Starting phenix.real_space_refine on Fri Oct 23 06:03:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9yyd_73630/10_2026/9yyd_73630.cif Found real_map, /net/cci-nas-00/data/ceres_data/9yyd_73630/10_2026/9yyd_73630.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9yyd_73630/10_2026/9yyd_73630.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9yyd_73630/10_2026/9yyd_73630.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9yyd_73630/10_2026/9yyd_73630.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9yyd_73630/10_2026/9yyd_73630.map" } resolution = 2.8 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: 6 Type Number sf(0) Gaussians P 1 5.49 5 Mg 1 5.21 5 S 61 5.16 5 C 5479 2.51 5 N 1460 2.21 5 O 1518 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8520 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 8470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1077, 8470 Classifications: {'peptide': 1077} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 59, 'TRANS': 1017} Chain breaks: 6 Chain: "A" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 50 Unusual residues: {' MG': 1, 'PEV': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 1.88, per 1000 atoms: 0.22 Number of scatterers: 8520 At special positions: 0 Unit cell: (77.738, 93.451, 145.552, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 61 16.00 P 1 15.00 Mg 1 11.99 O 1518 8.00 N 1460 7.00 C 5479 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 604 " - pdb=" SG CYS A 641 " distance=2.03 Simple disulfide: pdb=" SG CYS A 641 " - pdb=" SG CYS A1039 " distance=2.04 Simple disulfide: pdb=" SG CYS A1205 " - pdb=" SG CYS A1216 " distance=2.03 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: 0.81 Conformation dependent library (CDL) restraints added in 304.5 milliseconds 2126 Ramachandran restraints generated. 1063 Oldfield, 0 Emsley, 1063 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2040 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 5 sheets defined 55.3% alpha, 10.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'A' and resid 28 through 54 Processing helix chain 'A' and resid 56 through 64 Processing helix chain 'A' and resid 76 through 92 Processing helix chain 'A' and resid 103 through 131 Processing helix chain 'A' and resid 132 through 151 removed outlier: 4.430A pdb=" N ASP A 151 " --> pdb=" O ASP A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 162 Processing helix chain 'A' and resid 190 through 192 No H-bonds generated for 'chain 'A' and resid 190 through 192' Processing helix chain 'A' and resid 259 through 270 removed outlier: 4.216A pdb=" N ASN A 263 " --> pdb=" O PRO A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 292 Processing helix chain 'A' and resid 294 through 313 Processing helix chain 'A' and resid 319 through 325 Processing helix chain 'A' and resid 325 through 333 Processing helix chain 'A' and resid 339 through 358 removed outlier: 3.736A pdb=" N GLN A 358 " --> pdb=" O ARG A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 401 removed outlier: 3.819A pdb=" N MET A 388 " --> pdb=" O SER A 384 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N LEU A 389 " --> pdb=" O SER A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 418 Processing helix chain 'A' and resid 582 through 589 removed outlier: 4.060A pdb=" N GLN A 586 " --> pdb=" O SER A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 591 through 603 Processing helix chain 'A' and resid 605 through 607 No H-bonds generated for 'chain 'A' and resid 605 through 607' Processing helix chain 'A' and resid 608 through 626 Processing helix chain 'A' and resid 640 through 648 removed outlier: 3.917A pdb=" N ALA A 644 " --> pdb=" O LEU A 640 " (cutoff:3.500A) Processing helix chain 'A' and resid 650 through 654 removed outlier: 3.976A pdb=" N LYS A 654 " --> pdb=" O PRO A 651 " (cutoff:3.500A) Processing helix chain 'A' and resid 715 through 720 Processing helix chain 'A' and resid 736 through 753 Processing helix chain 'A' and resid 844 through 857 Processing helix chain 'A' and resid 868 through 880 Processing helix chain 'A' and resid 964 through 966 No H-bonds generated for 'chain 'A' and resid 964 through 966' Processing helix chain 'A' and resid 967 through 975 Processing helix chain 'A' and resid 977 through 981 Processing helix chain 'A' and resid 989 through 1003 Processing helix chain 'A' and resid 1015 through 1017 No H-bonds generated for 'chain 'A' and resid 1015 through 1017' Processing helix chain 'A' and resid 1018 through 1025 Processing helix chain 'A' and resid 1053 through 1058 removed outlier: 4.591A pdb=" N ASP A1057 " --> pdb=" O ALA A1053 " (cutoff:3.500A) Processing helix chain 'A' and resid 1060 through 1070 Processing helix chain 'A' and resid 1081 through 1083 No H-bonds generated for 'chain 'A' and resid 1081 through 1083' Processing helix chain 'A' and resid 1084 through 1123 Processing helix chain 'A' and resid 1130 through 1140 Processing helix chain 'A' and resid 1140 through 1149 removed outlier: 3.739A pdb=" N LEU A1149 " --> pdb=" O LEU A1145 " (cutoff:3.500A) Processing helix chain 'A' and resid 1171 through 1211 removed outlier: 5.082A pdb=" N LEU A1188 " --> pdb=" O LEU A1184 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N THR A1189 " --> pdb=" O LYS A1185 " (cutoff:3.500A) Processing helix chain 'A' and resid 1235 through 1260 removed outlier: 3.864A pdb=" N THR A1260 " --> pdb=" O PHE A1256 " (cutoff:3.500A) Processing helix chain 'A' and resid 1272 through 1275 removed outlier: 3.576A pdb=" N THR A1275 " --> pdb=" O SER A1272 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1272 through 1275' Processing helix chain 'A' and resid 1276 through 1301 Proline residue: A1284 - end of helix Processing helix chain 'A' and resid 1311 through 1315 Processing helix chain 'A' and resid 1316 through 1358 removed outlier: 3.610A pdb=" N VAL A1328 " --> pdb=" O CYS A1324 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N THR A1358 " --> pdb=" O LEU A1354 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 175 through 180 Processing sheet with id=AA2, first strand: chain 'A' and resid 197 through 200 Processing sheet with id=AA3, first strand: chain 'A' and resid 888 through 890 removed outlier: 6.489A pdb=" N ILE A 889 " --> pdb=" O THR A 986 " (cutoff:3.500A) removed outlier: 7.922A pdb=" N PHE A 985 " --> pdb=" O PHE A 861 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N TYR A 863 " --> pdb=" O PHE A 985 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N VAL A 422 " --> pdb=" O CYS A1008 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N LEU A1010 " --> pdb=" O VAL A 422 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N CYS A 424 " --> pdb=" O LEU A1010 " (cutoff:3.500A) removed outlier: 8.500A pdb=" N SER A1012 " --> pdb=" O CYS A 424 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N THR A1007 " --> pdb=" O ILE A1027 " (cutoff:3.500A) removed outlier: 8.011A pdb=" N ILE A1029 " --> pdb=" O THR A1007 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N CYS A1009 " --> pdb=" O ILE A1029 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N LEU A1031 " --> pdb=" O CYS A1009 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N GLY A1011 " --> pdb=" O LEU A1031 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 452 through 454 removed outlier: 6.663A pdb=" N SER A 838 " --> pdb=" O GLU A 440 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N VAL A 442 " --> pdb=" O MET A 836 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N MET A 836 " --> pdb=" O VAL A 442 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N CYS A 723 " --> pdb=" O GLN A 831 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N PHE A 833 " --> pdb=" O CYS A 723 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N ASP A 725 " --> pdb=" O PHE A 833 " (cutoff:3.500A) removed outlier: 8.391A pdb=" N GLY A 835 " --> pdb=" O ASP A 725 " (cutoff:3.500A) removed outlier: 9.523A pdb=" N TRP A 727 " --> pdb=" O GLY A 835 " (cutoff:3.500A) removed outlier: 12.541A pdb=" N VAL A 837 " --> pdb=" O TRP A 727 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 452 through 454 removed outlier: 6.663A pdb=" N SER A 838 " --> pdb=" O GLU A 440 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N VAL A 442 " --> pdb=" O MET A 836 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N MET A 836 " --> pdb=" O VAL A 442 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N PHE A 833 " --> pdb=" O TYR A 761 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N TYR A 761 " --> pdb=" O PHE A 833 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLY A 835 " --> pdb=" O PHE A 759 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N SER A 693 " --> pdb=" O TYR A 666 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N TYR A 666 " --> pdb=" O SER A 693 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N MET A 695 " --> pdb=" O ALA A 664 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N ALA A 664 " --> pdb=" O MET A 695 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N SER A 697 " --> pdb=" O HIS A 662 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N HIS A 662 " --> pdb=" O SER A 697 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N PHE A 699 " --> pdb=" O GLU A 660 " (cutoff:3.500A) removed outlier: 10.317A pdb=" N LYS A 775 " --> pdb=" O GLU A 660 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N HIS A 662 " --> pdb=" O LYS A 775 " (cutoff:3.500A) removed outlier: 8.088A pdb=" N ILE A 777 " --> pdb=" O HIS A 662 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N ALA A 664 " --> pdb=" O ILE A 777 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N LEU A 779 " --> pdb=" O ALA A 664 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N TYR A 666 " --> pdb=" O LEU A 779 " (cutoff:3.500A) 469 hydrogen bonds defined for protein. 1350 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: 1.54 Time building geometry restraints manager: 1.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1462 1.32 - 1.45: 2189 1.45 - 1.57: 4983 1.57 - 1.69: 2 1.69 - 1.81: 82 Bond restraints: 8718 Sorted by residual: bond pdb=" CA GLN A 771 " pdb=" CB GLN A 771 " ideal model delta sigma weight residual 1.524 1.535 -0.011 1.31e-02 5.83e+03 6.92e-01 bond pdb=" CA VAL A 295 " pdb=" CB VAL A 295 " ideal model delta sigma weight residual 1.539 1.543 -0.004 5.40e-03 3.43e+04 6.49e-01 bond pdb=" CB PRO A 451 " pdb=" CG PRO A 451 " ideal model delta sigma weight residual 1.492 1.527 -0.035 5.00e-02 4.00e+02 4.92e-01 bond pdb=" C ARG A 667 " pdb=" N LEU A 668 " ideal model delta sigma weight residual 1.331 1.351 -0.020 2.83e-02 1.25e+03 4.81e-01 bond pdb=" N GLN A1054 " pdb=" CA GLN A1054 " ideal model delta sigma weight residual 1.462 1.472 -0.010 1.54e-02 4.22e+03 4.64e-01 ... (remaining 8713 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.21: 11591 1.21 - 2.42: 180 2.42 - 3.64: 56 3.64 - 4.85: 10 4.85 - 6.06: 4 Bond angle restraints: 11841 Sorted by residual: angle pdb=" N SER A 23 " pdb=" CA SER A 23 " pdb=" CB SER A 23 " ideal model delta sigma weight residual 113.65 110.74 2.91 1.47e+00 4.63e-01 3.92e+00 angle pdb=" C LYS A 214 " pdb=" N ASP A 215 " pdb=" CA ASP A 215 " ideal model delta sigma weight residual 122.61 125.62 -3.01 1.56e+00 4.11e-01 3.71e+00 angle pdb=" CA ASP A1234 " pdb=" C ASP A1234 " pdb=" N PHE A1235 " ideal model delta sigma weight residual 115.75 118.15 -2.40 1.34e+00 5.57e-01 3.21e+00 angle pdb=" C ALA A1053 " pdb=" N GLN A1054 " pdb=" CA GLN A1054 " ideal model delta sigma weight residual 122.08 124.69 -2.61 1.47e+00 4.63e-01 3.15e+00 angle pdb=" N ASP A1234 " pdb=" CA ASP A1234 " pdb=" C ASP A1234 " ideal model delta sigma weight residual 109.65 106.89 2.76 1.56e+00 4.11e-01 3.14e+00 ... (remaining 11836 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 4947 17.95 - 35.91: 243 35.91 - 53.86: 48 53.86 - 71.81: 13 71.81 - 89.76: 4 Dihedral angle restraints: 5255 sinusoidal: 2127 harmonic: 3128 Sorted by residual: dihedral pdb=" CB CYS A 604 " pdb=" SG CYS A 604 " pdb=" SG CYS A 641 " pdb=" CB CYS A 641 " ideal model delta sinusoidal sigma weight residual -86.00 -124.41 38.41 1 1.00e+01 1.00e-02 2.08e+01 dihedral pdb=" CB CYS A 641 " pdb=" SG CYS A 641 " pdb=" SG CYS A1039 " pdb=" CB CYS A1039 " ideal model delta sinusoidal sigma weight residual -86.00 -122.45 36.45 1 1.00e+01 1.00e-02 1.88e+01 dihedral pdb=" N LEU A1150 " pdb=" CA LEU A1150 " pdb=" CB LEU A1150 " pdb=" CG LEU A1150 " ideal model delta sinusoidal sigma weight residual -60.00 -119.94 59.94 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 5252 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 831 0.025 - 0.051: 325 0.051 - 0.076: 145 0.076 - 0.101: 41 0.101 - 0.126: 31 Chirality restraints: 1373 Sorted by residual: chirality pdb=" CA ILE A1170 " pdb=" N ILE A1170 " pdb=" C ILE A1170 " pdb=" CB ILE A1170 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.99e-01 chirality pdb=" CA TRP A 77 " pdb=" N TRP A 77 " pdb=" C TRP A 77 " pdb=" CB TRP A 77 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.78e-01 chirality pdb=" CA ILE A 889 " pdb=" N ILE A 889 " pdb=" C ILE A 889 " pdb=" CB ILE A 889 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.60e-01 ... (remaining 1370 not shown) Planarity restraints: 1484 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG A 201 " 0.023 5.00e-02 4.00e+02 3.52e-02 1.98e+00 pdb=" N PRO A 202 " -0.061 5.00e-02 4.00e+02 pdb=" CA PRO A 202 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 202 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 978 " 0.023 5.00e-02 4.00e+02 3.46e-02 1.92e+00 pdb=" N PRO A 979 " -0.060 5.00e-02 4.00e+02 pdb=" CA PRO A 979 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 979 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR A1142 " 0.022 5.00e-02 4.00e+02 3.31e-02 1.75e+00 pdb=" N PRO A1143 " -0.057 5.00e-02 4.00e+02 pdb=" CA PRO A1143 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO A1143 " 0.019 5.00e-02 4.00e+02 ... (remaining 1481 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1698 2.78 - 3.31: 8368 3.31 - 3.84: 14729 3.84 - 4.37: 17120 4.37 - 4.90: 29734 Nonbonded interactions: 71649 Sorted by model distance: nonbonded pdb=" ND2 ASN A 436 " pdb=" OG SER A1040 " model vdw 2.249 3.120 nonbonded pdb=" O LEU A1298 " pdb=" OG1 THR A1302 " model vdw 2.254 3.040 nonbonded pdb=" O SER A 753 " pdb=" NE2 GLN A 840 " model vdw 2.264 3.120 nonbonded pdb=" OG SER A 319 " pdb=" OE1 GLN A 321 " model vdw 2.297 3.040 nonbonded pdb=" NZ LYS A1244 " pdb=" OD2 ASP A1297 " model vdw 2.309 3.120 ... (remaining 71644 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: 0.810 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: 0.170 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.560 Find NCS groups from input model: 0.150 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:6.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8977 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 : 0.002 0.035 8721 Z= 0.102 Angle : 0.455 6.062 11847 Z= 0.232 Chirality : 0.036 0.126 1373 Planarity : 0.004 0.035 1484 Dihedral : 11.513 89.763 3206 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.08 % Allowed : 5.41 % Favored : 92.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.10 (0.27), residues: 1063 helix: 2.71 (0.22), residues: 563 sheet: 0.37 (0.54), residues: 95 loop : -0.27 (0.32), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 283 TYR 0.009 0.001 TYR A 293 PHE 0.013 0.001 PHE A 396 TRP 0.007 0.001 TRP A1301 HIS 0.002 0.001 HIS A 694 Details of bonding type rmsd/Z covalent geometry : bond 0.00224 / 0.10 ( 8718) covalent geometry : angle 0.45514 / 0.23 (11841) SS BOND : bond 0.00238 / 0.17 ( 3) SS BOND : angle 0.42710 / 0.33 ( 6) hydrogen bonds : bond 0.09190 / 6.49 ( 464) hydrogen bonds : angle 4.35765 / 3.22 ( 1350) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2126 Ramachandran restraints generated. 1063 Oldfield, 0 Emsley, 1063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2126 Ramachandran restraints generated. 1063 Oldfield, 0 Emsley, 1063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 52 time to evaluate : 0.351 Fit side-chains revert: symmetry clash REVERT: A 25 LEU cc_start: 0.8914 (OUTLIER) cc_final: 0.8400 (tt) REVERT: A 453 HIS cc_start: 0.7779 (m-70) cc_final: 0.7373 (m-70) REVERT: A 600 LEU cc_start: 0.6712 (OUTLIER) cc_final: 0.6186 (pp) REVERT: A 695 MET cc_start: 0.7256 (ttp) cc_final: 0.6968 (ttt) outliers start: 20 outliers final: 6 residues processed: 70 average time/residue: 0.4941 time to fit residues: 37.5037 Evaluate side-chains 52 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 44 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 436 ASN Chi-restraints excluded: chain A residue 600 LEU Chi-restraints excluded: chain A residue 710 MET Chi-restraints excluded: chain A residue 1031 LEU Chi-restraints excluded: chain A residue 1039 CYS Chi-restraints excluded: chain A residue 1102 CYS Chi-restraints excluded: chain A residue 1184 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: [49, 97, 53, 5, 33, 65, 62, 51, 100, 106, 38] chunk 49 optimal weight: 20.0000 chunk 97 optimal weight: 4.9990 chunk 53 optimal weight: 0.0170 chunk 5 optimal weight: 0.5980 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 6.9990 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 20.0000 chunk 100 optimal weight: 0.9980 chunk 106 optimal weight: 2.9990 chunk 38 optimal weight: 0.7980 overall best weight: 0.6218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 108 ASN A 144 GLN A 395 HIS A 436 ASN A 574 ASN ** A 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 621 ASN A 840 GLN A1063 GLN A1067 GLN A1108 GLN A1355 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.143884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.094768 restraints weight = 12659.901| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 2.06 r_work: 0.3059 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2936 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9002 moved from start: 0.0671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8721 Z= 0.105 Angle : 0.463 6.055 11847 Z= 0.235 Chirality : 0.037 0.126 1373 Planarity : 0.004 0.046 1484 Dihedral : 6.767 53.085 1205 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.60 % Allowed : 6.56 % Favored : 90.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.09 (0.27), residues: 1063 helix: 2.75 (0.22), residues: 562 sheet: -0.02 (0.52), residues: 97 loop : -0.23 (0.32), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 614 TYR 0.009 0.001 TYR A 293 PHE 0.029 0.001 PHE A 615 TRP 0.007 0.001 TRP A 320 HIS 0.002 0.000 HIS A 166 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.10 ( 8718) covalent geometry : angle 0.46283 / 0.23 (11841) SS BOND : bond 0.00261 / 0.18 ( 3) SS BOND : angle 0.86709 / 0.74 ( 6) hydrogen bonds : bond 0.03538 / 2.32 ( 464) hydrogen bonds : angle 3.72772 / 2.73 ( 1350) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2126 Ramachandran restraints generated. 1063 Oldfield, 0 Emsley, 1063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2126 Ramachandran restraints generated. 1063 Oldfield, 0 Emsley, 1063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 45 time to evaluate : 0.319 Fit side-chains revert: symmetry clash REVERT: A 25 LEU cc_start: 0.8885 (OUTLIER) cc_final: 0.8254 (tt) REVERT: A 443 LEU cc_start: 0.7792 (OUTLIER) cc_final: 0.7131 (mt) REVERT: A 453 HIS cc_start: 0.7931 (m-70) cc_final: 0.7604 (m-70) REVERT: A 586 GLN cc_start: 0.7035 (mt0) cc_final: 0.6814 (mp10) REVERT: A 600 LEU cc_start: 0.6557 (OUTLIER) cc_final: 0.6055 (pp) REVERT: A 749 ARG cc_start: 0.7933 (ptp90) cc_final: 0.7696 (ptp90) outliers start: 25 outliers final: 3 residues processed: 63 average time/residue: 0.4611 time to fit residues: 31.6135 Evaluate side-chains 47 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 41 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 600 LEU Chi-restraints excluded: chain A residue 1031 LEU Chi-restraints excluded: chain A residue 1039 CYS Chi-restraints excluded: chain A residue 1102 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: [76, 64, 97, 22, 18, 85, 6, 94, 30, 12, 75] chunk 76 optimal weight: 0.0170 chunk 64 optimal weight: 6.9990 chunk 97 optimal weight: 0.6980 chunk 22 optimal weight: 0.4980 chunk 18 optimal weight: 3.9990 chunk 85 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 94 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 12 optimal weight: 0.5980 chunk 75 optimal weight: 8.9990 overall best weight: 0.5620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 436 ASN ** A 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 621 ASN A 662 HIS ** A 842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.144233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.095228 restraints weight = 12560.003| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 2.05 r_work: 0.3067 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2944 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8994 moved from start: 0.0863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8721 Z= 0.096 Angle : 0.449 6.115 11847 Z= 0.226 Chirality : 0.036 0.131 1373 Planarity : 0.004 0.047 1484 Dihedral : 6.223 52.666 1198 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.98 % Allowed : 8.53 % Favored : 89.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.15 (0.27), residues: 1063 helix: 2.86 (0.22), residues: 558 sheet: -0.29 (0.50), residues: 97 loop : -0.17 (0.32), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 614 TYR 0.008 0.001 TYR A 293 PHE 0.018 0.001 PHE A 615 TRP 0.008 0.001 TRP A 320 HIS 0.002 0.000 HIS A 166 Details of bonding type rmsd/Z covalent geometry : bond 0.00216 / 0.10 ( 8718) covalent geometry : angle 0.44875 / 0.23 (11841) SS BOND : bond 0.00229 / 0.16 ( 3) SS BOND : angle 0.82065 / 0.71 ( 6) hydrogen bonds : bond 0.03324 / 2.19 ( 464) hydrogen bonds : angle 3.57772 / 2.61 ( 1350) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2126 Ramachandran restraints generated. 1063 Oldfield, 0 Emsley, 1063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2126 Ramachandran restraints generated. 1063 Oldfield, 0 Emsley, 1063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 45 time to evaluate : 0.273 Fit side-chains revert: symmetry clash REVERT: A 25 LEU cc_start: 0.8863 (OUTLIER) cc_final: 0.8229 (tt) REVERT: A 443 LEU cc_start: 0.7805 (OUTLIER) cc_final: 0.7160 (mt) REVERT: A 453 HIS cc_start: 0.7949 (m-70) cc_final: 0.7630 (m-70) REVERT: A 586 GLN cc_start: 0.7074 (mt0) cc_final: 0.6841 (mp10) REVERT: A 600 LEU cc_start: 0.6482 (OUTLIER) cc_final: 0.5988 (pp) REVERT: A 749 ARG cc_start: 0.7941 (ptp90) cc_final: 0.7716 (ptp90) REVERT: A 1349 GLN cc_start: 0.7490 (mm110) cc_final: 0.7095 (tm-30) REVERT: A 1362 MET cc_start: 0.4481 (mpm) cc_final: 0.4224 (mpt) outliers start: 19 outliers final: 7 residues processed: 61 average time/residue: 0.5078 time to fit residues: 33.5299 Evaluate side-chains 53 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 43 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 292 HIS Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 600 LEU Chi-restraints excluded: chain A residue 1031 LEU Chi-restraints excluded: chain A residue 1039 CYS Chi-restraints excluded: chain A residue 1102 CYS Chi-restraints excluded: chain A residue 1184 LEU Chi-restraints excluded: chain A residue 1317 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: [25, 15, 7, 52, 33, 76, 98, 17, 97, 16, 29] chunk 25 optimal weight: 0.8980 chunk 15 optimal weight: 4.9990 chunk 7 optimal weight: 3.9990 chunk 52 optimal weight: 40.0000 chunk 33 optimal weight: 0.9980 chunk 76 optimal weight: 0.0980 chunk 98 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 97 optimal weight: 0.6980 chunk 16 optimal weight: 0.9990 chunk 29 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 436 ASN ** A 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 621 ASN ** A 842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1349 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.143825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.094560 restraints weight = 12877.456| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 2.08 r_work: 0.3060 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2937 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9003 moved from start: 0.0933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8721 Z= 0.103 Angle : 0.449 6.176 11847 Z= 0.225 Chirality : 0.036 0.136 1373 Planarity : 0.004 0.044 1484 Dihedral : 6.293 56.214 1198 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.77 % Allowed : 9.05 % Favored : 89.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.17 (0.27), residues: 1063 helix: 2.88 (0.22), residues: 558 sheet: -0.40 (0.50), residues: 98 loop : -0.14 (0.32), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 132 TYR 0.008 0.001 TYR A 293 PHE 0.014 0.001 PHE A 615 TRP 0.007 0.001 TRP A 320 HIS 0.002 0.000 HIS A 67 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.10 ( 8718) covalent geometry : angle 0.44896 / 0.22 (11841) SS BOND : bond 0.00205 / 0.14 ( 3) SS BOND : angle 0.79957 / 0.68 ( 6) hydrogen bonds : bond 0.03331 / 2.19 ( 464) hydrogen bonds : angle 3.54292 / 2.59 ( 1350) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2126 Ramachandran restraints generated. 1063 Oldfield, 0 Emsley, 1063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2126 Ramachandran restraints generated. 1063 Oldfield, 0 Emsley, 1063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 43 time to evaluate : 0.311 Fit side-chains revert: symmetry clash REVERT: A 25 LEU cc_start: 0.8853 (OUTLIER) cc_final: 0.8201 (tt) REVERT: A 443 LEU cc_start: 0.7850 (OUTLIER) cc_final: 0.7173 (mt) REVERT: A 453 HIS cc_start: 0.7973 (m-70) cc_final: 0.7656 (m-70) REVERT: A 586 GLN cc_start: 0.7102 (mt0) cc_final: 0.6840 (mp10) REVERT: A 600 LEU cc_start: 0.6457 (OUTLIER) cc_final: 0.5951 (pp) REVERT: A 749 ARG cc_start: 0.7963 (ptp90) cc_final: 0.7733 (ptp90) REVERT: A 1349 GLN cc_start: 0.7570 (mm-40) cc_final: 0.7149 (tm-30) REVERT: A 1358 THR cc_start: 0.6628 (OUTLIER) cc_final: 0.6419 (t) REVERT: A 1362 MET cc_start: 0.4588 (mpm) cc_final: 0.4187 (mmt) outliers start: 17 outliers final: 7 residues processed: 58 average time/residue: 0.4787 time to fit residues: 30.1935 Evaluate side-chains 55 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 44 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 292 HIS Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 600 LEU Chi-restraints excluded: chain A residue 1031 LEU Chi-restraints excluded: chain A residue 1039 CYS Chi-restraints excluded: chain A residue 1102 CYS Chi-restraints excluded: chain A residue 1184 LEU Chi-restraints excluded: chain A residue 1317 LEU Chi-restraints excluded: chain A residue 1358 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: [6, 46, 59, 82, 13, 16, 18, 79, 27, 100, 45] chunk 6 optimal weight: 1.9990 chunk 46 optimal weight: 4.9990 chunk 59 optimal weight: 0.6980 chunk 82 optimal weight: 0.7980 chunk 13 optimal weight: 1.9990 chunk 16 optimal weight: 4.9990 chunk 18 optimal weight: 6.9990 chunk 79 optimal weight: 0.9980 chunk 27 optimal weight: 3.9990 chunk 100 optimal weight: 0.8980 chunk 45 optimal weight: 8.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 436 ASN ** A 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 621 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.142994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.093255 restraints weight = 12723.536| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 2.09 r_work: 0.3038 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2914 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9023 moved from start: 0.0980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8721 Z= 0.122 Angle : 0.463 6.241 11847 Z= 0.231 Chirality : 0.037 0.143 1373 Planarity : 0.004 0.046 1484 Dihedral : 6.369 54.427 1198 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.98 % Allowed : 9.57 % Favored : 88.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.18 (0.26), residues: 1063 helix: 2.90 (0.21), residues: 551 sheet: -0.37 (0.50), residues: 97 loop : -0.10 (0.32), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 614 TYR 0.008 0.001 TYR A 293 PHE 0.015 0.001 PHE A1103 TRP 0.007 0.001 TRP A 320 HIS 0.002 0.001 HIS A 395 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.12 ( 8718) covalent geometry : angle 0.46259 / 0.23 (11841) SS BOND : bond 0.00125 / 0.09 ( 3) SS BOND : angle 0.75571 / 0.61 ( 6) hydrogen bonds : bond 0.03533 / 2.32 ( 464) hydrogen bonds : angle 3.58654 / 2.62 ( 1350) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2126 Ramachandran restraints generated. 1063 Oldfield, 0 Emsley, 1063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2126 Ramachandran restraints generated. 1063 Oldfield, 0 Emsley, 1063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 43 time to evaluate : 0.250 Fit side-chains revert: symmetry clash REVERT: A 25 LEU cc_start: 0.8841 (OUTLIER) cc_final: 0.8175 (tt) REVERT: A 50 GLU cc_start: 0.8313 (OUTLIER) cc_final: 0.8002 (tp30) REVERT: A 443 LEU cc_start: 0.7870 (OUTLIER) cc_final: 0.7190 (mt) REVERT: A 453 HIS cc_start: 0.7866 (m-70) cc_final: 0.7563 (m-70) REVERT: A 586 GLN cc_start: 0.7108 (mt0) cc_final: 0.6799 (mp10) REVERT: A 600 LEU cc_start: 0.6486 (OUTLIER) cc_final: 0.5960 (pp) REVERT: A 749 ARG cc_start: 0.7985 (ptp90) cc_final: 0.7764 (ptp90) REVERT: A 1349 GLN cc_start: 0.7632 (mm-40) cc_final: 0.7208 (tm-30) REVERT: A 1358 THR cc_start: 0.6663 (OUTLIER) cc_final: 0.6455 (t) REVERT: A 1362 MET cc_start: 0.4730 (mpm) cc_final: 0.4350 (mmt) outliers start: 19 outliers final: 8 residues processed: 59 average time/residue: 0.4849 time to fit residues: 31.0650 Evaluate side-chains 54 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 41 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 50 GLU Chi-restraints excluded: chain A residue 292 HIS Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 600 LEU Chi-restraints excluded: chain A residue 982 VAL Chi-restraints excluded: chain A residue 1031 LEU Chi-restraints excluded: chain A residue 1039 CYS Chi-restraints excluded: chain A residue 1102 CYS Chi-restraints excluded: chain A residue 1184 LEU Chi-restraints excluded: chain A residue 1317 LEU Chi-restraints excluded: chain A residue 1358 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: [94, 86, 37, 27, 53, 43, 32, 85, 82, 50, 45] chunk 94 optimal weight: 2.9990 chunk 86 optimal weight: 6.9990 chunk 37 optimal weight: 0.9980 chunk 27 optimal weight: 3.9990 chunk 53 optimal weight: 10.0000 chunk 43 optimal weight: 8.9990 chunk 32 optimal weight: 3.9990 chunk 85 optimal weight: 0.8980 chunk 82 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 621 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.141884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.091939 restraints weight = 12613.010| |-----------------------------------------------------------------------------| r_work (start): 0.3124 rms_B_bonded: 2.07 r_work: 0.3012 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2888 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9043 moved from start: 0.1023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8721 Z= 0.157 Angle : 0.494 6.467 11847 Z= 0.246 Chirality : 0.038 0.148 1373 Planarity : 0.004 0.047 1484 Dihedral : 6.546 53.896 1198 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.08 % Allowed : 9.78 % Favored : 88.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.07 (0.26), residues: 1063 helix: 2.80 (0.21), residues: 552 sheet: -0.40 (0.50), residues: 97 loop : -0.15 (0.31), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 614 TYR 0.009 0.001 TYR A1003 PHE 0.017 0.001 PHE A1103 TRP 0.006 0.001 TRP A 320 HIS 0.002 0.001 HIS A1261 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.16 ( 8718) covalent geometry : angle 0.49422 / 0.25 (11841) SS BOND : bond 0.00067 / 0.05 ( 3) SS BOND : angle 0.68131 / 0.53 ( 6) hydrogen bonds : bond 0.03849 / 2.53 ( 464) hydrogen bonds : angle 3.67246 / 2.68 ( 1350) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2126 Ramachandran restraints generated. 1063 Oldfield, 0 Emsley, 1063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2126 Ramachandran restraints generated. 1063 Oldfield, 0 Emsley, 1063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 40 time to evaluate : 0.339 Fit side-chains revert: symmetry clash REVERT: A 25 LEU cc_start: 0.8853 (OUTLIER) cc_final: 0.8216 (tt) REVERT: A 50 GLU cc_start: 0.8318 (OUTLIER) cc_final: 0.7990 (tp30) REVERT: A 443 LEU cc_start: 0.7975 (OUTLIER) cc_final: 0.7273 (mt) REVERT: A 453 HIS cc_start: 0.7807 (m-70) cc_final: 0.7530 (m-70) REVERT: A 586 GLN cc_start: 0.7114 (mt0) cc_final: 0.6788 (mp10) REVERT: A 600 LEU cc_start: 0.6526 (OUTLIER) cc_final: 0.5994 (pp) REVERT: A 1112 THR cc_start: 0.9294 (OUTLIER) cc_final: 0.9052 (m) REVERT: A 1349 GLN cc_start: 0.7649 (mm-40) cc_final: 0.7215 (tm-30) REVERT: A 1358 THR cc_start: 0.6708 (OUTLIER) cc_final: 0.6490 (t) REVERT: A 1362 MET cc_start: 0.4809 (mpm) cc_final: 0.4441 (mmt) outliers start: 20 outliers final: 9 residues processed: 58 average time/residue: 0.4520 time to fit residues: 28.5580 Evaluate side-chains 55 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 40 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 50 GLU Chi-restraints excluded: chain A residue 292 HIS Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 600 LEU Chi-restraints excluded: chain A residue 982 VAL Chi-restraints excluded: chain A residue 1031 LEU Chi-restraints excluded: chain A residue 1039 CYS Chi-restraints excluded: chain A residue 1102 CYS Chi-restraints excluded: chain A residue 1112 THR Chi-restraints excluded: chain A residue 1184 LEU Chi-restraints excluded: chain A residue 1317 LEU Chi-restraints excluded: chain A residue 1358 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: [80, 61, 74, 59, 15, 37, 71, 11, 50, 34, 24] chunk 80 optimal weight: 0.8980 chunk 61 optimal weight: 5.9990 chunk 74 optimal weight: 0.0040 chunk 59 optimal weight: 3.9990 chunk 15 optimal weight: 5.9990 chunk 37 optimal weight: 0.9980 chunk 71 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 chunk 50 optimal weight: 0.3980 chunk 34 optimal weight: 0.9980 chunk 24 optimal weight: 0.9980 overall best weight: 0.6592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 436 ASN ** A 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 621 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.143434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.094073 restraints weight = 12776.054| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 2.08 r_work: 0.3050 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2926 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9012 moved from start: 0.1043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8721 Z= 0.100 Angle : 0.452 6.467 11847 Z= 0.225 Chirality : 0.036 0.139 1373 Planarity : 0.004 0.048 1484 Dihedral : 6.262 52.169 1198 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.98 % Allowed : 10.20 % Favored : 87.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.22 (0.26), residues: 1063 helix: 2.96 (0.22), residues: 550 sheet: -0.48 (0.50), residues: 97 loop : -0.08 (0.32), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 614 TYR 0.008 0.001 TYR A 293 PHE 0.013 0.001 PHE A1103 TRP 0.010 0.001 TRP A 320 HIS 0.002 0.000 HIS A 166 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.10 ( 8718) covalent geometry : angle 0.45215 / 0.22 (11841) SS BOND : bond 0.00162 / 0.11 ( 3) SS BOND : angle 0.74030 / 0.59 ( 6) hydrogen bonds : bond 0.03334 / 2.19 ( 464) hydrogen bonds : angle 3.54405 / 2.59 ( 1350) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2126 Ramachandran restraints generated. 1063 Oldfield, 0 Emsley, 1063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2126 Ramachandran restraints generated. 1063 Oldfield, 0 Emsley, 1063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 42 time to evaluate : 0.264 Fit side-chains revert: symmetry clash REVERT: A 25 LEU cc_start: 0.8839 (OUTLIER) cc_final: 0.8201 (tt) REVERT: A 443 LEU cc_start: 0.7896 (OUTLIER) cc_final: 0.7253 (mt) REVERT: A 453 HIS cc_start: 0.7836 (m-70) cc_final: 0.7567 (m-70) REVERT: A 586 GLN cc_start: 0.7171 (mt0) cc_final: 0.6824 (mp10) REVERT: A 600 LEU cc_start: 0.6485 (OUTLIER) cc_final: 0.5984 (pp) REVERT: A 1349 GLN cc_start: 0.7627 (mm-40) cc_final: 0.7206 (tm-30) REVERT: A 1358 THR cc_start: 0.6698 (OUTLIER) cc_final: 0.6481 (t) REVERT: A 1362 MET cc_start: 0.4750 (mpm) cc_final: 0.4360 (mmt) outliers start: 19 outliers final: 10 residues processed: 57 average time/residue: 0.4586 time to fit residues: 28.4060 Evaluate side-chains 55 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 41 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 292 HIS Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 600 LEU Chi-restraints excluded: chain A residue 982 VAL Chi-restraints excluded: chain A residue 1031 LEU Chi-restraints excluded: chain A residue 1039 CYS Chi-restraints excluded: chain A residue 1102 CYS Chi-restraints excluded: chain A residue 1184 LEU Chi-restraints excluded: chain A residue 1312 LEU Chi-restraints excluded: chain A residue 1317 LEU Chi-restraints excluded: chain A residue 1358 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: [34, 45, 25, 72, 44, 48, 89, 13, 52, 24, 87] chunk 34 optimal weight: 0.4980 chunk 45 optimal weight: 8.9990 chunk 25 optimal weight: 0.9980 chunk 72 optimal weight: 6.9990 chunk 44 optimal weight: 5.9990 chunk 48 optimal weight: 30.0000 chunk 89 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 52 optimal weight: 20.0000 chunk 24 optimal weight: 0.9990 chunk 87 optimal weight: 0.8980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 621 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.142465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.092542 restraints weight = 12647.900| |-----------------------------------------------------------------------------| r_work (start): 0.3134 rms_B_bonded: 2.07 r_work: 0.3020 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2896 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9036 moved from start: 0.1091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8721 Z= 0.135 Angle : 0.481 7.446 11847 Z= 0.238 Chirality : 0.037 0.146 1373 Planarity : 0.004 0.047 1484 Dihedral : 6.408 53.351 1198 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.08 % Allowed : 10.20 % Favored : 87.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.15 (0.26), residues: 1063 helix: 2.89 (0.22), residues: 552 sheet: -0.47 (0.51), residues: 97 loop : -0.12 (0.32), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 614 TYR 0.008 0.001 TYR A1003 PHE 0.016 0.001 PHE A1103 TRP 0.007 0.001 TRP A 320 HIS 0.002 0.001 HIS A1261 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.13 ( 8718) covalent geometry : angle 0.48084 / 0.24 (11841) SS BOND : bond 0.00099 / 0.07 ( 3) SS BOND : angle 0.73687 / 0.57 ( 6) hydrogen bonds : bond 0.03638 / 2.39 ( 464) hydrogen bonds : angle 3.60874 / 2.64 ( 1350) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2126 Ramachandran restraints generated. 1063 Oldfield, 0 Emsley, 1063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2126 Ramachandran restraints generated. 1063 Oldfield, 0 Emsley, 1063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 41 time to evaluate : 0.286 Fit side-chains revert: symmetry clash REVERT: A 25 LEU cc_start: 0.8838 (OUTLIER) cc_final: 0.8212 (tt) REVERT: A 443 LEU cc_start: 0.7949 (OUTLIER) cc_final: 0.7286 (mt) REVERT: A 453 HIS cc_start: 0.7846 (m-70) cc_final: 0.7579 (m-70) REVERT: A 586 GLN cc_start: 0.7148 (mt0) cc_final: 0.6793 (mp10) REVERT: A 600 LEU cc_start: 0.6524 (OUTLIER) cc_final: 0.6029 (pp) REVERT: A 1349 GLN cc_start: 0.7644 (mm-40) cc_final: 0.7174 (tm-30) REVERT: A 1358 THR cc_start: 0.6711 (OUTLIER) cc_final: 0.6493 (t) REVERT: A 1362 MET cc_start: 0.4837 (mpm) cc_final: 0.4475 (mmt) outliers start: 20 outliers final: 11 residues processed: 57 average time/residue: 0.4744 time to fit residues: 29.4766 Evaluate side-chains 56 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 41 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 292 HIS Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 600 LEU Chi-restraints excluded: chain A residue 892 THR Chi-restraints excluded: chain A residue 982 VAL Chi-restraints excluded: chain A residue 1031 LEU Chi-restraints excluded: chain A residue 1039 CYS Chi-restraints excluded: chain A residue 1102 CYS Chi-restraints excluded: chain A residue 1184 LEU Chi-restraints excluded: chain A residue 1312 LEU Chi-restraints excluded: chain A residue 1317 LEU Chi-restraints excluded: chain A residue 1358 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: [86, 37, 53, 43, 29, 100, 42, 5, 13, 7, 4] chunk 86 optimal weight: 0.0370 chunk 37 optimal weight: 0.3980 chunk 53 optimal weight: 5.9990 chunk 43 optimal weight: 5.9990 chunk 29 optimal weight: 0.6980 chunk 100 optimal weight: 0.6980 chunk 42 optimal weight: 6.9990 chunk 5 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 7 optimal weight: 2.9990 chunk 4 optimal weight: 0.8980 overall best weight: 0.5258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.143693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.094153 restraints weight = 12742.880| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 2.08 r_work: 0.3058 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2934 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9005 moved from start: 0.1140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8721 Z= 0.093 Angle : 0.465 9.144 11847 Z= 0.227 Chirality : 0.036 0.136 1373 Planarity : 0.004 0.049 1484 Dihedral : 6.191 51.869 1198 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.14 % Allowed : 11.13 % Favored : 87.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.26 (0.27), residues: 1063 helix: 3.01 (0.22), residues: 550 sheet: -0.50 (0.51), residues: 97 loop : -0.08 (0.32), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 749 TYR 0.008 0.001 TYR A 293 PHE 0.012 0.001 PHE A1103 TRP 0.010 0.001 TRP A 320 HIS 0.002 0.000 HIS A 166 Details of bonding type rmsd/Z covalent geometry : bond 0.00208 / 0.09 ( 8718) covalent geometry : angle 0.46445 / 0.23 (11841) SS BOND : bond 0.00182 / 0.13 ( 3) SS BOND : angle 0.76652 / 0.62 ( 6) hydrogen bonds : bond 0.03235 / 2.12 ( 464) hydrogen bonds : angle 3.51983 / 2.58 ( 1350) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2126 Ramachandran restraints generated. 1063 Oldfield, 0 Emsley, 1063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2126 Ramachandran restraints generated. 1063 Oldfield, 0 Emsley, 1063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 42 time to evaluate : 0.372 Fit side-chains revert: symmetry clash REVERT: A 25 LEU cc_start: 0.8838 (OUTLIER) cc_final: 0.8197 (tt) REVERT: A 443 LEU cc_start: 0.7919 (OUTLIER) cc_final: 0.7279 (mt) REVERT: A 453 HIS cc_start: 0.7851 (m-70) cc_final: 0.7608 (m-70) REVERT: A 586 GLN cc_start: 0.7204 (mt0) cc_final: 0.6927 (mp10) REVERT: A 600 LEU cc_start: 0.6464 (OUTLIER) cc_final: 0.5960 (pp) REVERT: A 749 ARG cc_start: 0.7973 (ptp90) cc_final: 0.7737 (ptp90) REVERT: A 1052 MET cc_start: 0.2554 (mpm) cc_final: 0.1153 (pp-130) REVERT: A 1349 GLN cc_start: 0.7641 (mm-40) cc_final: 0.7222 (tm-30) outliers start: 11 outliers final: 7 residues processed: 51 average time/residue: 0.5255 time to fit residues: 28.8550 Evaluate side-chains 52 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 42 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 600 LEU Chi-restraints excluded: chain A residue 982 VAL Chi-restraints excluded: chain A residue 1031 LEU Chi-restraints excluded: chain A residue 1039 CYS Chi-restraints excluded: chain A residue 1102 CYS Chi-restraints excluded: chain A residue 1312 LEU Chi-restraints excluded: chain A residue 1317 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: [70, 4, 7, 106, 52, 38, 3, 15, 34, 101, 51] chunk 70 optimal weight: 0.8980 chunk 4 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 106 optimal weight: 4.9990 chunk 52 optimal weight: 30.0000 chunk 38 optimal weight: 8.9990 chunk 3 optimal weight: 2.9990 chunk 15 optimal weight: 6.9990 chunk 34 optimal weight: 2.9990 chunk 101 optimal weight: 0.9980 chunk 51 optimal weight: 6.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 453 HIS ** A 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.141123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.090420 restraints weight = 12668.724| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 2.10 r_work: 0.2991 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2866 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9063 moved from start: 0.1227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 8721 Z= 0.196 Angle : 0.538 8.497 11847 Z= 0.263 Chirality : 0.039 0.155 1373 Planarity : 0.004 0.045 1484 Dihedral : 6.727 55.407 1198 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.77 % Allowed : 10.51 % Favored : 87.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.99 (0.26), residues: 1063 helix: 2.77 (0.21), residues: 550 sheet: -0.43 (0.51), residues: 97 loop : -0.23 (0.31), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 614 TYR 0.011 0.001 TYR A1003 PHE 0.018 0.002 PHE A1103 TRP 0.008 0.001 TRP A1278 HIS 0.004 0.001 HIS A1261 Details of bonding type rmsd/Z covalent geometry : bond 0.00471 / 0.20 ( 8718) covalent geometry : angle 0.53774 / 0.26 (11841) SS BOND : bond 0.00044 / 0.03 ( 3) SS BOND : angle 0.73944 / 0.54 ( 6) hydrogen bonds : bond 0.04106 / 2.69 ( 464) hydrogen bonds : angle 3.73783 / 2.73 ( 1350) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2126 Ramachandran restraints generated. 1063 Oldfield, 0 Emsley, 1063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2126 Ramachandran restraints generated. 1063 Oldfield, 0 Emsley, 1063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 40 time to evaluate : 0.336 Fit side-chains revert: symmetry clash REVERT: A 25 LEU cc_start: 0.8846 (OUTLIER) cc_final: 0.8216 (tt) REVERT: A 443 LEU cc_start: 0.7979 (OUTLIER) cc_final: 0.7314 (mt) REVERT: A 453 HIS cc_start: 0.7712 (m90) cc_final: 0.7422 (m-70) REVERT: A 586 GLN cc_start: 0.7193 (mt0) cc_final: 0.6803 (mp10) REVERT: A 600 LEU cc_start: 0.6515 (OUTLIER) cc_final: 0.6006 (pp) REVERT: A 1052 MET cc_start: 0.2719 (mpm) cc_final: 0.1194 (pp-130) REVERT: A 1349 GLN cc_start: 0.7690 (mm-40) cc_final: 0.7207 (tm-30) outliers start: 17 outliers final: 10 residues processed: 54 average time/residue: 0.4915 time to fit residues: 28.8014 Evaluate side-chains 54 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 41 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 292 HIS Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 600 LEU Chi-restraints excluded: chain A residue 892 THR Chi-restraints excluded: chain A residue 982 VAL Chi-restraints excluded: chain A residue 1031 LEU Chi-restraints excluded: chain A residue 1039 CYS Chi-restraints excluded: chain A residue 1102 CYS Chi-restraints excluded: chain A residue 1184 LEU Chi-restraints excluded: chain A residue 1317 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: [23, 41, 44, 10, 35, 5, 4, 66, 18, 38, 20] chunk 23 optimal weight: 0.0370 chunk 41 optimal weight: 7.9990 chunk 44 optimal weight: 7.9990 chunk 10 optimal weight: 0.6980 chunk 35 optimal weight: 0.6980 chunk 5 optimal weight: 0.0570 chunk 4 optimal weight: 0.8980 chunk 66 optimal weight: 8.9990 chunk 18 optimal weight: 4.9990 chunk 38 optimal weight: 6.9990 chunk 20 optimal weight: 6.9990 overall best weight: 0.4776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 840 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.143728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.093956 restraints weight = 12716.125| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 2.09 r_work: 0.3059 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2935 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9007 moved from start: 0.1197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8721 Z= 0.094 Angle : 0.461 8.631 11847 Z= 0.227 Chirality : 0.036 0.135 1373 Planarity : 0.004 0.048 1484 Dihedral : 6.266 52.916 1198 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.66 % Allowed : 10.61 % Favored : 87.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.23 (0.27), residues: 1063 helix: 2.97 (0.22), residues: 550 sheet: -0.43 (0.51), residues: 97 loop : -0.09 (0.32), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 132 TYR 0.007 0.001 TYR A 293 PHE 0.012 0.001 PHE A1103 TRP 0.010 0.001 TRP A 320 HIS 0.002 0.000 HIS A 67 Details of bonding type rmsd/Z covalent geometry : bond 0.00209 / 0.09 ( 8718) covalent geometry : angle 0.46075 / 0.23 (11841) SS BOND : bond 0.00178 / 0.12 ( 3) SS BOND : angle 0.75771 / 0.60 ( 6) hydrogen bonds : bond 0.03229 / 2.12 ( 464) hydrogen bonds : angle 3.54100 / 2.60 ( 1350) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2914.49 seconds wall clock time: 50 minutes 19.33 seconds (3019.33 seconds total)