Starting phenix.real_space_refine on Sat Oct 24 19:53:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/29xz_57440/10_2026/29xz_57440.cif Found real_map, /net/cci-nas-00/data/ceres_data/29xz_57440/10_2026/29xz_57440.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.16 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/29xz_57440/10_2026/29xz_57440.map" default_real_map = "/net/cci-nas-00/data/ceres_data/29xz_57440/10_2026/29xz_57440.map" model { file = "/net/cci-nas-00/data/ceres_data/29xz_57440/10_2026/29xz_57440.cif" } default_model = "/net/cci-nas-00/data/ceres_data/29xz_57440/10_2026/29xz_57440.cif" } resolution = 2.16 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= 0.007 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 Fe 10 7.16 5 S 80 5.16 5 C 9228 2.51 5 N 2230 2.21 5 O 2663 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14211 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 1354 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1354 Classifications: {'peptide': 180} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 169} Chain: "B" Number of atoms: 3510 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 436, 3500 Classifications: {'peptide': 436} Link IDs: {'PCIS': 3, 'PTRANS': 27, 'TRANS': 405} Conformer: "B" Number of residues, atoms: 436, 3500 Classifications: {'peptide': 436} Link IDs: {'PCIS': 3, 'PTRANS': 27, 'TRANS': 405} bond proxies already assigned to first conformer: 3625 Chain: "C" Number of atoms: 1848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1848 Classifications: {'peptide': 238} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 222} Chain breaks: 1 Chain: "A" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 38 Unusual residues: {'FES': 1, 'UMQ': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 224 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 6, 206 Unusual residues: {'HEM': 2, 'UMQ': 3, 'UQ1': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Conformer: "B" Number of residues, atoms: 6, 206 Unusual residues: {'HEM': 2, 'UMQ': 3, 'UQ1': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} bond proxies already assigned to first conformer: 205 Chain: "C" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEC': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "B" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 55 Classifications: {'water': 55} Link IDs: {None: 54} Chain: "C" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 26 Classifications: {'water': 26} Link IDs: {None: 25} Chain: "D" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "E" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 52 Classifications: {'water': 52} Link IDs: {None: 51} Chain: "F" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 26 Classifications: {'water': 26} Link IDs: {None: 25} Restraints were copied for chains: D, E, F List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 922 SG CYS A 133 83.852 56.085 84.838 1.00 96.22 S ATOM 1068 SG CYS A 153 82.663 53.905 87.690 1.00 97.71 S ATOM 7634 SG CYS D 133 29.451 38.630 84.783 1.00 97.91 S ATOM 7780 SG CYS D 153 30.641 40.799 87.643 1.00 98.87 S Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N AHIS B 8 " occ=0.53 ... (18 atoms not shown) pdb=" NE2BHIS B 8 " occ=0.47 residue: pdb=" N AHIS E 8 " occ=0.53 ... (18 atoms not shown) pdb=" NE2BHIS E 8 " occ=0.47 residue: pdb=" C1 AUQ1 B 503 " occ=0.35 ... (34 atoms not shown) pdb=" O4 BUQ1 B 503 " occ=0.65 residue: pdb=" C1 AUQ1 E 503 " occ=0.35 ... (34 atoms not shown) pdb=" O4 BUQ1 E 503 " occ=0.65 Time building chain proxies: 4.61, per 1000 atoms: 0.32 Number of scatterers: 14211 At special positions: 0 Unit cell: (114.156, 95.5528, 111.619, 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) Fe 10 26.01 S 80 16.00 O 2663 8.00 N 2230 7.00 C 9228 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 138 " - pdb=" SG CYS A 155 " distance=2.03 Simple disulfide: pdb=" SG CYS C 144 " - pdb=" SG CYS C 167 " distance=2.03 Simple disulfide: pdb=" SG CYS D 138 " - pdb=" SG CYS D 155 " distance=2.03 Simple disulfide: pdb=" SG CYS F 144 " - pdb=" SG CYS F 167 " distance=2.03 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=10, symmetry=0 Number of additional bonds: simple=10, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.14 Conformation dependent library (CDL) restraints added in 836.9 milliseconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES A 501 " pdb="FE2 FES A 501 " - pdb=" ND1 HIS A 135 " pdb="FE2 FES A 501 " - pdb=" ND1 HIS A 156 " pdb="FE1 FES A 501 " - pdb=" SG CYS A 133 " pdb="FE1 FES A 501 " - pdb=" SG CYS A 153 " pdb=" FES D 501 " pdb="FE2 FES D 501 " - pdb=" ND1 HIS D 135 " pdb="FE2 FES D 501 " - pdb=" ND1 HIS D 156 " pdb="FE1 FES D 501 " - pdb=" SG CYS D 133 " pdb="FE1 FES D 501 " - pdb=" SG CYS D 153 " Number of angles added : 6 3396 Ramachandran restraints generated. 1698 Oldfield, 0 Emsley, 1698 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3116 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 12 sheets defined 57.6% alpha, 4.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'A' and resid 13 through 37 removed outlier: 4.129A pdb=" N HIS A 17 " --> pdb=" O ASP A 13 " (cutoff:3.500A) Proline residue: A 33 - end of helix Processing helix chain 'A' and resid 41 through 47 removed outlier: 3.518A pdb=" N MET A 47 " --> pdb=" O ASP A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 86 Processing helix chain 'A' and resid 110 through 114 removed outlier: 4.026A pdb=" N THR A 114 " --> pdb=" O GLU A 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 13 through 21 Processing helix chain 'B' and resid 24 through 34 Processing helix chain 'B' and resid 42 through 45 Processing helix chain 'B' and resid 46 through 67 removed outlier: 3.678A pdb=" N VAL B 50 " --> pdb=" O ILE B 46 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N MET B 67 " --> pdb=" O ILE B 63 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 86 Processing helix chain 'B' and resid 89 through 119 removed outlier: 3.505A pdb=" N ALA B 101 " --> pdb=" O HIS B 97 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N SER B 102 " --> pdb=" O ALA B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 149 removed outlier: 3.749A pdb=" N VAL B 148 " --> pdb=" O PHE B 144 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LEU B 149 " --> pdb=" O MET B 145 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 164 Processing helix chain 'B' and resid 165 through 169 Processing helix chain 'B' and resid 172 through 182 Processing helix chain 'B' and resid 187 through 220 Proline residue: B 202 - end of helix removed outlier: 3.569A pdb=" N PHE B 216 " --> pdb=" O HIS B 212 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N THR B 219 " --> pdb=" O ALA B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 239 Processing helix chain 'B' and resid 244 through 270 removed outlier: 6.860A pdb=" N VAL B 249 " --> pdb=" O TRP B 245 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LYS B 251 " --> pdb=" O TYR B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 281 Processing helix chain 'B' and resid 295 through 297 No H-bonds generated for 'chain 'B' and resid 295 through 297' Processing helix chain 'B' and resid 298 through 308 removed outlier: 3.665A pdb=" N ILE B 304 " --> pdb=" O PRO B 300 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N PHE B 308 " --> pdb=" O ILE B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 312 through 322 Processing helix chain 'B' and resid 327 through 345 removed outlier: 3.757A pdb=" N ILE B 340 " --> pdb=" O MET B 336 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N MET B 343 " --> pdb=" O ALA B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 350 Processing helix chain 'B' and resid 356 through 359 removed outlier: 3.790A pdb=" N TYR B 359 " --> pdb=" O SER B 356 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 356 through 359' Processing helix chain 'B' and resid 360 through 381 removed outlier: 3.945A pdb=" N MET B 365 " --> pdb=" O PRO B 361 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N TRP B 366 " --> pdb=" O LYS B 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 388 through 406 removed outlier: 3.542A pdb=" N PHE B 401 " --> pdb=" O SER B 397 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N PHE B 404 " --> pdb=" O TRP B 400 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 412 removed outlier: 3.777A pdb=" N GLY B 412 " --> pdb=" O LEU B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 423 through 433 removed outlier: 3.588A pdb=" N HIS B 431 " --> pdb=" O ASP B 427 " (cutoff:3.500A) Processing helix chain 'C' and resid 19 through 33 Processing helix chain 'C' and resid 34 through 37 Processing helix chain 'C' and resid 44 through 50 Processing helix chain 'C' and resid 57 through 67 Processing helix chain 'C' and resid 102 through 107 Processing helix chain 'C' and resid 126 through 136 removed outlier: 3.501A pdb=" N ILE C 136 " --> pdb=" O TYR C 132 " (cutoff:3.500A) Processing helix chain 'C' and resid 164 through 168 Processing helix chain 'C' and resid 201 through 218 Processing helix chain 'C' and resid 220 through 250 removed outlier: 3.669A pdb=" N LEU C 229 " --> pdb=" O LYS C 225 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 255 Processing helix chain 'C' and resid 256 through 258 No H-bonds generated for 'chain 'C' and resid 256 through 258' Processing helix chain 'D' and resid 13 through 37 removed outlier: 4.129A pdb=" N HIS D 17 " --> pdb=" O ASP D 13 " (cutoff:3.500A) Proline residue: D 33 - end of helix Processing helix chain 'D' and resid 41 through 47 removed outlier: 3.518A pdb=" N MET D 47 " --> pdb=" O ASP D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 79 through 86 Processing helix chain 'D' and resid 110 through 114 removed outlier: 4.027A pdb=" N THR D 114 " --> pdb=" O GLU D 111 " (cutoff:3.500A) Processing helix chain 'E' and resid 13 through 21 Processing helix chain 'E' and resid 24 through 34 Processing helix chain 'E' and resid 42 through 45 Processing helix chain 'E' and resid 46 through 67 removed outlier: 3.678A pdb=" N VAL E 50 " --> pdb=" O ILE E 46 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N MET E 67 " --> pdb=" O ILE E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 75 through 86 Processing helix chain 'E' and resid 89 through 119 removed outlier: 3.506A pdb=" N ALA E 101 " --> pdb=" O HIS E 97 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N SER E 102 " --> pdb=" O ALA E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 125 through 149 removed outlier: 3.750A pdb=" N VAL E 148 " --> pdb=" O PHE E 144 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N LEU E 149 " --> pdb=" O MET E 145 " (cutoff:3.500A) Processing helix chain 'E' and resid 152 through 164 Processing helix chain 'E' and resid 165 through 169 Processing helix chain 'E' and resid 172 through 182 Processing helix chain 'E' and resid 187 through 220 Proline residue: E 202 - end of helix removed outlier: 3.569A pdb=" N PHE E 216 " --> pdb=" O HIS E 212 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N THR E 219 " --> pdb=" O ALA E 215 " (cutoff:3.500A) Processing helix chain 'E' and resid 233 through 239 Processing helix chain 'E' and resid 244 through 270 removed outlier: 6.860A pdb=" N VAL E 249 " --> pdb=" O TRP E 245 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LYS E 251 " --> pdb=" O TYR E 247 " (cutoff:3.500A) Processing helix chain 'E' and resid 276 through 281 Processing helix chain 'E' and resid 295 through 297 No H-bonds generated for 'chain 'E' and resid 295 through 297' Processing helix chain 'E' and resid 298 through 308 removed outlier: 3.665A pdb=" N ILE E 304 " --> pdb=" O PRO E 300 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N PHE E 308 " --> pdb=" O ILE E 304 " (cutoff:3.500A) Processing helix chain 'E' and resid 312 through 322 Processing helix chain 'E' and resid 327 through 345 removed outlier: 3.758A pdb=" N ILE E 340 " --> pdb=" O MET E 336 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N MET E 343 " --> pdb=" O ALA E 339 " (cutoff:3.500A) Processing helix chain 'E' and resid 345 through 350 Processing helix chain 'E' and resid 356 through 359 removed outlier: 3.790A pdb=" N TYR E 359 " --> pdb=" O SER E 356 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 356 through 359' Processing helix chain 'E' and resid 360 through 381 removed outlier: 3.945A pdb=" N MET E 365 " --> pdb=" O PRO E 361 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N TRP E 366 " --> pdb=" O LYS E 362 " (cutoff:3.500A) Processing helix chain 'E' and resid 388 through 406 removed outlier: 3.539A pdb=" N PHE E 401 " --> pdb=" O SER E 397 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N PHE E 404 " --> pdb=" O TRP E 400 " (cutoff:3.500A) Processing helix chain 'E' and resid 406 through 412 removed outlier: 3.777A pdb=" N GLY E 412 " --> pdb=" O LEU E 408 " (cutoff:3.500A) Processing helix chain 'E' and resid 423 through 433 removed outlier: 3.587A pdb=" N HIS E 431 " --> pdb=" O ASP E 427 " (cutoff:3.500A) Processing helix chain 'F' and resid 19 through 33 Processing helix chain 'F' and resid 34 through 37 Processing helix chain 'F' and resid 44 through 50 Processing helix chain 'F' and resid 57 through 67 Processing helix chain 'F' and resid 102 through 107 Processing helix chain 'F' and resid 126 through 136 removed outlier: 3.501A pdb=" N ILE F 136 " --> pdb=" O TYR F 132 " (cutoff:3.500A) Processing helix chain 'F' and resid 164 through 168 Processing helix chain 'F' and resid 201 through 218 Processing helix chain 'F' and resid 220 through 250 removed outlier: 3.669A pdb=" N LEU F 229 " --> pdb=" O LYS F 225 " (cutoff:3.500A) Processing helix chain 'F' and resid 250 through 255 Processing helix chain 'F' and resid 256 through 258 No H-bonds generated for 'chain 'F' and resid 256 through 258' Processing sheet with id=AA1, first strand: chain 'A' and resid 51 through 53 Processing sheet with id=AA2, first strand: chain 'A' and resid 62 through 67 Processing sheet with id=AA3, first strand: chain 'A' and resid 151 through 153 removed outlier: 3.789A pdb=" N LYS A 168 " --> pdb=" O HIS A 159 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 36 through 38 Processing sheet with id=AA5, first strand: chain 'C' and resid 71 through 72 Processing sheet with id=AA6, first strand: chain 'C' and resid 153 through 155 Processing sheet with id=AA7, first strand: chain 'D' and resid 51 through 53 Processing sheet with id=AA8, first strand: chain 'D' and resid 62 through 67 Processing sheet with id=AA9, first strand: chain 'D' and resid 151 through 153 removed outlier: 3.789A pdb=" N LYS D 168 " --> pdb=" O HIS D 159 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 36 through 38 Processing sheet with id=AB2, first strand: chain 'F' and resid 71 through 72 Processing sheet with id=AB3, first strand: chain 'F' and resid 153 through 155 686 hydrogen bonds defined for protein. 1920 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: 2.10 Time building geometry restraints manager: 1.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.41: 6198 1.41 - 1.61: 8148 1.61 - 1.81: 122 1.81 - 2.01: 14 2.01 - 2.20: 32 Bond restraints: 14514 Sorted by residual: bond pdb=" C ILE A 50 " pdb=" N PHE A 51 " ideal model delta sigma weight residual 1.330 1.282 0.048 1.32e-02 5.74e+03 1.32e+01 bond pdb=" C ILE D 50 " pdb=" N PHE D 51 " ideal model delta sigma weight residual 1.330 1.282 0.048 1.32e-02 5.74e+03 1.30e+01 bond pdb=" C THR D 64 " pdb=" N VAL D 65 " ideal model delta sigma weight residual 1.331 1.294 0.038 1.36e-02 5.41e+03 7.69e+00 bond pdb=" C THR A 64 " pdb=" N VAL A 65 " ideal model delta sigma weight residual 1.331 1.294 0.037 1.36e-02 5.41e+03 7.51e+00 bond pdb=" N SER B 2 " pdb=" CA SER B 2 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.98e+00 ... (remaining 14509 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.32: 19480 1.32 - 2.63: 288 2.63 - 3.95: 108 3.95 - 5.26: 4 5.26 - 6.58: 4 Bond angle restraints: 19884 Sorted by residual: angle pdb=" C6 BUQ1 E 503 " pdb=" C7 BUQ1 E 503 " pdb=" C8 BUQ1 E 503 " ideal model delta sigma weight residual 110.15 116.73 -6.58 3.00e+00 1.11e-01 4.81e+00 angle pdb=" C6 BUQ1 B 503 " pdb=" C7 BUQ1 B 503 " pdb=" C8 BUQ1 B 503 " ideal model delta sigma weight residual 110.15 116.73 -6.58 3.00e+00 1.11e-01 4.81e+00 angle pdb=" C5 BUQ1 B 503 " pdb=" C6 BUQ1 B 503 " pdb=" C7 BUQ1 B 503 " ideal model delta sigma weight residual 123.11 128.78 -5.67 3.00e+00 1.11e-01 3.57e+00 angle pdb=" C5 BUQ1 E 503 " pdb=" C6 BUQ1 E 503 " pdb=" C7 BUQ1 E 503 " ideal model delta sigma weight residual 123.11 128.78 -5.67 3.00e+00 1.11e-01 3.57e+00 angle pdb=" O ILE A 50 " pdb=" C ILE A 50 " pdb=" N PHE A 51 " ideal model delta sigma weight residual 123.00 121.21 1.79 1.07e+00 8.73e-01 2.80e+00 ... (remaining 19879 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 8066 17.89 - 35.79: 322 35.79 - 53.68: 90 53.68 - 71.57: 16 71.57 - 89.47: 20 Dihedral angle restraints: 8514 sinusoidal: 3620 harmonic: 4894 Sorted by residual: dihedral pdb=" C1A HEM E 501 " pdb=" C2A HEM E 501 " pdb=" CAA HEM E 501 " pdb=" CBA HEM E 501 " ideal model delta sinusoidal sigma weight residual -180.00 -91.85 -88.15 2 2.00e+01 2.50e-03 1.20e+01 dihedral pdb=" C1A HEM B 501 " pdb=" C2A HEM B 501 " pdb=" CAA HEM B 501 " pdb=" CBA HEM B 501 " ideal model delta sinusoidal sigma weight residual -180.00 -91.87 -88.13 2 2.00e+01 2.50e-03 1.20e+01 dihedral pdb=" C2D HEM E 501 " pdb=" C3D HEM E 501 " pdb=" CAD HEM E 501 " pdb=" CBD HEM E 501 " ideal model delta sinusoidal sigma weight residual -180.00 -92.19 -87.81 2 2.00e+01 2.50e-03 1.20e+01 ... (remaining 8511 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 1384 0.031 - 0.061: 492 0.061 - 0.092: 151 0.092 - 0.122: 85 0.122 - 0.153: 12 Chirality restraints: 2124 Sorted by residual: chirality pdb=" CA ILE D 177 " pdb=" N ILE D 177 " pdb=" C ILE D 177 " pdb=" CB ILE D 177 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.83e-01 chirality pdb=" CA ILE A 177 " pdb=" N ILE A 177 " pdb=" C ILE A 177 " pdb=" CB ILE A 177 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.82e-01 chirality pdb=" CA ILE E 35 " pdb=" N ILE E 35 " pdb=" C ILE E 35 " pdb=" CB ILE E 35 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.03e-01 ... (remaining 2121 not shown) Planarity restraints: 2450 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN B 434 " -0.028 5.00e-02 4.00e+02 4.27e-02 2.92e+00 pdb=" N PRO B 435 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO B 435 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 435 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN E 434 " 0.028 5.00e-02 4.00e+02 4.21e-02 2.84e+00 pdb=" N PRO E 435 " -0.073 5.00e-02 4.00e+02 pdb=" CA PRO E 435 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO E 435 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA D 171 " -0.022 5.00e-02 4.00e+02 3.40e-02 1.85e+00 pdb=" N PRO D 172 " 0.059 5.00e-02 4.00e+02 pdb=" CA PRO D 172 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO D 172 " -0.019 5.00e-02 4.00e+02 ... (remaining 2447 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1422 2.74 - 3.28: 13905 3.28 - 3.82: 22963 3.82 - 4.36: 29320 4.36 - 4.90: 48503 Nonbonded interactions: 116113 Sorted by model distance: nonbonded pdb=" NE2 HIS B 97 " pdb="FE HEM B 501 " model vdw 2.204 3.080 nonbonded pdb=" NE2 HIS E 97 " pdb="FE HEM E 501 " model vdw 2.204 3.080 nonbonded pdb=" SD MET F 183 " pdb="FE HEC F 501 " model vdw 2.265 3.360 nonbonded pdb=" SD MET C 183 " pdb="FE HEC C 501 " model vdw 2.265 3.360 nonbonded pdb=" NE2 HIS B 111 " pdb="FE HEM B 502 " model vdw 2.310 3.080 ... (remaining 116108 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' } ncs_group { reference = chain 'B' selection = chain 'E' } ncs_group { reference = chain 'C' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.35 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.360 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: 0.250 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 16.690 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.030 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:5.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9079 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.181 14536 Z= 0.305 Angle : 0.479 6.577 19898 Z= 0.234 Chirality : 0.039 0.153 2124 Planarity : 0.004 0.043 2450 Dihedral : 11.813 89.466 5386 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 1.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 0.58 % Allowed : 4.48 % Favored : 94.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % 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: -0.02 (0.21), residues: 1698 helix: 0.67 (0.18), residues: 840 sheet: -1.13 (0.58), residues: 92 loop : -0.55 (0.23), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 224 TYR 0.007 0.001 TYR E 302 PHE 0.017 0.001 PHE E 216 TRP 0.006 0.001 TRP B 47 HIS 0.004 0.001 HIS B 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 (14514) covalent geometry : angle 0.47399 / 0.23 (19884) SS BOND : bond 0.00170 / 0.09 ( 4) SS BOND : angle 0.51957 / 0.37 ( 8) hydrogen bonds : bond 0.23819 / 16.33 ( 686) hydrogen bonds : angle 6.37871 / 4.54 ( 1920) metal coordination : bond 0.04251 / 2.42 ( 8) metal coordination : angle 3.94677 / 2.14 ( 6) Misc. bond : bond 0.11728 / 7.30 ( 10) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3396 Ramachandran restraints generated. 1698 Oldfield, 0 Emsley, 1698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3396 Ramachandran restraints generated. 1698 Oldfield, 0 Emsley, 1698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 127 time to evaluate : 0.553 Fit side-chains REVERT: A 182 PHE cc_start: 0.8426 (OUTLIER) cc_final: 0.7313 (t80) REVERT: B 434 ASN cc_start: 0.7507 (OUTLIER) cc_final: 0.7115 (t0) REVERT: C 74 LYS cc_start: 0.9122 (ptpt) cc_final: 0.8908 (pttm) REVERT: D 182 PHE cc_start: 0.8551 (OUTLIER) cc_final: 0.7618 (t80) REVERT: E 434 ASN cc_start: 0.7486 (OUTLIER) cc_final: 0.7103 (t0) REVERT: F 74 LYS cc_start: 0.9126 (ptpt) cc_final: 0.8899 (pttm) outliers start: 8 outliers final: 2 residues processed: 131 average time/residue: 0.4890 time to fit residues: 71.8179 Evaluate side-chains 121 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 115 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 182 PHE Chi-restraints excluded: chain B residue 434 ASN Chi-restraints excluded: chain D residue 74 ILE Chi-restraints excluded: chain D residue 182 PHE Chi-restraints excluded: chain E residue 434 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: [98, 107, 10, 66, 130, 124, 103, 77, 122, 91, 149] chunk 98 optimal weight: 20.0000 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 20.0000 chunk 66 optimal weight: 0.5980 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 0.0980 chunk 149 optimal weight: 0.0000 overall best weight: 0.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 221 ASN ** D 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 221 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.098913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.2716 r_free = 0.2716 target = 0.055637 restraints weight = 48290.903| |-----------------------------------------------------------------------------| r_work (start): 0.2601 rms_B_bonded: 3.20 r_work: 0.2460 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2349 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2349 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2350 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2350 r_free = 0.2350 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2350 r_free = 0.2350 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.2350 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9102 moved from start: 0.1413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.128 14536 Z= 0.118 Angle : 0.583 8.943 19898 Z= 0.275 Chirality : 0.042 0.181 2124 Planarity : 0.005 0.047 2450 Dihedral : 9.963 87.138 2414 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 1.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 0.72 % Allowed : 6.50 % Favored : 92.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % 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: 0.80 (0.21), residues: 1698 helix: 1.53 (0.18), residues: 856 sheet: -0.69 (0.67), residues: 72 loop : -0.44 (0.23), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 114 TYR 0.008 0.001 TYR E 302 PHE 0.014 0.001 PHE B 216 TRP 0.012 0.001 TRP C 215 HIS 0.004 0.001 HIS B 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.12 (14514) covalent geometry : angle 0.58034 / 0.28 (19884) SS BOND : bond 0.00242 / 0.12 ( 4) SS BOND : angle 0.93966 / 0.69 ( 8) hydrogen bonds : bond 0.05558 / 3.86 ( 686) hydrogen bonds : angle 4.18353 / 2.97 ( 1920) metal coordination : bond 0.00238 / 0.10 ( 8) metal coordination : angle 3.10911 / 1.80 ( 6) Misc. bond : bond 0.08009 / 4.85 ( 10) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3396 Ramachandran restraints generated. 1698 Oldfield, 0 Emsley, 1698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3396 Ramachandran restraints generated. 1698 Oldfield, 0 Emsley, 1698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 114 time to evaluate : 0.518 Fit side-chains REVERT: A 182 PHE cc_start: 0.7027 (OUTLIER) cc_final: 0.6080 (t80) REVERT: D 182 PHE cc_start: 0.7255 (OUTLIER) cc_final: 0.6474 (t80) outliers start: 10 outliers final: 4 residues processed: 120 average time/residue: 0.4914 time to fit residues: 66.0610 Evaluate side-chains 111 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 105 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 182 PHE Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain D residue 74 ILE Chi-restraints excluded: chain D residue 182 PHE Chi-restraints excluded: chain F residue 229 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: [19, 108, 83, 148, 107, 37, 81, 57, 98, 129, 103] chunk 19 optimal weight: 0.9990 chunk 108 optimal weight: 0.8980 chunk 83 optimal weight: 1.9990 chunk 148 optimal weight: 0.1980 chunk 107 optimal weight: 0.5980 chunk 37 optimal weight: 5.9990 chunk 81 optimal weight: 0.8980 chunk 57 optimal weight: 2.9990 chunk 98 optimal weight: 6.9990 chunk 129 optimal weight: 0.9980 chunk 103 optimal weight: 0.9980 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 = 0.3412 r_free = 0.3412 target = 0.098386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2703 r_free = 0.2703 target = 0.054998 restraints weight = 53125.604| |-----------------------------------------------------------------------------| r_work (start): 0.2585 rms_B_bonded: 3.23 r_work: 0.2436 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2323 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2323 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2326 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2326 r_free = 0.2326 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2326 r_free = 0.2326 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2326 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9115 moved from start: 0.1535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.160 14536 Z= 0.115 Angle : 0.570 11.201 19898 Z= 0.261 Chirality : 0.042 0.164 2124 Planarity : 0.005 0.050 2450 Dihedral : 9.713 88.121 2410 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 2.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 1.01 % Allowed : 7.88 % Favored : 91.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % 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: 1.07 (0.21), residues: 1698 helix: 1.86 (0.18), residues: 858 sheet: -0.71 (0.66), residues: 72 loop : -0.45 (0.22), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 113 TYR 0.007 0.001 TYR E 297 PHE 0.019 0.001 PHE E 216 TRP 0.009 0.001 TRP E 368 HIS 0.006 0.001 HIS E 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.11 (14514) covalent geometry : angle 0.56754 / 0.26 (19884) SS BOND : bond 0.00231 / 0.12 ( 4) SS BOND : angle 2.03583 / 1.54 ( 8) hydrogen bonds : bond 0.05525 / 3.82 ( 686) hydrogen bonds : angle 3.90288 / 2.76 ( 1920) metal coordination : bond 0.00317 / 0.17 ( 8) metal coordination : angle 2.24743 / 1.29 ( 6) Misc. bond : bond 0.09860 / 5.70 ( 10) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3396 Ramachandran restraints generated. 1698 Oldfield, 0 Emsley, 1698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3396 Ramachandran restraints generated. 1698 Oldfield, 0 Emsley, 1698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 114 time to evaluate : 0.509 Fit side-chains REVERT: A 182 PHE cc_start: 0.7005 (OUTLIER) cc_final: 0.6038 (t80) REVERT: B 238 GLU cc_start: 0.8913 (tt0) cc_final: 0.8663 (tt0) REVERT: D 182 PHE cc_start: 0.7286 (OUTLIER) cc_final: 0.6527 (t80) REVERT: E 238 GLU cc_start: 0.8937 (tt0) cc_final: 0.8691 (tt0) outliers start: 14 outliers final: 7 residues processed: 122 average time/residue: 0.5098 time to fit residues: 69.3084 Evaluate side-chains 116 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 107 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 182 PHE Chi-restraints excluded: chain B residue 336 MET Chi-restraints excluded: chain C residue 31 ASN Chi-restraints excluded: chain C residue 167 CYS Chi-restraints excluded: chain D residue 74 ILE Chi-restraints excluded: chain D residue 182 PHE Chi-restraints excluded: chain F residue 31 ASN Chi-restraints excluded: chain F residue 167 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: [149, 154, 42, 167, 127, 18, 156, 106, 150, 56, 103] chunk 149 optimal weight: 1.9990 chunk 154 optimal weight: 0.7980 chunk 42 optimal weight: 2.9990 chunk 167 optimal weight: 0.8980 chunk 127 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 chunk 156 optimal weight: 0.2980 chunk 106 optimal weight: 1.9990 chunk 150 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 chunk 103 optimal weight: 0.0060 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 100 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.099739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2734 r_free = 0.2734 target = 0.056177 restraints weight = 53967.317| |-----------------------------------------------------------------------------| r_work (start): 0.2616 rms_B_bonded: 3.35 r_work: 0.2471 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2360 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2360 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2365 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2365 r_free = 0.2365 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2365 r_free = 0.2365 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2365 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9095 moved from start: 0.1815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.148 14536 Z= 0.106 Angle : 0.545 10.213 19898 Z= 0.249 Chirality : 0.041 0.169 2124 Planarity : 0.005 0.051 2450 Dihedral : 9.199 88.200 2410 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 2.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 1.37 % Allowed : 8.09 % Favored : 90.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % 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 (0.21), residues: 1698 helix: 2.00 (0.18), residues: 860 sheet: -0.54 (0.66), residues: 72 loop : -0.41 (0.22), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 114 TYR 0.007 0.001 TYR E 302 PHE 0.018 0.001 PHE B 216 TRP 0.009 0.001 TRP F 215 HIS 0.005 0.001 HIS E 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.10 (14514) covalent geometry : angle 0.54370 / 0.25 (19884) SS BOND : bond 0.00402 / 0.20 ( 4) SS BOND : angle 1.37407 / 1.04 ( 8) hydrogen bonds : bond 0.04828 / 3.35 ( 686) hydrogen bonds : angle 3.68170 / 2.60 ( 1920) metal coordination : bond 0.00404 / 0.21 ( 8) metal coordination : angle 2.00936 / 1.18 ( 6) Misc. bond : bond 0.08984 / 5.01 ( 10) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3396 Ramachandran restraints generated. 1698 Oldfield, 0 Emsley, 1698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3396 Ramachandran restraints generated. 1698 Oldfield, 0 Emsley, 1698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 111 time to evaluate : 0.501 Fit side-chains REVERT: A 182 PHE cc_start: 0.6992 (OUTLIER) cc_final: 0.6661 (t80) REVERT: B 238 GLU cc_start: 0.8879 (tt0) cc_final: 0.8622 (tt0) REVERT: C 74 LYS cc_start: 0.9115 (ptpt) cc_final: 0.8816 (pttm) REVERT: C 125 MET cc_start: 0.5831 (mtm) cc_final: 0.5429 (ttp) REVERT: C 183 MET cc_start: 0.8954 (ttt) cc_final: 0.8269 (ttt) REVERT: D 182 PHE cc_start: 0.7131 (OUTLIER) cc_final: 0.6774 (t80) REVERT: E 238 GLU cc_start: 0.8878 (tt0) cc_final: 0.8629 (tt0) REVERT: F 74 LYS cc_start: 0.9120 (ptpt) cc_final: 0.8822 (pttm) REVERT: F 183 MET cc_start: 0.8961 (ttt) cc_final: 0.8281 (ttt) outliers start: 19 outliers final: 7 residues processed: 123 average time/residue: 0.5017 time to fit residues: 68.7789 Evaluate side-chains 114 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 105 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 182 PHE Chi-restraints excluded: chain B residue 270 MET Chi-restraints excluded: chain C residue 167 CYS Chi-restraints excluded: chain D residue 74 ILE Chi-restraints excluded: chain D residue 182 PHE Chi-restraints excluded: chain E residue 270 MET Chi-restraints excluded: chain E residue 336 MET Chi-restraints excluded: chain F residue 167 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: [65, 20, 117, 107, 144, 128, 22, 111, 51, 148, 143] chunk 65 optimal weight: 0.9990 chunk 20 optimal weight: 5.9990 chunk 117 optimal weight: 0.9980 chunk 107 optimal weight: 0.4980 chunk 144 optimal weight: 0.9990 chunk 128 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 111 optimal weight: 4.9990 chunk 51 optimal weight: 5.9990 chunk 148 optimal weight: 0.0370 chunk 143 optimal weight: 2.9990 overall best weight: 0.7062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 100 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.099175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2713 r_free = 0.2713 target = 0.055126 restraints weight = 65280.071| |-----------------------------------------------------------------------------| r_work (start): 0.2591 rms_B_bonded: 3.59 r_work: 0.2439 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work: 0.2328 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2328 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2333 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2333 r_free = 0.2333 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2333 r_free = 0.2333 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2333 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9107 moved from start: 0.1844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.157 14536 Z= 0.109 Angle : 0.548 10.894 19898 Z= 0.249 Chirality : 0.041 0.162 2124 Planarity : 0.005 0.051 2450 Dihedral : 9.158 87.544 2410 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 2.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.23 % Allowed : 8.16 % Favored : 90.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % 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: 1.31 (0.21), residues: 1698 helix: 2.05 (0.18), residues: 860 sheet: -0.31 (0.67), residues: 72 loop : -0.38 (0.23), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 113 TYR 0.007 0.001 TYR E 399 PHE 0.019 0.001 PHE E 216 TRP 0.010 0.001 TRP E 47 HIS 0.005 0.001 HIS E 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.11 (14514) covalent geometry : angle 0.54652 / 0.25 (19884) SS BOND : bond 0.00187 / 0.09 ( 4) SS BOND : angle 1.18542 / 0.89 ( 8) hydrogen bonds : bond 0.05076 / 3.51 ( 686) hydrogen bonds : angle 3.64861 / 2.58 ( 1920) metal coordination : bond 0.00344 / 0.18 ( 8) metal coordination : angle 1.93338 / 1.12 ( 6) Misc. bond : bond 0.09366 / 5.19 ( 10) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3396 Ramachandran restraints generated. 1698 Oldfield, 0 Emsley, 1698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3396 Ramachandran restraints generated. 1698 Oldfield, 0 Emsley, 1698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 108 time to evaluate : 0.548 Fit side-chains REVERT: A 182 PHE cc_start: 0.6968 (OUTLIER) cc_final: 0.6127 (t80) REVERT: B 238 GLU cc_start: 0.8868 (tt0) cc_final: 0.8613 (tt0) REVERT: C 125 MET cc_start: 0.5827 (mtm) cc_final: 0.5498 (ttp) REVERT: C 183 MET cc_start: 0.9058 (ttt) cc_final: 0.8379 (ttt) REVERT: D 182 PHE cc_start: 0.7102 (OUTLIER) cc_final: 0.6700 (t80) REVERT: E 238 GLU cc_start: 0.8868 (tt0) cc_final: 0.8616 (tt0) REVERT: F 125 MET cc_start: 0.5720 (mtm) cc_final: 0.5517 (ttp) REVERT: F 183 MET cc_start: 0.9065 (ttt) cc_final: 0.8390 (ttt) outliers start: 17 outliers final: 3 residues processed: 121 average time/residue: 0.5287 time to fit residues: 71.3813 Evaluate side-chains 107 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 102 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 PHE Chi-restraints excluded: chain C residue 167 CYS Chi-restraints excluded: chain D residue 74 ILE Chi-restraints excluded: chain D residue 182 PHE Chi-restraints excluded: chain F residue 167 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: [79, 65, 140, 40, 113, 145, 107, 160, 162, 58, 161] chunk 79 optimal weight: 2.9990 chunk 65 optimal weight: 0.8980 chunk 140 optimal weight: 0.7980 chunk 40 optimal weight: 0.0980 chunk 113 optimal weight: 1.9990 chunk 145 optimal weight: 0.0030 chunk 107 optimal weight: 0.7980 chunk 160 optimal weight: 0.4980 chunk 162 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 161 optimal weight: 4.9990 overall best weight: 0.4390 ------------------------------------------------------------------------------- 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 = 0.3454 r_free = 0.3454 target = 0.101156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2773 r_free = 0.2773 target = 0.057986 restraints weight = 51869.146| |-----------------------------------------------------------------------------| r_work (start): 0.2656 rms_B_bonded: 3.32 r_work: 0.2511 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2402 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2402 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2406 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2406 r_free = 0.2406 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2406 r_free = 0.2406 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2406 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9070 moved from start: 0.2100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.155 14536 Z= 0.097 Angle : 0.511 9.178 19898 Z= 0.237 Chirality : 0.041 0.168 2124 Planarity : 0.005 0.051 2450 Dihedral : 8.858 88.282 2408 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 2.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.08 % Allowed : 8.67 % Favored : 90.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % 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: 1.46 (0.21), residues: 1698 helix: 2.16 (0.18), residues: 860 sheet: -0.22 (0.67), residues: 72 loop : -0.28 (0.23), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 114 TYR 0.006 0.001 TYR B 302 PHE 0.018 0.001 PHE B 216 TRP 0.009 0.001 TRP C 215 HIS 0.004 0.000 HIS E 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.10 (14514) covalent geometry : angle 0.50897 / 0.24 (19884) SS BOND : bond 0.00141 / 0.07 ( 4) SS BOND : angle 1.05422 / 0.79 ( 8) hydrogen bonds : bond 0.04279 / 2.97 ( 686) hydrogen bonds : angle 3.51871 / 2.49 ( 1920) metal coordination : bond 0.00456 / 0.23 ( 8) metal coordination : angle 2.17154 / 1.28 ( 6) Misc. bond : bond 0.08688 / 4.51 ( 10) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3396 Ramachandran restraints generated. 1698 Oldfield, 0 Emsley, 1698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3396 Ramachandran restraints generated. 1698 Oldfield, 0 Emsley, 1698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 110 time to evaluate : 0.532 Fit side-chains REVERT: A 141 MET cc_start: 0.8197 (ttt) cc_final: 0.7982 (ptm) REVERT: A 182 PHE cc_start: 0.6926 (OUTLIER) cc_final: 0.6531 (t80) REVERT: B 238 GLU cc_start: 0.8787 (tt0) cc_final: 0.8552 (tt0) REVERT: C 125 MET cc_start: 0.5881 (mtm) cc_final: 0.5619 (ttp) REVERT: C 183 MET cc_start: 0.8877 (ttt) cc_final: 0.8537 (ttt) REVERT: D 141 MET cc_start: 0.8179 (ttt) cc_final: 0.7961 (ptm) REVERT: D 182 PHE cc_start: 0.7041 (OUTLIER) cc_final: 0.6587 (t80) REVERT: E 238 GLU cc_start: 0.8790 (tt0) cc_final: 0.8556 (tt0) REVERT: F 183 MET cc_start: 0.8879 (ttt) cc_final: 0.8541 (ttt) outliers start: 15 outliers final: 4 residues processed: 121 average time/residue: 0.5212 time to fit residues: 70.4085 Evaluate side-chains 113 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 107 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 PHE Chi-restraints excluded: chain B residue 217 HIS Chi-restraints excluded: chain C residue 167 CYS Chi-restraints excluded: chain D residue 182 PHE Chi-restraints excluded: chain E residue 217 HIS Chi-restraints excluded: chain F residue 167 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: [81, 25, 63, 110, 14, 15, 8, 150, 1, 0, 141] chunk 81 optimal weight: 0.5980 chunk 25 optimal weight: 0.7980 chunk 63 optimal weight: 0.9990 chunk 110 optimal weight: 4.9990 chunk 14 optimal weight: 7.9990 chunk 15 optimal weight: 1.9990 chunk 8 optimal weight: 4.9990 chunk 150 optimal weight: 0.0970 chunk 1 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 chunk 141 optimal weight: 3.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 = 0.3415 r_free = 0.3415 target = 0.098694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.2697 r_free = 0.2697 target = 0.054502 restraints weight = 60769.568| |-----------------------------------------------------------------------------| r_work (start): 0.2577 rms_B_bonded: 3.53 r_work: 0.2426 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work: 0.2314 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2314 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2318 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2318 r_free = 0.2318 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2318 r_free = 0.2318 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2318 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9121 moved from start: 0.1932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.154 14536 Z= 0.117 Angle : 0.561 11.690 19898 Z= 0.253 Chirality : 0.042 0.186 2124 Planarity : 0.005 0.050 2450 Dihedral : 9.048 87.441 2406 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 2.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 0.65 % Allowed : 9.39 % Favored : 89.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % 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: 1.38 (0.21), residues: 1698 helix: 2.08 (0.18), residues: 860 sheet: -0.27 (0.67), residues: 72 loop : -0.29 (0.23), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 94 TYR 0.008 0.001 TYR E 399 PHE 0.021 0.001 PHE B 216 TRP 0.010 0.001 TRP B 47 HIS 0.005 0.001 HIS E 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.12 (14514) covalent geometry : angle 0.55967 / 0.25 (19884) SS BOND : bond 0.00225 / 0.12 ( 4) SS BOND : angle 1.07806 / 0.80 ( 8) hydrogen bonds : bond 0.05358 / 3.70 ( 686) hydrogen bonds : angle 3.62449 / 2.56 ( 1920) metal coordination : bond 0.00282 / 0.15 ( 8) metal coordination : angle 1.95297 / 1.14 ( 6) Misc. bond : bond 0.09290 / 5.19 ( 10) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3396 Ramachandran restraints generated. 1698 Oldfield, 0 Emsley, 1698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3396 Ramachandran restraints generated. 1698 Oldfield, 0 Emsley, 1698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 107 time to evaluate : 0.417 Fit side-chains REVERT: A 182 PHE cc_start: 0.6901 (OUTLIER) cc_final: 0.6178 (t80) REVERT: B 238 GLU cc_start: 0.8843 (tt0) cc_final: 0.8612 (tt0) REVERT: C 125 MET cc_start: 0.5825 (mtm) cc_final: 0.5559 (ttp) REVERT: C 183 MET cc_start: 0.9161 (ttt) cc_final: 0.8710 (ttt) REVERT: D 182 PHE cc_start: 0.6979 (OUTLIER) cc_final: 0.6270 (t80) REVERT: E 238 GLU cc_start: 0.8844 (tt0) cc_final: 0.8613 (tt0) REVERT: F 183 MET cc_start: 0.9163 (ttt) cc_final: 0.8714 (ttt) outliers start: 9 outliers final: 4 residues processed: 114 average time/residue: 0.5088 time to fit residues: 64.5382 Evaluate side-chains 112 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 106 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 PHE Chi-restraints excluded: chain B residue 217 HIS Chi-restraints excluded: chain C residue 167 CYS Chi-restraints excluded: chain D residue 182 PHE Chi-restraints excluded: chain E residue 217 HIS Chi-restraints excluded: chain F residue 167 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: [125, 158, 124, 140, 78, 112, 72, 132, 42, 0, 129] chunk 125 optimal weight: 1.9990 chunk 158 optimal weight: 3.9990 chunk 124 optimal weight: 0.1980 chunk 140 optimal weight: 0.7980 chunk 78 optimal weight: 2.9990 chunk 112 optimal weight: 1.9990 chunk 72 optimal weight: 0.5980 chunk 132 optimal weight: 0.8980 chunk 42 optimal weight: 0.5980 chunk 0 optimal weight: 7.9990 chunk 129 optimal weight: 0.4980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 = 0.3440 r_free = 0.3440 target = 0.100363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2745 r_free = 0.2745 target = 0.056683 restraints weight = 55723.284| |-----------------------------------------------------------------------------| r_work (start): 0.2626 rms_B_bonded: 3.36 r_work: 0.2480 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2367 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2367 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2371 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2371 r_free = 0.2371 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2371 r_free = 0.2371 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2371 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9088 moved from start: 0.2119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.152 14536 Z= 0.102 Angle : 0.522 9.651 19898 Z= 0.241 Chirality : 0.041 0.179 2124 Planarity : 0.005 0.051 2450 Dihedral : 8.855 88.006 2406 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 2.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 0.79 % Allowed : 9.10 % Favored : 90.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % 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: 1.43 (0.21), residues: 1698 helix: 2.15 (0.18), residues: 860 sheet: -0.56 (0.64), residues: 76 loop : -0.26 (0.23), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 165 TYR 0.006 0.001 TYR E 399 PHE 0.018 0.001 PHE B 216 TRP 0.010 0.001 TRP C 215 HIS 0.004 0.000 HIS E 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.10 (14514) covalent geometry : angle 0.52051 / 0.24 (19884) SS BOND : bond 0.00178 / 0.09 ( 4) SS BOND : angle 1.00125 / 0.75 ( 8) hydrogen bonds : bond 0.04570 / 3.17 ( 686) hydrogen bonds : angle 3.53801 / 2.50 ( 1920) metal coordination : bond 0.00383 / 0.20 ( 8) metal coordination : angle 2.00783 / 1.16 ( 6) Misc. bond : bond 0.08670 / 4.55 ( 10) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3396 Ramachandran restraints generated. 1698 Oldfield, 0 Emsley, 1698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3396 Ramachandran restraints generated. 1698 Oldfield, 0 Emsley, 1698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 109 time to evaluate : 0.509 Fit side-chains REVERT: A 182 PHE cc_start: 0.6881 (OUTLIER) cc_final: 0.6155 (t80) REVERT: B 238 GLU cc_start: 0.8795 (tt0) cc_final: 0.8563 (tt0) REVERT: C 125 MET cc_start: 0.5839 (mtm) cc_final: 0.5593 (ttp) REVERT: C 183 MET cc_start: 0.8990 (ttt) cc_final: 0.8390 (ttt) REVERT: D 182 PHE cc_start: 0.6976 (OUTLIER) cc_final: 0.6260 (t80) REVERT: E 238 GLU cc_start: 0.8800 (tt0) cc_final: 0.8566 (tt0) REVERT: F 183 MET cc_start: 0.8989 (ttt) cc_final: 0.8392 (ttt) outliers start: 11 outliers final: 4 residues processed: 118 average time/residue: 0.5095 time to fit residues: 67.1848 Evaluate side-chains 114 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 108 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 PHE Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 217 HIS Chi-restraints excluded: chain D residue 182 PHE Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 217 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: [43, 142, 152, 164, 156, 153, 150, 11, 54, 100, 69] chunk 43 optimal weight: 0.9990 chunk 142 optimal weight: 0.1980 chunk 152 optimal weight: 0.5980 chunk 164 optimal weight: 1.9990 chunk 156 optimal weight: 3.9990 chunk 153 optimal weight: 0.6980 chunk 150 optimal weight: 2.9990 chunk 11 optimal weight: 8.9990 chunk 54 optimal weight: 2.9990 chunk 100 optimal weight: 0.0870 chunk 69 optimal weight: 4.9990 overall best weight: 0.5160 ------------------------------------------------------------------------------- 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 = 0.3450 r_free = 0.3450 target = 0.101278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.2757 r_free = 0.2757 target = 0.057534 restraints weight = 53110.214| |-----------------------------------------------------------------------------| r_work (start): 0.2636 rms_B_bonded: 3.39 r_work: 0.2488 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2375 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2375 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2376 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2376 r_free = 0.2376 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2376 r_free = 0.2376 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2376 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9054 moved from start: 0.2203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.160 14536 Z= 0.101 Angle : 0.522 10.129 19898 Z= 0.239 Chirality : 0.041 0.178 2124 Planarity : 0.005 0.050 2450 Dihedral : 8.748 87.885 2406 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 2.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 0.72 % Allowed : 9.61 % Favored : 89.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % 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: 1.47 (0.21), residues: 1698 helix: 2.17 (0.18), residues: 860 sheet: -0.51 (0.64), residues: 76 loop : -0.24 (0.23), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 113 TYR 0.007 0.001 TYR E 297 PHE 0.019 0.001 PHE E 216 TRP 0.009 0.001 TRP C 215 HIS 0.004 0.000 HIS B 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.10 (14514) covalent geometry : angle 0.52021 / 0.24 (19884) SS BOND : bond 0.00133 / 0.07 ( 4) SS BOND : angle 1.13597 / 0.85 ( 8) hydrogen bonds : bond 0.04554 / 3.16 ( 686) hydrogen bonds : angle 3.50916 / 2.48 ( 1920) metal coordination : bond 0.00431 / 0.22 ( 8) metal coordination : angle 2.20693 / 1.29 ( 6) Misc. bond : bond 0.09026 / 4.72 ( 10) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3396 Ramachandran restraints generated. 1698 Oldfield, 0 Emsley, 1698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3396 Ramachandran restraints generated. 1698 Oldfield, 0 Emsley, 1698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 110 time to evaluate : 0.549 Fit side-chains REVERT: A 182 PHE cc_start: 0.6821 (OUTLIER) cc_final: 0.6350 (t80) REVERT: B 238 GLU cc_start: 0.8751 (tt0) cc_final: 0.8522 (tt0) REVERT: C 183 MET cc_start: 0.9011 (ttt) cc_final: 0.8783 (ttt) REVERT: D 182 PHE cc_start: 0.6890 (OUTLIER) cc_final: 0.6178 (t80) REVERT: E 238 GLU cc_start: 0.8741 (tt0) cc_final: 0.8513 (tt0) REVERT: F 183 MET cc_start: 0.9016 (ttt) cc_final: 0.8788 (ttt) outliers start: 10 outliers final: 4 residues processed: 120 average time/residue: 0.4980 time to fit residues: 66.9066 Evaluate side-chains 115 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 109 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 PHE Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 217 HIS Chi-restraints excluded: chain D residue 182 PHE Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 217 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: [78, 123, 111, 156, 55, 81, 149, 84, 69, 14, 87] chunk 78 optimal weight: 4.9990 chunk 123 optimal weight: 1.9990 chunk 111 optimal weight: 0.8980 chunk 156 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 chunk 81 optimal weight: 1.9990 chunk 149 optimal weight: 0.7980 chunk 84 optimal weight: 7.9990 chunk 69 optimal weight: 5.9990 chunk 14 optimal weight: 6.9990 chunk 87 optimal weight: 0.7980 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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 = 0.3402 r_free = 0.3402 target = 0.098193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.2666 r_free = 0.2666 target = 0.053499 restraints weight = 61990.045| |-----------------------------------------------------------------------------| r_work (start): 0.2546 rms_B_bonded: 3.57 r_work: 0.2389 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work: 0.2276 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2276 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2277 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2277 r_free = 0.2277 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2277 r_free = 0.2277 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2277 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9112 moved from start: 0.1932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.152 14536 Z= 0.139 Angle : 0.588 12.030 19898 Z= 0.266 Chirality : 0.043 0.177 2124 Planarity : 0.005 0.048 2450 Dihedral : 9.141 86.927 2406 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 1.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 0.43 % Allowed : 9.97 % Favored : 89.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % 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: 1.31 (0.21), residues: 1698 helix: 2.00 (0.18), residues: 860 sheet: -0.53 (0.63), residues: 76 loop : -0.27 (0.23), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 94 TYR 0.009 0.001 TYR E 399 PHE 0.022 0.001 PHE B 216 TRP 0.010 0.001 TRP B 47 HIS 0.005 0.001 HIS B 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.14 (14514) covalent geometry : angle 0.58646 / 0.27 (19884) SS BOND : bond 0.00299 / 0.15 ( 4) SS BOND : angle 1.34214 / 0.99 ( 8) hydrogen bonds : bond 0.05951 / 4.11 ( 686) hydrogen bonds : angle 3.71424 / 2.63 ( 1920) metal coordination : bond 0.00166 / 0.09 ( 8) metal coordination : angle 1.84107 / 1.09 ( 6) Misc. bond : bond 0.09386 / 5.37 ( 10) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3396 Ramachandran restraints generated. 1698 Oldfield, 0 Emsley, 1698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3396 Ramachandran restraints generated. 1698 Oldfield, 0 Emsley, 1698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 110 time to evaluate : 0.541 Fit side-chains REVERT: A 182 PHE cc_start: 0.6960 (OUTLIER) cc_final: 0.6177 (t80) REVERT: B 238 GLU cc_start: 0.8830 (tt0) cc_final: 0.8595 (tt0) REVERT: C 183 MET cc_start: 0.9243 (ttt) cc_final: 0.8934 (ttt) REVERT: D 182 PHE cc_start: 0.7004 (OUTLIER) cc_final: 0.6175 (t80) REVERT: E 238 GLU cc_start: 0.8823 (tt0) cc_final: 0.8588 (tt0) REVERT: F 183 MET cc_start: 0.9245 (ttt) cc_final: 0.8938 (ttt) outliers start: 6 outliers final: 4 residues processed: 116 average time/residue: 0.5274 time to fit residues: 68.0018 Evaluate side-chains 113 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 107 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 PHE Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 217 HIS Chi-restraints excluded: chain D residue 182 PHE Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 217 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: [92, 142, 165, 65, 139, 12, 130, 17, 87, 112, 2] chunk 92 optimal weight: 20.0000 chunk 142 optimal weight: 1.9990 chunk 165 optimal weight: 2.9990 chunk 65 optimal weight: 0.5980 chunk 139 optimal weight: 3.9990 chunk 12 optimal weight: 0.0370 chunk 130 optimal weight: 3.9990 chunk 17 optimal weight: 10.0000 chunk 87 optimal weight: 0.3980 chunk 112 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 overall best weight: 0.8060 ------------------------------------------------------------------------------- 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 = 0.3421 r_free = 0.3421 target = 0.099471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2703 r_free = 0.2703 target = 0.055212 restraints weight = 55687.158| |-----------------------------------------------------------------------------| r_work (start): 0.2585 rms_B_bonded: 3.43 r_work: 0.2433 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2321 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2321 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2323 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2323 r_free = 0.2323 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2323 r_free = 0.2323 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2323 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9085 moved from start: 0.2054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.149 14536 Z= 0.113 Angle : 0.550 10.253 19898 Z= 0.252 Chirality : 0.042 0.177 2124 Planarity : 0.005 0.049 2450 Dihedral : 9.019 87.359 2406 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 1.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 0.58 % Allowed : 9.97 % Favored : 89.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % 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: 1.36 (0.21), residues: 1698 helix: 2.06 (0.18), residues: 862 sheet: -0.53 (0.63), residues: 76 loop : -0.26 (0.23), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 224 TYR 0.007 0.001 TYR E 399 PHE 0.020 0.001 PHE B 216 TRP 0.010 0.001 TRP E 157 HIS 0.005 0.001 HIS E 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.11 (14514) covalent geometry : angle 0.54877 / 0.25 (19884) SS BOND : bond 0.00212 / 0.11 ( 4) SS BOND : angle 1.24208 / 0.93 ( 8) hydrogen bonds : bond 0.05180 / 3.59 ( 686) hydrogen bonds : angle 3.63268 / 2.57 ( 1920) metal coordination : bond 0.00324 / 0.18 ( 8) metal coordination : angle 1.90371 / 1.12 ( 6) Misc. bond : bond 0.08933 / 4.97 ( 10) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7767.05 seconds wall clock time: 132 minutes 8.87 seconds (7928.87 seconds total)