Starting phenix.real_space_refine on Wed Sep 17 14:04:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8y91_39066/09_2025/8y91_39066.cif Found real_map, /net/cci-nas-00/data/ceres_data/8y91_39066/09_2025/8y91_39066.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.13 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8y91_39066/09_2025/8y91_39066.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8y91_39066/09_2025/8y91_39066.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8y91_39066/09_2025/8y91_39066.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8y91_39066/09_2025/8y91_39066.map" } resolution = 3.13 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= 0.057 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians S 40 5.16 5 Cl 2 4.86 5 Na 2 4.78 5 C 6084 2.51 5 N 1416 2.21 5 O 1528 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9072 Number of models: 1 Model: "" Number of chains: 4 Chain: "D" Number of atoms: 4516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 565, 4516 Classifications: {'peptide': 565} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 544} Chain: "A" Number of atoms: 4516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 565, 4516 Classifications: {'peptide': 565} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 544} Chain: "D" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 20 Unusual residues: {' CL': 1, ' NA': 1, 'A1LX5': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 20 Unusual residues: {' CL': 1, ' NA': 1, 'A1LX5': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 2.06, per 1000 atoms: 0.23 Number of scatterers: 9072 At special positions: 0 Unit cell: (78.11, 120.45, 89.79, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 2 17.00 S 40 16.00 Na 2 11.00 O 1528 8.00 N 1416 7.00 C 6084 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: 0.74 Conformation dependent library (CDL) restraints added in 351.7 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2076 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 0 sheets defined 78.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'D' and resid 61 through 74 removed outlier: 3.669A pdb=" N PHE D 65 " --> pdb=" O LYS D 61 " (cutoff:3.500A) Processing helix chain 'D' and resid 75 through 81 removed outlier: 3.621A pdb=" N VAL D 79 " --> pdb=" O ASP D 75 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 89 Processing helix chain 'D' and resid 90 through 93 Processing helix chain 'D' and resid 94 through 107 removed outlier: 3.905A pdb=" N LEU D 100 " --> pdb=" O ILE D 96 " (cutoff:3.500A) Processing helix chain 'D' and resid 107 through 120 Processing helix chain 'D' and resid 124 through 133 removed outlier: 3.835A pdb=" N VAL D 127 " --> pdb=" O ALA D 124 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N TRP D 128 " --> pdb=" O ALA D 125 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N LYS D 129 " --> pdb=" O THR D 126 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N ILE D 130 " --> pdb=" O VAL D 127 " (cutoff:3.500A) Proline residue: D 132 - end of helix Processing helix chain 'D' and resid 134 through 151 removed outlier: 3.761A pdb=" N ILE D 142 " --> pdb=" O GLY D 138 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLY D 149 " --> pdb=" O ALA D 145 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N TYR D 151 " --> pdb=" O TYR D 147 " (cutoff:3.500A) Processing helix chain 'D' and resid 151 through 166 removed outlier: 3.641A pdb=" N ILE D 156 " --> pdb=" O TYR D 152 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N TYR D 162 " --> pdb=" O TRP D 158 " (cutoff:3.500A) Processing helix chain 'D' and resid 208 through 219 removed outlier: 4.013A pdb=" N TYR D 214 " --> pdb=" O ALA D 210 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLU D 215 " --> pdb=" O ALA D 211 " (cutoff:3.500A) Processing helix chain 'D' and resid 220 through 224 Processing helix chain 'D' and resid 234 through 253 Processing helix chain 'D' and resid 255 through 267 removed outlier: 3.769A pdb=" N SER D 259 " --> pdb=" O GLY D 255 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N LYS D 261 " --> pdb=" O LYS D 257 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N TRP D 264 " --> pdb=" O GLY D 260 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N ILE D 265 " --> pdb=" O LYS D 261 " (cutoff:3.500A) Processing helix chain 'D' and resid 268 through 283 removed outlier: 3.554A pdb=" N PHE D 272 " --> pdb=" O THR D 268 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N THR D 283 " --> pdb=" O VAL D 279 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 295 removed outlier: 3.652A pdb=" N GLY D 290 " --> pdb=" O GLY D 286 " (cutoff:3.500A) Processing helix chain 'D' and resid 303 through 320 removed outlier: 4.838A pdb=" N ILE D 309 " --> pdb=" O ALA D 305 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N ASP D 310 " --> pdb=" O THR D 306 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLY D 320 " --> pdb=" O PHE D 316 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 331 Processing helix chain 'D' and resid 338 through 372 removed outlier: 3.610A pdb=" N ASP D 342 " --> pdb=" O ASN D 338 " (cutoff:3.500A) Processing helix chain 'D' and resid 375 through 380 removed outlier: 3.930A pdb=" N VAL D 379 " --> pdb=" O ASN D 375 " (cutoff:3.500A) Processing helix chain 'D' and resid 383 through 389 removed outlier: 3.730A pdb=" N VAL D 387 " --> pdb=" O GLY D 383 " (cutoff:3.500A) Processing helix chain 'D' and resid 390 through 398 removed outlier: 3.684A pdb=" N THR D 397 " --> pdb=" O GLU D 393 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU D 398 " --> pdb=" O ALA D 394 " (cutoff:3.500A) Processing helix chain 'D' and resid 400 through 435 removed outlier: 3.704A pdb=" N TRP D 404 " --> pdb=" O GLY D 400 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N SER D 419 " --> pdb=" O LEU D 415 " (cutoff:3.500A) Processing helix chain 'D' and resid 435 through 441 removed outlier: 3.812A pdb=" N LYS D 439 " --> pdb=" O PHE D 435 " (cutoff:3.500A) Processing helix chain 'D' and resid 441 through 456 Processing helix chain 'D' and resid 464 through 494 removed outlier: 3.866A pdb=" N VAL D 468 " --> pdb=" O GLY D 464 " (cutoff:3.500A) Processing helix chain 'D' and resid 497 through 509 Processing helix chain 'D' and resid 514 through 523 removed outlier: 3.505A pdb=" N ARG D 518 " --> pdb=" O GLY D 514 " (cutoff:3.500A) Processing helix chain 'D' and resid 524 through 529 Processing helix chain 'D' and resid 530 through 539 Processing helix chain 'D' and resid 551 through 579 removed outlier: 3.811A pdb=" N ASN D 555 " --> pdb=" O PRO D 551 " (cutoff:3.500A) Proline residue: D 570 - end of helix Processing helix chain 'D' and resid 583 through 589 Processing helix chain 'D' and resid 598 through 604 removed outlier: 3.929A pdb=" N ALA D 602 " --> pdb=" O HIS D 598 " (cutoff:3.500A) Processing helix chain 'D' and resid 610 through 615 removed outlier: 4.030A pdb=" N TRP D 614 " --> pdb=" O GLN D 610 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 74 removed outlier: 3.661A pdb=" N PHE A 65 " --> pdb=" O LYS A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 81 removed outlier: 3.632A pdb=" N VAL A 79 " --> pdb=" O ASP A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 89 Processing helix chain 'A' and resid 90 through 93 Processing helix chain 'A' and resid 94 through 107 removed outlier: 3.914A pdb=" N LEU A 100 " --> pdb=" O ILE A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 120 Processing helix chain 'A' and resid 124 through 128 removed outlier: 3.824A pdb=" N VAL A 127 " --> pdb=" O ALA A 124 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N TRP A 128 " --> pdb=" O ALA A 125 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 124 through 128' Processing helix chain 'A' and resid 131 through 133 No H-bonds generated for 'chain 'A' and resid 131 through 133' Processing helix chain 'A' and resid 134 through 151 removed outlier: 3.764A pdb=" N ILE A 142 " --> pdb=" O GLY A 138 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLY A 149 " --> pdb=" O ALA A 145 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N TYR A 151 " --> pdb=" O TYR A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 166 removed outlier: 3.640A pdb=" N ILE A 156 " --> pdb=" O TYR A 152 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N TYR A 162 " --> pdb=" O TRP A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 219 removed outlier: 4.012A pdb=" N TYR A 214 " --> pdb=" O ALA A 210 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLU A 215 " --> pdb=" O ALA A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 224 Processing helix chain 'A' and resid 234 through 253 Processing helix chain 'A' and resid 255 through 267 removed outlier: 3.762A pdb=" N SER A 259 " --> pdb=" O GLY A 255 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N LYS A 261 " --> pdb=" O LYS A 257 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N TRP A 264 " --> pdb=" O GLY A 260 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ILE A 265 " --> pdb=" O LYS A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 283 removed outlier: 3.557A pdb=" N PHE A 272 " --> pdb=" O THR A 268 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N THR A 283 " --> pdb=" O VAL A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 295 removed outlier: 3.653A pdb=" N GLY A 290 " --> pdb=" O GLY A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 320 removed outlier: 3.511A pdb=" N VAL A 307 " --> pdb=" O LYS A 303 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N ILE A 309 " --> pdb=" O ALA A 305 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N ASP A 310 " --> pdb=" O THR A 306 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLY A 320 " --> pdb=" O PHE A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 331 Processing helix chain 'A' and resid 338 through 372 removed outlier: 3.617A pdb=" N ASP A 342 " --> pdb=" O ASN A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 380 removed outlier: 3.932A pdb=" N VAL A 379 " --> pdb=" O ASN A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 389 removed outlier: 3.722A pdb=" N VAL A 387 " --> pdb=" O GLY A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 398 removed outlier: 3.684A pdb=" N THR A 397 " --> pdb=" O GLU A 393 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEU A 398 " --> pdb=" O ALA A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 435 removed outlier: 3.707A pdb=" N TRP A 404 " --> pdb=" O GLY A 400 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N SER A 419 " --> pdb=" O LEU A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 441 removed outlier: 3.816A pdb=" N LYS A 439 " --> pdb=" O PHE A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 456 Processing helix chain 'A' and resid 464 through 494 removed outlier: 3.864A pdb=" N VAL A 468 " --> pdb=" O GLY A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 509 Processing helix chain 'A' and resid 514 through 523 removed outlier: 3.527A pdb=" N ARG A 518 " --> pdb=" O GLY A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 539 Processing helix chain 'A' and resid 551 through 579 removed outlier: 3.809A pdb=" N ASN A 555 " --> pdb=" O PRO A 551 " (cutoff:3.500A) Proline residue: A 570 - end of helix Processing helix chain 'A' and resid 583 through 589 Processing helix chain 'A' and resid 598 through 604 removed outlier: 3.924A pdb=" N ALA A 602 " --> pdb=" O HIS A 598 " (cutoff:3.500A) Processing helix chain 'A' and resid 610 through 615 removed outlier: 4.036A pdb=" N TRP A 614 " --> pdb=" O GLN A 610 " (cutoff:3.500A) 546 hydrogen bonds defined for protein. 1617 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: 1.15 Time building geometry restraints manager: 0.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2671 1.34 - 1.46: 2605 1.46 - 1.58: 4026 1.58 - 1.70: 2 1.70 - 1.81: 62 Bond restraints: 9366 Sorted by residual: bond pdb=" C01 A1LX5 D 703 " pdb=" N02 A1LX5 D 703 " ideal model delta sigma weight residual 1.444 1.290 0.154 2.00e-02 2.50e+03 5.93e+01 bond pdb=" C01 A1LX5 A 701 " pdb=" N02 A1LX5 A 701 " ideal model delta sigma weight residual 1.444 1.291 0.153 2.00e-02 2.50e+03 5.84e+01 bond pdb=" C07 A1LX5 A 701 " pdb=" N02 A1LX5 A 701 " ideal model delta sigma weight residual 1.444 1.375 0.069 2.00e-02 2.50e+03 1.19e+01 bond pdb=" C07 A1LX5 D 703 " pdb=" N02 A1LX5 D 703 " ideal model delta sigma weight residual 1.444 1.376 0.068 2.00e-02 2.50e+03 1.16e+01 bond pdb=" C05 A1LX5 D 703 " pdb=" C06 A1LX5 D 703 " ideal model delta sigma weight residual 1.391 1.325 0.066 2.00e-02 2.50e+03 1.10e+01 ... (remaining 9361 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.64: 12521 1.64 - 3.27: 222 3.27 - 4.91: 29 4.91 - 6.54: 8 6.54 - 8.18: 2 Bond angle restraints: 12782 Sorted by residual: angle pdb=" C GLY D 106 " pdb=" N MET D 107 " pdb=" CA MET D 107 " ideal model delta sigma weight residual 121.80 113.62 8.18 2.44e+00 1.68e-01 1.12e+01 angle pdb=" C GLY A 106 " pdb=" N MET A 107 " pdb=" CA MET A 107 " ideal model delta sigma weight residual 121.80 113.65 8.15 2.44e+00 1.68e-01 1.12e+01 angle pdb=" N ASP D 546 " pdb=" CA ASP D 546 " pdb=" C ASP D 546 " ideal model delta sigma weight residual 111.11 107.54 3.57 1.20e+00 6.94e-01 8.85e+00 angle pdb=" N ASP A 546 " pdb=" CA ASP A 546 " pdb=" C ASP A 546 " ideal model delta sigma weight residual 111.11 107.59 3.52 1.20e+00 6.94e-01 8.63e+00 angle pdb=" C ASP D 546 " pdb=" CA ASP D 546 " pdb=" CB ASP D 546 " ideal model delta sigma weight residual 110.81 115.42 -4.61 1.60e+00 3.91e-01 8.30e+00 ... (remaining 12777 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.97: 4884 14.97 - 29.93: 238 29.93 - 44.90: 93 44.90 - 59.86: 19 59.86 - 74.83: 8 Dihedral angle restraints: 5242 sinusoidal: 1978 harmonic: 3264 Sorted by residual: dihedral pdb=" CA THR A 179 " pdb=" C THR A 179 " pdb=" N TRP A 180 " pdb=" CA TRP A 180 " ideal model delta harmonic sigma weight residual -180.00 -129.07 -50.93 0 5.00e+00 4.00e-02 1.04e+02 dihedral pdb=" CA THR D 179 " pdb=" C THR D 179 " pdb=" N TRP D 180 " pdb=" CA TRP D 180 " ideal model delta harmonic sigma weight residual 180.00 -129.08 -50.92 0 5.00e+00 4.00e-02 1.04e+02 dihedral pdb=" CA HIS A 178 " pdb=" C HIS A 178 " pdb=" N THR A 179 " pdb=" CA THR A 179 " ideal model delta harmonic sigma weight residual 180.00 149.81 30.19 0 5.00e+00 4.00e-02 3.65e+01 ... (remaining 5239 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 1392 0.093 - 0.185: 26 0.185 - 0.278: 0 0.278 - 0.371: 0 0.371 - 0.464: 2 Chirality restraints: 1420 Sorted by residual: chirality pdb=" C04 A1LX5 D 703 " pdb=" C03 A1LX5 D 703 " pdb=" C05 A1LX5 D 703 " pdb=" C13 A1LX5 D 703 " both_signs ideal model delta sigma weight residual False 2.49 2.96 -0.46 2.00e-01 2.50e+01 5.37e+00 chirality pdb=" C04 A1LX5 A 701 " pdb=" C03 A1LX5 A 701 " pdb=" C05 A1LX5 A 701 " pdb=" C13 A1LX5 A 701 " both_signs ideal model delta sigma weight residual False 2.49 2.95 -0.46 2.00e-01 2.50e+01 5.30e+00 chirality pdb=" CA MET A 107 " pdb=" N MET A 107 " pdb=" C MET A 107 " pdb=" CB MET A 107 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.88e-01 ... (remaining 1417 not shown) Planarity restraints: 1556 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE D 104 " 0.011 2.00e-02 2.50e+03 2.22e-02 4.94e+00 pdb=" C ILE D 104 " -0.038 2.00e-02 2.50e+03 pdb=" O ILE D 104 " 0.014 2.00e-02 2.50e+03 pdb=" N ALA D 105 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 104 " -0.011 2.00e-02 2.50e+03 2.11e-02 4.45e+00 pdb=" C ILE A 104 " 0.036 2.00e-02 2.50e+03 pdb=" O ILE A 104 " -0.014 2.00e-02 2.50e+03 pdb=" N ALA A 105 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 103 " -0.010 2.00e-02 2.50e+03 1.94e-02 3.77e+00 pdb=" C ILE A 103 " 0.034 2.00e-02 2.50e+03 pdb=" O ILE A 103 " -0.013 2.00e-02 2.50e+03 pdb=" N ILE A 104 " -0.011 2.00e-02 2.50e+03 ... (remaining 1553 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 44 2.53 - 3.12: 7168 3.12 - 3.72: 14844 3.72 - 4.31: 20964 4.31 - 4.90: 34263 Nonbonded interactions: 77283 Sorted by model distance: nonbonded pdb=" O GLY A 71 " pdb="NA NA A 702 " model vdw 1.938 2.470 nonbonded pdb=" O GLY D 71 " pdb="NA NA D 701 " model vdw 2.046 2.470 nonbonded pdb=" O ALA A 476 " pdb=" OG SER A 480 " model vdw 2.224 3.040 nonbonded pdb=" O ALA D 476 " pdb=" OG SER D 480 " model vdw 2.228 3.040 nonbonded pdb=" O TRP D 264 " pdb=" OG1 THR D 268 " model vdw 2.267 3.040 ... (remaining 77278 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: 0.02 Found NCS groups: ncs_group { reference = (chain 'A' and resid 53 through 617) selection = (chain 'D' and resid 53 through 617) } 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: 2.180 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: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 8.810 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6260 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 0.154 9366 Z= 0.199 Angle : 0.553 8.181 12782 Z= 0.332 Chirality : 0.039 0.464 1420 Planarity : 0.004 0.035 1556 Dihedral : 11.479 74.830 3166 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 5.04 % Allowed : 6.93 % Favored : 88.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.37 % 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 aren not related in a simple way. whole: -1.65 (0.24), residues: 1126 helix: -0.80 (0.17), residues: 746 sheet: None (None), residues: 0 loop : -1.42 (0.33), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 216 TYR 0.013 0.001 TYR D 98 PHE 0.012 0.001 PHE A 362 TRP 0.007 0.001 TRP D 553 HIS 0.001 0.000 HIS D 222 Details of bonding type rmsd covalent geometry : bond 0.00370 ( 9366) covalent geometry : angle 0.55347 (12782) hydrogen bonds : bond 0.16178 ( 546) hydrogen bonds : angle 6.52136 ( 1617) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 278 time to evaluate : 0.223 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 119 TYR cc_start: 0.7341 (t80) cc_final: 0.6938 (t80) REVERT: D 264 TRP cc_start: 0.5833 (m100) cc_final: 0.5394 (m-10) REVERT: D 303 LYS cc_start: 0.7237 (OUTLIER) cc_final: 0.6993 (ptmt) REVERT: D 341 ARG cc_start: 0.7259 (ttp-110) cc_final: 0.6742 (ttm-80) REVERT: D 344 LEU cc_start: 0.7082 (mt) cc_final: 0.6835 (mp) REVERT: D 376 ILE cc_start: 0.8364 (OUTLIER) cc_final: 0.7933 (mt) REVERT: D 507 GLN cc_start: 0.8029 (tt0) cc_final: 0.7709 (tt0) REVERT: D 544 THR cc_start: 0.7020 (p) cc_final: 0.6751 (t) REVERT: D 545 TYR cc_start: 0.6371 (t80) cc_final: 0.5415 (t80) REVERT: A 119 TYR cc_start: 0.7339 (t80) cc_final: 0.6934 (t80) REVERT: A 264 TRP cc_start: 0.5841 (m100) cc_final: 0.5385 (m-10) REVERT: A 341 ARG cc_start: 0.7264 (ttp-110) cc_final: 0.6753 (ttm-80) REVERT: A 344 LEU cc_start: 0.7073 (mt) cc_final: 0.6825 (mp) REVERT: A 376 ILE cc_start: 0.8353 (OUTLIER) cc_final: 0.7951 (mt) REVERT: A 507 GLN cc_start: 0.8028 (tt0) cc_final: 0.7703 (tt0) REVERT: A 544 THR cc_start: 0.7022 (p) cc_final: 0.6769 (t) REVERT: A 545 TYR cc_start: 0.6360 (t80) cc_final: 0.5450 (t80) outliers start: 48 outliers final: 11 residues processed: 313 average time/residue: 0.0854 time to fit residues: 37.8920 Evaluate side-chains 174 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 160 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 173 TRP Chi-restraints excluded: chain D residue 227 ILE Chi-restraints excluded: chain D residue 303 LYS Chi-restraints excluded: chain D residue 309 ILE Chi-restraints excluded: chain D residue 315 ILE Chi-restraints excluded: chain D residue 376 ILE Chi-restraints excluded: chain D residue 598 HIS Chi-restraints excluded: chain A residue 173 TRP Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 376 ILE Chi-restraints excluded: chain A residue 528 PHE Chi-restraints excluded: chain A residue 598 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 108 optimal weight: 0.7980 chunk 49 optimal weight: 0.6980 chunk 97 optimal weight: 0.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 100 optimal weight: 0.7980 chunk 106 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.189758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.165701 restraints weight = 11251.500| |-----------------------------------------------------------------------------| r_work (start): 0.3906 rms_B_bonded: 1.58 r_work: 0.3813 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3693 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.2831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9366 Z= 0.146 Angle : 0.590 8.447 12782 Z= 0.297 Chirality : 0.040 0.167 1420 Planarity : 0.005 0.046 1556 Dihedral : 6.479 49.396 1276 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 3.89 % Allowed : 14.29 % Favored : 81.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.37 % 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 aren not related in a simple way. whole: -0.28 (0.25), residues: 1126 helix: 0.28 (0.18), residues: 764 sheet: None (None), residues: 0 loop : -1.00 (0.34), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 81 TYR 0.016 0.002 TYR A 575 PHE 0.021 0.002 PHE A 94 TRP 0.012 0.001 TRP D 128 HIS 0.008 0.001 HIS A 370 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 9366) covalent geometry : angle 0.59020 (12782) hydrogen bonds : bond 0.04986 ( 546) hydrogen bonds : angle 5.08802 ( 1617) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 196 time to evaluate : 0.279 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 250 PHE cc_start: 0.8306 (m-10) cc_final: 0.7940 (m-80) REVERT: D 264 TRP cc_start: 0.6530 (m100) cc_final: 0.5763 (m-10) REVERT: D 309 ILE cc_start: 0.7412 (OUTLIER) cc_final: 0.6831 (mp) REVERT: D 376 ILE cc_start: 0.8109 (OUTLIER) cc_final: 0.7571 (mt) REVERT: D 585 TRP cc_start: 0.6099 (m100) cc_final: 0.5718 (m100) REVERT: D 604 ARG cc_start: 0.5492 (tpt170) cc_final: 0.5208 (mtt-85) REVERT: A 250 PHE cc_start: 0.8309 (m-10) cc_final: 0.7928 (m-80) REVERT: A 264 TRP cc_start: 0.6558 (m100) cc_final: 0.5777 (m-10) REVERT: A 376 ILE cc_start: 0.8113 (OUTLIER) cc_final: 0.7612 (mt) REVERT: A 585 TRP cc_start: 0.6100 (m100) cc_final: 0.5727 (m100) outliers start: 37 outliers final: 18 residues processed: 221 average time/residue: 0.0843 time to fit residues: 26.9592 Evaluate side-chains 183 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 162 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 173 TRP Chi-restraints excluded: chain D residue 227 ILE Chi-restraints excluded: chain D residue 230 ILE Chi-restraints excluded: chain D residue 309 ILE Chi-restraints excluded: chain D residue 315 ILE Chi-restraints excluded: chain D residue 364 ILE Chi-restraints excluded: chain D residue 376 ILE Chi-restraints excluded: chain D residue 378 ASP Chi-restraints excluded: chain D residue 437 VAL Chi-restraints excluded: chain D residue 598 HIS Chi-restraints excluded: chain A residue 173 TRP Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 376 ILE Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 528 PHE Chi-restraints excluded: chain A residue 598 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 26 optimal weight: 0.5980 chunk 50 optimal weight: 4.9990 chunk 60 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 2 optimal weight: 0.7980 chunk 34 optimal weight: 0.3980 chunk 80 optimal weight: 0.7980 chunk 99 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 chunk 72 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.186146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.161647 restraints weight = 11194.074| |-----------------------------------------------------------------------------| r_work (start): 0.3848 rms_B_bonded: 1.59 r_work: 0.3747 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3622 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.3353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9366 Z= 0.136 Angle : 0.574 8.886 12782 Z= 0.288 Chirality : 0.039 0.139 1420 Planarity : 0.004 0.031 1556 Dihedral : 6.180 47.390 1272 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 3.89 % Allowed : 15.02 % Favored : 81.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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 aren not related in a simple way. whole: 0.23 (0.25), residues: 1126 helix: 0.69 (0.19), residues: 764 sheet: None (None), residues: 0 loop : -0.85 (0.34), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 81 TYR 0.016 0.001 TYR A 152 PHE 0.021 0.002 PHE A 540 TRP 0.012 0.001 TRP D 80 HIS 0.005 0.001 HIS D 370 Details of bonding type rmsd covalent geometry : bond 0.00295 ( 9366) covalent geometry : angle 0.57382 (12782) hydrogen bonds : bond 0.04824 ( 546) hydrogen bonds : angle 5.07168 ( 1617) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 171 time to evaluate : 0.335 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 250 PHE cc_start: 0.8390 (m-10) cc_final: 0.8037 (m-80) REVERT: D 264 TRP cc_start: 0.6509 (m100) cc_final: 0.5668 (m-10) REVERT: D 298 ASP cc_start: 0.7324 (t70) cc_final: 0.6847 (t0) REVERT: D 309 ILE cc_start: 0.7424 (OUTLIER) cc_final: 0.6978 (mp) REVERT: D 376 ILE cc_start: 0.8144 (OUTLIER) cc_final: 0.7528 (mt) REVERT: D 585 TRP cc_start: 0.6095 (m100) cc_final: 0.5698 (m100) REVERT: D 604 ARG cc_start: 0.5653 (tpt170) cc_final: 0.5321 (mtt-85) REVERT: A 250 PHE cc_start: 0.8373 (m-10) cc_final: 0.8010 (m-80) REVERT: A 264 TRP cc_start: 0.6472 (m100) cc_final: 0.5655 (m-10) REVERT: A 298 ASP cc_start: 0.7316 (t70) cc_final: 0.6796 (t0) REVERT: A 376 ILE cc_start: 0.8136 (OUTLIER) cc_final: 0.7585 (mt) REVERT: A 585 TRP cc_start: 0.6009 (m100) cc_final: 0.5721 (m100) outliers start: 37 outliers final: 21 residues processed: 198 average time/residue: 0.0880 time to fit residues: 25.1061 Evaluate side-chains 187 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 163 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 173 TRP Chi-restraints excluded: chain D residue 227 ILE Chi-restraints excluded: chain D residue 230 ILE Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 309 ILE Chi-restraints excluded: chain D residue 364 ILE Chi-restraints excluded: chain D residue 376 ILE Chi-restraints excluded: chain D residue 437 VAL Chi-restraints excluded: chain D residue 481 ILE Chi-restraints excluded: chain D residue 529 LEU Chi-restraints excluded: chain D residue 598 HIS Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 173 TRP Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 376 ILE Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 528 PHE Chi-restraints excluded: chain A residue 598 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 82 optimal weight: 0.9990 chunk 95 optimal weight: 0.7980 chunk 7 optimal weight: 3.9990 chunk 96 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 53 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 91 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 90 optimal weight: 0.7980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.182151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.157100 restraints weight = 11471.944| |-----------------------------------------------------------------------------| r_work (start): 0.3798 rms_B_bonded: 1.62 r_work: 0.3697 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3573 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.3891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9366 Z= 0.146 Angle : 0.572 8.276 12782 Z= 0.290 Chirality : 0.039 0.134 1420 Planarity : 0.004 0.037 1556 Dihedral : 6.039 44.480 1268 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 3.78 % Allowed : 15.13 % Favored : 81.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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 aren not related in a simple way. whole: 0.41 (0.25), residues: 1126 helix: 0.89 (0.19), residues: 750 sheet: None (None), residues: 0 loop : -0.88 (0.34), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 81 TYR 0.016 0.001 TYR A 152 PHE 0.017 0.002 PHE D 316 TRP 0.011 0.001 TRP D 80 HIS 0.007 0.001 HIS D 372 Details of bonding type rmsd covalent geometry : bond 0.00327 ( 9366) covalent geometry : angle 0.57223 (12782) hydrogen bonds : bond 0.05100 ( 546) hydrogen bonds : angle 5.14362 ( 1617) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 184 time to evaluate : 0.348 Fit side-chains revert: symmetry clash REVERT: D 173 TRP cc_start: 0.6685 (OUTLIER) cc_final: 0.6308 (m-90) REVERT: D 264 TRP cc_start: 0.6509 (m100) cc_final: 0.5679 (m-10) REVERT: D 309 ILE cc_start: 0.7492 (OUTLIER) cc_final: 0.7095 (mp) REVERT: D 376 ILE cc_start: 0.8201 (OUTLIER) cc_final: 0.7544 (mt) REVERT: D 585 TRP cc_start: 0.6127 (m100) cc_final: 0.5696 (m100) REVERT: D 604 ARG cc_start: 0.5553 (tpt170) cc_final: 0.5298 (mtt-85) REVERT: A 173 TRP cc_start: 0.6715 (OUTLIER) cc_final: 0.6343 (m-90) REVERT: A 264 TRP cc_start: 0.6497 (m100) cc_final: 0.5666 (m-10) REVERT: A 309 ILE cc_start: 0.7410 (OUTLIER) cc_final: 0.7038 (mp) REVERT: A 376 ILE cc_start: 0.8200 (OUTLIER) cc_final: 0.7672 (mt) REVERT: A 585 TRP cc_start: 0.6033 (m100) cc_final: 0.5721 (m100) outliers start: 36 outliers final: 23 residues processed: 209 average time/residue: 0.0928 time to fit residues: 27.5818 Evaluate side-chains 179 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 150 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 173 TRP Chi-restraints excluded: chain D residue 199 HIS Chi-restraints excluded: chain D residue 227 ILE Chi-restraints excluded: chain D residue 230 ILE Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 309 ILE Chi-restraints excluded: chain D residue 364 ILE Chi-restraints excluded: chain D residue 376 ILE Chi-restraints excluded: chain D residue 381 THR Chi-restraints excluded: chain D residue 386 LEU Chi-restraints excluded: chain D residue 437 VAL Chi-restraints excluded: chain D residue 481 ILE Chi-restraints excluded: chain D residue 529 LEU Chi-restraints excluded: chain D residue 598 HIS Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 173 TRP Chi-restraints excluded: chain A residue 199 HIS Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 376 ILE Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 528 PHE Chi-restraints excluded: chain A residue 598 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 26 optimal weight: 0.6980 chunk 51 optimal weight: 0.3980 chunk 99 optimal weight: 2.9990 chunk 38 optimal weight: 0.7980 chunk 97 optimal weight: 2.9990 chunk 79 optimal weight: 0.9980 chunk 34 optimal weight: 0.5980 chunk 67 optimal weight: 2.9990 chunk 104 optimal weight: 0.9980 chunk 24 optimal weight: 8.9990 chunk 98 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.182582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.157538 restraints weight = 11407.102| |-----------------------------------------------------------------------------| r_work (start): 0.3799 rms_B_bonded: 1.61 r_work: 0.3696 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3574 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.4060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9366 Z= 0.135 Angle : 0.553 7.822 12782 Z= 0.281 Chirality : 0.039 0.141 1420 Planarity : 0.004 0.035 1556 Dihedral : 5.963 43.751 1268 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 4.31 % Allowed : 15.55 % Favored : 80.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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 aren not related in a simple way. whole: 0.65 (0.26), residues: 1126 helix: 1.07 (0.19), residues: 746 sheet: None (None), residues: 0 loop : -0.77 (0.33), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 81 TYR 0.016 0.001 TYR A 152 PHE 0.023 0.002 PHE A 213 TRP 0.009 0.001 TRP D 80 HIS 0.004 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 9366) covalent geometry : angle 0.55307 (12782) hydrogen bonds : bond 0.04945 ( 546) hydrogen bonds : angle 5.10788 ( 1617) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 153 time to evaluate : 0.359 Fit side-chains REVERT: D 118 GLN cc_start: 0.8274 (OUTLIER) cc_final: 0.8049 (tt0) REVERT: D 173 TRP cc_start: 0.6784 (OUTLIER) cc_final: 0.6501 (m-90) REVERT: D 190 LEU cc_start: 0.7708 (tt) cc_final: 0.7353 (pp) REVERT: D 264 TRP cc_start: 0.6517 (m100) cc_final: 0.5644 (m-10) REVERT: D 298 ASP cc_start: 0.7278 (t70) cc_final: 0.6706 (t0) REVERT: D 309 ILE cc_start: 0.7430 (OUTLIER) cc_final: 0.7081 (mp) REVERT: D 376 ILE cc_start: 0.8155 (OUTLIER) cc_final: 0.7475 (mt) REVERT: D 585 TRP cc_start: 0.6109 (m100) cc_final: 0.5678 (m100) REVERT: D 604 ARG cc_start: 0.5452 (tpt170) cc_final: 0.5236 (mtt-85) REVERT: A 173 TRP cc_start: 0.6775 (OUTLIER) cc_final: 0.6481 (m-90) REVERT: A 189 LYS cc_start: 0.7039 (pttp) cc_final: 0.6837 (pptt) REVERT: A 264 TRP cc_start: 0.6469 (m100) cc_final: 0.5628 (m-10) REVERT: A 298 ASP cc_start: 0.7246 (t70) cc_final: 0.6619 (t0) REVERT: A 309 ILE cc_start: 0.7436 (OUTLIER) cc_final: 0.7010 (mp) REVERT: A 376 ILE cc_start: 0.8109 (OUTLIER) cc_final: 0.7485 (mt) REVERT: A 585 TRP cc_start: 0.6058 (m100) cc_final: 0.5711 (m100) outliers start: 41 outliers final: 29 residues processed: 183 average time/residue: 0.0805 time to fit residues: 21.6414 Evaluate side-chains 184 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 148 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain D residue 118 GLN Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 173 TRP Chi-restraints excluded: chain D residue 191 LEU Chi-restraints excluded: chain D residue 199 HIS Chi-restraints excluded: chain D residue 227 ILE Chi-restraints excluded: chain D residue 230 ILE Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 309 ILE Chi-restraints excluded: chain D residue 364 ILE Chi-restraints excluded: chain D residue 376 ILE Chi-restraints excluded: chain D residue 381 THR Chi-restraints excluded: chain D residue 386 LEU Chi-restraints excluded: chain D residue 437 VAL Chi-restraints excluded: chain D residue 479 THR Chi-restraints excluded: chain D residue 481 ILE Chi-restraints excluded: chain D residue 529 LEU Chi-restraints excluded: chain D residue 598 HIS Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 173 TRP Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 199 HIS Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 376 ILE Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 598 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 92 optimal weight: 3.9990 chunk 72 optimal weight: 0.8980 chunk 11 optimal weight: 0.6980 chunk 47 optimal weight: 3.9990 chunk 6 optimal weight: 0.8980 chunk 39 optimal weight: 3.9990 chunk 23 optimal weight: 0.4980 chunk 0 optimal weight: 10.0000 chunk 56 optimal weight: 10.0000 chunk 97 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.181293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.156076 restraints weight = 11335.397| |-----------------------------------------------------------------------------| r_work (start): 0.3782 rms_B_bonded: 1.61 r_work: 0.3676 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3552 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.4239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9366 Z= 0.140 Angle : 0.564 11.011 12782 Z= 0.282 Chirality : 0.039 0.124 1420 Planarity : 0.004 0.036 1556 Dihedral : 5.833 39.389 1266 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 4.31 % Allowed : 15.55 % Favored : 80.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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 aren not related in a simple way. whole: 0.69 (0.26), residues: 1126 helix: 1.08 (0.19), residues: 750 sheet: None (None), residues: 0 loop : -0.72 (0.34), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 81 TYR 0.016 0.001 TYR D 111 PHE 0.017 0.002 PHE D 362 TRP 0.011 0.001 TRP A 80 HIS 0.004 0.001 HIS D 220 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 9366) covalent geometry : angle 0.56373 (12782) hydrogen bonds : bond 0.05065 ( 546) hydrogen bonds : angle 5.14962 ( 1617) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 164 time to evaluate : 0.348 Fit side-chains REVERT: D 173 TRP cc_start: 0.6833 (OUTLIER) cc_final: 0.6566 (m-90) REVERT: D 264 TRP cc_start: 0.6554 (m100) cc_final: 0.6245 (t60) REVERT: D 298 ASP cc_start: 0.7252 (t70) cc_final: 0.6697 (t0) REVERT: D 309 ILE cc_start: 0.7411 (OUTLIER) cc_final: 0.7084 (mp) REVERT: D 376 ILE cc_start: 0.8175 (OUTLIER) cc_final: 0.7576 (mt) REVERT: D 585 TRP cc_start: 0.6160 (m100) cc_final: 0.5718 (m100) REVERT: D 604 ARG cc_start: 0.5483 (tpt170) cc_final: 0.5225 (mtt-85) REVERT: A 173 TRP cc_start: 0.6828 (OUTLIER) cc_final: 0.6558 (m-90) REVERT: A 264 TRP cc_start: 0.6552 (m100) cc_final: 0.6265 (t60) REVERT: A 298 ASP cc_start: 0.7303 (t70) cc_final: 0.6703 (t0) REVERT: A 309 ILE cc_start: 0.7468 (OUTLIER) cc_final: 0.7163 (mp) REVERT: A 376 ILE cc_start: 0.8116 (OUTLIER) cc_final: 0.7460 (mt) REVERT: A 433 ASP cc_start: 0.7377 (m-30) cc_final: 0.7103 (m-30) outliers start: 41 outliers final: 31 residues processed: 187 average time/residue: 0.0823 time to fit residues: 22.6015 Evaluate side-chains 189 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 152 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 173 TRP Chi-restraints excluded: chain D residue 191 LEU Chi-restraints excluded: chain D residue 199 HIS Chi-restraints excluded: chain D residue 227 ILE Chi-restraints excluded: chain D residue 230 ILE Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 265 ILE Chi-restraints excluded: chain D residue 309 ILE Chi-restraints excluded: chain D residue 364 ILE Chi-restraints excluded: chain D residue 376 ILE Chi-restraints excluded: chain D residue 381 THR Chi-restraints excluded: chain D residue 386 LEU Chi-restraints excluded: chain D residue 437 VAL Chi-restraints excluded: chain D residue 479 THR Chi-restraints excluded: chain D residue 481 ILE Chi-restraints excluded: chain D residue 529 LEU Chi-restraints excluded: chain D residue 598 HIS Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 173 TRP Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 199 HIS Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 376 ILE Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 598 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 42 optimal weight: 0.7980 chunk 20 optimal weight: 6.9990 chunk 50 optimal weight: 0.9990 chunk 3 optimal weight: 0.5980 chunk 106 optimal weight: 0.8980 chunk 26 optimal weight: 0.9990 chunk 103 optimal weight: 0.0370 chunk 48 optimal weight: 0.2980 chunk 88 optimal weight: 3.9990 chunk 109 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 overall best weight: 0.5258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.183872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.158973 restraints weight = 11375.126| |-----------------------------------------------------------------------------| r_work (start): 0.3815 rms_B_bonded: 1.61 r_work: 0.3711 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3587 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.4256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9366 Z= 0.125 Angle : 0.549 9.376 12782 Z= 0.274 Chirality : 0.038 0.156 1420 Planarity : 0.004 0.032 1556 Dihedral : 5.724 39.838 1266 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 4.10 % Allowed : 16.60 % Favored : 79.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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 aren not related in a simple way. whole: 0.85 (0.26), residues: 1126 helix: 1.21 (0.19), residues: 750 sheet: None (None), residues: 0 loop : -0.67 (0.33), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 81 TYR 0.015 0.001 TYR D 152 PHE 0.015 0.001 PHE D 511 TRP 0.008 0.001 TRP D 80 HIS 0.004 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00271 ( 9366) covalent geometry : angle 0.54892 (12782) hydrogen bonds : bond 0.04808 ( 546) hydrogen bonds : angle 5.12272 ( 1617) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 156 time to evaluate : 0.289 Fit side-chains revert: symmetry clash REVERT: D 173 TRP cc_start: 0.6806 (OUTLIER) cc_final: 0.6122 (m-90) REVERT: D 264 TRP cc_start: 0.6518 (m100) cc_final: 0.6213 (t60) REVERT: D 298 ASP cc_start: 0.7311 (t70) cc_final: 0.6788 (t0) REVERT: D 309 ILE cc_start: 0.7483 (OUTLIER) cc_final: 0.7124 (mp) REVERT: D 376 ILE cc_start: 0.8170 (OUTLIER) cc_final: 0.7418 (mt) REVERT: A 107 MET cc_start: 0.7332 (mmt) cc_final: 0.6559 (mmt) REVERT: A 173 TRP cc_start: 0.6799 (OUTLIER) cc_final: 0.6118 (m-90) REVERT: A 264 TRP cc_start: 0.6465 (m100) cc_final: 0.6189 (t60) REVERT: A 309 ILE cc_start: 0.7483 (OUTLIER) cc_final: 0.7197 (mp) REVERT: A 376 ILE cc_start: 0.8102 (OUTLIER) cc_final: 0.7430 (mt) outliers start: 39 outliers final: 25 residues processed: 177 average time/residue: 0.0820 time to fit residues: 21.1631 Evaluate side-chains 183 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 152 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 173 TRP Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 191 LEU Chi-restraints excluded: chain D residue 199 HIS Chi-restraints excluded: chain D residue 227 ILE Chi-restraints excluded: chain D residue 230 ILE Chi-restraints excluded: chain D residue 242 MET Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 309 ILE Chi-restraints excluded: chain D residue 376 ILE Chi-restraints excluded: chain D residue 381 THR Chi-restraints excluded: chain D residue 386 LEU Chi-restraints excluded: chain D residue 437 VAL Chi-restraints excluded: chain D residue 479 THR Chi-restraints excluded: chain D residue 481 ILE Chi-restraints excluded: chain D residue 529 LEU Chi-restraints excluded: chain D residue 598 HIS Chi-restraints excluded: chain A residue 173 TRP Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 199 HIS Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 376 ILE Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 598 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 31 optimal weight: 0.8980 chunk 85 optimal weight: 0.6980 chunk 22 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 70 optimal weight: 9.9990 chunk 56 optimal weight: 9.9990 chunk 8 optimal weight: 0.6980 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.176404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.150045 restraints weight = 11357.807| |-----------------------------------------------------------------------------| r_work (start): 0.3717 rms_B_bonded: 1.66 r_work: 0.3606 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3479 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.4602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 9366 Z= 0.190 Angle : 0.631 11.422 12782 Z= 0.318 Chirality : 0.042 0.144 1420 Planarity : 0.005 0.038 1556 Dihedral : 6.076 39.772 1266 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 4.41 % Allowed : 16.07 % Favored : 79.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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 aren not related in a simple way. whole: 0.54 (0.25), residues: 1126 helix: 0.89 (0.19), residues: 764 sheet: None (None), residues: 0 loop : -0.67 (0.33), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 81 TYR 0.032 0.002 TYR A 111 PHE 0.021 0.002 PHE A 409 TRP 0.015 0.001 TRP D 80 HIS 0.006 0.001 HIS D 220 Details of bonding type rmsd covalent geometry : bond 0.00444 ( 9366) covalent geometry : angle 0.63128 (12782) hydrogen bonds : bond 0.05806 ( 546) hydrogen bonds : angle 5.37259 ( 1617) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 149 time to evaluate : 0.290 Fit side-chains revert: symmetry clash REVERT: D 173 TRP cc_start: 0.6993 (OUTLIER) cc_final: 0.6480 (m-90) REVERT: D 264 TRP cc_start: 0.6552 (m100) cc_final: 0.6238 (t60) REVERT: D 309 ILE cc_start: 0.7450 (OUTLIER) cc_final: 0.6969 (mp) REVERT: D 376 ILE cc_start: 0.8215 (OUTLIER) cc_final: 0.7543 (mt) REVERT: A 173 TRP cc_start: 0.6980 (OUTLIER) cc_final: 0.6462 (m-90) REVERT: A 264 TRP cc_start: 0.6513 (m100) cc_final: 0.6216 (t60) REVERT: A 298 ASP cc_start: 0.7439 (t70) cc_final: 0.6752 (t0) REVERT: A 309 ILE cc_start: 0.7525 (OUTLIER) cc_final: 0.7273 (mp) REVERT: A 376 ILE cc_start: 0.8153 (OUTLIER) cc_final: 0.7509 (mt) outliers start: 42 outliers final: 32 residues processed: 174 average time/residue: 0.0826 time to fit residues: 21.1971 Evaluate side-chains 184 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 146 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 173 TRP Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 191 LEU Chi-restraints excluded: chain D residue 199 HIS Chi-restraints excluded: chain D residue 212 GLU Chi-restraints excluded: chain D residue 227 ILE Chi-restraints excluded: chain D residue 230 ILE Chi-restraints excluded: chain D residue 242 MET Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 265 ILE Chi-restraints excluded: chain D residue 309 ILE Chi-restraints excluded: chain D residue 364 ILE Chi-restraints excluded: chain D residue 376 ILE Chi-restraints excluded: chain D residue 381 THR Chi-restraints excluded: chain D residue 386 LEU Chi-restraints excluded: chain D residue 437 VAL Chi-restraints excluded: chain D residue 479 THR Chi-restraints excluded: chain D residue 481 ILE Chi-restraints excluded: chain D residue 544 THR Chi-restraints excluded: chain D residue 598 HIS Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 173 TRP Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 199 HIS Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 376 ILE Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 598 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 14 optimal weight: 20.0000 chunk 105 optimal weight: 9.9990 chunk 62 optimal weight: 0.9980 chunk 27 optimal weight: 0.3980 chunk 44 optimal weight: 0.5980 chunk 50 optimal weight: 0.8980 chunk 10 optimal weight: 0.6980 chunk 60 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 8 optimal weight: 0.2980 chunk 95 optimal weight: 3.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.181315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.156267 restraints weight = 11280.186| |-----------------------------------------------------------------------------| r_work (start): 0.3794 rms_B_bonded: 1.60 r_work: 0.3695 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3571 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.4488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9366 Z= 0.131 Angle : 0.585 11.186 12782 Z= 0.290 Chirality : 0.039 0.140 1420 Planarity : 0.004 0.033 1556 Dihedral : 5.842 39.354 1266 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 3.57 % Allowed : 17.86 % Favored : 78.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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 aren not related in a simple way. whole: 0.67 (0.25), residues: 1126 helix: 1.02 (0.19), residues: 766 sheet: None (None), residues: 0 loop : -0.70 (0.34), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 81 TYR 0.022 0.001 TYR A 111 PHE 0.014 0.001 PHE D 362 TRP 0.009 0.001 TRP D 80 HIS 0.004 0.001 HIS D 220 Details of bonding type rmsd covalent geometry : bond 0.00284 ( 9366) covalent geometry : angle 0.58508 (12782) hydrogen bonds : bond 0.05026 ( 546) hydrogen bonds : angle 5.17819 ( 1617) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 156 time to evaluate : 0.335 Fit side-chains REVERT: D 264 TRP cc_start: 0.6490 (m100) cc_final: 0.6223 (t60) REVERT: D 298 ASP cc_start: 0.7271 (t70) cc_final: 0.6595 (t0) REVERT: D 309 ILE cc_start: 0.7398 (OUTLIER) cc_final: 0.7058 (mp) REVERT: D 376 ILE cc_start: 0.8193 (OUTLIER) cc_final: 0.7531 (mt) REVERT: A 264 TRP cc_start: 0.6475 (m100) cc_final: 0.6231 (t60) REVERT: A 298 ASP cc_start: 0.7301 (t70) cc_final: 0.6591 (t0) REVERT: A 309 ILE cc_start: 0.7550 (OUTLIER) cc_final: 0.7319 (mp) REVERT: A 376 ILE cc_start: 0.8125 (OUTLIER) cc_final: 0.7467 (mt) outliers start: 34 outliers final: 29 residues processed: 172 average time/residue: 0.0824 time to fit residues: 20.8335 Evaluate side-chains 184 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 151 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 191 LEU Chi-restraints excluded: chain D residue 199 HIS Chi-restraints excluded: chain D residue 212 GLU Chi-restraints excluded: chain D residue 227 ILE Chi-restraints excluded: chain D residue 230 ILE Chi-restraints excluded: chain D residue 242 MET Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 309 ILE Chi-restraints excluded: chain D residue 364 ILE Chi-restraints excluded: chain D residue 376 ILE Chi-restraints excluded: chain D residue 381 THR Chi-restraints excluded: chain D residue 386 LEU Chi-restraints excluded: chain D residue 437 VAL Chi-restraints excluded: chain D residue 479 THR Chi-restraints excluded: chain D residue 481 ILE Chi-restraints excluded: chain D residue 598 HIS Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 199 HIS Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 376 ILE Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 598 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 76 optimal weight: 6.9990 chunk 37 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 68 optimal weight: 0.0980 chunk 4 optimal weight: 0.5980 chunk 80 optimal weight: 1.9990 chunk 105 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.178687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.153272 restraints weight = 11296.365| |-----------------------------------------------------------------------------| r_work (start): 0.3756 rms_B_bonded: 1.60 r_work: 0.3649 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3526 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.4627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9366 Z= 0.152 Angle : 0.611 10.878 12782 Z= 0.303 Chirality : 0.040 0.149 1420 Planarity : 0.004 0.034 1556 Dihedral : 5.684 39.497 1262 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 3.68 % Allowed : 18.07 % Favored : 78.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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 aren not related in a simple way. whole: 0.65 (0.25), residues: 1126 helix: 1.00 (0.19), residues: 764 sheet: None (None), residues: 0 loop : -0.67 (0.34), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 81 TYR 0.025 0.002 TYR A 111 PHE 0.017 0.002 PHE A 409 TRP 0.012 0.001 TRP A 80 HIS 0.005 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00344 ( 9366) covalent geometry : angle 0.61063 (12782) hydrogen bonds : bond 0.05368 ( 546) hydrogen bonds : angle 5.25598 ( 1617) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 149 time to evaluate : 0.241 Fit side-chains REVERT: D 264 TRP cc_start: 0.6544 (m100) cc_final: 0.6258 (t60) REVERT: D 298 ASP cc_start: 0.7328 (t70) cc_final: 0.6643 (t0) REVERT: D 309 ILE cc_start: 0.7444 (OUTLIER) cc_final: 0.6948 (mp) REVERT: D 376 ILE cc_start: 0.8224 (OUTLIER) cc_final: 0.7587 (mt) REVERT: A 264 TRP cc_start: 0.6535 (m100) cc_final: 0.6273 (t60) REVERT: A 298 ASP cc_start: 0.7363 (t70) cc_final: 0.6651 (t0) REVERT: A 309 ILE cc_start: 0.7550 (OUTLIER) cc_final: 0.7323 (mp) REVERT: A 376 ILE cc_start: 0.8142 (OUTLIER) cc_final: 0.7495 (mt) outliers start: 35 outliers final: 31 residues processed: 167 average time/residue: 0.0841 time to fit residues: 20.3918 Evaluate side-chains 187 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 152 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 191 LEU Chi-restraints excluded: chain D residue 199 HIS Chi-restraints excluded: chain D residue 212 GLU Chi-restraints excluded: chain D residue 227 ILE Chi-restraints excluded: chain D residue 230 ILE Chi-restraints excluded: chain D residue 242 MET Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 265 ILE Chi-restraints excluded: chain D residue 309 ILE Chi-restraints excluded: chain D residue 364 ILE Chi-restraints excluded: chain D residue 376 ILE Chi-restraints excluded: chain D residue 381 THR Chi-restraints excluded: chain D residue 386 LEU Chi-restraints excluded: chain D residue 437 VAL Chi-restraints excluded: chain D residue 479 THR Chi-restraints excluded: chain D residue 481 ILE Chi-restraints excluded: chain D residue 529 LEU Chi-restraints excluded: chain D residue 598 HIS Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 199 HIS Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 376 ILE Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 598 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 71 optimal weight: 0.7980 chunk 85 optimal weight: 0.7980 chunk 14 optimal weight: 20.0000 chunk 76 optimal weight: 7.9990 chunk 51 optimal weight: 1.9990 chunk 62 optimal weight: 0.6980 chunk 111 optimal weight: 10.0000 chunk 92 optimal weight: 0.7980 chunk 45 optimal weight: 2.9990 chunk 87 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.177185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.151602 restraints weight = 11205.338| |-----------------------------------------------------------------------------| r_work (start): 0.3731 rms_B_bonded: 1.60 r_work: 0.3618 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3491 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.4744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 9366 Z= 0.159 Angle : 0.621 10.509 12782 Z= 0.308 Chirality : 0.041 0.147 1420 Planarity : 0.004 0.034 1556 Dihedral : 5.794 40.247 1262 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 3.89 % Allowed : 18.17 % Favored : 77.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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 aren not related in a simple way. whole: 0.71 (0.25), residues: 1126 helix: 1.09 (0.19), residues: 750 sheet: None (None), residues: 0 loop : -0.69 (0.33), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 81 TYR 0.025 0.002 TYR A 111 PHE 0.018 0.002 PHE D 409 TRP 0.014 0.001 TRP D 80 HIS 0.005 0.001 HIS D 220 Details of bonding type rmsd covalent geometry : bond 0.00363 ( 9366) covalent geometry : angle 0.62087 (12782) hydrogen bonds : bond 0.05560 ( 546) hydrogen bonds : angle 5.29934 ( 1617) Origin is already at (0, 0, 0), no shifts will be applied Model does not fit in PDB format. =============================================================================== Job complete usr+sys time: 2333.86 seconds wall clock time: 40 minutes 22.13 seconds (2422.13 seconds total)