.19), residues: 708 sheet: -0.52 (0.26), residues: 392 loop : 0.52 (0.22), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 164 HIS 0.004 0.001 HIS D 186 PHE 0.014 0.002 PHE A 88 TYR 0.019 0.002 TYR D 118 ARG 0.006 0.001 ARG A 487 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 212 time to evaluate : 1.816 Fit side-chains REVERT: A 58 ASP cc_start: 0.7469 (m-30) cc_final: 0.7229 (m-30) REVERT: A 102 PHE cc_start: 0.7346 (m-80) cc_final: 0.6923 (m-80) REVERT: A 404 MET cc_start: 0.8454 (OUTLIER) cc_final: 0.8193 (ppp) REVERT: A 476 LYS cc_start: 0.8670 (OUTLIER) cc_final: 0.8071 (mmtm) REVERT: B 66 PHE cc_start: 0.7992 (m-80) cc_final: 0.7787 (m-80) REVERT: B 102 PHE cc_start: 0.7310 (m-80) cc_final: 0.6966 (m-80) REVERT: B 178 GLN cc_start: 0.7703 (OUTLIER) cc_final: 0.7483 (mp-120) REVERT: B 404 MET cc_start: 0.8452 (OUTLIER) cc_final: 0.8190 (ppp) REVERT: B 411 MET cc_start: 0.4955 (OUTLIER) cc_final: 0.4124 (tmt) REVERT: C 66 PHE cc_start: 0.7999 (m-80) cc_final: 0.7795 (m-80) REVERT: C 102 PHE cc_start: 0.7284 (m-80) cc_final: 0.6900 (m-80) REVERT: C 404 MET cc_start: 0.8454 (OUTLIER) cc_final: 0.8192 (ppp) REVERT: C 411 MET cc_start: 0.4947 (OUTLIER) cc_final: 0.4075 (tmt) REVERT: D 102 PHE cc_start: 0.7354 (m-80) cc_final: 0.6924 (m-80) REVERT: D 404 MET cc_start: 0.8452 (OUTLIER) cc_final: 0.8190 (ppp) outliers start: 35 outliers final: 14 residues processed: 228 average time/residue: 1.5132 time to fit residues: 377.3061 Evaluate side-chains 216 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 194 time to evaluate : 1.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 404 MET Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 476 LYS Chi-restraints excluded: chain B residue 178 GLN Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 404 MET Chi-restraints excluded: chain B residue 411 MET Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 404 MET Chi-restraints excluded: chain C residue 411 MET Chi-restraints excluded: chain C residue 423 THR Chi-restraints excluded: chain D residue 132 SER Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 298 VAL Chi-restraints excluded: chain D residue 404 MET Chi-restraints excluded: chain D residue 423 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 94 optimal weight: 30.0000 chunk 52 optimal weight: 0.0050 chunk 142 optimal weight: 9.9990 chunk 116 optimal weight: 9.9990 chunk 47 optimal weight: 30.0000 chunk 171 optimal weight: 10.0000 chunk 184 optimal weight: 8.9990 chunk 152 optimal weight: 10.0000 chunk 169 optimal weight: 10.0000 chunk 58 optimal weight: 0.4980 chunk 137 optimal weight: 3.9990 overall best weight: 4.7000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 GLN B 133 GLN C 133 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.1037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 16228 Z= 0.274 Angle : 0.594 5.757 22028 Z= 0.318 Chirality : 0.046 0.144 2344 Planarity : 0.006 0.085 2816 Dihedral : 14.467 83.838 2644 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 3.30 % Allowed : 17.93 % Favored : 78.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.19), residues: 1888 helix: 0.78 (0.19), residues: 704 sheet: -0.58 (0.26), residues: 392 loop : 0.52 (0.22), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 164 HIS 0.003 0.001 HIS A 186 PHE 0.017 0.002 PHE A 88 TYR 0.019 0.002 TYR A 118 ARG 0.005 0.001 ARG D 487 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 208 time to evaluate : 1.858 Fit side-chains REVERT: A 64 ASN cc_start: 0.7658 (OUTLIER) cc_final: 0.6985 (m-40) REVERT: A 102 PHE cc_start: 0.7332 (m-80) cc_final: 0.6910 (m-80) REVERT: A 404 MET cc_start: 0.8447 (OUTLIER) cc_final: 0.8192 (ppp) REVERT: A 411 MET cc_start: 0.4990 (OUTLIER) cc_final: 0.4110 (tmt) REVERT: A 476 LYS cc_start: 0.8651 (OUTLIER) cc_final: 0.8049 (mmtm) REVERT: B 64 ASN cc_start: 0.7672 (OUTLIER) cc_final: 0.7031 (m-40) REVERT: B 102 PHE cc_start: 0.7358 (m-80) cc_final: 0.7021 (m-80) REVERT: B 404 MET cc_start: 0.8449 (OUTLIER) cc_final: 0.8197 (ppp) REVERT: B 411 MET cc_start: 0.5049 (OUTLIER) cc_final: 0.4136 (tmt) REVERT: C 64 ASN cc_start: 0.7655 (OUTLIER) cc_final: 0.7022 (m-40) REVERT: C 102 PHE cc_start: 0.7350 (m-80) cc_final: 0.7047 (m-80) REVERT: C 404 MET cc_start: 0.8447 (OUTLIER) cc_final: 0.8192 (ppp) REVERT: C 411 MET cc_start: 0.5041 (OUTLIER) cc_final: 0.4200 (tmt) REVERT: D 64 ASN cc_start: 0.7642 (OUTLIER) cc_final: 0.6969 (m-40) REVERT: D 102 PHE cc_start: 0.7300 (m-80) cc_final: 0.6885 (m-80) REVERT: D 404 MET cc_start: 0.8450 (OUTLIER) cc_final: 0.8197 (ppp) REVERT: D 411 MET cc_start: 0.4972 (OUTLIER) cc_final: 0.4102 (tmt) outliers start: 55 outliers final: 16 residues processed: 245 average time/residue: 1.5560 time to fit residues: 416.4194 Evaluate side-chains 222 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 193 time to evaluate : 1.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ASN Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 404 MET Chi-restraints excluded: chain A residue 411 MET Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 476 LYS Chi-restraints excluded: chain B residue 64 ASN Chi-restraints excluded: chain B residue 132 SER Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 404 MET Chi-restraints excluded: chain B residue 411 MET Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain C residue 64 ASN Chi-restraints excluded: chain C residue 132 SER Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 404 MET Chi-restraints excluded: chain C residue 411 MET Chi-restraints excluded: chain C residue 423 THR Chi-restraints excluded: chain D residue 64 ASN Chi-restraints excluded: chain D residue 132 SER Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 298 VAL Chi-restraints excluded: chain D residue 404 MET Chi-restraints excluded: chain D residue 411 MET Chi-restraints excluded: chain D residue 423 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 168 optimal weight: 9.9990 chunk 128 optimal weight: 8.9990 chunk 88 optimal weight: 7.9990 chunk 18 optimal weight: 0.0770 chunk 81 optimal weight: 10.0000 chunk 114 optimal weight: 4.9990 chunk 171 optimal weight: 20.0000 chunk 181 optimal weight: 6.9990 chunk 89 optimal weight: 5.9990 chunk 162 optimal weight: 2.9990 chunk 48 optimal weight: 5.9990 overall best weight: 4.0146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 GLN A 186 HIS B 133 GLN C 133 GLN C 178 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.1206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 16228 Z= 0.247 Angle : 0.576 5.510 22028 Z= 0.308 Chirality : 0.045 0.141 2344 Planarity : 0.006 0.074 2816 Dihedral : 14.143 83.120 2644 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 3.54 % Allowed : 18.05 % Favored : 78.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.19), residues: 1888 helix: 0.83 (0.19), residues: 708 sheet: -0.53 (0.26), residues: 388 loop : 0.50 (0.22), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 164 HIS 0.003 0.001 HIS A 186 PHE 0.018 0.002 PHE A 88 TYR 0.018 0.002 TYR B 118 ARG 0.004 0.000 ARG A 487 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 199 time to evaluate : 1.736 Fit side-chains REVERT: A 64 ASN cc_start: 0.7627 (OUTLIER) cc_final: 0.6957 (m-40) REVERT: A 404 MET cc_start: 0.8434 (OUTLIER) cc_final: 0.8184 (ppp) REVERT: A 411 MET cc_start: 0.5042 (OUTLIER) cc_final: 0.4128 (tmt) REVERT: A 476 LYS cc_start: 0.8637 (OUTLIER) cc_final: 0.8041 (mmtm) REVERT: B 64 ASN cc_start: 0.7654 (OUTLIER) cc_final: 0.7002 (m-40) REVERT: B 404 MET cc_start: 0.8428 (OUTLIER) cc_final: 0.8182 (ppp) REVERT: B 411 MET cc_start: 0.5089 (OUTLIER) cc_final: 0.4160 (tmt) REVERT: C 64 ASN cc_start: 0.7652 (OUTLIER) cc_final: 0.6997 (m-40) REVERT: C 102 PHE cc_start: 0.7337 (m-80) cc_final: 0.6976 (m-80) REVERT: C 404 MET cc_start: 0.8433 (OUTLIER) cc_final: 0.8188 (ppp) REVERT: C 411 MET cc_start: 0.5134 (OUTLIER) cc_final: 0.4274 (tmt) REVERT: D 64 ASN cc_start: 0.7612 (OUTLIER) cc_final: 0.6941 (m-40) REVERT: D 102 PHE cc_start: 0.7312 (m-80) cc_final: 0.6886 (m-80) REVERT: D 404 MET cc_start: 0.8431 (OUTLIER) cc_final: 0.8185 (ppp) REVERT: D 411 MET cc_start: 0.5025 (OUTLIER) cc_final: 0.4117 (tmt) outliers start: 59 outliers final: 16 residues processed: 238 average time/residue: 1.3919 time to fit residues: 364.4704 Evaluate side-chains 216 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 187 time to evaluate : 1.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ASN Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 404 MET Chi-restraints excluded: chain A residue 411 MET Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 476 LYS Chi-restraints excluded: chain B residue 64 ASN Chi-restraints excluded: chain B residue 132 SER Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 404 MET Chi-restraints excluded: chain B residue 411 MET Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain C residue 64 ASN Chi-restraints excluded: chain C residue 132 SER Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 404 MET Chi-restraints excluded: chain C residue 411 MET Chi-restraints excluded: chain C residue 423 THR Chi-restraints excluded: chain D residue 64 ASN Chi-restraints excluded: chain D residue 132 SER Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 298 VAL Chi-restraints excluded: chain D residue 404 MET Chi-restraints excluded: chain D residue 411 MET Chi-restraints excluded: chain D residue 423 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 151 optimal weight: 0.6980 chunk 103 optimal weight: 10.0000 chunk 2 optimal weight: 6.9990 chunk 135 optimal weight: 7.9990 chunk 74 optimal weight: 8.9990 chunk 155 optimal weight: 10.0000 chunk 125 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 chunk 92 optimal weight: 20.0000 chunk 163 optimal weight: 0.5980 chunk 45 optimal weight: 2.9990 overall best weight: 3.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 GLN A 186 HIS B 133 GLN B 178 GLN C 133 GLN C 186 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.1331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 16228 Z= 0.216 Angle : 0.552 5.305 22028 Z= 0.295 Chirality : 0.044 0.140 2344 Planarity : 0.005 0.058 2816 Dihedral : 13.517 81.365 2644 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 3.00 % Allowed : 18.65 % Favored : 78.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.19), residues: 1888 helix: 0.92 (0.20), residues: 708 sheet: -0.55 (0.26), residues: 388 loop : 0.52 (0.22), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 164 HIS 0.003 0.001 HIS A 186 PHE 0.019 0.001 PHE A 88 TYR 0.018 0.002 TYR A 118 ARG 0.003 0.000 ARG A 439 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 203 time to evaluate : 1.841 Fit side-chains REVERT: A 64 ASN cc_start: 0.7601 (OUTLIER) cc_final: 0.6925 (m-40) REVERT: A 411 MET cc_start: 0.5056 (OUTLIER) cc_final: 0.4125 (tmt) REVERT: A 476 LYS cc_start: 0.8623 (OUTLIER) cc_final: 0.8046 (mmtm) REVERT: B 64 ASN cc_start: 0.7621 (OUTLIER) cc_final: 0.6943 (m-40) REVERT: B 411 MET cc_start: 0.5126 (OUTLIER) cc_final: 0.4305 (tmt) REVERT: C 64 ASN cc_start: 0.7625 (OUTLIER) cc_final: 0.6952 (m-40) REVERT: C 411 MET cc_start: 0.5140 (OUTLIER) cc_final: 0.4280 (tmt) REVERT: D 64 ASN cc_start: 0.7587 (OUTLIER) cc_final: 0.6912 (m-40) REVERT: D 102 PHE cc_start: 0.7293 (m-80) cc_final: 0.6858 (m-80) REVERT: D 411 MET cc_start: 0.5045 (OUTLIER) cc_final: 0.4113 (tmt) outliers start: 50 outliers final: 14 residues processed: 233 average time/residue: 1.4113 time to fit residues: 361.5131 Evaluate side-chains 210 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 187 time to evaluate : 1.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ASN Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 411 MET Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 476 LYS Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain B residue 64 ASN Chi-restraints excluded: chain B residue 132 SER Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 411 MET Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain C residue 64 ASN Chi-restraints excluded: chain C residue 132 SER Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 411 MET Chi-restraints excluded: chain C residue 423 THR Chi-restraints excluded: chain D residue 64 ASN Chi-restraints excluded: chain D residue 132 SER Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 411 MET Chi-restraints excluded: chain D residue 423 THR Chi-restraints excluded: chain D residue 510 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 61 optimal weight: 10.0000 chunk 163 optimal weight: 10.0000 chunk 35 optimal weight: 20.0000 chunk 106 optimal weight: 5.9990 chunk 44 optimal weight: 6.9990 chunk 181 optimal weight: 5.9990 chunk 150 optimal weight: 10.0000 chunk 84 optimal weight: 8.9990 chunk 15 optimal weight: 5.9990 chunk 60 optimal weight: 6.9990 chunk 95 optimal weight: 7.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 GLN A 186 HIS B 133 GLN C 133 GLN C 155 HIS C 186 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.1406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 16228 Z= 0.347 Angle : 0.640 6.699 22028 Z= 0.341 Chirality : 0.047 0.135 2344 Planarity : 0.007 0.121 2816 Dihedral : 13.504 78.638 2640 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.70 % Allowed : 18.76 % Favored : 78.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.19), residues: 1888 helix: 0.73 (0.20), residues: 712 sheet: -0.46 (0.27), residues: 388 loop : 0.47 (0.22), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 164 HIS 0.003 0.001 HIS A 186 PHE 0.021 0.002 PHE A 88 TYR 0.023 0.002 TYR A 118 ARG 0.006 0.001 ARG D 487 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 193 time to evaluate : 1.832 Fit side-chains REVERT: A 57 ARG cc_start: 0.7428 (OUTLIER) cc_final: 0.7073 (tmm160) REVERT: A 64 ASN cc_start: 0.7633 (OUTLIER) cc_final: 0.6981 (m-40) REVERT: A 411 MET cc_start: 0.5221 (OUTLIER) cc_final: 0.4335 (tmt) REVERT: A 476 LYS cc_start: 0.8667 (OUTLIER) cc_final: 0.8060 (mmtm) REVERT: B 64 ASN cc_start: 0.7622 (OUTLIER) cc_final: 0.6963 (m-40) REVERT: B 411 MET cc_start: 0.5212 (OUTLIER) cc_final: 0.4348 (tmt) REVERT: C 57 ARG cc_start: 0.7413 (OUTLIER) cc_final: 0.7070 (tmm160) REVERT: C 64 ASN cc_start: 0.7599 (OUTLIER) cc_final: 0.6934 (m-40) REVERT: C 102 PHE cc_start: 0.7354 (m-80) cc_final: 0.6899 (m-80) REVERT: C 411 MET cc_start: 0.5226 (OUTLIER) cc_final: 0.4322 (tmt) REVERT: D 57 ARG cc_start: 0.7357 (OUTLIER) cc_final: 0.7063 (tmm160) REVERT: D 64 ASN cc_start: 0.7616 (OUTLIER) cc_final: 0.6966 (m-40) REVERT: D 102 PHE cc_start: 0.7292 (m-80) cc_final: 0.6803 (m-80) REVERT: D 411 MET cc_start: 0.5196 (OUTLIER) cc_final: 0.4313 (tmt) outliers start: 45 outliers final: 20 residues processed: 229 average time/residue: 1.4846 time to fit residues: 373.0048 Evaluate side-chains 212 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 180 time to evaluate : 1.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ARG Chi-restraints excluded: chain A residue 64 ASN Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 411 MET Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 476 LYS Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain B residue 64 ASN Chi-restraints excluded: chain B residue 132 SER Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 411 MET Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain C residue 57 ARG Chi-restraints excluded: chain C residue 64 ASN Chi-restraints excluded: chain C residue 132 SER Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 411 MET Chi-restraints excluded: chain C residue 423 THR Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain D residue 57 ARG Chi-restraints excluded: chain D residue 64 ASN Chi-restraints excluded: chain D residue 132 SER Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 298 VAL Chi-restraints excluded: chain D residue 411 MET Chi-restraints excluded: chain D residue 423 THR Chi-restraints excluded: chain D residue 510 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 175 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 103 optimal weight: 6.9990 chunk 132 optimal weight: 10.0000 chunk 102 optimal weight: 6.9990 chunk 153 optimal weight: 10.0000 chunk 101 optimal weight: 10.0000 chunk 181 optimal weight: 5.9990 chunk 113 optimal weight: 0.5980 chunk 110 optimal weight: 3.9990 chunk 83 optimal weight: 0.7980 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 GLN A 186 HIS B 133 GLN C 133 GLN C 186 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.1452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 16228 Z= 0.180 Angle : 0.539 8.237 22028 Z= 0.286 Chirality : 0.043 0.141 2344 Planarity : 0.004 0.038 2816 Dihedral : 12.558 73.891 2640 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 2.82 % Allowed : 18.76 % Favored : 78.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.19), residues: 1888 helix: 0.98 (0.20), residues: 708 sheet: -0.58 (0.26), residues: 388 loop : 0.52 (0.22), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 164 HIS 0.003 0.001 HIS A 186 PHE 0.019 0.001 PHE A 88 TYR 0.016 0.001 TYR A 118 ARG 0.003 0.000 ARG B 439 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 202 time to evaluate : 1.912 Fit side-chains REVERT: A 64 ASN cc_start: 0.7608 (OUTLIER) cc_final: 0.6943 (m-40) REVERT: A 476 LYS cc_start: 0.8653 (OUTLIER) cc_final: 0.8034 (mmtm) REVERT: B 64 ASN cc_start: 0.7584 (OUTLIER) cc_final: 0.6903 (m-40) REVERT: B 102 PHE cc_start: 0.7284 (m-80) cc_final: 0.6863 (m-80) REVERT: B 205 LYS cc_start: 0.8152 (OUTLIER) cc_final: 0.7717 (mttm) REVERT: B 411 MET cc_start: 0.5114 (OUTLIER) cc_final: 0.4282 (tmt) REVERT: C 64 ASN cc_start: 0.7613 (OUTLIER) cc_final: 0.6932 (m-40) REVERT: C 411 MET cc_start: 0.5079 (OUTLIER) cc_final: 0.4202 (tmt) REVERT: D 64 ASN cc_start: 0.7593 (OUTLIER) cc_final: 0.6930 (m-40) REVERT: D 102 PHE cc_start: 0.7217 (m-80) cc_final: 0.6781 (m-80) REVERT: D 205 LYS cc_start: 0.8160 (OUTLIER) cc_final: 0.7728 (mttm) outliers start: 47 outliers final: 16 residues processed: 233 average time/residue: 1.4192 time to fit residues: 363.7559 Evaluate side-chains 215 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 190 time to evaluate : 1.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ASN Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 476 LYS Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain B residue 64 ASN Chi-restraints excluded: chain B residue 132 SER Chi-restraints excluded: chain B residue 205 LYS Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 411 MET Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain C residue 64 ASN Chi-restraints excluded: chain C residue 132 SER Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 411 MET Chi-restraints excluded: chain C residue 423 THR Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain D residue 64 ASN Chi-restraints excluded: chain D residue 132 SER Chi-restraints excluded: chain D residue 205 LYS Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 423 THR Chi-restraints excluded: chain D residue 510 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 112 optimal weight: 0.9980 chunk 72 optimal weight: 8.9990 chunk 108 optimal weight: 7.9990 chunk 54 optimal weight: 30.0000 chunk 35 optimal weight: 4.9990 chunk 115 optimal weight: 9.9990 chunk 123 optimal weight: 0.4980 chunk 89 optimal weight: 10.0000 chunk 16 optimal weight: 3.9990 chunk 142 optimal weight: 20.0000 chunk 164 optimal weight: 0.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 GLN ** A 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 133 GLN C 133 GLN ** C 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.1532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 16228 Z= 0.181 Angle : 0.539 7.188 22028 Z= 0.285 Chirality : 0.043 0.144 2344 Planarity : 0.005 0.045 2816 Dihedral : 12.069 66.541 2640 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.22 % Allowed : 19.30 % Favored : 78.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.19), residues: 1888 helix: 1.01 (0.20), residues: 704 sheet: -0.66 (0.26), residues: 396 loop : 0.54 (0.22), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 164 HIS 0.003 0.001 HIS C 186 PHE 0.018 0.001 PHE A 88 TYR 0.020 0.001 TYR C 118 ARG 0.006 0.000 ARG D 175 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 195 time to evaluate : 1.895 Fit side-chains REVERT: A 476 LYS cc_start: 0.8645 (OUTLIER) cc_final: 0.8056 (mmtm) REVERT: B 64 ASN cc_start: 0.7550 (OUTLIER) cc_final: 0.6861 (m-40) REVERT: B 205 LYS cc_start: 0.8152 (OUTLIER) cc_final: 0.7716 (mttm) REVERT: B 411 MET cc_start: 0.5060 (OUTLIER) cc_final: 0.4252 (tmt) REVERT: C 64 ASN cc_start: 0.7546 (OUTLIER) cc_final: 0.6857 (m-40) REVERT: C 411 MET cc_start: 0.5078 (OUTLIER) cc_final: 0.4216 (tmt) REVERT: D 102 PHE cc_start: 0.7222 (m-80) cc_final: 0.6755 (m-80) REVERT: D 205 LYS cc_start: 0.8154 (OUTLIER) cc_final: 0.7720 (mttm) outliers start: 37 outliers final: 11 residues processed: 220 average time/residue: 1.4686 time to fit residues: 354.3697 Evaluate side-chains 210 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 192 time to evaluate : 1.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 476 LYS Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain B residue 64 ASN Chi-restraints excluded: chain B residue 132 SER Chi-restraints excluded: chain B residue 205 LYS Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 411 MET Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain C residue 64 ASN Chi-restraints excluded: chain C residue 132 SER Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 411 MET Chi-restraints excluded: chain D residue 132 SER Chi-restraints excluded: chain D residue 205 LYS Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 510 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 173 optimal weight: 5.9990 chunk 158 optimal weight: 2.9990 chunk 168 optimal weight: 0.6980 chunk 101 optimal weight: 30.0000 chunk 73 optimal weight: 9.9990 chunk 132 optimal weight: 0.0770 chunk 51 optimal weight: 6.9990 chunk 152 optimal weight: 0.9990 chunk 159 optimal weight: 6.9990 chunk 110 optimal weight: 5.9990 chunk 178 optimal weight: 9.9990 overall best weight: 2.1544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 GLN A 186 HIS B 133 GLN B 155 HIS C 133 GLN ** C 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.1579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 16228 Z= 0.173 Angle : 0.530 7.023 22028 Z= 0.280 Chirality : 0.043 0.145 2344 Planarity : 0.004 0.037 2816 Dihedral : 11.470 59.362 2640 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Rotamer: Outliers : 1.68 % Allowed : 19.36 % Favored : 78.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.19), residues: 1888 helix: 1.08 (0.20), residues: 704 sheet: -0.56 (0.26), residues: 404 loop : 0.53 (0.22), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 164 HIS 0.003 0.001 HIS C 186 PHE 0.016 0.001 PHE A 88 TYR 0.015 0.001 TYR C 118 ARG 0.006 0.000 ARG D 175 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 199 time to evaluate : 1.895 Fit side-chains REVERT: B 205 LYS cc_start: 0.8147 (OUTLIER) cc_final: 0.7711 (mttm) REVERT: D 102 PHE cc_start: 0.7243 (m-80) cc_final: 0.6758 (m-80) REVERT: D 205 LYS cc_start: 0.8158 (OUTLIER) cc_final: 0.7723 (mttm) outliers start: 28 outliers final: 12 residues processed: 221 average time/residue: 1.4663 time to fit residues: 356.6136 Evaluate side-chains 203 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 189 time to evaluate : 1.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain B residue 132 SER Chi-restraints excluded: chain B residue 205 LYS Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain C residue 132 SER Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain D residue 132 SER Chi-restraints excluded: chain D residue 205 LYS Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 510 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 108 optimal weight: 10.0000 chunk 84 optimal weight: 9.9990 chunk 124 optimal weight: 7.9990 chunk 187 optimal weight: 10.0000 chunk 172 optimal weight: 6.9990 chunk 149 optimal weight: 0.0030 chunk 15 optimal weight: 10.0000 chunk 115 optimal weight: 0.0020 chunk 91 optimal weight: 7.9990 chunk 118 optimal weight: 9.9990 chunk 158 optimal weight: 0.8980 overall best weight: 3.1802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 GLN ** A 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 133 GLN C 133 GLN C 186 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.1579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16228 Z= 0.214 Angle : 0.562 7.007 22028 Z= 0.296 Chirality : 0.044 0.139 2344 Planarity : 0.005 0.060 2816 Dihedral : 11.548 59.373 2640 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 1.02 % Allowed : 20.14 % Favored : 78.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.19), residues: 1888 helix: 0.95 (0.20), residues: 708 sheet: -0.52 (0.27), residues: 388 loop : 0.51 (0.22), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 164 HIS 0.003 0.001 HIS A 186 PHE 0.018 0.001 PHE A 88 TYR 0.016 0.002 TYR A 118 ARG 0.006 0.000 ARG D 175 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 194 time to evaluate : 1.922 Fit side-chains REVERT: B 205 LYS cc_start: 0.8169 (OUTLIER) cc_final: 0.7736 (mttm) REVERT: D 102 PHE cc_start: 0.7230 (m-80) cc_final: 0.6753 (m-80) REVERT: D 205 LYS cc_start: 0.8183 (OUTLIER) cc_final: 0.7758 (mttm) outliers start: 17 outliers final: 12 residues processed: 210 average time/residue: 1.5098 time to fit residues: 348.5760 Evaluate side-chains 204 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 190 time to evaluate : 1.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain B residue 132 SER Chi-restraints excluded: chain B residue 205 LYS Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain C residue 132 SER Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain D residue 132 SER Chi-restraints excluded: chain D residue 205 LYS Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 510 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 45 optimal weight: 0.9980 chunk 137 optimal weight: 7.9990 chunk 22 optimal weight: 20.0000 chunk 41 optimal weight: 6.9990 chunk 149 optimal weight: 8.9990 chunk 62 optimal weight: 7.9990 chunk 153 optimal weight: 10.0000 chunk 18 optimal weight: 0.9990 chunk 27 optimal weight: 0.9990 chunk 131 optimal weight: 7.9990 chunk 8 optimal weight: 10.0000 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 GLN ** A 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 133 GLN C 133 GLN ** C 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.175479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.135135 restraints weight = 13298.246| |-----------------------------------------------------------------------------| r_work (start): 0.3511 rms_B_bonded: 1.74 r_work: 0.3152 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3026 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8728 moved from start: 0.1569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 16228 Z= 0.230 Angle : 0.571 6.889 22028 Z= 0.302 Chirality : 0.044 0.142 2344 Planarity : 0.005 0.068 2816 Dihedral : 11.616 59.449 2640 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 1.20 % Allowed : 19.78 % Favored : 79.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.19), residues: 1888 helix: 0.94 (0.20), residues: 708 sheet: -0.50 (0.27), residues: 388 loop : 0.51 (0.22), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 164 HIS 0.004 0.001 HIS C 186 PHE 0.020 0.002 PHE A 88 TYR 0.016 0.002 TYR B 118 ARG 0.006 0.000 ARG D 175 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5958.44 seconds wall clock time: 108 minutes 20.49 seconds (6500.49 seconds total)