Starting phenix.real_space_refine on Sun Jul 27 03:17:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8y91_39066/07_2025/8y91_39066.cif Found real_map, /net/cci-nas-00/data/ceres_data/8y91_39066/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8y91_39066/07_2025/8y91_39066.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8y91_39066/07_2025/8y91_39066.map" model { file = "/net/cci-nas-00/data/ceres_data/8y91_39066/07_2025/8y91_39066.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8y91_39066/07_2025/8y91_39066.cif" } resolution = 3.13 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 5.93, per 1000 atoms: 0.65 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: 2.37 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 1.03 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: 2.47 Time building geometry restraints manager: 2.75 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: 0.04 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: 2.850 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: 0.400 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 23.500 Find NCS groups from input model: 0.450 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:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.180 ------------------------------------------------------------------------------- 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 : 9.24 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.007 0.001 TRP D 553 HIS 0.001 0.000 HIS D 222 PHE 0.012 0.001 PHE A 362 TYR 0.013 0.001 TYR D 98 ARG 0.001 0.000 ARG D 216 Details of bonding type rmsd hydrogen bonds : bond 0.16178 ( 546) hydrogen bonds : angle 6.52136 ( 1617) covalent geometry : bond 0.00370 ( 9366) covalent geometry : angle 0.55347 (12782) *********************** 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 : 1.008 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: 0.2393 time to fit residues: 106.7211 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 : 0.984 ------------------------------------------------------------------------------- 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 94 optimal weight: 0.9990 chunk 84 optimal weight: 6.9990 chunk 47 optimal weight: 0.8980 chunk 28 optimal weight: 4.9990 chunk 57 optimal weight: 0.7980 chunk 45 optimal weight: 3.9990 chunk 87 optimal weight: 0.1980 chunk 33 optimal weight: 4.9990 chunk 53 optimal weight: 2.9990 chunk 65 optimal weight: 0.8980 chunk 101 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.4166 r_free = 0.4166 target = 0.192073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.168441 restraints weight = 11103.735| |-----------------------------------------------------------------------------| r_work (start): 0.3926 rms_B_bonded: 1.56 r_work: 0.3828 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3707 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.2715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9366 Z= 0.142 Angle : 0.581 8.610 12782 Z= 0.292 Chirality : 0.039 0.152 1420 Planarity : 0.004 0.047 1556 Dihedral : 6.437 50.009 1276 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 4.10 % Allowed : 13.87 % Favored : 82.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.37 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.25), residues: 1126 helix: 0.32 (0.18), residues: 764 sheet: None (None), residues: 0 loop : -1.00 (0.34), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 128 HIS 0.008 0.001 HIS A 370 PHE 0.023 0.002 PHE A 408 TYR 0.016 0.002 TYR D 575 ARG 0.006 0.001 ARG D 81 Details of bonding type rmsd hydrogen bonds : bond 0.04815 ( 546) hydrogen bonds : angle 5.04486 ( 1617) covalent geometry : bond 0.00300 ( 9366) covalent geometry : angle 0.58087 (12782) *********************** 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 237 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 198 time to evaluate : 0.911 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 250 PHE cc_start: 0.8249 (m-10) cc_final: 0.7722 (m-80) REVERT: D 264 TRP cc_start: 0.6499 (m100) cc_final: 0.5710 (m-10) REVERT: D 376 ILE cc_start: 0.8068 (OUTLIER) cc_final: 0.7523 (mt) REVERT: D 585 TRP cc_start: 0.6079 (m100) cc_final: 0.5699 (m100) REVERT: D 604 ARG cc_start: 0.5518 (tpt170) cc_final: 0.5216 (mtt-85) REVERT: A 250 PHE cc_start: 0.8238 (m-10) cc_final: 0.7699 (m-80) REVERT: A 264 TRP cc_start: 0.6531 (m100) cc_final: 0.5731 (m-10) REVERT: A 376 ILE cc_start: 0.8085 (OUTLIER) cc_final: 0.7575 (mt) REVERT: A 585 TRP cc_start: 0.6091 (m100) cc_final: 0.5726 (m100) REVERT: A 604 ARG cc_start: 0.5550 (tpt170) cc_final: 0.5342 (mtt-85) outliers start: 39 outliers final: 19 residues processed: 225 average time/residue: 0.1817 time to fit residues: 58.6169 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 : 0.991 ------------------------------------------------------------------------------- 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 107 optimal weight: 0.5980 chunk 16 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 59 optimal weight: 1.9990 chunk 72 optimal weight: 0.9990 chunk 54 optimal weight: 0.0030 chunk 13 optimal weight: 9.9990 chunk 22 optimal weight: 0.9990 chunk 50 optimal weight: 5.9990 chunk 64 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 overall best weight: 0.6594 ------------------------------------------------------------------------------- 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 = 0.4120 r_free = 0.4120 target = 0.187355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.162862 restraints weight = 11278.981| |-----------------------------------------------------------------------------| r_work (start): 0.3866 rms_B_bonded: 1.60 r_work: 0.3768 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3643 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.3254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9366 Z= 0.133 Angle : 0.568 8.764 12782 Z= 0.284 Chirality : 0.039 0.136 1420 Planarity : 0.004 0.031 1556 Dihedral : 6.168 47.798 1272 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 3.47 % Allowed : 15.23 % Favored : 81.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.25), residues: 1126 helix: 0.72 (0.19), residues: 764 sheet: None (None), residues: 0 loop : -0.83 (0.35), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 80 HIS 0.005 0.001 HIS D 370 PHE 0.020 0.002 PHE A 540 TYR 0.016 0.001 TYR D 152 ARG 0.006 0.001 ARG D 81 Details of bonding type rmsd hydrogen bonds : bond 0.04745 ( 546) hydrogen bonds : angle 5.04564 ( 1617) covalent geometry : bond 0.00289 ( 9366) covalent geometry : angle 0.56839 (12782) *********************** 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: 33 poor density : 175 time to evaluate : 0.919 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 250 PHE cc_start: 0.8358 (m-10) cc_final: 0.8003 (m-80) REVERT: D 264 TRP cc_start: 0.6471 (m100) cc_final: 0.5656 (m-10) REVERT: D 298 ASP cc_start: 0.7267 (t70) cc_final: 0.6782 (t0) REVERT: D 376 ILE cc_start: 0.8155 (OUTLIER) cc_final: 0.7527 (mt) REVERT: D 585 TRP cc_start: 0.6096 (m100) cc_final: 0.5706 (m100) REVERT: D 604 ARG cc_start: 0.5624 (tpt170) cc_final: 0.5412 (mtt-85) REVERT: A 250 PHE cc_start: 0.8358 (m-10) cc_final: 0.7997 (m-80) REVERT: A 264 TRP cc_start: 0.6489 (m100) cc_final: 0.5662 (m-10) REVERT: A 298 ASP cc_start: 0.7316 (t70) cc_final: 0.6808 (t0) REVERT: A 376 ILE cc_start: 0.8153 (OUTLIER) cc_final: 0.7574 (mt) REVERT: A 585 TRP cc_start: 0.6108 (m100) cc_final: 0.5703 (m100) REVERT: A 604 ARG cc_start: 0.5593 (tpt170) cc_final: 0.5321 (mtt-85) outliers start: 33 outliers final: 18 residues processed: 198 average time/residue: 0.1904 time to fit residues: 54.0448 Evaluate side-chains 178 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 158 time to evaluate : 0.956 ------------------------------------------------------------------------------- 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 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 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 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 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 52 optimal weight: 0.7980 chunk 63 optimal weight: 1.9990 chunk 24 optimal weight: 8.9990 chunk 85 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 111 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 100 optimal weight: 0.5980 chunk 82 optimal weight: 0.5980 chunk 14 optimal weight: 2.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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 = 0.4060 r_free = 0.4060 target = 0.181641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.156502 restraints weight = 11320.885| |-----------------------------------------------------------------------------| r_work (start): 0.3798 rms_B_bonded: 1.61 r_work: 0.3700 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3576 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.3821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9366 Z= 0.155 Angle : 0.580 8.341 12782 Z= 0.295 Chirality : 0.040 0.140 1420 Planarity : 0.004 0.038 1556 Dihedral : 6.082 44.959 1268 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 3.68 % Allowed : 15.23 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.25), residues: 1126 helix: 0.75 (0.19), residues: 764 sheet: None (None), residues: 0 loop : -0.80 (0.34), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 80 HIS 0.006 0.001 HIS D 372 PHE 0.018 0.002 PHE A 409 TYR 0.017 0.001 TYR D 152 ARG 0.007 0.001 ARG A 81 Details of bonding type rmsd hydrogen bonds : bond 0.05182 ( 546) hydrogen bonds : angle 5.16625 ( 1617) covalent geometry : bond 0.00347 ( 9366) covalent geometry : angle 0.57953 (12782) *********************** 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 213 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 178 time to evaluate : 0.920 Fit side-chains revert: symmetry clash REVERT: D 264 TRP cc_start: 0.6522 (m100) cc_final: 0.5697 (m-10) REVERT: D 309 ILE cc_start: 0.7488 (OUTLIER) cc_final: 0.7090 (mp) REVERT: D 376 ILE cc_start: 0.8197 (OUTLIER) cc_final: 0.7540 (mt) REVERT: D 585 TRP cc_start: 0.6134 (m100) cc_final: 0.5707 (m100) REVERT: D 604 ARG cc_start: 0.5562 (tpt170) cc_final: 0.5358 (mtt-85) REVERT: A 264 TRP cc_start: 0.6494 (m100) cc_final: 0.5681 (m-10) REVERT: A 309 ILE cc_start: 0.7443 (OUTLIER) cc_final: 0.7042 (mp) REVERT: A 376 ILE cc_start: 0.8199 (OUTLIER) cc_final: 0.7636 (mt) REVERT: A 585 TRP cc_start: 0.6125 (m100) cc_final: 0.5710 (m100) REVERT: A 604 ARG cc_start: 0.5595 (tpt170) cc_final: 0.5384 (mtt-85) outliers start: 35 outliers final: 25 residues processed: 203 average time/residue: 0.1935 time to fit residues: 55.9501 Evaluate side-chains 182 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 153 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 57 GLU 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 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 481 ILE 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 38 optimal weight: 0.9980 chunk 104 optimal weight: 0.8980 chunk 60 optimal weight: 1.9990 chunk 100 optimal weight: 0.9980 chunk 27 optimal weight: 0.8980 chunk 92 optimal weight: 0.0770 chunk 69 optimal weight: 0.0770 chunk 39 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 109 optimal weight: 0.9980 chunk 106 optimal weight: 3.9990 overall best weight: 0.5896 ------------------------------------------------------------------------------- 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 = 0.4084 r_free = 0.4084 target = 0.184225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.159488 restraints weight = 11331.463| |-----------------------------------------------------------------------------| r_work (start): 0.3822 rms_B_bonded: 1.60 r_work: 0.3720 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3596 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.3981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9366 Z= 0.130 Angle : 0.565 8.959 12782 Z= 0.280 Chirality : 0.038 0.123 1420 Planarity : 0.004 0.035 1556 Dihedral : 5.929 43.894 1268 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 3.89 % Allowed : 16.18 % Favored : 79.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.26), residues: 1126 helix: 1.06 (0.19), residues: 750 sheet: None (None), residues: 0 loop : -0.79 (0.34), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 80 HIS 0.004 0.001 HIS A 220 PHE 0.022 0.002 PHE A 213 TYR 0.016 0.001 TYR A 152 ARG 0.005 0.001 ARG A 81 Details of bonding type rmsd hydrogen bonds : bond 0.04803 ( 546) hydrogen bonds : angle 5.08358 ( 1617) covalent geometry : bond 0.00281 ( 9366) covalent geometry : angle 0.56495 (12782) *********************** 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: 37 poor density : 157 time to evaluate : 0.984 Fit side-chains revert: symmetry clash REVERT: D 118 GLN cc_start: 0.8263 (OUTLIER) cc_final: 0.8061 (tt0) REVERT: D 264 TRP cc_start: 0.6509 (m100) cc_final: 0.5623 (m-10) REVERT: D 298 ASP cc_start: 0.7207 (t70) cc_final: 0.6652 (t0) REVERT: D 309 ILE cc_start: 0.7423 (OUTLIER) cc_final: 0.7059 (mp) REVERT: D 376 ILE cc_start: 0.8214 (OUTLIER) cc_final: 0.7515 (mt) REVERT: D 585 TRP cc_start: 0.6120 (m100) cc_final: 0.5703 (m100) REVERT: A 107 MET cc_start: 0.7405 (mmt) cc_final: 0.6459 (mmt) REVERT: A 118 GLN cc_start: 0.8262 (OUTLIER) cc_final: 0.8055 (tt0) REVERT: A 264 TRP cc_start: 0.6443 (m100) cc_final: 0.5599 (m-10) REVERT: A 298 ASP cc_start: 0.7215 (t70) cc_final: 0.6580 (t0) REVERT: A 309 ILE cc_start: 0.7430 (OUTLIER) cc_final: 0.7007 (mp) REVERT: A 367 TYR cc_start: 0.8477 (t80) cc_final: 0.8263 (t80) REVERT: A 376 ILE cc_start: 0.8131 (OUTLIER) cc_final: 0.7466 (mt) REVERT: A 585 TRP cc_start: 0.6135 (m100) cc_final: 0.5704 (m100) outliers start: 37 outliers final: 27 residues processed: 182 average time/residue: 0.1932 time to fit residues: 50.6954 Evaluate side-chains 180 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 147 time to evaluate : 0.944 ------------------------------------------------------------------------------- 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 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 118 GLN 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 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 66 optimal weight: 0.5980 chunk 15 optimal weight: 4.9990 chunk 18 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 108 optimal weight: 0.8980 chunk 54 optimal weight: 0.8980 chunk 78 optimal weight: 4.9990 chunk 74 optimal weight: 2.9990 chunk 6 optimal weight: 0.8980 chunk 22 optimal weight: 3.9990 chunk 103 optimal weight: 2.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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 = 0.4028 r_free = 0.4028 target = 0.179017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.153698 restraints weight = 11283.231| |-----------------------------------------------------------------------------| r_work (start): 0.3762 rms_B_bonded: 1.60 r_work: 0.3658 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3534 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.4325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9366 Z= 0.160 Angle : 0.594 9.110 12782 Z= 0.297 Chirality : 0.040 0.139 1420 Planarity : 0.004 0.038 1556 Dihedral : 5.947 39.081 1266 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 4.31 % Allowed : 16.07 % Favored : 79.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.26), residues: 1126 helix: 1.02 (0.19), residues: 750 sheet: None (None), residues: 0 loop : -0.74 (0.33), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 80 HIS 0.005 0.001 HIS A 220 PHE 0.018 0.002 PHE A 409 TYR 0.017 0.001 TYR D 152 ARG 0.004 0.001 ARG A 341 Details of bonding type rmsd hydrogen bonds : bond 0.05394 ( 546) hydrogen bonds : angle 5.23045 ( 1617) covalent geometry : bond 0.00365 ( 9366) covalent geometry : angle 0.59393 (12782) *********************** 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 194 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 153 time to evaluate : 1.618 Fit side-chains REVERT: D 173 TRP cc_start: 0.6945 (OUTLIER) cc_final: 0.6665 (m-90) REVERT: D 264 TRP cc_start: 0.6551 (m100) cc_final: 0.5662 (m-10) REVERT: D 298 ASP cc_start: 0.7309 (t70) cc_final: 0.6754 (t0) REVERT: D 309 ILE cc_start: 0.7418 (OUTLIER) cc_final: 0.7113 (mp) REVERT: D 376 ILE cc_start: 0.8227 (OUTLIER) cc_final: 0.7518 (mt) REVERT: D 585 TRP cc_start: 0.6104 (m100) cc_final: 0.5757 (m100) REVERT: A 173 TRP cc_start: 0.6904 (OUTLIER) cc_final: 0.6544 (m-90) REVERT: A 264 TRP cc_start: 0.6519 (m100) cc_final: 0.6241 (t60) REVERT: A 298 ASP cc_start: 0.7302 (t70) cc_final: 0.6696 (t0) REVERT: A 309 ILE cc_start: 0.7500 (OUTLIER) cc_final: 0.7204 (mp) REVERT: A 376 ILE cc_start: 0.8199 (OUTLIER) cc_final: 0.7526 (mt) outliers start: 41 outliers final: 29 residues processed: 179 average time/residue: 0.2893 time to fit residues: 73.9257 Evaluate side-chains 180 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 145 time to evaluate : 1.019 ------------------------------------------------------------------------------- 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 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 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 22 optimal weight: 3.9990 chunk 13 optimal weight: 6.9990 chunk 98 optimal weight: 0.6980 chunk 109 optimal weight: 4.9990 chunk 91 optimal weight: 4.9990 chunk 95 optimal weight: 3.9990 chunk 34 optimal weight: 7.9990 chunk 82 optimal weight: 0.7980 chunk 40 optimal weight: 0.1980 chunk 103 optimal weight: 0.8980 chunk 65 optimal weight: 0.8980 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 = 0.4054 r_free = 0.4054 target = 0.181727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.156319 restraints weight = 11353.069| |-----------------------------------------------------------------------------| r_work (start): 0.3792 rms_B_bonded: 1.63 r_work: 0.3692 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3569 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.4347 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 : 0.568 9.511 12782 Z= 0.283 Chirality : 0.039 0.134 1420 Planarity : 0.004 0.035 1556 Dihedral : 5.853 39.553 1266 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 4.20 % Allowed : 17.02 % Favored : 78.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.26), residues: 1126 helix: 1.09 (0.19), residues: 750 sheet: None (None), residues: 0 loop : -0.70 (0.33), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 80 HIS 0.005 0.001 HIS A 220 PHE 0.016 0.001 PHE D 511 TYR 0.016 0.001 TYR D 111 ARG 0.004 0.000 ARG D 81 Details of bonding type rmsd hydrogen bonds : bond 0.05067 ( 546) hydrogen bonds : angle 5.18708 ( 1617) covalent geometry : bond 0.00298 ( 9366) covalent geometry : angle 0.56829 (12782) *********************** 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 200 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 160 time to evaluate : 1.138 Fit side-chains REVERT: D 173 TRP cc_start: 0.6871 (OUTLIER) cc_final: 0.6257 (m-90) REVERT: D 264 TRP cc_start: 0.6544 (m100) cc_final: 0.6256 (t60) REVERT: D 298 ASP cc_start: 0.7332 (t70) cc_final: 0.6785 (t0) REVERT: D 309 ILE cc_start: 0.7426 (OUTLIER) cc_final: 0.7098 (mp) REVERT: D 376 ILE cc_start: 0.8186 (OUTLIER) cc_final: 0.7480 (mt) REVERT: A 173 TRP cc_start: 0.6875 (OUTLIER) cc_final: 0.6264 (m-90) REVERT: A 264 TRP cc_start: 0.6486 (m100) cc_final: 0.6221 (t60) REVERT: A 309 ILE cc_start: 0.7531 (OUTLIER) cc_final: 0.7256 (mp) REVERT: A 376 ILE cc_start: 0.8157 (OUTLIER) cc_final: 0.7509 (mt) outliers start: 40 outliers final: 30 residues processed: 181 average time/residue: 0.1763 time to fit residues: 46.5118 Evaluate side-chains 186 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 150 time to evaluate : 1.038 ------------------------------------------------------------------------------- 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 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 79 optimal weight: 0.5980 chunk 8 optimal weight: 0.8980 chunk 75 optimal weight: 0.8980 chunk 39 optimal weight: 3.9990 chunk 64 optimal weight: 0.7980 chunk 14 optimal weight: 20.0000 chunk 9 optimal weight: 0.9980 chunk 87 optimal weight: 0.9990 chunk 84 optimal weight: 5.9990 chunk 27 optimal weight: 0.7980 chunk 36 optimal weight: 2.9990 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 = 0.4046 r_free = 0.4046 target = 0.180614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.155246 restraints weight = 11414.565| |-----------------------------------------------------------------------------| r_work (start): 0.3783 rms_B_bonded: 1.62 r_work: 0.3683 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3559 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.4459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9366 Z= 0.142 Angle : 0.591 11.927 12782 Z= 0.290 Chirality : 0.039 0.141 1420 Planarity : 0.004 0.035 1556 Dihedral : 5.835 39.220 1266 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 4.52 % Allowed : 16.60 % Favored : 78.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.25), residues: 1126 helix: 1.12 (0.19), residues: 752 sheet: None (None), residues: 0 loop : -0.65 (0.33), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 80 HIS 0.004 0.001 HIS A 220 PHE 0.015 0.001 PHE A 409 TYR 0.016 0.001 TYR D 111 ARG 0.003 0.000 ARG D 81 Details of bonding type rmsd hydrogen bonds : bond 0.05164 ( 546) hydrogen bonds : angle 5.20284 ( 1617) covalent geometry : bond 0.00318 ( 9366) covalent geometry : angle 0.59145 (12782) *********************** 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 197 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 154 time to evaluate : 1.001 Fit side-chains REVERT: D 173 TRP cc_start: 0.6930 (OUTLIER) cc_final: 0.6366 (m-90) REVERT: D 264 TRP cc_start: 0.6557 (m100) cc_final: 0.6279 (t60) REVERT: D 309 ILE cc_start: 0.7424 (OUTLIER) cc_final: 0.7108 (mp) REVERT: D 376 ILE cc_start: 0.8217 (OUTLIER) cc_final: 0.7512 (mt) REVERT: A 173 TRP cc_start: 0.6907 (OUTLIER) cc_final: 0.6336 (m-90) REVERT: A 264 TRP cc_start: 0.6461 (m100) cc_final: 0.6206 (t60) REVERT: A 298 ASP cc_start: 0.7299 (t70) cc_final: 0.6592 (t0) REVERT: A 309 ILE cc_start: 0.7565 (OUTLIER) cc_final: 0.7309 (mp) REVERT: A 376 ILE cc_start: 0.8141 (OUTLIER) cc_final: 0.7493 (mt) outliers start: 43 outliers final: 31 residues processed: 181 average time/residue: 0.1796 time to fit residues: 47.4056 Evaluate side-chains 184 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 147 time to evaluate : 0.883 ------------------------------------------------------------------------------- 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 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 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 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 212 GLU 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 45 optimal weight: 0.8980 chunk 23 optimal weight: 3.9990 chunk 3 optimal weight: 0.7980 chunk 106 optimal weight: 0.9980 chunk 74 optimal weight: 0.2980 chunk 76 optimal weight: 6.9990 chunk 67 optimal weight: 2.9990 chunk 20 optimal weight: 6.9990 chunk 55 optimal weight: 3.9990 chunk 19 optimal weight: 0.9990 chunk 6 optimal weight: 0.1980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.4059 r_free = 0.4059 target = 0.182227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.157326 restraints weight = 11275.832| |-----------------------------------------------------------------------------| r_work (start): 0.3807 rms_B_bonded: 1.60 r_work: 0.3707 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3583 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.4469 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= 0.132 Angle : 0.585 11.207 12782 Z= 0.286 Chirality : 0.039 0.137 1420 Planarity : 0.004 0.032 1556 Dihedral : 5.761 39.627 1266 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 4.10 % Allowed : 17.65 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.25), residues: 1126 helix: 1.04 (0.19), residues: 768 sheet: None (None), residues: 0 loop : -0.70 (0.34), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 80 HIS 0.004 0.001 HIS A 220 PHE 0.014 0.001 PHE A 409 TYR 0.015 0.001 TYR A 111 ARG 0.003 0.000 ARG A 81 Details of bonding type rmsd hydrogen bonds : bond 0.04979 ( 546) hydrogen bonds : angle 5.16122 ( 1617) covalent geometry : bond 0.00291 ( 9366) covalent geometry : angle 0.58536 (12782) *********************** 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: 39 poor density : 151 time to evaluate : 0.984 Fit side-chains REVERT: D 173 TRP cc_start: 0.6901 (OUTLIER) cc_final: 0.6269 (m-90) REVERT: D 264 TRP cc_start: 0.6481 (m100) cc_final: 0.6224 (t60) REVERT: D 298 ASP cc_start: 0.7279 (t70) cc_final: 0.6602 (t0) REVERT: D 309 ILE cc_start: 0.7432 (OUTLIER) cc_final: 0.7078 (mp) REVERT: D 376 ILE cc_start: 0.8239 (OUTLIER) cc_final: 0.7546 (mt) REVERT: A 173 TRP cc_start: 0.6899 (OUTLIER) cc_final: 0.6197 (m-90) REVERT: A 264 TRP cc_start: 0.6436 (m100) cc_final: 0.6210 (t60) REVERT: A 298 ASP cc_start: 0.7296 (t70) cc_final: 0.6584 (t0) REVERT: A 309 ILE cc_start: 0.7540 (OUTLIER) cc_final: 0.7292 (mp) REVERT: A 376 ILE cc_start: 0.8118 (OUTLIER) cc_final: 0.7493 (mt) outliers start: 39 outliers final: 33 residues processed: 172 average time/residue: 0.1794 time to fit residues: 44.9474 Evaluate side-chains 189 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 150 time to evaluate : 0.917 ------------------------------------------------------------------------------- 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 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 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 598 HIS Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 173 TRP Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 199 HIS Chi-restraints excluded: chain A residue 212 GLU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 61 optimal weight: 0.3980 chunk 72 optimal weight: 0.9980 chunk 49 optimal weight: 0.0000 chunk 37 optimal weight: 1.9990 chunk 80 optimal weight: 3.9990 chunk 88 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 106 optimal weight: 3.9990 chunk 104 optimal weight: 0.6980 chunk 21 optimal weight: 0.8980 overall best weight: 0.5984 ------------------------------------------------------------------------------- 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 = 0.4068 r_free = 0.4068 target = 0.182821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.157765 restraints weight = 11287.071| |-----------------------------------------------------------------------------| r_work (start): 0.3816 rms_B_bonded: 1.62 r_work: 0.3717 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3595 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.4503 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= 0.129 Angle : 0.581 11.188 12782 Z= 0.282 Chirality : 0.039 0.138 1420 Planarity : 0.004 0.033 1556 Dihedral : 5.676 39.894 1266 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 4.10 % Allowed : 17.23 % Favored : 78.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.26), residues: 1126 helix: 1.12 (0.19), residues: 768 sheet: None (None), residues: 0 loop : -0.67 (0.34), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 80 HIS 0.004 0.001 HIS D 220 PHE 0.014 0.001 PHE D 316 TYR 0.015 0.001 TYR A 152 ARG 0.003 0.000 ARG D 81 Details of bonding type rmsd hydrogen bonds : bond 0.04883 ( 546) hydrogen bonds : angle 5.12072 ( 1617) covalent geometry : bond 0.00283 ( 9366) covalent geometry : angle 0.58078 (12782) ********************** 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 198 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 159 time to evaluate : 0.984 Fit side-chains REVERT: D 173 TRP cc_start: 0.6921 (OUTLIER) cc_final: 0.6272 (m-90) REVERT: D 264 TRP cc_start: 0.6486 (m100) cc_final: 0.6235 (t60) REVERT: D 298 ASP cc_start: 0.7189 (t70) cc_final: 0.6484 (t0) REVERT: D 309 ILE cc_start: 0.7457 (OUTLIER) cc_final: 0.7101 (mp) REVERT: D 376 ILE cc_start: 0.8235 (OUTLIER) cc_final: 0.7567 (mt) REVERT: A 264 TRP cc_start: 0.6460 (m100) cc_final: 0.6248 (t60) REVERT: A 298 ASP cc_start: 0.7268 (t70) cc_final: 0.6576 (t0) REVERT: A 309 ILE cc_start: 0.7549 (OUTLIER) cc_final: 0.7297 (mp) REVERT: A 376 ILE cc_start: 0.8164 (OUTLIER) cc_final: 0.7566 (mt) outliers start: 39 outliers final: 32 residues processed: 180 average time/residue: 0.1823 time to fit residues: 47.4278 Evaluate side-chains 187 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 150 time to evaluate : 0.985 ------------------------------------------------------------------------------- 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 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 247 VAL Chi-restraints excluded: chain D residue 265 ILE 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 126 THR Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 199 HIS Chi-restraints excluded: chain A residue 212 GLU 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 65 optimal weight: 1.9990 chunk 54 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 76 optimal weight: 6.9990 chunk 42 optimal weight: 0.9980 chunk 5 optimal weight: 0.5980 chunk 97 optimal weight: 0.8980 chunk 69 optimal weight: 9.9990 chunk 83 optimal weight: 0.9990 chunk 104 optimal weight: 0.9990 chunk 87 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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 = 0.4041 r_free = 0.4041 target = 0.179964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.154465 restraints weight = 11280.208| |-----------------------------------------------------------------------------| r_work (start): 0.3774 rms_B_bonded: 1.61 r_work: 0.3669 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3548 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.4621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9366 Z= 0.149 Angle : 0.617 12.403 12782 Z= 0.299 Chirality : 0.040 0.132 1420 Planarity : 0.004 0.033 1556 Dihedral : 5.715 39.771 1264 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 4.10 % Allowed : 17.54 % Favored : 78.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.25), residues: 1126 helix: 1.05 (0.19), residues: 768 sheet: None (None), residues: 0 loop : -0.74 (0.34), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 80 HIS 0.005 0.001 HIS A 220 PHE 0.028 0.002 PHE A 540 TYR 0.017 0.001 TYR D 111 ARG 0.006 0.000 ARG A 81 Details of bonding type rmsd hydrogen bonds : bond 0.05254 ( 546) hydrogen bonds : angle 5.22667 ( 1617) covalent geometry : bond 0.00337 ( 9366) covalent geometry : angle 0.61715 (12782) Origin is already at (0, 0, 0), no shifts will be applied Model does not fit in PDB format. =============================================================================== Job complete usr+sys time: 4707.74 seconds wall clock time: 83 minutes 43.59 seconds (5023.59 seconds total)