Starting phenix.real_space_refine on Fri Mar 14 06:05:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8d49_27178/03_2025/8d49_27178.cif Found real_map, /net/cci-nas-00/data/ceres_data/8d49_27178/03_2025/8d49_27178.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8d49_27178/03_2025/8d49_27178.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8d49_27178/03_2025/8d49_27178.map" model { file = "/net/cci-nas-00/data/ceres_data/8d49_27178/03_2025/8d49_27178.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8d49_27178/03_2025/8d49_27178.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.018 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 25 5.49 5 S 24 5.16 5 C 5812 2.51 5 N 1568 2.21 5 O 1852 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 87 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 9281 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 8748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1072, 8748 Classifications: {'peptide': 1072} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 27, 'TRANS': 1044} Chain breaks: 4 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 533 Classifications: {'RNA': 26} Modifications used: {'5*END': 1, 'rna2p_pur': 2, 'rna2p_pyr': 5, 'rna3p_pur': 5, 'rna3p_pyr': 14} Link IDs: {'rna2p': 6, 'rna3p': 19} Chain breaks: 1 Time building chain proxies: 5.85, per 1000 atoms: 0.63 Number of scatterers: 9281 At special positions: 0 Unit cell: (86.48, 96.82, 125.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 24 16.00 P 25 15.00 O 1852 8.00 N 1568 7.00 C 5812 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.23 Conformation dependent library (CDL) restraints added in 976.6 milliseconds 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2046 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 10 sheets defined 55.8% alpha, 11.8% beta 4 base pairs and 16 stacking pairs defined. Time for finding SS restraints: 3.16 Creating SS restraints... Processing helix chain 'A' and resid 34 through 49 removed outlier: 3.703A pdb=" N SER A 47 " --> pdb=" O GLU A 43 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N SER A 48 " --> pdb=" O ASN A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 79 Processing helix chain 'A' and resid 92 through 102 Processing helix chain 'A' and resid 117 through 119 No H-bonds generated for 'chain 'A' and resid 117 through 119' Processing helix chain 'A' and resid 128 through 163 removed outlier: 3.601A pdb=" N ILE A 132 " --> pdb=" O LEU A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 197 removed outlier: 4.066A pdb=" N ILE A 190 " --> pdb=" O LEU A 186 " (cutoff:3.500A) Proline residue: A 193 - end of helix Processing helix chain 'A' and resid 201 through 205 removed outlier: 4.619A pdb=" N SER A 205 " --> pdb=" O PRO A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 220 removed outlier: 3.961A pdb=" N ILE A 216 " --> pdb=" O GLU A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 239 Processing helix chain 'A' and resid 263 through 274 Processing helix chain 'A' and resid 275 through 284 removed outlier: 3.530A pdb=" N LEU A 279 " --> pdb=" O LYS A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 297 Processing helix chain 'A' and resid 299 through 305 Processing helix chain 'A' and resid 310 through 319 Processing helix chain 'A' and resid 324 through 340 removed outlier: 4.386A pdb=" N HIS A 329 " --> pdb=" O PHE A 325 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N GLN A 330 " --> pdb=" O LEU A 326 " (cutoff:3.500A) Proline residue: A 338 - end of helix Processing helix chain 'A' and resid 342 through 352 removed outlier: 3.910A pdb=" N VAL A 349 " --> pdb=" O ALA A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 366 Processing helix chain 'A' and resid 376 through 392 removed outlier: 3.698A pdb=" N LEU A 392 " --> pdb=" O LEU A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 412 removed outlier: 4.276A pdb=" N CYS A 403 " --> pdb=" O PRO A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 417 Processing helix chain 'A' and resid 418 through 438 removed outlier: 3.674A pdb=" N VAL A 436 " --> pdb=" O LYS A 432 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU A 437 " --> pdb=" O ASN A 433 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 443 removed outlier: 4.134A pdb=" N LEU A 443 " --> pdb=" O LYS A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 461 removed outlier: 3.766A pdb=" N PHE A 450 " --> pdb=" O ASN A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 481 Processing helix chain 'A' and resid 488 through 503 Processing helix chain 'A' and resid 504 through 506 No H-bonds generated for 'chain 'A' and resid 504 through 506' Processing helix chain 'A' and resid 531 through 559 removed outlier: 3.762A pdb=" N GLN A 539 " --> pdb=" O ASN A 535 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N PHE A 548 " --> pdb=" O TYR A 544 " (cutoff:3.500A) Processing helix chain 'A' and resid 592 through 597 Processing helix chain 'A' and resid 716 through 727 Processing helix chain 'A' and resid 747 through 757 removed outlier: 3.719A pdb=" N PHE A 757 " --> pdb=" O TRP A 753 " (cutoff:3.500A) Processing helix chain 'A' and resid 808 through 818 Processing helix chain 'A' and resid 818 through 839 removed outlier: 3.825A pdb=" N GLN A 822 " --> pdb=" O ASP A 818 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N ASP A 839 " --> pdb=" O HIS A 835 " (cutoff:3.500A) Processing helix chain 'A' and resid 882 through 886 removed outlier: 3.727A pdb=" N SER A 886 " --> pdb=" O ARG A 883 " (cutoff:3.500A) Processing helix chain 'A' and resid 920 through 922 No H-bonds generated for 'chain 'A' and resid 920 through 922' Processing helix chain 'A' and resid 939 through 961 removed outlier: 3.535A pdb=" N THR A 960 " --> pdb=" O HIS A 956 " (cutoff:3.500A) Processing helix chain 'A' and resid 961 through 967 Processing helix chain 'A' and resid 968 through 970 No H-bonds generated for 'chain 'A' and resid 968 through 970' Processing helix chain 'A' and resid 974 through 986 removed outlier: 3.829A pdb=" N GLY A 984 " --> pdb=" O LYS A 980 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LEU A 985 " --> pdb=" O ARG A 981 " (cutoff:3.500A) Processing helix chain 'A' and resid 999 through 1016 removed outlier: 3.811A pdb=" N ASP A1009 " --> pdb=" O GLU A1005 " (cutoff:3.500A) Processing helix chain 'A' and resid 1019 through 1028 removed outlier: 3.969A pdb=" N ILE A1026 " --> pdb=" O GLU A1022 " (cutoff:3.500A) Processing helix chain 'A' and resid 1030 through 1034 removed outlier: 4.376A pdb=" N ASN A1034 " --> pdb=" O ALA A1031 " (cutoff:3.500A) Processing helix chain 'A' and resid 1035 through 1054 removed outlier: 3.924A pdb=" N ALA A1041 " --> pdb=" O GLN A1037 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ASN A1042 " --> pdb=" O GLY A1038 " (cutoff:3.500A) Processing helix chain 'A' and resid 1065 through 1070 Processing helix chain 'A' and resid 1090 through 1096 Processing helix chain 'A' and resid 1102 through 1119 removed outlier: 3.778A pdb=" N LYS A1119 " --> pdb=" O LYS A1115 " (cutoff:3.500A) Processing helix chain 'A' and resid 1139 through 1144 Processing helix chain 'A' and resid 1213 through 1232 removed outlier: 4.256A pdb=" N ALA A1217 " --> pdb=" O ASP A1213 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LYS A1232 " --> pdb=" O LEU A1228 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 11 through 14 Processing sheet with id=AA2, first strand: chain 'A' and resid 17 through 18 removed outlier: 6.617A pdb=" N LYS A 248 " --> pdb=" O HIS A 566 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N GLY A 568 " --> pdb=" O LYS A 248 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N THR A 250 " --> pdb=" O GLY A 568 " (cutoff:3.500A) removed outlier: 8.121A pdb=" N ILE A 570 " --> pdb=" O THR A 250 " (cutoff:3.500A) removed outlier: 16.277A pdb=" N HIS A 566 " --> pdb=" O SER A 613 " (cutoff:3.500A) removed outlier: 13.920A pdb=" N SER A 613 " --> pdb=" O HIS A 566 " (cutoff:3.500A) removed outlier: 9.122A pdb=" N GLY A 568 " --> pdb=" O VAL A 611 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N VAL A 611 " --> pdb=" O GLY A 568 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 17 through 18 removed outlier: 6.617A pdb=" N LYS A 248 " --> pdb=" O HIS A 566 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N GLY A 568 " --> pdb=" O LYS A 248 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N THR A 250 " --> pdb=" O GLY A 568 " (cutoff:3.500A) removed outlier: 8.121A pdb=" N ILE A 570 " --> pdb=" O THR A 250 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 113 through 115 Processing sheet with id=AA5, first strand: chain 'A' and resid 122 through 123 Processing sheet with id=AA6, first strand: chain 'A' and resid 866 through 867 removed outlier: 4.462A pdb=" N VAL A 859 " --> pdb=" O LEU A 867 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 866 through 867 removed outlier: 4.462A pdb=" N VAL A 859 " --> pdb=" O LEU A 867 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N GLU A1063 " --> pdb=" O ILE A 847 " (cutoff:3.500A) removed outlier: 8.516A pdb=" N HIS A1159 " --> pdb=" O ALA A1058 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ILE A1060 " --> pdb=" O HIS A1159 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N ILE A1161 " --> pdb=" O ILE A1060 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N LEU A1062 " --> pdb=" O ILE A1161 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 891 through 896 removed outlier: 5.702A pdb=" N GLN A 892 " --> pdb=" O LYS A 874 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N LYS A 874 " --> pdb=" O GLN A 892 " (cutoff:3.500A) removed outlier: 8.797A pdb=" N GLU A 871 " --> pdb=" O LYS A 914 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N LEU A 916 " --> pdb=" O GLU A 871 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 877 through 878 Processing sheet with id=AB1, first strand: chain 'A' and resid 1120 through 1121 467 hydrogen bonds defined for protein. 1326 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 9 hydrogen bonds 18 hydrogen bond angles 0 basepair planarities 4 basepair parallelities 16 stacking parallelities Total time for adding SS restraints: 3.61 Time building geometry restraints manager: 2.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1531 1.31 - 1.44: 2613 1.44 - 1.56: 5277 1.56 - 1.68: 49 1.68 - 1.81: 35 Bond restraints: 9505 Sorted by residual: bond pdb=" C THR A 244 " pdb=" O THR A 244 " ideal model delta sigma weight residual 1.242 1.203 0.039 9.70e-03 1.06e+04 1.63e+01 bond pdb=" C TYR A 579 " pdb=" O TYR A 579 " ideal model delta sigma weight residual 1.234 1.187 0.047 1.28e-02 6.10e+03 1.35e+01 bond pdb=" N VAL A 593 " pdb=" CA VAL A 593 " ideal model delta sigma weight residual 1.461 1.500 -0.039 1.17e-02 7.31e+03 1.12e+01 bond pdb=" C PRO A 245 " pdb=" O PRO A 245 " ideal model delta sigma weight residual 1.235 1.197 0.038 1.30e-02 5.92e+03 8.64e+00 bond pdb=" CA GLY A 242 " pdb=" C GLY A 242 " ideal model delta sigma weight residual 1.512 1.488 0.024 8.70e-03 1.32e+04 7.66e+00 ... (remaining 9500 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.75: 12720 2.75 - 5.50: 169 5.50 - 8.25: 13 8.25 - 11.00: 3 11.00 - 13.74: 2 Bond angle restraints: 12907 Sorted by residual: angle pdb=" C THR A 244 " pdb=" CA THR A 244 " pdb=" CB THR A 244 " ideal model delta sigma weight residual 111.01 100.12 10.89 1.38e+00 5.25e-01 6.22e+01 angle pdb=" C ASP A 601 " pdb=" CA ASP A 601 " pdb=" CB ASP A 601 " ideal model delta sigma weight residual 114.40 105.14 9.26 1.25e+00 6.40e-01 5.49e+01 angle pdb=" C ASN A 240 " pdb=" CA ASN A 240 " pdb=" CB ASN A 240 " ideal model delta sigma weight residual 112.44 100.27 12.17 1.72e+00 3.38e-01 5.01e+01 angle pdb=" N PRO A 245 " pdb=" CA PRO A 245 " pdb=" CB PRO A 245 " ideal model delta sigma weight residual 103.25 96.75 6.50 1.05e+00 9.07e-01 3.83e+01 angle pdb=" C GLY A 241 " pdb=" N GLY A 242 " pdb=" CA GLY A 242 " ideal model delta sigma weight residual 121.65 117.70 3.95 6.80e-01 2.16e+00 3.38e+01 ... (remaining 12902 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.56: 5577 30.56 - 61.12: 219 61.12 - 91.67: 30 91.67 - 122.23: 1 122.23 - 152.79: 2 Dihedral angle restraints: 5829 sinusoidal: 2664 harmonic: 3165 Sorted by residual: dihedral pdb=" O4' U B 14 " pdb=" C1' U B 14 " pdb=" N1 U B 14 " pdb=" C2 U B 14 " ideal model delta sinusoidal sigma weight residual 200.00 47.21 152.79 1 1.50e+01 4.44e-03 8.06e+01 dihedral pdb=" O4' C B 22 " pdb=" C1' C B 22 " pdb=" N1 C B 22 " pdb=" C2 C B 22 " ideal model delta sinusoidal sigma weight residual -128.00 6.39 -134.39 1 1.70e+01 3.46e-03 5.65e+01 dihedral pdb=" CA PHE A 325 " pdb=" C PHE A 325 " pdb=" N LEU A 326 " pdb=" CA LEU A 326 " ideal model delta harmonic sigma weight residual -180.00 -149.63 -30.37 0 5.00e+00 4.00e-02 3.69e+01 ... (remaining 5826 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 1138 0.059 - 0.119: 257 0.119 - 0.178: 26 0.178 - 0.237: 9 0.237 - 0.296: 3 Chirality restraints: 1433 Sorted by residual: chirality pdb=" CA LYS A 874 " pdb=" N LYS A 874 " pdb=" C LYS A 874 " pdb=" CB LYS A 874 " both_signs ideal model delta sigma weight residual False 2.51 2.81 -0.30 2.00e-01 2.50e+01 2.19e+00 chirality pdb=" CA THR A 244 " pdb=" N THR A 244 " pdb=" C THR A 244 " pdb=" CB THR A 244 " both_signs ideal model delta sigma weight residual False 2.53 2.78 -0.25 2.00e-01 2.50e+01 1.59e+00 chirality pdb=" P U B 33 " pdb=" OP1 U B 33 " pdb=" OP2 U B 33 " pdb=" O5' U B 33 " both_signs ideal model delta sigma weight residual True 2.41 -2.65 -0.24 2.00e-01 2.50e+01 1.48e+00 ... (remaining 1430 not shown) Planarity restraints: 1570 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU A 337 " -0.084 5.00e-02 4.00e+02 1.25e-01 2.50e+01 pdb=" N PRO A 338 " 0.216 5.00e-02 4.00e+02 pdb=" CA PRO A 338 " -0.064 5.00e-02 4.00e+02 pdb=" CD PRO A 338 " -0.068 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 325 " -0.026 2.00e-02 2.50e+03 1.84e-02 5.93e+00 pdb=" CG PHE A 325 " 0.040 2.00e-02 2.50e+03 pdb=" CD1 PHE A 325 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE A 325 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE A 325 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE A 325 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE A 325 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 596 " 0.010 2.00e-02 2.50e+03 2.09e-02 4.38e+00 pdb=" C ILE A 596 " -0.036 2.00e-02 2.50e+03 pdb=" O ILE A 596 " 0.013 2.00e-02 2.50e+03 pdb=" N LEU A 597 " 0.012 2.00e-02 2.50e+03 ... (remaining 1567 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 133 2.66 - 3.22: 8728 3.22 - 3.78: 13891 3.78 - 4.34: 19659 4.34 - 4.90: 32565 Nonbonded interactions: 74976 Sorted by model distance: nonbonded pdb=" OH TYR A 135 " pdb=" OE2 GLU A 189 " model vdw 2.098 3.040 nonbonded pdb=" OH TYR A 393 " pdb=" OD1 ASP A 426 " model vdw 2.128 3.040 nonbonded pdb=" CD1 ILE A 51 " pdb=" CG2 THR A 775 " model vdw 2.201 3.880 nonbonded pdb=" O ILE A 986 " pdb=" OH TYR A 995 " model vdw 2.219 3.040 nonbonded pdb=" OE2 GLU A 841 " pdb=" NH1 ARG A 863 " model vdw 2.225 3.120 ... (remaining 74971 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.900 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: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 26.320 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 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 : 0.009 0.061 9505 Z= 0.559 Angle : 0.842 13.744 12907 Z= 0.502 Chirality : 0.052 0.296 1433 Planarity : 0.005 0.125 1570 Dihedral : 16.096 152.791 3783 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.05 % Favored : 95.86 % Rotamer: Outliers : 1.14 % Allowed : 0.83 % Favored : 98.03 % Cbeta Deviations : 0.29 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.25), residues: 1062 helix: 0.32 (0.21), residues: 545 sheet: -1.42 (0.43), residues: 136 loop : -1.12 (0.31), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 78 HIS 0.007 0.002 HIS A 798 PHE 0.040 0.003 PHE A 325 TYR 0.029 0.002 TYR A 579 ARG 0.011 0.001 ARG A 883 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 37 time to evaluate : 1.138 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 1 residues processed: 47 average time/residue: 0.3169 time to fit residues: 20.3389 Evaluate side-chains 27 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 26 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 92 optimal weight: 0.6980 chunk 82 optimal weight: 0.6980 chunk 45 optimal weight: 8.9990 chunk 28 optimal weight: 4.9990 chunk 55 optimal weight: 3.9990 chunk 44 optimal weight: 0.9980 chunk 85 optimal weight: 0.8980 chunk 33 optimal weight: 4.9990 chunk 51 optimal weight: 1.9990 chunk 63 optimal weight: 0.4980 chunk 98 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 175 ASN A 812 GLN A1141 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.080945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.062489 restraints weight = 24395.409| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 3.10 r_work: 0.2920 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.1196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9505 Z= 0.183 Angle : 0.536 11.742 12907 Z= 0.285 Chirality : 0.039 0.172 1433 Planarity : 0.004 0.080 1570 Dihedral : 12.861 152.107 1554 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 0.21 % Allowed : 5.60 % Favored : 94.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.26), residues: 1062 helix: 1.13 (0.22), residues: 555 sheet: -1.46 (0.42), residues: 139 loop : -0.90 (0.32), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 480 HIS 0.003 0.001 HIS A 587 PHE 0.033 0.001 PHE A 325 TYR 0.010 0.001 TYR A 157 ARG 0.005 0.001 ARG A 896 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 32 time to evaluate : 0.997 Fit side-chains revert: symmetry clash REVERT: A 1151 LYS cc_start: 0.8859 (mtpt) cc_final: 0.8544 (ttmt) outliers start: 2 outliers final: 1 residues processed: 34 average time/residue: 0.2294 time to fit residues: 11.9401 Evaluate side-chains 25 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 24 time to evaluate : 1.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 59 optimal weight: 0.7980 chunk 103 optimal weight: 0.9990 chunk 54 optimal weight: 2.9990 chunk 75 optimal weight: 0.8980 chunk 21 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 92 optimal weight: 1.9990 chunk 102 optimal weight: 0.9980 chunk 0 optimal weight: 5.9990 chunk 10 optimal weight: 5.9990 chunk 47 optimal weight: 8.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1118 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.079827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.060909 restraints weight = 24991.736| |-----------------------------------------------------------------------------| r_work (start): 0.3058 rms_B_bonded: 3.15 r_work: 0.2892 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.1549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9505 Z= 0.220 Angle : 0.493 11.642 12907 Z= 0.259 Chirality : 0.038 0.158 1433 Planarity : 0.004 0.062 1570 Dihedral : 12.732 149.029 1554 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 0.52 % Allowed : 6.95 % Favored : 92.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.26), residues: 1062 helix: 1.57 (0.22), residues: 555 sheet: -1.39 (0.42), residues: 140 loop : -0.72 (0.32), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 480 HIS 0.003 0.001 HIS A 798 PHE 0.026 0.001 PHE A 325 TYR 0.011 0.001 TYR A 579 ARG 0.004 0.000 ARG A 896 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 24 time to evaluate : 1.027 Fit side-chains revert: symmetry clash REVERT: A 386 GLU cc_start: 0.8347 (OUTLIER) cc_final: 0.7401 (mp0) outliers start: 5 outliers final: 2 residues processed: 29 average time/residue: 0.2548 time to fit residues: 11.1617 Evaluate side-chains 24 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 21 time to evaluate : 1.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 386 GLU Chi-restraints excluded: chain A residue 871 GLU Chi-restraints excluded: chain A residue 906 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 93 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 36 optimal weight: 5.9990 chunk 55 optimal weight: 7.9990 chunk 89 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 102 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 108 optimal weight: 4.9990 chunk 49 optimal weight: 5.9990 chunk 57 optimal weight: 1.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1118 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.078013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.059229 restraints weight = 24986.633| |-----------------------------------------------------------------------------| r_work (start): 0.3017 rms_B_bonded: 3.17 r_work: 0.2851 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 moved from start: 0.1676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.032 9505 Z= 0.367 Angle : 0.562 13.754 12907 Z= 0.291 Chirality : 0.041 0.172 1433 Planarity : 0.004 0.054 1570 Dihedral : 12.715 148.915 1553 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.14 % Allowed : 7.78 % Favored : 91.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.26), residues: 1062 helix: 1.63 (0.22), residues: 555 sheet: -1.34 (0.42), residues: 147 loop : -0.72 (0.33), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 78 HIS 0.005 0.001 HIS A 798 PHE 0.042 0.002 PHE A 325 TYR 0.013 0.001 TYR A 544 ARG 0.003 0.000 ARG A 883 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 22 time to evaluate : 1.246 Fit side-chains revert: symmetry clash outliers start: 11 outliers final: 5 residues processed: 31 average time/residue: 0.1996 time to fit residues: 10.3752 Evaluate side-chains 27 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 22 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 PHE Chi-restraints excluded: chain A residue 386 GLU Chi-restraints excluded: chain A residue 771 VAL Chi-restraints excluded: chain A residue 906 VAL Chi-restraints excluded: chain A residue 1220 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 108 optimal weight: 3.9990 chunk 46 optimal weight: 0.7980 chunk 97 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 80 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 98 optimal weight: 0.8980 chunk 63 optimal weight: 0.9980 chunk 23 optimal weight: 3.9990 chunk 81 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1118 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.077302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.058856 restraints weight = 24517.196| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 3.10 r_work: 0.2885 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.1938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 9505 Z= 0.239 Angle : 0.496 12.679 12907 Z= 0.257 Chirality : 0.038 0.160 1433 Planarity : 0.003 0.049 1570 Dihedral : 12.638 147.927 1553 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 0.62 % Allowed : 8.92 % Favored : 90.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.27), residues: 1062 helix: 1.83 (0.22), residues: 557 sheet: -1.25 (0.44), residues: 137 loop : -0.67 (0.33), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 480 HIS 0.003 0.001 HIS A 798 PHE 0.039 0.001 PHE A 325 TYR 0.010 0.001 TYR A 544 ARG 0.002 0.000 ARG A 883 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 24 time to evaluate : 1.013 Fit side-chains revert: symmetry clash REVERT: A 402 MET cc_start: 0.8887 (ttp) cc_final: 0.8619 (ttp) outliers start: 6 outliers final: 4 residues processed: 29 average time/residue: 0.2105 time to fit residues: 9.9470 Evaluate side-chains 25 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 21 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 PHE Chi-restraints excluded: chain A residue 386 GLU Chi-restraints excluded: chain A residue 771 VAL Chi-restraints excluded: chain A residue 871 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 48 optimal weight: 6.9990 chunk 5 optimal weight: 5.9990 chunk 90 optimal weight: 2.9990 chunk 2 optimal weight: 5.9990 chunk 74 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 79 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 chunk 85 optimal weight: 4.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 887 HIS A 919 GLN A1118 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.074526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.055637 restraints weight = 24676.969| |-----------------------------------------------------------------------------| r_work (start): 0.2937 rms_B_bonded: 3.18 r_work: 0.2775 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.1943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.050 9505 Z= 0.579 Angle : 0.673 17.286 12907 Z= 0.344 Chirality : 0.045 0.177 1433 Planarity : 0.004 0.050 1570 Dihedral : 12.725 149.002 1553 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 0.93 % Allowed : 9.13 % Favored : 89.94 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.26), residues: 1062 helix: 1.58 (0.22), residues: 557 sheet: -1.44 (0.42), residues: 147 loop : -0.86 (0.32), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 78 HIS 0.006 0.001 HIS A 798 PHE 0.043 0.002 PHE A 325 TYR 0.017 0.002 TYR A 544 ARG 0.003 0.000 ARG A 103 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 21 time to evaluate : 1.517 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 7 residues processed: 29 average time/residue: 0.2516 time to fit residues: 11.8031 Evaluate side-chains 26 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 19 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 PHE Chi-restraints excluded: chain A residue 386 GLU Chi-restraints excluded: chain A residue 771 VAL Chi-restraints excluded: chain A residue 871 GLU Chi-restraints excluded: chain A residue 906 VAL Chi-restraints excluded: chain A residue 1159 HIS Chi-restraints excluded: chain A residue 1220 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 31 optimal weight: 0.9990 chunk 50 optimal weight: 0.8980 chunk 29 optimal weight: 0.8980 chunk 97 optimal weight: 0.0050 chunk 79 optimal weight: 0.8980 chunk 20 optimal weight: 0.8980 chunk 83 optimal weight: 0.8980 chunk 1 optimal weight: 0.7980 chunk 65 optimal weight: 3.9990 chunk 38 optimal weight: 0.7980 chunk 41 optimal weight: 0.9990 overall best weight: 0.6794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.078235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.059567 restraints weight = 24781.195| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 3.22 r_work: 0.2894 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.2163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9505 Z= 0.154 Angle : 0.473 12.037 12907 Z= 0.245 Chirality : 0.038 0.154 1433 Planarity : 0.003 0.045 1570 Dihedral : 12.646 147.269 1553 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 0.62 % Allowed : 9.75 % Favored : 89.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.27), residues: 1062 helix: 1.91 (0.22), residues: 557 sheet: -1.24 (0.45), residues: 137 loop : -0.64 (0.33), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 480 HIS 0.002 0.000 HIS A 798 PHE 0.041 0.001 PHE A 325 TYR 0.010 0.001 TYR A 579 ARG 0.003 0.000 ARG A 896 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 22 time to evaluate : 1.724 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 5 residues processed: 28 average time/residue: 0.2976 time to fit residues: 13.2074 Evaluate side-chains 24 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 19 time to evaluate : 1.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 PHE Chi-restraints excluded: chain A residue 386 GLU Chi-restraints excluded: chain A residue 580 LEU Chi-restraints excluded: chain A residue 771 VAL Chi-restraints excluded: chain A residue 906 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 57 optimal weight: 3.9990 chunk 78 optimal weight: 4.9990 chunk 5 optimal weight: 5.9990 chunk 100 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 chunk 49 optimal weight: 4.9990 chunk 31 optimal weight: 3.9990 chunk 94 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.075995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.057190 restraints weight = 25135.165| |-----------------------------------------------------------------------------| r_work (start): 0.2992 rms_B_bonded: 3.20 r_work: 0.2828 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.2104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.036 9505 Z= 0.392 Angle : 0.570 14.816 12907 Z= 0.292 Chirality : 0.041 0.166 1433 Planarity : 0.003 0.044 1570 Dihedral : 12.644 148.457 1553 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 0.83 % Allowed : 9.96 % Favored : 89.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.27), residues: 1062 helix: 1.83 (0.22), residues: 557 sheet: -1.35 (0.43), residues: 147 loop : -0.68 (0.33), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 78 HIS 0.004 0.001 HIS A 798 PHE 0.041 0.002 PHE A 325 TYR 0.014 0.001 TYR A 544 ARG 0.003 0.000 ARG A1016 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 19 time to evaluate : 1.020 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 4 residues processed: 26 average time/residue: 0.1804 time to fit residues: 8.2307 Evaluate side-chains 23 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 19 time to evaluate : 1.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 PHE Chi-restraints excluded: chain A residue 386 GLU Chi-restraints excluded: chain A residue 771 VAL Chi-restraints excluded: chain A residue 906 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 25 optimal weight: 2.9990 chunk 46 optimal weight: 0.1980 chunk 1 optimal weight: 1.9990 chunk 45 optimal weight: 4.9990 chunk 105 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 97 optimal weight: 0.8980 chunk 52 optimal weight: 3.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.076973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.058133 restraints weight = 24612.646| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 3.22 r_work: 0.2851 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.2192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9505 Z= 0.279 Angle : 0.513 13.661 12907 Z= 0.264 Chirality : 0.039 0.162 1433 Planarity : 0.003 0.043 1570 Dihedral : 12.610 147.995 1553 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 0.73 % Allowed : 10.27 % Favored : 89.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.27), residues: 1062 helix: 1.89 (0.22), residues: 557 sheet: -1.26 (0.43), residues: 140 loop : -0.73 (0.33), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 78 HIS 0.004 0.001 HIS A 798 PHE 0.040 0.001 PHE A 325 TYR 0.012 0.001 TYR A 544 ARG 0.003 0.000 ARG A1016 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 20 time to evaluate : 1.104 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 6 residues processed: 27 average time/residue: 0.1773 time to fit residues: 8.3957 Evaluate side-chains 26 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 20 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 PHE Chi-restraints excluded: chain A residue 386 GLU Chi-restraints excluded: chain A residue 771 VAL Chi-restraints excluded: chain A residue 906 VAL Chi-restraints excluded: chain A residue 969 ILE Chi-restraints excluded: chain A residue 1120 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 105 optimal weight: 0.9990 chunk 25 optimal weight: 0.7980 chunk 92 optimal weight: 0.5980 chunk 104 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 15 optimal weight: 6.9990 chunk 9 optimal weight: 0.7980 chunk 59 optimal weight: 3.9990 chunk 90 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 99 optimal weight: 0.5980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.078329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.059468 restraints weight = 24362.254| |-----------------------------------------------------------------------------| r_work (start): 0.3027 rms_B_bonded: 3.31 r_work: 0.2862 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.2403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9505 Z= 0.159 Angle : 0.452 10.731 12907 Z= 0.235 Chirality : 0.037 0.154 1433 Planarity : 0.003 0.043 1570 Dihedral : 12.559 146.859 1553 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 0.52 % Allowed : 10.58 % Favored : 88.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.27), residues: 1062 helix: 2.07 (0.22), residues: 558 sheet: -1.24 (0.45), residues: 137 loop : -0.59 (0.33), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 480 HIS 0.002 0.000 HIS A 798 PHE 0.036 0.001 PHE A 325 TYR 0.011 0.001 TYR A 579 ARG 0.003 0.000 ARG A1016 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 27 time to evaluate : 1.085 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 5 residues processed: 31 average time/residue: 0.1762 time to fit residues: 9.4443 Evaluate side-chains 27 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 22 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 PHE Chi-restraints excluded: chain A residue 386 GLU Chi-restraints excluded: chain A residue 771 VAL Chi-restraints excluded: chain A residue 906 VAL Chi-restraints excluded: chain A residue 969 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 74 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 41 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 chunk 32 optimal weight: 0.5980 chunk 5 optimal weight: 6.9990 chunk 68 optimal weight: 8.9990 chunk 92 optimal weight: 1.9990 chunk 86 optimal weight: 4.9990 chunk 54 optimal weight: 3.9990 chunk 106 optimal weight: 0.9980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.079556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.060628 restraints weight = 24748.190| |-----------------------------------------------------------------------------| r_work (start): 0.3048 rms_B_bonded: 3.22 r_work: 0.2885 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.2414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9505 Z= 0.200 Angle : 0.465 11.289 12907 Z= 0.241 Chirality : 0.038 0.154 1433 Planarity : 0.003 0.043 1570 Dihedral : 12.497 147.213 1553 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 0.73 % Allowed : 10.68 % Favored : 88.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.27), residues: 1062 helix: 2.09 (0.22), residues: 557 sheet: -1.20 (0.44), residues: 140 loop : -0.63 (0.33), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 78 HIS 0.003 0.001 HIS A 75 PHE 0.035 0.001 PHE A 325 TYR 0.010 0.001 TYR A 544 ARG 0.003 0.000 ARG A1016 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3983.00 seconds wall clock time: 70 minutes 15.53 seconds (4215.53 seconds total)