Starting phenix.real_space_refine on Thu Jul 2 19:15:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wcs_37448/07_2026/8wcs_37448.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wcs_37448/07_2026/8wcs_37448.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wcs_37448/07_2026/8wcs_37448.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wcs_37448/07_2026/8wcs_37448.map" model { file = "/net/cci-nas-00/data/ceres_data/8wcs_37448/07_2026/8wcs_37448.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wcs_37448/07_2026/8wcs_37448.cif" } resolution = 3.1 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= 0.001 sd= 0.077 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 66 5.49 5 Mg 1 5.21 5 S 31 5.16 5 C 6245 2.51 5 N 1692 2.21 5 O 2061 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: 10096 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 8685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1044, 8685 Classifications: {'peptide': 1044} Link IDs: {'PTRANS': 26, 'TRANS': 1017} Chain breaks: 2 Chain: "G" Number of atoms: 1410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 1410 Classifications: {'RNA': 66} Modifications used: {'rna2p_pur': 11, 'rna2p_pyr': 10, 'rna3p_pur': 26, 'rna3p_pyr': 19} Link IDs: {'rna2p': 20, 'rna3p': 45} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.96, per 1000 atoms: 0.19 Number of scatterers: 10096 At special positions: 0 Unit cell: (93.5, 86.7, 119.85, 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 31 16.00 P 66 15.00 Mg 1 11.99 O 2061 8.00 N 1692 7.00 C 6245 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: 0.83 Conformation dependent library (CDL) restraints added in 221.2 milliseconds 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1994 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 3 sheets defined 56.7% alpha, 1.5% beta 8 base pairs and 23 stacking pairs defined. Time for finding SS restraints: 1.17 Creating SS restraints... Processing helix chain 'A' and resid 9 through 30 Processing helix chain 'A' and resid 41 through 50 removed outlier: 3.502A pdb=" N LYS A 44 " --> pdb=" O LEU A 41 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N LEU A 45 " --> pdb=" O ALA A 42 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N GLY A 46 " --> pdb=" O ASP A 43 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N ASN A 47 " --> pdb=" O LYS A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 60 removed outlier: 3.873A pdb=" N LYS A 59 " --> pdb=" O LYS A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 132 removed outlier: 3.852A pdb=" N LEU A 105 " --> pdb=" O HIS A 101 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLU A 132 " --> pdb=" O ALA A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 163 removed outlier: 3.513A pdb=" N LEU A 156 " --> pdb=" O GLY A 152 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N PHE A 163 " --> pdb=" O SER A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 177 Processing helix chain 'A' and resid 180 through 204 removed outlier: 4.465A pdb=" N GLU A 184 " --> pdb=" O GLU A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 261 removed outlier: 3.666A pdb=" N GLU A 261 " --> pdb=" O ALA A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 280 Processing helix chain 'A' and resid 290 through 303 removed outlier: 4.313A pdb=" N ALA A 294 " --> pdb=" O ILE A 290 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU A 295 " --> pdb=" O SER A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 316 Processing helix chain 'A' and resid 322 through 324 No H-bonds generated for 'chain 'A' and resid 322 through 324' Processing helix chain 'A' and resid 325 through 334 removed outlier: 4.678A pdb=" N PHE A 332 " --> pdb=" O THR A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 361 Processing helix chain 'A' and resid 371 through 390 removed outlier: 3.826A pdb=" N GLU A 387 " --> pdb=" O ASP A 383 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LYS A 388 " --> pdb=" O SER A 384 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLU A 390 " --> pdb=" O SER A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 403 removed outlier: 3.733A pdb=" N GLU A 399 " --> pdb=" O LYS A 395 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LYS A 400 " --> pdb=" O GLU A 396 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ILE A 401 " --> pdb=" O GLU A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 425 Processing helix chain 'A' and resid 438 through 449 removed outlier: 3.559A pdb=" N ASN A 449 " --> pdb=" O TYR A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 504 removed outlier: 3.506A pdb=" N ARG A 504 " --> pdb=" O LYS A 500 " (cutoff:3.500A) Processing helix chain 'A' and resid 532 through 536 removed outlier: 3.639A pdb=" N GLY A 535 " --> pdb=" O GLU A 532 " (cutoff:3.500A) Processing helix chain 'A' and resid 545 through 559 removed outlier: 3.843A pdb=" N LEU A 549 " --> pdb=" O SER A 545 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N MET A 550 " --> pdb=" O PRO A 546 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LYS A 551 " --> pdb=" O ASP A 547 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 591 removed outlier: 3.615A pdb=" N ILE A 578 " --> pdb=" O LYS A 574 " (cutoff:3.500A) Processing helix chain 'A' and resid 623 through 647 removed outlier: 3.786A pdb=" N ILE A 627 " --> pdb=" O ASP A 623 " (cutoff:3.500A) Processing helix chain 'A' and resid 650 through 654 removed outlier: 3.556A pdb=" N ARG A 653 " --> pdb=" O ALA A 650 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N PHE A 654 " --> pdb=" O PRO A 651 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 650 through 654' Processing helix chain 'A' and resid 658 through 677 removed outlier: 3.594A pdb=" N ILE A 663 " --> pdb=" O LYS A 659 " (cutoff:3.500A) Processing helix chain 'A' and resid 682 through 688 removed outlier: 3.846A pdb=" N ARG A 686 " --> pdb=" O VAL A 682 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLU A 688 " --> pdb=" O ALA A 684 " (cutoff:3.500A) Processing helix chain 'A' and resid 691 through 704 Processing helix chain 'A' and resid 711 through 718 removed outlier: 3.864A pdb=" N LYS A 715 " --> pdb=" O THR A 711 " (cutoff:3.500A) Processing helix chain 'A' and resid 740 through 759 removed outlier: 3.706A pdb=" N ASN A 744 " --> pdb=" O GLU A 740 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N PHE A 745 " --> pdb=" O GLY A 741 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ALA A 746 " --> pdb=" O VAL A 742 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N SER A 759 " --> pdb=" O LYS A 755 " (cutoff:3.500A) Processing helix chain 'A' and resid 784 through 789 removed outlier: 3.588A pdb=" N GLU A 789 " --> pdb=" O GLY A 785 " (cutoff:3.500A) Processing helix chain 'A' and resid 809 through 817 Processing helix chain 'A' and resid 824 through 836 removed outlier: 3.898A pdb=" N PHE A 828 " --> pdb=" O SER A 824 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ARG A 836 " --> pdb=" O VAL A 832 " (cutoff:3.500A) Processing helix chain 'A' and resid 849 through 853 Processing helix chain 'A' and resid 865 through 893 removed outlier: 4.458A pdb=" N VAL A 871 " --> pdb=" O THR A 867 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ALA A 872 " --> pdb=" O GLN A 868 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ASN A 879 " --> pdb=" O ARG A 875 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N GLU A 885 " --> pdb=" O LEU A 881 " (cutoff:3.500A) Processing helix chain 'A' and resid 917 through 922 Processing helix chain 'A' and resid 922 through 928 Processing helix chain 'A' and resid 962 through 979 removed outlier: 3.837A pdb=" N GLN A 970 " --> pdb=" O GLN A 966 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N VAL A 974 " --> pdb=" O GLN A 970 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N ASP A 975 " --> pdb=" O GLU A 971 " (cutoff:3.500A) Processing helix chain 'A' and resid 992 through 1005 removed outlier: 4.221A pdb=" N ARG A1005 " --> pdb=" O ASP A1001 " (cutoff:3.500A) Processing helix chain 'A' and resid 1005 through 1023 removed outlier: 3.944A pdb=" N LYS A1023 " --> pdb=" O HIS A1019 " (cutoff:3.500A) Processing helix chain 'A' and resid 1024 through 1030 Processing helix chain 'A' and resid 1053 through 1059 Processing helix chain 'A' and resid 1068 through 1082 Processing helix chain 'A' and resid 1087 through 1105 removed outlier: 3.509A pdb=" N TYR A1091 " --> pdb=" O LYS A1087 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ASN A1105 " --> pdb=" O TYR A1101 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 433 through 436 removed outlier: 3.532A pdb=" N LYS A 509 " --> pdb=" O ILE A 433 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 525 through 529 removed outlier: 3.656A pdb=" N PHE A 527 " --> pdb=" O LEU A 542 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 954 through 955 382 hydrogen bonds defined for protein. 1119 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 20 hydrogen bonds 36 hydrogen bond angles 0 basepair planarities 8 basepair parallelities 23 stacking parallelities Total time for adding SS restraints: 1.33 Time building geometry restraints manager: 1.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 2406 1.33 - 1.45: 2487 1.45 - 1.57: 5374 1.57 - 1.69: 131 1.69 - 1.81: 56 Bond restraints: 10454 Sorted by residual: bond pdb=" CA ASP A1008 " pdb=" C ASP A1008 " ideal model delta sigma weight residual 1.524 1.487 0.037 1.29e-02 6.01e+03 8.22e+00 bond pdb=" N9 G G 11 " pdb=" C4 G G 11 " ideal model delta sigma weight residual 1.375 1.392 -0.017 8.00e-03 1.56e+04 4.30e+00 bond pdb=" CA LEU A 187 " pdb=" C LEU A 187 " ideal model delta sigma weight residual 1.524 1.498 0.026 1.27e-02 6.20e+03 4.12e+00 bond pdb=" N ASP A 721 " pdb=" CA ASP A 721 " ideal model delta sigma weight residual 1.457 1.483 -0.026 1.29e-02 6.01e+03 4.09e+00 bond pdb=" C ASP A1008 " pdb=" N ASP A1009 " ideal model delta sigma weight residual 1.335 1.312 0.023 1.31e-02 5.83e+03 3.14e+00 ... (remaining 10449 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.98: 13948 1.98 - 3.96: 332 3.96 - 5.94: 63 5.94 - 7.92: 14 7.92 - 9.91: 5 Bond angle restraints: 14362 Sorted by residual: angle pdb=" N ASP A1008 " pdb=" CA ASP A1008 " pdb=" C ASP A1008 " ideal model delta sigma weight residual 111.36 105.86 5.50 1.09e+00 8.42e-01 2.54e+01 angle pdb=" C5 G G 11 " pdb=" C4 G G 11 " pdb=" N3 G G 11 " ideal model delta sigma weight residual 128.60 126.29 2.31 5.00e-01 4.00e+00 2.14e+01 angle pdb=" C1' G G 11 " pdb=" N9 G G 11 " pdb=" C4 G G 11 " ideal model delta sigma weight residual 126.50 132.15 -5.65 1.30e+00 5.92e-01 1.89e+01 angle pdb=" N9 G G 11 " pdb=" C4 G G 11 " pdb=" N3 G G 11 " ideal model delta sigma weight residual 126.00 128.59 -2.59 6.00e-01 2.78e+00 1.86e+01 angle pdb=" C ILE A 568 " pdb=" N THR A 569 " pdb=" CA THR A 569 " ideal model delta sigma weight residual 121.54 129.60 -8.06 1.91e+00 2.74e-01 1.78e+01 ... (remaining 14357 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.32: 5900 34.32 - 68.65: 466 68.65 - 102.97: 33 102.97 - 137.29: 0 137.29 - 171.61: 5 Dihedral angle restraints: 6404 sinusoidal: 3308 harmonic: 3096 Sorted by residual: dihedral pdb=" O4' C G -24 " pdb=" C1' C G -24 " pdb=" N1 C G -24 " pdb=" C2 C G -24 " ideal model delta sinusoidal sigma weight residual 200.00 51.20 148.80 1 1.50e+01 4.44e-03 7.92e+01 dihedral pdb=" O4' U G 18 " pdb=" C1' U G 18 " pdb=" N1 U G 18 " pdb=" C2 U G 18 " ideal model delta sinusoidal sigma weight residual 200.00 56.08 143.92 1 1.50e+01 4.44e-03 7.72e+01 dihedral pdb=" O4' C G -8 " pdb=" C1' C G -8 " pdb=" N1 C G -8 " pdb=" C2 C G -8 " ideal model delta sinusoidal sigma weight residual 232.00 62.06 169.94 1 1.70e+01 3.46e-03 6.59e+01 ... (remaining 6401 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 1327 0.064 - 0.128: 221 0.128 - 0.193: 34 0.193 - 0.257: 4 0.257 - 0.321: 3 Chirality restraints: 1589 Sorted by residual: chirality pdb=" CB ILE A1044 " pdb=" CA ILE A1044 " pdb=" CG1 ILE A1044 " pdb=" CG2 ILE A1044 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.32 2.00e-01 2.50e+01 2.58e+00 chirality pdb=" CG LEU A 16 " pdb=" CB LEU A 16 " pdb=" CD1 LEU A 16 " pdb=" CD2 LEU A 16 " both_signs ideal model delta sigma weight residual False -2.59 -2.30 -0.29 2.00e-01 2.50e+01 2.14e+00 chirality pdb=" CB VAL A1021 " pdb=" CA VAL A1021 " pdb=" CG1 VAL A1021 " pdb=" CG2 VAL A1021 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.66e+00 ... (remaining 1586 not shown) Planarity restraints: 1558 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 211 " -0.037 5.00e-02 4.00e+02 5.57e-02 4.96e+00 pdb=" N PRO A 212 " 0.096 5.00e-02 4.00e+02 pdb=" CA PRO A 212 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 212 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLU A 25 " 0.010 2.00e-02 2.50e+03 2.11e-02 4.46e+00 pdb=" CD GLU A 25 " -0.037 2.00e-02 2.50e+03 pdb=" OE1 GLU A 25 " 0.013 2.00e-02 2.50e+03 pdb=" OE2 GLU A 25 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A1007 " -0.010 2.00e-02 2.50e+03 2.04e-02 4.16e+00 pdb=" C LEU A1007 " 0.035 2.00e-02 2.50e+03 pdb=" O LEU A1007 " -0.013 2.00e-02 2.50e+03 pdb=" N ASP A1008 " -0.012 2.00e-02 2.50e+03 ... (remaining 1555 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 364 2.70 - 3.25: 9184 3.25 - 3.80: 16329 3.80 - 4.35: 20398 4.35 - 4.90: 33314 Nonbonded interactions: 79589 Sorted by model distance: nonbonded pdb=" OP1 A G 22 " pdb="MG MG G 101 " model vdw 2.148 2.170 nonbonded pdb=" OH TYR A1006 " pdb=" O ILE A1083 " model vdw 2.211 3.040 nonbonded pdb=" O PHE A 325 " pdb=" OG1 THR A 328 " model vdw 2.231 3.040 nonbonded pdb=" OD2 ASP A 673 " pdb=" OH TYR A 753 " model vdw 2.287 3.040 nonbonded pdb=" OD2 ASP A 424 " pdb=" OH TYR A 890 " model vdw 2.304 3.040 ... (remaining 79584 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: 0.880 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: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.740 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:1.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 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 : 0.004 0.049 10454 Z= 0.214 Angle : 0.771 9.905 14362 Z= 0.477 Chirality : 0.051 0.321 1589 Planarity : 0.005 0.056 1558 Dihedral : 21.585 171.613 4410 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.57 % Favored : 91.43 % Rotamer: Outliers : 0.74 % Allowed : 31.72 % Favored : 67.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.55 (0.22), residues: 1038 helix: -0.94 (0.19), residues: 557 sheet: -2.54 (0.76), residues: 30 loop : -2.59 (0.25), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 36 TYR 0.023 0.002 TYR A 695 PHE 0.026 0.002 PHE A 331 TRP 0.010 0.001 TRP A 884 HIS 0.004 0.001 HIS A 787 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.21 (10454) covalent geometry : angle 0.77112 / 0.48 (14362) hydrogen bonds : bond 0.14026 / 8.98 ( 402) hydrogen bonds : angle 5.60782 / 4.08 ( 1155) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 99 time to evaluate : 0.367 Fit side-chains REVERT: A 1006 TYR cc_start: 0.5842 (OUTLIER) cc_final: 0.5537 (t80) outliers start: 7 outliers final: 0 residues processed: 105 average time/residue: 0.0936 time to fit residues: 14.4318 Evaluate side-chains 92 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 91 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1006 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 108 optimal weight: 10.0000 chunk 49 optimal weight: 5.9990 chunk 97 optimal weight: 0.9980 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 0.0170 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 chunk 100 optimal weight: 0.7980 chunk 106 optimal weight: 20.0000 overall best weight: 0.7218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 329 GLN A 996 ASN A1081 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.158640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.132674 restraints weight = 15115.085| |-----------------------------------------------------------------------------| r_work (start): 0.3847 rms_B_bonded: 2.64 r_work: 0.3716 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.0712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 10454 Z= 0.116 Angle : 0.518 6.570 14362 Z= 0.294 Chirality : 0.040 0.233 1589 Planarity : 0.004 0.045 1558 Dihedral : 19.252 173.365 2143 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.57 % Favored : 91.43 % Rotamer: Outliers : 2.42 % Allowed : 30.24 % Favored : 67.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.32 (0.25), residues: 1038 helix: 0.29 (0.22), residues: 562 sheet: -1.25 (0.81), residues: 38 loop : -2.44 (0.26), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 36 TYR 0.017 0.001 TYR A 155 PHE 0.010 0.001 PHE A 110 TRP 0.011 0.001 TRP A 884 HIS 0.003 0.000 HIS A 687 Details of bonding type rmsd/Z covalent geometry : bond 0.00223 / 0.12 (10454) covalent geometry : angle 0.51755 / 0.29 (14362) hydrogen bonds : bond 0.05150 / 3.31 ( 402) hydrogen bonds : angle 4.07562 / 2.93 ( 1155) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 99 time to evaluate : 0.249 Fit side-chains REVERT: A 313 LYS cc_start: 0.8527 (pttp) cc_final: 0.8123 (pttp) REVERT: A 329 GLN cc_start: 0.8922 (OUTLIER) cc_final: 0.8652 (mm-40) REVERT: A 591 ILE cc_start: 0.8657 (OUTLIER) cc_final: 0.8362 (tt) outliers start: 23 outliers final: 8 residues processed: 116 average time/residue: 0.0798 time to fit residues: 13.6435 Evaluate side-chains 101 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 91 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 301 MET Chi-restraints excluded: chain A residue 329 GLN Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 818 LYS Chi-restraints excluded: chain A residue 849 VAL Chi-restraints excluded: chain A residue 974 VAL Chi-restraints excluded: chain A residue 1053 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 56 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 14 optimal weight: 7.9990 chunk 45 optimal weight: 10.0000 chunk 9 optimal weight: 10.0000 chunk 62 optimal weight: 4.9990 chunk 42 optimal weight: 3.9990 chunk 67 optimal weight: 0.9990 chunk 50 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1081 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.156372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.130287 restraints weight = 15325.520| |-----------------------------------------------------------------------------| r_work (start): 0.3817 rms_B_bonded: 2.64 r_work: 0.3692 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.0979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10454 Z= 0.128 Angle : 0.513 6.610 14362 Z= 0.290 Chirality : 0.040 0.218 1589 Planarity : 0.003 0.046 1558 Dihedral : 19.098 172.301 2141 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.67 % Favored : 91.33 % Rotamer: Outliers : 2.95 % Allowed : 29.61 % Favored : 67.44 % 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 (0.26), residues: 1038 helix: 0.73 (0.22), residues: 560 sheet: -1.78 (0.76), residues: 42 loop : -2.29 (0.27), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 432 TYR 0.019 0.001 TYR A 155 PHE 0.008 0.001 PHE A 676 TRP 0.015 0.001 TRP A 884 HIS 0.004 0.001 HIS A 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.13 (10454) covalent geometry : angle 0.51286 / 0.29 (14362) hydrogen bonds : bond 0.05034 / 3.24 ( 402) hydrogen bonds : angle 3.81374 / 2.75 ( 1155) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 100 time to evaluate : 0.347 Fit side-chains revert: symmetry clash REVERT: A 591 ILE cc_start: 0.8661 (OUTLIER) cc_final: 0.8378 (tt) REVERT: A 1008 ASP cc_start: 0.7592 (t0) cc_final: 0.7112 (t0) outliers start: 28 outliers final: 18 residues processed: 119 average time/residue: 0.0810 time to fit residues: 14.3539 Evaluate side-chains 110 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 91 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 88 TRP Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 261 GLU Chi-restraints excluded: chain A residue 578 ILE Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 672 SER Chi-restraints excluded: chain A residue 687 HIS Chi-restraints excluded: chain A residue 738 SER Chi-restraints excluded: chain A residue 757 ILE Chi-restraints excluded: chain A residue 762 THR Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 818 LYS Chi-restraints excluded: chain A residue 823 ILE Chi-restraints excluded: chain A residue 849 VAL Chi-restraints excluded: chain A residue 974 VAL Chi-restraints excluded: chain A residue 1053 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 4 optimal weight: 10.0000 chunk 49 optimal weight: 7.9990 chunk 28 optimal weight: 0.8980 chunk 2 optimal weight: 6.9990 chunk 101 optimal weight: 0.9990 chunk 35 optimal weight: 0.9980 chunk 93 optimal weight: 0.9990 chunk 65 optimal weight: 5.9990 chunk 21 optimal weight: 0.9990 chunk 79 optimal weight: 6.9990 chunk 48 optimal weight: 0.9980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1081 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.157300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.131361 restraints weight = 15203.019| |-----------------------------------------------------------------------------| r_work (start): 0.3829 rms_B_bonded: 2.63 r_work: 0.3696 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.1200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 10454 Z= 0.105 Angle : 0.488 6.502 14362 Z= 0.276 Chirality : 0.039 0.200 1589 Planarity : 0.003 0.047 1558 Dihedral : 18.979 175.130 2141 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.29 % Favored : 91.71 % Rotamer: Outliers : 2.74 % Allowed : 29.61 % Favored : 67.65 % 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: -0.57 (0.26), residues: 1038 helix: 1.06 (0.22), residues: 561 sheet: -1.82 (0.76), residues: 42 loop : -2.24 (0.27), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 442 TYR 0.016 0.001 TYR A 155 PHE 0.006 0.001 PHE A 506 TRP 0.024 0.001 TRP A 884 HIS 0.003 0.000 HIS A 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00209 / 0.11 (10454) covalent geometry : angle 0.48779 / 0.28 (14362) hydrogen bonds : bond 0.04382 / 2.81 ( 402) hydrogen bonds : angle 3.64817 / 2.61 ( 1155) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 99 time to evaluate : 0.244 Fit side-chains revert: symmetry clash REVERT: A 36 ARG cc_start: 0.8131 (ptt90) cc_final: 0.7786 (ptm160) REVERT: A 131 TYR cc_start: 0.6729 (t80) cc_final: 0.6396 (t80) REVERT: A 241 PHE cc_start: 0.7676 (m-10) cc_final: 0.7309 (m-80) REVERT: A 591 ILE cc_start: 0.8678 (OUTLIER) cc_final: 0.8395 (tt) REVERT: A 882 MET cc_start: 0.7952 (tpt) cc_final: 0.7738 (mmm) REVERT: A 884 TRP cc_start: 0.8466 (t60) cc_final: 0.7922 (t-100) outliers start: 26 outliers final: 18 residues processed: 118 average time/residue: 0.0916 time to fit residues: 15.6845 Evaluate side-chains 110 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 91 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 88 TRP Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 261 GLU Chi-restraints excluded: chain A residue 301 MET Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 578 ILE Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 672 SER Chi-restraints excluded: chain A residue 687 HIS Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 818 LYS Chi-restraints excluded: chain A residue 849 VAL Chi-restraints excluded: chain A residue 974 VAL Chi-restraints excluded: chain A residue 1053 LEU Chi-restraints excluded: chain A residue 1108 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 24 optimal weight: 0.0050 chunk 104 optimal weight: 30.0000 chunk 38 optimal weight: 0.0000 chunk 55 optimal weight: 9.9990 chunk 59 optimal weight: 0.8980 chunk 32 optimal weight: 7.9990 chunk 58 optimal weight: 5.9990 chunk 19 optimal weight: 9.9990 chunk 36 optimal weight: 0.9990 chunk 85 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 overall best weight: 0.9802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1081 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.156847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.130968 restraints weight = 15107.658| |-----------------------------------------------------------------------------| r_work (start): 0.3825 rms_B_bonded: 2.61 r_work: 0.3692 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.1305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 10454 Z= 0.105 Angle : 0.488 7.910 14362 Z= 0.272 Chirality : 0.039 0.194 1589 Planarity : 0.003 0.046 1558 Dihedral : 18.928 175.469 2141 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.48 % Favored : 91.52 % Rotamer: Outliers : 3.16 % Allowed : 29.40 % Favored : 67.44 % 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 (0.27), residues: 1038 helix: 1.21 (0.22), residues: 567 sheet: -1.79 (0.76), residues: 42 loop : -2.22 (0.28), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 304 TYR 0.018 0.001 TYR A 155 PHE 0.007 0.001 PHE A 533 TRP 0.018 0.001 TRP A 884 HIS 0.003 0.001 HIS A 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00212 / 0.11 (10454) covalent geometry : angle 0.48809 / 0.27 (14362) hydrogen bonds : bond 0.04275 / 2.74 ( 402) hydrogen bonds : angle 3.55044 / 2.53 ( 1155) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 98 time to evaluate : 0.387 Fit side-chains revert: symmetry clash REVERT: A 131 TYR cc_start: 0.6802 (t80) cc_final: 0.6523 (t80) REVERT: A 591 ILE cc_start: 0.8700 (OUTLIER) cc_final: 0.8422 (tt) REVERT: A 884 TRP cc_start: 0.8415 (t60) cc_final: 0.7894 (t-100) outliers start: 30 outliers final: 23 residues processed: 121 average time/residue: 0.0925 time to fit residues: 16.3429 Evaluate side-chains 113 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 89 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 88 TRP Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 261 GLU Chi-restraints excluded: chain A residue 301 MET Chi-restraints excluded: chain A residue 545 SER Chi-restraints excluded: chain A residue 578 ILE Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 672 SER Chi-restraints excluded: chain A residue 687 HIS Chi-restraints excluded: chain A residue 762 THR Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 776 THR Chi-restraints excluded: chain A residue 818 LYS Chi-restraints excluded: chain A residue 823 ILE Chi-restraints excluded: chain A residue 849 VAL Chi-restraints excluded: chain A residue 974 VAL Chi-restraints excluded: chain A residue 1010 ILE Chi-restraints excluded: chain A residue 1053 LEU Chi-restraints excluded: chain A residue 1102 CYS Chi-restraints excluded: chain A residue 1108 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 68 optimal weight: 4.9990 chunk 63 optimal weight: 4.9990 chunk 3 optimal weight: 10.0000 chunk 43 optimal weight: 8.9990 chunk 16 optimal weight: 7.9990 chunk 109 optimal weight: 20.0000 chunk 37 optimal weight: 6.9990 chunk 97 optimal weight: 0.7980 chunk 60 optimal weight: 4.9990 chunk 53 optimal weight: 8.9990 chunk 33 optimal weight: 2.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 103 ASN A1081 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.148675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.122636 restraints weight = 15674.202| |-----------------------------------------------------------------------------| r_work (start): 0.3719 rms_B_bonded: 2.63 r_work: 0.3591 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.1784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 10454 Z= 0.236 Angle : 0.643 7.610 14362 Z= 0.354 Chirality : 0.046 0.221 1589 Planarity : 0.004 0.044 1558 Dihedral : 19.166 165.781 2141 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.10 % Allowed : 10.02 % Favored : 89.88 % Rotamer: Outliers : 4.21 % Allowed : 29.29 % Favored : 66.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.94 (0.26), residues: 1038 helix: 0.79 (0.22), residues: 569 sheet: -2.60 (0.70), residues: 41 loop : -2.46 (0.27), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 432 TYR 0.025 0.002 TYR A 155 PHE 0.017 0.002 PHE A 506 TRP 0.015 0.002 TRP A 884 HIS 0.006 0.002 HIS A 251 Details of bonding type rmsd/Z covalent geometry : bond 0.00529 / 0.24 (10454) covalent geometry : angle 0.64335 / 0.35 (14362) hydrogen bonds : bond 0.06117 / 3.86 ( 402) hydrogen bonds : angle 3.90212 / 2.75 ( 1155) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 95 time to evaluate : 0.385 Fit side-chains REVERT: A 88 TRP cc_start: 0.2564 (OUTLIER) cc_final: 0.2241 (t60) REVERT: A 131 TYR cc_start: 0.6826 (t80) cc_final: 0.6416 (t80) REVERT: A 150 LEU cc_start: 0.6933 (mt) cc_final: 0.6693 (mt) REVERT: A 180 GLU cc_start: 0.7974 (tp30) cc_final: 0.7670 (tp30) REVERT: A 400 LYS cc_start: 0.7574 (OUTLIER) cc_final: 0.6999 (mmtm) REVERT: A 591 ILE cc_start: 0.8762 (OUTLIER) cc_final: 0.8505 (tt) REVERT: A 1006 TYR cc_start: 0.6640 (m-80) cc_final: 0.6259 (m-80) REVERT: A 1050 ASP cc_start: 0.7749 (OUTLIER) cc_final: 0.7505 (p0) outliers start: 40 outliers final: 24 residues processed: 129 average time/residue: 0.0961 time to fit residues: 18.0705 Evaluate side-chains 117 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 89 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 88 TRP Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 261 GLU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 381 ASN Chi-restraints excluded: chain A residue 400 LYS Chi-restraints excluded: chain A residue 545 SER Chi-restraints excluded: chain A residue 564 ILE Chi-restraints excluded: chain A residue 578 ILE Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 672 SER Chi-restraints excluded: chain A residue 687 HIS Chi-restraints excluded: chain A residue 738 SER Chi-restraints excluded: chain A residue 757 ILE Chi-restraints excluded: chain A residue 762 THR Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 791 PHE Chi-restraints excluded: chain A residue 792 SER Chi-restraints excluded: chain A residue 818 LYS Chi-restraints excluded: chain A residue 849 VAL Chi-restraints excluded: chain A residue 1044 ILE Chi-restraints excluded: chain A residue 1050 ASP Chi-restraints excluded: chain A residue 1051 ILE Chi-restraints excluded: chain A residue 1053 LEU Chi-restraints excluded: chain A residue 1067 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 80 optimal weight: 5.9990 chunk 79 optimal weight: 0.0370 chunk 26 optimal weight: 0.8980 chunk 19 optimal weight: 6.9990 chunk 8 optimal weight: 0.0170 chunk 21 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 40 optimal weight: 6.9990 chunk 60 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 86 optimal weight: 3.9990 overall best weight: 0.9900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 767 ASN A 970 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.153016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.127569 restraints weight = 14963.953| |-----------------------------------------------------------------------------| r_work (start): 0.3788 rms_B_bonded: 2.60 r_work: 0.3659 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.1687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 10454 Z= 0.114 Angle : 0.518 6.305 14362 Z= 0.290 Chirality : 0.040 0.182 1589 Planarity : 0.003 0.050 1558 Dihedral : 19.066 174.986 2141 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.09 % Favored : 91.91 % Rotamer: Outliers : 3.27 % Allowed : 30.24 % Favored : 66.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.48 (0.26), residues: 1038 helix: 1.15 (0.22), residues: 577 sheet: -2.06 (0.73), residues: 42 loop : -2.32 (0.28), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 442 TYR 0.016 0.001 TYR A1075 PHE 0.007 0.001 PHE A 241 TRP 0.022 0.001 TRP A 884 HIS 0.003 0.001 HIS A 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.11 (10454) covalent geometry : angle 0.51825 / 0.29 (14362) hydrogen bonds : bond 0.04679 / 3.00 ( 402) hydrogen bonds : angle 3.65464 / 2.58 ( 1155) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 102 time to evaluate : 0.374 Fit side-chains revert: symmetry clash REVERT: A 36 ARG cc_start: 0.8059 (ptt90) cc_final: 0.7753 (ptm160) REVERT: A 131 TYR cc_start: 0.6783 (t80) cc_final: 0.6385 (t80) REVERT: A 150 LEU cc_start: 0.6792 (mt) cc_final: 0.6571 (mt) REVERT: A 884 TRP cc_start: 0.8428 (t60) cc_final: 0.7916 (t-100) REVERT: A 1006 TYR cc_start: 0.6472 (m-80) cc_final: 0.6059 (m-80) REVERT: A 1050 ASP cc_start: 0.7788 (OUTLIER) cc_final: 0.7539 (p0) outliers start: 31 outliers final: 25 residues processed: 126 average time/residue: 0.0961 time to fit residues: 17.4497 Evaluate side-chains 121 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 95 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 56 TYR Chi-restraints excluded: chain A residue 88 TRP Chi-restraints excluded: chain A residue 261 GLU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 381 ASN Chi-restraints excluded: chain A residue 545 SER Chi-restraints excluded: chain A residue 578 ILE Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 672 SER Chi-restraints excluded: chain A residue 687 HIS Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 757 ILE Chi-restraints excluded: chain A residue 762 THR Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 776 THR Chi-restraints excluded: chain A residue 791 PHE Chi-restraints excluded: chain A residue 818 LYS Chi-restraints excluded: chain A residue 849 VAL Chi-restraints excluded: chain A residue 1010 ILE Chi-restraints excluded: chain A residue 1050 ASP Chi-restraints excluded: chain A residue 1053 LEU Chi-restraints excluded: chain A residue 1070 ASP Chi-restraints excluded: chain A residue 1105 ASN Chi-restraints excluded: chain A residue 1108 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 32 optimal weight: 7.9990 chunk 53 optimal weight: 7.9990 chunk 50 optimal weight: 4.9990 chunk 39 optimal weight: 0.9980 chunk 86 optimal weight: 0.7980 chunk 13 optimal weight: 2.9990 chunk 66 optimal weight: 7.9990 chunk 52 optimal weight: 4.9990 chunk 70 optimal weight: 4.9990 chunk 71 optimal weight: 5.9990 chunk 6 optimal weight: 6.9990 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 970 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.150114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.124044 restraints weight = 15442.092| |-----------------------------------------------------------------------------| r_work (start): 0.3741 rms_B_bonded: 2.63 r_work: 0.3613 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.1832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 10454 Z= 0.192 Angle : 0.577 6.607 14362 Z= 0.319 Chirality : 0.043 0.198 1589 Planarity : 0.004 0.047 1558 Dihedral : 19.084 168.718 2141 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.83 % Favored : 90.17 % Rotamer: Outliers : 3.79 % Allowed : 30.24 % Favored : 65.96 % 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: -0.63 (0.26), residues: 1038 helix: 1.03 (0.22), residues: 572 sheet: -2.52 (0.70), residues: 41 loop : -2.30 (0.28), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 432 TYR 0.021 0.002 TYR A 155 PHE 0.011 0.002 PHE A 443 TRP 0.017 0.001 TRP A 884 HIS 0.003 0.001 HIS A 989 Details of bonding type rmsd/Z covalent geometry : bond 0.00437 / 0.19 (10454) covalent geometry : angle 0.57710 / 0.32 (14362) hydrogen bonds : bond 0.05345 / 3.39 ( 402) hydrogen bonds : angle 3.78212 / 2.66 ( 1155) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 96 time to evaluate : 0.419 Fit side-chains revert: symmetry clash REVERT: A 150 LEU cc_start: 0.6884 (mt) cc_final: 0.6653 (mt) REVERT: A 591 ILE cc_start: 0.8684 (OUTLIER) cc_final: 0.8406 (tt) REVERT: A 882 MET cc_start: 0.8074 (mmt) cc_final: 0.7841 (tpt) REVERT: A 939 LYS cc_start: 0.7274 (mtpt) cc_final: 0.7008 (tttp) REVERT: A 1006 TYR cc_start: 0.6604 (m-80) cc_final: 0.6115 (m-80) REVERT: A 1050 ASP cc_start: 0.7913 (OUTLIER) cc_final: 0.7661 (p0) outliers start: 36 outliers final: 30 residues processed: 123 average time/residue: 0.0863 time to fit residues: 15.4150 Evaluate side-chains 126 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 94 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 56 TYR Chi-restraints excluded: chain A residue 88 TRP Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 261 GLU Chi-restraints excluded: chain A residue 301 MET Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 381 ASN Chi-restraints excluded: chain A residue 545 SER Chi-restraints excluded: chain A residue 578 ILE Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 672 SER Chi-restraints excluded: chain A residue 687 HIS Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 757 ILE Chi-restraints excluded: chain A residue 762 THR Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 776 THR Chi-restraints excluded: chain A residue 788 SER Chi-restraints excluded: chain A residue 791 PHE Chi-restraints excluded: chain A residue 792 SER Chi-restraints excluded: chain A residue 818 LYS Chi-restraints excluded: chain A residue 849 VAL Chi-restraints excluded: chain A residue 970 GLN Chi-restraints excluded: chain A residue 1010 ILE Chi-restraints excluded: chain A residue 1044 ILE Chi-restraints excluded: chain A residue 1050 ASP Chi-restraints excluded: chain A residue 1053 LEU Chi-restraints excluded: chain A residue 1070 ASP Chi-restraints excluded: chain A residue 1105 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 4 optimal weight: 8.9990 chunk 15 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 69 optimal weight: 8.9990 chunk 90 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 86 optimal weight: 4.9990 chunk 44 optimal weight: 0.9990 chunk 53 optimal weight: 5.9990 chunk 7 optimal weight: 20.0000 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 970 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.150543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.125140 restraints weight = 15074.036| |-----------------------------------------------------------------------------| r_work (start): 0.3756 rms_B_bonded: 2.54 r_work: 0.3630 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.1847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10454 Z= 0.147 Angle : 0.551 9.717 14362 Z= 0.304 Chirality : 0.041 0.194 1589 Planarity : 0.003 0.050 1558 Dihedral : 19.076 170.604 2141 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.44 % Favored : 90.56 % Rotamer: Outliers : 3.58 % Allowed : 30.56 % Favored : 65.86 % 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 (0.26), residues: 1038 helix: 1.07 (0.22), residues: 577 sheet: -2.40 (0.72), residues: 43 loop : -2.34 (0.28), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1048 TYR 0.019 0.002 TYR A 155 PHE 0.009 0.001 PHE A 526 TRP 0.019 0.001 TRP A 884 HIS 0.003 0.001 HIS A 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.15 (10454) covalent geometry : angle 0.55132 / 0.30 (14362) hydrogen bonds : bond 0.05050 / 3.22 ( 402) hydrogen bonds : angle 3.74501 / 2.64 ( 1155) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 98 time to evaluate : 0.375 Fit side-chains revert: symmetry clash REVERT: A 36 ARG cc_start: 0.8104 (ptt90) cc_final: 0.7845 (ptm160) REVERT: A 591 ILE cc_start: 0.8682 (OUTLIER) cc_final: 0.8404 (tt) REVERT: A 882 MET cc_start: 0.8057 (mmt) cc_final: 0.7834 (tpt) REVERT: A 1006 TYR cc_start: 0.6554 (m-80) cc_final: 0.6086 (m-80) REVERT: A 1050 ASP cc_start: 0.7937 (OUTLIER) cc_final: 0.7664 (p0) outliers start: 34 outliers final: 28 residues processed: 125 average time/residue: 0.0939 time to fit residues: 17.0319 Evaluate side-chains 124 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 94 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 88 TRP Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 261 GLU Chi-restraints excluded: chain A residue 301 MET Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 381 ASN Chi-restraints excluded: chain A residue 545 SER Chi-restraints excluded: chain A residue 578 ILE Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 672 SER Chi-restraints excluded: chain A residue 687 HIS Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 757 ILE Chi-restraints excluded: chain A residue 762 THR Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 776 THR Chi-restraints excluded: chain A residue 791 PHE Chi-restraints excluded: chain A residue 792 SER Chi-restraints excluded: chain A residue 818 LYS Chi-restraints excluded: chain A residue 849 VAL Chi-restraints excluded: chain A residue 945 VAL Chi-restraints excluded: chain A residue 1010 ILE Chi-restraints excluded: chain A residue 1044 ILE Chi-restraints excluded: chain A residue 1050 ASP Chi-restraints excluded: chain A residue 1053 LEU Chi-restraints excluded: chain A residue 1070 ASP Chi-restraints excluded: chain A residue 1105 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 36 optimal weight: 1.9990 chunk 108 optimal weight: 10.0000 chunk 47 optimal weight: 1.9990 chunk 81 optimal weight: 0.7980 chunk 49 optimal weight: 2.9990 chunk 3 optimal weight: 9.9990 chunk 26 optimal weight: 2.9990 chunk 92 optimal weight: 9.9990 chunk 75 optimal weight: 7.9990 chunk 102 optimal weight: 0.8980 chunk 32 optimal weight: 6.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 970 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.152458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.126494 restraints weight = 15233.383| |-----------------------------------------------------------------------------| r_work (start): 0.3767 rms_B_bonded: 2.61 r_work: 0.3640 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.1906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10454 Z= 0.135 Angle : 0.544 9.910 14362 Z= 0.300 Chirality : 0.041 0.198 1589 Planarity : 0.003 0.050 1558 Dihedral : 19.037 172.431 2141 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.25 % Favored : 90.75 % Rotamer: Outliers : 3.37 % Allowed : 30.87 % Favored : 65.75 % 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 (0.26), residues: 1038 helix: 1.15 (0.22), residues: 577 sheet: -2.40 (0.71), residues: 43 loop : -2.33 (0.28), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1048 TYR 0.021 0.001 TYR A 131 PHE 0.008 0.001 PHE A 526 TRP 0.019 0.001 TRP A 884 HIS 0.003 0.001 HIS A 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.14 (10454) covalent geometry : angle 0.54444 / 0.30 (14362) hydrogen bonds : bond 0.04782 / 3.05 ( 402) hydrogen bonds : angle 3.71278 / 2.62 ( 1155) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 96 time to evaluate : 0.368 Fit side-chains revert: symmetry clash REVERT: A 36 ARG cc_start: 0.8143 (ptt90) cc_final: 0.7879 (ptm160) REVERT: A 102 TYR cc_start: 0.8221 (m-80) cc_final: 0.7806 (m-80) REVERT: A 882 MET cc_start: 0.8038 (mmt) cc_final: 0.7835 (tpt) REVERT: A 1006 TYR cc_start: 0.6506 (m-80) cc_final: 0.6054 (m-80) REVERT: A 1050 ASP cc_start: 0.7922 (OUTLIER) cc_final: 0.7657 (p0) outliers start: 32 outliers final: 30 residues processed: 120 average time/residue: 0.0963 time to fit residues: 16.8434 Evaluate side-chains 124 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 93 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 56 TYR Chi-restraints excluded: chain A residue 88 TRP Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 261 GLU Chi-restraints excluded: chain A residue 301 MET Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 381 ASN Chi-restraints excluded: chain A residue 545 SER Chi-restraints excluded: chain A residue 578 ILE Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 672 SER Chi-restraints excluded: chain A residue 687 HIS Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 757 ILE Chi-restraints excluded: chain A residue 762 THR Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 776 THR Chi-restraints excluded: chain A residue 791 PHE Chi-restraints excluded: chain A residue 792 SER Chi-restraints excluded: chain A residue 818 LYS Chi-restraints excluded: chain A residue 849 VAL Chi-restraints excluded: chain A residue 945 VAL Chi-restraints excluded: chain A residue 1010 ILE Chi-restraints excluded: chain A residue 1044 ILE Chi-restraints excluded: chain A residue 1050 ASP Chi-restraints excluded: chain A residue 1053 LEU Chi-restraints excluded: chain A residue 1070 ASP Chi-restraints excluded: chain A residue 1105 ASN Chi-restraints excluded: chain A residue 1108 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 68 optimal weight: 2.9990 chunk 85 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 45 optimal weight: 8.9990 chunk 71 optimal weight: 10.0000 chunk 58 optimal weight: 2.9990 chunk 6 optimal weight: 9.9990 chunk 66 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 5 optimal weight: 0.0030 chunk 0 optimal weight: 10.0000 overall best weight: 1.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 970 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.155211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.129258 restraints weight = 15137.034| |-----------------------------------------------------------------------------| r_work (start): 0.3773 rms_B_bonded: 2.62 r_work: 0.3647 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.1923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10454 Z= 0.130 Angle : 0.543 10.122 14362 Z= 0.299 Chirality : 0.041 0.203 1589 Planarity : 0.003 0.050 1558 Dihedral : 19.001 172.457 2141 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.86 % Favored : 91.14 % Rotamer: Outliers : 3.48 % Allowed : 31.19 % Favored : 65.33 % 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: -0.44 (0.26), residues: 1038 helix: 1.20 (0.22), residues: 577 sheet: -2.35 (0.72), residues: 43 loop : -2.30 (0.28), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1095 TYR 0.019 0.001 TYR A1075 PHE 0.008 0.001 PHE A 855 TRP 0.020 0.001 TRP A 884 HIS 0.003 0.001 HIS A 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.13 (10454) covalent geometry : angle 0.54321 / 0.30 (14362) hydrogen bonds : bond 0.04707 / 3.00 ( 402) hydrogen bonds : angle 3.67837 / 2.59 ( 1155) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2003.57 seconds wall clock time: 35 minutes 21.86 seconds (2121.86 seconds total)