Starting phenix.real_space_refine on Thu Jan 16 03:42:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8y91_39066/01_2025/8y91_39066.cif Found real_map, /net/cci-nas-00/data/ceres_data/8y91_39066/01_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_39066/01_2025/8y91_39066.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8y91_39066/01_2025/8y91_39066.map" model { file = "/net/cci-nas-00/data/ceres_data/8y91_39066/01_2025/8y91_39066.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8y91_39066/01_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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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: 5.72, per 1000 atoms: 0.63 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: 2.31 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: 0.67 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: 2.63 Time building geometry restraints manager: 2.62 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: 2.580 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: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 22.350 Find NCS groups from input model: 0.410 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:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.560 ------------------------------------------------------------------------------- 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= 0.257 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 *********************** 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 : 0.902 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: 0.2000 time to fit residues: 87.6314 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 : 0.957 ------------------------------------------------------------------------------- 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 = 40)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.168471 restraints weight = 11103.733| |-----------------------------------------------------------------------------| r_work (start): 0.3925 rms_B_bonded: 1.56 r_work: 0.3828 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3705 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 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= 0.192 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 *********************** 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 : 0.983 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 250 PHE cc_start: 0.8258 (m-10) cc_final: 0.7729 (m-80) REVERT: D 264 TRP cc_start: 0.6487 (m100) cc_final: 0.5708 (m-10) REVERT: D 376 ILE cc_start: 0.8063 (OUTLIER) cc_final: 0.7520 (mt) REVERT: D 585 TRP cc_start: 0.6080 (m100) cc_final: 0.5700 (m100) REVERT: D 604 ARG cc_start: 0.5518 (tpt170) cc_final: 0.5216 (mtt-85) REVERT: A 250 PHE cc_start: 0.8246 (m-10) cc_final: 0.7707 (m-80) REVERT: A 264 TRP cc_start: 0.6523 (m100) cc_final: 0.5729 (m-10) REVERT: A 376 ILE cc_start: 0.8082 (OUTLIER) cc_final: 0.7574 (mt) REVERT: A 585 TRP cc_start: 0.6092 (m100) cc_final: 0.5726 (m100) REVERT: A 604 ARG cc_start: 0.5553 (tpt170) cc_final: 0.5343 (mtt-85) outliers start: 39 outliers final: 19 residues processed: 225 average time/residue: 0.1896 time to fit residues: 60.9009 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 : 0.976 ------------------------------------------------------------------------------- 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: 0.8980 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: 0.1980 chunk 13 optimal weight: 9.9990 chunk 22 optimal weight: 0.9980 chunk 50 optimal weight: 4.9990 chunk 64 optimal weight: 0.3980 chunk 97 optimal weight: 2.9990 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 = 0.4122 r_free = 0.4122 target = 0.187593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.163307 restraints weight = 11288.597| |-----------------------------------------------------------------------------| r_work (start): 0.3870 rms_B_bonded: 1.59 r_work: 0.3774 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3649 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.3191 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= 0.184 Angle : 0.566 8.857 12782 Z= 0.283 Chirality : 0.039 0.136 1420 Planarity : 0.004 0.031 1556 Dihedral : 6.167 48.119 1272 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 3.57 % Allowed : 15.02 % Favored : 81.41 % 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: 0.71 (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 0.019 0.002 PHE A 540 TYR 0.015 0.001 TYR D 152 ARG 0.006 0.000 ARG D 81 *********************** 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 210 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 176 time to evaluate : 0.997 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 250 PHE cc_start: 0.8332 (m-10) cc_final: 0.7977 (m-80) REVERT: D 264 TRP cc_start: 0.6463 (m100) cc_final: 0.5651 (m-10) REVERT: D 298 ASP cc_start: 0.7295 (t70) cc_final: 0.6805 (t0) REVERT: D 376 ILE cc_start: 0.8152 (OUTLIER) cc_final: 0.7528 (mt) REVERT: D 585 TRP cc_start: 0.6083 (m100) cc_final: 0.5699 (m100) REVERT: D 604 ARG cc_start: 0.5617 (tpt170) cc_final: 0.5412 (mtt-85) REVERT: A 250 PHE cc_start: 0.8339 (m-10) cc_final: 0.7970 (m-80) REVERT: A 264 TRP cc_start: 0.6481 (m100) cc_final: 0.5672 (m-10) REVERT: A 298 ASP cc_start: 0.7304 (t70) cc_final: 0.6789 (t0) REVERT: A 376 ILE cc_start: 0.8136 (OUTLIER) cc_final: 0.7561 (mt) REVERT: A 585 TRP cc_start: 0.6117 (m100) cc_final: 0.5714 (m100) REVERT: A 604 ARG cc_start: 0.5563 (tpt170) cc_final: 0.5321 (mtt-85) outliers start: 34 outliers final: 19 residues processed: 200 average time/residue: 0.2025 time to fit residues: 57.6568 Evaluate side-chains 176 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 155 time to evaluate : 0.934 ------------------------------------------------------------------------------- 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 529 LEU 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: 1.9990 chunk 63 optimal weight: 1.9990 chunk 24 optimal weight: 9.9990 chunk 85 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 38 optimal weight: 3.9990 chunk 111 optimal weight: 0.9990 chunk 2 optimal weight: 3.9990 chunk 100 optimal weight: 0.6980 chunk 82 optimal weight: 0.6980 chunk 14 optimal weight: 0.0050 overall best weight: 0.6798 ------------------------------------------------------------------------------- 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 = 0.4097 r_free = 0.4097 target = 0.185486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.161026 restraints weight = 11309.938| |-----------------------------------------------------------------------------| r_work (start): 0.3847 rms_B_bonded: 1.59 r_work: 0.3751 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3630 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.3638 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= 0.187 Angle : 0.552 8.208 12782 Z= 0.279 Chirality : 0.039 0.136 1420 Planarity : 0.004 0.031 1556 Dihedral : 5.981 46.562 1268 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 3.47 % Allowed : 15.55 % Favored : 80.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.40 (0.26), residues: 1126 helix: 0.83 (0.19), residues: 766 sheet: None (None), residues: 0 loop : -0.84 (0.34), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 80 HIS 0.007 0.001 HIS D 372 PHE 0.016 0.002 PHE D 540 TYR 0.016 0.001 TYR A 152 ARG 0.006 0.001 ARG A 81 *********************** 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 204 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 171 time to evaluate : 0.945 Fit side-chains REVERT: D 250 PHE cc_start: 0.8379 (m-10) cc_final: 0.8042 (m-80) REVERT: D 264 TRP cc_start: 0.6485 (m100) cc_final: 0.5677 (m-10) REVERT: D 309 ILE cc_start: 0.7474 (OUTLIER) cc_final: 0.7054 (mp) REVERT: D 376 ILE cc_start: 0.8193 (OUTLIER) cc_final: 0.7530 (mt) REVERT: D 585 TRP cc_start: 0.6099 (m100) cc_final: 0.5697 (m100) REVERT: A 250 PHE cc_start: 0.8377 (m-10) cc_final: 0.8018 (m-80) REVERT: A 264 TRP cc_start: 0.6505 (m100) cc_final: 0.5684 (m-10) REVERT: A 376 ILE cc_start: 0.8186 (OUTLIER) cc_final: 0.7618 (mt) REVERT: A 585 TRP cc_start: 0.6117 (m100) cc_final: 0.5691 (m100) outliers start: 33 outliers final: 26 residues processed: 196 average time/residue: 0.2058 time to fit residues: 56.5755 Evaluate side-chains 181 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 152 time to evaluate : 0.942 ------------------------------------------------------------------------------- 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 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 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: 2.9990 chunk 104 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 92 optimal weight: 0.8980 chunk 69 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 97 optimal weight: 4.9990 chunk 109 optimal weight: 3.9990 chunk 106 optimal weight: 2.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- 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 = 0.3990 r_free = 0.3990 target = 0.175231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.148990 restraints weight = 11387.326| |-----------------------------------------------------------------------------| r_work (start): 0.3628 rms_B_bonded: 1.62 r_work: 0.3521 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3395 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.4458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 9366 Z= 0.307 Angle : 0.651 9.387 12782 Z= 0.331 Chirality : 0.042 0.161 1420 Planarity : 0.005 0.038 1556 Dihedral : 6.430 42.355 1268 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 4.31 % Allowed : 15.34 % Favored : 80.36 % 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: 0.26 (0.26), residues: 1126 helix: 0.73 (0.19), residues: 760 sheet: None (None), residues: 0 loop : -0.87 (0.34), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 80 HIS 0.006 0.001 HIS D 220 PHE 0.025 0.002 PHE A 409 TYR 0.020 0.002 TYR D 111 ARG 0.006 0.001 ARG A 341 *********************** 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 199 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 158 time to evaluate : 1.012 Fit side-chains revert: symmetry clash REVERT: D 173 TRP cc_start: 0.6890 (OUTLIER) cc_final: 0.6405 (m-90) REVERT: D 190 LEU cc_start: 0.7755 (tt) cc_final: 0.7443 (pp) REVERT: D 264 TRP cc_start: 0.6612 (m100) cc_final: 0.5640 (m-10) REVERT: D 298 ASP cc_start: 0.7442 (t70) cc_final: 0.6850 (t0) REVERT: D 309 ILE cc_start: 0.7413 (OUTLIER) cc_final: 0.7146 (mp) REVERT: D 376 ILE cc_start: 0.8221 (OUTLIER) cc_final: 0.7516 (mt) REVERT: D 585 TRP cc_start: 0.6048 (m100) cc_final: 0.5720 (m100) REVERT: A 173 TRP cc_start: 0.6849 (OUTLIER) cc_final: 0.6307 (m-90) REVERT: A 190 LEU cc_start: 0.7761 (tt) cc_final: 0.7438 (pp) REVERT: A 264 TRP cc_start: 0.6595 (m100) cc_final: 0.5619 (m-10) REVERT: A 298 ASP cc_start: 0.7449 (t70) cc_final: 0.6798 (t0) REVERT: A 309 ILE cc_start: 0.7441 (OUTLIER) cc_final: 0.7152 (mp) REVERT: A 376 ILE cc_start: 0.8194 (OUTLIER) cc_final: 0.7594 (mt) REVERT: A 585 TRP cc_start: 0.6049 (m100) cc_final: 0.5708 (m100) outliers start: 41 outliers final: 31 residues processed: 189 average time/residue: 0.1903 time to fit residues: 52.1578 Evaluate side-chains 183 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 146 time to evaluate : 0.850 ------------------------------------------------------------------------------- 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 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 598 HIS Chi-restraints excluded: chain A residue 57 GLU 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 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 368 MET 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 528 PHE 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: 0.6980 chunk 15 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 108 optimal weight: 1.9990 chunk 54 optimal weight: 4.9990 chunk 78 optimal weight: 3.9990 chunk 74 optimal weight: 0.9990 chunk 6 optimal weight: 0.7980 chunk 22 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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 = 0.4005 r_free = 0.4005 target = 0.177052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.151285 restraints weight = 11264.805| |-----------------------------------------------------------------------------| r_work (start): 0.3732 rms_B_bonded: 1.61 r_work: 0.3630 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3506 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.4495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9366 Z= 0.237 Angle : 0.600 9.432 12782 Z= 0.306 Chirality : 0.041 0.143 1420 Planarity : 0.004 0.041 1556 Dihedral : 6.135 41.551 1266 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 4.41 % Allowed : 16.49 % Favored : 79.10 % 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: 0.33 (0.25), residues: 1126 helix: 0.79 (0.19), residues: 752 sheet: None (None), residues: 0 loop : -0.83 (0.33), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 80 HIS 0.005 0.001 HIS A 220 PHE 0.019 0.002 PHE A 409 TYR 0.018 0.002 TYR D 111 ARG 0.005 0.001 ARG A 81 *********************** 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 193 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 151 time to evaluate : 0.907 Fit side-chains REVERT: D 133 PHE cc_start: 0.8750 (OUTLIER) cc_final: 0.8268 (m-80) REVERT: D 173 TRP cc_start: 0.6877 (OUTLIER) cc_final: 0.6280 (m-90) REVERT: D 264 TRP cc_start: 0.6554 (m100) cc_final: 0.5658 (m-10) REVERT: D 298 ASP cc_start: 0.7354 (t70) cc_final: 0.6766 (t0) REVERT: D 309 ILE cc_start: 0.7445 (OUTLIER) cc_final: 0.6979 (mp) REVERT: D 376 ILE cc_start: 0.8250 (OUTLIER) cc_final: 0.7506 (mt) REVERT: D 585 TRP cc_start: 0.6120 (m100) cc_final: 0.5767 (m100) REVERT: A 173 TRP cc_start: 0.6873 (OUTLIER) cc_final: 0.6308 (m-90) REVERT: A 264 TRP cc_start: 0.6554 (m100) cc_final: 0.6310 (t60) REVERT: A 298 ASP cc_start: 0.7401 (t70) cc_final: 0.6772 (t0) REVERT: A 309 ILE cc_start: 0.7502 (OUTLIER) cc_final: 0.7207 (mp) REVERT: A 376 ILE cc_start: 0.8251 (OUTLIER) cc_final: 0.7635 (mt) outliers start: 42 outliers final: 32 residues processed: 179 average time/residue: 0.1864 time to fit residues: 48.3774 Evaluate side-chains 182 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 143 time to evaluate : 0.924 ------------------------------------------------------------------------------- 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 133 PHE 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 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 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 212 GLU Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 242 MET 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 22 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 98 optimal weight: 0.5980 chunk 109 optimal weight: 5.9990 chunk 91 optimal weight: 0.9980 chunk 95 optimal weight: 0.8980 chunk 34 optimal weight: 0.3980 chunk 82 optimal weight: 0.7980 chunk 40 optimal weight: 2.9990 chunk 103 optimal weight: 0.9980 chunk 65 optimal weight: 0.7980 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 = 0.4039 r_free = 0.4039 target = 0.180586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.155299 restraints weight = 11349.925| |-----------------------------------------------------------------------------| r_work (start): 0.3772 rms_B_bonded: 1.61 r_work: 0.3670 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3544 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.4472 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= 0.194 Angle : 0.569 9.379 12782 Z= 0.288 Chirality : 0.039 0.151 1420 Planarity : 0.004 0.037 1556 Dihedral : 5.840 39.871 1264 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 4.62 % Allowed : 16.60 % 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: 0.54 (0.26), residues: 1126 helix: 0.96 (0.19), residues: 750 sheet: None (None), residues: 0 loop : -0.76 (0.33), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 80 HIS 0.004 0.001 HIS D 220 PHE 0.017 0.001 PHE D 316 TYR 0.016 0.001 TYR D 152 ARG 0.005 0.000 ARG A 81 *********************** 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 210 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 166 time to evaluate : 0.834 Fit side-chains REVERT: D 173 TRP cc_start: 0.6859 (OUTLIER) cc_final: 0.6173 (m-90) REVERT: D 264 TRP cc_start: 0.6544 (m100) cc_final: 0.6317 (t60) REVERT: D 298 ASP cc_start: 0.7408 (t70) cc_final: 0.6850 (t0) REVERT: D 309 ILE cc_start: 0.7390 (OUTLIER) cc_final: 0.7087 (mp) REVERT: D 376 ILE cc_start: 0.8224 (OUTLIER) cc_final: 0.7489 (mt) REVERT: A 173 TRP cc_start: 0.6854 (OUTLIER) cc_final: 0.6138 (m-90) REVERT: A 264 TRP cc_start: 0.6518 (m100) cc_final: 0.6298 (t60) REVERT: A 309 ILE cc_start: 0.7512 (OUTLIER) cc_final: 0.7263 (mp) REVERT: A 376 ILE cc_start: 0.8156 (OUTLIER) cc_final: 0.7533 (mt) outliers start: 44 outliers final: 31 residues processed: 190 average time/residue: 0.1875 time to fit residues: 51.5056 Evaluate side-chains 179 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 142 time to evaluate : 1.067 ------------------------------------------------------------------------------- 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 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 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 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 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 ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 69.3768 > 50: distance: 3 - 23: 36.343 distance: 21 - 23: 34.072 distance: 25 - 26: 36.036 distance: 25 - 30: 40.292 distance: 27 - 28: 23.538 distance: 27 - 29: 18.995 distance: 30 - 31: 6.346 distance: 31 - 32: 37.302 distance: 31 - 34: 6.275 distance: 32 - 33: 45.452 distance: 32 - 37: 40.249 distance: 34 - 35: 50.366 distance: 37 - 38: 15.309 distance: 38 - 39: 34.879 distance: 38 - 41: 22.450 distance: 39 - 40: 39.621 distance: 39 - 45: 49.661 distance: 41 - 42: 33.757 distance: 42 - 43: 29.553 distance: 42 - 44: 55.731 distance: 45 - 46: 25.775 distance: 45 - 51: 57.219 distance: 46 - 47: 23.673 distance: 46 - 49: 42.484 distance: 47 - 48: 3.209 distance: 47 - 52: 8.719 distance: 52 - 53: 43.190 distance: 53 - 54: 45.753 distance: 54 - 55: 4.127 distance: 54 - 56: 45.436 distance: 56 - 57: 11.661 distance: 58 - 59: 13.272 distance: 58 - 61: 23.530 distance: 59 - 79: 54.777 distance: 61 - 62: 12.029 distance: 62 - 63: 36.467 distance: 62 - 65: 4.642 distance: 63 - 67: 55.860 distance: 64 - 87: 35.358 distance: 67 - 68: 12.895 distance: 69 - 75: 15.983 distance: 70 - 95: 36.070 distance: 71 - 72: 41.019 distance: 72 - 73: 10.350 distance: 72 - 74: 29.452 distance: 75 - 76: 7.682 distance: 76 - 77: 12.983 distance: 77 - 78: 6.843 distance: 78 - 100: 33.541 distance: 79 - 80: 13.479 distance: 80 - 81: 7.565 distance: 80 - 83: 11.041 distance: 81 - 82: 37.079 distance: 81 - 87: 24.244 distance: 82 - 107: 33.748 distance: 83 - 84: 22.294 distance: 83 - 85: 21.045 distance: 84 - 86: 16.290