Starting phenix.real_space_refine on Thu Jul 2 18:01:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zqc_60382/07_2026/8zqc_60382.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zqc_60382/07_2026/8zqc_60382.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8zqc_60382/07_2026/8zqc_60382.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zqc_60382/07_2026/8zqc_60382.map" model { file = "/net/cci-nas-00/data/ceres_data/8zqc_60382/07_2026/8zqc_60382.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zqc_60382/07_2026/8zqc_60382.cif" } resolution = 3.4 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: 5 Type Number sf(0) Gaussians P 99 5.49 5 S 27 5.16 5 C 5784 2.51 5 N 1703 2.21 5 O 2067 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.00s 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: 9680 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 7612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 930, 7612 Classifications: {'peptide': 930} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 22, 'TRANS': 907} Chain breaks: 3 Chain: "B" Number of atoms: 1167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 1167 Classifications: {'RNA': 55} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 8, 'rna3p_pur': 20, 'rna3p_pyr': 20} Link IDs: {'rna2p': 15, 'rna3p': 39} Chain: "C" Number of atoms: 542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 542 Classifications: {'DNA': 26} Link IDs: {'rna3p': 25} Chain: "D" Number of atoms: 359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 359 Classifications: {'DNA': 18} Link IDs: {'rna3p': 17} Time building chain proxies: 1.64, per 1000 atoms: 0.17 Number of scatterers: 9680 At special positions: 0 Unit cell: (84.48, 104.94, 126.06, 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 27 16.00 P 99 15.00 O 2067 8.00 N 1703 7.00 C 5784 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: 0.94 Conformation dependent library (CDL) restraints added in 287.8 milliseconds 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1774 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 6 sheets defined 51.1% alpha, 10.2% beta 20 base pairs and 52 stacking pairs defined. Time for finding SS restraints: 1.12 Creating SS restraints... Processing helix chain 'A' and resid 15 through 47 Processing helix chain 'A' and resid 52 through 62 Processing helix chain 'A' and resid 64 through 76 removed outlier: 4.171A pdb=" N SER A 73 " --> pdb=" O ARG A 69 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N CYS A 74 " --> pdb=" O ALA A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 98 Processing helix chain 'A' and resid 106 through 115 removed outlier: 3.741A pdb=" N LEU A 110 " --> pdb=" O THR A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 171 removed outlier: 4.232A pdb=" N ALA A 148 " --> pdb=" O LYS A 144 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N ASN A 152 " --> pdb=" O ALA A 148 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N LYS A 153 " --> pdb=" O LYS A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 182 Processing helix chain 'A' and resid 186 through 229 removed outlier: 3.519A pdb=" N LEU A 190 " --> pdb=" O ASN A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 251 removed outlier: 3.991A pdb=" N LEU A 251 " --> pdb=" O ARG A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 272 removed outlier: 3.654A pdb=" N ALA A 265 " --> pdb=" O LEU A 261 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N LYS A 266 " --> pdb=" O GLN A 262 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ARG A 269 " --> pdb=" O ALA A 265 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N LYS A 270 " --> pdb=" O LYS A 266 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N PHE A 272 " --> pdb=" O TRP A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 275 No H-bonds generated for 'chain 'A' and resid 273 through 275' Processing helix chain 'A' and resid 284 through 295 removed outlier: 3.727A pdb=" N HIS A 295 " --> pdb=" O LYS A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 298 No H-bonds generated for 'chain 'A' and resid 296 through 298' Processing helix chain 'A' and resid 301 through 319 removed outlier: 3.758A pdb=" N LEU A 305 " --> pdb=" O ASP A 301 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N LYS A 308 " --> pdb=" O TYR A 304 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N GLU A 309 " --> pdb=" O LEU A 305 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N ASP A 310 " --> pdb=" O PHE A 306 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU A 311 " --> pdb=" O GLY A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 436 Processing helix chain 'A' and resid 452 through 458 Processing helix chain 'A' and resid 459 through 462 removed outlier: 3.866A pdb=" N THR A 462 " --> pdb=" O LEU A 459 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 459 through 462' Processing helix chain 'A' and resid 469 through 474 Processing helix chain 'A' and resid 537 through 565 removed outlier: 3.806A pdb=" N LYS A 541 " --> pdb=" O ASN A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 597 through 605 removed outlier: 3.531A pdb=" N GLY A 605 " --> pdb=" O LEU A 601 " (cutoff:3.500A) Processing helix chain 'A' and resid 606 through 611 removed outlier: 3.574A pdb=" N PHE A 610 " --> pdb=" O LEU A 606 " (cutoff:3.500A) Processing helix chain 'A' and resid 621 through 635 Processing helix chain 'A' and resid 638 through 657 removed outlier: 3.517A pdb=" N PHE A 642 " --> pdb=" O THR A 638 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ILE A 657 " --> pdb=" O ILE A 653 " (cutoff:3.500A) Processing helix chain 'A' and resid 657 through 666 Processing helix chain 'A' and resid 679 through 700 Processing helix chain 'A' and resid 715 through 743 removed outlier: 3.668A pdb=" N GLN A 719 " --> pdb=" O PHE A 715 " (cutoff:3.500A) Processing helix chain 'A' and resid 766 through 770 removed outlier: 4.115A pdb=" N ARG A 769 " --> pdb=" O ASP A 766 " (cutoff:3.500A) Processing helix chain 'A' and resid 775 through 789 removed outlier: 3.815A pdb=" N GLU A 789 " --> pdb=" O GLU A 785 " (cutoff:3.500A) Processing helix chain 'A' and resid 801 through 805 removed outlier: 3.536A pdb=" N GLN A 804 " --> pdb=" O HIS A 801 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N LEU A 805 " --> pdb=" O SER A 802 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 801 through 805' Processing helix chain 'A' and resid 835 through 850 Processing helix chain 'A' and resid 881 through 890 Processing helix chain 'A' and resid 908 through 916 removed outlier: 3.608A pdb=" N LEU A 916 " --> pdb=" O GLN A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 933 through 951 removed outlier: 4.089A pdb=" N ARG A 947 " --> pdb=" O GLU A 943 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N THR A 948 " --> pdb=" O ILE A 944 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N ASN A 949 " --> pdb=" O GLY A 945 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N VAL A 950 " --> pdb=" O ALA A 946 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLN A 951 " --> pdb=" O ARG A 947 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 338 through 339 removed outlier: 4.921A pdb=" N PHE A 439 " --> pdb=" O LEU A 12 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLU A 13 " --> pdb=" O LYS A 372 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LYS A 372 " --> pdb=" O GLU A 13 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 379 through 383 Processing sheet with id=AA3, first strand: chain 'A' and resid 509 through 510 removed outlier: 6.955A pdb=" N ILE A 497 " --> pdb=" O VAL A 527 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N GLU A 529 " --> pdb=" O MET A 495 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N MET A 495 " --> pdb=" O GLU A 529 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU A 748 " --> pdb=" O ARG A 481 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N GLU A 752 " --> pdb=" O VAL A 485 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 814 through 815 Processing sheet with id=AA5, first strand: chain 'A' and resid 857 through 858 Processing sheet with id=AA6, first strand: chain 'A' and resid 861 through 863 removed outlier: 3.653A pdb=" N GLY A 920 " --> pdb=" O LEU A 862 " (cutoff:3.500A) 380 hydrogen bonds defined for protein. 1092 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 53 hydrogen bonds 104 hydrogen bond angles 0 basepair planarities 20 basepair parallelities 52 stacking parallelities Total time for adding SS restraints: 1.80 Time building geometry restraints manager: 1.20 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: 2276 1.33 - 1.45: 2497 1.45 - 1.57: 5065 1.57 - 1.69: 195 1.69 - 1.81: 39 Bond restraints: 10072 Sorted by residual: bond pdb=" C3' DG C 1 " pdb=" C2' DG C 1 " ideal model delta sigma weight residual 1.516 1.545 -0.029 8.00e-03 1.56e+04 1.28e+01 bond pdb=" C3' DC D -1 " pdb=" C2' DC D -1 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.11e+01 bond pdb=" C3' DG D 8 " pdb=" C2' DG D 8 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.10e+01 bond pdb=" C3' DT D -3 " pdb=" O3' DT D -3 " ideal model delta sigma weight residual 1.435 1.393 0.042 1.30e-02 5.92e+03 1.06e+01 bond pdb=" C3' DT C -6 " pdb=" C2' DT C -6 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.32e+00 ... (remaining 10067 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.72: 13560 1.72 - 3.44: 383 3.44 - 5.17: 50 5.17 - 6.89: 18 6.89 - 8.61: 4 Bond angle restraints: 14015 Sorted by residual: angle pdb=" O4' DA C -9 " pdb=" C4' DA C -9 " pdb=" C3' DA C -9 " ideal model delta sigma weight residual 106.00 102.87 3.13 6.00e-01 2.78e+00 2.72e+01 angle pdb=" C1' U B 5 " pdb=" N1 U B 5 " pdb=" C2 U B 5 " ideal model delta sigma weight residual 117.70 123.67 -5.97 1.20e+00 6.94e-01 2.47e+01 angle pdb=" C1' C B 3 " pdb=" N1 C B 3 " pdb=" C2 C B 3 " ideal model delta sigma weight residual 118.80 124.21 -5.41 1.10e+00 8.26e-01 2.42e+01 angle pdb=" C4' DG C 1 " pdb=" O4' DG C 1 " pdb=" C1' DG C 1 " ideal model delta sigma weight residual 110.10 105.71 4.39 1.00e+00 1.00e+00 1.93e+01 angle pdb=" N3 DT D 0 " pdb=" C4 DT D 0 " pdb=" O4 DT D 0 " ideal model delta sigma weight residual 119.90 122.49 -2.59 6.00e-01 2.78e+00 1.86e+01 ... (remaining 14010 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.84: 5502 34.84 - 69.68: 501 69.68 - 104.52: 40 104.52 - 139.36: 4 139.36 - 174.21: 2 Dihedral angle restraints: 6049 sinusoidal: 3314 harmonic: 2735 Sorted by residual: dihedral pdb=" O4' U B -32 " pdb=" C1' U B -32 " pdb=" N1 U B -32 " pdb=" C2 U B -32 " ideal model delta sinusoidal sigma weight residual -128.00 46.21 -174.21 1 1.70e+01 3.46e-03 6.63e+01 dihedral pdb=" O4' G B -11 " pdb=" C1' G B -11 " pdb=" N9 G B -11 " pdb=" C4 G B -11 " ideal model delta sinusoidal sigma weight residual 70.00 -2.59 72.59 1 2.00e+01 2.50e-03 1.68e+01 dihedral pdb=" O4' A B -18 " pdb=" C1' A B -18 " pdb=" N9 A B -18 " pdb=" C4 A B -18 " ideal model delta sinusoidal sigma weight residual 70.00 -1.28 71.28 1 2.00e+01 2.50e-03 1.63e+01 ... (remaining 6046 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 1203 0.046 - 0.092: 300 0.092 - 0.138: 64 0.138 - 0.184: 9 0.184 - 0.229: 3 Chirality restraints: 1579 Sorted by residual: chirality pdb=" C3' A B -8 " pdb=" C4' A B -8 " pdb=" O3' A B -8 " pdb=" C2' A B -8 " both_signs ideal model delta sigma weight residual False -2.48 -2.71 0.23 2.00e-01 2.50e+01 1.32e+00 chirality pdb=" C1' U B 5 " pdb=" O4' U B 5 " pdb=" C2' U B 5 " pdb=" N1 U B 5 " both_signs ideal model delta sigma weight residual False 2.47 2.28 0.19 2.00e-01 2.50e+01 8.95e-01 chirality pdb=" C1' G B -36 " pdb=" O4' G B -36 " pdb=" C2' G B -36 " pdb=" N9 G B -36 " both_signs ideal model delta sigma weight residual False 2.46 2.27 0.19 2.00e-01 2.50e+01 8.59e-01 ... (remaining 1576 not shown) Planarity restraints: 1438 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 806 " 0.065 5.00e-02 4.00e+02 9.82e-02 1.54e+01 pdb=" N PRO A 807 " -0.170 5.00e-02 4.00e+02 pdb=" CA PRO A 807 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO A 807 " 0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' A B -31 " 0.035 2.00e-02 2.50e+03 1.61e-02 7.12e+00 pdb=" N9 A B -31 " -0.037 2.00e-02 2.50e+03 pdb=" C8 A B -31 " -0.001 2.00e-02 2.50e+03 pdb=" N7 A B -31 " 0.003 2.00e-02 2.50e+03 pdb=" C5 A B -31 " 0.002 2.00e-02 2.50e+03 pdb=" C6 A B -31 " 0.007 2.00e-02 2.50e+03 pdb=" N6 A B -31 " 0.006 2.00e-02 2.50e+03 pdb=" N1 A B -31 " 0.004 2.00e-02 2.50e+03 pdb=" C2 A B -31 " -0.002 2.00e-02 2.50e+03 pdb=" N3 A B -31 " -0.005 2.00e-02 2.50e+03 pdb=" C4 A B -31 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C B 1 " 0.028 2.00e-02 2.50e+03 1.54e-02 5.31e+00 pdb=" N1 C B 1 " -0.036 2.00e-02 2.50e+03 pdb=" C2 C B 1 " -0.002 2.00e-02 2.50e+03 pdb=" O2 C B 1 " 0.000 2.00e-02 2.50e+03 pdb=" N3 C B 1 " 0.000 2.00e-02 2.50e+03 pdb=" C4 C B 1 " 0.002 2.00e-02 2.50e+03 pdb=" N4 C B 1 " 0.008 2.00e-02 2.50e+03 pdb=" C5 C B 1 " 0.003 2.00e-02 2.50e+03 pdb=" C6 C B 1 " -0.004 2.00e-02 2.50e+03 ... (remaining 1435 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1030 2.74 - 3.28: 9166 3.28 - 3.82: 17008 3.82 - 4.36: 18905 4.36 - 4.90: 30721 Nonbonded interactions: 76830 Sorted by model distance: nonbonded pdb=" OG SER A 125 " pdb=" N4 DC D 1 " model vdw 2.198 3.120 nonbonded pdb=" OD1 ASN A 124 " pdb=" N SER A 125 " model vdw 2.210 3.120 nonbonded pdb=" OH TYR A 107 " pdb=" NZ LYS A 144 " model vdw 2.221 3.120 nonbonded pdb=" O SER A 892 " pdb=" OG SER A 892 " model vdw 2.237 3.040 nonbonded pdb=" OP2 G B -15 " pdb=" N2 G B -15 " model vdw 2.245 3.120 ... (remaining 76825 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 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: 3.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.240 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 10.030 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: 0.000 Load rotamer database and sin/cos tables:1.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 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 0.051 10072 Z= 0.338 Angle : 0.692 8.609 14015 Z= 0.488 Chirality : 0.043 0.229 1579 Planarity : 0.004 0.098 1438 Dihedral : 22.960 174.205 4275 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.29 % Favored : 93.60 % Rotamer: Outliers : 0.83 % Allowed : 33.06 % Favored : 66.11 % 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: 0.38 (0.28), residues: 922 helix: 1.86 (0.26), residues: 425 sheet: 0.44 (0.46), residues: 126 loop : -1.84 (0.31), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 668 TYR 0.011 0.001 TYR A 92 PHE 0.017 0.002 PHE A 325 TRP 0.016 0.002 TRP A 382 HIS 0.012 0.001 HIS A 376 Details of bonding type rmsd/Z covalent geometry : bond 0.00468 / 0.34 (10072) covalent geometry : angle 0.69167 / 0.49 (14015) hydrogen bonds : bond 0.11553 / 7.57 ( 433) hydrogen bonds : angle 4.65810 / 3.29 ( 1196) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 134 time to evaluate : 0.417 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 2 residues processed: 138 average time/residue: 0.1120 time to fit residues: 20.6761 Evaluate side-chains 68 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 66 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 886 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 10.0000 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 9.9990 chunk 51 optimal weight: 0.4980 chunk 100 optimal weight: 9.9990 chunk 38 optimal weight: 9.9990 chunk 61 optimal weight: 0.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 214 ASN A 338 GLN A 344 GLN A 429 GLN A 768 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.088968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.063772 restraints weight = 32652.172| |-----------------------------------------------------------------------------| r_work (start): 0.3129 rms_B_bonded: 4.24 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.1540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 10072 Z= 0.165 Angle : 0.632 10.469 14015 Z= 0.357 Chirality : 0.041 0.228 1579 Planarity : 0.004 0.066 1438 Dihedral : 22.878 176.941 2336 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.99 % Favored : 94.90 % Rotamer: Outliers : 3.91 % Allowed : 29.03 % Favored : 67.06 % 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: 0.53 (0.28), residues: 922 helix: 1.94 (0.25), residues: 425 sheet: 0.43 (0.48), residues: 125 loop : -1.66 (0.31), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 6 TYR 0.010 0.001 TYR A 721 PHE 0.017 0.001 PHE A 552 TRP 0.013 0.001 TRP A 382 HIS 0.007 0.001 HIS A 376 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.17 (10072) covalent geometry : angle 0.63180 / 0.36 (14015) hydrogen bonds : bond 0.05177 / 3.48 ( 433) hydrogen bonds : angle 3.99632 / 2.82 ( 1196) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 71 time to evaluate : 0.296 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 MET cc_start: 0.9108 (mtm) cc_final: 0.8770 (mtp) REVERT: A 280 TRP cc_start: 0.7523 (m-10) cc_final: 0.7259 (m-10) REVERT: A 501 ASN cc_start: 0.8846 (OUTLIER) cc_final: 0.8017 (t0) REVERT: A 709 GLU cc_start: 0.9014 (OUTLIER) cc_final: 0.8382 (mt-10) outliers start: 33 outliers final: 12 residues processed: 101 average time/residue: 0.1091 time to fit residues: 14.9136 Evaluate side-chains 70 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 56 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 127 PHE Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 269 ARG Chi-restraints excluded: chain A residue 344 GLN Chi-restraints excluded: chain A residue 501 ASN Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 551 ILE Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 709 GLU Chi-restraints excluded: chain A residue 776 HIS Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 840 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 34 optimal weight: 6.9990 chunk 40 optimal weight: 2.9990 chunk 3 optimal weight: 6.9990 chunk 64 optimal weight: 4.9990 chunk 98 optimal weight: 20.0000 chunk 77 optimal weight: 6.9990 chunk 0 optimal weight: 5.9990 chunk 73 optimal weight: 4.9990 chunk 49 optimal weight: 0.5980 chunk 30 optimal weight: 9.9990 chunk 58 optimal weight: 0.7980 overall best weight: 2.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 294 GLN A 338 GLN A 388 ASN A 634 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.085768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.059976 restraints weight = 33410.889| |-----------------------------------------------------------------------------| r_work (start): 0.3026 rms_B_bonded: 4.28 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.2209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 10072 Z= 0.242 Angle : 0.650 8.861 14015 Z= 0.364 Chirality : 0.042 0.234 1579 Planarity : 0.004 0.060 1438 Dihedral : 22.869 176.382 2334 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.77 % Favored : 95.12 % Rotamer: Outliers : 4.86 % Allowed : 28.08 % Favored : 67.06 % 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: 0.40 (0.28), residues: 922 helix: 1.90 (0.25), residues: 425 sheet: 0.28 (0.50), residues: 115 loop : -1.72 (0.30), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 431 TYR 0.017 0.002 TYR A 229 PHE 0.024 0.002 PHE A 552 TRP 0.013 0.001 TRP A 382 HIS 0.008 0.002 HIS A 376 Details of bonding type rmsd/Z covalent geometry : bond 0.00504 / 0.24 (10072) covalent geometry : angle 0.65036 / 0.36 (14015) hydrogen bonds : bond 0.04957 / 3.32 ( 433) hydrogen bonds : angle 4.01323 / 2.84 ( 1196) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 55 time to evaluate : 0.250 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 MET cc_start: 0.9210 (mtm) cc_final: 0.8901 (mtt) REVERT: A 154 MET cc_start: 0.8919 (tpp) cc_final: 0.8513 (ttm) REVERT: A 431 ARG cc_start: 0.8218 (mtp-110) cc_final: 0.7450 (ptm160) REVERT: A 501 ASN cc_start: 0.8805 (OUTLIER) cc_final: 0.8002 (t0) REVERT: A 583 ARG cc_start: 0.8130 (OUTLIER) cc_final: 0.7698 (ptm160) REVERT: A 709 GLU cc_start: 0.8979 (mm-30) cc_final: 0.8236 (mt-10) REVERT: A 784 GLU cc_start: 0.8976 (tp30) cc_final: 0.8584 (tp30) outliers start: 41 outliers final: 17 residues processed: 91 average time/residue: 0.1056 time to fit residues: 12.8443 Evaluate side-chains 67 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 48 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 SER Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 125 SER Chi-restraints excluded: chain A residue 127 PHE Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 501 ASN Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 551 ILE Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 583 ARG Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 776 HIS Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 840 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 1 optimal weight: 0.7980 chunk 12 optimal weight: 4.9990 chunk 17 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 72 optimal weight: 0.6980 chunk 26 optimal weight: 9.9990 chunk 10 optimal weight: 7.9990 chunk 4 optimal weight: 0.9990 chunk 7 optimal weight: 3.9990 chunk 13 optimal weight: 7.9990 chunk 5 optimal weight: 4.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 344 GLN A 584 GLN ** A 912 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.086079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.061017 restraints weight = 32649.136| |-----------------------------------------------------------------------------| r_work (start): 0.3069 rms_B_bonded: 4.10 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.2570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 10072 Z= 0.175 Angle : 0.592 8.593 14015 Z= 0.333 Chirality : 0.041 0.318 1579 Planarity : 0.003 0.054 1438 Dihedral : 22.824 177.767 2334 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.56 % Favored : 95.34 % Rotamer: Outliers : 4.38 % Allowed : 28.32 % Favored : 67.30 % 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: 0.70 (0.28), residues: 922 helix: 2.19 (0.26), residues: 421 sheet: 0.66 (0.49), residues: 113 loop : -1.65 (0.30), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 947 TYR 0.010 0.001 TYR A 627 PHE 0.016 0.001 PHE A 306 TRP 0.014 0.001 TRP A 382 HIS 0.007 0.001 HIS A 376 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.17 (10072) covalent geometry : angle 0.59247 / 0.33 (14015) hydrogen bonds : bond 0.04679 / 3.13 ( 433) hydrogen bonds : angle 3.80515 / 2.68 ( 1196) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 51 time to evaluate : 0.266 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 MET cc_start: 0.8909 (tpp) cc_final: 0.8558 (ttm) REVERT: A 431 ARG cc_start: 0.8243 (mtp-110) cc_final: 0.8028 (ptm160) REVERT: A 479 GLN cc_start: 0.8890 (tm-30) cc_final: 0.8518 (tm-30) REVERT: A 501 ASN cc_start: 0.8812 (OUTLIER) cc_final: 0.8183 (t0) REVERT: A 583 ARG cc_start: 0.8023 (OUTLIER) cc_final: 0.7634 (ptm160) REVERT: A 709 GLU cc_start: 0.8966 (mm-30) cc_final: 0.8168 (mt-10) REVERT: A 784 GLU cc_start: 0.8992 (tp30) cc_final: 0.8540 (tp30) outliers start: 37 outliers final: 23 residues processed: 83 average time/residue: 0.0964 time to fit residues: 11.2117 Evaluate side-chains 72 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 47 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 SER Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 127 PHE Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 501 ASN Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 551 ILE Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 583 ARG Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 644 SER Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 776 HIS Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 840 SER Chi-restraints excluded: chain A residue 869 SER Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain A residue 936 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 46 optimal weight: 0.6980 chunk 84 optimal weight: 2.9990 chunk 69 optimal weight: 5.9990 chunk 52 optimal weight: 0.7980 chunk 74 optimal weight: 3.9990 chunk 8 optimal weight: 4.9990 chunk 87 optimal weight: 0.8980 chunk 77 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 94 optimal weight: 9.9990 chunk 83 optimal weight: 2.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 912 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.086204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.061165 restraints weight = 33018.774| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 4.14 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.2817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 10072 Z= 0.156 Angle : 0.586 9.169 14015 Z= 0.329 Chirality : 0.041 0.301 1579 Planarity : 0.004 0.055 1438 Dihedral : 22.752 178.533 2334 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.56 % Favored : 95.34 % Rotamer: Outliers : 4.03 % Allowed : 28.91 % Favored : 67.06 % 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: 0.82 (0.28), residues: 922 helix: 2.32 (0.26), residues: 420 sheet: 0.70 (0.49), residues: 113 loop : -1.61 (0.30), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 121 TYR 0.020 0.001 TYR A 241 PHE 0.014 0.001 PHE A 552 TRP 0.011 0.001 TRP A 382 HIS 0.006 0.001 HIS A 376 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.16 (10072) covalent geometry : angle 0.58576 / 0.33 (14015) hydrogen bonds : bond 0.04504 / 3.03 ( 433) hydrogen bonds : angle 3.72939 / 2.63 ( 1196) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 51 time to evaluate : 0.314 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 153 LYS cc_start: 0.9105 (OUTLIER) cc_final: 0.8860 (ptpp) REVERT: A 154 MET cc_start: 0.8890 (tpp) cc_final: 0.8584 (ttm) REVERT: A 284 GLU cc_start: 0.8489 (mp0) cc_final: 0.7764 (pm20) REVERT: A 314 LEU cc_start: 0.8540 (OUTLIER) cc_final: 0.8081 (tp) REVERT: A 407 LYS cc_start: 0.9289 (OUTLIER) cc_final: 0.8885 (tptp) REVERT: A 431 ARG cc_start: 0.8354 (mtp-110) cc_final: 0.7969 (ptm160) REVERT: A 479 GLN cc_start: 0.8898 (tm-30) cc_final: 0.8507 (tm-30) REVERT: A 501 ASN cc_start: 0.8939 (OUTLIER) cc_final: 0.7986 (t0) REVERT: A 583 ARG cc_start: 0.7993 (OUTLIER) cc_final: 0.7556 (ptm160) outliers start: 34 outliers final: 17 residues processed: 80 average time/residue: 0.1023 time to fit residues: 11.5025 Evaluate side-chains 71 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 49 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 125 SER Chi-restraints excluded: chain A residue 127 PHE Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 153 LYS Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 407 LYS Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 501 ASN Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain A residue 583 ARG Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 776 HIS Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 840 SER Chi-restraints excluded: chain A residue 936 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 37 optimal weight: 1.9990 chunk 31 optimal weight: 9.9990 chunk 92 optimal weight: 1.9990 chunk 60 optimal weight: 0.0010 chunk 98 optimal weight: 20.0000 chunk 61 optimal weight: 5.9990 chunk 34 optimal weight: 6.9990 chunk 90 optimal weight: 6.9990 chunk 99 optimal weight: 10.0000 chunk 25 optimal weight: 7.9990 chunk 73 optimal weight: 0.6980 overall best weight: 2.1392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 912 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.085142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.060122 restraints weight = 33042.455| |-----------------------------------------------------------------------------| r_work (start): 0.3049 rms_B_bonded: 4.13 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.3047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 10072 Z= 0.187 Angle : 0.593 9.897 14015 Z= 0.331 Chirality : 0.041 0.290 1579 Planarity : 0.003 0.053 1438 Dihedral : 22.734 177.803 2334 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.88 % Favored : 95.01 % Rotamer: Outliers : 4.15 % Allowed : 29.27 % Favored : 66.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.81 (0.28), residues: 922 helix: 2.34 (0.26), residues: 421 sheet: 0.62 (0.49), residues: 113 loop : -1.64 (0.30), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 639 TYR 0.012 0.001 TYR A 241 PHE 0.009 0.001 PHE A 204 TRP 0.011 0.001 TRP A 382 HIS 0.005 0.001 HIS A 376 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.19 (10072) covalent geometry : angle 0.59342 / 0.33 (14015) hydrogen bonds : bond 0.04457 / 2.99 ( 433) hydrogen bonds : angle 3.77963 / 2.67 ( 1196) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 49 time to evaluate : 0.328 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 153 LYS cc_start: 0.9133 (OUTLIER) cc_final: 0.8895 (ptpp) REVERT: A 284 GLU cc_start: 0.8474 (mp0) cc_final: 0.7778 (pm20) REVERT: A 407 LYS cc_start: 0.9303 (OUTLIER) cc_final: 0.8907 (tptp) REVERT: A 431 ARG cc_start: 0.8377 (mtp-110) cc_final: 0.7959 (ptm160) REVERT: A 479 GLN cc_start: 0.8881 (tm-30) cc_final: 0.8488 (tm-30) REVERT: A 501 ASN cc_start: 0.8864 (OUTLIER) cc_final: 0.8215 (t0) REVERT: A 583 ARG cc_start: 0.8053 (OUTLIER) cc_final: 0.7665 (ptm160) REVERT: A 639 ARG cc_start: 0.8228 (mmt90) cc_final: 0.7922 (mmt180) REVERT: A 777 ARG cc_start: 0.8179 (tpp80) cc_final: 0.7731 (mtp85) outliers start: 35 outliers final: 23 residues processed: 77 average time/residue: 0.1046 time to fit residues: 11.2868 Evaluate side-chains 74 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 47 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 SER Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 125 SER Chi-restraints excluded: chain A residue 127 PHE Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 153 LYS Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 407 LYS Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 501 ASN Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 583 ARG Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 776 HIS Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 840 SER Chi-restraints excluded: chain A residue 936 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 71 optimal weight: 0.9980 chunk 40 optimal weight: 0.9990 chunk 45 optimal weight: 5.9990 chunk 80 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 7 optimal weight: 5.9990 chunk 87 optimal weight: 1.9990 chunk 79 optimal weight: 3.9990 chunk 47 optimal weight: 4.9990 chunk 11 optimal weight: 8.9990 chunk 99 optimal weight: 10.0000 overall best weight: 2.1988 ------------------------------------------------------------------------------- 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 = 0.3617 r_free = 0.3617 target = 0.084510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.059559 restraints weight = 32750.021| |-----------------------------------------------------------------------------| r_work (start): 0.3038 rms_B_bonded: 4.05 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.3254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 10072 Z= 0.187 Angle : 0.583 9.904 14015 Z= 0.328 Chirality : 0.041 0.260 1579 Planarity : 0.003 0.052 1438 Dihedral : 22.740 177.731 2334 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.99 % Favored : 94.90 % Rotamer: Outliers : 3.79 % Allowed : 29.98 % Favored : 66.23 % 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: 0.80 (0.28), residues: 922 helix: 2.36 (0.26), residues: 420 sheet: 0.64 (0.48), residues: 113 loop : -1.68 (0.29), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 121 TYR 0.016 0.001 TYR A 627 PHE 0.020 0.001 PHE A 552 TRP 0.011 0.001 TRP A 382 HIS 0.008 0.001 HIS A 631 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.19 (10072) covalent geometry : angle 0.58325 / 0.33 (14015) hydrogen bonds : bond 0.04470 / 2.99 ( 433) hydrogen bonds : angle 3.81996 / 2.69 ( 1196) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 50 time to evaluate : 0.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 LYS cc_start: 0.9128 (OUTLIER) cc_final: 0.8878 (ptpp) REVERT: A 154 MET cc_start: 0.8959 (tpp) cc_final: 0.8652 (ttm) REVERT: A 407 LYS cc_start: 0.9328 (OUTLIER) cc_final: 0.8929 (tptp) REVERT: A 428 LEU cc_start: 0.8771 (OUTLIER) cc_final: 0.8527 (tt) REVERT: A 501 ASN cc_start: 0.8929 (OUTLIER) cc_final: 0.8183 (t0) REVERT: A 583 ARG cc_start: 0.8034 (OUTLIER) cc_final: 0.7598 (ptm160) REVERT: A 639 ARG cc_start: 0.8253 (mmt90) cc_final: 0.7951 (mmt180) REVERT: A 777 ARG cc_start: 0.8186 (tpp80) cc_final: 0.7826 (mmm-85) outliers start: 32 outliers final: 21 residues processed: 77 average time/residue: 0.1195 time to fit residues: 12.7620 Evaluate side-chains 73 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 47 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 SER Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 125 SER Chi-restraints excluded: chain A residue 127 PHE Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 153 LYS Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 407 LYS Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 501 ASN Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 551 ILE Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain A residue 583 ARG Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 776 HIS Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 840 SER Chi-restraints excluded: chain A residue 936 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 38 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 37 optimal weight: 0.0980 chunk 54 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 64 optimal weight: 4.9990 chunk 91 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 57 optimal weight: 4.9990 chunk 90 optimal weight: 5.9990 chunk 85 optimal weight: 1.9990 overall best weight: 1.6188 ------------------------------------------------------------------------------- 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 = 0.3626 r_free = 0.3626 target = 0.084903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.059723 restraints weight = 33226.467| |-----------------------------------------------------------------------------| r_work (start): 0.3041 rms_B_bonded: 4.16 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.3383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 10072 Z= 0.156 Angle : 0.582 10.880 14015 Z= 0.324 Chirality : 0.041 0.336 1579 Planarity : 0.003 0.051 1438 Dihedral : 22.727 178.192 2334 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.77 % Favored : 95.12 % Rotamer: Outliers : 3.67 % Allowed : 30.21 % Favored : 66.11 % 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: 0.84 (0.28), residues: 922 helix: 2.41 (0.26), residues: 420 sheet: 0.65 (0.48), residues: 113 loop : -1.69 (0.30), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 431 TYR 0.010 0.001 TYR A 627 PHE 0.012 0.001 PHE A 552 TRP 0.012 0.001 TRP A 382 HIS 0.006 0.001 HIS A 631 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.16 (10072) covalent geometry : angle 0.58154 / 0.32 (14015) hydrogen bonds : bond 0.04372 / 2.93 ( 433) hydrogen bonds : angle 3.76454 / 2.65 ( 1196) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 48 time to evaluate : 0.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 LYS cc_start: 0.9128 (OUTLIER) cc_final: 0.8878 (ptpp) REVERT: A 154 MET cc_start: 0.8944 (tpp) cc_final: 0.8645 (ttm) REVERT: A 407 LYS cc_start: 0.9332 (OUTLIER) cc_final: 0.8941 (tptp) REVERT: A 479 GLN cc_start: 0.8851 (tm-30) cc_final: 0.8332 (tm-30) REVERT: A 501 ASN cc_start: 0.8916 (OUTLIER) cc_final: 0.8146 (t0) REVERT: A 583 ARG cc_start: 0.7995 (OUTLIER) cc_final: 0.7699 (ptm160) REVERT: A 639 ARG cc_start: 0.8269 (mmt90) cc_final: 0.7972 (mmt180) REVERT: A 777 ARG cc_start: 0.8241 (tpp80) cc_final: 0.7782 (mtp85) outliers start: 31 outliers final: 23 residues processed: 75 average time/residue: 0.1199 time to fit residues: 12.3286 Evaluate side-chains 76 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 49 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 SER Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 125 SER Chi-restraints excluded: chain A residue 127 PHE Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 153 LYS Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 407 LYS Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 501 ASN Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain A residue 583 ARG Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 776 HIS Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 840 SER Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 936 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 54 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 15 optimal weight: 5.9990 chunk 8 optimal weight: 3.9990 chunk 22 optimal weight: 4.9990 chunk 80 optimal weight: 0.6980 chunk 30 optimal weight: 7.9990 chunk 1 optimal weight: 0.8980 chunk 55 optimal weight: 4.9990 chunk 97 optimal weight: 10.0000 overall best weight: 1.5184 ------------------------------------------------------------------------------- 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 = 0.3624 r_free = 0.3624 target = 0.084880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.059595 restraints weight = 33235.475| |-----------------------------------------------------------------------------| r_work (start): 0.3041 rms_B_bonded: 4.13 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.3518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 10072 Z= 0.151 Angle : 0.575 11.299 14015 Z= 0.321 Chirality : 0.040 0.281 1579 Planarity : 0.003 0.051 1438 Dihedral : 22.693 178.207 2334 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.10 % Favored : 94.79 % Rotamer: Outliers : 3.55 % Allowed : 30.45 % Favored : 66.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.88 (0.28), residues: 922 helix: 2.48 (0.26), residues: 419 sheet: 0.67 (0.48), residues: 110 loop : -1.67 (0.29), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 431 TYR 0.009 0.001 TYR A 627 PHE 0.014 0.001 PHE A 552 TRP 0.012 0.001 TRP A 382 HIS 0.010 0.001 HIS A 634 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.15 (10072) covalent geometry : angle 0.57523 / 0.32 (14015) hydrogen bonds : bond 0.04262 / 2.86 ( 433) hydrogen bonds : angle 3.72386 / 2.63 ( 1196) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 48 time to evaluate : 0.344 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 LYS cc_start: 0.9134 (OUTLIER) cc_final: 0.8887 (ptpp) REVERT: A 154 MET cc_start: 0.8945 (tpp) cc_final: 0.8656 (ttm) REVERT: A 407 LYS cc_start: 0.9338 (OUTLIER) cc_final: 0.8963 (tptp) REVERT: A 428 LEU cc_start: 0.8750 (OUTLIER) cc_final: 0.8547 (tt) REVERT: A 479 GLN cc_start: 0.8843 (tm-30) cc_final: 0.8379 (tm-30) REVERT: A 583 ARG cc_start: 0.7997 (OUTLIER) cc_final: 0.7737 (ptm160) REVERT: A 622 GLU cc_start: 0.9240 (tp30) cc_final: 0.8721 (tp30) REVERT: A 639 ARG cc_start: 0.8261 (mmt90) cc_final: 0.7977 (mmt180) REVERT: A 777 ARG cc_start: 0.8278 (tpp80) cc_final: 0.7832 (mtp85) outliers start: 30 outliers final: 23 residues processed: 76 average time/residue: 0.1215 time to fit residues: 12.7011 Evaluate side-chains 73 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 46 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 SER Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 125 SER Chi-restraints excluded: chain A residue 127 PHE Chi-restraints excluded: chain A residue 153 LYS Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 407 LYS Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain A residue 583 ARG Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 776 HIS Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 840 SER Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 936 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 66 optimal weight: 3.9990 chunk 85 optimal weight: 10.0000 chunk 35 optimal weight: 6.9990 chunk 25 optimal weight: 20.0000 chunk 81 optimal weight: 0.7980 chunk 43 optimal weight: 3.9990 chunk 98 optimal weight: 20.0000 chunk 69 optimal weight: 7.9990 chunk 16 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 30 optimal weight: 3.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 215 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.083381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.058303 restraints weight = 33113.838| |-----------------------------------------------------------------------------| r_work (start): 0.3021 rms_B_bonded: 4.08 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 moved from start: 0.3675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 10072 Z= 0.205 Angle : 0.606 10.442 14015 Z= 0.337 Chirality : 0.041 0.292 1579 Planarity : 0.003 0.051 1438 Dihedral : 22.722 176.949 2334 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.42 % Favored : 94.47 % Rotamer: Outliers : 3.32 % Allowed : 30.69 % Favored : 66.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.85 (0.28), residues: 922 helix: 2.43 (0.26), residues: 420 sheet: 0.47 (0.48), residues: 118 loop : -1.66 (0.30), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 431 TYR 0.008 0.001 TYR A 594 PHE 0.011 0.001 PHE A 552 TRP 0.009 0.001 TRP A 244 HIS 0.007 0.001 HIS A 631 Details of bonding type rmsd/Z covalent geometry : bond 0.00425 / 0.21 (10072) covalent geometry : angle 0.60587 / 0.34 (14015) hydrogen bonds : bond 0.04548 / 3.05 ( 433) hydrogen bonds : angle 3.88599 / 2.74 ( 1196) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 46 time to evaluate : 0.333 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 154 MET cc_start: 0.9010 (tpp) cc_final: 0.8648 (ttm) REVERT: A 407 LYS cc_start: 0.9342 (OUTLIER) cc_final: 0.8958 (tptp) REVERT: A 428 LEU cc_start: 0.8803 (OUTLIER) cc_final: 0.8570 (tt) REVERT: A 583 ARG cc_start: 0.8051 (OUTLIER) cc_final: 0.7637 (ptm160) REVERT: A 622 GLU cc_start: 0.9293 (tp30) cc_final: 0.8777 (tp30) REVERT: A 639 ARG cc_start: 0.8275 (mmt90) cc_final: 0.7980 (mmt180) outliers start: 28 outliers final: 21 residues processed: 71 average time/residue: 0.1112 time to fit residues: 11.0654 Evaluate side-chains 68 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 44 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 SER Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 125 SER Chi-restraints excluded: chain A residue 127 PHE Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 407 LYS Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain A residue 583 ARG Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 840 SER Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 936 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 45 optimal weight: 5.9990 chunk 16 optimal weight: 0.7980 chunk 94 optimal weight: 10.0000 chunk 41 optimal weight: 3.9990 chunk 85 optimal weight: 5.9990 chunk 8 optimal weight: 3.9990 chunk 32 optimal weight: 5.9990 chunk 42 optimal weight: 3.9990 chunk 21 optimal weight: 0.9990 chunk 20 optimal weight: 5.9990 chunk 69 optimal weight: 4.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- 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 = 0.3593 r_free = 0.3593 target = 0.083094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.057959 restraints weight = 33208.059| |-----------------------------------------------------------------------------| r_work (start): 0.3000 rms_B_bonded: 4.06 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 moved from start: 0.3789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 10072 Z= 0.221 Angle : 0.613 10.429 14015 Z= 0.342 Chirality : 0.042 0.291 1579 Planarity : 0.003 0.051 1438 Dihedral : 22.698 176.973 2332 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.10 % Favored : 94.79 % Rotamer: Outliers : 3.20 % Allowed : 30.69 % Favored : 66.11 % 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: 0.77 (0.28), residues: 922 helix: 2.32 (0.26), residues: 421 sheet: 0.37 (0.47), residues: 119 loop : -1.62 (0.30), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 431 TYR 0.009 0.001 TYR A 594 PHE 0.014 0.002 PHE A 552 TRP 0.010 0.001 TRP A 382 HIS 0.008 0.001 HIS A 631 Details of bonding type rmsd/Z covalent geometry : bond 0.00465 / 0.22 (10072) covalent geometry : angle 0.61350 / 0.34 (14015) hydrogen bonds : bond 0.04615 / 3.10 ( 433) hydrogen bonds : angle 3.92954 / 2.78 ( 1196) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1782.69 seconds wall clock time: 31 minutes 39.60 seconds (1899.60 seconds total)