Starting phenix.real_space_refine on Fri Oct 23 08:55:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/24ye_69907/10_2026/24ye_69907.cif Found real_map, /net/cci-nas-00/data/ceres_data/24ye_69907/10_2026/24ye_69907.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/24ye_69907/10_2026/24ye_69907.map" default_real_map = "/net/cci-nas-00/data/ceres_data/24ye_69907/10_2026/24ye_69907.map" model { file = "/net/cci-nas-00/data/ceres_data/24ye_69907/10_2026/24ye_69907.cif" } default_model = "/net/cci-nas-00/data/ceres_data/24ye_69907/10_2026/24ye_69907.cif" } resolution = 2.9 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= 0.001 sd= 0.013 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: 4 Type Number sf(0) Gaussians S 15 5.16 5 C 5676 2.51 5 N 1611 2.21 5 O 1746 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 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: 9048 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 2210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 2210 Classifications: {'peptide': 299} Link IDs: {'PTRANS': 15, 'TRANS': 283} Chain breaks: 1 Chain: "B" Number of atoms: 2210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 2210 Classifications: {'peptide': 299} Link IDs: {'PTRANS': 15, 'TRANS': 283} Chain breaks: 1 Chain: "C" Number of atoms: 708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 708 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 3, 'TRANS': 90} Chain: "D" Number of atoms: 708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 708 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 3, 'TRANS': 90} Chain: "E" Number of atoms: 2210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 2210 Classifications: {'peptide': 299} Link IDs: {'PTRANS': 15, 'TRANS': 283} Chain breaks: 1 Chain: "F" Number of atoms: 708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 708 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 3, 'TRANS': 90} Chain: "G" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 98 Classifications: {'peptide': 14} Link IDs: {'TRANS': 13} Chain breaks: 1 Chain: "H" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 98 Classifications: {'peptide': 14} Link IDs: {'TRANS': 13} Chain breaks: 1 Chain: "I" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 98 Classifications: {'peptide': 14} Link IDs: {'TRANS': 13} Chain breaks: 1 Time building chain proxies: 1.93, per 1000 atoms: 0.21 Number of scatterers: 9048 At special positions: 0 Unit cell: (102.82, 110.58, 119.31, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 15 16.00 O 1746 8.00 N 1611 7.00 C 5676 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.72 Conformation dependent library (CDL) restraints added in 332.8 milliseconds 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2202 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 24 sheets defined 19.3% alpha, 31.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'A' and resid 30 through 38 Processing helix chain 'A' and resid 39 through 41 No H-bonds generated for 'chain 'A' and resid 39 through 41' Processing helix chain 'A' and resid 112 through 117 removed outlier: 3.861A pdb=" N VAL A 116 " --> pdb=" O ASN A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 265 Processing helix chain 'A' and resid 280 through 287 Processing helix chain 'A' and resid 304 through 309 Processing helix chain 'A' and resid 329 through 337 removed outlier: 4.218A pdb=" N HIS A 333 " --> pdb=" O ALA A 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 38 Processing helix chain 'B' and resid 112 through 117 removed outlier: 3.580A pdb=" N VAL B 116 " --> pdb=" O ASN B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 264 Processing helix chain 'B' and resid 280 through 287 Processing helix chain 'B' and resid 304 through 310 removed outlier: 3.639A pdb=" N LYS B 308 " --> pdb=" O GLY B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 337 removed outlier: 4.057A pdb=" N HIS B 333 " --> pdb=" O ALA B 329 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ASN B 337 " --> pdb=" O HIS B 333 " (cutoff:3.500A) Processing helix chain 'C' and resid 394 through 401 Processing helix chain 'C' and resid 415 through 420 removed outlier: 3.765A pdb=" N VAL C 419 " --> pdb=" O GLY C 415 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE C 420 " --> pdb=" O PRO C 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 415 through 420' Processing helix chain 'C' and resid 438 through 448 Processing helix chain 'D' and resid 394 through 401 Processing helix chain 'D' and resid 415 through 420 Processing helix chain 'D' and resid 438 through 448 Processing helix chain 'E' and resid 30 through 38 Processing helix chain 'E' and resid 112 through 117 removed outlier: 3.862A pdb=" N VAL E 116 " --> pdb=" O ASN E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 251 through 264 Processing helix chain 'E' and resid 280 through 287 Processing helix chain 'E' and resid 304 through 310 removed outlier: 3.622A pdb=" N GLY E 310 " --> pdb=" O ALA E 306 " (cutoff:3.500A) Processing helix chain 'E' and resid 329 through 337 removed outlier: 3.882A pdb=" N HIS E 333 " --> pdb=" O ALA E 329 " (cutoff:3.500A) Processing helix chain 'F' and resid 394 through 400 Processing helix chain 'F' and resid 415 through 420 removed outlier: 3.734A pdb=" N VAL F 419 " --> pdb=" O GLY F 415 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ILE F 420 " --> pdb=" O PRO F 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 415 through 420' Processing helix chain 'F' and resid 438 through 448 Processing sheet with id=AA1, first strand: chain 'A' and resid 94 through 98 removed outlier: 3.658A pdb=" N SER A 96 " --> pdb=" O THR A 46 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ARG A 47 " --> pdb=" O GLU A 121 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N GLU A 121 " --> pdb=" O ARG A 47 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ILE A 122 " --> pdb=" O ALA A 134 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 101 through 104 removed outlier: 3.783A pdb=" N PHE A 101 " --> pdb=" O LEU A 110 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N TYR A 108 " --> pdb=" O ILE A 103 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N VAL A 145 " --> pdb=" O ASP A 140 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLY A 138 " --> pdb=" O VAL A 147 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 221 through 223 removed outlier: 3.543A pdb=" N GLY A 176 " --> pdb=" O SER A 184 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N PHE A 247 " --> pdb=" O SER A 233 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 270 through 271 Processing sheet with id=AA5, first strand: chain 'A' and resid 323 through 324 removed outlier: 6.991A pdb=" N ASP A 347 " --> pdb=" O LEU A 318 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N LEU A 320 " --> pdb=" O ASN A 345 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ASN A 345 " --> pdb=" O LEU A 320 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL A 348 " --> pdb=" O LYS A 355 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 323 through 324 removed outlier: 7.230A pdb=" N VAL A 275 " --> pdb=" O ALA A 298 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL A 274 " --> pdb=" O ALA I 388 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 131 through 134 removed outlier: 4.208A pdb=" N ILE B 122 " --> pdb=" O ALA B 134 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N GLU B 121 " --> pdb=" O ARG B 47 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ARG B 47 " --> pdb=" O GLU B 121 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 101 through 104 removed outlier: 3.667A pdb=" N PHE B 101 " --> pdb=" O LEU B 110 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N TYR B 108 " --> pdb=" O ILE B 103 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N THR B 111 " --> pdb=" O ALA B 146 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N VAL B 145 " --> pdb=" O ASP B 140 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ASP B 140 " --> pdb=" O VAL B 145 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N GLY B 138 " --> pdb=" O VAL B 147 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 159 through 160 removed outlier: 7.290A pdb=" N LYS B 159 " --> pdb=" O VAL B 228 " (cutoff:3.500A) removed outlier: 8.192A pdb=" N GLY B 230 " --> pdb=" O LYS B 159 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N VAL B 228 " --> pdb=" O ASN B 223 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ASN B 223 " --> pdb=" O VAL B 228 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N GLY B 230 " --> pdb=" O LEU B 221 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N VAL B 172 " --> pdb=" O GLY B 188 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLY B 188 " --> pdb=" O VAL B 172 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLY B 176 " --> pdb=" O SER B 184 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 159 through 160 removed outlier: 7.290A pdb=" N LYS B 159 " --> pdb=" O VAL B 228 " (cutoff:3.500A) removed outlier: 8.192A pdb=" N GLY B 230 " --> pdb=" O LYS B 159 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 274 through 278 removed outlier: 6.695A pdb=" N VAL B 275 " --> pdb=" O ALA B 298 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 274 through 278 removed outlier: 6.695A pdb=" N VAL B 275 " --> pdb=" O ALA B 298 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N ASP B 347 " --> pdb=" O LEU B 318 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N LEU B 320 " --> pdb=" O ASN B 345 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ASN B 345 " --> pdb=" O LEU B 320 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL B 348 " --> pdb=" O LYS B 355 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS B 355 " --> pdb=" O VAL B 348 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 388 through 391 removed outlier: 6.928A pdb=" N THR C 389 " --> pdb=" O LYS C 410 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LYS C 410 " --> pdb=" O THR C 389 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N ARG C 458 " --> pdb=" O THR C 429 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N LEU C 431 " --> pdb=" O SER C 456 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N SER C 456 " --> pdb=" O LEU C 431 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N VAL C 459 " --> pdb=" O SER C 466 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N SER C 466 " --> pdb=" O VAL C 459 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 388 through 390 removed outlier: 7.467A pdb=" N THR D 389 " --> pdb=" O LYS D 410 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 434 through 435 removed outlier: 3.529A pdb=" N LEU D 431 " --> pdb=" O LYS D 434 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N HIS D 430 " --> pdb=" O ARG D 458 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL D 455 " --> pdb=" O PHE D 470 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 41 through 48 removed outlier: 3.743A pdb=" N GLY E 100 " --> pdb=" O VAL E 42 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE E 44 " --> pdb=" O GLY E 98 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N PHE E 101 " --> pdb=" O LEU E 110 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N TYR E 108 " --> pdb=" O ILE E 103 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N VAL E 145 " --> pdb=" O ALA E 139 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N ALA E 139 " --> pdb=" O VAL E 145 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N VAL E 147 " --> pdb=" O ILE E 137 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ILE E 137 " --> pdb=" O VAL E 147 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N ILE E 122 " --> pdb=" O ALA E 134 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N GLU E 121 " --> pdb=" O ARG E 47 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ARG E 47 " --> pdb=" O GLU E 121 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ARG E 125 " --> pdb=" O ASN E 43 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 159 through 160 removed outlier: 7.477A pdb=" N LYS E 159 " --> pdb=" O VAL E 228 " (cutoff:3.500A) removed outlier: 8.628A pdb=" N GLY E 230 " --> pdb=" O LYS E 159 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N PHE E 247 " --> pdb=" O SER E 233 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N PHE E 205 " --> pdb=" O GLY E 194 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 187 through 188 removed outlier: 6.953A pdb=" N LEU E 221 " --> pdb=" O VAL E 229 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N GLU E 227 " --> pdb=" O ASN E 223 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 270 through 271 Processing sheet with id=AC2, first strand: chain 'E' and resid 274 through 278 removed outlier: 6.748A pdb=" N VAL E 275 " --> pdb=" O ALA E 298 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 274 through 278 removed outlier: 6.748A pdb=" N VAL E 275 " --> pdb=" O ALA E 298 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N VAL E 316 " --> pdb=" O ILE E 349 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N ASP E 347 " --> pdb=" O LEU E 318 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N LEU E 320 " --> pdb=" O ASN E 345 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N ASN E 345 " --> pdb=" O LEU E 320 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 381 through 383 removed outlier: 3.541A pdb=" N SER F 383 " --> pdb=" O VAL F 388 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N VAL F 388 " --> pdb=" O SER F 383 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 407 through 408 removed outlier: 4.151A pdb=" N VAL F 407 " --> pdb=" O ILE F 428 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ILE F 428 " --> pdb=" O VAL F 407 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 407 through 408 removed outlier: 4.151A pdb=" N VAL F 407 " --> pdb=" O ILE F 428 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ILE F 428 " --> pdb=" O VAL F 407 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N ILE F 428 " --> pdb=" O LEU F 460 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N LEU F 460 " --> pdb=" O ILE F 428 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N HIS F 430 " --> pdb=" O ARG F 458 " (cutoff:3.500A) 319 hydrogen bonds defined for protein. 843 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: 1.40 Time building geometry restraints manager: 0.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3067 1.34 - 1.45: 886 1.45 - 1.57: 5179 1.57 - 1.69: 0 1.69 - 1.81: 30 Bond restraints: 9162 Sorted by residual: bond pdb=" CA PRO B 220 " pdb=" C PRO B 220 " ideal model delta sigma weight residual 1.521 1.481 0.040 1.24e-02 6.50e+03 1.04e+01 bond pdb=" C GLY E 219 " pdb=" N PRO E 220 " ideal model delta sigma weight residual 1.328 1.367 -0.039 1.26e-02 6.30e+03 9.49e+00 bond pdb=" CA ALA D 446 " pdb=" C ALA D 446 " ideal model delta sigma weight residual 1.523 1.495 0.028 1.34e-02 5.57e+03 4.43e+00 bond pdb=" C ASN B 213 " pdb=" N PRO B 214 " ideal model delta sigma weight residual 1.332 1.358 -0.027 1.30e-02 5.92e+03 4.19e+00 bond pdb=" CA LYS A 266 " pdb=" C LYS A 266 " ideal model delta sigma weight residual 1.521 1.496 0.025 1.21e-02 6.83e+03 4.13e+00 ... (remaining 9157 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.07: 12073 2.07 - 4.13: 267 4.13 - 6.20: 44 6.20 - 8.26: 4 8.26 - 10.33: 2 Bond angle restraints: 12390 Sorted by residual: angle pdb=" C PRO B 220 " pdb=" CA PRO B 220 " pdb=" CB PRO B 220 " ideal model delta sigma weight residual 111.23 104.88 6.35 1.28e+00 6.10e-01 2.46e+01 angle pdb=" C PRO B 220 " pdb=" N LEU B 221 " pdb=" CA LEU B 221 " ideal model delta sigma weight residual 123.23 115.46 7.77 1.57e+00 4.06e-01 2.45e+01 angle pdb=" C TYR B 202 " pdb=" N VAL B 203 " pdb=" CA VAL B 203 " ideal model delta sigma weight residual 122.85 118.65 4.20 8.70e-01 1.32e+00 2.33e+01 angle pdb=" N VAL E 229 " pdb=" CA VAL E 229 " pdb=" C VAL E 229 " ideal model delta sigma weight residual 113.53 109.65 3.88 9.80e-01 1.04e+00 1.57e+01 angle pdb=" C HIS B 183 " pdb=" N SER B 184 " pdb=" CA SER B 184 " ideal model delta sigma weight residual 122.77 117.70 5.07 1.33e+00 5.65e-01 1.45e+01 ... (remaining 12385 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.37: 4960 15.37 - 30.74: 461 30.74 - 46.12: 154 46.12 - 61.49: 17 61.49 - 76.86: 3 Dihedral angle restraints: 5595 sinusoidal: 2181 harmonic: 3414 Sorted by residual: dihedral pdb=" CA VAL F 408 " pdb=" C VAL F 408 " pdb=" N ILE F 409 " pdb=" CA ILE F 409 " ideal model delta harmonic sigma weight residual 180.00 154.30 25.70 0 5.00e+00 4.00e-02 2.64e+01 dihedral pdb=" CA GLU C 380 " pdb=" C GLU C 380 " pdb=" N ARG C 381 " pdb=" CA ARG C 381 " ideal model delta harmonic sigma weight residual 180.00 154.97 25.03 0 5.00e+00 4.00e-02 2.51e+01 dihedral pdb=" CA ASP D 402 " pdb=" C ASP D 402 " pdb=" N ILE D 403 " pdb=" CA ILE D 403 " ideal model delta harmonic sigma weight residual 180.00 163.13 16.87 0 5.00e+00 4.00e-02 1.14e+01 ... (remaining 5592 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 893 0.036 - 0.071: 340 0.071 - 0.107: 166 0.107 - 0.142: 66 0.142 - 0.178: 5 Chirality restraints: 1470 Sorted by residual: chirality pdb=" CA ILE B 206 " pdb=" N ILE B 206 " pdb=" C ILE B 206 " pdb=" CB ILE B 206 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 7.91e-01 chirality pdb=" CB ILE E 349 " pdb=" CA ILE E 349 " pdb=" CG1 ILE E 349 " pdb=" CG2 ILE E 349 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.16 2.00e-01 2.50e+01 6.40e-01 chirality pdb=" CA ILE E 249 " pdb=" N ILE E 249 " pdb=" C ILE E 249 " pdb=" CB ILE E 249 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.79e-01 ... (remaining 1467 not shown) Planarity restraints: 1626 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY B 215 " -0.012 2.00e-02 2.50e+03 2.41e-02 5.82e+00 pdb=" C GLY B 215 " 0.042 2.00e-02 2.50e+03 pdb=" O GLY B 215 " -0.015 2.00e-02 2.50e+03 pdb=" N ASN B 216 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY E 219 " 0.010 2.00e-02 2.50e+03 2.08e-02 4.31e+00 pdb=" C GLY E 219 " -0.036 2.00e-02 2.50e+03 pdb=" O GLY E 219 " 0.014 2.00e-02 2.50e+03 pdb=" N PRO E 220 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 265 " 0.009 2.00e-02 2.50e+03 1.95e-02 3.82e+00 pdb=" C GLY A 265 " -0.034 2.00e-02 2.50e+03 pdb=" O GLY A 265 " 0.013 2.00e-02 2.50e+03 pdb=" N LYS A 266 " 0.012 2.00e-02 2.50e+03 ... (remaining 1623 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1324 2.77 - 3.30: 8647 3.30 - 3.83: 14391 3.83 - 4.37: 16315 4.37 - 4.90: 28459 Nonbonded interactions: 69136 Sorted by model distance: nonbonded pdb=" O GLY E 244 " pdb=" CD1 LEU E 245 " model vdw 2.236 3.460 nonbonded pdb=" N ASN D 452 " pdb=" O LEU D 472 " model vdw 2.275 3.120 nonbonded pdb=" CD1 PHE E 236 " pdb=" CD2 LEU G 372 " model vdw 2.314 3.760 nonbonded pdb=" CD2 LEU A 197 " pdb=" CE2 PHE A 205 " model vdw 2.322 3.760 nonbonded pdb=" CG2 THR E 237 " pdb=" CD1 ILE G 373 " model vdw 2.323 3.880 ... (remaining 69131 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'E' } ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' } 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: 1.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.290 Find NCS groups from input model: 0.150 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:6.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4841 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 0.049 9162 Z= 0.221 Angle : 0.749 10.326 12390 Z= 0.430 Chirality : 0.049 0.178 1470 Planarity : 0.004 0.045 1626 Dihedral : 13.387 76.860 3393 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 16.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 0.00 % Allowed : 15.29 % Favored : 84.71 % 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: -0.85 (0.24), residues: 1191 helix: -0.18 (0.39), residues: 195 sheet: 0.15 (0.33), residues: 240 loop : -0.91 (0.22), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 381 TYR 0.007 0.002 TYR B 202 PHE 0.020 0.002 PHE B 205 TRP 0.029 0.003 TRP B 171 HIS 0.006 0.001 HIS E 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.22 ( 9162) covalent geometry : angle 0.74894 / 0.43 (12390) hydrogen bonds : bond 0.23527 / 15.26 ( 307) hydrogen bonds : angle 9.88550 / 6.78 ( 843) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 285 time to evaluate : 0.242 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 276 ILE cc_start: 0.8099 (pt) cc_final: 0.7884 (pp) REVERT: E 233 SER cc_start: 0.8123 (t) cc_final: 0.7824 (t) REVERT: F 396 GLU cc_start: 0.5359 (tp30) cc_final: 0.4960 (tm-30) REVERT: F 399 LYS cc_start: 0.5475 (ptpp) cc_final: 0.5006 (mmpt) REVERT: F 436 VAL cc_start: 0.7205 (t) cc_final: 0.6987 (m) outliers start: 0 outliers final: 0 residues processed: 285 average time/residue: 0.4765 time to fit residues: 145.7503 Evaluate side-chains 146 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 146 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: [108, 49, 97, 113, 53, 5, 33, 65, 62, 51, 100] chunk 108 optimal weight: 0.8980 chunk 49 optimal weight: 8.9990 chunk 97 optimal weight: 8.9990 chunk 113 optimal weight: 0.9990 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 0.0870 chunk 51 optimal weight: 3.9990 chunk 100 optimal weight: 8.9990 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 112 ASN A 234 GLN A 333 HIS A 353 GLN B 299 GLN B 333 HIS ** B 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4859 r_free = 0.4859 target = 0.223659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4677 r_free = 0.4677 target = 0.203228 restraints weight = 20114.662| |-----------------------------------------------------------------------------| r_work (start): 0.4661 rms_B_bonded: 3.87 r_work: 0.4584 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work (final): 0.4584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5742 moved from start: 0.4281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9162 Z= 0.153 Angle : 0.783 10.263 12390 Z= 0.387 Chirality : 0.051 0.176 1470 Planarity : 0.005 0.060 1626 Dihedral : 4.088 15.988 1266 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 4.49 % Allowed : 23.65 % Favored : 71.87 % 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: -0.76 (0.23), residues: 1191 helix: -0.06 (0.38), residues: 198 sheet: 0.21 (0.29), residues: 300 loop : -0.96 (0.22), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 464 TYR 0.013 0.002 TYR E 202 PHE 0.021 0.002 PHE A 242 TRP 0.009 0.001 TRP A 271 HIS 0.005 0.001 HIS B 333 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.15 ( 9162) covalent geometry : angle 0.78289 / 0.39 (12390) hydrogen bonds : bond 0.03899 / 2.47 ( 307) hydrogen bonds : angle 6.26973 / 4.32 ( 843) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 193 time to evaluate : 0.302 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 ASP cc_start: 0.8123 (t0) cc_final: 0.7804 (t0) REVERT: A 209 ASP cc_start: 0.7872 (t0) cc_final: 0.7664 (t0) REVERT: A 337 ASN cc_start: 0.8852 (m-40) cc_final: 0.8364 (m110) REVERT: B 103 ILE cc_start: 0.8797 (OUTLIER) cc_final: 0.8570 (pt) REVERT: B 287 PHE cc_start: 0.8149 (m-10) cc_final: 0.7886 (m-10) REVERT: B 331 LEU cc_start: 0.8988 (OUTLIER) cc_final: 0.8748 (pp) REVERT: C 396 GLU cc_start: 0.6669 (OUTLIER) cc_final: 0.6468 (pp20) REVERT: C 401 LEU cc_start: 0.8154 (OUTLIER) cc_final: 0.7877 (tm) REVERT: D 426 ASP cc_start: 0.6250 (t0) cc_final: 0.5933 (t0) REVERT: D 432 ASP cc_start: 0.7840 (t0) cc_final: 0.7147 (t0) REVERT: E 233 SER cc_start: 0.8422 (t) cc_final: 0.8211 (t) REVERT: E 243 MET cc_start: 0.8663 (mtm) cc_final: 0.8440 (mtm) REVERT: E 287 PHE cc_start: 0.8055 (m-10) cc_final: 0.7655 (m-10) REVERT: E 296 LEU cc_start: 0.7767 (tp) cc_final: 0.7521 (tp) REVERT: F 396 GLU cc_start: 0.5771 (tp30) cc_final: 0.5389 (tm-30) REVERT: F 397 GLN cc_start: 0.3953 (tt0) cc_final: 0.3736 (tp-100) REVERT: F 399 LYS cc_start: 0.5645 (ptpp) cc_final: 0.5135 (mmpt) REVERT: I 374 LEU cc_start: 0.8719 (OUTLIER) cc_final: 0.8371 (tt) outliers start: 44 outliers final: 13 residues processed: 220 average time/residue: 0.4720 time to fit residues: 111.3927 Evaluate side-chains 164 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 146 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 103 ILE Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain C residue 390 VAL Chi-restraints excluded: chain C residue 396 GLU Chi-restraints excluded: chain C residue 401 LEU Chi-restraints excluded: chain C residue 439 THR Chi-restraints excluded: chain D residue 401 LEU Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain E residue 109 ILE Chi-restraints excluded: chain E residue 222 LEU Chi-restraints excluded: chain G residue 373 ILE Chi-restraints excluded: chain I residue 374 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: [88, 42, 20, 31, 61, 50, 21, 12, 46, 58, 91] chunk 88 optimal weight: 4.9990 chunk 42 optimal weight: 4.9990 chunk 20 optimal weight: 4.9990 chunk 31 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 50 optimal weight: 0.7980 chunk 21 optimal weight: 2.9990 chunk 12 optimal weight: 6.9990 chunk 46 optimal weight: 3.9990 chunk 58 optimal weight: 0.9990 chunk 91 optimal weight: 1.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 95 GLN ** A 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 95 GLN B 353 GLN C 413 GLN C 452 ASN ** E 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 154 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4713 r_free = 0.4713 target = 0.209691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4526 r_free = 0.4526 target = 0.189377 restraints weight = 19575.021| |-----------------------------------------------------------------------------| r_work (start): 0.4511 rms_B_bonded: 3.63 r_work: 0.4403 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.4403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6214 moved from start: 0.6468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 9162 Z= 0.243 Angle : 0.887 9.414 12390 Z= 0.464 Chirality : 0.054 0.257 1470 Planarity : 0.006 0.068 1626 Dihedral : 5.409 29.202 1266 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 15.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 5.71 % Allowed : 24.77 % Favored : 69.52 % 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: -1.04 (0.23), residues: 1191 helix: -0.71 (0.36), residues: 198 sheet: -0.24 (0.27), residues: 366 loop : -0.88 (0.24), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 381 TYR 0.015 0.002 TYR E 202 PHE 0.027 0.003 PHE F 442 TRP 0.015 0.002 TRP E 171 HIS 0.013 0.001 HIS H 371 Details of bonding type rmsd/Z covalent geometry : bond 0.00537 / 0.24 ( 9162) covalent geometry : angle 0.88669 / 0.46 (12390) hydrogen bonds : bond 0.05006 / 3.11 ( 307) hydrogen bonds : angle 6.43843 / 4.43 ( 843) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 168 time to evaluate : 0.240 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 ASP cc_start: 0.8383 (t0) cc_final: 0.8057 (t0) REVERT: A 317 ILE cc_start: 0.9080 (tp) cc_final: 0.8809 (pp) REVERT: A 337 ASN cc_start: 0.8558 (m-40) cc_final: 0.8286 (m110) REVERT: B 45 SER cc_start: 0.8803 (OUTLIER) cc_final: 0.8534 (p) REVERT: B 48 GLN cc_start: 0.8232 (OUTLIER) cc_final: 0.8027 (tp40) REVERT: B 287 PHE cc_start: 0.8402 (m-10) cc_final: 0.8131 (m-10) REVERT: C 396 GLU cc_start: 0.6654 (pt0) cc_final: 0.6407 (pp20) REVERT: C 423 ARG cc_start: 0.6603 (ptp90) cc_final: 0.6362 (pmm150) REVERT: C 457 MET cc_start: 0.7501 (mmm) cc_final: 0.7196 (mtt) REVERT: D 399 LYS cc_start: 0.5902 (mmtm) cc_final: 0.5582 (mmtm) REVERT: D 426 ASP cc_start: 0.6586 (t0) cc_final: 0.6340 (t0) REVERT: D 432 ASP cc_start: 0.8026 (t0) cc_final: 0.7394 (t0) REVERT: D 439 THR cc_start: -0.0108 (OUTLIER) cc_final: -0.0536 (p) REVERT: F 431 LEU cc_start: 0.8108 (tm) cc_final: 0.7754 (tp) outliers start: 56 outliers final: 20 residues processed: 204 average time/residue: 0.5218 time to fit residues: 113.6960 Evaluate side-chains 168 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 145 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 48 GLN Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 259 ASP Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 426 ASP Chi-restraints excluded: chain D residue 389 THR Chi-restraints excluded: chain D residue 390 VAL Chi-restraints excluded: chain D residue 397 GLN Chi-restraints excluded: chain D residue 401 LEU Chi-restraints excluded: chain D residue 412 VAL Chi-restraints excluded: chain D residue 439 THR Chi-restraints excluded: chain D residue 455 VAL Chi-restraints excluded: chain E residue 145 VAL Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 297 VAL Chi-restraints excluded: chain F residue 410 LYS Chi-restraints excluded: chain F residue 449 LEU Chi-restraints excluded: chain G residue 373 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: [28, 15, 104, 76, 75, 78, 71, 100, 19, 37, 79] chunk 28 optimal weight: 2.9990 chunk 15 optimal weight: 0.7980 chunk 104 optimal weight: 0.9990 chunk 76 optimal weight: 0.6980 chunk 75 optimal weight: 5.9990 chunk 78 optimal weight: 10.0000 chunk 71 optimal weight: 3.9990 chunk 100 optimal weight: 0.6980 chunk 19 optimal weight: 3.9990 chunk 37 optimal weight: 5.9990 chunk 79 optimal weight: 0.5980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 462 GLN ** E 114 HIS ** 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 = 0.4772 r_free = 0.4772 target = 0.213677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4600 r_free = 0.4600 target = 0.193309 restraints weight = 19887.626| |-----------------------------------------------------------------------------| r_work (start): 0.4572 rms_B_bonded: 3.78 r_work: 0.4454 rms_B_bonded: 4.69 restraints_weight: 0.5000 r_work (final): 0.4454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6154 moved from start: 0.6940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9162 Z= 0.146 Angle : 0.771 9.345 12390 Z= 0.381 Chirality : 0.050 0.182 1470 Planarity : 0.005 0.052 1626 Dihedral : 4.509 24.562 1266 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 5.20 % Allowed : 27.83 % Favored : 66.97 % 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: -0.80 (0.24), residues: 1191 helix: -0.34 (0.37), residues: 198 sheet: 0.10 (0.28), residues: 345 loop : -0.91 (0.23), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 129 TYR 0.010 0.001 TYR A 202 PHE 0.019 0.002 PHE F 442 TRP 0.006 0.001 TRP B 271 HIS 0.004 0.001 HIS I 371 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.15 ( 9162) covalent geometry : angle 0.77078 / 0.38 (12390) hydrogen bonds : bond 0.03658 / 2.34 ( 307) hydrogen bonds : angle 5.78580 / 3.98 ( 843) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 159 time to evaluate : 0.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 ASP cc_start: 0.8405 (t0) cc_final: 0.8086 (t0) REVERT: A 337 ASN cc_start: 0.8381 (m-40) cc_final: 0.8177 (m110) REVERT: B 48 GLN cc_start: 0.8097 (OUTLIER) cc_final: 0.7823 (tp40) REVERT: B 287 PHE cc_start: 0.8427 (m-10) cc_final: 0.8104 (m-10) REVERT: C 423 ARG cc_start: 0.6614 (ptp90) cc_final: 0.6351 (pmm150) REVERT: C 455 VAL cc_start: 0.6084 (t) cc_final: 0.5727 (t) REVERT: D 432 ASP cc_start: 0.7998 (t0) cc_final: 0.7412 (t0) REVERT: E 106 ASP cc_start: 0.7885 (t0) cc_final: 0.7390 (p0) REVERT: E 122 ILE cc_start: 0.8678 (OUTLIER) cc_final: 0.8467 (tp) REVERT: E 287 PHE cc_start: 0.7823 (m-10) cc_final: 0.7601 (m-10) REVERT: I 387 LEU cc_start: 0.8659 (mp) cc_final: 0.8401 (mm) outliers start: 51 outliers final: 22 residues processed: 191 average time/residue: 0.5275 time to fit residues: 107.5614 Evaluate side-chains 163 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 139 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 48 GLN Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain C residue 390 VAL Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 439 THR Chi-restraints excluded: chain C residue 459 VAL Chi-restraints excluded: chain D residue 381 ARG Chi-restraints excluded: chain D residue 401 LEU Chi-restraints excluded: chain D residue 412 VAL Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain E residue 222 LEU Chi-restraints excluded: chain E residue 272 LEU Chi-restraints excluded: chain E residue 297 VAL Chi-restraints excluded: chain F residue 419 VAL Chi-restraints excluded: chain I residue 385 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: [65, 71, 50, 41, 63, 79, 18, 100, 61, 103, 29] chunk 65 optimal weight: 0.0010 chunk 71 optimal weight: 0.3980 chunk 50 optimal weight: 0.0040 chunk 41 optimal weight: 5.9990 chunk 63 optimal weight: 3.9990 chunk 79 optimal weight: 7.9990 chunk 18 optimal weight: 0.0970 chunk 100 optimal weight: 0.2980 chunk 61 optimal weight: 0.9980 chunk 103 optimal weight: 6.9990 chunk 29 optimal weight: 0.0170 overall best weight: 0.0834 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 114 HIS A 234 GLN ** A 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 95 GLN ** E 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4804 r_free = 0.4804 target = 0.217439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4642 r_free = 0.4642 target = 0.197666 restraints weight = 20175.387| |-----------------------------------------------------------------------------| r_work (start): 0.4638 rms_B_bonded: 3.83 r_work: 0.4555 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.4555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5966 moved from start: 0.7053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9162 Z= 0.128 Angle : 0.762 9.712 12390 Z= 0.365 Chirality : 0.049 0.175 1470 Planarity : 0.004 0.045 1626 Dihedral : 3.914 15.777 1266 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 3.26 % Allowed : 29.56 % Favored : 67.18 % 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: -0.61 (0.23), residues: 1191 helix: -0.10 (0.37), residues: 198 sheet: 0.27 (0.29), residues: 327 loop : -0.82 (0.22), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 129 TYR 0.012 0.001 TYR A 202 PHE 0.011 0.001 PHE E 242 TRP 0.004 0.000 TRP E 271 HIS 0.003 0.000 HIS I 371 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 ( 9162) covalent geometry : angle 0.76179 / 0.37 (12390) hydrogen bonds : bond 0.03005 / 1.94 ( 307) hydrogen bonds : angle 5.34175 / 3.67 ( 843) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 142 time to evaluate : 0.322 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 ASP cc_start: 0.8355 (t0) cc_final: 0.8088 (t0) REVERT: B 238 ARG cc_start: 0.7294 (ttm-80) cc_final: 0.7086 (ttm-80) REVERT: B 272 LEU cc_start: 0.7914 (tm) cc_final: 0.7150 (mt) REVERT: B 287 PHE cc_start: 0.8281 (m-10) cc_final: 0.7950 (m-10) REVERT: B 300 LEU cc_start: 0.7829 (OUTLIER) cc_final: 0.7595 (mt) REVERT: C 396 GLU cc_start: 0.6287 (pp20) cc_final: 0.5660 (tp30) REVERT: C 455 VAL cc_start: 0.6009 (t) cc_final: 0.4681 (t) REVERT: D 432 ASP cc_start: 0.7894 (t0) cc_final: 0.7618 (t0) REVERT: E 113 ASN cc_start: 0.8334 (OUTLIER) cc_final: 0.8125 (t0) REVERT: E 287 PHE cc_start: 0.7834 (m-10) cc_final: 0.7545 (m-10) outliers start: 32 outliers final: 16 residues processed: 164 average time/residue: 0.5055 time to fit residues: 88.7127 Evaluate side-chains 143 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 125 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 439 THR Chi-restraints excluded: chain C residue 459 VAL Chi-restraints excluded: chain D residue 401 LEU Chi-restraints excluded: chain D residue 412 VAL Chi-restraints excluded: chain E residue 113 ASN Chi-restraints excluded: chain E residue 279 VAL Chi-restraints excluded: chain E residue 297 VAL Chi-restraints excluded: chain F residue 408 VAL Chi-restraints excluded: chain F residue 419 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: [83, 12, 43, 93, 49, 45, 90, 34, 15, 65, 79] chunk 83 optimal weight: 6.9990 chunk 12 optimal weight: 4.9990 chunk 43 optimal weight: 0.3980 chunk 93 optimal weight: 6.9990 chunk 49 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 90 optimal weight: 4.9990 chunk 34 optimal weight: 8.9990 chunk 15 optimal weight: 3.9990 chunk 65 optimal weight: 0.0970 chunk 79 optimal weight: 3.9990 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 114 HIS ** 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 = 0.4717 r_free = 0.4717 target = 0.208214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4552 r_free = 0.4552 target = 0.187698 restraints weight = 19346.873| |-----------------------------------------------------------------------------| r_work (start): 0.4525 rms_B_bonded: 3.81 r_work: 0.4402 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.4402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6353 moved from start: 0.7773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 9162 Z= 0.238 Angle : 0.863 10.795 12390 Z= 0.438 Chirality : 0.053 0.233 1470 Planarity : 0.005 0.051 1626 Dihedral : 5.154 34.296 1266 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 16.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 4.38 % Allowed : 29.36 % Favored : 66.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.87 (0.23), residues: 1191 helix: -0.73 (0.35), residues: 205 sheet: 0.15 (0.29), residues: 330 loop : -0.87 (0.23), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.002 ARG C 381 TYR 0.013 0.002 TYR A 202 PHE 0.026 0.002 PHE F 442 TRP 0.009 0.001 TRP B 271 HIS 0.003 0.001 HIS I 371 Details of bonding type rmsd/Z covalent geometry : bond 0.00545 / 0.24 ( 9162) covalent geometry : angle 0.86324 / 0.44 (12390) hydrogen bonds : bond 0.04432 / 2.76 ( 307) hydrogen bonds : angle 6.05242 / 4.15 ( 843) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 142 time to evaluate : 0.421 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 ASP cc_start: 0.8417 (t0) cc_final: 0.8138 (t0) REVERT: A 125 ARG cc_start: 0.7461 (ptm-80) cc_final: 0.7057 (ttp80) REVERT: B 238 ARG cc_start: 0.7609 (ttm-80) cc_final: 0.7254 (tpp-160) REVERT: B 287 PHE cc_start: 0.8496 (m-10) cc_final: 0.8009 (m-10) REVERT: C 449 LEU cc_start: 0.5404 (mt) cc_final: 0.5194 (tt) REVERT: D 412 VAL cc_start: 0.6811 (OUTLIER) cc_final: 0.6382 (t) REVERT: D 432 ASP cc_start: 0.8153 (t0) cc_final: 0.7799 (t0) outliers start: 43 outliers final: 26 residues processed: 171 average time/residue: 0.5189 time to fit residues: 95.0750 Evaluate side-chains 155 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 128 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 259 ASP Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 390 VAL Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 439 THR Chi-restraints excluded: chain C residue 459 VAL Chi-restraints excluded: chain D residue 390 VAL Chi-restraints excluded: chain D residue 401 LEU Chi-restraints excluded: chain D residue 412 VAL Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 222 LEU Chi-restraints excluded: chain E residue 272 LEU Chi-restraints excluded: chain E residue 297 VAL Chi-restraints excluded: chain F residue 410 LYS Chi-restraints excluded: chain F residue 439 THR Chi-restraints excluded: chain I residue 387 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: [24, 112, 68, 34, 2, 37, 56, 35, 33, 45, 1] chunk 24 optimal weight: 20.0000 chunk 112 optimal weight: 2.9990 chunk 68 optimal weight: 0.6980 chunk 34 optimal weight: 4.9990 chunk 2 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 56 optimal weight: 0.0020 chunk 35 optimal weight: 6.9990 chunk 33 optimal weight: 3.9990 chunk 45 optimal weight: 5.9990 chunk 1 optimal weight: 0.9980 overall best weight: 1.5392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 114 HIS ** A 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 337 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4675 r_free = 0.4675 target = 0.205665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4485 r_free = 0.4485 target = 0.184901 restraints weight = 19367.581| |-----------------------------------------------------------------------------| r_work (start): 0.4465 rms_B_bonded: 3.64 r_work: 0.4356 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.4356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6343 moved from start: 0.8161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 9162 Z= 0.210 Angle : 0.859 10.102 12390 Z= 0.433 Chirality : 0.052 0.217 1470 Planarity : 0.005 0.059 1626 Dihedral : 5.209 35.828 1266 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 16.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 4.59 % Allowed : 30.17 % Favored : 65.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.99 (0.23), residues: 1191 helix: -0.88 (0.35), residues: 205 sheet: 0.07 (0.29), residues: 331 loop : -0.93 (0.23), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.002 ARG B 129 TYR 0.012 0.001 TYR A 202 PHE 0.019 0.002 PHE F 442 TRP 0.009 0.001 TRP B 271 HIS 0.004 0.001 HIS I 371 Details of bonding type rmsd/Z covalent geometry : bond 0.00491 / 0.21 ( 9162) covalent geometry : angle 0.85935 / 0.43 (12390) hydrogen bonds : bond 0.04243 / 2.73 ( 307) hydrogen bonds : angle 6.05264 / 4.15 ( 843) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 136 time to evaluate : 0.290 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 ASP cc_start: 0.8451 (t0) cc_final: 0.8153 (t0) REVERT: A 113 ASN cc_start: 0.8336 (OUTLIER) cc_final: 0.8107 (t0) REVERT: A 125 ARG cc_start: 0.7563 (ptm-80) cc_final: 0.7297 (ttm-80) REVERT: B 287 PHE cc_start: 0.8610 (m-10) cc_final: 0.8045 (m-10) REVERT: B 320 LEU cc_start: 0.9073 (mp) cc_final: 0.8833 (tt) REVERT: D 412 VAL cc_start: 0.6966 (OUTLIER) cc_final: 0.6594 (t) REVERT: D 432 ASP cc_start: 0.8149 (t0) cc_final: 0.7815 (t0) outliers start: 45 outliers final: 27 residues processed: 167 average time/residue: 0.4688 time to fit residues: 84.3927 Evaluate side-chains 156 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 127 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 113 ASN Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 199 ASN Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 390 VAL Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 426 ASP Chi-restraints excluded: chain C residue 439 THR Chi-restraints excluded: chain C residue 459 VAL Chi-restraints excluded: chain D residue 381 ARG Chi-restraints excluded: chain D residue 393 LEU Chi-restraints excluded: chain D residue 397 GLN Chi-restraints excluded: chain D residue 401 LEU Chi-restraints excluded: chain D residue 412 VAL Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 145 VAL Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 222 LEU Chi-restraints excluded: chain E residue 272 LEU Chi-restraints excluded: chain E residue 297 VAL Chi-restraints excluded: chain F residue 390 VAL Chi-restraints excluded: chain F residue 408 VAL Chi-restraints excluded: chain H residue 371 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: [101, 51, 4, 27, 61, 50, 53, 83, 73, 63, 31] chunk 101 optimal weight: 8.9990 chunk 51 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 27 optimal weight: 5.9990 chunk 61 optimal weight: 0.7980 chunk 50 optimal weight: 6.9990 chunk 53 optimal weight: 4.9990 chunk 83 optimal weight: 3.9990 chunk 73 optimal weight: 0.4980 chunk 63 optimal weight: 0.4980 chunk 31 optimal weight: 7.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 337 ASN F 462 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4667 r_free = 0.4667 target = 0.204721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4472 r_free = 0.4472 target = 0.183520 restraints weight = 19175.520| |-----------------------------------------------------------------------------| r_work (start): 0.4449 rms_B_bonded: 3.76 r_work: 0.4335 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.4335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6390 moved from start: 0.8532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 9162 Z= 0.214 Angle : 0.884 11.682 12390 Z= 0.444 Chirality : 0.053 0.269 1470 Planarity : 0.005 0.067 1626 Dihedral : 5.382 35.893 1266 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 15.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 4.59 % Allowed : 29.87 % Favored : 65.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.00 (0.23), residues: 1191 helix: -0.91 (0.35), residues: 205 sheet: 0.14 (0.29), residues: 325 loop : -0.97 (0.22), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG C 381 TYR 0.015 0.001 TYR A 202 PHE 0.023 0.002 PHE F 442 TRP 0.011 0.001 TRP B 271 HIS 0.003 0.001 HIS I 371 Details of bonding type rmsd/Z covalent geometry : bond 0.00502 / 0.21 ( 9162) covalent geometry : angle 0.88447 / 0.44 (12390) hydrogen bonds : bond 0.04360 / 2.76 ( 307) hydrogen bonds : angle 6.04463 / 4.15 ( 843) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 139 time to evaluate : 0.350 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 ASP cc_start: 0.8544 (t0) cc_final: 0.8224 (t0) REVERT: A 125 ARG cc_start: 0.7633 (ptm-80) cc_final: 0.7254 (ttm-80) REVERT: A 350 ARG cc_start: 0.5817 (ttm170) cc_final: 0.5469 (ttp-110) REVERT: B 238 ARG cc_start: 0.7884 (ttm-80) cc_final: 0.7542 (tpp-160) REVERT: B 287 PHE cc_start: 0.8667 (m-10) cc_final: 0.8131 (m-10) REVERT: C 396 GLU cc_start: 0.6962 (pp20) cc_final: 0.6638 (pp20) REVERT: D 393 LEU cc_start: 0.4460 (OUTLIER) cc_final: 0.1695 (mp) REVERT: D 412 VAL cc_start: 0.6944 (OUTLIER) cc_final: 0.6663 (t) REVERT: D 432 ASP cc_start: 0.7935 (t0) cc_final: 0.7672 (t0) REVERT: E 125 ARG cc_start: 0.7874 (ptm-80) cc_final: 0.7458 (ptm-80) REVERT: F 382 SER cc_start: 0.2208 (m) cc_final: 0.1737 (t) outliers start: 45 outliers final: 29 residues processed: 171 average time/residue: 0.5039 time to fit residues: 92.4286 Evaluate side-chains 161 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 130 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 199 ASN Chi-restraints excluded: chain B residue 263 LYS Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 390 VAL Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 426 ASP Chi-restraints excluded: chain C residue 439 THR Chi-restraints excluded: chain C residue 440 LYS Chi-restraints excluded: chain C residue 459 VAL Chi-restraints excluded: chain D residue 386 LEU Chi-restraints excluded: chain D residue 393 LEU Chi-restraints excluded: chain D residue 397 GLN Chi-restraints excluded: chain D residue 401 LEU Chi-restraints excluded: chain D residue 412 VAL Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 145 VAL Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 222 LEU Chi-restraints excluded: chain E residue 272 LEU Chi-restraints excluded: chain E residue 279 VAL Chi-restraints excluded: chain E residue 297 VAL Chi-restraints excluded: chain F residue 410 LYS Chi-restraints excluded: chain F residue 439 THR Chi-restraints excluded: chain H residue 371 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: [9, 2, 81, 29, 88, 71, 70, 36, 44, 91, 90] chunk 9 optimal weight: 2.9990 chunk 2 optimal weight: 4.9990 chunk 81 optimal weight: 6.9990 chunk 29 optimal weight: 1.9990 chunk 88 optimal weight: 3.9990 chunk 71 optimal weight: 0.0030 chunk 70 optimal weight: 0.6980 chunk 36 optimal weight: 0.9980 chunk 44 optimal weight: 2.9990 chunk 91 optimal weight: 0.9980 chunk 90 optimal weight: 0.7980 overall best weight: 0.6990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 114 HIS A 207 GLN ** A 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4688 r_free = 0.4688 target = 0.207435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4486 r_free = 0.4486 target = 0.186359 restraints weight = 19743.762| |-----------------------------------------------------------------------------| r_work (start): 0.4477 rms_B_bonded: 3.63 r_work: 0.4373 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.4373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6280 moved from start: 0.8574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 9162 Z= 0.154 Angle : 0.855 11.995 12390 Z= 0.419 Chirality : 0.051 0.186 1470 Planarity : 0.005 0.075 1626 Dihedral : 4.840 26.393 1266 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.53 % Favored : 96.39 % Rotamer: Outliers : 3.06 % Allowed : 31.50 % Favored : 65.44 % 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: -0.92 (0.23), residues: 1191 helix: -0.68 (0.36), residues: 205 sheet: 0.10 (0.29), residues: 318 loop : -0.92 (0.22), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG D 461 TYR 0.010 0.001 TYR A 202 PHE 0.021 0.002 PHE E 287 TRP 0.007 0.001 TRP B 271 HIS 0.003 0.001 HIS I 371 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.15 ( 9162) covalent geometry : angle 0.85502 / 0.42 (12390) hydrogen bonds : bond 0.03651 / 2.33 ( 307) hydrogen bonds : angle 5.62092 / 3.88 ( 843) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 140 time to evaluate : 0.314 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 ASP cc_start: 0.8492 (t0) cc_final: 0.8187 (t0) REVERT: A 125 ARG cc_start: 0.7532 (ptm-80) cc_final: 0.7311 (ttm-80) REVERT: A 312 GLN cc_start: 0.8338 (pm20) cc_final: 0.7870 (pm20) REVERT: A 317 ILE cc_start: 0.9163 (tp) cc_final: 0.8782 (pp) REVERT: B 287 PHE cc_start: 0.8621 (m-10) cc_final: 0.8101 (m-10) REVERT: C 396 GLU cc_start: 0.6934 (pp20) cc_final: 0.6562 (pp20) REVERT: D 412 VAL cc_start: 0.6862 (OUTLIER) cc_final: 0.6614 (t) REVERT: D 432 ASP cc_start: 0.8006 (t0) cc_final: 0.7765 (t0) REVERT: F 434 LYS cc_start: 0.6464 (ptmt) cc_final: 0.6154 (pttt) outliers start: 30 outliers final: 21 residues processed: 159 average time/residue: 0.5350 time to fit residues: 90.8913 Evaluate side-chains 149 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 127 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain B residue 199 ASN Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 439 THR Chi-restraints excluded: chain C residue 455 VAL Chi-restraints excluded: chain C residue 459 VAL Chi-restraints excluded: chain D residue 401 LEU Chi-restraints excluded: chain D residue 412 VAL Chi-restraints excluded: chain D residue 429 THR Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 222 LEU Chi-restraints excluded: chain E residue 272 LEU Chi-restraints excluded: chain E residue 297 VAL Chi-restraints excluded: chain F residue 410 LYS Chi-restraints excluded: chain F residue 437 THR Chi-restraints excluded: chain H residue 371 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: [103, 24, 63, 85, 67, 0, 37, 58, 64, 60, 114] chunk 103 optimal weight: 8.9990 chunk 24 optimal weight: 8.9990 chunk 63 optimal weight: 3.9990 chunk 85 optimal weight: 0.0670 chunk 67 optimal weight: 0.3980 chunk 0 optimal weight: 5.9990 chunk 37 optimal weight: 3.9990 chunk 58 optimal weight: 0.5980 chunk 64 optimal weight: 0.5980 chunk 60 optimal weight: 0.6980 chunk 114 optimal weight: 9.9990 overall best weight: 0.4718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 95 GLN ** D 462 GLN ** 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 = 0.4708 r_free = 0.4708 target = 0.209286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4503 r_free = 0.4503 target = 0.187794 restraints weight = 19515.087| |-----------------------------------------------------------------------------| r_work (start): 0.4491 rms_B_bonded: 3.51 r_work: 0.4400 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.4400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6214 moved from start: 0.8677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9162 Z= 0.148 Angle : 0.866 12.131 12390 Z= 0.422 Chirality : 0.050 0.205 1470 Planarity : 0.005 0.076 1626 Dihedral : 4.574 22.944 1266 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 2.45 % Allowed : 32.93 % Favored : 64.63 % 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: -0.83 (0.23), residues: 1191 helix: -0.49 (0.37), residues: 205 sheet: 0.08 (0.29), residues: 321 loop : -0.85 (0.22), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG D 461 TYR 0.007 0.001 TYR A 202 PHE 0.019 0.002 PHE E 236 TRP 0.006 0.001 TRP B 271 HIS 0.003 0.001 HIS I 371 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.15 ( 9162) covalent geometry : angle 0.86610 / 0.42 (12390) hydrogen bonds : bond 0.03413 / 2.22 ( 307) hydrogen bonds : angle 5.50216 / 3.80 ( 843) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 133 time to evaluate : 0.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 ASP cc_start: 0.8419 (t0) cc_final: 0.8113 (t0) REVERT: A 202 TYR cc_start: 0.7454 (m-80) cc_final: 0.7242 (m-80) REVERT: B 238 ARG cc_start: 0.7842 (ttm-80) cc_final: 0.7519 (tpp-160) REVERT: B 287 PHE cc_start: 0.8613 (m-10) cc_final: 0.8042 (m-10) REVERT: C 396 GLU cc_start: 0.6856 (pp20) cc_final: 0.6502 (pp20) REVERT: D 412 VAL cc_start: 0.6838 (OUTLIER) cc_final: 0.6619 (t) outliers start: 24 outliers final: 21 residues processed: 151 average time/residue: 0.5115 time to fit residues: 82.7780 Evaluate side-chains 143 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 121 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 199 ASN Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 439 THR Chi-restraints excluded: chain C residue 459 VAL Chi-restraints excluded: chain D residue 401 LEU Chi-restraints excluded: chain D residue 412 VAL Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 222 LEU Chi-restraints excluded: chain E residue 272 LEU Chi-restraints excluded: chain E residue 279 VAL Chi-restraints excluded: chain E residue 297 VAL Chi-restraints excluded: chain F residue 390 VAL Chi-restraints excluded: chain F residue 410 LYS Chi-restraints excluded: chain F residue 437 THR Chi-restraints excluded: chain H residue 371 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: [103, 44, 76, 90, 111, 23, 13, 14, 65, 31, 0] chunk 103 optimal weight: 6.9990 chunk 44 optimal weight: 0.8980 chunk 76 optimal weight: 0.4980 chunk 90 optimal weight: 5.9990 chunk 111 optimal weight: 0.5980 chunk 23 optimal weight: 0.0570 chunk 13 optimal weight: 3.9990 chunk 14 optimal weight: 0.7980 chunk 65 optimal weight: 0.7980 chunk 31 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 353 GLN ** 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 = 0.4707 r_free = 0.4707 target = 0.209185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4499 r_free = 0.4499 target = 0.187466 restraints weight = 19357.744| |-----------------------------------------------------------------------------| r_work (start): 0.4487 rms_B_bonded: 3.48 r_work: 0.4396 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.4396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6217 moved from start: 0.8785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 9162 Z= 0.152 Angle : 0.890 12.565 12390 Z= 0.433 Chirality : 0.051 0.232 1470 Planarity : 0.005 0.066 1626 Dihedral : 4.534 24.144 1266 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 13.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 2.55 % Allowed : 33.03 % Favored : 64.42 % 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: -0.79 (0.23), residues: 1191 helix: -0.54 (0.37), residues: 205 sheet: 0.18 (0.30), residues: 300 loop : -0.80 (0.22), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 461 TYR 0.007 0.001 TYR A 202 PHE 0.021 0.002 PHE E 287 TRP 0.005 0.001 TRP B 271 HIS 0.014 0.001 HIS E 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.15 ( 9162) covalent geometry : angle 0.88978 / 0.43 (12390) hydrogen bonds : bond 0.03486 / 2.27 ( 307) hydrogen bonds : angle 5.47416 / 3.76 ( 843) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3488.37 seconds wall clock time: 59 minutes 58.36 seconds (3598.36 seconds total)