Starting phenix.real_space_refine on Thu Jul 2 06:28:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8huj_35041/07_2026/8huj_35041.cif Found real_map, /net/cci-nas-00/data/ceres_data/8huj_35041/07_2026/8huj_35041.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8huj_35041/07_2026/8huj_35041.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8huj_35041/07_2026/8huj_35041.cif" model { file = "/net/cci-nas-00/data/ceres_data/8huj_35041/07_2026/8huj_35041.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8huj_35041/07_2026/8huj_35041.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8huj_35041/07_2026/8huj_35041.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8huj_35041/07_2026/8huj_35041.map" } resolution = 3.76 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= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 99 5.49 5 Mg 3 5.21 5 S 35 5.16 5 C 4108 2.51 5 N 1261 2.21 5 O 1637 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7143 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3067 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 3067 Classifications: {'peptide': 383} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 372} Chain: "B" Number of atoms: 1951 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1951 Classifications: {'peptide': 238} Link IDs: {'PTRANS': 5, 'TRANS': 232} Chain: "C" Number of atoms: 2121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 2121 Classifications: {'RNA': 99} Modifications used: {'rna2p_pur': 11, 'rna2p_pyr': 3, 'rna3p_pur': 44, 'rna3p_pyr': 41} Link IDs: {'rna2p': 14, 'rna3p': 84} Chain breaks: 2 Chain: "C" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' MG': 3} Classifications: {'undetermined': 3, 'water': 1} Link IDs: {None: 3} Time building chain proxies: 1.23, per 1000 atoms: 0.17 Number of scatterers: 7143 At special positions: 0 Unit cell: (100.98, 94.095, 119.34, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 35 16.00 P 99 15.00 Mg 3 11.99 O 1637 8.00 N 1261 7.00 C 4108 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: 0.57 Conformation dependent library (CDL) restraints added in 315.6 milliseconds 1234 Ramachandran restraints generated. 617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1186 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 3 sheets defined 65.1% alpha, 6.9% beta 37 base pairs and 55 stacking pairs defined. Time for finding SS restraints: 0.87 Creating SS restraints... Processing helix chain 'A' and resid 34 through 38 removed outlier: 4.101A pdb=" N ASN A 38 " --> pdb=" O ASP A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 40 through 51 Processing helix chain 'A' and resid 56 through 62 Processing helix chain 'A' and resid 63 through 69 removed outlier: 3.564A pdb=" N GLY A 69 " --> pdb=" O PRO A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 94 removed outlier: 4.207A pdb=" N PHE A 86 " --> pdb=" O LYS A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 123 Processing helix chain 'A' and resid 139 through 150 Processing helix chain 'A' and resid 158 through 167 Processing helix chain 'A' and resid 183 through 191 Processing helix chain 'A' and resid 192 through 203 Processing helix chain 'A' and resid 217 through 228 removed outlier: 3.585A pdb=" N LYS A 225 " --> pdb=" O LEU A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 246 Processing helix chain 'A' and resid 257 through 269 removed outlier: 4.416A pdb=" N ASP A 261 " --> pdb=" O GLU A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 295 removed outlier: 3.570A pdb=" N ASP A 286 " --> pdb=" O ARG A 282 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ARG A 295 " --> pdb=" O LYS A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 321 Processing helix chain 'A' and resid 329 through 336 Processing helix chain 'A' and resid 354 through 361 removed outlier: 3.926A pdb=" N HIS A 358 " --> pdb=" O GLU A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 365 removed outlier: 3.555A pdb=" N ARG A 365 " --> pdb=" O ARG A 362 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 362 through 365' Processing helix chain 'A' and resid 377 through 379 No H-bonds generated for 'chain 'A' and resid 377 through 379' Processing helix chain 'A' and resid 380 through 391 Processing helix chain 'A' and resid 401 through 406 removed outlier: 4.310A pdb=" N LEU A 405 " --> pdb=" O ASN A 401 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 771 Processing helix chain 'B' and resid 775 through 785 removed outlier: 3.714A pdb=" N LEU B 779 " --> pdb=" O MET B 775 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LYS B 781 " --> pdb=" O GLN B 777 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N GLN B 782 " --> pdb=" O GLN B 778 " (cutoff:3.500A) Processing helix chain 'B' and resid 790 through 808 Processing helix chain 'B' and resid 811 through 822 removed outlier: 3.574A pdb=" N LEU B 822 " --> pdb=" O MET B 818 " (cutoff:3.500A) Processing helix chain 'B' and resid 838 through 852 Processing helix chain 'B' and resid 853 through 871 removed outlier: 3.807A pdb=" N ASP B 858 " --> pdb=" O ASP B 854 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N GLU B 859 " --> pdb=" O LYS B 855 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS B 866 " --> pdb=" O GLU B 862 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N GLU B 867 " --> pdb=" O LYS B 863 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N MET B 868 " --> pdb=" O LYS B 864 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ASP B 869 " --> pdb=" O GLN B 865 " (cutoff:3.500A) Processing helix chain 'B' and resid 873 through 908 removed outlier: 3.609A pdb=" N LEU B 908 " --> pdb=" O GLU B 904 " (cutoff:3.500A) Processing helix chain 'B' and resid 912 through 926 removed outlier: 3.591A pdb=" N MET B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N VAL B 921 " --> pdb=" O HIS B 917 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LYS B 922 " --> pdb=" O ASP B 918 " (cutoff:3.500A) Processing helix chain 'B' and resid 928 through 947 removed outlier: 5.967A pdb=" N LYS B 944 " --> pdb=" O THR B 940 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N ASP B 945 " --> pdb=" O THR B 941 " (cutoff:3.500A) Processing helix chain 'B' and resid 948 through 950 No H-bonds generated for 'chain 'B' and resid 948 through 950' Processing helix chain 'B' and resid 951 through 969 removed outlier: 3.570A pdb=" N PHE B 959 " --> pdb=" O MET B 955 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ASN B 960 " --> pdb=" O ASP B 956 " (cutoff:3.500A) Processing helix chain 'B' and resid 972 through 988 Processing sheet with id=AA1, first strand: chain 'A' and resid 131 through 133 removed outlier: 6.462A pdb=" N HIS A 132 " --> pdb=" O VAL A 156 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N LEU A 104 " --> pdb=" O VAL A 180 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N ASP A 182 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N LEU A 106 " --> pdb=" O ASP A 182 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N PHE A 179 " --> pdb=" O VAL A 210 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N LEU A 212 " --> pdb=" O PHE A 179 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N LEU A 181 " --> pdb=" O LEU A 212 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N VAL A 72 " --> pdb=" O LEU A 211 " (cutoff:3.500A) removed outlier: 8.126A pdb=" N SER A 213 " --> pdb=" O VAL A 72 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N ALA A 74 " --> pdb=" O SER A 213 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 300 through 301 removed outlier: 6.490A pdb=" N SER A 300 " --> pdb=" O ILE A 327 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ALA A 275 " --> pdb=" O LEU A 326 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N THR A 328 " --> pdb=" O ALA A 275 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N ILE A 277 " --> pdb=" O THR A 328 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 827 through 828 269 hydrogen bonds defined for protein. 792 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 93 hydrogen bonds 146 hydrogen bond angles 0 basepair planarities 37 basepair parallelities 55 stacking parallelities Total time for adding SS restraints: 1.49 Time building geometry restraints manager: 0.79 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: 1756 1.33 - 1.46: 1895 1.46 - 1.58: 3551 1.58 - 1.70: 195 1.70 - 1.82: 60 Bond restraints: 7457 Sorted by residual: bond pdb=" N VAL B 835 " pdb=" CA VAL B 835 " ideal model delta sigma weight residual 1.455 1.493 -0.038 1.32e-02 5.74e+03 8.07e+00 bond pdb=" N THR B 829 " pdb=" CA THR B 829 " ideal model delta sigma weight residual 1.456 1.488 -0.032 1.23e-02 6.61e+03 6.87e+00 bond pdb=" N MET A 187 " pdb=" CA MET A 187 " ideal model delta sigma weight residual 1.459 1.491 -0.032 1.21e-02 6.83e+03 6.79e+00 bond pdb=" N LYS A 369 " pdb=" CA LYS A 369 " ideal model delta sigma weight residual 1.457 1.488 -0.031 1.19e-02 7.06e+03 6.73e+00 bond pdb=" N VAL A 180 " pdb=" CA VAL A 180 " ideal model delta sigma weight residual 1.458 1.488 -0.030 1.19e-02 7.06e+03 6.41e+00 ... (remaining 7452 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.97: 10096 1.97 - 3.93: 369 3.93 - 5.90: 52 5.90 - 7.87: 9 7.87 - 9.83: 1 Bond angle restraints: 10527 Sorted by residual: angle pdb=" CA PHE B 839 " pdb=" CB PHE B 839 " pdb=" CG PHE B 839 " ideal model delta sigma weight residual 113.80 119.00 -5.20 1.00e+00 1.00e+00 2.70e+01 angle pdb=" O3' U C 778 " pdb=" C3' U C 778 " pdb=" C2' U C 778 " ideal model delta sigma weight residual 113.70 121.48 -7.78 1.50e+00 4.44e-01 2.69e+01 angle pdb=" N ARG A 368 " pdb=" CA ARG A 368 " pdb=" C ARG A 368 " ideal model delta sigma weight residual 111.28 106.15 5.13 1.09e+00 8.42e-01 2.22e+01 angle pdb=" C4' U C 778 " pdb=" C3' U C 778 " pdb=" O3' U C 778 " ideal model delta sigma weight residual 113.00 119.98 -6.98 1.50e+00 4.44e-01 2.17e+01 angle pdb=" CA VAL B 835 " pdb=" C VAL B 835 " pdb=" O VAL B 835 " ideal model delta sigma weight residual 121.92 117.02 4.90 1.17e+00 7.31e-01 1.75e+01 ... (remaining 10522 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.18: 4037 31.18 - 62.37: 284 62.37 - 93.55: 26 93.55 - 124.74: 2 124.74 - 155.92: 1 Dihedral angle restraints: 4350 sinusoidal: 2531 harmonic: 1819 Sorted by residual: dihedral pdb=" C5' A C 687 " pdb=" C4' A C 687 " pdb=" C3' A C 687 " pdb=" O3' A C 687 " ideal model delta sinusoidal sigma weight residual 147.00 108.10 38.90 1 8.00e+00 1.56e-02 3.33e+01 dihedral pdb=" O4' A C 687 " pdb=" C4' A C 687 " pdb=" C3' A C 687 " pdb=" C2' A C 687 " ideal model delta sinusoidal sigma weight residual 24.00 -8.41 32.41 1 8.00e+00 1.56e-02 2.34e+01 dihedral pdb=" O4' A C 687 " pdb=" C1' A C 687 " pdb=" N9 A C 687 " pdb=" C4 A C 687 " ideal model delta sinusoidal sigma weight residual -106.00 -172.85 66.85 1 1.70e+01 3.46e-03 2.02e+01 ... (remaining 4347 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.101: 1157 0.101 - 0.202: 94 0.202 - 0.302: 22 0.302 - 0.403: 1 0.403 - 0.504: 1 Chirality restraints: 1275 Sorted by residual: chirality pdb=" C3' U C 778 " pdb=" C4' U C 778 " pdb=" O3' U C 778 " pdb=" C2' U C 778 " both_signs ideal model delta sigma weight residual False -2.48 -1.97 -0.50 2.00e-01 2.50e+01 6.35e+00 chirality pdb=" C3' A C 771 " pdb=" C4' A C 771 " pdb=" O3' A C 771 " pdb=" C2' A C 771 " both_signs ideal model delta sigma weight residual False -2.48 -2.78 0.31 2.00e-01 2.50e+01 2.33e+00 chirality pdb=" P G C 766 " pdb=" OP1 G C 766 " pdb=" OP2 G C 766 " pdb=" O5' G C 766 " both_signs ideal model delta sigma weight residual True 2.41 -2.69 -0.28 2.00e-01 2.50e+01 2.01e+00 ... (remaining 1272 not shown) Planarity restraints: 979 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR A 158 " -0.014 2.00e-02 2.50e+03 2.74e-02 7.48e+00 pdb=" C THR A 158 " 0.047 2.00e-02 2.50e+03 pdb=" O THR A 158 " -0.017 2.00e-02 2.50e+03 pdb=" N PRO A 159 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 64 " 0.032 5.00e-02 4.00e+02 4.84e-02 3.74e+00 pdb=" N PRO A 65 " -0.084 5.00e-02 4.00e+02 pdb=" CA PRO A 65 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 65 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 86 " 0.013 2.00e-02 2.50e+03 1.39e-02 3.37e+00 pdb=" CG PHE A 86 " -0.032 2.00e-02 2.50e+03 pdb=" CD1 PHE A 86 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE A 86 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 PHE A 86 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 86 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE A 86 " 0.002 2.00e-02 2.50e+03 ... (remaining 976 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 829 2.74 - 3.28: 7178 3.28 - 3.82: 13651 3.82 - 4.36: 15716 4.36 - 4.90: 22689 Nonbonded interactions: 60063 Sorted by model distance: nonbonded pdb=" O ASP A 348 " pdb=" NH1 ARG A 359 " model vdw 2.203 3.120 nonbonded pdb=" O CYS B 936 " pdb=" OG1 THR B 940 " model vdw 2.209 3.040 nonbonded pdb=" O ILE A 246 " pdb=" NE2 GLN A 248 " model vdw 2.244 3.120 nonbonded pdb=" O2 C C 746 " pdb=" N6 A C 750 " model vdw 2.249 3.120 nonbonded pdb=" N GLU A 379 " pdb=" OE1 GLU A 379 " model vdw 2.278 3.120 ... (remaining 60058 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.160 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: 8.270 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 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 0.038 7457 Z= 0.305 Angle : 0.828 9.832 10527 Z= 0.518 Chirality : 0.062 0.504 1275 Planarity : 0.004 0.048 979 Dihedral : 18.745 155.919 3164 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 13.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.51 % Allowed : 26.21 % Favored : 71.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.39 (0.34), residues: 617 helix: 0.44 (0.28), residues: 340 sheet: -0.76 (0.64), residues: 61 loop : -1.08 (0.43), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 190 TYR 0.009 0.002 TYR A 170 PHE 0.032 0.003 PHE A 86 TRP 0.010 0.002 TRP A 287 HIS 0.003 0.001 HIS A 303 Details of bonding type rmsd/Z covalent geometry : bond 0.00496 / 0.31 ( 7457) covalent geometry : angle 0.82765 / 0.52 (10527) hydrogen bonds : bond 0.17853 / 12.31 ( 362) hydrogen bonds : angle 6.49450 / 4.54 ( 938) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1234 Ramachandran restraints generated. 617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1234 Ramachandran restraints generated. 617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 62 time to evaluate : 0.275 Fit side-chains revert: symmetry clash REVERT: A 178 MET cc_start: 0.5083 (mtm) cc_final: 0.4264 (mtm) REVERT: A 228 MET cc_start: 0.4751 (tmm) cc_final: 0.4451 (tmm) REVERT: B 845 ASN cc_start: 0.8227 (OUTLIER) cc_final: 0.7996 (t0) REVERT: B 890 ILE cc_start: 0.8839 (mm) cc_final: 0.8495 (mm) outliers start: 14 outliers final: 5 residues processed: 75 average time/residue: 0.0910 time to fit residues: 9.0132 Evaluate side-chains 66 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 60 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 303 HIS Chi-restraints excluded: chain A residue 368 ARG Chi-restraints excluded: chain B residue 827 VAL Chi-restraints excluded: chain B residue 829 THR Chi-restraints excluded: chain B residue 845 ASN Chi-restraints excluded: chain B residue 893 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 49 optimal weight: 4.9990 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 6.9990 chunk 65 optimal weight: 10.0000 chunk 62 optimal weight: 10.0000 chunk 51 optimal weight: 6.9990 chunk 38 optimal weight: 8.9990 chunk 61 optimal weight: 10.0000 chunk 45 optimal weight: 4.9990 chunk 27 optimal weight: 5.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 195 GLN B 777 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.102892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.070121 restraints weight = 22107.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.072261 restraints weight = 10829.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.073549 restraints weight = 7526.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.074213 restraints weight = 6275.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.074455 restraints weight = 5759.084| |-----------------------------------------------------------------------------| r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.1439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 7457 Z= 0.208 Angle : 0.675 14.450 10527 Z= 0.338 Chirality : 0.039 0.215 1275 Planarity : 0.004 0.042 979 Dihedral : 14.970 164.386 1872 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 13.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 3.95 % Allowed : 26.39 % Favored : 69.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.35), residues: 617 helix: 0.73 (0.27), residues: 357 sheet: -0.91 (0.60), residues: 68 loop : -0.56 (0.50), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 362 TYR 0.017 0.002 TYR A 48 PHE 0.041 0.003 PHE B 977 TRP 0.012 0.002 TRP A 287 HIS 0.003 0.001 HIS B 927 Details of bonding type rmsd/Z covalent geometry : bond 0.00453 / 0.21 ( 7457) covalent geometry : angle 0.67474 / 0.34 (10527) hydrogen bonds : bond 0.05574 / 3.73 ( 362) hydrogen bonds : angle 4.40113 / 3.05 ( 938) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1234 Ramachandran restraints generated. 617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1234 Ramachandran restraints generated. 617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 66 time to evaluate : 0.230 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 178 MET cc_start: 0.5133 (mtm) cc_final: 0.4895 (mtm) REVERT: A 187 MET cc_start: 0.6417 (tmm) cc_final: 0.5993 (ppp) REVERT: A 228 MET cc_start: 0.4774 (tmm) cc_final: 0.4372 (tmm) REVERT: A 258 TRP cc_start: 0.8169 (m-10) cc_final: 0.7929 (m-10) REVERT: A 293 HIS cc_start: 0.7939 (t-90) cc_final: 0.7705 (t-90) REVERT: B 853 LYS cc_start: 0.7362 (OUTLIER) cc_final: 0.6830 (ptpt) REVERT: B 890 ILE cc_start: 0.8747 (mm) cc_final: 0.8432 (mm) REVERT: B 961 GLN cc_start: 0.8828 (OUTLIER) cc_final: 0.8569 (tp-100) outliers start: 22 outliers final: 13 residues processed: 84 average time/residue: 0.0797 time to fit residues: 9.0320 Evaluate side-chains 76 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 61 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain B residue 783 VAL Chi-restraints excluded: chain B residue 798 ILE Chi-restraints excluded: chain B residue 827 VAL Chi-restraints excluded: chain B residue 829 THR Chi-restraints excluded: chain B residue 834 THR Chi-restraints excluded: chain B residue 853 LYS Chi-restraints excluded: chain B residue 884 LEU Chi-restraints excluded: chain B residue 893 ARG Chi-restraints excluded: chain B residue 899 ILE Chi-restraints excluded: chain B residue 961 GLN Chi-restraints excluded: chain B residue 975 ILE Chi-restraints excluded: chain B residue 981 ASP Chi-restraints excluded: chain B residue 982 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 1 optimal weight: 7.9990 chunk 43 optimal weight: 2.9990 chunk 7 optimal weight: 40.0000 chunk 44 optimal weight: 0.9990 chunk 21 optimal weight: 0.0170 chunk 52 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 55 optimal weight: 4.9990 chunk 18 optimal weight: 40.0000 chunk 58 optimal weight: 0.9980 chunk 60 optimal weight: 0.9990 overall best weight: 1.0024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.105734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.073332 restraints weight = 22211.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.075833 restraints weight = 10749.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.076906 restraints weight = 7216.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.077997 restraints weight = 6124.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.077930 restraints weight = 5534.262| |-----------------------------------------------------------------------------| r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.2010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 7457 Z= 0.105 Angle : 0.537 14.145 10527 Z= 0.268 Chirality : 0.036 0.183 1275 Planarity : 0.003 0.040 979 Dihedral : 14.164 162.646 1864 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 3.95 % Allowed : 25.31 % Favored : 70.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.35), residues: 617 helix: 1.27 (0.28), residues: 363 sheet: -0.98 (0.60), residues: 67 loop : -0.90 (0.47), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 161 TYR 0.008 0.001 TYR B 815 PHE 0.031 0.002 PHE B 977 TRP 0.011 0.001 TRP A 287 HIS 0.003 0.001 HIS A 132 Details of bonding type rmsd/Z covalent geometry : bond 0.00218 / 0.11 ( 7457) covalent geometry : angle 0.53723 / 0.27 (10527) hydrogen bonds : bond 0.04066 / 2.78 ( 362) hydrogen bonds : angle 3.77703 / 2.62 ( 938) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1234 Ramachandran restraints generated. 617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1234 Ramachandran restraints generated. 617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 77 time to evaluate : 0.291 Fit side-chains REVERT: A 149 MET cc_start: 0.2062 (ptt) cc_final: 0.1019 (mtm) REVERT: A 161 ARG cc_start: 0.7579 (mtt-85) cc_final: 0.7375 (mtp85) REVERT: A 181 LEU cc_start: 0.7758 (OUTLIER) cc_final: 0.7304 (tp) REVERT: A 187 MET cc_start: 0.6513 (tmm) cc_final: 0.5992 (ppp) REVERT: A 193 LYS cc_start: 0.4947 (OUTLIER) cc_final: 0.4733 (tptt) REVERT: A 228 MET cc_start: 0.4781 (tmm) cc_final: 0.4578 (tmm) REVERT: A 229 ARG cc_start: 0.6148 (ptp-170) cc_final: 0.5424 (mmp-170) REVERT: A 293 HIS cc_start: 0.7819 (t-90) cc_final: 0.7584 (t-90) REVERT: A 366 PHE cc_start: 0.3284 (OUTLIER) cc_final: 0.3009 (p90) REVERT: B 853 LYS cc_start: 0.7225 (OUTLIER) cc_final: 0.6865 (ptpt) REVERT: B 855 LYS cc_start: 0.7247 (mmtm) cc_final: 0.6774 (mttm) REVERT: B 890 ILE cc_start: 0.8725 (mm) cc_final: 0.8412 (mm) REVERT: B 893 ARG cc_start: 0.8388 (OUTLIER) cc_final: 0.8140 (ttm-80) REVERT: B 986 ARG cc_start: 0.7411 (OUTLIER) cc_final: 0.6923 (ttt-90) outliers start: 22 outliers final: 7 residues processed: 94 average time/residue: 0.1029 time to fit residues: 12.5240 Evaluate side-chains 78 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 65 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 193 LYS Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 366 PHE Chi-restraints excluded: chain B residue 798 ILE Chi-restraints excluded: chain B residue 827 VAL Chi-restraints excluded: chain B residue 853 LYS Chi-restraints excluded: chain B residue 893 ARG Chi-restraints excluded: chain B residue 899 ILE Chi-restraints excluded: chain B residue 918 ASP Chi-restraints excluded: chain B residue 936 CYS Chi-restraints excluded: chain B residue 986 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 38 optimal weight: 7.9990 chunk 17 optimal weight: 5.9990 chunk 37 optimal weight: 9.9990 chunk 68 optimal weight: 20.0000 chunk 51 optimal weight: 20.0000 chunk 49 optimal weight: 20.0000 chunk 3 optimal weight: 6.9990 chunk 36 optimal weight: 10.0000 chunk 66 optimal weight: 10.0000 chunk 4 optimal weight: 10.0000 chunk 65 optimal weight: 10.0000 overall best weight: 8.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 960 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.100600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.067317 restraints weight = 22089.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.069403 restraints weight = 10780.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 69)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.070715 restraints weight = 7428.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.071354 restraints weight = 6154.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.071542 restraints weight = 5639.351| |-----------------------------------------------------------------------------| r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.2237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.041 7457 Z= 0.303 Angle : 0.744 18.137 10527 Z= 0.370 Chirality : 0.042 0.250 1275 Planarity : 0.005 0.038 979 Dihedral : 14.733 162.641 1863 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 14.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 6.64 % Allowed : 24.96 % Favored : 68.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.10 (0.34), residues: 617 helix: 0.81 (0.27), residues: 358 sheet: -1.05 (0.61), residues: 67 loop : -0.74 (0.50), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 362 TYR 0.022 0.003 TYR A 48 PHE 0.037 0.003 PHE B 977 TRP 0.021 0.003 TRP A 27 HIS 0.004 0.001 HIS A 303 Details of bonding type rmsd/Z covalent geometry : bond 0.00652 / 0.30 ( 7457) covalent geometry : angle 0.74399 / 0.37 (10527) hydrogen bonds : bond 0.06286 / 4.21 ( 362) hydrogen bonds : angle 4.29263 / 3.00 ( 938) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1234 Ramachandran restraints generated. 617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1234 Ramachandran restraints generated. 617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 62 time to evaluate : 0.245 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 178 MET cc_start: 0.5336 (mtm) cc_final: 0.4435 (mtm) REVERT: A 181 LEU cc_start: 0.7771 (OUTLIER) cc_final: 0.7346 (tp) REVERT: A 187 MET cc_start: 0.6456 (tmm) cc_final: 0.5956 (ppp) REVERT: A 193 LYS cc_start: 0.4827 (OUTLIER) cc_final: 0.4616 (tptt) REVERT: A 228 MET cc_start: 0.4749 (tmm) cc_final: 0.4395 (tmm) REVERT: A 229 ARG cc_start: 0.6114 (ptp-170) cc_final: 0.5539 (mmp-170) REVERT: B 791 GLU cc_start: 0.8365 (OUTLIER) cc_final: 0.8105 (tt0) REVERT: B 855 LYS cc_start: 0.7208 (mmtm) cc_final: 0.6862 (mttm) REVERT: B 986 ARG cc_start: 0.7376 (OUTLIER) cc_final: 0.6946 (ttt-90) outliers start: 37 outliers final: 19 residues processed: 90 average time/residue: 0.0886 time to fit residues: 10.5337 Evaluate side-chains 82 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 59 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 TRP Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 193 LYS Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain B residue 783 VAL Chi-restraints excluded: chain B residue 791 GLU Chi-restraints excluded: chain B residue 798 ILE Chi-restraints excluded: chain B residue 827 VAL Chi-restraints excluded: chain B residue 834 THR Chi-restraints excluded: chain B residue 869 ASP Chi-restraints excluded: chain B residue 884 LEU Chi-restraints excluded: chain B residue 889 ASP Chi-restraints excluded: chain B residue 899 ILE Chi-restraints excluded: chain B residue 918 ASP Chi-restraints excluded: chain B residue 936 CYS Chi-restraints excluded: chain B residue 962 MET Chi-restraints excluded: chain B residue 982 VAL Chi-restraints excluded: chain B residue 986 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 42 optimal weight: 1.9990 chunk 51 optimal weight: 5.9990 chunk 16 optimal weight: 30.0000 chunk 67 optimal weight: 30.0000 chunk 45 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 36 optimal weight: 10.0000 chunk 46 optimal weight: 4.9990 chunk 1 optimal weight: 5.9990 chunk 3 optimal weight: 0.2980 overall best weight: 1.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 248 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.104917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.072401 restraints weight = 22265.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.074771 restraints weight = 10658.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.075881 restraints weight = 7318.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.076540 restraints weight = 6109.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.076654 restraints weight = 5679.643| |-----------------------------------------------------------------------------| r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.2406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 7457 Z= 0.111 Angle : 0.552 16.161 10527 Z= 0.275 Chirality : 0.036 0.187 1275 Planarity : 0.003 0.040 979 Dihedral : 13.876 162.161 1859 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 4.13 % Allowed : 28.73 % Favored : 67.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.35), residues: 617 helix: 1.35 (0.28), residues: 361 sheet: -0.80 (0.66), residues: 60 loop : -0.97 (0.46), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 255 TYR 0.006 0.001 TYR A 48 PHE 0.023 0.002 PHE B 977 TRP 0.022 0.003 TRP A 27 HIS 0.002 0.001 HIS A 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.11 ( 7457) covalent geometry : angle 0.55237 / 0.27 (10527) hydrogen bonds : bond 0.04195 / 2.87 ( 362) hydrogen bonds : angle 3.69699 / 2.55 ( 938) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1234 Ramachandran restraints generated. 617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1234 Ramachandran restraints generated. 617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 68 time to evaluate : 0.221 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 149 MET cc_start: 0.1684 (ptt) cc_final: 0.0479 (mtm) REVERT: A 178 MET cc_start: 0.5271 (mtm) cc_final: 0.4872 (mtm) REVERT: A 181 LEU cc_start: 0.7752 (OUTLIER) cc_final: 0.7355 (tp) REVERT: A 228 MET cc_start: 0.4715 (tmm) cc_final: 0.4431 (tmm) REVERT: B 855 LYS cc_start: 0.7088 (mmtm) cc_final: 0.6658 (mttm) REVERT: B 977 PHE cc_start: 0.7851 (m-10) cc_final: 0.7612 (m-80) REVERT: B 986 ARG cc_start: 0.7435 (OUTLIER) cc_final: 0.6959 (ttt-90) outliers start: 23 outliers final: 14 residues processed: 85 average time/residue: 0.0872 time to fit residues: 9.9881 Evaluate side-chains 80 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 64 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain B residue 772 THR Chi-restraints excluded: chain B residue 798 ILE Chi-restraints excluded: chain B residue 827 VAL Chi-restraints excluded: chain B residue 899 ILE Chi-restraints excluded: chain B residue 918 ASP Chi-restraints excluded: chain B residue 936 CYS Chi-restraints excluded: chain B residue 962 MET Chi-restraints excluded: chain B residue 981 ASP Chi-restraints excluded: chain B residue 986 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 6 optimal weight: 6.9990 chunk 46 optimal weight: 0.8980 chunk 41 optimal weight: 7.9990 chunk 7 optimal weight: 30.0000 chunk 27 optimal weight: 8.9990 chunk 58 optimal weight: 0.9990 chunk 30 optimal weight: 0.7980 chunk 42 optimal weight: 8.9990 chunk 34 optimal weight: 8.9990 chunk 56 optimal weight: 10.0000 chunk 49 optimal weight: 20.0000 overall best weight: 3.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.102549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.069263 restraints weight = 21665.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.071502 restraints weight = 10083.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.072905 restraints weight = 6786.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.073633 restraints weight = 5566.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.073895 restraints weight = 5067.808| |-----------------------------------------------------------------------------| r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.2510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7457 Z= 0.154 Angle : 0.594 16.665 10527 Z= 0.294 Chirality : 0.037 0.206 1275 Planarity : 0.003 0.039 979 Dihedral : 13.916 161.278 1859 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 4.67 % Allowed : 28.37 % Favored : 66.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.35), residues: 617 helix: 1.42 (0.28), residues: 359 sheet: -0.90 (0.61), residues: 68 loop : -1.03 (0.47), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 877 TYR 0.012 0.002 TYR A 48 PHE 0.022 0.002 PHE B 977 TRP 0.010 0.002 TRP A 287 HIS 0.003 0.001 HIS A 303 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.15 ( 7457) covalent geometry : angle 0.59450 / 0.29 (10527) hydrogen bonds : bond 0.04717 / 3.21 ( 362) hydrogen bonds : angle 3.78797 / 2.61 ( 938) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1234 Ramachandran restraints generated. 617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1234 Ramachandran restraints generated. 617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 61 time to evaluate : 0.251 Fit side-chains revert: symmetry clash REVERT: A 149 MET cc_start: 0.1708 (ptt) cc_final: 0.0380 (mtm) REVERT: A 178 MET cc_start: 0.5391 (mtm) cc_final: 0.5074 (mtm) REVERT: A 181 LEU cc_start: 0.7594 (OUTLIER) cc_final: 0.7212 (tp) REVERT: A 187 MET cc_start: 0.6641 (tmm) cc_final: 0.6361 (tmm) REVERT: A 258 TRP cc_start: 0.8286 (m-10) cc_final: 0.8046 (m-10) REVERT: B 791 GLU cc_start: 0.8325 (OUTLIER) cc_final: 0.8014 (tt0) REVERT: B 855 LYS cc_start: 0.7060 (mmtm) cc_final: 0.6709 (mttm) REVERT: B 977 PHE cc_start: 0.7909 (m-10) cc_final: 0.7678 (m-10) REVERT: B 986 ARG cc_start: 0.7354 (OUTLIER) cc_final: 0.6959 (ttt-90) outliers start: 26 outliers final: 18 residues processed: 81 average time/residue: 0.0906 time to fit residues: 9.8209 Evaluate side-chains 81 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 60 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain B residue 772 THR Chi-restraints excluded: chain B residue 791 GLU Chi-restraints excluded: chain B residue 798 ILE Chi-restraints excluded: chain B residue 827 VAL Chi-restraints excluded: chain B residue 884 LEU Chi-restraints excluded: chain B residue 890 ILE Chi-restraints excluded: chain B residue 899 ILE Chi-restraints excluded: chain B residue 918 ASP Chi-restraints excluded: chain B residue 936 CYS Chi-restraints excluded: chain B residue 962 MET Chi-restraints excluded: chain B residue 981 ASP Chi-restraints excluded: chain B residue 982 VAL Chi-restraints excluded: chain B residue 986 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 40 optimal weight: 2.9990 chunk 61 optimal weight: 10.0000 chunk 59 optimal weight: 9.9990 chunk 28 optimal weight: 20.0000 chunk 1 optimal weight: 9.9990 chunk 3 optimal weight: 4.9990 chunk 51 optimal weight: 10.0000 chunk 9 optimal weight: 20.0000 chunk 11 optimal weight: 9.9990 chunk 24 optimal weight: 3.9990 chunk 34 optimal weight: 20.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 374 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.101251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.067954 restraints weight = 21794.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.070059 restraints weight = 10592.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.071299 restraints weight = 7345.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.071844 restraints weight = 6141.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 56)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.072291 restraints weight = 5685.104| |-----------------------------------------------------------------------------| r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.2716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 7457 Z= 0.240 Angle : 0.678 17.171 10527 Z= 0.338 Chirality : 0.040 0.234 1275 Planarity : 0.004 0.038 979 Dihedral : 14.316 162.027 1859 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 13.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 5.57 % Allowed : 27.83 % Favored : 66.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.34), residues: 617 helix: 0.97 (0.27), residues: 359 sheet: -0.95 (0.68), residues: 54 loop : -1.04 (0.46), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 877 TYR 0.018 0.002 TYR A 48 PHE 0.023 0.003 PHE B 977 TRP 0.010 0.002 TRP A 27 HIS 0.003 0.001 HIS A 303 Details of bonding type rmsd/Z covalent geometry : bond 0.00516 / 0.24 ( 7457) covalent geometry : angle 0.67823 / 0.34 (10527) hydrogen bonds : bond 0.05819 / 3.94 ( 362) hydrogen bonds : angle 4.09160 / 2.84 ( 938) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1234 Ramachandran restraints generated. 617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1234 Ramachandran restraints generated. 617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 62 time to evaluate : 0.272 Fit side-chains revert: symmetry clash REVERT: A 178 MET cc_start: 0.5765 (mtm) cc_final: 0.5551 (mtm) REVERT: A 181 LEU cc_start: 0.7670 (OUTLIER) cc_final: 0.7265 (tp) REVERT: A 187 MET cc_start: 0.6537 (tmm) cc_final: 0.6279 (tmm) REVERT: A 229 ARG cc_start: 0.5985 (ptt-90) cc_final: 0.5424 (mmp-170) REVERT: A 258 TRP cc_start: 0.8392 (m-10) cc_final: 0.8185 (m-10) REVERT: B 791 GLU cc_start: 0.8361 (OUTLIER) cc_final: 0.8069 (tt0) REVERT: B 855 LYS cc_start: 0.6995 (mmtm) cc_final: 0.6671 (mttm) REVERT: B 977 PHE cc_start: 0.7990 (m-10) cc_final: 0.7772 (m-10) REVERT: B 986 ARG cc_start: 0.7341 (OUTLIER) cc_final: 0.6910 (ttt-90) outliers start: 31 outliers final: 22 residues processed: 87 average time/residue: 0.0857 time to fit residues: 10.2563 Evaluate side-chains 85 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 60 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 302 MET Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain B residue 772 THR Chi-restraints excluded: chain B residue 783 VAL Chi-restraints excluded: chain B residue 791 GLU Chi-restraints excluded: chain B residue 798 ILE Chi-restraints excluded: chain B residue 827 VAL Chi-restraints excluded: chain B residue 834 THR Chi-restraints excluded: chain B residue 836 THR Chi-restraints excluded: chain B residue 884 LEU Chi-restraints excluded: chain B residue 899 ILE Chi-restraints excluded: chain B residue 918 ASP Chi-restraints excluded: chain B residue 936 CYS Chi-restraints excluded: chain B residue 962 MET Chi-restraints excluded: chain B residue 982 VAL Chi-restraints excluded: chain B residue 986 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 34 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 chunk 28 optimal weight: 10.0000 chunk 31 optimal weight: 0.3980 chunk 53 optimal weight: 0.8980 chunk 24 optimal weight: 4.9990 chunk 12 optimal weight: 30.0000 chunk 29 optimal weight: 2.9990 chunk 65 optimal weight: 10.0000 chunk 5 optimal weight: 20.0000 chunk 54 optimal weight: 1.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.103476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.070491 restraints weight = 21670.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 69)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.072777 restraints weight = 9933.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.074216 restraints weight = 6606.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.074926 restraints weight = 5411.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.075063 restraints weight = 4922.997| |-----------------------------------------------------------------------------| r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.2805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 7457 Z= 0.112 Angle : 0.554 15.660 10527 Z= 0.275 Chirality : 0.036 0.187 1275 Planarity : 0.003 0.040 979 Dihedral : 13.747 161.939 1859 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 4.67 % Allowed : 29.80 % Favored : 65.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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 (0.34), residues: 617 helix: 1.44 (0.28), residues: 360 sheet: -0.80 (0.67), residues: 55 loop : -1.12 (0.44), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 877 TYR 0.008 0.001 TYR A 48 PHE 0.027 0.002 PHE B 776 TRP 0.013 0.002 TRP A 287 HIS 0.001 0.000 HIS A 303 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.11 ( 7457) covalent geometry : angle 0.55401 / 0.27 (10527) hydrogen bonds : bond 0.04247 / 2.91 ( 362) hydrogen bonds : angle 3.72157 / 2.56 ( 938) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1234 Ramachandran restraints generated. 617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1234 Ramachandran restraints generated. 617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 64 time to evaluate : 0.224 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 149 MET cc_start: 0.1879 (ptt) cc_final: 0.0568 (mtm) REVERT: A 181 LEU cc_start: 0.7726 (OUTLIER) cc_final: 0.7266 (tp) REVERT: A 187 MET cc_start: 0.6535 (tmm) cc_final: 0.6118 (tmm) REVERT: A 229 ARG cc_start: 0.5810 (ptt-90) cc_final: 0.5313 (mmp-170) REVERT: B 791 GLU cc_start: 0.8337 (OUTLIER) cc_final: 0.7949 (tt0) REVERT: B 855 LYS cc_start: 0.7124 (mmtm) cc_final: 0.6778 (mttm) REVERT: B 857 ASP cc_start: 0.7064 (OUTLIER) cc_final: 0.6800 (m-30) REVERT: B 977 PHE cc_start: 0.7944 (m-10) cc_final: 0.7722 (m-10) REVERT: B 986 ARG cc_start: 0.7312 (OUTLIER) cc_final: 0.6768 (ttt-90) outliers start: 26 outliers final: 18 residues processed: 83 average time/residue: 0.0831 time to fit residues: 9.3412 Evaluate side-chains 83 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 61 time to evaluate : 0.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 302 MET Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain B residue 772 THR Chi-restraints excluded: chain B residue 791 GLU Chi-restraints excluded: chain B residue 798 ILE Chi-restraints excluded: chain B residue 827 VAL Chi-restraints excluded: chain B residue 857 ASP Chi-restraints excluded: chain B residue 884 LEU Chi-restraints excluded: chain B residue 899 ILE Chi-restraints excluded: chain B residue 918 ASP Chi-restraints excluded: chain B residue 936 CYS Chi-restraints excluded: chain B residue 981 ASP Chi-restraints excluded: chain B residue 982 VAL Chi-restraints excluded: chain B residue 986 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 47 optimal weight: 2.9990 chunk 7 optimal weight: 0.0070 chunk 56 optimal weight: 0.9980 chunk 66 optimal weight: 20.0000 chunk 41 optimal weight: 4.9990 chunk 64 optimal weight: 20.0000 chunk 1 optimal weight: 5.9990 chunk 59 optimal weight: 6.9990 chunk 21 optimal weight: 10.0000 chunk 62 optimal weight: 10.0000 chunk 53 optimal weight: 0.6980 overall best weight: 1.9402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.103831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.070721 restraints weight = 21371.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.072889 restraints weight = 9866.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.074342 restraints weight = 6698.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.075109 restraints weight = 5459.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.075508 restraints weight = 4946.571| |-----------------------------------------------------------------------------| r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.2958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 7457 Z= 0.114 Angle : 0.550 14.410 10527 Z= 0.273 Chirality : 0.036 0.195 1275 Planarity : 0.003 0.041 979 Dihedral : 13.636 161.524 1859 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 4.49 % Allowed : 29.26 % Favored : 66.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.35), residues: 617 helix: 1.59 (0.28), residues: 360 sheet: -0.64 (0.67), residues: 55 loop : -1.07 (0.44), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 877 TYR 0.009 0.001 TYR A 48 PHE 0.028 0.002 PHE A 86 TRP 0.009 0.002 TRP A 287 HIS 0.002 0.001 HIS A 303 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 ( 7457) covalent geometry : angle 0.55046 / 0.27 (10527) hydrogen bonds : bond 0.04073 / 2.77 ( 362) hydrogen bonds : angle 3.64097 / 2.50 ( 938) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1234 Ramachandran restraints generated. 617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1234 Ramachandran restraints generated. 617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 64 time to evaluate : 0.220 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 48 TYR cc_start: 0.7039 (m-80) cc_final: 0.6745 (m-80) REVERT: A 127 MET cc_start: 0.7001 (mmm) cc_final: 0.6773 (mmm) REVERT: A 143 GLU cc_start: 0.2468 (OUTLIER) cc_final: 0.2110 (mt-10) REVERT: A 149 MET cc_start: 0.1628 (ptt) cc_final: 0.0461 (mtm) REVERT: A 178 MET cc_start: 0.5627 (mtm) cc_final: 0.5342 (mtm) REVERT: A 181 LEU cc_start: 0.7662 (OUTLIER) cc_final: 0.7186 (tp) REVERT: A 187 MET cc_start: 0.6424 (tmm) cc_final: 0.6012 (tmm) REVERT: A 229 ARG cc_start: 0.5972 (ptt-90) cc_final: 0.5243 (mmp-170) REVERT: A 258 TRP cc_start: 0.8103 (m-10) cc_final: 0.7880 (m-10) REVERT: B 791 GLU cc_start: 0.8379 (OUTLIER) cc_final: 0.7982 (tt0) REVERT: B 855 LYS cc_start: 0.7118 (mmtm) cc_final: 0.6784 (mttm) REVERT: B 857 ASP cc_start: 0.7135 (OUTLIER) cc_final: 0.6859 (m-30) REVERT: B 977 PHE cc_start: 0.8045 (m-10) cc_final: 0.7837 (m-10) REVERT: B 986 ARG cc_start: 0.7362 (OUTLIER) cc_final: 0.6960 (ttt-90) outliers start: 25 outliers final: 18 residues processed: 83 average time/residue: 0.0696 time to fit residues: 7.9486 Evaluate side-chains 82 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 59 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 GLU Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 302 MET Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain B residue 772 THR Chi-restraints excluded: chain B residue 791 GLU Chi-restraints excluded: chain B residue 798 ILE Chi-restraints excluded: chain B residue 827 VAL Chi-restraints excluded: chain B residue 857 ASP Chi-restraints excluded: chain B residue 884 LEU Chi-restraints excluded: chain B residue 899 ILE Chi-restraints excluded: chain B residue 918 ASP Chi-restraints excluded: chain B residue 936 CYS Chi-restraints excluded: chain B residue 981 ASP Chi-restraints excluded: chain B residue 982 VAL Chi-restraints excluded: chain B residue 986 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 9 optimal weight: 20.0000 chunk 13 optimal weight: 20.0000 chunk 7 optimal weight: 10.0000 chunk 65 optimal weight: 10.0000 chunk 15 optimal weight: 20.0000 chunk 53 optimal weight: 6.9990 chunk 66 optimal weight: 20.0000 chunk 26 optimal weight: 3.9990 chunk 68 optimal weight: 20.0000 chunk 18 optimal weight: 40.0000 chunk 40 optimal weight: 8.9990 overall best weight: 7.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.100645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.067492 restraints weight = 21820.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.069594 restraints weight = 10706.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 60)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.070887 restraints weight = 7410.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.071509 restraints weight = 6183.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 61)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.071867 restraints weight = 5674.407| |-----------------------------------------------------------------------------| r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.3005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 7457 Z= 0.289 Angle : 0.738 16.069 10527 Z= 0.367 Chirality : 0.042 0.249 1275 Planarity : 0.004 0.036 979 Dihedral : 14.370 162.205 1859 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 14.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 5.03 % Allowed : 28.90 % Favored : 66.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.34), residues: 617 helix: 0.91 (0.27), residues: 365 sheet: -0.81 (0.64), residues: 60 loop : -1.11 (0.48), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 319 TYR 0.019 0.003 TYR A 48 PHE 0.036 0.003 PHE A 86 TRP 0.012 0.003 TRP A 258 HIS 0.004 0.002 HIS B 927 Details of bonding type rmsd/Z covalent geometry : bond 0.00622 / 0.29 ( 7457) covalent geometry : angle 0.73756 / 0.37 (10527) hydrogen bonds : bond 0.06305 / 4.27 ( 362) hydrogen bonds : angle 4.21225 / 2.92 ( 938) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1234 Ramachandran restraints generated. 617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1234 Ramachandran restraints generated. 617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 61 time to evaluate : 0.200 Fit side-chains REVERT: A 127 MET cc_start: 0.7120 (mmm) cc_final: 0.6893 (mmm) REVERT: A 181 LEU cc_start: 0.7684 (OUTLIER) cc_final: 0.7236 (tt) REVERT: A 187 MET cc_start: 0.6417 (tmm) cc_final: 0.6051 (tmm) REVERT: A 216 MET cc_start: 0.6062 (ptp) cc_final: 0.5711 (ptm) REVERT: A 229 ARG cc_start: 0.6008 (ptt-90) cc_final: 0.5407 (mmp80) REVERT: B 791 GLU cc_start: 0.8375 (OUTLIER) cc_final: 0.8119 (tt0) REVERT: B 855 LYS cc_start: 0.7232 (mmtm) cc_final: 0.6883 (mttm) REVERT: B 857 ASP cc_start: 0.7058 (OUTLIER) cc_final: 0.6846 (m-30) REVERT: B 977 PHE cc_start: 0.8036 (m-10) cc_final: 0.7809 (m-10) REVERT: B 986 ARG cc_start: 0.7423 (OUTLIER) cc_final: 0.6955 (ttt-90) outliers start: 28 outliers final: 21 residues processed: 82 average time/residue: 0.0735 time to fit residues: 8.1497 Evaluate side-chains 84 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 59 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 302 MET Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain B residue 772 THR Chi-restraints excluded: chain B residue 791 GLU Chi-restraints excluded: chain B residue 798 ILE Chi-restraints excluded: chain B residue 827 VAL Chi-restraints excluded: chain B residue 857 ASP Chi-restraints excluded: chain B residue 869 ASP Chi-restraints excluded: chain B residue 884 LEU Chi-restraints excluded: chain B residue 889 ASP Chi-restraints excluded: chain B residue 899 ILE Chi-restraints excluded: chain B residue 918 ASP Chi-restraints excluded: chain B residue 936 CYS Chi-restraints excluded: chain B residue 962 MET Chi-restraints excluded: chain B residue 982 VAL Chi-restraints excluded: chain B residue 986 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 43 optimal weight: 6.9990 chunk 8 optimal weight: 6.9990 chunk 22 optimal weight: 0.6980 chunk 28 optimal weight: 9.9990 chunk 58 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 68 optimal weight: 20.0000 chunk 48 optimal weight: 30.0000 chunk 13 optimal weight: 0.9990 chunk 50 optimal weight: 7.9990 chunk 32 optimal weight: 2.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.104194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.071784 restraints weight = 21812.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.074064 restraints weight = 10584.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.075122 restraints weight = 7358.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.075997 restraints weight = 6183.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.075880 restraints weight = 5638.334| |-----------------------------------------------------------------------------| r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.3098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 7457 Z= 0.110 Angle : 0.554 15.145 10527 Z= 0.276 Chirality : 0.036 0.183 1275 Planarity : 0.003 0.040 979 Dihedral : 13.614 161.425 1859 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 4.31 % Allowed : 29.44 % Favored : 66.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.66 (0.35), residues: 617 helix: 1.46 (0.28), residues: 366 sheet: -0.78 (0.66), residues: 55 loop : -1.12 (0.45), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 877 TYR 0.009 0.001 TYR A 267 PHE 0.029 0.002 PHE A 86 TRP 0.024 0.003 TRP A 27 HIS 0.001 0.000 HIS B 917 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.11 ( 7457) covalent geometry : angle 0.55404 / 0.28 (10527) hydrogen bonds : bond 0.04110 / 2.83 ( 362) hydrogen bonds : angle 3.69020 / 2.53 ( 938) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1263.36 seconds wall clock time: 22 minutes 30.28 seconds (1350.28 seconds total)