Starting phenix.real_space_refine on Thu Jul 2 13:36:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9md1_48164/07_2026/9md1_48164_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9md1_48164/07_2026/9md1_48164.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.03 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9md1_48164/07_2026/9md1_48164_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9md1_48164/07_2026/9md1_48164_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9md1_48164/07_2026/9md1_48164.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9md1_48164/07_2026/9md1_48164.map" } resolution = 3.03 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.032 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 4 5.49 5 S 63 5.16 5 C 5572 2.51 5 N 1375 2.21 5 O 1493 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8507 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 948 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'TRANS': 119} Chain breaks: 4 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 31 Planarities with less than four sites: {'ARG:plan': 4, 'GLN:plan1': 1, 'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 35 Chain: "B" Number of atoms: 2444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2444 Classifications: {'peptide': 321} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 315} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "C" Number of atoms: 2197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2197 Classifications: {'peptide': 280} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 12, 'TRANS': 267} Chain breaks: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'TYR:plan': 1, 'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "G" Number of atoms: 327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 327 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 4, 'TRANS': 38} Chain: "R" Number of atoms: 2197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2197 Classifications: {'peptide': 280} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 12, 'TRANS': 267} Chain breaks: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'TYR:plan': 1, 'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "C" Number of atoms: 197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 197 Unusual residues: {'CLR': 4, 'J40': 1, 'YLX': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "R" Number of atoms: 197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 197 Unusual residues: {'CLR': 4, 'J40': 1, 'YLX': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Time building chain proxies: 1.60, per 1000 atoms: 0.19 Number of scatterers: 8507 At special positions: 0 Unit cell: (92.055, 100.719, 152.703, 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 63 16.00 P 4 15.00 O 1493 8.00 N 1375 7.00 C 5572 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS C 109 " - pdb=" SG CYS C 187 " distance=2.05 Simple disulfide: pdb=" SG CYS R 109 " - pdb=" SG CYS R 187 " distance=2.05 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: 0.49 Conformation dependent library (CDL) restraints added in 350.9 milliseconds 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1976 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 8 sheets defined 55.1% alpha, 14.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'A' and resid 6 through 32 removed outlier: 4.273A pdb=" N ARG A 32 " --> pdb=" O GLN A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 352 removed outlier: 3.522A pdb=" N TYR A 351 " --> pdb=" O ASN A 347 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ILE A 352 " --> pdb=" O ASN A 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 16 through 26 removed outlier: 3.657A pdb=" N ARG B 22 " --> pdb=" O ILE B 18 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N LYS B 23 " --> pdb=" O ARG B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'C' and resid 36 through 64 removed outlier: 4.074A pdb=" N ALA C 55 " --> pdb=" O VAL C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 69 through 89 Processing helix chain 'C' and resid 89 through 100 Processing helix chain 'C' and resid 105 through 140 removed outlier: 3.528A pdb=" N SER C 123 " --> pdb=" O CYS C 119 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE C 124 " --> pdb=" O CYS C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 140 through 147 removed outlier: 3.513A pdb=" N TYR C 144 " --> pdb=" O ASP C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 149 through 167 removed outlier: 3.821A pdb=" N ALA C 153 " --> pdb=" O THR C 149 " (cutoff:3.500A) Processing helix chain 'C' and resid 169 through 173 Processing helix chain 'C' and resid 192 through 204 Processing helix chain 'C' and resid 204 through 228 Processing helix chain 'C' and resid 331 through 368 removed outlier: 3.611A pdb=" N THR C 346 " --> pdb=" O LYS C 342 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N LEU C 347 " --> pdb=" O THR C 343 " (cutoff:3.500A) Proline residue: C 360 - end of helix Processing helix chain 'C' and resid 369 through 371 No H-bonds generated for 'chain 'C' and resid 369 through 371' Processing helix chain 'C' and resid 378 through 391 Processing helix chain 'C' and resid 391 through 401 Proline residue: C 397 - end of helix Processing helix chain 'C' and resid 404 through 415 Processing helix chain 'G' and resid 20 through 25 Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.517A pdb=" N ALA G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 48 Processing helix chain 'R' and resid 36 through 63 removed outlier: 3.767A pdb=" N ALA R 55 " --> pdb=" O VAL R 51 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL R 58 " --> pdb=" O ASN R 54 " (cutoff:3.500A) Processing helix chain 'R' and resid 69 through 89 removed outlier: 3.706A pdb=" N LEU R 74 " --> pdb=" O VAL R 70 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE R 75 " --> pdb=" O ALA R 71 " (cutoff:3.500A) Processing helix chain 'R' and resid 89 through 100 removed outlier: 3.530A pdb=" N LEU R 95 " --> pdb=" O PRO R 91 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N TYR R 96 " --> pdb=" O MET R 92 " (cutoff:3.500A) Processing helix chain 'R' and resid 105 through 140 removed outlier: 3.655A pdb=" N ILE R 138 " --> pdb=" O ARG R 134 " (cutoff:3.500A) Processing helix chain 'R' and resid 140 through 147 Processing helix chain 'R' and resid 149 through 168 removed outlier: 3.898A pdb=" N ALA R 153 " --> pdb=" O THR R 149 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ILE R 167 " --> pdb=" O ILE R 163 " (cutoff:3.500A) Processing helix chain 'R' and resid 192 through 204 Processing helix chain 'R' and resid 204 through 228 Processing helix chain 'R' and resid 331 through 338 Processing helix chain 'R' and resid 344 through 368 Proline residue: R 360 - end of helix Processing helix chain 'R' and resid 369 through 371 No H-bonds generated for 'chain 'R' and resid 369 through 371' Processing helix chain 'R' and resid 378 through 391 removed outlier: 3.839A pdb=" N ASN R 386 " --> pdb=" O GLY R 382 " (cutoff:3.500A) Processing helix chain 'R' and resid 391 through 401 Proline residue: R 397 - end of helix Processing helix chain 'R' and resid 404 through 415 removed outlier: 3.808A pdb=" N LYS R 412 " --> pdb=" O GLN R 408 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 186 through 191 removed outlier: 6.295A pdb=" N ILE A 34 " --> pdb=" O LYS A 198 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N VAL A 200 " --> pdb=" O ILE A 34 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N LEU A 36 " --> pdb=" O VAL A 200 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ALA A 221 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU A 37 " --> pdb=" O ALA A 221 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N ILE A 222 " --> pdb=" O ILE A 266 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N PHE A 268 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N PHE A 224 " --> pdb=" O PHE A 268 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N ASN A 270 " --> pdb=" O PHE A 224 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N VAL A 226 " --> pdb=" O ASN A 270 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N LEU A 269 " --> pdb=" O HIS A 323 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 49 through 52 removed outlier: 3.665A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ILE B 338 " --> pdb=" O ARG B 49 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N SER B 331 " --> pdb=" O PHE B 335 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.653A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 102 through 105 removed outlier: 3.766A pdb=" N GLY B 115 " --> pdb=" O THR B 102 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ALA B 113 " --> pdb=" O ALA B 104 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.928A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.228A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU B 168 " --> pdb=" O THR B 178 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 189 through 192 removed outlier: 6.751A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.332A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 4.338A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) 483 hydrogen bonds defined for protein. 1422 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: 0.95 Time building geometry restraints manager: 0.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1453 1.32 - 1.45: 2147 1.45 - 1.57: 5011 1.57 - 1.70: 7 1.70 - 1.82: 87 Bond restraints: 8705 Sorted by residual: bond pdb=" N LEU R 368 " pdb=" CA LEU R 368 " ideal model delta sigma weight residual 1.461 1.496 -0.035 9.20e-03 1.18e+04 1.44e+01 bond pdb=" C ARG A 21 " pdb=" O ARG A 21 " ideal model delta sigma weight residual 1.236 1.280 -0.043 1.15e-02 7.56e+03 1.40e+01 bond pdb=" C4 YLX R 501 " pdb=" C5 YLX R 501 " ideal model delta sigma weight residual 1.546 1.472 0.074 2.00e-02 2.50e+03 1.36e+01 bond pdb=" N LYS R 147 " pdb=" CA LYS R 147 " ideal model delta sigma weight residual 1.459 1.493 -0.034 9.10e-03 1.21e+04 1.36e+01 bond pdb=" N ILE B 93 " pdb=" CA ILE B 93 " ideal model delta sigma weight residual 1.461 1.494 -0.034 9.10e-03 1.21e+04 1.36e+01 ... (remaining 8700 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.23: 11564 3.23 - 6.46: 291 6.46 - 9.69: 7 9.69 - 12.92: 2 12.92 - 16.15: 2 Bond angle restraints: 11866 Sorted by residual: angle pdb=" O1 J40 C 506 " pdb=" P1 J40 C 506 " pdb=" O13 J40 C 506 " ideal model delta sigma weight residual 92.86 109.01 -16.15 3.00e+00 1.11e-01 2.90e+01 angle pdb=" O1 J40 R 506 " pdb=" P1 J40 R 506 " pdb=" O13 J40 R 506 " ideal model delta sigma weight residual 92.86 108.89 -16.03 3.00e+00 1.11e-01 2.86e+01 angle pdb=" CA GLY R 164 " pdb=" C GLY R 164 " pdb=" O GLY R 164 " ideal model delta sigma weight residual 120.90 115.22 5.68 1.12e+00 7.97e-01 2.58e+01 angle pdb=" N CYS A 215 " pdb=" CA CYS A 215 " pdb=" C CYS A 215 " ideal model delta sigma weight residual 111.82 106.43 5.39 1.16e+00 7.43e-01 2.16e+01 angle pdb=" N PRO C 170 " pdb=" CA PRO C 170 " pdb=" C PRO C 170 " ideal model delta sigma weight residual 110.70 116.24 -5.54 1.22e+00 6.72e-01 2.06e+01 ... (remaining 11861 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.13: 5420 24.13 - 48.26: 195 48.26 - 72.39: 31 72.39 - 96.52: 3 96.52 - 120.65: 8 Dihedral angle restraints: 5657 sinusoidal: 2616 harmonic: 3041 Sorted by residual: dihedral pdb=" CB CYS R 109 " pdb=" SG CYS R 109 " pdb=" SG CYS R 187 " pdb=" CB CYS R 187 " ideal model delta sinusoidal sigma weight residual 93.00 156.95 -63.95 1 1.00e+01 1.00e-02 5.38e+01 dihedral pdb=" CA TRP B 169 " pdb=" C TRP B 169 " pdb=" N ASP B 170 " pdb=" CA ASP B 170 " ideal model delta harmonic sigma weight residual 180.00 158.91 21.09 0 5.00e+00 4.00e-02 1.78e+01 dihedral pdb=" SG CYS R 109 " pdb=" CB CYS R 187 " pdb=" SG CYS R 187 " pdb=" CA CYS R 187 " ideal model delta sinusoidal sigma weight residual -73.00 -1.34 -71.66 1 2.00e+01 2.50e-03 1.64e+01 ... (remaining 5654 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 705 0.056 - 0.111: 434 0.111 - 0.166: 211 0.166 - 0.222: 57 0.222 - 0.277: 4 Chirality restraints: 1411 Sorted by residual: chirality pdb=" CA VAL B 327 " pdb=" N VAL B 327 " pdb=" C VAL B 327 " pdb=" CB VAL B 327 " both_signs ideal model delta sigma weight residual False 2.44 2.72 -0.28 2.00e-01 2.50e+01 1.92e+00 chirality pdb=" CA ILE B 58 " pdb=" N ILE B 58 " pdb=" C ILE B 58 " pdb=" CB ILE B 58 " both_signs ideal model delta sigma weight residual False 2.43 2.69 -0.25 2.00e-01 2.50e+01 1.59e+00 chirality pdb=" CA ILE B 81 " pdb=" N ILE B 81 " pdb=" C ILE B 81 " pdb=" CB ILE B 81 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.24 2.00e-01 2.50e+01 1.44e+00 ... (remaining 1408 not shown) Planarity restraints: 1409 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" N YLX C 501 " 0.024 2.00e-02 2.50e+03 7.47e-02 8.37e+01 pdb=" C YLX C 501 " 0.011 2.00e-02 2.50e+03 pdb=" O YLX C 501 " -0.102 2.00e-02 2.50e+03 pdb=" C1 YLX C 501 " 0.082 2.00e-02 2.50e+03 pdb=" C8 YLX C 501 " -0.096 2.00e-02 2.50e+03 pdb=" C9 YLX C 501 " 0.081 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C15 YLX C 501 " 0.024 2.00e-02 2.50e+03 2.63e-02 1.21e+01 pdb=" C16 YLX C 501 " 0.002 2.00e-02 2.50e+03 pdb=" C17 YLX C 501 " -0.031 2.00e-02 2.50e+03 pdb=" C18 YLX C 501 " -0.005 2.00e-02 2.50e+03 pdb=" N2 YLX C 501 " -0.043 2.00e-02 2.50e+03 pdb=" N3 YLX C 501 " 0.023 2.00e-02 2.50e+03 pdb=" N4 YLX C 501 " 0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE R 130 " 0.013 2.00e-02 2.50e+03 2.59e-02 6.71e+00 pdb=" C ILE R 130 " -0.045 2.00e-02 2.50e+03 pdb=" O ILE R 130 " 0.017 2.00e-02 2.50e+03 pdb=" N ALA R 131 " 0.015 2.00e-02 2.50e+03 ... (remaining 1406 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.83: 2247 2.83 - 3.35: 7969 3.35 - 3.87: 13439 3.87 - 4.38: 15874 4.38 - 4.90: 26375 Nonbonded interactions: 65904 Sorted by model distance: nonbonded pdb=" O13 J40 C 506 " pdb=" O2 J40 C 506 " model vdw 2.316 3.040 nonbonded pdb=" OH TYR B 264 " pdb=" O ALA B 299 " model vdw 2.323 3.040 nonbonded pdb=" O13 J40 R 506 " pdb=" O2 J40 R 506 " model vdw 2.371 3.040 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.393 3.040 nonbonded pdb=" O ASP B 333 " pdb=" OG SER B 334 " model vdw 2.446 3.040 ... (remaining 65899 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 'C' selection = chain 'R' } 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: 1.010 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: 0.000 Extract box with map and model: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 7.420 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.010 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:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5368 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 : 0.011 0.074 8707 Z= 0.834 Angle : 1.345 16.154 11870 Z= 0.984 Chirality : 0.083 0.277 1411 Planarity : 0.005 0.075 1409 Dihedral : 13.332 120.650 3675 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.82 (0.25), residues: 1020 helix: -0.24 (0.22), residues: 537 sheet: -0.74 (0.40), residues: 165 loop : -3.07 (0.29), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 251 TYR 0.018 0.002 TYR C 390 PHE 0.012 0.002 PHE B 241 TRP 0.030 0.003 TRP B 82 HIS 0.005 0.001 HIS C 126 Details of bonding type rmsd/Z covalent geometry : bond 0.01138 / 0.83 ( 8705) covalent geometry : angle 1.34478 / 0.98 (11866) SS BOND : bond 0.01436 / 0.72 ( 2) SS BOND : angle 1.61178 / 0.76 ( 4) hydrogen bonds : bond 0.21846 / 14.45 ( 483) hydrogen bonds : angle 7.85658 / 5.45 ( 1422) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 115 time to evaluate : 0.290 Fit side-chains revert: symmetry clash REVERT: B 188 MET cc_start: 0.5518 (mtt) cc_final: 0.5076 (mtt) REVERT: B 323 ASP cc_start: 0.7274 (p0) cc_final: 0.6797 (p0) REVERT: C 335 MET cc_start: 0.3269 (mmt) cc_final: 0.2979 (mmt) outliers start: 0 outliers final: 0 residues processed: 115 average time/residue: 0.0750 time to fit residues: 12.1371 Evaluate side-chains 83 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 49 optimal weight: 0.5980 chunk 97 optimal weight: 0.5980 chunk 53 optimal weight: 0.5980 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 0.5980 chunk 51 optimal weight: 0.1980 chunk 100 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 126 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.196811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.120605 restraints weight = 8760.287| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 2.33 r_work: 0.3018 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2864 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7347 moved from start: 0.1886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8707 Z= 0.135 Angle : 0.606 11.601 11870 Z= 0.307 Chirality : 0.041 0.202 1411 Planarity : 0.004 0.045 1409 Dihedral : 9.867 89.339 1872 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.49 % Allowed : 7.89 % Favored : 90.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.27), residues: 1020 helix: 1.35 (0.23), residues: 554 sheet: -0.57 (0.38), residues: 183 loop : -2.45 (0.33), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 225 TYR 0.018 0.001 TYR C 198 PHE 0.017 0.001 PHE R 165 TRP 0.024 0.002 TRP B 211 HIS 0.005 0.001 HIS R 193 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.14 ( 8705) covalent geometry : angle 0.60623 / 0.31 (11866) SS BOND : bond 0.00147 / 0.07 ( 2) SS BOND : angle 0.70205 / 0.36 ( 4) hydrogen bonds : bond 0.05528 / 3.62 ( 483) hydrogen bonds : angle 4.74594 / 3.36 ( 1422) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 106 time to evaluate : 0.278 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 63 TRP cc_start: 0.8447 (m100) cc_final: 0.8067 (m100) REVERT: B 105 TYR cc_start: 0.8434 (t80) cc_final: 0.8091 (t80) REVERT: B 188 MET cc_start: 0.5083 (mtt) cc_final: 0.4743 (mtt) REVERT: C 176 ARG cc_start: 0.8591 (mtp85) cc_final: 0.8280 (mtp85) REVERT: C 335 MET cc_start: 0.4329 (mmt) cc_final: 0.3833 (mmt) REVERT: R 133 ASP cc_start: 0.8089 (t0) cc_final: 0.7829 (t0) REVERT: R 341 ARG cc_start: 0.7499 (mtt180) cc_final: 0.6754 (ttp-170) outliers start: 13 outliers final: 6 residues processed: 113 average time/residue: 0.1051 time to fit residues: 15.3242 Evaluate side-chains 94 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 88 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 108 SER Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain G residue 38 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 5 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 35 optimal weight: 20.0000 chunk 78 optimal weight: 0.6980 chunk 51 optimal weight: 0.5980 chunk 88 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 28 optimal weight: 9.9990 chunk 29 optimal weight: 0.3980 chunk 82 optimal weight: 1.9990 chunk 103 optimal weight: 0.7980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.183342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.105488 restraints weight = 8932.518| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 2.85 r_work: 0.2927 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2775 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 moved from start: 0.2690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8707 Z= 0.130 Angle : 0.548 7.705 11870 Z= 0.281 Chirality : 0.041 0.205 1411 Planarity : 0.004 0.048 1409 Dihedral : 9.509 89.213 1872 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.49 % Allowed : 9.37 % Favored : 89.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.27), residues: 1020 helix: 2.05 (0.23), residues: 541 sheet: -0.22 (0.39), residues: 181 loop : -2.54 (0.32), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 227 TYR 0.018 0.002 TYR C 198 PHE 0.012 0.001 PHE B 253 TRP 0.018 0.002 TRP B 211 HIS 0.002 0.001 HIS R 126 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 ( 8705) covalent geometry : angle 0.54835 / 0.28 (11866) SS BOND : bond 0.00012 / 0.01 ( 2) SS BOND : angle 0.45320 / 0.24 ( 4) hydrogen bonds : bond 0.05288 / 3.44 ( 483) hydrogen bonds : angle 4.31052 / 3.08 ( 1422) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 103 time to evaluate : 0.279 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 199 MET cc_start: 0.7506 (mtm) cc_final: 0.7087 (mpp) REVERT: B 105 TYR cc_start: 0.8526 (t80) cc_final: 0.8185 (t80) REVERT: B 188 MET cc_start: 0.5372 (mtt) cc_final: 0.5134 (mtt) REVERT: C 335 MET cc_start: 0.4255 (mmt) cc_final: 0.3750 (mmt) REVERT: R 133 ASP cc_start: 0.8319 (t0) cc_final: 0.7982 (t70) REVERT: R 227 ARG cc_start: 0.6531 (tpp80) cc_final: 0.6191 (mtm-85) outliers start: 13 outliers final: 9 residues processed: 110 average time/residue: 0.0931 time to fit residues: 13.6163 Evaluate side-chains 109 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 100 time to evaluate : 0.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 172 MET Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain R residue 139 THR Chi-restraints excluded: chain R residue 176 ARG Chi-restraints excluded: chain R residue 187 CYS Chi-restraints excluded: chain R residue 356 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 36 optimal weight: 10.0000 chunk 31 optimal weight: 9.9990 chunk 84 optimal weight: 0.5980 chunk 39 optimal weight: 3.9990 chunk 94 optimal weight: 0.9990 chunk 102 optimal weight: 0.6980 chunk 25 optimal weight: 0.4980 chunk 90 optimal weight: 3.9990 chunk 4 optimal weight: 0.8980 chunk 21 optimal weight: 0.8980 chunk 2 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.191322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.113567 restraints weight = 9002.652| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 2.33 r_work: 0.2910 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2761 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 moved from start: 0.3117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8707 Z= 0.126 Angle : 0.530 7.977 11870 Z= 0.272 Chirality : 0.040 0.207 1411 Planarity : 0.004 0.049 1409 Dihedral : 9.467 89.203 1872 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.97 % Allowed : 10.51 % Favored : 86.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.82 (0.27), residues: 1020 helix: 2.30 (0.23), residues: 533 sheet: -0.11 (0.39), residues: 180 loop : -2.36 (0.31), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 227 TYR 0.017 0.001 TYR C 198 PHE 0.010 0.001 PHE B 253 TRP 0.020 0.001 TRP B 211 HIS 0.002 0.001 HIS B 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 ( 8705) covalent geometry : angle 0.53034 / 0.27 (11866) SS BOND : bond 0.00042 / 0.02 ( 2) SS BOND : angle 0.47868 / 0.26 ( 4) hydrogen bonds : bond 0.05027 / 3.26 ( 483) hydrogen bonds : angle 4.17338 / 2.99 ( 1422) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 108 time to evaluate : 0.207 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 350 LYS cc_start: 0.6887 (mttt) cc_final: 0.6235 (mptt) REVERT: B 88 ASN cc_start: 0.7362 (m-40) cc_final: 0.7117 (t0) REVERT: B 101 MET cc_start: 0.7671 (mmt) cc_final: 0.7112 (mmt) REVERT: B 105 TYR cc_start: 0.8495 (t80) cc_final: 0.8214 (t80) REVERT: C 335 MET cc_start: 0.4199 (mmt) cc_final: 0.3698 (mmt) REVERT: R 133 ASP cc_start: 0.8374 (t0) cc_final: 0.8076 (t0) REVERT: R 342 LYS cc_start: 0.8250 (ttpp) cc_final: 0.7947 (tttt) outliers start: 26 outliers final: 15 residues processed: 121 average time/residue: 0.0987 time to fit residues: 15.8405 Evaluate side-chains 117 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 102 time to evaluate : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 ARG Chi-restraints excluded: chain A residue 322 SER Chi-restraints excluded: chain A residue 352 ILE Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 172 MET Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain R residue 69 ASN Chi-restraints excluded: chain R residue 139 THR Chi-restraints excluded: chain R residue 176 ARG Chi-restraints excluded: chain R residue 187 CYS Chi-restraints excluded: chain R residue 356 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 43 optimal weight: 4.9990 chunk 65 optimal weight: 0.8980 chunk 4 optimal weight: 0.8980 chunk 29 optimal weight: 0.9980 chunk 37 optimal weight: 4.9990 chunk 87 optimal weight: 0.5980 chunk 98 optimal weight: 0.6980 chunk 85 optimal weight: 0.7980 chunk 53 optimal weight: 0.5980 chunk 55 optimal weight: 0.8980 chunk 88 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 125 ASN B 239 ASN C 386 ASN R 54 ASN R 126 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.191007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.113237 restraints weight = 8912.025| |-----------------------------------------------------------------------------| r_work (start): 0.3032 rms_B_bonded: 2.30 r_work: 0.2893 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2745 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.3435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8707 Z= 0.124 Angle : 0.530 7.798 11870 Z= 0.270 Chirality : 0.040 0.202 1411 Planarity : 0.004 0.050 1409 Dihedral : 9.475 89.231 1872 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.97 % Allowed : 11.43 % Favored : 85.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.08 (0.27), residues: 1020 helix: 2.48 (0.23), residues: 533 sheet: 0.07 (0.39), residues: 176 loop : -2.19 (0.31), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 227 TYR 0.016 0.001 TYR C 198 PHE 0.010 0.001 PHE B 253 TRP 0.021 0.001 TRP B 211 HIS 0.002 0.000 HIS C 126 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.12 ( 8705) covalent geometry : angle 0.53051 / 0.27 (11866) SS BOND : bond 0.00053 / 0.03 ( 2) SS BOND : angle 0.49233 / 0.27 ( 4) hydrogen bonds : bond 0.04979 / 3.23 ( 483) hydrogen bonds : angle 4.11307 / 2.95 ( 1422) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 107 time to evaluate : 0.229 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 199 MET cc_start: 0.7456 (mtm) cc_final: 0.7062 (mpp) REVERT: A 350 LYS cc_start: 0.6899 (mttt) cc_final: 0.6233 (mptt) REVERT: A 352 ILE cc_start: 0.7075 (OUTLIER) cc_final: 0.6795 (mt) REVERT: B 63 TRP cc_start: 0.8877 (m100) cc_final: 0.8635 (m100) REVERT: B 88 ASN cc_start: 0.7367 (m-40) cc_final: 0.7132 (t0) REVERT: B 155 ASN cc_start: 0.7575 (t0) cc_final: 0.6868 (t0) REVERT: B 170 ASP cc_start: 0.6847 (t0) cc_final: 0.6579 (t0) REVERT: B 262 MET cc_start: 0.1990 (tpp) cc_final: 0.1751 (mtt) REVERT: C 335 MET cc_start: 0.4147 (mmt) cc_final: 0.3651 (mmt) REVERT: R 133 ASP cc_start: 0.8420 (t0) cc_final: 0.8159 (t0) REVERT: R 342 LYS cc_start: 0.8283 (ttpp) cc_final: 0.7970 (tttt) REVERT: R 371 CYS cc_start: 0.7661 (m) cc_final: 0.6355 (p) outliers start: 26 outliers final: 18 residues processed: 118 average time/residue: 0.1056 time to fit residues: 16.5174 Evaluate side-chains 118 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 99 time to evaluate : 0.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 ARG Chi-restraints excluded: chain A residue 322 SER Chi-restraints excluded: chain A residue 346 GLN Chi-restraints excluded: chain A residue 352 ILE Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 211 TRP Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 172 MET Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain R residue 69 ASN Chi-restraints excluded: chain R residue 139 THR Chi-restraints excluded: chain R residue 173 LEU Chi-restraints excluded: chain R residue 176 ARG Chi-restraints excluded: chain R residue 187 CYS Chi-restraints excluded: chain R residue 356 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 90 optimal weight: 0.0370 chunk 25 optimal weight: 0.3980 chunk 57 optimal weight: 0.5980 chunk 47 optimal weight: 1.9990 chunk 51 optimal weight: 0.5980 chunk 82 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 80 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 32 optimal weight: 6.9990 overall best weight: 0.5260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 239 ASN C 126 HIS R 126 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.192540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.115460 restraints weight = 8794.246| |-----------------------------------------------------------------------------| r_work (start): 0.3057 rms_B_bonded: 2.29 r_work: 0.2920 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2772 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.3630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 8707 Z= 0.109 Angle : 0.510 7.727 11870 Z= 0.259 Chirality : 0.040 0.194 1411 Planarity : 0.004 0.050 1409 Dihedral : 9.396 89.842 1872 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 2.29 % Allowed : 12.11 % Favored : 85.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.33 (0.27), residues: 1020 helix: 2.54 (0.23), residues: 545 sheet: 0.14 (0.40), residues: 174 loop : -1.93 (0.32), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 227 TYR 0.014 0.001 TYR C 198 PHE 0.009 0.001 PHE B 253 TRP 0.024 0.001 TRP B 211 HIS 0.004 0.001 HIS C 126 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.11 ( 8705) covalent geometry : angle 0.50989 / 0.26 (11866) SS BOND : bond 0.00043 / 0.02 ( 2) SS BOND : angle 0.39506 / 0.22 ( 4) hydrogen bonds : bond 0.04514 / 2.92 ( 483) hydrogen bonds : angle 4.00227 / 2.87 ( 1422) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 94 time to evaluate : 0.310 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 350 LYS cc_start: 0.6877 (mttt) cc_final: 0.6250 (mptt) REVERT: A 352 ILE cc_start: 0.6929 (OUTLIER) cc_final: 0.6581 (mt) REVERT: B 63 TRP cc_start: 0.8875 (m100) cc_final: 0.8650 (m100) REVERT: B 88 ASN cc_start: 0.7174 (m-40) cc_final: 0.6950 (t0) REVERT: B 155 ASN cc_start: 0.7571 (t0) cc_final: 0.6814 (t0) REVERT: C 176 ARG cc_start: 0.8607 (ttp80) cc_final: 0.8285 (mtp-110) REVERT: C 335 MET cc_start: 0.4144 (mmt) cc_final: 0.3651 (mmt) REVERT: R 133 ASP cc_start: 0.8429 (t0) cc_final: 0.8188 (t0) REVERT: R 342 LYS cc_start: 0.8320 (ttpp) cc_final: 0.7995 (tttt) REVERT: R 371 CYS cc_start: 0.7730 (m) cc_final: 0.6461 (p) outliers start: 20 outliers final: 18 residues processed: 104 average time/residue: 0.1103 time to fit residues: 15.1958 Evaluate side-chains 108 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 89 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 ARG Chi-restraints excluded: chain A residue 322 SER Chi-restraints excluded: chain A residue 346 GLN Chi-restraints excluded: chain A residue 352 ILE Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 211 TRP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 172 MET Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain R residue 69 ASN Chi-restraints excluded: chain R residue 139 THR Chi-restraints excluded: chain R residue 173 LEU Chi-restraints excluded: chain R residue 176 ARG Chi-restraints excluded: chain R residue 356 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 66 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 chunk 93 optimal weight: 0.0870 chunk 88 optimal weight: 0.5980 chunk 46 optimal weight: 0.9990 chunk 61 optimal weight: 0.5980 chunk 67 optimal weight: 0.7980 chunk 8 optimal weight: 4.9990 chunk 11 optimal weight: 0.9990 chunk 30 optimal weight: 4.9990 chunk 52 optimal weight: 0.9980 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 239 ASN B 340 ASN R 54 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.191966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.114376 restraints weight = 8892.868| |-----------------------------------------------------------------------------| r_work (start): 0.3043 rms_B_bonded: 2.31 r_work: 0.2905 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2758 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.3810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8707 Z= 0.112 Angle : 0.509 7.726 11870 Z= 0.258 Chirality : 0.040 0.194 1411 Planarity : 0.004 0.050 1409 Dihedral : 9.233 89.891 1872 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 2.86 % Allowed : 12.11 % Favored : 85.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.45 (0.27), residues: 1020 helix: 2.78 (0.22), residues: 535 sheet: 0.07 (0.39), residues: 178 loop : -1.94 (0.33), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 227 TYR 0.015 0.001 TYR C 198 PHE 0.009 0.001 PHE C 112 TRP 0.017 0.001 TRP B 211 HIS 0.001 0.000 HIS B 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.11 ( 8705) covalent geometry : angle 0.50937 / 0.26 (11866) SS BOND : bond 0.00043 / 0.02 ( 2) SS BOND : angle 0.43053 / 0.24 ( 4) hydrogen bonds : bond 0.04604 / 2.98 ( 483) hydrogen bonds : angle 3.96458 / 2.84 ( 1422) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 92 time to evaluate : 0.203 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 350 LYS cc_start: 0.6907 (mttt) cc_final: 0.6257 (mptt) REVERT: A 352 ILE cc_start: 0.6863 (OUTLIER) cc_final: 0.6523 (mt) REVERT: B 63 TRP cc_start: 0.8962 (m100) cc_final: 0.8753 (m100) REVERT: B 88 ASN cc_start: 0.7049 (m-40) cc_final: 0.6844 (t0) REVERT: B 155 ASN cc_start: 0.7552 (t0) cc_final: 0.6771 (t0) REVERT: C 176 ARG cc_start: 0.8604 (ttp80) cc_final: 0.8292 (mtp-110) REVERT: C 335 MET cc_start: 0.4139 (mmt) cc_final: 0.3661 (mmt) REVERT: R 133 ASP cc_start: 0.8415 (t0) cc_final: 0.8186 (t0) REVERT: R 342 LYS cc_start: 0.8391 (ttpp) cc_final: 0.8090 (tttt) REVERT: R 371 CYS cc_start: 0.7716 (m) cc_final: 0.6451 (p) outliers start: 25 outliers final: 23 residues processed: 103 average time/residue: 0.1050 time to fit residues: 14.4610 Evaluate side-chains 113 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 89 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 ARG Chi-restraints excluded: chain A residue 322 SER Chi-restraints excluded: chain A residue 346 GLN Chi-restraints excluded: chain A residue 352 ILE Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 108 SER Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 211 TRP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 172 MET Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain R residue 63 LEU Chi-restraints excluded: chain R residue 139 THR Chi-restraints excluded: chain R residue 173 LEU Chi-restraints excluded: chain R residue 176 ARG Chi-restraints excluded: chain R residue 187 CYS Chi-restraints excluded: chain R residue 356 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 36 optimal weight: 6.9990 chunk 28 optimal weight: 4.9990 chunk 14 optimal weight: 5.9990 chunk 63 optimal weight: 3.9990 chunk 79 optimal weight: 0.8980 chunk 78 optimal weight: 0.8980 chunk 31 optimal weight: 7.9990 chunk 5 optimal weight: 2.9990 chunk 25 optimal weight: 5.9990 chunk 40 optimal weight: 8.9990 chunk 66 optimal weight: 0.4980 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 340 ASN ** R 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.175851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.092323 restraints weight = 9068.743| |-----------------------------------------------------------------------------| r_work (start): 0.2963 rms_B_bonded: 2.38 r_work: 0.2821 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2675 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.3969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 8707 Z= 0.240 Angle : 0.643 8.517 11870 Z= 0.324 Chirality : 0.045 0.193 1411 Planarity : 0.004 0.045 1409 Dihedral : 9.894 89.663 1872 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 2.74 % Allowed : 12.57 % Favored : 84.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.27), residues: 1020 helix: 2.12 (0.22), residues: 545 sheet: -0.08 (0.38), residues: 182 loop : -1.88 (0.33), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 15 TYR 0.017 0.002 TYR C 198 PHE 0.014 0.002 PHE C 112 TRP 0.019 0.002 TRP B 211 HIS 0.003 0.001 HIS C 193 Details of bonding type rmsd/Z covalent geometry : bond 0.00610 / 0.24 ( 8705) covalent geometry : angle 0.64310 / 0.32 (11866) SS BOND : bond 0.00157 / 0.08 ( 2) SS BOND : angle 0.85599 / 0.42 ( 4) hydrogen bonds : bond 0.06780 / 4.38 ( 483) hydrogen bonds : angle 4.33211 / 3.11 ( 1422) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 108 time to evaluate : 0.297 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 352 ILE cc_start: 0.7238 (OUTLIER) cc_final: 0.6942 (mt) REVERT: B 101 MET cc_start: 0.7747 (mmt) cc_final: 0.7528 (mmt) REVERT: B 155 ASN cc_start: 0.7491 (t0) cc_final: 0.6879 (t0) REVERT: B 178 THR cc_start: 0.6227 (p) cc_final: 0.5930 (p) REVERT: C 176 ARG cc_start: 0.8727 (ttp80) cc_final: 0.8481 (mtp85) REVERT: C 335 MET cc_start: 0.4220 (mmt) cc_final: 0.3783 (mmt) REVERT: R 133 ASP cc_start: 0.8584 (t0) cc_final: 0.8326 (t0) REVERT: R 342 LYS cc_start: 0.8415 (ttpp) cc_final: 0.8080 (tttt) REVERT: R 371 CYS cc_start: 0.8006 (m) cc_final: 0.6712 (p) outliers start: 24 outliers final: 20 residues processed: 122 average time/residue: 0.0994 time to fit residues: 16.0648 Evaluate side-chains 117 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 96 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 ARG Chi-restraints excluded: chain A residue 322 SER Chi-restraints excluded: chain A residue 352 ILE Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 211 TRP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 172 MET Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain R residue 63 LEU Chi-restraints excluded: chain R residue 69 ASN Chi-restraints excluded: chain R residue 139 THR Chi-restraints excluded: chain R residue 176 ARG Chi-restraints excluded: chain R residue 187 CYS Chi-restraints excluded: chain R residue 356 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 80 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 chunk 9 optimal weight: 3.9990 chunk 7 optimal weight: 6.9990 chunk 102 optimal weight: 0.5980 chunk 93 optimal weight: 0.8980 chunk 10 optimal weight: 0.7980 chunk 43 optimal weight: 0.9980 chunk 77 optimal weight: 0.6980 chunk 48 optimal weight: 0.9990 chunk 91 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.179991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.103331 restraints weight = 9037.099| |-----------------------------------------------------------------------------| r_work (start): 0.3054 rms_B_bonded: 2.58 r_work: 0.2827 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2680 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.4094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8707 Z= 0.131 Angle : 0.543 7.785 11870 Z= 0.275 Chirality : 0.041 0.186 1411 Planarity : 0.004 0.048 1409 Dihedral : 9.540 89.472 1872 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.74 % Allowed : 13.60 % Favored : 83.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.23 (0.27), residues: 1020 helix: 2.57 (0.22), residues: 533 sheet: 0.06 (0.38), residues: 177 loop : -1.99 (0.32), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG R 227 TYR 0.016 0.001 TYR C 198 PHE 0.010 0.001 PHE C 112 TRP 0.018 0.001 TRP B 211 HIS 0.002 0.001 HIS B 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.13 ( 8705) covalent geometry : angle 0.54315 / 0.28 (11866) SS BOND : bond 0.00099 / 0.05 ( 2) SS BOND : angle 0.47271 / 0.26 ( 4) hydrogen bonds : bond 0.05198 / 3.35 ( 483) hydrogen bonds : angle 4.12035 / 2.96 ( 1422) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 97 time to evaluate : 0.319 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 350 LYS cc_start: 0.7188 (mttt) cc_final: 0.6453 (mptt) REVERT: A 352 ILE cc_start: 0.6965 (OUTLIER) cc_final: 0.6759 (mt) REVERT: B 101 MET cc_start: 0.7606 (mmt) cc_final: 0.7360 (mmt) REVERT: B 155 ASN cc_start: 0.7497 (t0) cc_final: 0.6914 (t0) REVERT: B 178 THR cc_start: 0.6203 (p) cc_final: 0.5894 (p) REVERT: C 176 ARG cc_start: 0.8682 (ttp80) cc_final: 0.8400 (mtp-110) REVERT: C 335 MET cc_start: 0.4135 (mmt) cc_final: 0.3716 (mmt) REVERT: R 133 ASP cc_start: 0.8435 (t0) cc_final: 0.8216 (t0) REVERT: R 342 LYS cc_start: 0.8427 (ttpp) cc_final: 0.8092 (tttt) REVERT: R 371 CYS cc_start: 0.7948 (m) cc_final: 0.6612 (p) outliers start: 24 outliers final: 19 residues processed: 109 average time/residue: 0.1110 time to fit residues: 16.0254 Evaluate side-chains 114 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 94 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 322 SER Chi-restraints excluded: chain A residue 352 ILE Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 108 SER Chi-restraints excluded: chain B residue 211 TRP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 172 MET Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain R residue 63 LEU Chi-restraints excluded: chain R residue 69 ASN Chi-restraints excluded: chain R residue 139 THR Chi-restraints excluded: chain R residue 176 ARG Chi-restraints excluded: chain R residue 187 CYS Chi-restraints excluded: chain R residue 356 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 27 optimal weight: 5.9990 chunk 94 optimal weight: 0.9980 chunk 24 optimal weight: 8.9990 chunk 60 optimal weight: 0.5980 chunk 18 optimal weight: 4.9990 chunk 57 optimal weight: 0.6980 chunk 59 optimal weight: 4.9990 chunk 88 optimal weight: 1.9990 chunk 55 optimal weight: 0.4980 chunk 12 optimal weight: 20.0000 chunk 83 optimal weight: 0.0010 overall best weight: 0.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 54 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.181011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.097631 restraints weight = 8987.591| |-----------------------------------------------------------------------------| r_work (start): 0.3018 rms_B_bonded: 2.43 r_work: 0.2879 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2730 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.4187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8707 Z= 0.114 Angle : 0.524 7.686 11870 Z= 0.265 Chirality : 0.040 0.185 1411 Planarity : 0.004 0.050 1409 Dihedral : 9.295 89.641 1872 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.29 % Allowed : 14.40 % Favored : 83.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.39 (0.27), residues: 1020 helix: 2.58 (0.22), residues: 547 sheet: 0.04 (0.37), residues: 180 loop : -1.84 (0.33), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG R 227 TYR 0.014 0.001 TYR C 198 PHE 0.009 0.001 PHE C 112 TRP 0.017 0.001 TRP B 211 HIS 0.005 0.001 HIS B 311 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.11 ( 8705) covalent geometry : angle 0.52371 / 0.27 (11866) SS BOND : bond 0.00054 / 0.03 ( 2) SS BOND : angle 0.43277 / 0.24 ( 4) hydrogen bonds : bond 0.04657 / 3.01 ( 483) hydrogen bonds : angle 4.01539 / 2.89 ( 1422) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 94 time to evaluate : 0.276 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 350 LYS cc_start: 0.7047 (mttt) cc_final: 0.6316 (mptt) REVERT: B 101 MET cc_start: 0.7503 (mmt) cc_final: 0.7248 (mmt) REVERT: B 155 ASN cc_start: 0.7442 (t0) cc_final: 0.6861 (t0) REVERT: B 178 THR cc_start: 0.6139 (p) cc_final: 0.5835 (p) REVERT: C 176 ARG cc_start: 0.8629 (ttp80) cc_final: 0.8290 (mtp85) REVERT: C 335 MET cc_start: 0.4072 (mmt) cc_final: 0.3643 (mmt) REVERT: R 133 ASP cc_start: 0.8376 (t0) cc_final: 0.8154 (t0) REVERT: R 342 LYS cc_start: 0.8281 (ttpp) cc_final: 0.7952 (tttt) REVERT: R 371 CYS cc_start: 0.7765 (m) cc_final: 0.6408 (p) outliers start: 20 outliers final: 19 residues processed: 104 average time/residue: 0.1179 time to fit residues: 16.2881 Evaluate side-chains 113 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 94 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 322 SER Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 108 SER Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 211 TRP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 172 MET Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain R residue 63 LEU Chi-restraints excluded: chain R residue 69 ASN Chi-restraints excluded: chain R residue 139 THR Chi-restraints excluded: chain R residue 176 ARG Chi-restraints excluded: chain R residue 187 CYS Chi-restraints excluded: chain R residue 356 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 37 optimal weight: 0.6980 chunk 35 optimal weight: 3.9990 chunk 5 optimal weight: 0.0980 chunk 87 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 chunk 90 optimal weight: 0.1980 chunk 85 optimal weight: 0.8980 chunk 66 optimal weight: 0.5980 chunk 77 optimal weight: 2.9990 chunk 100 optimal weight: 0.9980 chunk 45 optimal weight: 0.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 125 ASN B 340 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.192027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.109747 restraints weight = 8952.238| |-----------------------------------------------------------------------------| r_work (start): 0.3066 rms_B_bonded: 2.41 r_work: 0.2937 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2786 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.4291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 8707 Z= 0.107 Angle : 0.510 7.585 11870 Z= 0.258 Chirality : 0.039 0.182 1411 Planarity : 0.004 0.052 1409 Dihedral : 9.122 89.834 1872 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.40 % Allowed : 14.63 % Favored : 82.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.55 (0.27), residues: 1020 helix: 2.72 (0.22), residues: 547 sheet: 0.13 (0.38), residues: 180 loop : -1.81 (0.33), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG R 227 TYR 0.014 0.001 TYR C 198 PHE 0.008 0.001 PHE C 112 TRP 0.017 0.001 TRP B 211 HIS 0.001 0.000 HIS R 193 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.11 ( 8705) covalent geometry : angle 0.50985 / 0.26 (11866) SS BOND : bond 0.00043 / 0.02 ( 2) SS BOND : angle 0.44438 / 0.24 ( 4) hydrogen bonds : bond 0.04372 / 2.83 ( 483) hydrogen bonds : angle 3.93492 / 2.84 ( 1422) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2639.09 seconds wall clock time: 45 minutes 39.79 seconds (2739.79 seconds total)