Starting phenix.real_space_refine on Wed Aug 5 22:41:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sfr_40449/08_2026/8sfr_40449.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sfr_40449/08_2026/8sfr_40449.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8sfr_40449/08_2026/8sfr_40449.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sfr_40449/08_2026/8sfr_40449.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8sfr_40449/08_2026/8sfr_40449.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sfr_40449/08_2026/8sfr_40449.map" } resolution = 3.5 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= 0.031 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 91 5.49 5 S 23 5.16 5 C 7395 2.51 5 N 2050 2.21 5 O 2486 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12045 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 10138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1240, 10138 Classifications: {'peptide': 1240} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 46, 'TRANS': 1193} Chain breaks: 2 Chain: "B" Number of atoms: 826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 826 Classifications: {'RNA': 39} Modifications used: {'5*END': 1, 'rna2p_pur': 3, 'rna2p_pyr': 4, 'rna3p_pur': 17, 'rna3p_pyr': 15} Link IDs: {'rna2p': 7, 'rna3p': 31} Chain: "C" Number of atoms: 696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 696 Classifications: {'DNA': 34} Link IDs: {'rna3p': 33} Chain: "D" Number of atoms: 385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 385 Classifications: {'DNA': 19} Link IDs: {'rna3p': 18} Time building chain proxies: 2.86, per 1000 atoms: 0.24 Number of scatterers: 12045 At special positions: 0 Unit cell: (90.797, 106.624, 140.777, 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 23 16.00 P 91 15.00 O 2486 8.00 N 2050 7.00 C 7395 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: 1.04 Conformation dependent library (CDL) restraints added in 463.4 milliseconds 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2368 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 9 sheets defined 53.6% alpha, 10.8% beta 40 base pairs and 67 stacking pairs defined. Time for finding SS restraints: 1.58 Creating SS restraints... Processing helix chain 'A' and resid 3 through 7 Processing helix chain 'A' and resid 26 through 35 removed outlier: 3.875A pdb=" N GLN A 32 " --> pdb=" O LEU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 35 through 67 Proline residue: A 52 - end of helix removed outlier: 3.787A pdb=" N ARG A 56 " --> pdb=" O PRO A 52 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ILE A 57 " --> pdb=" O ILE A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 86 removed outlier: 3.549A pdb=" N GLU A 86 " --> pdb=" O SER A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 112 removed outlier: 3.862A pdb=" N TYR A 109 " --> pdb=" O ALA A 105 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N PHE A 110 " --> pdb=" O ILE A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 130 Processing helix chain 'A' and resid 140 through 147 removed outlier: 3.579A pdb=" N LYS A 144 " --> pdb=" O GLY A 140 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLN A 145 " --> pdb=" O LYS A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 160 Processing helix chain 'A' and resid 161 through 163 No H-bonds generated for 'chain 'A' and resid 161 through 163' Processing helix chain 'A' and resid 165 through 168 Processing helix chain 'A' and resid 169 through 178 Processing helix chain 'A' and resid 188 through 196 Processing helix chain 'A' and resid 196 through 215 removed outlier: 3.944A pdb=" N LYS A 200 " --> pdb=" O ASP A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 230 removed outlier: 3.774A pdb=" N HIS A 221 " --> pdb=" O SER A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 248 removed outlier: 5.913A pdb=" N PHE A 243 " --> pdb=" O VAL A 240 " (cutoff:3.500A) Proline residue: A 244 - end of helix Processing helix chain 'A' and resid 251 through 264 removed outlier: 3.507A pdb=" N ILE A 255 " --> pdb=" O THR A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 286 Processing helix chain 'A' and resid 289 through 297 Processing helix chain 'A' and resid 325 through 343 Processing helix chain 'A' and resid 344 through 356 removed outlier: 3.534A pdb=" N THR A 348 " --> pdb=" O ASN A 344 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LEU A 356 " --> pdb=" O LEU A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 359 No H-bonds generated for 'chain 'A' and resid 357 through 359' Processing helix chain 'A' and resid 370 through 379 Processing helix chain 'A' and resid 382 through 396 removed outlier: 4.410A pdb=" N ARG A 386 " --> pdb=" O TRP A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 415 removed outlier: 3.801A pdb=" N HIS A 415 " --> pdb=" O ARG A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 428 Processing helix chain 'A' and resid 428 through 452 removed outlier: 3.507A pdb=" N SER A 432 " --> pdb=" O GLY A 428 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 482 removed outlier: 3.510A pdb=" N LYS A 464 " --> pdb=" O LYS A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 508 Processing helix chain 'A' and resid 509 through 522 Processing helix chain 'A' and resid 570 through 574 removed outlier: 4.157A pdb=" N GLY A 573 " --> pdb=" O LYS A 570 " (cutoff:3.500A) Processing helix chain 'A' and resid 600 through 610 Proline residue: A 606 - end of helix Processing helix chain 'A' and resid 612 through 622 Processing helix chain 'A' and resid 639 through 647 Processing helix chain 'A' and resid 656 through 664 removed outlier: 3.789A pdb=" N ALA A 660 " --> pdb=" O GLN A 656 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 687 Processing helix chain 'A' and resid 700 through 704 Processing helix chain 'A' and resid 706 through 719 Proline residue: A 716 - end of helix removed outlier: 3.830A pdb=" N TYR A 719 " --> pdb=" O ASN A 715 " (cutoff:3.500A) Processing helix chain 'A' and resid 728 through 737 Processing helix chain 'A' and resid 759 through 769 removed outlier: 3.784A pdb=" N PHE A 769 " --> pdb=" O TRP A 765 " (cutoff:3.500A) Processing helix chain 'A' and resid 770 through 776 Processing helix chain 'A' and resid 861 through 865 removed outlier: 3.642A pdb=" N PHE A 864 " --> pdb=" O ASP A 861 " (cutoff:3.500A) Processing helix chain 'A' and resid 887 through 899 Processing helix chain 'A' and resid 939 through 956 removed outlier: 4.180A pdb=" N LYS A 943 " --> pdb=" O ASP A 939 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N GLN A 956 " --> pdb=" O VAL A 952 " (cutoff:3.500A) Processing helix chain 'A' and resid 964 through 987 removed outlier: 3.745A pdb=" N GLN A 974 " --> pdb=" O GLY A 970 " (cutoff:3.500A) Processing helix chain 'A' and resid 1008 through 1025 removed outlier: 3.643A pdb=" N GLU A1016 " --> pdb=" O TYR A1012 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N LYS A1017 " --> pdb=" O GLN A1013 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N MET A1018 " --> pdb=" O GLN A1014 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU A1019 " --> pdb=" O PHE A1015 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N CYS A1025 " --> pdb=" O ASP A1021 " (cutoff:3.500A) Processing helix chain 'A' and resid 1090 through 1100 removed outlier: 3.568A pdb=" N GLY A1100 " --> pdb=" O HIS A1096 " (cutoff:3.500A) Processing helix chain 'A' and resid 1177 through 1190 Processing helix chain 'A' and resid 1199 through 1206 removed outlier: 4.095A pdb=" N ASN A1206 " --> pdb=" O LYS A1202 " (cutoff:3.500A) Processing helix chain 'A' and resid 1208 through 1224 Processing helix chain 'A' and resid 1252 through 1254 No H-bonds generated for 'chain 'A' and resid 1252 through 1254' Processing helix chain 'A' and resid 1261 through 1284 Processing helix chain 'A' and resid 1294 through 1307 Processing sheet with id=AA1, first strand: chain 'A' and resid 531 through 532 removed outlier: 4.333A pdb=" N PHE A 869 " --> pdb=" O LEU A 21 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N TYR A 563 " --> pdb=" O ILE A 745 " (cutoff:3.500A) removed outlier: 11.191A pdb=" N ALA A 554 " --> pdb=" O TYR A 595 " (cutoff:3.500A) removed outlier: 8.142A pdb=" N TYR A 595 " --> pdb=" O ALA A 554 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N LEU A 556 " --> pdb=" O MET A 593 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 531 through 532 Processing sheet with id=AA3, first strand: chain 'A' and resid 418 through 419 removed outlier: 4.266A pdb=" N PHE A 365 " --> pdb=" O ALA A 485 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 626 through 628 Processing sheet with id=AA5, first strand: chain 'A' and resid 926 through 931 removed outlier: 6.509A pdb=" N VAL A 919 " --> pdb=" O LEU A 927 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N GLN A 929 " --> pdb=" O ILE A 917 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N ILE A 917 " --> pdb=" O GLN A 929 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N GLU A 993 " --> pdb=" O ILE A 907 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1103 through 1107 Processing sheet with id=AA7, first strand: chain 'A' and resid 1145 through 1147 Processing sheet with id=AA8, first strand: chain 'A' and resid 1159 through 1162 Processing sheet with id=AA9, first strand: chain 'A' and resid 1226 through 1229 removed outlier: 3.719A pdb=" N PHE A1249 " --> pdb=" O SER A1239 " (cutoff:3.500A) 519 hydrogen bonds defined for protein. 1461 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 96 hydrogen bonds 188 hydrogen bond angles 0 basepair planarities 40 basepair parallelities 67 stacking parallelities Total time for adding SS restraints: 2.90 Time building geometry restraints manager: 1.40 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: 3119 1.33 - 1.45: 3194 1.45 - 1.58: 5969 1.58 - 1.70: 180 1.70 - 1.82: 38 Bond restraints: 12500 Sorted by residual: bond pdb=" N1 U B 12 " pdb=" C2 U B 12 " ideal model delta sigma weight residual 1.381 1.413 -0.032 9.00e-03 1.23e+04 1.27e+01 bond pdb=" C GLU A 508 " pdb=" N PRO A 509 " ideal model delta sigma weight residual 1.334 1.362 -0.028 8.40e-03 1.42e+04 1.13e+01 bond pdb=" C3' DT D 12 " pdb=" O3' DT D 12 " ideal model delta sigma weight residual 1.435 1.393 0.042 1.30e-02 5.92e+03 1.04e+01 bond pdb=" C3' DC C 7 " pdb=" C2' DC C 7 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 1.01e+01 bond pdb=" C3' DT D 8 " pdb=" O3' DT D 8 " ideal model delta sigma weight residual 1.435 1.395 0.040 1.30e-02 5.92e+03 9.54e+00 ... (remaining 12495 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.98: 17173 4.98 - 9.96: 101 9.96 - 14.94: 18 14.94 - 19.92: 3 19.92 - 24.90: 1 Bond angle restraints: 17296 Sorted by residual: angle pdb=" C1' U B 12 " pdb=" N1 U B 12 " pdb=" C2 U B 12 " ideal model delta sigma weight residual 117.70 130.10 -12.40 1.20e+00 6.94e-01 1.07e+02 angle pdb=" N1 U B 12 " pdb=" C2 U B 12 " pdb=" O2 U B 12 " ideal model delta sigma weight residual 122.80 129.77 -6.97 7.00e-01 2.04e+00 9.93e+01 angle pdb=" O2 U B 12 " pdb=" C2 U B 12 " pdb=" N3 U B 12 " ideal model delta sigma weight residual 122.20 115.52 6.68 7.00e-01 2.04e+00 9.12e+01 angle pdb=" O3' DG D 6 " pdb=" P DA D 7 " pdb=" OP1 DA D 7 " ideal model delta sigma weight residual 108.00 132.90 -24.90 3.00e+00 1.11e-01 6.89e+01 angle pdb=" C1' U B 12 " pdb=" N1 U B 12 " pdb=" C6 U B 12 " ideal model delta sigma weight residual 121.20 111.81 9.39 1.40e+00 5.10e-01 4.50e+01 ... (remaining 17291 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.54: 6965 35.54 - 71.09: 443 71.09 - 106.63: 28 106.63 - 142.18: 0 142.18 - 177.72: 3 Dihedral angle restraints: 7439 sinusoidal: 3781 harmonic: 3658 Sorted by residual: dihedral pdb=" O4' C B 11 " pdb=" C1' C B 11 " pdb=" N1 C B 11 " pdb=" C2 C B 11 " ideal model delta sinusoidal sigma weight residual -128.00 49.72 -177.72 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' U B 12 " pdb=" C1' U B 12 " pdb=" N1 U B 12 " pdb=" C2 U B 12 " ideal model delta sinusoidal sigma weight residual 200.00 101.79 98.21 1 1.50e+01 4.44e-03 4.88e+01 dihedral pdb=" CA ALA A1007 " pdb=" C ALA A1007 " pdb=" N GLU A1008 " pdb=" CA GLU A1008 " ideal model delta harmonic sigma weight residual 180.00 152.46 27.54 0 5.00e+00 4.00e-02 3.03e+01 ... (remaining 7436 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.143: 1889 0.143 - 0.285: 24 0.285 - 0.428: 13 0.428 - 0.570: 2 0.570 - 0.713: 2 Chirality restraints: 1930 Sorted by residual: chirality pdb=" P DA D 7 " pdb=" OP1 DA D 7 " pdb=" OP2 DA D 7 " pdb=" O5' DA D 7 " both_signs ideal model delta sigma weight residual True 2.34 -3.05 -0.71 2.00e-01 2.50e+01 1.27e+01 chirality pdb=" P DA C 8 " pdb=" OP1 DA C 8 " pdb=" OP2 DA C 8 " pdb=" O5' DA C 8 " both_signs ideal model delta sigma weight residual True 2.34 -2.95 -0.62 2.00e-01 2.50e+01 9.47e+00 chirality pdb=" CG LEU A 645 " pdb=" CB LEU A 645 " pdb=" CD1 LEU A 645 " pdb=" CD2 LEU A 645 " both_signs ideal model delta sigma weight residual False -2.59 -2.13 -0.46 2.00e-01 2.50e+01 5.29e+00 ... (remaining 1927 not shown) Planarity restraints: 1895 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN A 784 " 0.017 2.00e-02 2.50e+03 3.43e-02 1.17e+01 pdb=" C GLN A 784 " -0.059 2.00e-02 2.50e+03 pdb=" O GLN A 784 " 0.023 2.00e-02 2.50e+03 pdb=" N ALA A 785 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP A 908 " 0.015 2.00e-02 2.50e+03 2.99e-02 8.92e+00 pdb=" CG ASP A 908 " -0.052 2.00e-02 2.50e+03 pdb=" OD1 ASP A 908 " 0.019 2.00e-02 2.50e+03 pdb=" OD2 ASP A 908 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT D 11 " -0.033 2.00e-02 2.50e+03 1.59e-02 6.28e+00 pdb=" N1 DT D 11 " 0.030 2.00e-02 2.50e+03 pdb=" C2 DT D 11 " 0.006 2.00e-02 2.50e+03 pdb=" O2 DT D 11 " 0.010 2.00e-02 2.50e+03 pdb=" N3 DT D 11 " -0.005 2.00e-02 2.50e+03 pdb=" C4 DT D 11 " -0.007 2.00e-02 2.50e+03 pdb=" O4 DT D 11 " -0.011 2.00e-02 2.50e+03 pdb=" C5 DT D 11 " -0.005 2.00e-02 2.50e+03 pdb=" C7 DT D 11 " 0.010 2.00e-02 2.50e+03 pdb=" C6 DT D 11 " 0.005 2.00e-02 2.50e+03 ... (remaining 1892 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1674 2.75 - 3.29: 12343 3.29 - 3.82: 23069 3.82 - 4.36: 25824 4.36 - 4.90: 40318 Nonbonded interactions: 103228 Sorted by model distance: nonbonded pdb=" O ALA A1067 " pdb=" OG1 THR A1070 " model vdw 2.210 3.040 nonbonded pdb=" O LYS A 370 " pdb=" OG1 THR A 373 " model vdw 2.280 3.040 nonbonded pdb=" O ILE A 605 " pdb=" OG SER A 609 " model vdw 2.280 3.040 nonbonded pdb=" O GLY A 767 " pdb=" OG SER A 770 " model vdw 2.285 3.040 nonbonded pdb=" O LYS A1282 " pdb=" NZ LYS A1285 " model vdw 2.302 3.120 ... (remaining 103223 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.260 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: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 13.590 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8790 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 : 0.007 0.058 12500 Z= 0.458 Angle : 1.064 24.904 17296 Z= 0.640 Chirality : 0.066 0.713 1930 Planarity : 0.005 0.050 1895 Dihedral : 20.280 177.720 5071 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 0.18 % Allowed : 20.40 % Favored : 79.42 % 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: -0.36 (0.23), residues: 1234 helix: 0.02 (0.20), residues: 601 sheet: -0.70 (0.47), residues: 121 loop : -0.22 (0.27), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 392 TYR 0.038 0.002 TYR A 526 PHE 0.031 0.002 PHE A 619 TRP 0.022 0.002 TRP A 382 HIS 0.008 0.001 HIS A 363 Details of bonding type rmsd/Z covalent geometry : bond 0.00660 / 0.46 (12500) covalent geometry : angle 1.06429 / 0.64 (17296) hydrogen bonds : bond 0.15586 / 10.02 ( 607) hydrogen bonds : angle 6.46303 / 4.68 ( 1649) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 52 time to evaluate : 0.388 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 537 MET cc_start: 0.9387 (mmt) cc_final: 0.8844 (mmm) REVERT: A 604 MET cc_start: 0.9314 (mmm) cc_final: 0.9097 (mmm) outliers start: 2 outliers final: 1 residues processed: 52 average time/residue: 0.1115 time to fit residues: 8.8987 Evaluate side-chains 50 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 49 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 969 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 98 optimal weight: 0.5980 chunk 107 optimal weight: 20.0000 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 20.0000 chunk 124 optimal weight: 20.0000 chunk 103 optimal weight: 20.0000 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 9.9990 chunk 91 optimal weight: 3.9990 chunk 55 optimal weight: 5.9990 overall best weight: 4.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 178 ASN A 560 ASN A1206 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.039920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2590 r_free = 0.2590 target = 0.028129 restraints weight = 84326.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.2629 r_free = 0.2629 target = 0.029287 restraints weight = 42826.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2655 r_free = 0.2655 target = 0.030031 restraints weight = 28774.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2671 r_free = 0.2671 target = 0.030503 restraints weight = 22585.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2681 r_free = 0.2681 target = 0.030789 restraints weight = 19331.563| |-----------------------------------------------------------------------------| r_work (final): 0.2653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8804 moved from start: 0.0871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 12500 Z= 0.274 Angle : 0.699 10.653 17296 Z= 0.383 Chirality : 0.045 0.290 1930 Planarity : 0.004 0.043 1895 Dihedral : 20.252 179.916 2524 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.71 % Allowed : 19.58 % Favored : 78.70 % 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: 0.45 (0.24), residues: 1234 helix: 0.90 (0.21), residues: 604 sheet: -0.77 (0.45), residues: 132 loop : 0.04 (0.29), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 313 TYR 0.014 0.002 TYR A 526 PHE 0.015 0.002 PHE A 655 TRP 0.010 0.001 TRP A1085 HIS 0.004 0.001 HIS A 191 Details of bonding type rmsd/Z covalent geometry : bond 0.00535 / 0.27 (12500) covalent geometry : angle 0.69918 / 0.38 (17296) hydrogen bonds : bond 0.05596 / 3.51 ( 607) hydrogen bonds : angle 5.26911 / 3.83 ( 1649) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 48 time to evaluate : 0.463 Fit side-chains REVERT: A 1 MET cc_start: 0.8919 (tpp) cc_final: 0.8312 (tmm) REVERT: A 271 THR cc_start: 0.8638 (OUTLIER) cc_final: 0.8279 (p) REVERT: A 604 MET cc_start: 0.9336 (mmm) cc_final: 0.9075 (mmm) REVERT: A 784 GLN cc_start: 0.8111 (tt0) cc_final: 0.7351 (tm-30) REVERT: A 786 GLU cc_start: 0.8696 (OUTLIER) cc_final: 0.7540 (mp0) REVERT: A 908 ASP cc_start: 0.7177 (t0) cc_final: 0.6893 (t0) REVERT: A 969 GLN cc_start: 0.8661 (OUTLIER) cc_final: 0.8079 (pp30) REVERT: A 1092 GLU cc_start: 0.9674 (OUTLIER) cc_final: 0.9329 (mp0) outliers start: 19 outliers final: 5 residues processed: 64 average time/residue: 0.1188 time to fit residues: 11.6422 Evaluate side-chains 56 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 47 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 786 GLU Chi-restraints excluded: chain A residue 969 GLN Chi-restraints excluded: chain A residue 1088 ILE Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1307 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 124 optimal weight: 30.0000 chunk 104 optimal weight: 20.0000 chunk 37 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 chunk 80 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 28 optimal weight: 9.9990 chunk 50 optimal weight: 7.9990 chunk 32 optimal weight: 2.9990 chunk 105 optimal weight: 5.9990 chunk 10 optimal weight: 10.0000 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1105 HIS ** 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 = 0.3036 r_free = 0.3036 target = 0.040022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2600 r_free = 0.2600 target = 0.028315 restraints weight = 83970.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.2640 r_free = 0.2640 target = 0.029481 restraints weight = 42774.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2665 r_free = 0.2665 target = 0.030218 restraints weight = 28703.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.2681 r_free = 0.2681 target = 0.030686 restraints weight = 22437.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2691 r_free = 0.2691 target = 0.030966 restraints weight = 19230.433| |-----------------------------------------------------------------------------| r_work (final): 0.2664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8780 moved from start: 0.1140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 12500 Z= 0.208 Angle : 0.625 11.253 17296 Z= 0.342 Chirality : 0.043 0.291 1930 Planarity : 0.003 0.035 1895 Dihedral : 20.157 179.679 2524 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.53 % Allowed : 18.59 % Favored : 78.88 % 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: 0.72 (0.25), residues: 1234 helix: 1.23 (0.21), residues: 606 sheet: -0.95 (0.46), residues: 121 loop : 0.07 (0.29), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 912 TYR 0.015 0.001 TYR A 61 PHE 0.014 0.001 PHE A 655 TRP 0.010 0.001 TRP A 382 HIS 0.005 0.001 HIS A 754 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.21 (12500) covalent geometry : angle 0.62500 / 0.34 (17296) hydrogen bonds : bond 0.04761 / 2.99 ( 607) hydrogen bonds : angle 4.85506 / 3.53 ( 1649) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 52 time to evaluate : 0.512 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.8890 (tpp) cc_final: 0.8158 (tmm) REVERT: A 48 LYS cc_start: 0.9435 (pttm) cc_final: 0.9202 (ptpp) REVERT: A 537 MET cc_start: 0.9301 (mmt) cc_final: 0.8637 (mmm) REVERT: A 604 MET cc_start: 0.9358 (mmm) cc_final: 0.9068 (mmm) REVERT: A 784 GLN cc_start: 0.8091 (tt0) cc_final: 0.7366 (tm-30) REVERT: A 786 GLU cc_start: 0.8654 (OUTLIER) cc_final: 0.7547 (mp0) REVERT: A 908 ASP cc_start: 0.7519 (t0) cc_final: 0.7270 (t0) REVERT: A 1092 GLU cc_start: 0.9689 (OUTLIER) cc_final: 0.9358 (mp0) outliers start: 28 outliers final: 15 residues processed: 76 average time/residue: 0.1147 time to fit residues: 13.0666 Evaluate side-chains 65 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 48 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LYS Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain A residue 754 HIS Chi-restraints excluded: chain A residue 786 GLU Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 933 ASN Chi-restraints excluded: chain A residue 969 GLN Chi-restraints excluded: chain A residue 1004 THR Chi-restraints excluded: chain A residue 1046 THR Chi-restraints excluded: chain A residue 1050 THR Chi-restraints excluded: chain A residue 1088 ILE Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1235 ASP Chi-restraints excluded: chain A residue 1307 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 55 optimal weight: 7.9990 chunk 56 optimal weight: 6.9990 chunk 39 optimal weight: 9.9990 chunk 97 optimal weight: 0.0030 chunk 9 optimal weight: 7.9990 chunk 79 optimal weight: 10.0000 chunk 26 optimal weight: 7.9990 chunk 107 optimal weight: 20.0000 chunk 124 optimal weight: 20.0000 chunk 99 optimal weight: 0.3980 chunk 24 optimal weight: 0.4980 overall best weight: 3.1794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 913 ASN ** A1105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1238 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.040147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2597 r_free = 0.2597 target = 0.028380 restraints weight = 83536.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.2636 r_free = 0.2636 target = 0.029575 restraints weight = 41630.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2662 r_free = 0.2662 target = 0.030335 restraints weight = 27676.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2677 r_free = 0.2677 target = 0.030780 restraints weight = 21483.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2690 r_free = 0.2690 target = 0.031131 restraints weight = 18499.660| |-----------------------------------------------------------------------------| r_work (final): 0.2662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8784 moved from start: 0.1324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 12500 Z= 0.195 Angle : 0.617 12.316 17296 Z= 0.335 Chirality : 0.043 0.315 1930 Planarity : 0.004 0.062 1895 Dihedral : 20.088 179.229 2524 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 3.34 % Allowed : 18.95 % Favored : 77.71 % 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: 0.83 (0.25), residues: 1234 helix: 1.37 (0.21), residues: 607 sheet: -1.08 (0.46), residues: 121 loop : 0.11 (0.29), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 313 TYR 0.016 0.001 TYR A 61 PHE 0.011 0.001 PHE A1079 TRP 0.012 0.001 TRP A 382 HIS 0.005 0.001 HIS A 754 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.20 (12500) covalent geometry : angle 0.61698 / 0.34 (17296) hydrogen bonds : bond 0.04477 / 2.79 ( 607) hydrogen bonds : angle 4.67451 / 3.38 ( 1649) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 50 time to evaluate : 0.433 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.8884 (tpp) cc_final: 0.8124 (tmm) REVERT: A 20 GLU cc_start: 0.8513 (tm-30) cc_final: 0.8021 (tm-30) REVERT: A 48 LYS cc_start: 0.9410 (pttm) cc_final: 0.9158 (ptpp) REVERT: A 271 THR cc_start: 0.8706 (OUTLIER) cc_final: 0.8370 (p) REVERT: A 507 MET cc_start: 0.9279 (ppp) cc_final: 0.9021 (ppp) REVERT: A 604 MET cc_start: 0.9362 (mmm) cc_final: 0.9056 (mmm) REVERT: A 784 GLN cc_start: 0.8152 (tt0) cc_final: 0.7915 (tm-30) REVERT: A 786 GLU cc_start: 0.8633 (OUTLIER) cc_final: 0.7342 (mp0) REVERT: A 908 ASP cc_start: 0.7595 (t0) cc_final: 0.7308 (t0) REVERT: A 927 LEU cc_start: 0.9710 (OUTLIER) cc_final: 0.9495 (mm) REVERT: A 969 GLN cc_start: 0.8662 (OUTLIER) cc_final: 0.8341 (mm110) REVERT: A 1092 GLU cc_start: 0.9696 (OUTLIER) cc_final: 0.9339 (mp0) REVERT: A 1119 MET cc_start: 0.9136 (mmm) cc_final: 0.8876 (mmm) outliers start: 37 outliers final: 21 residues processed: 82 average time/residue: 0.1072 time to fit residues: 13.4611 Evaluate side-chains 74 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 48 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 123 LYS Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 623 THR Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain A residue 703 GLN Chi-restraints excluded: chain A residue 752 LYS Chi-restraints excluded: chain A residue 754 HIS Chi-restraints excluded: chain A residue 786 GLU Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 927 LEU Chi-restraints excluded: chain A residue 969 GLN Chi-restraints excluded: chain A residue 1004 THR Chi-restraints excluded: chain A residue 1046 THR Chi-restraints excluded: chain A residue 1050 THR Chi-restraints excluded: chain A residue 1073 ILE Chi-restraints excluded: chain A residue 1088 ILE Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1182 LEU Chi-restraints excluded: chain A residue 1235 ASP Chi-restraints excluded: chain A residue 1307 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 34 optimal weight: 0.0370 chunk 96 optimal weight: 7.9990 chunk 111 optimal weight: 9.9990 chunk 81 optimal weight: 7.9990 chunk 119 optimal weight: 9.9990 chunk 126 optimal weight: 20.0000 chunk 44 optimal weight: 5.9990 chunk 69 optimal weight: 7.9990 chunk 13 optimal weight: 7.9990 chunk 17 optimal weight: 5.9990 chunk 48 optimal weight: 20.0000 overall best weight: 5.6066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1105 HIS ** 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 = 0.3006 r_free = 0.3006 target = 0.039312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2562 r_free = 0.2562 target = 0.027618 restraints weight = 87325.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.2601 r_free = 0.2601 target = 0.028783 restraints weight = 43964.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2627 r_free = 0.2627 target = 0.029522 restraints weight = 29382.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2643 r_free = 0.2643 target = 0.029981 restraints weight = 22957.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.2652 r_free = 0.2652 target = 0.030234 restraints weight = 19699.022| |-----------------------------------------------------------------------------| r_work (final): 0.2625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8822 moved from start: 0.1613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 12500 Z= 0.312 Angle : 0.703 10.959 17296 Z= 0.382 Chirality : 0.045 0.277 1930 Planarity : 0.004 0.035 1895 Dihedral : 20.090 179.671 2524 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 13.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 3.70 % Allowed : 19.31 % Favored : 76.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.24), residues: 1234 helix: 1.21 (0.21), residues: 613 sheet: -1.40 (0.45), residues: 121 loop : -0.01 (0.30), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 313 TYR 0.023 0.002 TYR A1012 PHE 0.017 0.002 PHE A1079 TRP 0.011 0.001 TRP A 382 HIS 0.006 0.001 HIS A 191 Details of bonding type rmsd/Z covalent geometry : bond 0.00609 / 0.31 (12500) covalent geometry : angle 0.70251 / 0.38 (17296) hydrogen bonds : bond 0.05307 / 3.36 ( 607) hydrogen bonds : angle 4.81070 / 3.48 ( 1649) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 50 time to evaluate : 0.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.8968 (tpp) cc_final: 0.8132 (tmm) REVERT: A 20 GLU cc_start: 0.8457 (tm-30) cc_final: 0.8099 (tm-30) REVERT: A 48 LYS cc_start: 0.9401 (pttm) cc_final: 0.9153 (ptpp) REVERT: A 271 THR cc_start: 0.8614 (OUTLIER) cc_final: 0.8239 (p) REVERT: A 507 MET cc_start: 0.9232 (ppp) cc_final: 0.8941 (ppp) REVERT: A 604 MET cc_start: 0.9401 (mmm) cc_final: 0.9053 (mmm) REVERT: A 784 GLN cc_start: 0.8337 (tt0) cc_final: 0.7742 (tm-30) REVERT: A 786 GLU cc_start: 0.8694 (OUTLIER) cc_final: 0.7668 (mp0) REVERT: A 908 ASP cc_start: 0.7854 (t0) cc_final: 0.7553 (t0) REVERT: A 927 LEU cc_start: 0.9725 (OUTLIER) cc_final: 0.9506 (mm) REVERT: A 969 GLN cc_start: 0.8618 (OUTLIER) cc_final: 0.8360 (mm110) REVERT: A 1046 THR cc_start: 0.9138 (OUTLIER) cc_final: 0.8918 (p) REVERT: A 1092 GLU cc_start: 0.9699 (OUTLIER) cc_final: 0.9338 (mp0) outliers start: 41 outliers final: 22 residues processed: 87 average time/residue: 0.1110 time to fit residues: 14.3625 Evaluate side-chains 78 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 50 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 123 LYS Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 622 HIS Chi-restraints excluded: chain A residue 623 THR Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain A residue 703 GLN Chi-restraints excluded: chain A residue 754 HIS Chi-restraints excluded: chain A residue 786 GLU Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 927 LEU Chi-restraints excluded: chain A residue 969 GLN Chi-restraints excluded: chain A residue 1004 THR Chi-restraints excluded: chain A residue 1046 THR Chi-restraints excluded: chain A residue 1050 THR Chi-restraints excluded: chain A residue 1073 ILE Chi-restraints excluded: chain A residue 1074 ASP Chi-restraints excluded: chain A residue 1088 ILE Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1182 LEU Chi-restraints excluded: chain A residue 1235 ASP Chi-restraints excluded: chain A residue 1307 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 60 optimal weight: 0.0170 chunk 1 optimal weight: 6.9990 chunk 101 optimal weight: 4.9990 chunk 96 optimal weight: 6.9990 chunk 49 optimal weight: 1.9990 chunk 91 optimal weight: 0.2980 chunk 44 optimal weight: 6.9990 chunk 56 optimal weight: 6.9990 chunk 104 optimal weight: 20.0000 chunk 16 optimal weight: 7.9990 chunk 52 optimal weight: 3.9990 overall best weight: 2.2624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 64 GLN ** A 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1105 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.040348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2604 r_free = 0.2604 target = 0.028557 restraints weight = 83024.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2645 r_free = 0.2645 target = 0.029762 restraints weight = 41424.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.2671 r_free = 0.2671 target = 0.030541 restraints weight = 27444.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2686 r_free = 0.2686 target = 0.030989 restraints weight = 21228.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2698 r_free = 0.2698 target = 0.031320 restraints weight = 18240.709| |-----------------------------------------------------------------------------| r_work (final): 0.2672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8773 moved from start: 0.1654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12500 Z= 0.155 Angle : 0.607 14.263 17296 Z= 0.328 Chirality : 0.043 0.286 1930 Planarity : 0.003 0.031 1895 Dihedral : 20.022 178.749 2524 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 3.25 % Allowed : 19.31 % Favored : 77.44 % 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: 0.86 (0.25), residues: 1234 helix: 1.42 (0.21), residues: 613 sheet: -1.19 (0.45), residues: 121 loop : 0.11 (0.30), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 951 TYR 0.017 0.001 TYR A1012 PHE 0.012 0.001 PHE A1140 TRP 0.014 0.001 TRP A 382 HIS 0.005 0.001 HIS A 754 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.15 (12500) covalent geometry : angle 0.60662 / 0.33 (17296) hydrogen bonds : bond 0.04109 / 2.57 ( 607) hydrogen bonds : angle 4.46505 / 3.23 ( 1649) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 53 time to evaluate : 0.421 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.8937 (tpp) cc_final: 0.8058 (tmm) REVERT: A 20 GLU cc_start: 0.8485 (tm-30) cc_final: 0.8070 (tm-30) REVERT: A 48 LYS cc_start: 0.9420 (pttm) cc_final: 0.9195 (ptpp) REVERT: A 165 PHE cc_start: 0.8922 (OUTLIER) cc_final: 0.8594 (t80) REVERT: A 271 THR cc_start: 0.8656 (OUTLIER) cc_final: 0.8304 (p) REVERT: A 507 MET cc_start: 0.9231 (ppp) cc_final: 0.9030 (ppp) REVERT: A 537 MET cc_start: 0.9296 (mmt) cc_final: 0.8622 (mmm) REVERT: A 604 MET cc_start: 0.9315 (mmm) cc_final: 0.8976 (mmm) REVERT: A 754 HIS cc_start: 0.8211 (OUTLIER) cc_final: 0.7879 (t-90) REVERT: A 784 GLN cc_start: 0.8319 (tt0) cc_final: 0.7699 (tm-30) REVERT: A 786 GLU cc_start: 0.8637 (OUTLIER) cc_final: 0.7528 (mp0) REVERT: A 908 ASP cc_start: 0.7816 (t0) cc_final: 0.7546 (t0) REVERT: A 969 GLN cc_start: 0.8658 (OUTLIER) cc_final: 0.8389 (mm-40) REVERT: A 1065 VAL cc_start: 0.9658 (OUTLIER) cc_final: 0.9399 (p) REVERT: A 1074 ASP cc_start: 0.9550 (OUTLIER) cc_final: 0.8784 (p0) REVERT: A 1092 GLU cc_start: 0.9698 (OUTLIER) cc_final: 0.9331 (mp0) outliers start: 36 outliers final: 21 residues processed: 82 average time/residue: 0.1102 time to fit residues: 13.7019 Evaluate side-chains 80 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 51 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 123 LYS Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 165 PHE Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain A residue 703 GLN Chi-restraints excluded: chain A residue 752 LYS Chi-restraints excluded: chain A residue 754 HIS Chi-restraints excluded: chain A residue 786 GLU Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 969 GLN Chi-restraints excluded: chain A residue 1004 THR Chi-restraints excluded: chain A residue 1050 THR Chi-restraints excluded: chain A residue 1065 VAL Chi-restraints excluded: chain A residue 1073 ILE Chi-restraints excluded: chain A residue 1074 ASP Chi-restraints excluded: chain A residue 1088 ILE Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1182 LEU Chi-restraints excluded: chain A residue 1235 ASP Chi-restraints excluded: chain A residue 1307 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 24 optimal weight: 1.9990 chunk 112 optimal weight: 10.0000 chunk 6 optimal weight: 3.9990 chunk 41 optimal weight: 20.0000 chunk 75 optimal weight: 4.9990 chunk 30 optimal weight: 0.4980 chunk 55 optimal weight: 6.9990 chunk 115 optimal weight: 4.9990 chunk 79 optimal weight: 4.9990 chunk 69 optimal weight: 8.9990 chunk 4 optimal weight: 6.9990 overall best weight: 3.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 195 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 = 0.3031 r_free = 0.3031 target = 0.040053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2593 r_free = 0.2593 target = 0.028286 restraints weight = 84910.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2633 r_free = 0.2633 target = 0.029476 restraints weight = 42588.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2658 r_free = 0.2658 target = 0.030237 restraints weight = 28443.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2673 r_free = 0.2673 target = 0.030673 restraints weight = 22173.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.2685 r_free = 0.2685 target = 0.030989 restraints weight = 19165.500| |-----------------------------------------------------------------------------| r_work (final): 0.2656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8790 moved from start: 0.1732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 12500 Z= 0.199 Angle : 0.632 13.585 17296 Z= 0.339 Chirality : 0.043 0.395 1930 Planarity : 0.003 0.031 1895 Dihedral : 19.974 179.096 2524 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 3.34 % Allowed : 19.77 % Favored : 76.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.90 (0.25), residues: 1234 helix: 1.46 (0.21), residues: 614 sheet: -1.16 (0.44), residues: 121 loop : 0.10 (0.30), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 951 TYR 0.017 0.001 TYR A 61 PHE 0.012 0.001 PHE A1113 TRP 0.013 0.001 TRP A 382 HIS 0.005 0.001 HIS A 754 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.20 (12500) covalent geometry : angle 0.63236 / 0.34 (17296) hydrogen bonds : bond 0.04332 / 2.73 ( 607) hydrogen bonds : angle 4.55342 / 3.26 ( 1649) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 54 time to evaluate : 0.486 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.8974 (tpp) cc_final: 0.8123 (tmm) REVERT: A 20 GLU cc_start: 0.8467 (tm-30) cc_final: 0.8081 (tm-30) REVERT: A 48 LYS cc_start: 0.9419 (pttm) cc_final: 0.9204 (ptpp) REVERT: A 271 THR cc_start: 0.8665 (OUTLIER) cc_final: 0.8318 (p) REVERT: A 507 MET cc_start: 0.9216 (ppp) cc_final: 0.9000 (ppp) REVERT: A 537 MET cc_start: 0.9278 (mmt) cc_final: 0.8582 (mmm) REVERT: A 604 MET cc_start: 0.9339 (mmm) cc_final: 0.8986 (mmm) REVERT: A 754 HIS cc_start: 0.8215 (OUTLIER) cc_final: 0.8010 (t-90) REVERT: A 784 GLN cc_start: 0.8418 (tt0) cc_final: 0.7776 (tm-30) REVERT: A 786 GLU cc_start: 0.8645 (OUTLIER) cc_final: 0.7583 (mp0) REVERT: A 908 ASP cc_start: 0.7783 (t0) cc_final: 0.7435 (t0) REVERT: A 969 GLN cc_start: 0.8622 (OUTLIER) cc_final: 0.8381 (mm110) REVERT: A 1065 VAL cc_start: 0.9641 (OUTLIER) cc_final: 0.9370 (p) REVERT: A 1074 ASP cc_start: 0.9571 (OUTLIER) cc_final: 0.8737 (p0) REVERT: A 1092 GLU cc_start: 0.9704 (OUTLIER) cc_final: 0.9343 (mp0) outliers start: 37 outliers final: 22 residues processed: 86 average time/residue: 0.1096 time to fit residues: 14.1981 Evaluate side-chains 81 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 52 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 123 LYS Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 622 HIS Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain A residue 703 GLN Chi-restraints excluded: chain A residue 752 LYS Chi-restraints excluded: chain A residue 754 HIS Chi-restraints excluded: chain A residue 786 GLU Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 969 GLN Chi-restraints excluded: chain A residue 1004 THR Chi-restraints excluded: chain A residue 1046 THR Chi-restraints excluded: chain A residue 1050 THR Chi-restraints excluded: chain A residue 1065 VAL Chi-restraints excluded: chain A residue 1073 ILE Chi-restraints excluded: chain A residue 1074 ASP Chi-restraints excluded: chain A residue 1088 ILE Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1182 LEU Chi-restraints excluded: chain A residue 1235 ASP Chi-restraints excluded: chain A residue 1307 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 7 optimal weight: 8.9990 chunk 118 optimal weight: 8.9990 chunk 9 optimal weight: 5.9990 chunk 73 optimal weight: 9.9990 chunk 110 optimal weight: 9.9990 chunk 98 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 90 optimal weight: 6.9990 chunk 34 optimal weight: 6.9990 chunk 16 optimal weight: 8.9990 chunk 119 optimal weight: 1.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 913 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.039944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2588 r_free = 0.2588 target = 0.028195 restraints weight = 84688.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.2628 r_free = 0.2628 target = 0.029363 restraints weight = 42737.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2654 r_free = 0.2654 target = 0.030135 restraints weight = 28726.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2668 r_free = 0.2668 target = 0.030566 restraints weight = 22370.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.2680 r_free = 0.2680 target = 0.030887 restraints weight = 19351.817| |-----------------------------------------------------------------------------| r_work (final): 0.2651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8795 moved from start: 0.1840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 12500 Z= 0.219 Angle : 0.644 13.631 17296 Z= 0.346 Chirality : 0.044 0.366 1930 Planarity : 0.003 0.032 1895 Dihedral : 19.980 179.777 2524 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 3.61 % Allowed : 20.13 % Favored : 76.26 % 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 (0.25), residues: 1234 helix: 1.43 (0.21), residues: 619 sheet: -1.15 (0.44), residues: 121 loop : 0.03 (0.30), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 951 TYR 0.019 0.001 TYR A 61 PHE 0.015 0.001 PHE A1113 TRP 0.014 0.001 TRP A 382 HIS 0.005 0.001 HIS A 754 Details of bonding type rmsd/Z covalent geometry : bond 0.00432 / 0.22 (12500) covalent geometry : angle 0.64365 / 0.35 (17296) hydrogen bonds : bond 0.04427 / 2.81 ( 607) hydrogen bonds : angle 4.57246 / 3.27 ( 1649) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 55 time to evaluate : 0.457 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.9011 (tpp) cc_final: 0.8077 (tmm) REVERT: A 20 GLU cc_start: 0.8503 (tm-30) cc_final: 0.8144 (tm-30) REVERT: A 165 PHE cc_start: 0.8994 (OUTLIER) cc_final: 0.8624 (t80) REVERT: A 271 THR cc_start: 0.8653 (OUTLIER) cc_final: 0.8301 (p) REVERT: A 357 ASN cc_start: 0.9829 (OUTLIER) cc_final: 0.9462 (p0) REVERT: A 507 MET cc_start: 0.9209 (ppp) cc_final: 0.8977 (ppp) REVERT: A 604 MET cc_start: 0.9347 (mmm) cc_final: 0.8994 (mmm) REVERT: A 709 GLU cc_start: 0.9250 (OUTLIER) cc_final: 0.9048 (tm-30) REVERT: A 754 HIS cc_start: 0.8220 (OUTLIER) cc_final: 0.8015 (t-90) REVERT: A 784 GLN cc_start: 0.8518 (tt0) cc_final: 0.7850 (tm-30) REVERT: A 786 GLU cc_start: 0.8650 (OUTLIER) cc_final: 0.7578 (mp0) REVERT: A 908 ASP cc_start: 0.7792 (t0) cc_final: 0.7405 (t0) REVERT: A 969 GLN cc_start: 0.8614 (OUTLIER) cc_final: 0.8372 (mm110) REVERT: A 1065 VAL cc_start: 0.9615 (OUTLIER) cc_final: 0.9335 (p) REVERT: A 1074 ASP cc_start: 0.9574 (OUTLIER) cc_final: 0.8732 (p0) REVERT: A 1092 GLU cc_start: 0.9700 (OUTLIER) cc_final: 0.9336 (mp0) outliers start: 40 outliers final: 23 residues processed: 89 average time/residue: 0.1125 time to fit residues: 15.0225 Evaluate side-chains 84 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 51 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 123 LYS Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 165 PHE Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 357 ASN Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 622 HIS Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain A residue 703 GLN Chi-restraints excluded: chain A residue 709 GLU Chi-restraints excluded: chain A residue 754 HIS Chi-restraints excluded: chain A residue 786 GLU Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 960 VAL Chi-restraints excluded: chain A residue 969 GLN Chi-restraints excluded: chain A residue 1004 THR Chi-restraints excluded: chain A residue 1050 THR Chi-restraints excluded: chain A residue 1065 VAL Chi-restraints excluded: chain A residue 1073 ILE Chi-restraints excluded: chain A residue 1074 ASP Chi-restraints excluded: chain A residue 1088 ILE Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1182 LEU Chi-restraints excluded: chain A residue 1235 ASP Chi-restraints excluded: chain A residue 1305 LEU Chi-restraints excluded: chain A residue 1307 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 110 optimal weight: 8.9990 chunk 124 optimal weight: 30.0000 chunk 122 optimal weight: 8.9990 chunk 3 optimal weight: 0.9980 chunk 90 optimal weight: 0.9990 chunk 45 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 120 optimal weight: 8.9990 chunk 109 optimal weight: 6.9990 chunk 46 optimal weight: 5.9990 chunk 38 optimal weight: 8.9990 overall best weight: 4.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 195 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 = 0.3017 r_free = 0.3017 target = 0.039559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2577 r_free = 0.2577 target = 0.027869 restraints weight = 86096.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.2616 r_free = 0.2616 target = 0.029039 restraints weight = 43350.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2641 r_free = 0.2641 target = 0.029776 restraints weight = 29046.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2655 r_free = 0.2655 target = 0.030200 restraints weight = 22741.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2667 r_free = 0.2667 target = 0.030530 restraints weight = 19717.077| |-----------------------------------------------------------------------------| r_work (final): 0.2641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8809 moved from start: 0.1943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 12500 Z= 0.268 Angle : 0.690 13.275 17296 Z= 0.369 Chirality : 0.044 0.314 1930 Planarity : 0.003 0.032 1895 Dihedral : 20.014 179.371 2524 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 12.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 3.34 % Allowed : 20.67 % Favored : 75.99 % 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 (0.25), residues: 1234 helix: 1.34 (0.21), residues: 619 sheet: -1.28 (0.44), residues: 121 loop : -0.06 (0.29), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 951 TYR 0.019 0.002 TYR A 61 PHE 0.024 0.002 PHE A1113 TRP 0.014 0.001 TRP A 382 HIS 0.005 0.001 HIS A 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00527 / 0.27 (12500) covalent geometry : angle 0.68969 / 0.37 (17296) hydrogen bonds : bond 0.04757 / 3.02 ( 607) hydrogen bonds : angle 4.67620 / 3.35 ( 1649) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 52 time to evaluate : 0.443 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.9042 (tpp) cc_final: 0.8045 (tmm) REVERT: A 20 GLU cc_start: 0.8537 (tm-30) cc_final: 0.8253 (tm-30) REVERT: A 165 PHE cc_start: 0.9030 (OUTLIER) cc_final: 0.8651 (t80) REVERT: A 271 THR cc_start: 0.8618 (OUTLIER) cc_final: 0.8257 (p) REVERT: A 357 ASN cc_start: 0.9842 (OUTLIER) cc_final: 0.9485 (p0) REVERT: A 507 MET cc_start: 0.9199 (ppp) cc_final: 0.8963 (ppp) REVERT: A 604 MET cc_start: 0.9351 (mmm) cc_final: 0.9007 (mmm) REVERT: A 754 HIS cc_start: 0.8247 (OUTLIER) cc_final: 0.8015 (t-90) REVERT: A 784 GLN cc_start: 0.8641 (tt0) cc_final: 0.7991 (tm-30) REVERT: A 786 GLU cc_start: 0.8668 (OUTLIER) cc_final: 0.7587 (mp0) REVERT: A 908 ASP cc_start: 0.7953 (t0) cc_final: 0.7525 (t0) REVERT: A 969 GLN cc_start: 0.8567 (OUTLIER) cc_final: 0.8351 (mm110) REVERT: A 1065 VAL cc_start: 0.9604 (OUTLIER) cc_final: 0.9322 (p) REVERT: A 1074 ASP cc_start: 0.9582 (OUTLIER) cc_final: 0.8754 (p0) REVERT: A 1092 GLU cc_start: 0.9711 (OUTLIER) cc_final: 0.9347 (mp0) outliers start: 37 outliers final: 23 residues processed: 84 average time/residue: 0.1063 time to fit residues: 13.5544 Evaluate side-chains 84 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 52 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 123 LYS Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 165 PHE Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 357 ASN Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 622 HIS Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain A residue 703 GLN Chi-restraints excluded: chain A residue 754 HIS Chi-restraints excluded: chain A residue 786 GLU Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 960 VAL Chi-restraints excluded: chain A residue 969 GLN Chi-restraints excluded: chain A residue 1004 THR Chi-restraints excluded: chain A residue 1050 THR Chi-restraints excluded: chain A residue 1065 VAL Chi-restraints excluded: chain A residue 1073 ILE Chi-restraints excluded: chain A residue 1074 ASP Chi-restraints excluded: chain A residue 1088 ILE Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1095 LYS Chi-restraints excluded: chain A residue 1182 LEU Chi-restraints excluded: chain A residue 1235 ASP Chi-restraints excluded: chain A residue 1307 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 108 optimal weight: 5.9990 chunk 23 optimal weight: 2.9990 chunk 56 optimal weight: 5.9990 chunk 61 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 3 optimal weight: 0.8980 chunk 11 optimal weight: 0.9990 chunk 60 optimal weight: 4.9990 chunk 14 optimal weight: 7.9990 chunk 87 optimal weight: 9.9990 chunk 45 optimal weight: 30.0000 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 946 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.040061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2594 r_free = 0.2594 target = 0.028307 restraints weight = 85105.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2634 r_free = 0.2634 target = 0.029504 restraints weight = 42755.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2658 r_free = 0.2658 target = 0.030256 restraints weight = 28542.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.2674 r_free = 0.2674 target = 0.030720 restraints weight = 22262.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2684 r_free = 0.2684 target = 0.031015 restraints weight = 19094.906| |-----------------------------------------------------------------------------| r_work (final): 0.2655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8788 moved from start: 0.1961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 12500 Z= 0.191 Angle : 0.655 14.163 17296 Z= 0.347 Chirality : 0.044 0.338 1930 Planarity : 0.003 0.031 1895 Dihedral : 20.006 179.411 2524 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.98 % Allowed : 21.30 % Favored : 75.72 % 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: 0.79 (0.25), residues: 1234 helix: 1.39 (0.21), residues: 620 sheet: -1.16 (0.45), residues: 121 loop : -0.01 (0.30), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 951 TYR 0.016 0.001 TYR A 61 PHE 0.025 0.001 PHE A1113 TRP 0.015 0.001 TRP A 382 HIS 0.005 0.001 HIS A 754 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.19 (12500) covalent geometry : angle 0.65511 / 0.35 (17296) hydrogen bonds : bond 0.04203 / 2.66 ( 607) hydrogen bonds : angle 4.54406 / 3.26 ( 1649) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 55 time to evaluate : 0.263 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.9042 (tpp) cc_final: 0.8042 (tmm) REVERT: A 20 GLU cc_start: 0.8522 (tm-30) cc_final: 0.8195 (tm-30) REVERT: A 165 PHE cc_start: 0.8954 (OUTLIER) cc_final: 0.8603 (t80) REVERT: A 271 THR cc_start: 0.8613 (OUTLIER) cc_final: 0.8254 (p) REVERT: A 357 ASN cc_start: 0.9834 (OUTLIER) cc_final: 0.9486 (p0) REVERT: A 507 MET cc_start: 0.9191 (ppp) cc_final: 0.8942 (ppp) REVERT: A 604 MET cc_start: 0.9310 (mmm) cc_final: 0.8977 (mmm) REVERT: A 754 HIS cc_start: 0.8239 (OUTLIER) cc_final: 0.8032 (t-90) REVERT: A 784 GLN cc_start: 0.8657 (tt0) cc_final: 0.8051 (tm-30) REVERT: A 786 GLU cc_start: 0.8646 (OUTLIER) cc_final: 0.7508 (mp0) REVERT: A 908 ASP cc_start: 0.7877 (t0) cc_final: 0.7416 (t0) REVERT: A 1065 VAL cc_start: 0.9573 (OUTLIER) cc_final: 0.9283 (p) REVERT: A 1074 ASP cc_start: 0.9564 (OUTLIER) cc_final: 0.8796 (p0) REVERT: A 1092 GLU cc_start: 0.9711 (OUTLIER) cc_final: 0.9352 (mp0) outliers start: 33 outliers final: 24 residues processed: 82 average time/residue: 0.1019 time to fit residues: 12.3053 Evaluate side-chains 84 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 52 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 123 LYS Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 165 PHE Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 357 ASN Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 622 HIS Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain A residue 703 GLN Chi-restraints excluded: chain A residue 752 LYS Chi-restraints excluded: chain A residue 754 HIS Chi-restraints excluded: chain A residue 786 GLU Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 1004 THR Chi-restraints excluded: chain A residue 1050 THR Chi-restraints excluded: chain A residue 1065 VAL Chi-restraints excluded: chain A residue 1073 ILE Chi-restraints excluded: chain A residue 1074 ASP Chi-restraints excluded: chain A residue 1088 ILE Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1182 LEU Chi-restraints excluded: chain A residue 1194 ARG Chi-restraints excluded: chain A residue 1235 ASP Chi-restraints excluded: chain A residue 1305 LEU Chi-restraints excluded: chain A residue 1307 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 78 optimal weight: 8.9990 chunk 129 optimal weight: 20.0000 chunk 30 optimal weight: 0.0030 chunk 97 optimal weight: 8.9990 chunk 93 optimal weight: 8.9990 chunk 64 optimal weight: 10.0000 chunk 118 optimal weight: 5.9990 chunk 40 optimal weight: 5.9990 chunk 130 optimal weight: 20.0000 chunk 96 optimal weight: 0.9980 chunk 59 optimal weight: 1.9990 overall best weight: 2.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 195 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 = 0.3025 r_free = 0.3025 target = 0.040146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2596 r_free = 0.2596 target = 0.028605 restraints weight = 84472.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2635 r_free = 0.2635 target = 0.029758 restraints weight = 42190.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2660 r_free = 0.2660 target = 0.030517 restraints weight = 28155.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2675 r_free = 0.2675 target = 0.030969 restraints weight = 21810.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2687 r_free = 0.2687 target = 0.031293 restraints weight = 18717.841| |-----------------------------------------------------------------------------| r_work (final): 0.2660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8782 moved from start: 0.2018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 12500 Z= 0.187 Angle : 0.651 14.592 17296 Z= 0.345 Chirality : 0.043 0.316 1930 Planarity : 0.003 0.031 1895 Dihedral : 19.932 178.874 2521 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.89 % Allowed : 21.66 % Favored : 75.45 % 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 (0.25), residues: 1234 helix: 1.42 (0.21), residues: 620 sheet: -1.14 (0.45), residues: 121 loop : -0.01 (0.30), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 951 TYR 0.017 0.001 TYR A 61 PHE 0.026 0.001 PHE A1113 TRP 0.015 0.001 TRP A 382 HIS 0.005 0.001 HIS A 754 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.19 (12500) covalent geometry : angle 0.65115 / 0.34 (17296) hydrogen bonds : bond 0.04166 / 2.65 ( 607) hydrogen bonds : angle 4.51043 / 3.22 ( 1649) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2050.20 seconds wall clock time: 36 minutes 30.22 seconds (2190.22 seconds total)