Starting phenix.real_space_refine on Tue Mar 3 17:49:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6xov_22281/03_2026/6xov_22281.cif Found real_map, /net/cci-nas-00/data/ceres_data/6xov_22281/03_2026/6xov_22281.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6xov_22281/03_2026/6xov_22281.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6xov_22281/03_2026/6xov_22281.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6xov_22281/03_2026/6xov_22281.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6xov_22281/03_2026/6xov_22281.map" } resolution = 3.3 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= 0.002 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 39 5.16 5 C 4935 2.51 5 N 1313 2.21 5 O 1468 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7755 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 7713 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 966, 7699 Classifications: {'peptide': 966} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PTRANS': 60, 'TRANS': 903} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 966, 7699 Classifications: {'peptide': 966} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PTRANS': 60, 'TRANS': 903} Chain breaks: 1 bond proxies already assigned to first conformer: 7874 Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 27 Classifications: {'peptide': 3} Link IDs: {'TRANS': 2} Chain: "C" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 15 Classifications: {'peptide': 3} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'TRANS': 2} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'UNK:plan-1': 3} Unresolved non-hydrogen planarities: 3 Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N ASER A 723 " occ=0.42 ... (10 atoms not shown) pdb=" OG BSER A 723 " occ=0.58 residue: pdb=" N AASN A 915 " occ=0.59 ... (14 atoms not shown) pdb=" ND2BASN A 915 " occ=0.41 Time building chain proxies: 3.23, per 1000 atoms: 0.42 Number of scatterers: 7755 At special positions: 0 Unit cell: (86.355, 88.065, 98.325, 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 39 16.00 O 1468 8.00 N 1313 7.00 C 4935 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: 0.65 Conformation dependent library (CDL) restraints added in 580.3 milliseconds 1938 Ramachandran restraints generated. 969 Oldfield, 0 Emsley, 969 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1840 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 8 sheets defined 52.2% alpha, 16.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'A' and resid 32 through 38 Processing helix chain 'A' and resid 101 through 110 Processing helix chain 'A' and resid 122 through 127 Processing helix chain 'A' and resid 152 through 169 Processing helix chain 'A' and resid 173 through 181 Processing helix chain 'A' and resid 201 through 210 Processing helix chain 'A' and resid 212 through 226 Processing helix chain 'A' and resid 229 through 233 Processing helix chain 'A' and resid 241 through 245 removed outlier: 3.617A pdb=" N GLU A 244 " --> pdb=" O CYS A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 258 Processing helix chain 'A' and resid 259 through 261 No H-bonds generated for 'chain 'A' and resid 259 through 261' Processing helix chain 'A' and resid 272 through 282 removed outlier: 4.270A pdb=" N HIS A 276 " --> pdb=" O PRO A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 288 Processing helix chain 'A' and resid 339 through 355 Processing helix chain 'A' and resid 359 through 365 Processing helix chain 'A' and resid 366 through 369 removed outlier: 3.748A pdb=" N GLY A 369 " --> pdb=" O ILE A 366 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 366 through 369' Processing helix chain 'A' and resid 397 through 399 No H-bonds generated for 'chain 'A' and resid 397 through 399' Processing helix chain 'A' and resid 400 through 419 Processing helix chain 'A' and resid 421 through 438 Processing helix chain 'A' and resid 442 through 456 removed outlier: 5.376A pdb=" N SER A 453 " --> pdb=" O SER A 449 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N CYS A 454 " --> pdb=" O TYR A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 466 removed outlier: 3.547A pdb=" N LYS A 466 " --> pdb=" O VAL A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 481 removed outlier: 3.674A pdb=" N ASN A 481 " --> pdb=" O CYS A 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 494 Processing helix chain 'A' and resid 509 through 527 Processing helix chain 'A' and resid 530 through 550 Processing helix chain 'A' and resid 608 through 612 removed outlier: 3.574A pdb=" N LEU A 611 " --> pdb=" O PRO A 608 " (cutoff:3.500A) Processing helix chain 'A' and resid 614 through 623 removed outlier: 4.553A pdb=" N THR A 623 " --> pdb=" O CYS A 619 " (cutoff:3.500A) Processing helix chain 'A' and resid 631 through 643 Processing helix chain 'A' and resid 676 through 690 Processing helix chain 'A' and resid 696 through 713 removed outlier: 3.678A pdb=" N GLY A 713 " --> pdb=" O GLU A 709 " (cutoff:3.500A) Processing helix chain 'A' and resid 714 through 716 No H-bonds generated for 'chain 'A' and resid 714 through 716' Processing helix chain 'A' and resid 717 through 728 Processing helix chain 'A' and resid 731 through 742 Processing helix chain 'A' and resid 742 through 755 removed outlier: 3.758A pdb=" N VAL A 746 " --> pdb=" O GLY A 742 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N MET A 755 " --> pdb=" O ARG A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 763 Processing helix chain 'A' and resid 764 through 773 removed outlier: 4.120A pdb=" N HIS A 771 " --> pdb=" O ARG A 767 " (cutoff:3.500A) Processing helix chain 'A' and resid 788 through 802 Processing helix chain 'A' and resid 877 through 894 removed outlier: 3.775A pdb=" N ALA A 881 " --> pdb=" O ASP A 877 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N SER A 882 " --> pdb=" O PRO A 878 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ILE A 885 " --> pdb=" O ALA A 881 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ARG A 888 " --> pdb=" O LYS A 884 " (cutoff:3.500A) Processing helix chain 'A' and resid 894 through 899 Processing helix chain 'A' and resid 928 through 944 removed outlier: 3.516A pdb=" N VAL A 939 " --> pdb=" O PHE A 935 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASP A 940 " --> pdb=" O GLY A 936 " (cutoff:3.500A) Processing helix chain 'A' and resid 948 through 963 removed outlier: 3.813A pdb=" N ILE A 952 " --> pdb=" O THR A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 973 through 979 removed outlier: 3.763A pdb=" N PHE A 977 " --> pdb=" O GLY A 973 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 995 removed outlier: 3.526A pdb=" N PHE A 994 " --> pdb=" O ARG A 990 " (cutoff:3.500A) Processing helix chain 'A' and resid 997 through 1009 removed outlier: 3.509A pdb=" N ASP A1006 " --> pdb=" O LEU A1002 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ARG A1007 " --> pdb=" O ALA A1003 " (cutoff:3.500A) Processing helix chain 'A' and resid 1025 through 1031 removed outlier: 3.671A pdb=" N ASP A1031 " --> pdb=" O LYS A1027 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 45 through 46 removed outlier: 5.714A pdb=" N VAL A 51 " --> pdb=" O THR A 68 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N THR A 68 " --> pdb=" O VAL A 51 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLN A 53 " --> pdb=" O LYS A 66 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N ARG A 75 " --> pdb=" O PHE A 265 " (cutoff:3.500A) removed outlier: 7.808A pdb=" N THR A 267 " --> pdb=" O ARG A 75 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N LEU A 77 " --> pdb=" O THR A 267 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 46 removed outlier: 5.714A pdb=" N VAL A 51 " --> pdb=" O THR A 68 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N THR A 68 " --> pdb=" O VAL A 51 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLN A 53 " --> pdb=" O LYS A 66 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N ARG A 75 " --> pdb=" O PHE A 265 " (cutoff:3.500A) removed outlier: 7.808A pdb=" N THR A 267 " --> pdb=" O ARG A 75 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N LEU A 77 " --> pdb=" O THR A 267 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 182 through 185 Processing sheet with id=AA4, first strand: chain 'A' and resid 311 through 313 removed outlier: 7.175A pdb=" N VAL A 328 " --> pdb=" O GLN A 394 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N GLN A 394 " --> pdb=" O VAL A 328 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 577 through 578 Processing sheet with id=AA6, first strand: chain 'A' and resid 588 through 589 removed outlier: 5.474A pdb=" N CYS A 588 " --> pdb=" O ALA A 784 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N SER A 649 " --> pdb=" O LEU A 667 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 588 through 589 removed outlier: 5.474A pdb=" N CYS A 588 " --> pdb=" O ALA A 784 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 907 through 912 removed outlier: 3.557A pdb=" N VAL A 866 " --> pdb=" O SER A 922 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N ASN A 864 " --> pdb=" O ARG A 924 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLY A1017 " --> pdb=" O CYS A 869 " (cutoff:3.500A) removed outlier: 5.655A pdb=" N HIS A 856 " --> pdb=" O ARG A1037 " (cutoff:3.500A) 424 hydrogen bonds defined for protein. 1210 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: 1.52 Time building geometry restraints manager: 0.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1906 1.33 - 1.45: 1564 1.45 - 1.57: 4416 1.57 - 1.69: 0 1.69 - 1.81: 62 Bond restraints: 7948 Sorted by residual: bond pdb=" N PHE A 318 " pdb=" CA PHE A 318 " ideal model delta sigma weight residual 1.457 1.484 -0.026 1.29e-02 6.01e+03 4.12e+00 bond pdb=" C ILE A 242 " pdb=" N PRO A 243 " ideal model delta sigma weight residual 1.336 1.356 -0.020 1.08e-02 8.57e+03 3.49e+00 bond pdb=" CA PHE A 318 " pdb=" C PHE A 318 " ideal model delta sigma weight residual 1.523 1.542 -0.019 1.34e-02 5.57e+03 2.04e+00 bond pdb=" N GLY A 626 " pdb=" CA GLY A 626 " ideal model delta sigma weight residual 1.449 1.470 -0.020 1.45e-02 4.76e+03 1.98e+00 bond pdb=" CB ASN A 136 " pdb=" CG ASN A 136 " ideal model delta sigma weight residual 1.516 1.483 0.033 2.50e-02 1.60e+03 1.73e+00 ... (remaining 7943 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.48: 10604 2.48 - 4.96: 149 4.96 - 7.45: 20 7.45 - 9.93: 3 9.93 - 12.41: 1 Bond angle restraints: 10777 Sorted by residual: angle pdb=" N PHE A 318 " pdb=" CA PHE A 318 " pdb=" C PHE A 318 " ideal model delta sigma weight residual 110.80 123.21 -12.41 2.13e+00 2.20e-01 3.39e+01 angle pdb=" C SER A 317 " pdb=" CA SER A 317 " pdb=" CB SER A 317 " ideal model delta sigma weight residual 109.90 118.86 -8.96 1.56e+00 4.11e-01 3.30e+01 angle pdb=" N LYS A 324 " pdb=" CA LYS A 324 " pdb=" C LYS A 324 " ideal model delta sigma weight residual 108.56 117.67 -9.11 1.74e+00 3.30e-01 2.74e+01 angle pdb=" C ASP A 321 " pdb=" N PRO A 322 " pdb=" CA PRO A 322 " ideal model delta sigma weight residual 119.28 124.67 -5.39 1.10e+00 8.26e-01 2.41e+01 angle pdb=" N ILE A 758 " pdb=" CA ILE A 758 " pdb=" C ILE A 758 " ideal model delta sigma weight residual 112.17 108.46 3.71 9.50e-01 1.11e+00 1.52e+01 ... (remaining 10772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.82: 4339 17.82 - 35.64: 381 35.64 - 53.46: 62 53.46 - 71.27: 12 71.27 - 89.09: 8 Dihedral angle restraints: 4802 sinusoidal: 1960 harmonic: 2842 Sorted by residual: dihedral pdb=" C PHE A 318 " pdb=" N PHE A 318 " pdb=" CA PHE A 318 " pdb=" CB PHE A 318 " ideal model delta harmonic sigma weight residual -122.60 -135.25 12.65 0 2.50e+00 1.60e-01 2.56e+01 dihedral pdb=" CA PHE A 210 " pdb=" C PHE A 210 " pdb=" N THR A 211 " pdb=" CA THR A 211 " ideal model delta harmonic sigma weight residual 180.00 155.34 24.66 0 5.00e+00 4.00e-02 2.43e+01 dihedral pdb=" N PHE A 318 " pdb=" C PHE A 318 " pdb=" CA PHE A 318 " pdb=" CB PHE A 318 " ideal model delta harmonic sigma weight residual 122.80 134.48 -11.68 0 2.50e+00 1.60e-01 2.18e+01 ... (remaining 4799 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.110: 1156 0.110 - 0.220: 23 0.220 - 0.330: 1 0.330 - 0.440: 0 0.440 - 0.550: 1 Chirality restraints: 1181 Sorted by residual: chirality pdb=" CA PHE A 318 " pdb=" N PHE A 318 " pdb=" C PHE A 318 " pdb=" CB PHE A 318 " both_signs ideal model delta sigma weight residual False 2.51 1.96 0.55 2.00e-01 2.50e+01 7.57e+00 chirality pdb=" CA THR A 876 " pdb=" N THR A 876 " pdb=" C THR A 876 " pdb=" CB THR A 876 " both_signs ideal model delta sigma weight residual False 2.53 2.21 0.32 2.00e-01 2.50e+01 2.58e+00 chirality pdb=" CA LYS A 324 " pdb=" N LYS A 324 " pdb=" C LYS A 324 " pdb=" CB LYS A 324 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.44e-01 ... (remaining 1178 not shown) Planarity restraints: 1407 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 163 " -0.027 2.00e-02 2.50e+03 1.76e-02 6.17e+00 pdb=" CG TYR A 163 " 0.041 2.00e-02 2.50e+03 pdb=" CD1 TYR A 163 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 TYR A 163 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR A 163 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR A 163 " -0.002 2.00e-02 2.50e+03 pdb=" CZ TYR A 163 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR A 163 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 146 " -0.009 2.00e-02 2.50e+03 1.82e-02 3.32e+00 pdb=" C TYR A 146 " 0.032 2.00e-02 2.50e+03 pdb=" O TYR A 146 " -0.012 2.00e-02 2.50e+03 pdb=" N PRO A 147 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A 102 " 0.030 5.00e-02 4.00e+02 4.54e-02 3.29e+00 pdb=" N PRO A 103 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO A 103 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 103 " 0.026 5.00e-02 4.00e+02 ... (remaining 1404 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 160 2.66 - 3.22: 7612 3.22 - 3.78: 12070 3.78 - 4.34: 16710 4.34 - 4.90: 27480 Nonbonded interactions: 64032 Sorted by model distance: nonbonded pdb=" OD1 ASP A 373 " pdb=" N PHE A 374 " model vdw 2.100 3.120 nonbonded pdb=" O LEU A 365 " pdb=" OG SER A 368 " model vdw 2.199 3.040 nonbonded pdb=" OG SER A 997 " pdb=" OD1 ASP A 999 " model vdw 2.220 3.040 nonbonded pdb=" OG1 THR A 50 " pdb=" OD1 ASP A 70 " model vdw 2.234 3.040 nonbonded pdb=" O SER A 190 " pdb=" OH TYR A 538 " model vdw 2.235 3.040 ... (remaining 64027 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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=0.41 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 10.920 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 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 : 0.005 0.044 7948 Z= 0.210 Angle : 0.758 12.411 10777 Z= 0.433 Chirality : 0.048 0.550 1181 Planarity : 0.006 0.045 1407 Dihedral : 14.282 89.092 2962 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 13.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 0.35 % Allowed : 0.58 % Favored : 99.07 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % 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: -1.92 (0.27), residues: 969 helix: -0.29 (0.25), residues: 444 sheet: -2.18 (0.37), residues: 174 loop : -1.91 (0.34), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 725 TYR 0.041 0.002 TYR A 163 PHE 0.022 0.002 PHE B 20 TRP 0.031 0.002 TRP A 455 HIS 0.010 0.001 HIS A 108 Details of bonding type rmsd covalent geometry : bond 0.00457 ( 7948) covalent geometry : angle 0.75798 (10777) hydrogen bonds : bond 0.19194 ( 391) hydrogen bonds : angle 7.80080 ( 1210) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1938 Ramachandran restraints generated. 969 Oldfield, 0 Emsley, 969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1938 Ramachandran restraints generated. 969 Oldfield, 0 Emsley, 969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 93 time to evaluate : 0.330 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 76 TYR cc_start: 0.8126 (t80) cc_final: 0.7824 (t80) REVERT: A 106 LEU cc_start: 0.8882 (tp) cc_final: 0.8531 (tp) REVERT: A 517 VAL cc_start: 0.8318 (p) cc_final: 0.8008 (p) REVERT: A 520 THR cc_start: 0.8784 (m) cc_final: 0.8509 (p) REVERT: A 884 LYS cc_start: 0.8779 (ttmt) cc_final: 0.8565 (tppt) REVERT: A 953 ASP cc_start: 0.7911 (t70) cc_final: 0.7688 (t0) outliers start: 3 outliers final: 0 residues processed: 94 average time/residue: 0.0857 time to fit residues: 11.4284 Evaluate side-chains 66 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 49 optimal weight: 4.9990 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 4.9990 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 0.7980 chunk 45 optimal weight: 0.9990 chunk 74 optimal weight: 6.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 394 GLN A 514 GLN A 552 GLN ** A 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 987 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 = 0.3361 r_free = 0.3361 target = 0.072641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.058037 restraints weight = 55044.825| |-----------------------------------------------------------------------------| r_work (start): 0.3027 rms_B_bonded: 5.98 r_work: 0.2839 rms_B_bonded: 5.94 restraints_weight: 2.0000 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2849 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2849 r_free = 0.2849 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2849 r_free = 0.2849 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2849 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.1431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7948 Z= 0.147 Angle : 0.664 8.983 10777 Z= 0.341 Chirality : 0.044 0.190 1181 Planarity : 0.006 0.048 1407 Dihedral : 5.075 45.144 1043 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 0.81 % Allowed : 7.08 % Favored : 92.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % 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: -0.86 (0.28), residues: 969 helix: 0.56 (0.25), residues: 462 sheet: -1.56 (0.39), residues: 166 loop : -1.49 (0.35), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 751 TYR 0.018 0.002 TYR A 163 PHE 0.010 0.001 PHE A 688 TRP 0.023 0.002 TRP A 851 HIS 0.006 0.001 HIS A 108 Details of bonding type rmsd covalent geometry : bond 0.00330 ( 7948) covalent geometry : angle 0.66436 (10777) hydrogen bonds : bond 0.04040 ( 391) hydrogen bonds : angle 5.14925 ( 1210) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1938 Ramachandran restraints generated. 969 Oldfield, 0 Emsley, 969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1938 Ramachandran restraints generated. 969 Oldfield, 0 Emsley, 969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 81 time to evaluate : 0.306 Fit side-chains revert: symmetry clash REVERT: A 604 LEU cc_start: 0.8825 (mt) cc_final: 0.8595 (mt) REVERT: A 640 GLU cc_start: 0.8711 (mt-10) cc_final: 0.8269 (mp0) REVERT: A 755 MET cc_start: 0.8053 (mtm) cc_final: 0.7290 (ptp) REVERT: A 884 LYS cc_start: 0.8680 (ttmt) cc_final: 0.8385 (tppt) REVERT: A 917 ILE cc_start: 0.8845 (mm) cc_final: 0.8631 (mm) REVERT: A 925 ASP cc_start: 0.8431 (t0) cc_final: 0.7663 (t0) REVERT: A 953 ASP cc_start: 0.8342 (t70) cc_final: 0.8042 (t0) outliers start: 7 outliers final: 4 residues processed: 82 average time/residue: 0.0718 time to fit residues: 8.8248 Evaluate side-chains 75 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 71 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 931 THR Chi-restraints excluded: chain A residue 985 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 54 optimal weight: 7.9990 chunk 4 optimal weight: 7.9990 chunk 19 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 chunk 9 optimal weight: 0.0670 chunk 85 optimal weight: 8.9990 chunk 24 optimal weight: 0.9990 chunk 2 optimal weight: 3.9990 chunk 73 optimal weight: 0.9990 chunk 57 optimal weight: 0.9980 overall best weight: 0.7722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 128 ASN A 590 GLN ** A 987 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.073577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.058591 restraints weight = 70094.838| |-----------------------------------------------------------------------------| r_work (start): 0.3043 rms_B_bonded: 6.63 r_work: 0.2844 rms_B_bonded: 6.35 restraints_weight: 2.0000 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2852 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2852 r_free = 0.2852 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2852 r_free = 0.2852 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2852 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.1919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7948 Z= 0.113 Angle : 0.593 9.110 10777 Z= 0.302 Chirality : 0.042 0.182 1181 Planarity : 0.005 0.046 1407 Dihedral : 4.696 40.118 1043 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 0.81 % Allowed : 8.58 % Favored : 90.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % 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: -0.11 (0.28), residues: 969 helix: 1.08 (0.25), residues: 459 sheet: -1.07 (0.40), residues: 166 loop : -1.03 (0.36), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 751 TYR 0.009 0.001 TYR A 450 PHE 0.028 0.001 PHE A 389 TRP 0.021 0.002 TRP A 851 HIS 0.004 0.001 HIS A 186 Details of bonding type rmsd covalent geometry : bond 0.00254 ( 7948) covalent geometry : angle 0.59299 (10777) hydrogen bonds : bond 0.03344 ( 391) hydrogen bonds : angle 4.71413 ( 1210) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1938 Ramachandran restraints generated. 969 Oldfield, 0 Emsley, 969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1938 Ramachandran restraints generated. 969 Oldfield, 0 Emsley, 969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 80 time to evaluate : 0.343 Fit side-chains revert: symmetry clash REVERT: A 152 ASN cc_start: 0.8389 (t0) cc_final: 0.7982 (t0) REVERT: A 436 MET cc_start: 0.9044 (ttm) cc_final: 0.8727 (tmm) REVERT: A 550 LYS cc_start: 0.7940 (mtmm) cc_final: 0.7710 (mtmt) REVERT: A 573 GLU cc_start: 0.7921 (pm20) cc_final: 0.7338 (pm20) REVERT: A 640 GLU cc_start: 0.8734 (mt-10) cc_final: 0.8313 (mp0) REVERT: A 659 MET cc_start: 0.8008 (tpp) cc_final: 0.7580 (tpt) REVERT: A 755 MET cc_start: 0.8046 (mtm) cc_final: 0.7688 (ptp) REVERT: A 859 MET cc_start: 0.8956 (mmt) cc_final: 0.8724 (mmm) REVERT: A 884 LYS cc_start: 0.8736 (ttmt) cc_final: 0.8411 (tppt) REVERT: A 925 ASP cc_start: 0.8617 (t0) cc_final: 0.7918 (t0) REVERT: A 953 ASP cc_start: 0.8333 (t70) cc_final: 0.8109 (t0) outliers start: 7 outliers final: 5 residues processed: 81 average time/residue: 0.0770 time to fit residues: 9.1577 Evaluate side-chains 72 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 67 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 657 SER Chi-restraints excluded: chain A residue 931 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 73 optimal weight: 2.9990 chunk 14 optimal weight: 7.9990 chunk 43 optimal weight: 8.9990 chunk 49 optimal weight: 9.9990 chunk 25 optimal weight: 8.9990 chunk 47 optimal weight: 9.9990 chunk 89 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 86 optimal weight: 2.9990 chunk 44 optimal weight: 0.7980 chunk 64 optimal weight: 6.9990 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 223 ASN A 635 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.069438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.055524 restraints weight = 50528.735| |-----------------------------------------------------------------------------| r_work (start): 0.2973 rms_B_bonded: 5.52 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2974 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2974 r_free = 0.2974 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2974 r_free = 0.2974 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2974 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.2055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 7948 Z= 0.285 Angle : 0.709 9.101 10777 Z= 0.361 Chirality : 0.046 0.189 1181 Planarity : 0.005 0.046 1407 Dihedral : 5.115 44.329 1043 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 1.16 % Allowed : 9.05 % Favored : 89.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % 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: -0.42 (0.28), residues: 969 helix: 0.79 (0.24), residues: 466 sheet: -1.06 (0.40), residues: 171 loop : -1.25 (0.37), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 751 TYR 0.020 0.002 TYR A 388 PHE 0.024 0.002 PHE A 389 TRP 0.032 0.002 TRP A 455 HIS 0.006 0.001 HIS A 856 Details of bonding type rmsd covalent geometry : bond 0.00645 ( 7948) covalent geometry : angle 0.70920 (10777) hydrogen bonds : bond 0.04306 ( 391) hydrogen bonds : angle 4.82751 ( 1210) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1938 Ramachandran restraints generated. 969 Oldfield, 0 Emsley, 969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1938 Ramachandran restraints generated. 969 Oldfield, 0 Emsley, 969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 66 time to evaluate : 0.323 Fit side-chains revert: symmetry clash REVERT: A 187 GLU cc_start: 0.8136 (mm-30) cc_final: 0.7923 (mm-30) REVERT: A 436 MET cc_start: 0.8653 (ttm) cc_final: 0.8302 (tmm) REVERT: A 640 GLU cc_start: 0.8406 (mt-10) cc_final: 0.8032 (mp0) REVERT: A 755 MET cc_start: 0.7850 (mtm) cc_final: 0.7356 (ptp) REVERT: A 859 MET cc_start: 0.8652 (mmt) cc_final: 0.8433 (mmm) REVERT: A 884 LYS cc_start: 0.8663 (ttmt) cc_final: 0.8325 (tppt) REVERT: A 925 ASP cc_start: 0.8535 (t0) cc_final: 0.7957 (t0) outliers start: 10 outliers final: 7 residues processed: 73 average time/residue: 0.0707 time to fit residues: 7.8323 Evaluate side-chains 68 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 61 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 657 SER Chi-restraints excluded: chain A residue 669 SER Chi-restraints excluded: chain A residue 928 THR Chi-restraints excluded: chain A residue 931 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 58 optimal weight: 2.9990 chunk 47 optimal weight: 8.9990 chunk 1 optimal weight: 3.9990 chunk 87 optimal weight: 1.9990 chunk 4 optimal weight: 4.9990 chunk 94 optimal weight: 10.0000 chunk 27 optimal weight: 0.6980 chunk 62 optimal weight: 3.9990 chunk 19 optimal weight: 0.9980 chunk 64 optimal weight: 4.9990 chunk 81 optimal weight: 0.7980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 987 GLN ** 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 = 0.3346 r_free = 0.3346 target = 0.071907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.057373 restraints weight = 57353.409| |-----------------------------------------------------------------------------| r_work (start): 0.3011 rms_B_bonded: 6.00 r_work: 0.2823 rms_B_bonded: 5.92 restraints_weight: 2.0000 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2833 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2833 r_free = 0.2833 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2833 r_free = 0.2833 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2833 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.2274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7948 Z= 0.137 Angle : 0.606 11.943 10777 Z= 0.305 Chirality : 0.042 0.185 1181 Planarity : 0.005 0.048 1407 Dihedral : 4.775 41.238 1043 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 0.93 % Allowed : 10.79 % Favored : 88.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % 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: -0.01 (0.29), residues: 969 helix: 1.07 (0.24), residues: 471 sheet: -0.97 (0.39), residues: 178 loop : -0.93 (0.39), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 747 TYR 0.011 0.001 TYR A 380 PHE 0.027 0.001 PHE A 389 TRP 0.022 0.002 TRP A 455 HIS 0.003 0.001 HIS A 186 Details of bonding type rmsd covalent geometry : bond 0.00314 ( 7948) covalent geometry : angle 0.60604 (10777) hydrogen bonds : bond 0.03409 ( 391) hydrogen bonds : angle 4.56845 ( 1210) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1938 Ramachandran restraints generated. 969 Oldfield, 0 Emsley, 969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1938 Ramachandran restraints generated. 969 Oldfield, 0 Emsley, 969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 68 time to evaluate : 0.320 Fit side-chains revert: symmetry clash REVERT: A 187 GLU cc_start: 0.8136 (mm-30) cc_final: 0.7899 (mm-30) REVERT: A 436 MET cc_start: 0.9172 (ttm) cc_final: 0.8726 (tmm) REVERT: A 573 GLU cc_start: 0.8153 (pm20) cc_final: 0.7704 (pm20) REVERT: A 635 GLN cc_start: 0.8615 (OUTLIER) cc_final: 0.8266 (pt0) REVERT: A 640 GLU cc_start: 0.8703 (mt-10) cc_final: 0.8332 (mp0) REVERT: A 659 MET cc_start: 0.8010 (tpp) cc_final: 0.7705 (tpp) REVERT: A 736 LEU cc_start: 0.8130 (OUTLIER) cc_final: 0.7917 (mp) REVERT: A 859 MET cc_start: 0.8999 (mmt) cc_final: 0.8754 (mmm) REVERT: A 884 LYS cc_start: 0.8732 (ttmt) cc_final: 0.8407 (tppt) REVERT: A 925 ASP cc_start: 0.8688 (t0) cc_final: 0.8160 (t0) REVERT: A 1037 ARG cc_start: 0.7633 (mpt-90) cc_final: 0.7274 (mpt-90) outliers start: 8 outliers final: 4 residues processed: 71 average time/residue: 0.0794 time to fit residues: 8.3069 Evaluate side-chains 68 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 62 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 635 GLN Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 928 THR Chi-restraints excluded: chain A residue 931 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 56 optimal weight: 5.9990 chunk 63 optimal weight: 5.9990 chunk 0 optimal weight: 9.9990 chunk 76 optimal weight: 2.9990 chunk 9 optimal weight: 0.0770 chunk 66 optimal weight: 6.9990 chunk 30 optimal weight: 0.8980 chunk 50 optimal weight: 9.9990 chunk 87 optimal weight: 0.7980 chunk 32 optimal weight: 0.0270 chunk 22 optimal weight: 5.9990 overall best weight: 0.9598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 664 GLN ** A 987 GLN ** 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 = 0.3368 r_free = 0.3368 target = 0.072671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.058295 restraints weight = 55509.563| |-----------------------------------------------------------------------------| r_work (start): 0.3041 rms_B_bonded: 5.90 r_work: 0.2855 rms_B_bonded: 5.82 restraints_weight: 2.0000 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2862 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2862 r_free = 0.2862 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2862 r_free = 0.2862 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2862 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.2552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7948 Z= 0.112 Angle : 0.571 8.568 10777 Z= 0.288 Chirality : 0.041 0.133 1181 Planarity : 0.005 0.047 1407 Dihedral : 4.524 38.828 1043 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 0.93 % Allowed : 10.90 % Favored : 88.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % 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: 0.38 (0.29), residues: 969 helix: 1.39 (0.25), residues: 465 sheet: -0.76 (0.40), residues: 172 loop : -0.71 (0.38), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 747 TYR 0.009 0.001 TYR A 450 PHE 0.030 0.001 PHE A 389 TRP 0.021 0.001 TRP A 851 HIS 0.003 0.001 HIS A 186 Details of bonding type rmsd covalent geometry : bond 0.00260 ( 7948) covalent geometry : angle 0.57139 (10777) hydrogen bonds : bond 0.03051 ( 391) hydrogen bonds : angle 4.39953 ( 1210) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1938 Ramachandran restraints generated. 969 Oldfield, 0 Emsley, 969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1938 Ramachandran restraints generated. 969 Oldfield, 0 Emsley, 969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 66 time to evaluate : 0.330 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 187 GLU cc_start: 0.8130 (mm-30) cc_final: 0.7894 (mm-30) REVERT: A 436 MET cc_start: 0.9176 (ttm) cc_final: 0.8702 (tmm) REVERT: A 573 GLU cc_start: 0.8195 (pm20) cc_final: 0.7695 (pm20) REVERT: A 659 MET cc_start: 0.8068 (tpp) cc_final: 0.7787 (tpp) REVERT: A 853 MET cc_start: 0.8268 (mmt) cc_final: 0.8045 (mmt) REVERT: A 859 MET cc_start: 0.8991 (mmt) cc_final: 0.8781 (mmm) REVERT: A 884 LYS cc_start: 0.8705 (ttmt) cc_final: 0.8387 (tppt) REVERT: A 925 ASP cc_start: 0.8652 (t0) cc_final: 0.8146 (t0) REVERT: A 1037 ARG cc_start: 0.7545 (mpt-90) cc_final: 0.7306 (mpt-90) REVERT: B 20 PHE cc_start: 0.6193 (p90) cc_final: 0.5883 (p90) outliers start: 8 outliers final: 7 residues processed: 72 average time/residue: 0.0821 time to fit residues: 8.6494 Evaluate side-chains 67 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 60 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 647 SER Chi-restraints excluded: chain A residue 657 SER Chi-restraints excluded: chain A residue 669 SER Chi-restraints excluded: chain A residue 928 THR Chi-restraints excluded: chain A residue 931 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 58 optimal weight: 3.9990 chunk 25 optimal weight: 5.9990 chunk 18 optimal weight: 0.7980 chunk 7 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 chunk 45 optimal weight: 7.9990 chunk 8 optimal weight: 1.9990 chunk 3 optimal weight: 0.7980 chunk 54 optimal weight: 10.0000 chunk 39 optimal weight: 0.5980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 552 GLN ** A 987 GLN ** 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 = 0.3376 r_free = 0.3376 target = 0.072943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.058390 restraints weight = 61661.184| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 6.21 r_work: 0.2852 rms_B_bonded: 6.08 restraints_weight: 2.0000 r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2861 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2861 r_free = 0.2861 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2861 r_free = 0.2861 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2861 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.2688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7948 Z= 0.110 Angle : 0.569 8.608 10777 Z= 0.285 Chirality : 0.041 0.132 1181 Planarity : 0.005 0.044 1407 Dihedral : 4.381 33.799 1043 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 0.93 % Allowed : 11.48 % Favored : 87.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % 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: 0.51 (0.29), residues: 969 helix: 1.52 (0.25), residues: 467 sheet: -0.67 (0.40), residues: 178 loop : -0.71 (0.38), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 747 TYR 0.011 0.001 TYR A 450 PHE 0.029 0.001 PHE A 389 TRP 0.023 0.001 TRP A 851 HIS 0.003 0.001 HIS A 186 Details of bonding type rmsd covalent geometry : bond 0.00253 ( 7948) covalent geometry : angle 0.56858 (10777) hydrogen bonds : bond 0.03000 ( 391) hydrogen bonds : angle 4.32941 ( 1210) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1938 Ramachandran restraints generated. 969 Oldfield, 0 Emsley, 969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1938 Ramachandran restraints generated. 969 Oldfield, 0 Emsley, 969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 63 time to evaluate : 0.457 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 187 GLU cc_start: 0.8167 (mm-30) cc_final: 0.7923 (mm-30) REVERT: A 436 MET cc_start: 0.9184 (ttm) cc_final: 0.8691 (tmm) REVERT: A 550 LYS cc_start: 0.7640 (OUTLIER) cc_final: 0.7384 (pttm) REVERT: A 573 GLU cc_start: 0.8273 (pm20) cc_final: 0.7746 (pm20) REVERT: A 659 MET cc_start: 0.8080 (tpp) cc_final: 0.7456 (tpt) REVERT: A 859 MET cc_start: 0.9011 (mmt) cc_final: 0.8808 (mmm) REVERT: A 884 LYS cc_start: 0.8710 (ttmt) cc_final: 0.8399 (tppt) REVERT: A 925 ASP cc_start: 0.8660 (t0) cc_final: 0.8163 (t0) REVERT: A 1037 ARG cc_start: 0.7583 (mpt-90) cc_final: 0.7258 (mpt-90) REVERT: B 20 PHE cc_start: 0.6197 (p90) cc_final: 0.5891 (p90) outliers start: 8 outliers final: 6 residues processed: 68 average time/residue: 0.0801 time to fit residues: 8.0725 Evaluate side-chains 68 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 61 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 550 LYS Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 928 THR Chi-restraints excluded: chain A residue 931 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 45 optimal weight: 7.9990 chunk 64 optimal weight: 5.9990 chunk 54 optimal weight: 10.0000 chunk 30 optimal weight: 4.9990 chunk 74 optimal weight: 8.9990 chunk 41 optimal weight: 5.9990 chunk 57 optimal weight: 0.8980 chunk 42 optimal weight: 5.9990 chunk 3 optimal weight: 10.0000 chunk 9 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 987 GLN ** 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 = 0.3305 r_free = 0.3305 target = 0.069370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.056346 restraints weight = 34720.514| |-----------------------------------------------------------------------------| r_work (start): 0.3002 rms_B_bonded: 4.57 r_work: 0.2838 rms_B_bonded: 4.82 restraints_weight: 0.5000 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2846 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2846 r_free = 0.2846 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2846 r_free = 0.2846 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2846 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.2630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 7948 Z= 0.273 Angle : 0.686 7.931 10777 Z= 0.348 Chirality : 0.045 0.148 1181 Planarity : 0.005 0.042 1407 Dihedral : 4.868 41.544 1043 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 1.39 % Allowed : 11.02 % Favored : 87.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % 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: 0.14 (0.28), residues: 969 helix: 1.16 (0.24), residues: 468 sheet: -0.87 (0.39), residues: 180 loop : -0.77 (0.39), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 747 TYR 0.019 0.002 TYR A 388 PHE 0.023 0.002 PHE A 389 TRP 0.023 0.002 TRP A 851 HIS 0.012 0.001 HIS A 896 Details of bonding type rmsd covalent geometry : bond 0.00615 ( 7948) covalent geometry : angle 0.68641 (10777) hydrogen bonds : bond 0.04030 ( 391) hydrogen bonds : angle 4.57651 ( 1210) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1938 Ramachandran restraints generated. 969 Oldfield, 0 Emsley, 969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1938 Ramachandran restraints generated. 969 Oldfield, 0 Emsley, 969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 59 time to evaluate : 0.314 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 187 GLU cc_start: 0.8226 (mm-30) cc_final: 0.7972 (mm-30) REVERT: A 436 MET cc_start: 0.9171 (ttm) cc_final: 0.8636 (tmm) REVERT: A 550 LYS cc_start: 0.7632 (ptpt) cc_final: 0.7255 (ptpp) REVERT: A 573 GLU cc_start: 0.8297 (pm20) cc_final: 0.8033 (pm20) REVERT: A 659 MET cc_start: 0.8103 (tpp) cc_final: 0.7801 (tpp) REVERT: A 884 LYS cc_start: 0.8781 (ttmt) cc_final: 0.8429 (tppt) REVERT: A 925 ASP cc_start: 0.8668 (t0) cc_final: 0.8155 (t0) REVERT: B 20 PHE cc_start: 0.6504 (p90) cc_final: 0.6142 (p90) outliers start: 12 outliers final: 9 residues processed: 65 average time/residue: 0.0721 time to fit residues: 7.0998 Evaluate side-chains 67 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 58 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 647 SER Chi-restraints excluded: chain A residue 657 SER Chi-restraints excluded: chain A residue 669 SER Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 928 THR Chi-restraints excluded: chain A residue 931 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 68 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 37 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 73 optimal weight: 0.8980 chunk 22 optimal weight: 0.8980 chunk 52 optimal weight: 0.8980 chunk 69 optimal weight: 3.9990 chunk 59 optimal weight: 4.9990 chunk 44 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 987 GLN ** 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 = 0.3363 r_free = 0.3363 target = 0.072210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.058091 restraints weight = 51024.986| |-----------------------------------------------------------------------------| r_work (start): 0.3041 rms_B_bonded: 5.67 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3039 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3039 r_free = 0.3039 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3039 r_free = 0.3039 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3039 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.2826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7948 Z= 0.114 Angle : 0.586 8.764 10777 Z= 0.292 Chirality : 0.041 0.129 1181 Planarity : 0.004 0.045 1407 Dihedral : 4.491 37.207 1043 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.04 % Allowed : 11.48 % Favored : 87.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % 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: 0.61 (0.29), residues: 969 helix: 1.55 (0.25), residues: 469 sheet: -0.63 (0.40), residues: 176 loop : -0.60 (0.39), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 747 TYR 0.013 0.001 TYR A 163 PHE 0.029 0.001 PHE A 389 TRP 0.024 0.001 TRP A 851 HIS 0.010 0.001 HIS A 896 Details of bonding type rmsd covalent geometry : bond 0.00259 ( 7948) covalent geometry : angle 0.58590 (10777) hydrogen bonds : bond 0.03042 ( 391) hydrogen bonds : angle 4.37094 ( 1210) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1938 Ramachandran restraints generated. 969 Oldfield, 0 Emsley, 969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1938 Ramachandran restraints generated. 969 Oldfield, 0 Emsley, 969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 65 time to evaluate : 0.186 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 187 GLU cc_start: 0.8208 (mm-30) cc_final: 0.7970 (mm-30) REVERT: A 436 MET cc_start: 0.8624 (ttm) cc_final: 0.8314 (tmm) REVERT: A 595 MET cc_start: 0.8447 (OUTLIER) cc_final: 0.8158 (mtp) REVERT: A 659 MET cc_start: 0.7913 (tpp) cc_final: 0.7321 (tpt) REVERT: A 853 MET cc_start: 0.7671 (mmt) cc_final: 0.7443 (mmm) REVERT: A 884 LYS cc_start: 0.8571 (ttmt) cc_final: 0.8282 (tppt) REVERT: A 925 ASP cc_start: 0.8433 (t0) cc_final: 0.7967 (t0) REVERT: A 1037 ARG cc_start: 0.7438 (mpt-90) cc_final: 0.7155 (mpt-90) REVERT: B 20 PHE cc_start: 0.6310 (p90) cc_final: 0.5700 (p90) outliers start: 9 outliers final: 6 residues processed: 69 average time/residue: 0.0694 time to fit residues: 7.0322 Evaluate side-chains 68 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 61 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 595 MET Chi-restraints excluded: chain A residue 647 SER Chi-restraints excluded: chain A residue 928 THR Chi-restraints excluded: chain A residue 931 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 23 optimal weight: 4.9990 chunk 53 optimal weight: 8.9990 chunk 7 optimal weight: 4.9990 chunk 29 optimal weight: 0.4980 chunk 76 optimal weight: 0.9990 chunk 11 optimal weight: 0.4980 chunk 84 optimal weight: 7.9990 chunk 43 optimal weight: 6.9990 chunk 3 optimal weight: 5.9990 chunk 60 optimal weight: 0.7980 chunk 44 optimal weight: 1.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 987 GLN ** 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 = 0.3370 r_free = 0.3370 target = 0.072577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.058468 restraints weight = 50672.171| |-----------------------------------------------------------------------------| r_work (start): 0.3051 rms_B_bonded: 5.61 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3047 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3047 r_free = 0.3047 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3047 r_free = 0.3047 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3047 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.2921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 7948 Z= 0.114 Angle : 0.605 14.503 10777 Z= 0.297 Chirality : 0.041 0.127 1181 Planarity : 0.004 0.045 1407 Dihedral : 4.359 32.808 1043 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 0.58 % Allowed : 12.06 % Favored : 87.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % 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: 0.73 (0.29), residues: 969 helix: 1.65 (0.25), residues: 469 sheet: -0.51 (0.41), residues: 175 loop : -0.56 (0.38), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 747 TYR 0.012 0.001 TYR A 163 PHE 0.028 0.001 PHE A 389 TRP 0.024 0.001 TRP A 851 HIS 0.009 0.001 HIS A 896 Details of bonding type rmsd covalent geometry : bond 0.00262 ( 7948) covalent geometry : angle 0.60487 (10777) hydrogen bonds : bond 0.02939 ( 391) hydrogen bonds : angle 4.27847 ( 1210) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1938 Ramachandran restraints generated. 969 Oldfield, 0 Emsley, 969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1938 Ramachandran restraints generated. 969 Oldfield, 0 Emsley, 969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 61 time to evaluate : 0.313 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 187 GLU cc_start: 0.8229 (mm-30) cc_final: 0.7979 (mm-30) REVERT: A 436 MET cc_start: 0.8633 (ttm) cc_final: 0.8263 (tmm) REVERT: A 595 MET cc_start: 0.8434 (OUTLIER) cc_final: 0.8186 (mtp) REVERT: A 659 MET cc_start: 0.7930 (tpp) cc_final: 0.7369 (tpt) REVERT: A 884 LYS cc_start: 0.8554 (ttmt) cc_final: 0.8270 (tppt) REVERT: A 925 ASP cc_start: 0.8432 (t0) cc_final: 0.7957 (t0) REVERT: A 1037 ARG cc_start: 0.7415 (mpt-90) cc_final: 0.7140 (mpt-90) REVERT: B 20 PHE cc_start: 0.6298 (p90) cc_final: 0.5794 (p90) outliers start: 5 outliers final: 4 residues processed: 63 average time/residue: 0.0824 time to fit residues: 7.5623 Evaluate side-chains 65 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 60 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 595 MET Chi-restraints excluded: chain A residue 928 THR Chi-restraints excluded: chain A residue 931 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 90 optimal weight: 7.9990 chunk 76 optimal weight: 4.9990 chunk 54 optimal weight: 3.9990 chunk 52 optimal weight: 7.9990 chunk 55 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 62 optimal weight: 0.8980 chunk 63 optimal weight: 4.9990 chunk 89 optimal weight: 7.9990 chunk 77 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 987 GLN ** 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 = 0.3326 r_free = 0.3326 target = 0.070413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.056306 restraints weight = 52228.345| |-----------------------------------------------------------------------------| r_work (start): 0.2997 rms_B_bonded: 5.65 r_work: 0.2814 rms_B_bonded: 5.64 restraints_weight: 2.0000 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2826 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2826 r_free = 0.2826 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2826 r_free = 0.2826 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2826 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.2879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 7948 Z= 0.210 Angle : 0.668 13.683 10777 Z= 0.333 Chirality : 0.043 0.154 1181 Planarity : 0.005 0.042 1407 Dihedral : 4.674 34.435 1043 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 0.81 % Allowed : 12.30 % Favored : 86.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % 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: 0.52 (0.29), residues: 969 helix: 1.45 (0.25), residues: 469 sheet: -0.57 (0.40), residues: 177 loop : -0.65 (0.39), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 747 TYR 0.019 0.002 TYR A 721 PHE 0.025 0.002 PHE A 389 TRP 0.027 0.002 TRP A 851 HIS 0.009 0.001 HIS A 896 Details of bonding type rmsd covalent geometry : bond 0.00479 ( 7948) covalent geometry : angle 0.66760 (10777) hydrogen bonds : bond 0.03605 ( 391) hydrogen bonds : angle 4.43037 ( 1210) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1997.66 seconds wall clock time: 34 minutes 58.68 seconds (2098.68 seconds total)