Starting phenix.real_space_refine on Wed Feb 4 17:31:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sfr_40449/02_2026/8sfr_40449.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sfr_40449/02_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_40449/02_2026/8sfr_40449.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sfr_40449/02_2026/8sfr_40449.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8sfr_40449/02_2026/8sfr_40449.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sfr_40449/02_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-2.0-5952/lib/python3.9/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: 2.50, per 1000 atoms: 0.21 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: 0.74 Conformation dependent library (CDL) restraints added in 383.6 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: 1.54 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: 2.49 Time building geometry restraints manager: 0.98 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=" 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=" CB ASP A1021 " pdb=" CG ASP A1021 " ideal model delta sigma weight residual 1.516 1.472 0.044 2.50e-02 1.60e+03 3.06e+00 bond pdb=" CG ARG A 912 " pdb=" CD ARG A 912 " ideal model delta sigma weight residual 1.520 1.569 -0.049 3.00e-02 1.11e+03 2.71e+00 bond pdb=" N1 U B 12 " pdb=" C2 U B 12 " ideal model delta sigma weight residual 1.381 1.413 -0.032 2.00e-02 2.50e+03 2.58e+00 bond pdb=" CG LEU A 475 " pdb=" CD2 LEU A 475 " ideal model delta sigma weight residual 1.521 1.469 0.052 3.30e-02 9.18e+02 2.51e+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=" 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=" O3' DC C 7 " pdb=" P DA C 8 " pdb=" OP1 DA C 8 " ideal model delta sigma weight residual 108.00 126.22 -18.22 3.00e+00 1.11e-01 3.69e+01 angle pdb=" OP1 DA D 7 " pdb=" P DA D 7 " pdb=" OP2 DA D 7 " ideal model delta sigma weight residual 120.00 104.46 15.54 3.00e+00 1.11e-01 2.68e+01 angle pdb=" CA LYS A 48 " pdb=" CB LYS A 48 " pdb=" CG LYS A 48 " ideal model delta sigma weight residual 114.10 123.85 -9.75 2.00e+00 2.50e-01 2.38e+01 angle pdb=" OP1 DA C 8 " pdb=" P DA C 8 " pdb=" OP2 DA C 8 " ideal model delta sigma weight residual 120.00 105.73 14.27 3.00e+00 1.11e-01 2.26e+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 - 0.141: 1890 0.141 - 0.281: 26 0.281 - 0.422: 10 0.422 - 0.562: 2 0.562 - 0.703: 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 2.35 -3.05 -0.70 2.00e-01 2.50e+01 1.23e+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 2.35 -2.95 -0.61 2.00e-01 2.50e+01 9.16e+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: 2.530 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: 0.240 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 12.560 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.040 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:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8852 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 : 0.006 0.058 12500 Z= 0.298 Angle : 1.026 24.904 17296 Z= 0.490 Chirality : 0.062 0.703 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 covalent geometry : bond 0.00634 (12500) covalent geometry : angle 1.02616 (17296) hydrogen bonds : bond 0.15586 ( 607) hydrogen bonds : angle 6.46303 ( 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 : 0.441 Fit side-chains 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: 0.1075 time to fit residues: 8.5888 Evaluate side-chains 49 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 48 time to evaluate : 0.428 ------------------------------------------------------------------------------- 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: 6.9990 chunk 124 optimal weight: 10.0000 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... Flipped N/Q/H residues before XYZ refinement: ** A 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 178 ASN A 560 ASN ** A1105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1206 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.039535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2575 r_free = 0.2575 target = 0.027780 restraints weight = 85190.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.2614 r_free = 0.2614 target = 0.028929 restraints weight = 42764.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2640 r_free = 0.2640 target = 0.029674 restraints weight = 28675.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2654 r_free = 0.2654 target = 0.030115 restraints weight = 22442.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.2666 r_free = 0.2666 target = 0.030425 restraints weight = 19404.218| |-----------------------------------------------------------------------------| r_work (final): 0.2637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8870 moved from start: 0.1101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 12500 Z= 0.292 Angle : 0.682 9.518 17296 Z= 0.366 Chirality : 0.042 0.196 1930 Planarity : 0.004 0.040 1895 Dihedral : 20.327 179.911 2524 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.99 % Allowed : 18.50 % Favored : 79.51 % 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: 0.49 (0.24), residues: 1234 helix: 0.99 (0.21), residues: 604 sheet: -0.91 (0.46), residues: 121 loop : 0.00 (0.29), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 313 TYR 0.017 0.002 TYR A 61 PHE 0.017 0.002 PHE A 655 TRP 0.013 0.001 TRP A 382 HIS 0.005 0.001 HIS A 191 Details of bonding type rmsd covalent geometry : bond 0.00599 (12500) covalent geometry : angle 0.68218 (17296) hydrogen bonds : bond 0.05123 ( 607) hydrogen bonds : angle 5.08305 ( 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 73 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 51 time to evaluate : 0.449 Fit side-chains REVERT: A 1 MET cc_start: 0.8917 (tpp) cc_final: 0.8285 (tmm) REVERT: A 20 GLU cc_start: 0.8511 (tm-30) cc_final: 0.7995 (tm-30) REVERT: A 271 THR cc_start: 0.8689 (OUTLIER) cc_final: 0.8328 (p) REVERT: A 507 MET cc_start: 0.9251 (ppp) cc_final: 0.8991 (ppp) REVERT: A 604 MET cc_start: 0.9344 (mmm) cc_final: 0.9085 (mmm) REVERT: A 786 GLU cc_start: 0.8716 (OUTLIER) cc_final: 0.8380 (mp0) REVERT: A 908 ASP cc_start: 0.7396 (t0) cc_final: 0.7101 (t0) REVERT: A 912 ARG cc_start: 0.7936 (tpm170) cc_final: 0.7727 (tpm170) REVERT: A 969 GLN cc_start: 0.8644 (OUTLIER) cc_final: 0.8113 (pp30) REVERT: A 1092 GLU cc_start: 0.9677 (OUTLIER) cc_final: 0.9342 (mp0) outliers start: 22 outliers final: 6 residues processed: 70 average time/residue: 0.1034 time to fit residues: 10.8439 Evaluate side-chains 57 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 47 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 624 THR Chi-restraints excluded: chain A residue 786 GLU Chi-restraints excluded: chain A residue 969 GLN 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 1307 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 124 optimal weight: 10.0000 chunk 104 optimal weight: 20.0000 chunk 37 optimal weight: 0.0970 chunk 75 optimal weight: 0.9990 chunk 80 optimal weight: 0.9980 chunk 54 optimal weight: 5.9990 chunk 28 optimal weight: 3.9990 chunk 50 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 chunk 105 optimal weight: 3.9990 chunk 10 optimal weight: 10.0000 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1105 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.040992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2634 r_free = 0.2634 target = 0.029239 restraints weight = 82275.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2675 r_free = 0.2675 target = 0.030453 restraints weight = 41196.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2700 r_free = 0.2700 target = 0.031241 restraints weight = 27338.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.2717 r_free = 0.2717 target = 0.031734 restraints weight = 21197.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2728 r_free = 0.2728 target = 0.032043 restraints weight = 18028.809| |-----------------------------------------------------------------------------| r_work (final): 0.2700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8800 moved from start: 0.1369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 12500 Z= 0.124 Angle : 0.585 10.340 17296 Z= 0.303 Chirality : 0.040 0.265 1930 Planarity : 0.003 0.034 1895 Dihedral : 20.042 178.949 2524 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.53 % Allowed : 18.95 % Favored : 78.52 % 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: 0.95 (0.25), residues: 1234 helix: 1.45 (0.22), residues: 607 sheet: -0.70 (0.44), residues: 132 loop : 0.11 (0.29), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 313 TYR 0.014 0.001 TYR A 764 PHE 0.013 0.001 PHE A1113 TRP 0.009 0.001 TRP A 382 HIS 0.004 0.001 HIS A 754 Details of bonding type rmsd covalent geometry : bond 0.00265 (12500) covalent geometry : angle 0.58505 (17296) hydrogen bonds : bond 0.03722 ( 607) hydrogen bonds : angle 4.49065 ( 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 83 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 55 time to evaluate : 0.467 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.8855 (tpp) cc_final: 0.8220 (tmm) REVERT: A 20 GLU cc_start: 0.8440 (tm-30) cc_final: 0.7929 (tm-30) REVERT: A 48 LYS cc_start: 0.9394 (pttm) cc_final: 0.9140 (ptpp) REVERT: A 165 PHE cc_start: 0.8993 (OUTLIER) cc_final: 0.8753 (t80) REVERT: A 507 MET cc_start: 0.9239 (ppp) cc_final: 0.9030 (ppp) REVERT: A 604 MET cc_start: 0.9312 (mmm) cc_final: 0.8997 (mmm) REVERT: A 754 HIS cc_start: 0.8199 (OUTLIER) cc_final: 0.7987 (t-90) REVERT: A 786 GLU cc_start: 0.8574 (OUTLIER) cc_final: 0.8230 (mp0) REVERT: A 912 ARG cc_start: 0.7972 (tpm170) cc_final: 0.7747 (tpm170) REVERT: A 969 GLN cc_start: 0.8665 (OUTLIER) cc_final: 0.8008 (pp30) REVERT: A 1119 MET cc_start: 0.9177 (mmm) cc_final: 0.8941 (mmp) outliers start: 28 outliers final: 11 residues processed: 77 average time/residue: 0.0933 time to fit residues: 10.8596 Evaluate side-chains 66 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 51 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 165 PHE Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 467 LEU 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 1019 LEU Chi-restraints excluded: chain A residue 1073 ILE Chi-restraints excluded: chain A residue 1088 ILE Chi-restraints excluded: chain A residue 1235 ASP Chi-restraints excluded: chain A residue 1305 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 55 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 39 optimal weight: 9.9990 chunk 97 optimal weight: 1.9990 chunk 9 optimal weight: 9.9990 chunk 79 optimal weight: 8.9990 chunk 26 optimal weight: 9.9990 chunk 107 optimal weight: 9.9990 chunk 124 optimal weight: 10.0000 chunk 99 optimal weight: 6.9990 chunk 24 optimal weight: 7.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3011 r_free = 0.3011 target = 0.039448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2572 r_free = 0.2572 target = 0.027743 restraints weight = 86239.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2613 r_free = 0.2613 target = 0.028901 restraints weight = 43321.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.2637 r_free = 0.2637 target = 0.029655 restraints weight = 29115.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2652 r_free = 0.2652 target = 0.030087 restraints weight = 22746.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2664 r_free = 0.2664 target = 0.030398 restraints weight = 19684.065| |-----------------------------------------------------------------------------| r_work (final): 0.2639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8871 moved from start: 0.1656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 12500 Z= 0.293 Angle : 0.661 9.586 17296 Z= 0.350 Chirality : 0.041 0.166 1930 Planarity : 0.004 0.034 1895 Dihedral : 20.091 179.955 2524 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 12.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.98 % Allowed : 19.40 % Favored : 77.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.84 (0.25), residues: 1234 helix: 1.40 (0.21), residues: 619 sheet: -1.06 (0.45), residues: 121 loop : 0.02 (0.30), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 313 TYR 0.020 0.002 TYR A 61 PHE 0.015 0.002 PHE A 655 TRP 0.013 0.001 TRP A 382 HIS 0.005 0.001 HIS A 191 Details of bonding type rmsd covalent geometry : bond 0.00603 (12500) covalent geometry : angle 0.66061 (17296) hydrogen bonds : bond 0.04685 ( 607) hydrogen bonds : angle 4.59245 ( 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 84 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 51 time to evaluate : 0.365 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.8957 (tpp) cc_final: 0.8135 (tmm) REVERT: A 20 GLU cc_start: 0.8447 (tm-30) cc_final: 0.8127 (tm-30) REVERT: A 48 LYS cc_start: 0.9442 (pttm) cc_final: 0.9227 (ptpp) REVERT: A 271 THR cc_start: 0.8692 (OUTLIER) cc_final: 0.8345 (p) REVERT: A 507 MET cc_start: 0.9209 (ppp) cc_final: 0.8963 (ppp) REVERT: A 537 MET cc_start: 0.9294 (mmt) cc_final: 0.8581 (mmm) REVERT: A 604 MET cc_start: 0.9371 (mmm) cc_final: 0.9011 (mmm) REVERT: A 786 GLU cc_start: 0.8703 (OUTLIER) cc_final: 0.8329 (mp0) REVERT: A 908 ASP cc_start: 0.7510 (t0) cc_final: 0.7267 (t0) REVERT: A 912 ARG cc_start: 0.7982 (tpm170) cc_final: 0.7776 (tpm170) REVERT: A 927 LEU cc_start: 0.9706 (OUTLIER) cc_final: 0.9472 (mm) REVERT: A 969 GLN cc_start: 0.8633 (OUTLIER) cc_final: 0.8333 (pp30) REVERT: A 1046 THR cc_start: 0.9163 (OUTLIER) cc_final: 0.8946 (p) REVERT: A 1092 GLU cc_start: 0.9696 (OUTLIER) cc_final: 0.9313 (mp0) REVERT: A 1119 MET cc_start: 0.9200 (mmm) cc_final: 0.8961 (mmp) outliers start: 33 outliers final: 17 residues processed: 78 average time/residue: 0.0978 time to fit residues: 11.4192 Evaluate side-chains 72 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 49 time to evaluate : 0.346 ------------------------------------------------------------------------------- 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 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 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 927 LEU Chi-restraints excluded: chain A residue 969 GLN Chi-restraints excluded: chain A residue 1004 THR Chi-restraints excluded: chain A residue 1018 MET Chi-restraints excluded: chain A residue 1046 THR 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 34 optimal weight: 9.9990 chunk 96 optimal weight: 0.4980 chunk 111 optimal weight: 10.0000 chunk 81 optimal weight: 0.0970 chunk 119 optimal weight: 8.9990 chunk 126 optimal weight: 6.9990 chunk 44 optimal weight: 5.9990 chunk 69 optimal weight: 7.9990 chunk 13 optimal weight: 5.9990 chunk 17 optimal weight: 3.9990 chunk 48 optimal weight: 20.0000 overall best weight: 3.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3029 r_free = 0.3029 target = 0.039948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2595 r_free = 0.2595 target = 0.028298 restraints weight = 84624.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.2635 r_free = 0.2635 target = 0.029479 restraints weight = 42517.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2662 r_free = 0.2662 target = 0.030244 restraints weight = 28200.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2676 r_free = 0.2676 target = 0.030686 restraints weight = 21837.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.2687 r_free = 0.2687 target = 0.031010 restraints weight = 18764.946| |-----------------------------------------------------------------------------| r_work (final): 0.2661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8849 moved from start: 0.1764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 12500 Z= 0.209 Angle : 0.617 11.991 17296 Z= 0.321 Chirality : 0.040 0.272 1930 Planarity : 0.003 0.032 1895 Dihedral : 20.045 179.406 2524 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 3.52 % Allowed : 18.95 % Favored : 77.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.25), residues: 1234 helix: 1.53 (0.21), residues: 620 sheet: -1.09 (0.44), residues: 121 loop : 0.06 (0.30), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 313 TYR 0.016 0.001 TYR A 61 PHE 0.010 0.001 PHE A 655 TRP 0.013 0.001 TRP A 382 HIS 0.004 0.001 HIS A 754 Details of bonding type rmsd covalent geometry : bond 0.00437 (12500) covalent geometry : angle 0.61682 (17296) hydrogen bonds : bond 0.03951 ( 607) hydrogen bonds : angle 4.39922 ( 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 92 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 53 time to evaluate : 0.440 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.8974 (tpp) cc_final: 0.8093 (tmm) REVERT: A 20 GLU cc_start: 0.8464 (tm-30) cc_final: 0.8120 (tm-30) REVERT: A 48 LYS cc_start: 0.9422 (pttm) cc_final: 0.9198 (ptpp) REVERT: A 271 THR cc_start: 0.8678 (OUTLIER) cc_final: 0.8316 (p) REVERT: A 507 MET cc_start: 0.9207 (ppp) cc_final: 0.8938 (ppp) REVERT: A 604 MET cc_start: 0.9307 (mmm) cc_final: 0.8971 (mmm) REVERT: A 754 HIS cc_start: 0.8178 (OUTLIER) cc_final: 0.7796 (t-90) REVERT: A 786 GLU cc_start: 0.8670 (OUTLIER) cc_final: 0.8307 (mp0) REVERT: A 908 ASP cc_start: 0.7568 (t0) cc_final: 0.7295 (t0) REVERT: A 912 ARG cc_start: 0.7958 (tpm170) cc_final: 0.7729 (tpm170) REVERT: A 969 GLN cc_start: 0.8637 (OUTLIER) cc_final: 0.8308 (pp30) REVERT: A 1013 GLN cc_start: 0.9717 (tt0) cc_final: 0.9334 (pt0) REVERT: A 1046 THR cc_start: 0.9207 (OUTLIER) cc_final: 0.8991 (p) REVERT: A 1055 MET cc_start: 0.9578 (pmm) cc_final: 0.8938 (pmm) REVERT: A 1092 GLU cc_start: 0.9701 (OUTLIER) cc_final: 0.9332 (mp0) outliers start: 39 outliers final: 18 residues processed: 86 average time/residue: 0.1123 time to fit residues: 14.3960 Evaluate side-chains 75 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 51 time to evaluate : 0.420 ------------------------------------------------------------------------------- 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 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 1018 MET 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 60 optimal weight: 7.9990 chunk 1 optimal weight: 10.0000 chunk 101 optimal weight: 4.9990 chunk 96 optimal weight: 0.8980 chunk 49 optimal weight: 10.0000 chunk 91 optimal weight: 0.9980 chunk 44 optimal weight: 10.0000 chunk 56 optimal weight: 5.9990 chunk 104 optimal weight: 10.0000 chunk 16 optimal weight: 0.9980 chunk 52 optimal weight: 6.9990 overall best weight: 2.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3037 r_free = 0.3037 target = 0.040222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2603 r_free = 0.2603 target = 0.028516 restraints weight = 84125.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.2643 r_free = 0.2643 target = 0.029720 restraints weight = 41968.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.2669 r_free = 0.2669 target = 0.030493 restraints weight = 27739.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2684 r_free = 0.2684 target = 0.030937 restraints weight = 21462.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2697 r_free = 0.2697 target = 0.031285 restraints weight = 18435.778| |-----------------------------------------------------------------------------| r_work (final): 0.2669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8836 moved from start: 0.1901 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= 0.184 Angle : 0.602 12.727 17296 Z= 0.313 Chirality : 0.039 0.151 1930 Planarity : 0.003 0.032 1895 Dihedral : 19.984 179.933 2524 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.89 % Allowed : 19.68 % 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: 1.04 (0.25), residues: 1234 helix: 1.60 (0.21), residues: 620 sheet: -0.93 (0.45), residues: 121 loop : 0.07 (0.30), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 313 TYR 0.016 0.001 TYR A 61 PHE 0.011 0.001 PHE A1113 TRP 0.014 0.001 TRP A 382 HIS 0.004 0.001 HIS A 754 Details of bonding type rmsd covalent geometry : bond 0.00390 (12500) covalent geometry : angle 0.60170 (17296) hydrogen bonds : bond 0.03814 ( 607) hydrogen bonds : angle 4.34615 ( 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 87 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 55 time to evaluate : 0.396 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.8987 (tpp) cc_final: 0.8062 (tmm) REVERT: A 20 GLU cc_start: 0.8490 (tm-30) cc_final: 0.8121 (tm-30) REVERT: A 145 GLN cc_start: 0.9295 (OUTLIER) cc_final: 0.8994 (mp10) REVERT: A 271 THR cc_start: 0.8643 (OUTLIER) cc_final: 0.8268 (p) REVERT: A 507 MET cc_start: 0.9188 (ppp) cc_final: 0.8912 (ppp) REVERT: A 604 MET cc_start: 0.9306 (mmm) cc_final: 0.8964 (mmm) REVERT: A 610 THR cc_start: 0.9697 (OUTLIER) cc_final: 0.9383 (p) REVERT: A 709 GLU cc_start: 0.9251 (OUTLIER) cc_final: 0.9044 (tm-30) REVERT: A 754 HIS cc_start: 0.8197 (OUTLIER) cc_final: 0.7801 (t-90) REVERT: A 786 GLU cc_start: 0.8644 (OUTLIER) cc_final: 0.8296 (mp0) REVERT: A 908 ASP cc_start: 0.7670 (t0) cc_final: 0.7407 (t0) REVERT: A 912 ARG cc_start: 0.7943 (tpm170) cc_final: 0.7704 (tpm170) REVERT: A 969 GLN cc_start: 0.8629 (OUTLIER) cc_final: 0.8273 (pp30) REVERT: A 1046 THR cc_start: 0.9197 (OUTLIER) cc_final: 0.8985 (p) REVERT: A 1055 MET cc_start: 0.9574 (pmm) cc_final: 0.9246 (pmm) REVERT: A 1074 ASP cc_start: 0.9581 (OUTLIER) cc_final: 0.8787 (p0) REVERT: A 1092 GLU cc_start: 0.9718 (OUTLIER) cc_final: 0.9350 (mp0) REVERT: A 1119 MET cc_start: 0.9133 (mmm) cc_final: 0.8852 (mmm) outliers start: 32 outliers final: 18 residues processed: 83 average time/residue: 0.1131 time to fit residues: 13.9186 Evaluate side-chains 79 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 51 time to evaluate : 0.499 ------------------------------------------------------------------------------- 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 145 GLN 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 610 THR 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 969 GLN Chi-restraints excluded: chain A residue 1004 THR Chi-restraints excluded: chain A residue 1018 MET 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 24 optimal weight: 0.8980 chunk 112 optimal weight: 0.0060 chunk 6 optimal weight: 3.9990 chunk 41 optimal weight: 10.0000 chunk 75 optimal weight: 3.9990 chunk 30 optimal weight: 7.9990 chunk 55 optimal weight: 1.9990 chunk 115 optimal weight: 9.9990 chunk 79 optimal weight: 1.9990 chunk 69 optimal weight: 7.9990 chunk 4 optimal weight: 1.9990 overall best weight: 1.3802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 GLN A 206 HIS A 946 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.041146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2631 r_free = 0.2631 target = 0.029528 restraints weight = 82967.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.2672 r_free = 0.2672 target = 0.030750 restraints weight = 40974.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2698 r_free = 0.2698 target = 0.031544 restraints weight = 26990.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2713 r_free = 0.2713 target = 0.032020 restraints weight = 20776.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.2725 r_free = 0.2725 target = 0.032352 restraints weight = 17724.030| |-----------------------------------------------------------------------------| r_work (final): 0.2695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8805 moved from start: 0.2019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12500 Z= 0.126 Angle : 0.594 14.428 17296 Z= 0.303 Chirality : 0.039 0.156 1930 Planarity : 0.003 0.033 1895 Dihedral : 19.851 179.774 2524 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.80 % Allowed : 20.22 % 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: 1.22 (0.25), residues: 1234 helix: 1.72 (0.21), residues: 620 sheet: -0.69 (0.44), residues: 132 loop : 0.19 (0.30), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 313 TYR 0.014 0.001 TYR A 595 PHE 0.011 0.001 PHE A1113 TRP 0.013 0.001 TRP A 382 HIS 0.004 0.001 HIS A 754 Details of bonding type rmsd covalent geometry : bond 0.00275 (12500) covalent geometry : angle 0.59381 (17296) hydrogen bonds : bond 0.03417 ( 607) hydrogen bonds : angle 4.19522 ( 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 86 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 55 time to evaluate : 0.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.8962 (tpp) cc_final: 0.8051 (tmm) REVERT: A 20 GLU cc_start: 0.8488 (tm-30) cc_final: 0.8070 (tm-30) REVERT: A 145 GLN cc_start: 0.9337 (OUTLIER) cc_final: 0.9031 (mp10) REVERT: A 165 PHE cc_start: 0.8861 (OUTLIER) cc_final: 0.8446 (t80) REVERT: A 271 THR cc_start: 0.8649 (OUTLIER) cc_final: 0.8299 (p) REVERT: A 363 HIS cc_start: 0.9461 (OUTLIER) cc_final: 0.9048 (t70) REVERT: A 507 MET cc_start: 0.9183 (ppp) cc_final: 0.8784 (ppp) REVERT: A 604 MET cc_start: 0.9286 (mmm) cc_final: 0.8933 (mmm) REVERT: A 610 THR cc_start: 0.9686 (OUTLIER) cc_final: 0.9371 (p) REVERT: A 709 GLU cc_start: 0.9262 (OUTLIER) cc_final: 0.9042 (tm-30) REVERT: A 754 HIS cc_start: 0.8257 (OUTLIER) cc_final: 0.7994 (t70) REVERT: A 786 GLU cc_start: 0.8544 (OUTLIER) cc_final: 0.8202 (mp0) REVERT: A 908 ASP cc_start: 0.7628 (t0) cc_final: 0.7330 (t0) REVERT: A 912 ARG cc_start: 0.7965 (tpm170) cc_final: 0.7739 (tpm170) REVERT: A 969 GLN cc_start: 0.8635 (OUTLIER) cc_final: 0.8265 (pp30) REVERT: A 1055 MET cc_start: 0.9564 (pmm) cc_final: 0.9258 (pmm) REVERT: A 1074 ASP cc_start: 0.9594 (OUTLIER) cc_final: 0.8765 (p0) REVERT: A 1092 GLU cc_start: 0.9706 (OUTLIER) cc_final: 0.9333 (mp0) REVERT: A 1119 MET cc_start: 0.9154 (mmm) cc_final: 0.8915 (mmp) outliers start: 31 outliers final: 16 residues processed: 82 average time/residue: 0.1072 time to fit residues: 13.3030 Evaluate side-chains 79 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 52 time to evaluate : 0.456 ------------------------------------------------------------------------------- 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 145 GLN 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 363 HIS Chi-restraints excluded: chain A residue 610 THR Chi-restraints excluded: chain A residue 622 HIS Chi-restraints excluded: chain A residue 703 GLN Chi-restraints excluded: chain A residue 709 GLU 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 1018 MET 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 1305 LEU 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: 9.9990 chunk 9 optimal weight: 6.9990 chunk 73 optimal weight: 0.6980 chunk 110 optimal weight: 6.9990 chunk 98 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 90 optimal weight: 6.9990 chunk 34 optimal weight: 6.9990 chunk 16 optimal weight: 0.8980 chunk 119 optimal weight: 1.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.041467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2645 r_free = 0.2645 target = 0.029911 restraints weight = 82533.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2686 r_free = 0.2686 target = 0.031134 restraints weight = 40785.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2713 r_free = 0.2713 target = 0.031952 restraints weight = 26871.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2730 r_free = 0.2730 target = 0.032478 restraints weight = 20583.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2741 r_free = 0.2741 target = 0.032792 restraints weight = 17354.969| |-----------------------------------------------------------------------------| r_work (final): 0.2710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8803 moved from start: 0.2198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 12500 Z= 0.123 Angle : 0.591 14.422 17296 Z= 0.297 Chirality : 0.038 0.164 1930 Planarity : 0.003 0.031 1895 Dihedral : 19.672 178.562 2524 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.89 % Allowed : 20.49 % Favored : 76.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.30 (0.25), residues: 1234 helix: 1.79 (0.21), residues: 619 sheet: -0.60 (0.44), residues: 132 loop : 0.20 (0.30), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 313 TYR 0.014 0.001 TYR A 595 PHE 0.009 0.001 PHE A1140 TRP 0.014 0.001 TRP A 382 HIS 0.004 0.001 HIS A 754 Details of bonding type rmsd covalent geometry : bond 0.00269 (12500) covalent geometry : angle 0.59056 (17296) hydrogen bonds : bond 0.03326 ( 607) hydrogen bonds : angle 4.09169 ( 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 90 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 58 time to evaluate : 0.459 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.8964 (tpp) cc_final: 0.8017 (tmm) REVERT: A 20 GLU cc_start: 0.8473 (tm-30) cc_final: 0.8047 (tm-30) REVERT: A 145 GLN cc_start: 0.9350 (OUTLIER) cc_final: 0.9099 (mp10) REVERT: A 165 PHE cc_start: 0.8935 (OUTLIER) cc_final: 0.8579 (t80) REVERT: A 271 THR cc_start: 0.8718 (OUTLIER) cc_final: 0.8375 (p) REVERT: A 363 HIS cc_start: 0.9453 (OUTLIER) cc_final: 0.9042 (t70) REVERT: A 507 MET cc_start: 0.9196 (ppp) cc_final: 0.8794 (ppp) REVERT: A 604 MET cc_start: 0.9280 (mmm) cc_final: 0.8922 (mmm) REVERT: A 610 THR cc_start: 0.9695 (OUTLIER) cc_final: 0.9422 (p) REVERT: A 709 GLU cc_start: 0.9245 (OUTLIER) cc_final: 0.9013 (tm-30) REVERT: A 754 HIS cc_start: 0.8320 (OUTLIER) cc_final: 0.7993 (t70) REVERT: A 786 GLU cc_start: 0.8433 (OUTLIER) cc_final: 0.8145 (mp0) REVERT: A 908 ASP cc_start: 0.7593 (t0) cc_final: 0.7250 (t0) REVERT: A 912 ARG cc_start: 0.7985 (tpm170) cc_final: 0.7768 (tpm170) REVERT: A 969 GLN cc_start: 0.8624 (OUTLIER) cc_final: 0.7978 (pp30) REVERT: A 1055 MET cc_start: 0.9563 (pmm) cc_final: 0.9241 (pmm) REVERT: A 1074 ASP cc_start: 0.9595 (OUTLIER) cc_final: 0.8705 (p0) REVERT: A 1092 GLU cc_start: 0.9700 (OUTLIER) cc_final: 0.9322 (mp0) REVERT: A 1119 MET cc_start: 0.9165 (mmm) cc_final: 0.8916 (mmp) outliers start: 32 outliers final: 17 residues processed: 84 average time/residue: 0.1108 time to fit residues: 14.0912 Evaluate side-chains 82 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 54 time to evaluate : 0.399 ------------------------------------------------------------------------------- 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 145 GLN 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 363 HIS Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 610 THR Chi-restraints excluded: chain A residue 703 GLN Chi-restraints excluded: chain A residue 709 GLU 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 1018 MET 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 1305 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 110 optimal weight: 10.0000 chunk 124 optimal weight: 10.0000 chunk 122 optimal weight: 0.2980 chunk 3 optimal weight: 0.8980 chunk 90 optimal weight: 5.9990 chunk 45 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 120 optimal weight: 10.0000 chunk 109 optimal weight: 20.0000 chunk 46 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 overall best weight: 2.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.040980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2632 r_free = 0.2632 target = 0.029343 restraints weight = 82926.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.2672 r_free = 0.2672 target = 0.030554 restraints weight = 41801.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2698 r_free = 0.2698 target = 0.031339 restraints weight = 27792.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2713 r_free = 0.2713 target = 0.031798 restraints weight = 21548.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2725 r_free = 0.2725 target = 0.032132 restraints weight = 18576.101| |-----------------------------------------------------------------------------| r_work (final): 0.2699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8813 moved from start: 0.2229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12500 Z= 0.157 Angle : 0.609 14.410 17296 Z= 0.307 Chirality : 0.039 0.305 1930 Planarity : 0.003 0.031 1895 Dihedral : 19.662 177.499 2524 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.80 % Allowed : 20.58 % Favored : 76.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.31 (0.25), residues: 1234 helix: 1.78 (0.21), residues: 619 sheet: -0.59 (0.45), residues: 132 loop : 0.23 (0.30), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 313 TYR 0.015 0.001 TYR A 61 PHE 0.011 0.001 PHE A1113 TRP 0.015 0.001 TRP A 382 HIS 0.004 0.001 HIS A 754 Details of bonding type rmsd covalent geometry : bond 0.00337 (12500) covalent geometry : angle 0.60885 (17296) hydrogen bonds : bond 0.03456 ( 607) hydrogen bonds : angle 4.15026 ( 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 84 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 53 time to evaluate : 0.495 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.8993 (tpp) cc_final: 0.8004 (tmm) REVERT: A 20 GLU cc_start: 0.8466 (tm-30) cc_final: 0.8077 (tm-30) REVERT: A 145 GLN cc_start: 0.9344 (OUTLIER) cc_final: 0.9080 (mp10) REVERT: A 165 PHE cc_start: 0.8946 (OUTLIER) cc_final: 0.8535 (t80) REVERT: A 271 THR cc_start: 0.8696 (OUTLIER) cc_final: 0.8352 (p) REVERT: A 363 HIS cc_start: 0.9466 (OUTLIER) cc_final: 0.9073 (t70) REVERT: A 507 MET cc_start: 0.9203 (ppp) cc_final: 0.8810 (ppp) REVERT: A 604 MET cc_start: 0.9301 (mmm) cc_final: 0.8939 (mmm) REVERT: A 709 GLU cc_start: 0.9226 (OUTLIER) cc_final: 0.9005 (tm-30) REVERT: A 754 HIS cc_start: 0.8316 (OUTLIER) cc_final: 0.7992 (t70) REVERT: A 786 GLU cc_start: 0.8463 (OUTLIER) cc_final: 0.8163 (mp0) REVERT: A 908 ASP cc_start: 0.7735 (t0) cc_final: 0.7397 (t0) REVERT: A 912 ARG cc_start: 0.7972 (tpm170) cc_final: 0.7762 (tpm170) REVERT: A 969 GLN cc_start: 0.8614 (OUTLIER) cc_final: 0.7845 (pp30) REVERT: A 1013 GLN cc_start: 0.9718 (tt0) cc_final: 0.9341 (pt0) REVERT: A 1055 MET cc_start: 0.9575 (pmm) cc_final: 0.9273 (pmm) REVERT: A 1074 ASP cc_start: 0.9597 (OUTLIER) cc_final: 0.8713 (p0) REVERT: A 1092 GLU cc_start: 0.9710 (OUTLIER) cc_final: 0.9330 (mp0) outliers start: 31 outliers final: 16 residues processed: 80 average time/residue: 0.1100 time to fit residues: 12.9715 Evaluate side-chains 78 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 52 time to evaluate : 0.426 ------------------------------------------------------------------------------- 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 145 GLN 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 363 HIS Chi-restraints excluded: chain A residue 622 HIS 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 969 GLN Chi-restraints excluded: chain A residue 1004 THR Chi-restraints excluded: chain A residue 1018 MET 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 1305 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 108 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 56 optimal weight: 3.9990 chunk 61 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 3 optimal weight: 0.9990 chunk 11 optimal weight: 9.9990 chunk 60 optimal weight: 0.9990 chunk 14 optimal weight: 10.0000 chunk 87 optimal weight: 4.9990 chunk 45 optimal weight: 5.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.041226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2629 r_free = 0.2629 target = 0.029546 restraints weight = 83448.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2669 r_free = 0.2669 target = 0.030765 restraints weight = 41715.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2695 r_free = 0.2695 target = 0.031556 restraints weight = 27749.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2711 r_free = 0.2711 target = 0.032039 restraints weight = 21493.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.2723 r_free = 0.2723 target = 0.032368 restraints weight = 18401.705| |-----------------------------------------------------------------------------| r_work (final): 0.2695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8818 moved from start: 0.2272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 12500 Z= 0.164 Angle : 0.620 13.926 17296 Z= 0.312 Chirality : 0.040 0.305 1930 Planarity : 0.003 0.032 1895 Dihedral : 19.681 177.233 2524 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.53 % Allowed : 21.03 % Favored : 76.44 % 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: 1.30 (0.25), residues: 1234 helix: 1.77 (0.21), residues: 619 sheet: -0.63 (0.45), residues: 132 loop : 0.24 (0.30), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 951 TYR 0.016 0.001 TYR A 61 PHE 0.013 0.001 PHE A1113 TRP 0.015 0.001 TRP A 382 HIS 0.004 0.001 HIS A 754 Details of bonding type rmsd covalent geometry : bond 0.00352 (12500) covalent geometry : angle 0.62001 (17296) hydrogen bonds : bond 0.03498 ( 607) hydrogen bonds : angle 4.16401 ( 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 80 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 52 time to evaluate : 0.267 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.9014 (tpp) cc_final: 0.7994 (tmm) REVERT: A 20 GLU cc_start: 0.8515 (tm-30) cc_final: 0.8150 (tm-30) REVERT: A 145 GLN cc_start: 0.9347 (OUTLIER) cc_final: 0.9041 (mp10) REVERT: A 165 PHE cc_start: 0.8944 (OUTLIER) cc_final: 0.8533 (t80) REVERT: A 271 THR cc_start: 0.8674 (OUTLIER) cc_final: 0.8327 (p) REVERT: A 363 HIS cc_start: 0.9444 (OUTLIER) cc_final: 0.9044 (t70) REVERT: A 507 MET cc_start: 0.9195 (ppp) cc_final: 0.8780 (ppp) REVERT: A 604 MET cc_start: 0.9263 (mmm) cc_final: 0.8921 (mmm) REVERT: A 709 GLU cc_start: 0.9208 (OUTLIER) cc_final: 0.8995 (tm-30) REVERT: A 754 HIS cc_start: 0.8280 (OUTLIER) cc_final: 0.7971 (t70) REVERT: A 786 GLU cc_start: 0.8477 (OUTLIER) cc_final: 0.8177 (mp0) REVERT: A 908 ASP cc_start: 0.7888 (t0) cc_final: 0.7545 (t0) REVERT: A 912 ARG cc_start: 0.7969 (tpm170) cc_final: 0.7758 (tpm170) REVERT: A 969 GLN cc_start: 0.8596 (OUTLIER) cc_final: 0.7819 (pp30) REVERT: A 1013 GLN cc_start: 0.9727 (tt0) cc_final: 0.9347 (pt0) REVERT: A 1055 MET cc_start: 0.9576 (pmm) cc_final: 0.9270 (pmm) REVERT: A 1074 ASP cc_start: 0.9591 (OUTLIER) cc_final: 0.8709 (p0) REVERT: A 1092 GLU cc_start: 0.9712 (OUTLIER) cc_final: 0.9330 (mp0) outliers start: 28 outliers final: 16 residues processed: 77 average time/residue: 0.1058 time to fit residues: 12.0741 Evaluate side-chains 78 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 52 time to evaluate : 0.320 ------------------------------------------------------------------------------- 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 145 GLN 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 363 HIS Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 622 HIS 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 969 GLN Chi-restraints excluded: chain A residue 1004 THR Chi-restraints excluded: chain A residue 1018 MET 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 78 optimal weight: 7.9990 chunk 129 optimal weight: 5.9990 chunk 30 optimal weight: 1.9990 chunk 97 optimal weight: 6.9990 chunk 93 optimal weight: 10.0000 chunk 64 optimal weight: 6.9990 chunk 118 optimal weight: 4.9990 chunk 40 optimal weight: 8.9990 chunk 130 optimal weight: 6.9990 chunk 96 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 206 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.040181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2598 r_free = 0.2598 target = 0.028505 restraints weight = 85145.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.2638 r_free = 0.2638 target = 0.029692 restraints weight = 42622.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2664 r_free = 0.2664 target = 0.030460 restraints weight = 28303.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.2680 r_free = 0.2680 target = 0.030942 restraints weight = 21973.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.2692 r_free = 0.2692 target = 0.031253 restraints weight = 18757.538| |-----------------------------------------------------------------------------| r_work (final): 0.2663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8844 moved from start: 0.2319 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= 0.228 Angle : 0.651 14.120 17296 Z= 0.334 Chirality : 0.041 0.285 1930 Planarity : 0.003 0.032 1895 Dihedral : 19.804 176.560 2524 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.44 % Allowed : 21.48 % Favored : 76.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.19 (0.25), residues: 1234 helix: 1.69 (0.21), residues: 618 sheet: -0.71 (0.45), residues: 132 loop : 0.18 (0.30), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 951 TYR 0.019 0.001 TYR A 61 PHE 0.013 0.001 PHE A1113 TRP 0.016 0.001 TRP A 382 HIS 0.004 0.001 HIS A 191 Details of bonding type rmsd covalent geometry : bond 0.00478 (12500) covalent geometry : angle 0.65115 (17296) hydrogen bonds : bond 0.03977 ( 607) hydrogen bonds : angle 4.32533 ( 1649) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1979.32 seconds wall clock time: 35 minutes 5.93 seconds (2105.93 seconds total)