Starting phenix.real_space_refine on Thu Jul 2 04:49:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/10uj_75470/07_2026/10uj_75470.cif Found real_map, /net/cci-nas-00/data/ceres_data/10uj_75470/07_2026/10uj_75470.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/10uj_75470/07_2026/10uj_75470.cif" } default_model = "/net/cci-nas-00/data/ceres_data/10uj_75470/07_2026/10uj_75470.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/10uj_75470/07_2026/10uj_75470.map" default_real_map = "/net/cci-nas-00/data/ceres_data/10uj_75470/07_2026/10uj_75470.map" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.038 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6490 Number of models: 1 Model: "" Number of chains: 1 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 Time building chain proxies: 1.17, per 1000 atoms: 0.18 Number of scatterers: 6490 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: 4 Type Number sf(0) 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: 0.37 Conformation dependent library (CDL) restraints added in 225.7 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: 0.14 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: 3.955A pdb=" N HIS A 187 " --> pdb=" O GLU A 183 " (cutoff:3.500A) removed outlier: 5.537A 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: 3.833A 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: 3.534A 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: 4.204A 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: 3.785A 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: 3.709A 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: 3.592A 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: 3.867A 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: 3.610A 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: 4.036A 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: 3.500A pdb=" N LEU A 666 " --> pdb=" O SER A 662 " (cutoff:3.500A) removed outlier: 3.539A 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: 3.577A pdb=" N ASP A 813 " --> pdb=" O ASN A 810 " (cutoff:3.500A) removed outlier: 3.962A 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: 6.424A pdb=" N ILE A 159 " --> pdb=" O ILE A 289 " (cutoff:3.500A) removed outlier: 8.021A pdb=" N MET A 291 " --> pdb=" O ILE A 159 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N MET A 161 " --> pdb=" O MET A 291 " (cutoff:3.500A) removed outlier: 6.482A 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: 8.464A 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: 7.198A pdb=" N VAL A 471 " --> pdb=" O GLU A 326 " (cutoff:3.500A) removed outlier: 6.108A 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: 6.356A pdb=" N LEU A 330 " --> pdb=" O ALA A 473 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N LEU A 420 " --> pdb=" O VAL A 472 " (cutoff:3.500A) removed outlier: 7.711A pdb=" N ILE A 474 " --> pdb=" O LEU A 420 " (cutoff:3.500A) removed outlier: 6.080A 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: 7.103A pdb=" N TYR A 723 " --> pdb=" O LYS A 764 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N LEU A 766 " --> pdb=" O TYR A 723 " (cutoff:3.500A) removed outlier: 6.038A 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 739 313 hydrogen bonds defined for protein. 921 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: 0.72 Time building geometry restraints manager: 0.52 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: 1349 1.46 - 1.58: 3059 1.58 - 1.70: 0 1.70 - 1.81: 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 1.491 -0.033 1.33e-02 5.65e+03 6.18e+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 2.01e+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 1.99e+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=" CG LYS A 114 " pdb=" CD LYS A 114 " ideal model delta sigma weight residual 1.520 1.560 -0.040 3.00e-02 1.11e+03 1.81e+00 ... (remaining 6612 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.91: 8762 1.91 - 3.81: 155 3.81 - 5.72: 16 5.72 - 7.63: 12 7.63 - 9.53: 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 114.10 122.61 -8.51 2.00e+00 2.50e-01 1.81e+01 angle pdb=" CB LYS A 114 " pdb=" CG LYS A 114 " pdb=" CD LYS A 114 " ideal model delta sigma weight residual 111.30 120.83 -9.53 2.30e+00 1.89e-01 1.72e+01 angle pdb=" CG ARG A 625 " pdb=" CD ARG A 625 " pdb=" NE ARG A 625 " ideal model delta sigma weight residual 112.00 118.52 -6.52 2.20e+00 2.07e-01 8.77e+00 angle pdb=" CA GLU A 727 " pdb=" CB GLU A 727 " pdb=" CG GLU A 727 " ideal model delta sigma weight residual 114.10 119.61 -5.51 2.00e+00 2.50e-01 7.59e+00 angle pdb=" CB ARG A 625 " pdb=" CG ARG A 625 " pdb=" CD ARG A 625 " ideal model delta sigma weight residual 111.30 117.57 -6.27 2.30e+00 1.89e-01 7.43e+00 ... (remaining 8943 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.14: 3649 16.14 - 32.28: 272 32.28 - 48.42: 84 48.42 - 64.56: 14 64.56 - 80.69: 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 180.00 -135.02 -44.98 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 180.00 135.24 44.76 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 -136.91 -43.09 2 1.50e+01 4.44e-03 9.96e+00 ... (remaining 4020 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 771 0.050 - 0.100: 177 0.100 - 0.151: 43 0.151 - 0.201: 3 0.201 - 0.251: 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 1.57e+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 1.11e+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 0.19 2.00e-01 2.50e+01 9.48e-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 2.54e-02 6.44e+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 " 0.025 5.00e-02 4.00e+02 3.90e-02 2.43e+00 pdb=" N PRO A 519 " -0.067 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: 2.34 - 2.85: 2122 2.85 - 3.36: 5823 3.36 - 3.88: 10580 3.88 - 4.39: 12178 4.39 - 4.90: 21077 Nonbonded interactions: 51780 Sorted by model distance: nonbonded pdb=" OE1 GLU A 568 " pdb=" OH TYR A 607 " model vdw 2.340 3.040 nonbonded pdb=" OD1 ASP A 411 " pdb=" NH2 ARG A 463 " model vdw 2.346 3.120 nonbonded pdb=" OH TYR A 23 " pdb=" O GLY A 33 " model vdw 2.352 3.040 nonbonded pdb=" NH2 ARG A 60 " pdb=" O ALA A 283 " model vdw 2.355 3.120 nonbonded pdb=" OD1 ASP A 381 " pdb=" OG SER A 384 " model vdw 2.381 3.040 ... (remaining 51775 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 group one per residue 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: 1.580 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: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 5.530 Find NCS groups from input model: 0.020 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:0.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 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 0.047 6617 Z= 0.166 Angle : 0.665 9.533 8948 Z= 0.347 Chirality : 0.046 0.251 996 Planarity : 0.005 0.040 1159 Dihedral : 13.073 80.694 2475 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 2.54 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 0.009 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 826 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.17 ( 6617) covalent geometry : angle 0.66461 / 0.35 ( 8948) hydrogen bonds : bond 0.12238 / 8.00 ( 313) hydrogen bonds : angle 6.09915 / 4.47 ( 921) *********************** 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 169 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 166 time to evaluate : 0.162 Fit side-chains revert: symmetry clash REVERT: A 70 GLN cc_start: 0.5832 (mm-40) cc_final: 0.5360 (mm-40) REVERT: A 109 SER cc_start: 0.8828 (t) cc_final: 0.8588 (p) REVERT: A 173 ASP cc_start: 0.7985 (OUTLIER) cc_final: 0.7779 (m-30) REVERT: A 241 LYS cc_start: 0.6976 (mmtt) cc_final: 0.6689 (mmtm) REVERT: A 242 LYS cc_start: 0.7437 (mmtt) cc_final: 0.6545 (tptp) REVERT: A 286 LYS cc_start: 0.8767 (mttt) cc_final: 0.8328 (mtmm) REVERT: A 424 SER cc_start: 0.8887 (m) cc_final: 0.8551 (t) REVERT: A 448 MET cc_start: 0.7515 (mtp) cc_final: 0.7036 (mtp) REVERT: A 641 LYS cc_start: 0.8696 (mttm) cc_final: 0.8468 (mtpp) REVERT: A 722 GLN cc_start: 0.8218 (mm-40) cc_final: 0.7746 (tt0) REVERT: A 804 LYS cc_start: 0.7567 (tttt) cc_final: 0.7250 (mttm) outliers start: 3 outliers final: 0 residues processed: 167 average time/residue: 0.0915 time to fit residues: 18.8134 Evaluate side-chains 93 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 92 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 49 optimal weight: 0.9990 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.5980 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 0.6980 chunk 74 optimal weight: 0.3980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 107 GLN A 165 HIS ** A 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 430 ASN A 826 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.171086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.156385 restraints weight = 6549.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.155844 restraints weight = 7605.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.156914 restraints weight = 7796.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.157383 restraints weight = 5909.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.157468 restraints weight = 5130.334| |-----------------------------------------------------------------------------| r_work (final): 0.3620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.2318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6617 Z= 0.137 Angle : 0.503 5.766 8948 Z= 0.263 Chirality : 0.041 0.139 996 Planarity : 0.004 0.028 1159 Dihedral : 4.091 32.115 892 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 1.73 % Allowed : 9.37 % Favored : 88.90 % 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: 1.32 (0.29), residues: 817 helix: 1.38 (0.25), residues: 406 sheet: 1.26 (0.55), residues: 96 loop : 0.23 (0.33), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 213 TYR 0.013 0.002 TYR A 93 PHE 0.013 0.001 PHE A 193 TRP 0.013 0.001 TRP A 323 HIS 0.005 0.001 HIS A 67 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.14 ( 6617) covalent geometry : angle 0.50265 / 0.26 ( 8948) hydrogen bonds : bond 0.03539 / 2.27 ( 313) hydrogen bonds : angle 4.55609 / 3.32 ( 921) *********************** 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 106 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 94 time to evaluate : 0.177 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 66 LEU cc_start: 0.8053 (OUTLIER) cc_final: 0.7814 (pp) REVERT: A 213 ARG cc_start: 0.7505 (mtm-85) cc_final: 0.6932 (mpt180) REVERT: A 242 LYS cc_start: 0.7346 (mmtt) cc_final: 0.6913 (tptp) REVERT: A 600 TYR cc_start: 0.7868 (m-80) cc_final: 0.7598 (m-80) REVERT: A 667 ASP cc_start: 0.7661 (t70) cc_final: 0.7149 (t0) REVERT: A 747 MET cc_start: 0.8447 (tpt) cc_final: 0.8088 (tpp) outliers start: 12 outliers final: 8 residues processed: 104 average time/residue: 0.0869 time to fit residues: 11.9239 Evaluate side-chains 90 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 81 time to evaluate : 0.284 ------------------------------------------------------------------------------- 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 159 ILE Chi-restraints excluded: chain A residue 173 ASP Chi-restraints excluded: chain A residue 299 SER Chi-restraints excluded: chain A residue 308 SER Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 766 LEU Chi-restraints excluded: chain A residue 805 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 59 optimal weight: 5.9990 chunk 65 optimal weight: 0.7980 chunk 29 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 62 optimal weight: 6.9990 chunk 21 optimal weight: 4.9990 chunk 27 optimal weight: 2.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 85 ASN A 259 GLN A 624 HIS A 809 GLN A 818 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.155986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.137610 restraints weight = 6754.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.139010 restraints weight = 5663.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.139764 restraints weight = 4914.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.140941 restraints weight = 4494.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.141583 restraints weight = 4110.672| |-----------------------------------------------------------------------------| r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.3768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.050 6617 Z= 0.284 Angle : 0.666 6.256 8948 Z= 0.343 Chirality : 0.045 0.146 996 Planarity : 0.005 0.066 1159 Dihedral : 4.618 28.212 892 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.31 % Allowed : 10.37 % Favored : 87.32 % 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: 0.82 (0.29), residues: 817 helix: 1.15 (0.25), residues: 408 sheet: 0.08 (0.53), residues: 98 loop : 0.06 (0.35), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 452 TYR 0.026 0.003 TYR A 93 PHE 0.023 0.002 PHE A 780 TRP 0.015 0.002 TRP A 224 HIS 0.007 0.002 HIS A 624 Details of bonding type rmsd/Z covalent geometry : bond 0.00676 / 0.28 ( 6617) covalent geometry : angle 0.66552 / 0.34 ( 8948) hydrogen bonds : bond 0.04641 / 2.99 ( 313) hydrogen bonds : angle 4.85968 / 3.52 ( 921) *********************** 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 123 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 107 time to evaluate : 0.317 Fit side-chains revert: symmetry clash REVERT: A 66 LEU cc_start: 0.8351 (OUTLIER) cc_final: 0.8024 (pp) REVERT: A 212 LYS cc_start: 0.7767 (mmtp) cc_final: 0.7423 (mmtt) REVERT: A 213 ARG cc_start: 0.7729 (mtm-85) cc_final: 0.7202 (mpt90) REVERT: A 242 LYS cc_start: 0.7643 (mmtt) cc_final: 0.6931 (tptp) REVERT: A 298 ASP cc_start: 0.8433 (m-30) cc_final: 0.6320 (p0) REVERT: A 545 MET cc_start: 0.8804 (tpp) cc_final: 0.8502 (tpp) REVERT: A 667 ASP cc_start: 0.7560 (t70) cc_final: 0.7133 (t0) outliers start: 16 outliers final: 8 residues processed: 118 average time/residue: 0.0880 time to fit residues: 13.9243 Evaluate side-chains 97 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 88 time to evaluate : 0.300 ------------------------------------------------------------------------------- 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 159 ILE Chi-restraints excluded: chain A residue 259 GLN Chi-restraints excluded: chain A residue 308 SER Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 443 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 54 optimal weight: 2.9990 chunk 36 optimal weight: 7.9990 chunk 76 optimal weight: 0.9980 chunk 49 optimal weight: 0.9990 chunk 55 optimal weight: 0.2980 chunk 62 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 14 optimal weight: 0.9990 chunk 57 optimal weight: 0.5980 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 259 GLN A 529 GLN A 809 GLN A 818 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.161655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.145682 restraints weight = 6769.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.144682 restraints weight = 7101.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.145920 restraints weight = 6940.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.146494 restraints weight = 5810.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.146768 restraints weight = 5183.603| |-----------------------------------------------------------------------------| r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.3925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6617 Z= 0.141 Angle : 0.511 7.106 8948 Z= 0.263 Chirality : 0.042 0.158 996 Planarity : 0.004 0.041 1159 Dihedral : 4.052 18.942 890 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 2.02 % Allowed : 12.39 % Favored : 85.59 % 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: 1.17 (0.30), residues: 817 helix: 1.48 (0.25), residues: 408 sheet: -0.03 (0.54), residues: 98 loop : 0.26 (0.36), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 89 TYR 0.014 0.002 TYR A 282 PHE 0.009 0.001 PHE A 803 TRP 0.011 0.001 TRP A 222 HIS 0.004 0.001 HIS A 67 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.14 ( 6617) covalent geometry : angle 0.51063 / 0.26 ( 8948) hydrogen bonds : bond 0.03470 / 2.23 ( 313) hydrogen bonds : angle 4.42249 / 3.19 ( 921) *********************** 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 104 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 90 time to evaluate : 0.156 Fit side-chains revert: symmetry clash REVERT: A 66 LEU cc_start: 0.8179 (OUTLIER) cc_final: 0.7846 (pp) REVERT: A 212 LYS cc_start: 0.7524 (mmtp) cc_final: 0.7277 (mmtt) REVERT: A 213 ARG cc_start: 0.7624 (mtm-85) cc_final: 0.7128 (mpt90) REVERT: A 242 LYS cc_start: 0.7523 (mmtt) cc_final: 0.6807 (tptp) REVERT: A 463 ARG cc_start: 0.8029 (OUTLIER) cc_final: 0.7816 (mmm-85) REVERT: A 545 MET cc_start: 0.8715 (tpp) cc_final: 0.8134 (mmm) REVERT: A 667 ASP cc_start: 0.7521 (t70) cc_final: 0.7128 (t0) outliers start: 14 outliers final: 9 residues processed: 100 average time/residue: 0.0789 time to fit residues: 10.8072 Evaluate side-chains 92 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 81 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 79 ILE 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 308 SER Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 463 ARG Chi-restraints excluded: chain A residue 643 THR Chi-restraints excluded: chain A residue 644 ILE 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 77 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 28 optimal weight: 0.6980 chunk 78 optimal weight: 0.5980 chunk 46 optimal weight: 1.9990 chunk 71 optimal weight: 8.9990 chunk 23 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 165 HIS A 259 GLN A 529 GLN A 809 GLN A 818 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.159513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.140544 restraints weight = 6818.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.141871 restraints weight = 5654.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.143263 restraints weight = 4943.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.144448 restraints weight = 4372.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.144791 restraints weight = 4023.469| |-----------------------------------------------------------------------------| r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.4156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6617 Z= 0.166 Angle : 0.524 7.224 8948 Z= 0.269 Chirality : 0.042 0.142 996 Planarity : 0.004 0.040 1159 Dihedral : 4.016 19.829 890 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.59 % Allowed : 12.97 % Favored : 84.44 % 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: 1.08 (0.30), residues: 817 helix: 1.47 (0.25), residues: 416 sheet: -0.41 (0.53), residues: 98 loop : 0.19 (0.37), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 288 TYR 0.016 0.002 TYR A 282 PHE 0.011 0.001 PHE A 427 TRP 0.010 0.001 TRP A 323 HIS 0.003 0.001 HIS A 67 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.17 ( 6617) covalent geometry : angle 0.52380 / 0.27 ( 8948) hydrogen bonds : bond 0.03531 / 2.28 ( 313) hydrogen bonds : angle 4.33802 / 3.12 ( 921) *********************** 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 106 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 88 time to evaluate : 0.246 Fit side-chains revert: symmetry clash REVERT: A 66 LEU cc_start: 0.8219 (OUTLIER) cc_final: 0.7902 (pp) REVERT: A 212 LYS cc_start: 0.7563 (mmtp) cc_final: 0.7327 (mmtt) REVERT: A 213 ARG cc_start: 0.7605 (mtm-85) cc_final: 0.7148 (mpt90) REVERT: A 242 LYS cc_start: 0.7517 (mmtt) cc_final: 0.6696 (tptp) REVERT: A 272 HIS cc_start: 0.7311 (m-70) cc_final: 0.7101 (m-70) REVERT: A 366 PHE cc_start: 0.7139 (m-80) cc_final: 0.6851 (m-80) REVERT: A 463 ARG cc_start: 0.8088 (OUTLIER) cc_final: 0.7848 (mmm-85) REVERT: A 545 MET cc_start: 0.8757 (tpp) cc_final: 0.8530 (mmm) REVERT: A 667 ASP cc_start: 0.7505 (t70) cc_final: 0.7143 (t0) outliers start: 18 outliers final: 10 residues processed: 103 average time/residue: 0.0810 time to fit residues: 11.2372 Evaluate side-chains 92 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 80 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 259 GLN Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 308 SER Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 463 ARG Chi-restraints excluded: chain A residue 643 THR Chi-restraints excluded: chain A residue 644 ILE 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 73 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 chunk 76 optimal weight: 0.7980 chunk 41 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 chunk 21 optimal weight: 0.7980 chunk 47 optimal weight: 2.9990 chunk 62 optimal weight: 4.9990 chunk 80 optimal weight: 3.9990 chunk 78 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 809 GLN A 818 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.158412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.140826 restraints weight = 6784.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.140736 restraints weight = 6552.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.140940 restraints weight = 6782.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.141420 restraints weight = 5999.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.141695 restraints weight = 5409.462| |-----------------------------------------------------------------------------| r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.4362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 6617 Z= 0.173 Angle : 0.524 7.441 8948 Z= 0.269 Chirality : 0.042 0.134 996 Planarity : 0.004 0.041 1159 Dihedral : 4.011 19.458 890 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 2.74 % Allowed : 13.98 % Favored : 83.29 % 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: 1.05 (0.30), residues: 817 helix: 1.47 (0.25), residues: 416 sheet: -0.58 (0.53), residues: 98 loop : 0.22 (0.37), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 452 TYR 0.016 0.002 TYR A 282 PHE 0.011 0.001 PHE A 427 TRP 0.011 0.001 TRP A 323 HIS 0.004 0.001 HIS A 624 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.17 ( 6617) covalent geometry : angle 0.52440 / 0.27 ( 8948) hydrogen bonds : bond 0.03611 / 2.35 ( 313) hydrogen bonds : angle 4.33644 / 3.11 ( 921) *********************** 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 106 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 87 time to evaluate : 0.250 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 66 LEU cc_start: 0.8199 (OUTLIER) cc_final: 0.7902 (pp) REVERT: A 212 LYS cc_start: 0.7564 (mmtp) cc_final: 0.7351 (mmtt) REVERT: A 213 ARG cc_start: 0.7532 (mtm-85) cc_final: 0.7172 (mpt90) REVERT: A 242 LYS cc_start: 0.7519 (mmtt) cc_final: 0.6675 (tptp) REVERT: A 272 HIS cc_start: 0.7354 (m-70) cc_final: 0.7086 (m-70) REVERT: A 366 PHE cc_start: 0.7216 (m-80) cc_final: 0.6882 (m-80) REVERT: A 545 MET cc_start: 0.8752 (tpp) cc_final: 0.8533 (mmm) REVERT: A 667 ASP cc_start: 0.7517 (t70) cc_final: 0.7138 (t0) outliers start: 19 outliers final: 11 residues processed: 102 average time/residue: 0.0863 time to fit residues: 11.9117 Evaluate side-chains 93 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 81 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 259 GLN Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 308 SER Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 580 GLU Chi-restraints excluded: chain A residue 643 THR Chi-restraints excluded: chain A residue 644 ILE 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 42 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 43 optimal weight: 0.8980 chunk 36 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 72 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 chunk 34 optimal weight: 0.6980 chunk 62 optimal weight: 0.7980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 259 GLN A 809 GLN A 818 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.158287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.140941 restraints weight = 6706.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.140893 restraints weight = 6464.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.141392 restraints weight = 6462.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.142077 restraints weight = 5650.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.142271 restraints weight = 4980.745| |-----------------------------------------------------------------------------| r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.4584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6617 Z= 0.143 Angle : 0.500 7.641 8948 Z= 0.258 Chirality : 0.042 0.133 996 Planarity : 0.004 0.041 1159 Dihedral : 3.889 17.278 890 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.31 % Allowed : 14.55 % Favored : 83.14 % 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 (0.30), residues: 817 helix: 1.60 (0.26), residues: 415 sheet: -0.60 (0.53), residues: 98 loop : 0.33 (0.37), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 613 TYR 0.018 0.001 TYR A 282 PHE 0.012 0.001 PHE A 780 TRP 0.016 0.001 TRP A 323 HIS 0.004 0.001 HIS A 624 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.14 ( 6617) covalent geometry : angle 0.50008 / 0.26 ( 8948) hydrogen bonds : bond 0.03369 / 2.18 ( 313) hydrogen bonds : angle 4.23931 / 3.02 ( 921) *********************** 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 103 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 87 time to evaluate : 0.254 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 66 LEU cc_start: 0.8198 (OUTLIER) cc_final: 0.7900 (pp) REVERT: A 213 ARG cc_start: 0.7583 (mtm-85) cc_final: 0.7252 (mpt90) REVERT: A 242 LYS cc_start: 0.7512 (mmtt) cc_final: 0.6678 (tptp) REVERT: A 272 HIS cc_start: 0.7255 (m-70) cc_final: 0.7000 (m-70) REVERT: A 366 PHE cc_start: 0.7166 (m-80) cc_final: 0.6872 (m-80) REVERT: A 545 MET cc_start: 0.8736 (tpp) cc_final: 0.8499 (mmm) REVERT: A 667 ASP cc_start: 0.7432 (t70) cc_final: 0.7086 (t0) outliers start: 16 outliers final: 12 residues processed: 97 average time/residue: 0.0760 time to fit residues: 10.2502 Evaluate side-chains 96 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 83 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 259 GLN Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 308 SER Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain A residue 580 GLU Chi-restraints excluded: chain A residue 643 THR Chi-restraints excluded: chain A residue 644 ILE 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 23 optimal weight: 3.9990 chunk 79 optimal weight: 0.6980 chunk 16 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 61 optimal weight: 0.9980 chunk 39 optimal weight: 0.9990 chunk 42 optimal weight: 2.9990 chunk 77 optimal weight: 0.9990 chunk 50 optimal weight: 0.9990 chunk 64 optimal weight: 0.7980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 259 GLN A 809 GLN A 818 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.156019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.140493 restraints weight = 6701.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.139683 restraints weight = 6747.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.140117 restraints weight = 6660.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.140634 restraints weight = 6231.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.140871 restraints weight = 5549.514| |-----------------------------------------------------------------------------| r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.4708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 6617 Z= 0.154 Angle : 0.509 7.695 8948 Z= 0.262 Chirality : 0.042 0.135 996 Planarity : 0.004 0.041 1159 Dihedral : 3.866 17.248 890 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 2.31 % Allowed : 15.13 % Favored : 82.56 % 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: 1.20 (0.30), residues: 817 helix: 1.60 (0.25), residues: 415 sheet: -0.60 (0.54), residues: 97 loop : 0.31 (0.37), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 452 TYR 0.017 0.002 TYR A 282 PHE 0.008 0.001 PHE A 803 TRP 0.013 0.001 TRP A 323 HIS 0.004 0.001 HIS A 624 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.15 ( 6617) covalent geometry : angle 0.50885 / 0.26 ( 8948) hydrogen bonds : bond 0.03460 / 2.25 ( 313) hydrogen bonds : angle 4.27788 / 3.05 ( 921) *********************** 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 106 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 90 time to evaluate : 0.257 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 66 LEU cc_start: 0.8208 (OUTLIER) cc_final: 0.7923 (pp) REVERT: A 213 ARG cc_start: 0.7545 (mtm-85) cc_final: 0.7234 (mpt90) REVERT: A 242 LYS cc_start: 0.7541 (mmtt) cc_final: 0.6699 (tptp) REVERT: A 272 HIS cc_start: 0.7247 (m-70) cc_final: 0.6958 (m-70) REVERT: A 366 PHE cc_start: 0.7124 (m-80) cc_final: 0.6853 (m-80) REVERT: A 545 MET cc_start: 0.8700 (tpp) cc_final: 0.8479 (mmm) REVERT: A 667 ASP cc_start: 0.7459 (t70) cc_final: 0.7132 (t0) outliers start: 16 outliers final: 12 residues processed: 100 average time/residue: 0.0787 time to fit residues: 10.7796 Evaluate side-chains 98 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 85 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 259 GLN Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 308 SER Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain A residue 580 GLU Chi-restraints excluded: chain A residue 643 THR Chi-restraints excluded: chain A residue 785 ASP 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 41 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 55 optimal weight: 0.9980 chunk 28 optimal weight: 0.0870 chunk 59 optimal weight: 0.9980 chunk 27 optimal weight: 0.8980 chunk 71 optimal weight: 0.3980 chunk 7 optimal weight: 0.9980 chunk 10 optimal weight: 3.9990 chunk 32 optimal weight: 0.9980 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 584 GLN A 809 GLN A 818 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.157502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.141206 restraints weight = 6789.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.140505 restraints weight = 6719.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.141582 restraints weight = 6657.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.142405 restraints weight = 5732.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.142594 restraints weight = 4880.931| |-----------------------------------------------------------------------------| r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.4755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6617 Z= 0.128 Angle : 0.493 7.939 8948 Z= 0.252 Chirality : 0.041 0.136 996 Planarity : 0.003 0.040 1159 Dihedral : 3.781 16.407 890 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.16 % Allowed : 15.56 % Favored : 82.28 % 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: 1.30 (0.30), residues: 817 helix: 1.69 (0.25), residues: 415 sheet: -0.54 (0.54), residues: 97 loop : 0.34 (0.37), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 452 TYR 0.018 0.001 TYR A 282 PHE 0.009 0.001 PHE A 780 TRP 0.015 0.001 TRP A 323 HIS 0.004 0.001 HIS A 624 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 ( 6617) covalent geometry : angle 0.49322 / 0.25 ( 8948) hydrogen bonds : bond 0.03288 / 2.14 ( 313) hydrogen bonds : angle 4.20473 / 2.99 ( 921) *********************** 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 103 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 88 time to evaluate : 0.253 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 66 LEU cc_start: 0.8201 (OUTLIER) cc_final: 0.7900 (pp) REVERT: A 213 ARG cc_start: 0.7523 (mtm-85) cc_final: 0.7192 (mpt90) REVERT: A 242 LYS cc_start: 0.7541 (mmtt) cc_final: 0.6680 (tptp) REVERT: A 272 HIS cc_start: 0.7160 (m-70) cc_final: 0.6917 (m-70) REVERT: A 366 PHE cc_start: 0.7134 (m-80) cc_final: 0.6859 (m-80) REVERT: A 545 MET cc_start: 0.8706 (tpp) cc_final: 0.8486 (tpp) REVERT: A 667 ASP cc_start: 0.7421 (t70) cc_final: 0.7084 (t0) outliers start: 15 outliers final: 11 residues processed: 96 average time/residue: 0.0762 time to fit residues: 10.2252 Evaluate side-chains 94 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 82 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 308 SER Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain A residue 580 GLU Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain A residue 643 THR Chi-restraints excluded: chain A residue 785 ASP 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 30 optimal weight: 0.9980 chunk 74 optimal weight: 0.5980 chunk 61 optimal weight: 0.8980 chunk 66 optimal weight: 0.7980 chunk 31 optimal weight: 0.4980 chunk 5 optimal weight: 0.7980 chunk 0 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 chunk 54 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 259 GLN A 809 GLN A 818 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.160182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.143591 restraints weight = 6691.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.143340 restraints weight = 6312.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.143818 restraints weight = 6069.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.144460 restraints weight = 5569.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.144560 restraints weight = 4976.327| |-----------------------------------------------------------------------------| r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.4803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6617 Z= 0.133 Angle : 0.507 10.989 8948 Z= 0.257 Chirality : 0.042 0.135 996 Planarity : 0.004 0.040 1159 Dihedral : 3.772 18.076 890 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.16 % Allowed : 15.99 % Favored : 81.84 % 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: 1.28 (0.30), residues: 817 helix: 1.67 (0.25), residues: 416 sheet: -0.61 (0.54), residues: 97 loop : 0.36 (0.37), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 460 TYR 0.019 0.001 TYR A 282 PHE 0.008 0.001 PHE A 780 TRP 0.016 0.001 TRP A 323 HIS 0.004 0.001 HIS A 624 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.13 ( 6617) covalent geometry : angle 0.50679 / 0.26 ( 8948) hydrogen bonds : bond 0.03358 / 2.15 ( 313) hydrogen bonds : angle 4.17221 / 2.97 ( 921) ********************** 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 105 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 90 time to evaluate : 0.245 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 66 LEU cc_start: 0.8211 (OUTLIER) cc_final: 0.7926 (pp) REVERT: A 213 ARG cc_start: 0.7493 (mtm-85) cc_final: 0.7183 (mpt90) REVERT: A 242 LYS cc_start: 0.7547 (mmtt) cc_final: 0.6780 (tptp) REVERT: A 272 HIS cc_start: 0.7167 (m-70) cc_final: 0.6934 (m-70) REVERT: A 366 PHE cc_start: 0.7098 (m-80) cc_final: 0.6824 (m-80) REVERT: A 463 ARG cc_start: 0.8338 (mmm160) cc_final: 0.7947 (mmm-85) REVERT: A 545 MET cc_start: 0.8706 (tpp) cc_final: 0.8486 (tpp) REVERT: A 667 ASP cc_start: 0.7443 (t70) cc_final: 0.7119 (t0) outliers start: 15 outliers final: 11 residues processed: 100 average time/residue: 0.0763 time to fit residues: 10.4412 Evaluate side-chains 96 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 84 time to evaluate : 0.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 79 ILE 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 308 SER Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain A residue 580 GLU Chi-restraints excluded: chain A residue 631 LEU 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 37 optimal weight: 0.0670 chunk 15 optimal weight: 0.1980 chunk 13 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 74 optimal weight: 0.6980 chunk 70 optimal weight: 0.6980 chunk 78 optimal weight: 0.4980 chunk 60 optimal weight: 1.9990 overall best weight: 0.4318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 259 GLN A 809 GLN A 818 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.159288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.143630 restraints weight = 6705.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.142971 restraints weight = 7395.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.144012 restraints weight = 7413.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.144829 restraints weight = 6024.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.145146 restraints weight = 5125.229| |-----------------------------------------------------------------------------| r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.4836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.210 6617 Z= 0.259 Angle : 0.963 59.032 8948 Z= 0.561 Chirality : 0.057 1.233 996 Planarity : 0.004 0.040 1159 Dihedral : 3.803 18.026 890 Min Nonbonded Distance : 1.764 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.02 % Allowed : 15.71 % Favored : 82.28 % Cbeta Deviations : 0.13 % 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: 1.28 (0.30), residues: 817 helix: 1.67 (0.25), residues: 416 sheet: -0.64 (0.54), residues: 97 loop : 0.36 (0.37), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 736 TYR 0.017 0.001 TYR A 282 PHE 0.007 0.001 PHE A 803 TRP 0.014 0.001 TRP A 323 HIS 0.004 0.001 HIS A 624 Details of bonding type rmsd/Z covalent geometry : bond 0.00592 / 0.26 ( 6617) covalent geometry : angle 0.96340 / 0.56 ( 8948) hydrogen bonds : bond 0.03337 / 2.15 ( 313) hydrogen bonds : angle 4.20323 / 2.98 ( 921) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1071.54 seconds wall clock time: 19 minutes 14.49 seconds (1154.49 seconds total)