Starting phenix.real_space_refine on Tue Feb 3 20:08:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9yhn_72967/02_2026/9yhn_72967.cif Found real_map, /net/cci-nas-00/data/ceres_data/9yhn_72967/02_2026/9yhn_72967.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.38 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9yhn_72967/02_2026/9yhn_72967.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9yhn_72967/02_2026/9yhn_72967.map" model { file = "/net/cci-nas-00/data/ceres_data/9yhn_72967/02_2026/9yhn_72967.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9yhn_72967/02_2026/9yhn_72967.cif" } resolution = 3.38 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 3 9.91 5 S 26 5.16 5 C 4111 2.51 5 N 1134 2.21 5 O 1219 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6493 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 6490 Number of conformers: 1 Conformer: "" Number of residues, atoms: 821, 6490 Classifications: {'peptide': 821} Link IDs: {'PCIS': 1, 'PTRANS': 30, 'TRANS': 789} Chain breaks: 1 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 1.34, per 1000 atoms: 0.21 Number of scatterers: 6493 At special positions: 0 Unit cell: (67.68, 86.48, 103.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 3 19.99 S 26 16.00 O 1219 8.00 N 1134 7.00 C 4111 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.52 Conformation dependent library (CDL) restraints added in 213.2 milliseconds 1634 Ramachandran restraints generated. 817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1548 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 5 sheets defined 58.2% alpha, 10.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'A' and resid 18 through 26 removed outlier: 3.952A pdb=" N GLU A 24 " --> pdb=" O VAL A 20 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N THR A 25 " --> pdb=" O ALA A 21 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU A 26 " --> pdb=" O LEU A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 36 through 51 Processing helix chain 'A' and resid 71 through 86 removed outlier: 3.652A pdb=" N ASP A 86 " --> pdb=" O SER A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 112 Processing helix chain 'A' and resid 123 through 128 Processing helix chain 'A' and resid 137 through 141 Processing helix chain 'A' and resid 149 through 153 removed outlier: 3.651A pdb=" N SER A 153 " --> pdb=" O HIS A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 175 removed outlier: 3.529A pdb=" N CYS A 175 " --> pdb=" O ILE A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 199 removed outlier: 3.954A pdb=" N HIS A 187 " --> pdb=" O GLU A 183 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N THR A 195 " --> pdb=" O LYS A 191 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N GLU A 196 " --> pdb=" O LEU A 192 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LEU A 199 " --> pdb=" O THR A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 211 Processing helix chain 'A' and resid 220 through 227 removed outlier: 3.533A pdb=" N ALA A 226 " --> pdb=" O TRP A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 238 Processing helix chain 'A' and resid 241 through 246 removed outlier: 4.205A pdb=" N PHE A 246 " --> pdb=" O LYS A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 252 removed outlier: 3.592A pdb=" N LEU A 251 " --> pdb=" O THR A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 256 No H-bonds generated for 'chain 'A' and resid 254 through 256' Processing helix chain 'A' and resid 279 through 284 Processing helix chain 'A' and resid 297 through 299 No H-bonds generated for 'chain 'A' and resid 297 through 299' Processing helix chain 'A' and resid 300 through 305 Processing helix chain 'A' and resid 308 through 314 removed outlier: 3.786A pdb=" N ILE A 312 " --> pdb=" O SER A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 335 Processing helix chain 'A' and resid 340 through 349 removed outlier: 3.708A pdb=" N ILE A 344 " --> pdb=" O ASP A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 374 removed outlier: 3.668A pdb=" N TRP A 372 " --> pdb=" O ARG A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 394 Processing helix chain 'A' and resid 413 through 417 removed outlier: 3.593A pdb=" N CYS A 417 " --> pdb=" O ASP A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 440 Processing helix chain 'A' and resid 443 through 459 removed outlier: 3.560A pdb=" N LEU A 447 " --> pdb=" O SER A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 484 Processing helix chain 'A' and resid 484 through 489 removed outlier: 3.868A pdb=" N ARG A 489 " --> pdb=" O VAL A 485 " (cutoff:3.500A) Processing helix chain 'A' and resid 492 through 515 Processing helix chain 'A' and resid 518 through 532 Processing helix chain 'A' and resid 534 through 545 Processing helix chain 'A' and resid 546 through 548 No H-bonds generated for 'chain 'A' and resid 546 through 548' Processing helix chain 'A' and resid 554 through 573 Processing helix chain 'A' and resid 575 through 589 removed outlier: 3.611A pdb=" N ALA A 579 " --> pdb=" O ASP A 575 " (cutoff:3.500A) Processing helix chain 'A' and resid 593 through 595 No H-bonds generated for 'chain 'A' and resid 593 through 595' Processing helix chain 'A' and resid 596 through 608 removed outlier: 4.035A pdb=" N TYR A 600 " --> pdb=" O ASP A 596 " (cutoff:3.500A) Processing helix chain 'A' and resid 612 through 627 Processing helix chain 'A' and resid 648 through 659 Processing helix chain 'A' and resid 662 through 676 removed outlier: 3.538A pdb=" N ARG A 676 " --> pdb=" O ASP A 672 " (cutoff:3.500A) Processing helix chain 'A' and resid 682 through 697 Processing helix chain 'A' and resid 740 through 758 Processing helix chain 'A' and resid 788 through 805 removed outlier: 3.525A pdb=" N SER A 805 " --> pdb=" O ALA A 801 " (cutoff:3.500A) Processing helix chain 'A' and resid 810 through 814 removed outlier: 3.578A pdb=" N ASP A 813 " --> pdb=" O ASN A 810 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N LEU A 814 " --> pdb=" O LEU A 811 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 810 through 814' Processing helix chain 'A' and resid 815 through 826 Processing helix chain 'A' and resid 829 through 836 Processing sheet with id=AA1, first strand: chain 'A' and resid 61 through 65 removed outlier: 6.426A pdb=" N ILE A 159 " --> pdb=" O ILE A 289 " (cutoff:3.500A) removed outlier: 8.020A pdb=" N MET A 291 " --> pdb=" O ILE A 159 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N MET A 161 " --> pdb=" O MET A 291 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N VAL A 92 " --> pdb=" O LEU A 160 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N SER A 116 " --> pdb=" O VAL A 134 " (cutoff:3.500A) removed outlier: 8.465A pdb=" N SER A 136 " --> pdb=" O SER A 116 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 177 through 180 removed outlier: 4.732A pdb=" N CYS A 260 " --> pdb=" O VAL A 219 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 326 through 330 removed outlier: 6.620A pdb=" N GLU A 326 " --> pdb=" O SER A 469 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N VAL A 471 " --> pdb=" O GLU A 326 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N MET A 328 " --> pdb=" O VAL A 471 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N ALA A 473 " --> pdb=" O MET A 328 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N LEU A 330 " --> pdb=" O ALA A 473 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N LEU A 420 " --> pdb=" O VAL A 472 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N ILE A 474 " --> pdb=" O LEU A 420 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N PHE A 422 " --> pdb=" O ILE A 474 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ILE A 359 " --> pdb=" O LEU A 401 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N LEU A 403 " --> pdb=" O ILE A 359 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N ALA A 361 " --> pdb=" O LEU A 403 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N LYS A 378 " --> pdb=" O VAL A 402 " (cutoff:3.500A) removed outlier: 8.297A pdb=" N ALA A 404 " --> pdb=" O LYS A 378 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 700 through 702 removed outlier: 3.814A pdb=" N ALA A 700 " --> pdb=" O ALA A 717 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ASN A 714 " --> pdb=" O PHE A 726 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N TYR A 723 " --> pdb=" O LYS A 764 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N LEU A 766 " --> pdb=" O TYR A 723 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N LEU A 725 " --> pdb=" O LEU A 766 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N VAL A 768 " --> pdb=" O LEU A 725 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N GLU A 727 " --> pdb=" O VAL A 768 " (cutoff:3.500A) removed outlier: 8.651A pdb=" N ASP A 785 " --> pdb=" O VAL A 763 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N ARG A 765 " --> pdb=" O ASP A 785 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N MET A 787 " --> pdb=" O ARG A 765 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ILE A 767 " --> pdb=" O MET A 787 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 738 through 739 314 hydrogen bonds defined for protein. 924 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.10 Time building geometry restraints manager: 0.69 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: 2169 1.34 - 1.46: 1372 1.46 - 1.58: 3036 1.58 - 1.70: 0 1.70 - 1.82: 40 Bond restraints: 6617 Sorted by residual: bond pdb=" N MET A 545 " pdb=" CA MET A 545 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.33e-02 5.65e+03 5.91e+00 bond pdb=" C ALA A 349 " pdb=" N PRO A 350 " ideal model delta sigma weight residual 1.331 1.349 -0.019 1.31e-02 5.83e+03 2.06e+00 bond pdb=" CB LYS A 114 " pdb=" CG LYS A 114 " ideal model delta sigma weight residual 1.520 1.562 -0.042 3.00e-02 1.11e+03 1.94e+00 bond pdb=" CG ARG A 625 " pdb=" CD ARG A 625 " ideal model delta sigma weight residual 1.520 1.561 -0.041 3.00e-02 1.11e+03 1.90e+00 bond pdb=" CA ASP A 713 " pdb=" CB ASP A 713 " ideal model delta sigma weight residual 1.528 1.506 0.023 1.66e-02 3.63e+03 1.87e+00 ... (remaining 6612 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.92: 8766 1.92 - 3.84: 152 3.84 - 5.75: 17 5.75 - 7.67: 10 7.67 - 9.59: 3 Bond angle restraints: 8948 Sorted by residual: angle pdb=" CA LYS A 466 " pdb=" CB LYS A 466 " pdb=" CG LYS A 466 " ideal model delta sigma weight residual 114.10 122.58 -8.48 2.00e+00 2.50e-01 1.80e+01 angle pdb=" CB LYS A 114 " pdb=" CG LYS A 114 " pdb=" CD LYS A 114 " ideal model delta sigma weight residual 111.30 120.89 -9.59 2.30e+00 1.89e-01 1.74e+01 angle pdb=" CG ARG A 625 " pdb=" CD ARG A 625 " pdb=" NE ARG A 625 " ideal model delta sigma weight residual 112.00 118.56 -6.56 2.20e+00 2.07e-01 8.89e+00 angle pdb=" CA GLU A 727 " pdb=" CB GLU A 727 " pdb=" CG GLU A 727 " ideal model delta sigma weight residual 114.10 119.64 -5.54 2.00e+00 2.50e-01 7.66e+00 angle pdb=" CB ARG A 625 " pdb=" CG ARG A 625 " pdb=" CD ARG A 625 " ideal model delta sigma weight residual 111.30 117.56 -6.26 2.30e+00 1.89e-01 7.40e+00 ... (remaining 8943 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.16: 3648 16.16 - 32.31: 274 32.31 - 48.46: 83 48.46 - 64.62: 14 64.62 - 80.77: 4 Dihedral angle restraints: 4023 sinusoidal: 1633 harmonic: 2390 Sorted by residual: dihedral pdb=" CG ARG A 28 " pdb=" CD ARG A 28 " pdb=" NE ARG A 28 " pdb=" CZ ARG A 28 " ideal model delta sinusoidal sigma weight residual -90.00 -135.00 45.00 2 1.50e+01 4.44e-03 1.07e+01 dihedral pdb=" CG ARG A 256 " pdb=" CD ARG A 256 " pdb=" NE ARG A 256 " pdb=" CZ ARG A 256 " ideal model delta sinusoidal sigma weight residual 180.00 135.21 44.79 2 1.50e+01 4.44e-03 1.06e+01 dihedral pdb=" CG ARG A 254 " pdb=" CD ARG A 254 " pdb=" NE ARG A 254 " pdb=" CZ ARG A 254 " ideal model delta sinusoidal sigma weight residual -180.00 -136.84 -43.16 2 1.50e+01 4.44e-03 9.98e+00 ... (remaining 4020 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 773 0.050 - 0.101: 174 0.101 - 0.151: 44 0.151 - 0.202: 3 0.202 - 0.252: 2 Chirality restraints: 996 Sorted by residual: chirality pdb=" CB ILE A 159 " pdb=" CA ILE A 159 " pdb=" CG1 ILE A 159 " pdb=" CG2 ILE A 159 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.25 2.00e-01 2.50e+01 1.59e+00 chirality pdb=" CB THR A 135 " pdb=" CA THR A 135 " pdb=" OG1 THR A 135 " pdb=" CG2 THR A 135 " both_signs ideal model delta sigma weight residual False 2.55 2.34 0.21 2.00e-01 2.50e+01 1.12e+00 chirality pdb=" CB ILE A 767 " pdb=" CA ILE A 767 " pdb=" CG1 ILE A 767 " pdb=" CG2 ILE A 767 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.20 2.00e-01 2.50e+01 9.52e-01 ... (remaining 993 not shown) Planarity restraints: 1159 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP A 705 " -0.013 2.00e-02 2.50e+03 2.53e-02 6.39e+00 pdb=" CG ASP A 705 " 0.044 2.00e-02 2.50e+03 pdb=" OD1 ASP A 705 " -0.015 2.00e-02 2.50e+03 pdb=" OD2 ASP A 705 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 705 " -0.008 2.00e-02 2.50e+03 1.57e-02 2.47e+00 pdb=" C ASP A 705 " 0.027 2.00e-02 2.50e+03 pdb=" O ASP A 705 " -0.010 2.00e-02 2.50e+03 pdb=" N ALA A 706 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU A 518 " 0.026 5.00e-02 4.00e+02 3.93e-02 2.47e+00 pdb=" N PRO A 519 " -0.068 5.00e-02 4.00e+02 pdb=" CA PRO A 519 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 519 " 0.022 5.00e-02 4.00e+02 ... (remaining 1156 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 64 2.67 - 3.23: 5737 3.23 - 3.78: 9804 3.78 - 4.34: 13714 4.34 - 4.90: 22487 Nonbonded interactions: 51806 Sorted by model distance: nonbonded pdb=" OE2 GLU A 687 " pdb="CA CA A 902 " model vdw 2.111 2.510 nonbonded pdb=" OE1 GLU A 687 " pdb="CA CA A 902 " model vdw 2.312 2.510 nonbonded pdb=" OD1 ASP A 713 " pdb="CA CA A 901 " model vdw 2.320 2.510 nonbonded pdb=" OE1 GLU A 568 " pdb=" OH TYR A 607 " model vdw 2.339 3.040 nonbonded pdb=" OD1 ASP A 411 " pdb=" NH2 ARG A 463 " model vdw 2.346 3.120 ... (remaining 51801 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.870 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: 0.000 Extract box with map and model: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 6.940 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6690 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 : 0.003 0.046 6617 Z= 0.163 Angle : 0.663 9.588 8948 Z= 0.346 Chirality : 0.046 0.252 996 Planarity : 0.005 0.040 1159 Dihedral : 13.073 80.774 2475 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 0.43 % Allowed : 5.76 % Favored : 93.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.26 (0.27), residues: 817 helix: 0.23 (0.23), residues: 408 sheet: 1.26 (0.55), residues: 96 loop : -0.04 (0.32), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 625 TYR 0.015 0.001 TYR A 318 PHE 0.016 0.002 PHE A 803 TRP 0.013 0.002 TRP A 753 HIS 0.002 0.001 HIS A 287 Details of bonding type rmsd covalent geometry : bond 0.00345 ( 6617) covalent geometry : angle 0.66341 ( 8948) hydrogen bonds : bond 0.12689 ( 314) hydrogen bonds : angle 6.09327 ( 924) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1634 Ramachandran restraints generated. 817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1634 Ramachandran restraints generated. 817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 39 time to evaluate : 0.225 Fit side-chains revert: symmetry clash REVERT: A 114 LYS cc_start: 0.7598 (mmmt) cc_final: 0.7106 (tptp) REVERT: A 448 MET cc_start: 0.7570 (mtp) cc_final: 0.7342 (mtm) REVERT: A 626 ASN cc_start: 0.8032 (t0) cc_final: 0.7599 (m-40) REVERT: A 747 MET cc_start: 0.7426 (tpp) cc_final: 0.7203 (tpp) REVERT: A 764 LYS cc_start: 0.7476 (tptt) cc_final: 0.6843 (tptt) outliers start: 3 outliers final: 0 residues processed: 39 average time/residue: 0.1124 time to fit residues: 5.6396 Evaluate side-chains 37 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 37 time to evaluate : 0.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 49 optimal weight: 0.7980 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 0.5980 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.5980 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 0.1980 chunk 74 optimal weight: 0.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.4225 r_free = 0.4225 target = 0.207217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.185404 restraints weight = 5893.227| |-----------------------------------------------------------------------------| r_work (start): 0.4281 rms_B_bonded: 1.46 r_work: 0.4020 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.4020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6829 moved from start: 0.0946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 6617 Z= 0.161 Angle : 0.503 5.391 8948 Z= 0.258 Chirality : 0.041 0.140 996 Planarity : 0.004 0.029 1159 Dihedral : 4.027 13.649 890 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 1.30 % Allowed : 6.05 % Favored : 92.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.15 (0.28), residues: 817 helix: 1.23 (0.25), residues: 407 sheet: 0.97 (0.54), residues: 96 loop : 0.23 (0.33), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 625 TYR 0.010 0.001 TYR A 93 PHE 0.009 0.001 PHE A 803 TRP 0.012 0.001 TRP A 222 HIS 0.003 0.001 HIS A 438 Details of bonding type rmsd covalent geometry : bond 0.00372 ( 6617) covalent geometry : angle 0.50258 ( 8948) hydrogen bonds : bond 0.03816 ( 314) hydrogen bonds : angle 4.61902 ( 924) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1634 Ramachandran restraints generated. 817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1634 Ramachandran restraints generated. 817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 37 time to evaluate : 0.213 Fit side-chains REVERT: A 66 LEU cc_start: 0.7460 (OUTLIER) cc_final: 0.7196 (pp) REVERT: A 114 LYS cc_start: 0.7715 (mmmt) cc_final: 0.7179 (tptp) REVERT: A 448 MET cc_start: 0.7758 (mtp) cc_final: 0.7494 (mtp) REVERT: A 545 MET cc_start: 0.8592 (tpp) cc_final: 0.8050 (tpp) REVERT: A 551 LYS cc_start: 0.7268 (ttpp) cc_final: 0.6906 (ttpp) REVERT: A 764 LYS cc_start: 0.7512 (tptt) cc_final: 0.6831 (tptt) outliers start: 9 outliers final: 6 residues processed: 44 average time/residue: 0.0811 time to fit residues: 4.7837 Evaluate side-chains 43 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 36 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 259 GLN Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 299 SER Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 548 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 65 optimal weight: 0.9990 chunk 29 optimal weight: 0.7980 chunk 33 optimal weight: 0.4980 chunk 48 optimal weight: 0.6980 chunk 7 optimal weight: 0.5980 chunk 55 optimal weight: 2.9990 chunk 57 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 80 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.4156 r_free = 0.4156 target = 0.199251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.178858 restraints weight = 5916.655| |-----------------------------------------------------------------------------| r_work (start): 0.3968 rms_B_bonded: 1.37 r_work: 0.3822 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3663 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7033 moved from start: 0.2058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 6617 Z= 0.195 Angle : 0.546 5.396 8948 Z= 0.279 Chirality : 0.043 0.145 996 Planarity : 0.004 0.039 1159 Dihedral : 4.197 14.211 890 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.59 % Allowed : 6.92 % Favored : 91.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.21 (0.29), residues: 817 helix: 1.36 (0.26), residues: 406 sheet: 0.77 (0.56), residues: 96 loop : 0.22 (0.34), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 625 TYR 0.011 0.001 TYR A 758 PHE 0.014 0.002 PHE A 726 TRP 0.012 0.002 TRP A 222 HIS 0.005 0.001 HIS A 438 Details of bonding type rmsd covalent geometry : bond 0.00461 ( 6617) covalent geometry : angle 0.54643 ( 8948) hydrogen bonds : bond 0.04065 ( 314) hydrogen bonds : angle 4.38875 ( 924) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1634 Ramachandran restraints generated. 817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1634 Ramachandran restraints generated. 817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 43 time to evaluate : 0.154 Fit side-chains REVERT: A 66 LEU cc_start: 0.7703 (OUTLIER) cc_final: 0.7404 (pp) REVERT: A 114 LYS cc_start: 0.7837 (mmmt) cc_final: 0.7544 (mmmt) REVERT: A 242 LYS cc_start: 0.7166 (mmtt) cc_final: 0.6900 (mtpp) REVERT: A 338 ASP cc_start: 0.7133 (m-30) cc_final: 0.6882 (m-30) REVERT: A 378 LYS cc_start: 0.8108 (tttt) cc_final: 0.7451 (mtmt) REVERT: A 448 MET cc_start: 0.7915 (mtp) cc_final: 0.7685 (mtp) REVERT: A 466 LYS cc_start: 0.8120 (tptp) cc_final: 0.7910 (tptp) REVERT: A 551 LYS cc_start: 0.7319 (ttpp) cc_final: 0.6915 (ptmm) REVERT: A 764 LYS cc_start: 0.7648 (tptt) cc_final: 0.6763 (tptt) outliers start: 11 outliers final: 4 residues processed: 50 average time/residue: 0.0990 time to fit residues: 6.3088 Evaluate side-chains 43 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 38 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain A residue 662 SER Chi-restraints excluded: chain A residue 787 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 49 optimal weight: 0.6980 chunk 55 optimal weight: 2.9990 chunk 62 optimal weight: 0.6980 chunk 10 optimal weight: 0.7980 chunk 17 optimal weight: 0.0970 chunk 36 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 57 optimal weight: 0.0980 chunk 56 optimal weight: 0.5980 chunk 58 optimal weight: 0.7980 overall best weight: 0.4378 ------------------------------------------------------------------------------- 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 = 0.4421 r_free = 0.4421 target = 0.230617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.205682 restraints weight = 6299.315| |-----------------------------------------------------------------------------| r_work (start): 0.3965 rms_B_bonded: 1.70 r_work: 0.3812 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6844 moved from start: 0.2197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6617 Z= 0.127 Angle : 0.456 5.711 8948 Z= 0.233 Chirality : 0.040 0.136 996 Planarity : 0.003 0.035 1159 Dihedral : 3.841 13.448 890 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 0.72 % Allowed : 8.21 % Favored : 91.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.52 (0.29), residues: 817 helix: 1.66 (0.26), residues: 407 sheet: 0.74 (0.56), residues: 96 loop : 0.36 (0.35), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 625 TYR 0.010 0.001 TYR A 93 PHE 0.008 0.001 PHE A 803 TRP 0.008 0.001 TRP A 222 HIS 0.003 0.001 HIS A 438 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 6617) covalent geometry : angle 0.45631 ( 8948) hydrogen bonds : bond 0.03321 ( 314) hydrogen bonds : angle 4.13688 ( 924) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1634 Ramachandran restraints generated. 817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1634 Ramachandran restraints generated. 817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 37 time to evaluate : 0.162 Fit side-chains REVERT: A 66 LEU cc_start: 0.7516 (OUTLIER) cc_final: 0.7231 (pp) REVERT: A 242 LYS cc_start: 0.7084 (mmtt) cc_final: 0.6567 (mmtm) REVERT: A 378 LYS cc_start: 0.8081 (tttt) cc_final: 0.7396 (mtmt) REVERT: A 448 MET cc_start: 0.7811 (mtp) cc_final: 0.7607 (mtp) REVERT: A 466 LYS cc_start: 0.8046 (tptp) cc_final: 0.7489 (tptp) REVERT: A 545 MET cc_start: 0.8595 (tpp) cc_final: 0.8289 (tpp) REVERT: A 551 LYS cc_start: 0.7241 (ttpp) cc_final: 0.6884 (ptmm) REVERT: A 764 LYS cc_start: 0.7461 (tptt) cc_final: 0.6644 (tptt) outliers start: 5 outliers final: 4 residues processed: 41 average time/residue: 0.1034 time to fit residues: 5.4428 Evaluate side-chains 42 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 37 time to evaluate : 0.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 299 SER Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain A residue 787 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 46 optimal weight: 1.9990 chunk 71 optimal weight: 5.9990 chunk 23 optimal weight: 0.9980 chunk 11 optimal weight: 0.5980 chunk 41 optimal weight: 0.6980 chunk 70 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 chunk 43 optimal weight: 0.0870 chunk 49 optimal weight: 0.6980 chunk 53 optimal weight: 0.9980 chunk 75 optimal weight: 0.9980 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 494 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4394 r_free = 0.4394 target = 0.227372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.202327 restraints weight = 6365.690| |-----------------------------------------------------------------------------| r_work (start): 0.3933 rms_B_bonded: 1.74 r_work: 0.3782 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6875 moved from start: 0.2563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 6617 Z= 0.167 Angle : 0.496 5.153 8948 Z= 0.252 Chirality : 0.041 0.144 996 Planarity : 0.004 0.038 1159 Dihedral : 3.905 14.034 890 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.44 % Allowed : 7.78 % Favored : 90.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.48 (0.29), residues: 817 helix: 1.63 (0.26), residues: 408 sheet: 1.23 (0.60), residues: 80 loop : 0.19 (0.34), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 625 TYR 0.011 0.001 TYR A 93 PHE 0.009 0.001 PHE A 726 TRP 0.009 0.001 TRP A 222 HIS 0.003 0.001 HIS A 438 Details of bonding type rmsd covalent geometry : bond 0.00396 ( 6617) covalent geometry : angle 0.49562 ( 8948) hydrogen bonds : bond 0.03636 ( 314) hydrogen bonds : angle 4.11643 ( 924) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1634 Ramachandran restraints generated. 817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1634 Ramachandran restraints generated. 817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 46 time to evaluate : 0.252 Fit side-chains REVERT: A 66 LEU cc_start: 0.7511 (OUTLIER) cc_final: 0.7248 (pp) REVERT: A 114 LYS cc_start: 0.7756 (mmmt) cc_final: 0.7273 (tptp) REVERT: A 173 ASP cc_start: 0.7354 (OUTLIER) cc_final: 0.6677 (t70) REVERT: A 242 LYS cc_start: 0.7037 (mmtt) cc_final: 0.6525 (mmtm) REVERT: A 334 MET cc_start: 0.7935 (mmt) cc_final: 0.6851 (mtt) REVERT: A 378 LYS cc_start: 0.8003 (tttt) cc_final: 0.7323 (mtmt) REVERT: A 466 LYS cc_start: 0.8096 (tptp) cc_final: 0.7566 (tptp) REVERT: A 545 MET cc_start: 0.8686 (tpp) cc_final: 0.7987 (tpp) REVERT: A 546 LYS cc_start: 0.8318 (mttm) cc_final: 0.8071 (mttt) REVERT: A 551 LYS cc_start: 0.7172 (ttpp) cc_final: 0.6873 (ptmm) REVERT: A 764 LYS cc_start: 0.7505 (tptt) cc_final: 0.6573 (tptt) outliers start: 10 outliers final: 5 residues processed: 54 average time/residue: 0.1173 time to fit residues: 7.9683 Evaluate side-chains 51 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 44 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 173 ASP Chi-restraints excluded: chain A residue 212 LYS Chi-restraints excluded: chain A residue 299 SER Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain A residue 787 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 47 optimal weight: 0.2980 chunk 62 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 35 optimal weight: 0.0770 chunk 74 optimal weight: 0.7980 chunk 36 optimal weight: 0.8980 chunk 81 optimal weight: 0.6980 chunk 37 optimal weight: 0.0770 chunk 69 optimal weight: 0.1980 chunk 67 optimal weight: 0.7980 overall best weight: 0.2696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 HIS A 746 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.202707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.180555 restraints weight = 5992.609| |-----------------------------------------------------------------------------| r_work (start): 0.4208 rms_B_bonded: 1.54 r_work: 0.3993 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6890 moved from start: 0.2714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 6617 Z= 0.097 Angle : 0.434 6.505 8948 Z= 0.225 Chirality : 0.040 0.143 996 Planarity : 0.003 0.037 1159 Dihedral : 3.668 13.880 890 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 1.44 % Allowed : 8.50 % Favored : 90.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.81 (0.30), residues: 817 helix: 1.97 (0.26), residues: 406 sheet: 0.77 (0.56), residues: 96 loop : 0.44 (0.35), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 625 TYR 0.009 0.001 TYR A 93 PHE 0.007 0.001 PHE A 754 TRP 0.010 0.001 TRP A 222 HIS 0.002 0.000 HIS A 826 Details of bonding type rmsd covalent geometry : bond 0.00216 ( 6617) covalent geometry : angle 0.43391 ( 8948) hydrogen bonds : bond 0.02994 ( 314) hydrogen bonds : angle 3.93649 ( 924) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1634 Ramachandran restraints generated. 817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1634 Ramachandran restraints generated. 817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 38 time to evaluate : 0.171 Fit side-chains REVERT: A 66 LEU cc_start: 0.7592 (OUTLIER) cc_final: 0.7310 (pp) REVERT: A 114 LYS cc_start: 0.7734 (mmmt) cc_final: 0.7388 (mmmt) REVERT: A 173 ASP cc_start: 0.7549 (OUTLIER) cc_final: 0.6889 (t70) REVERT: A 212 LYS cc_start: 0.7654 (OUTLIER) cc_final: 0.7386 (mptt) REVERT: A 242 LYS cc_start: 0.7107 (mmtt) cc_final: 0.6864 (mtpp) REVERT: A 334 MET cc_start: 0.7965 (OUTLIER) cc_final: 0.6917 (mtt) REVERT: A 378 LYS cc_start: 0.8076 (tttt) cc_final: 0.7366 (mtmt) REVERT: A 466 LYS cc_start: 0.8146 (tptp) cc_final: 0.7613 (tptp) REVERT: A 545 MET cc_start: 0.8594 (tpp) cc_final: 0.8366 (tpp) REVERT: A 551 LYS cc_start: 0.7250 (ttpp) cc_final: 0.6900 (ptmm) REVERT: A 764 LYS cc_start: 0.7463 (tptt) cc_final: 0.6671 (tptt) outliers start: 10 outliers final: 5 residues processed: 45 average time/residue: 0.1187 time to fit residues: 6.6785 Evaluate side-chains 45 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 36 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 173 ASP Chi-restraints excluded: chain A residue 212 LYS Chi-restraints excluded: chain A residue 299 SER Chi-restraints excluded: chain A residue 334 MET Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain A residue 643 THR Chi-restraints excluded: chain A residue 787 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 18 optimal weight: 0.9980 chunk 16 optimal weight: 0.3980 chunk 70 optimal weight: 0.1980 chunk 2 optimal weight: 0.5980 chunk 78 optimal weight: 2.9990 chunk 23 optimal weight: 0.5980 chunk 7 optimal weight: 0.0070 chunk 44 optimal weight: 0.3980 chunk 69 optimal weight: 0.5980 chunk 43 optimal weight: 0.8980 chunk 3 optimal weight: 2.9990 overall best weight: 0.3198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.202343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.179813 restraints weight = 5988.508| |-----------------------------------------------------------------------------| r_work (start): 0.4202 rms_B_bonded: 1.59 r_work: 0.3905 rms_B_bonded: 4.88 restraints_weight: 0.5000 r_work (final): 0.3905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7013 moved from start: 0.2832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 6617 Z= 0.102 Angle : 0.429 6.011 8948 Z= 0.220 Chirality : 0.039 0.136 996 Planarity : 0.003 0.037 1159 Dihedral : 3.565 14.118 890 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 1.44 % Allowed : 9.51 % Favored : 89.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.95 (0.30), residues: 817 helix: 2.05 (0.26), residues: 413 sheet: 0.82 (0.57), residues: 96 loop : 0.54 (0.36), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 625 TYR 0.009 0.001 TYR A 93 PHE 0.007 0.001 PHE A 754 TRP 0.010 0.001 TRP A 222 HIS 0.002 0.000 HIS A 826 Details of bonding type rmsd covalent geometry : bond 0.00231 ( 6617) covalent geometry : angle 0.42939 ( 8948) hydrogen bonds : bond 0.02942 ( 314) hydrogen bonds : angle 3.83864 ( 924) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1634 Ramachandran restraints generated. 817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1634 Ramachandran restraints generated. 817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 38 time to evaluate : 0.155 Fit side-chains REVERT: A 66 LEU cc_start: 0.7650 (OUTLIER) cc_final: 0.7364 (pp) REVERT: A 114 LYS cc_start: 0.7726 (mmmt) cc_final: 0.7394 (mmmt) REVERT: A 173 ASP cc_start: 0.7524 (OUTLIER) cc_final: 0.6681 (t0) REVERT: A 242 LYS cc_start: 0.7141 (mmtt) cc_final: 0.6888 (mtpp) REVERT: A 334 MET cc_start: 0.8023 (OUTLIER) cc_final: 0.6935 (mtt) REVERT: A 378 LYS cc_start: 0.8134 (tttt) cc_final: 0.7381 (mtmt) REVERT: A 466 LYS cc_start: 0.8162 (tptp) cc_final: 0.7630 (tptp) REVERT: A 545 MET cc_start: 0.8610 (tpp) cc_final: 0.8036 (tpp) REVERT: A 551 LYS cc_start: 0.7303 (ttpp) cc_final: 0.6939 (ptmm) REVERT: A 764 LYS cc_start: 0.7572 (tptt) cc_final: 0.6746 (tptt) outliers start: 10 outliers final: 6 residues processed: 45 average time/residue: 0.1041 time to fit residues: 5.9109 Evaluate side-chains 44 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 35 time to evaluate : 0.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 173 ASP Chi-restraints excluded: chain A residue 299 SER Chi-restraints excluded: chain A residue 334 MET Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain A residue 643 THR Chi-restraints excluded: chain A residue 787 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 39 optimal weight: 0.9990 chunk 30 optimal weight: 0.7980 chunk 63 optimal weight: 0.7980 chunk 3 optimal weight: 0.6980 chunk 35 optimal weight: 1.9990 chunk 38 optimal weight: 0.5980 chunk 79 optimal weight: 0.6980 chunk 72 optimal weight: 3.9990 chunk 24 optimal weight: 0.5980 chunk 66 optimal weight: 0.5980 chunk 14 optimal weight: 1.9990 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 = 0.4125 r_free = 0.4125 target = 0.196753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.175265 restraints weight = 5994.594| |-----------------------------------------------------------------------------| r_work (start): 0.3909 rms_B_bonded: 1.48 r_work: 0.3788 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3628 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7041 moved from start: 0.3140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 6617 Z= 0.170 Angle : 0.502 5.913 8948 Z= 0.255 Chirality : 0.041 0.139 996 Planarity : 0.004 0.038 1159 Dihedral : 3.874 14.379 890 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.15 % Allowed : 9.80 % Favored : 89.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.73 (0.30), residues: 817 helix: 1.84 (0.26), residues: 407 sheet: 1.18 (0.62), residues: 80 loop : 0.36 (0.35), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 625 TYR 0.012 0.001 TYR A 93 PHE 0.009 0.001 PHE A 726 TRP 0.016 0.001 TRP A 222 HIS 0.003 0.001 HIS A 438 Details of bonding type rmsd covalent geometry : bond 0.00400 ( 6617) covalent geometry : angle 0.50190 ( 8948) hydrogen bonds : bond 0.03637 ( 314) hydrogen bonds : angle 4.02497 ( 924) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1634 Ramachandran restraints generated. 817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1634 Ramachandran restraints generated. 817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 42 time to evaluate : 0.141 Fit side-chains REVERT: A 66 LEU cc_start: 0.7662 (OUTLIER) cc_final: 0.7363 (pp) REVERT: A 114 LYS cc_start: 0.7683 (mmmt) cc_final: 0.7384 (mmmt) REVERT: A 173 ASP cc_start: 0.7464 (OUTLIER) cc_final: 0.6820 (t70) REVERT: A 242 LYS cc_start: 0.7047 (mmtt) cc_final: 0.6789 (mtpp) REVERT: A 334 MET cc_start: 0.7961 (OUTLIER) cc_final: 0.6940 (mtt) REVERT: A 378 LYS cc_start: 0.8121 (tttt) cc_final: 0.7407 (mtmt) REVERT: A 466 LYS cc_start: 0.8112 (tptp) cc_final: 0.7603 (tptp) REVERT: A 495 MET cc_start: 0.7802 (tpt) cc_final: 0.7134 (tpt) REVERT: A 551 LYS cc_start: 0.7145 (ttpp) cc_final: 0.6906 (ptmm) REVERT: A 764 LYS cc_start: 0.7618 (tptt) cc_final: 0.6629 (tptt) outliers start: 8 outliers final: 5 residues processed: 47 average time/residue: 0.0969 time to fit residues: 5.8542 Evaluate side-chains 49 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 41 time to evaluate : 0.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 173 ASP Chi-restraints excluded: chain A residue 299 SER Chi-restraints excluded: chain A residue 334 MET Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain A residue 643 THR Chi-restraints excluded: chain A residue 787 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 57 optimal weight: 0.9980 chunk 53 optimal weight: 0.8980 chunk 23 optimal weight: 0.4980 chunk 69 optimal weight: 0.9990 chunk 22 optimal weight: 0.4980 chunk 50 optimal weight: 0.6980 chunk 59 optimal weight: 0.7980 chunk 55 optimal weight: 2.9990 chunk 11 optimal weight: 0.0570 chunk 16 optimal weight: 0.4980 chunk 66 optimal weight: 0.5980 overall best weight: 0.4298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4412 r_free = 0.4412 target = 0.229936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.205025 restraints weight = 6411.611| |-----------------------------------------------------------------------------| r_work (start): 0.4182 rms_B_bonded: 1.74 r_work (final): 0.4182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6825 moved from start: 0.3192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6617 Z= 0.123 Angle : 0.453 7.055 8948 Z= 0.230 Chirality : 0.040 0.138 996 Planarity : 0.003 0.038 1159 Dihedral : 3.684 14.139 890 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 1.30 % Allowed : 10.09 % Favored : 88.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.87 (0.30), residues: 817 helix: 1.97 (0.26), residues: 407 sheet: 1.20 (0.62), residues: 80 loop : 0.44 (0.36), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 625 TYR 0.009 0.001 TYR A 93 PHE 0.007 0.001 PHE A 754 TRP 0.012 0.001 TRP A 222 HIS 0.002 0.001 HIS A 438 Details of bonding type rmsd covalent geometry : bond 0.00283 ( 6617) covalent geometry : angle 0.45320 ( 8948) hydrogen bonds : bond 0.03108 ( 314) hydrogen bonds : angle 3.91698 ( 924) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1634 Ramachandran restraints generated. 817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1634 Ramachandran restraints generated. 817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 42 time to evaluate : 0.231 Fit side-chains REVERT: A 66 LEU cc_start: 0.7364 (OUTLIER) cc_final: 0.7121 (pp) REVERT: A 173 ASP cc_start: 0.7528 (OUTLIER) cc_final: 0.6689 (t0) REVERT: A 334 MET cc_start: 0.7751 (OUTLIER) cc_final: 0.6861 (mtt) REVERT: A 378 LYS cc_start: 0.7819 (tttt) cc_final: 0.7405 (mtmt) REVERT: A 466 LYS cc_start: 0.7831 (tptp) cc_final: 0.7469 (tptp) REVERT: A 545 MET cc_start: 0.8186 (tpp) cc_final: 0.7880 (tpp) REVERT: A 764 LYS cc_start: 0.7206 (tptt) cc_final: 0.6337 (tptt) outliers start: 9 outliers final: 6 residues processed: 48 average time/residue: 0.1132 time to fit residues: 6.9606 Evaluate side-chains 50 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 41 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 173 ASP Chi-restraints excluded: chain A residue 299 SER Chi-restraints excluded: chain A residue 334 MET Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain A residue 643 THR Chi-restraints excluded: chain A residue 787 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 18 optimal weight: 0.0870 chunk 1 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 40 optimal weight: 0.0770 chunk 72 optimal weight: 1.9990 chunk 37 optimal weight: 0.5980 chunk 9 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4400 r_free = 0.4400 target = 0.228451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.203861 restraints weight = 6274.897| |-----------------------------------------------------------------------------| r_work (start): 0.4150 rms_B_bonded: 1.70 r_work: 0.3918 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6983 moved from start: 0.3351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 6617 Z= 0.151 Angle : 0.477 6.684 8948 Z= 0.241 Chirality : 0.040 0.140 996 Planarity : 0.003 0.039 1159 Dihedral : 3.761 14.260 890 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.44 % Allowed : 10.23 % Favored : 88.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.79 (0.30), residues: 817 helix: 1.90 (0.26), residues: 407 sheet: 1.16 (0.62), residues: 80 loop : 0.41 (0.35), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 625 TYR 0.010 0.001 TYR A 93 PHE 0.008 0.001 PHE A 726 TRP 0.012 0.001 TRP A 222 HIS 0.002 0.001 HIS A 438 Details of bonding type rmsd covalent geometry : bond 0.00356 ( 6617) covalent geometry : angle 0.47716 ( 8948) hydrogen bonds : bond 0.03346 ( 314) hydrogen bonds : angle 3.95406 ( 924) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1634 Ramachandran restraints generated. 817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1634 Ramachandran restraints generated. 817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 43 time to evaluate : 0.191 Fit side-chains REVERT: A 66 LEU cc_start: 0.7593 (OUTLIER) cc_final: 0.7315 (pp) REVERT: A 173 ASP cc_start: 0.7568 (OUTLIER) cc_final: 0.6869 (t70) REVERT: A 334 MET cc_start: 0.7875 (OUTLIER) cc_final: 0.6913 (mtt) REVERT: A 378 LYS cc_start: 0.8100 (tttt) cc_final: 0.7331 (mtmt) REVERT: A 466 LYS cc_start: 0.8112 (tptp) cc_final: 0.7616 (tptp) REVERT: A 545 MET cc_start: 0.8520 (tpp) cc_final: 0.8115 (tpp) REVERT: A 764 LYS cc_start: 0.7541 (tptt) cc_final: 0.6696 (tptt) outliers start: 10 outliers final: 6 residues processed: 50 average time/residue: 0.0893 time to fit residues: 5.7663 Evaluate side-chains 52 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 43 time to evaluate : 0.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 173 ASP Chi-restraints excluded: chain A residue 299 SER Chi-restraints excluded: chain A residue 334 MET Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain A residue 643 THR Chi-restraints excluded: chain A residue 787 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 40 optimal weight: 0.5980 chunk 27 optimal weight: 0.8980 chunk 28 optimal weight: 0.8980 chunk 33 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 chunk 75 optimal weight: 0.0030 chunk 50 optimal weight: 0.8980 chunk 45 optimal weight: 0.6980 chunk 35 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 chunk 72 optimal weight: 0.9980 overall best weight: 0.6190 ------------------------------------------------------------------------------- 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 = 0.4124 r_free = 0.4124 target = 0.196432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.176243 restraints weight = 5999.948| |-----------------------------------------------------------------------------| r_work (start): 0.3932 rms_B_bonded: 1.36 r_work: 0.3793 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3639 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7067 moved from start: 0.3552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 6617 Z= 0.164 Angle : 0.498 7.795 8948 Z= 0.251 Chirality : 0.041 0.143 996 Planarity : 0.004 0.038 1159 Dihedral : 3.843 14.537 890 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.30 % Allowed : 10.66 % Favored : 88.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.74 (0.30), residues: 817 helix: 1.85 (0.26), residues: 407 sheet: 1.13 (0.62), residues: 80 loop : 0.39 (0.35), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 625 TYR 0.011 0.001 TYR A 93 PHE 0.008 0.001 PHE A 726 TRP 0.013 0.001 TRP A 222 HIS 0.003 0.001 HIS A 438 Details of bonding type rmsd covalent geometry : bond 0.00387 ( 6617) covalent geometry : angle 0.49809 ( 8948) hydrogen bonds : bond 0.03505 ( 314) hydrogen bonds : angle 4.01143 ( 924) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1266.48 seconds wall clock time: 22 minutes 23.69 seconds (1343.69 seconds total)