Starting phenix.real_space_refine on Wed Jul 30 07:25:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sfr_40449/07_2025/8sfr_40449.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sfr_40449/07_2025/8sfr_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8sfr_40449/07_2025/8sfr_40449.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sfr_40449/07_2025/8sfr_40449.map" model { file = "/net/cci-nas-00/data/ceres_data/8sfr_40449/07_2025/8sfr_40449.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sfr_40449/07_2025/8sfr_40449.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 15.62, per 1000 atoms: 1.30 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: 3.25 Conformation dependent library (CDL) restraints added in 1.4 seconds 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: 4.79 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: 6.32 Time building geometry restraints manager: 3.80 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: 2.990 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: 0.510 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 46.050 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.050 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:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.790 ------------------------------------------------------------------------------- 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 : 8.73 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.022 0.002 TRP A 382 HIS 0.008 0.001 HIS A 363 PHE 0.031 0.002 PHE A 619 TYR 0.038 0.002 TYR A 526 ARG 0.006 0.001 ARG A 392 Details of bonding type rmsd hydrogen bonds : bond 0.15586 ( 607) hydrogen bonds : angle 6.46303 ( 1649) covalent geometry : bond 0.00634 (12500) covalent geometry : angle 1.02616 (17296) *********************** 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 : 1.268 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: 0.2587 time to fit residues: 20.6337 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 : 1.437 ------------------------------------------------------------------------------- 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 110 optimal weight: 6.9990 chunk 99 optimal weight: 1.9990 chunk 55 optimal weight: 5.9990 chunk 33 optimal weight: 4.9990 chunk 66 optimal weight: 5.9990 chunk 53 optimal weight: 0.7980 chunk 102 optimal weight: 10.0000 chunk 39 optimal weight: 9.9990 chunk 62 optimal weight: 0.9980 chunk 76 optimal weight: 0.8980 chunk 118 optimal weight: 5.9990 overall best weight: 1.9384 ------------------------------------------------------------------------------- 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** A1206 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.041041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2626 r_free = 0.2626 target = 0.029296 restraints weight = 81864.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2665 r_free = 0.2665 target = 0.030503 restraints weight = 40796.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2691 r_free = 0.2691 target = 0.031287 restraints weight = 26987.261| |-----------------------------------------------------------------------------| r_work (final): 0.2657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8838 moved from start: 0.1015 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 : 0.614 10.340 17296 Z= 0.322 Chirality : 0.040 0.211 1930 Planarity : 0.004 0.039 1895 Dihedral : 20.195 179.369 2524 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 1.53 % Allowed : 18.32 % Favored : 80.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.24), residues: 1234 helix: 1.07 (0.21), residues: 597 sheet: -0.60 (0.45), residues: 132 loop : 0.03 (0.28), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 382 HIS 0.005 0.001 HIS A 363 PHE 0.013 0.001 PHE A 353 TYR 0.015 0.001 TYR A 526 ARG 0.004 0.000 ARG A 313 Details of bonding type rmsd hydrogen bonds : bond 0.04316 ( 607) hydrogen bonds : angle 4.86115 ( 1649) covalent geometry : bond 0.00332 (12500) covalent geometry : angle 0.61357 (17296) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 50 time to evaluate : 1.327 Fit side-chains REVERT: A 1 MET cc_start: 0.8896 (tpp) cc_final: 0.8340 (tmm) REVERT: A 604 MET cc_start: 0.9292 (mmm) cc_final: 0.9043 (mmm) REVERT: A 754 HIS cc_start: 0.8092 (OUTLIER) cc_final: 0.7598 (t-90) REVERT: A 786 GLU cc_start: 0.8665 (OUTLIER) cc_final: 0.8292 (mp0) REVERT: A 908 ASP cc_start: 0.7341 (t0) cc_final: 0.7127 (t0) REVERT: A 912 ARG cc_start: 0.7970 (tpm170) cc_final: 0.7742 (tpm170) REVERT: A 969 GLN cc_start: 0.8650 (OUTLIER) cc_final: 0.8172 (pp30) REVERT: A 1092 GLU cc_start: 0.9684 (OUTLIER) cc_final: 0.9340 (mp0) outliers start: 17 outliers final: 3 residues processed: 64 average time/residue: 0.2797 time to fit residues: 27.6256 Evaluate side-chains 54 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 47 time to evaluate : 1.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 969 GLN Chi-restraints excluded: chain A residue 1088 ILE Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1307 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 104 optimal weight: 20.0000 chunk 51 optimal weight: 10.0000 chunk 90 optimal weight: 8.9990 chunk 102 optimal weight: 10.0000 chunk 114 optimal weight: 20.0000 chunk 69 optimal weight: 7.9990 chunk 29 optimal weight: 5.9990 chunk 107 optimal weight: 9.9990 chunk 77 optimal weight: 8.9990 chunk 73 optimal weight: 6.9990 chunk 20 optimal weight: 6.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- 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 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 560 ASN ** A1105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.038595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2539 r_free = 0.2539 target = 0.027083 restraints weight = 88672.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.2577 r_free = 0.2577 target = 0.028186 restraints weight = 44800.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.2602 r_free = 0.2602 target = 0.028896 restraints weight = 30233.457| |-----------------------------------------------------------------------------| r_work (final): 0.2567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8925 moved from start: 0.1644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.062 12500 Z= 0.428 Angle : 0.774 9.513 17296 Z= 0.415 Chirality : 0.045 0.198 1930 Planarity : 0.004 0.040 1895 Dihedral : 20.342 179.508 2524 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 16.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 3.52 % Allowed : 18.86 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.24), residues: 1234 helix: 0.98 (0.21), residues: 607 sheet: -1.10 (0.45), residues: 121 loop : -0.02 (0.29), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 382 HIS 0.007 0.001 HIS A 191 PHE 0.022 0.002 PHE A 655 TYR 0.020 0.002 TYR A 61 ARG 0.005 0.001 ARG A 313 Details of bonding type rmsd hydrogen bonds : bond 0.05897 ( 607) hydrogen bonds : angle 5.04245 ( 1649) covalent geometry : bond 0.00871 (12500) covalent geometry : angle 0.77434 (17296) *********************** 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 87 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 48 time to evaluate : 1.315 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.9020 (tpp) cc_final: 0.8240 (tmm) REVERT: A 20 GLU cc_start: 0.8529 (tm-30) cc_final: 0.8125 (tm-30) REVERT: A 48 LYS cc_start: 0.9448 (pttm) cc_final: 0.9223 (ptpp) REVERT: A 271 THR cc_start: 0.8563 (OUTLIER) cc_final: 0.8184 (p) REVERT: A 507 MET cc_start: 0.9244 (ppp) cc_final: 0.8983 (ppp) REVERT: A 604 MET cc_start: 0.9404 (mmm) cc_final: 0.9094 (mmm) REVERT: A 786 GLU cc_start: 0.8767 (OUTLIER) cc_final: 0.8396 (mp0) REVERT: A 908 ASP cc_start: 0.7903 (t0) cc_final: 0.7589 (t0) REVERT: A 969 GLN cc_start: 0.8710 (OUTLIER) cc_final: 0.8454 (pp30) REVERT: A 1055 MET cc_start: 0.9595 (pmm) cc_final: 0.9041 (pmm) REVERT: A 1092 GLU cc_start: 0.9683 (OUTLIER) cc_final: 0.9316 (mp0) outliers start: 39 outliers final: 15 residues processed: 80 average time/residue: 0.2695 time to fit residues: 31.8995 Evaluate side-chains 64 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 45 time to evaluate : 1.491 ------------------------------------------------------------------------------- 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 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 1050 THR Chi-restraints excluded: chain A residue 1088 ILE Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1235 ASP Chi-restraints excluded: chain A residue 1307 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 7 optimal weight: 6.9990 chunk 4 optimal weight: 2.9990 chunk 115 optimal weight: 0.9990 chunk 6 optimal weight: 0.9990 chunk 58 optimal weight: 6.9990 chunk 59 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 94 optimal weight: 6.9990 chunk 98 optimal weight: 8.9990 chunk 57 optimal weight: 6.9990 chunk 61 optimal weight: 0.9980 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 GLN A1105 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.040402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2608 r_free = 0.2608 target = 0.028747 restraints weight = 82703.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2649 r_free = 0.2649 target = 0.029947 restraints weight = 40759.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2675 r_free = 0.2675 target = 0.030724 restraints weight = 26810.145| |-----------------------------------------------------------------------------| r_work (final): 0.2643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8839 moved from start: 0.1597 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= 0.130 Angle : 0.591 10.434 17296 Z= 0.308 Chirality : 0.039 0.169 1930 Planarity : 0.003 0.034 1895 Dihedral : 20.074 177.997 2524 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.26 % Allowed : 20.40 % Favored : 77.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.25), residues: 1234 helix: 1.50 (0.21), residues: 613 sheet: -0.94 (0.45), residues: 121 loop : 0.11 (0.30), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 382 HIS 0.004 0.001 HIS A 754 PHE 0.013 0.001 PHE A1052 TYR 0.015 0.001 TYR A 61 ARG 0.004 0.000 ARG A 313 Details of bonding type rmsd hydrogen bonds : bond 0.03757 ( 607) hydrogen bonds : angle 4.40104 ( 1649) covalent geometry : bond 0.00279 (12500) covalent geometry : angle 0.59148 (17296) *********************** 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 77 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 52 time to evaluate : 1.767 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.8969 (tpp) cc_final: 0.8234 (tmm) REVERT: A 20 GLU cc_start: 0.8544 (tm-30) cc_final: 0.8047 (tm-30) REVERT: A 48 LYS cc_start: 0.9419 (pttm) cc_final: 0.9190 (ptpp) REVERT: A 271 THR cc_start: 0.8634 (OUTLIER) cc_final: 0.8284 (p) REVERT: A 507 MET cc_start: 0.9240 (ppp) cc_final: 0.9034 (ppp) REVERT: A 537 MET cc_start: 0.9287 (mmt) cc_final: 0.8595 (mmm) REVERT: A 604 MET cc_start: 0.9277 (mmm) cc_final: 0.8924 (mmm) REVERT: A 754 HIS cc_start: 0.8172 (OUTLIER) cc_final: 0.7964 (t-90) REVERT: A 786 GLU cc_start: 0.8657 (OUTLIER) cc_final: 0.8286 (mp0) REVERT: A 908 ASP cc_start: 0.7766 (t0) cc_final: 0.7463 (t0) REVERT: A 969 GLN cc_start: 0.8676 (OUTLIER) cc_final: 0.8382 (pp30) REVERT: A 1055 MET cc_start: 0.9556 (pmm) cc_final: 0.9266 (pmm) REVERT: A 1092 GLU cc_start: 0.9705 (OUTLIER) cc_final: 0.9343 (mp0) REVERT: A 1119 MET cc_start: 0.9172 (mmp) cc_final: 0.8887 (mmp) outliers start: 25 outliers final: 11 residues processed: 72 average time/residue: 0.3577 time to fit residues: 39.4599 Evaluate side-chains 65 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 49 time to evaluate : 1.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 752 LYS Chi-restraints excluded: chain A residue 754 HIS Chi-restraints excluded: chain A residue 786 GLU Chi-restraints excluded: chain A residue 933 ASN Chi-restraints excluded: chain A residue 969 GLN Chi-restraints excluded: chain A residue 1004 THR Chi-restraints excluded: chain A residue 1018 MET Chi-restraints excluded: chain A residue 1046 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 76 optimal weight: 7.9990 chunk 121 optimal weight: 9.9990 chunk 46 optimal weight: 8.9990 chunk 99 optimal weight: 5.9990 chunk 22 optimal weight: 4.9990 chunk 77 optimal weight: 5.9990 chunk 18 optimal weight: 7.9990 chunk 15 optimal weight: 8.9990 chunk 120 optimal weight: 0.8980 chunk 3 optimal weight: 0.7980 chunk 54 optimal weight: 8.9990 overall best weight: 3.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 946 ASN ** 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 = 0.3021 r_free = 0.3021 target = 0.039684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2586 r_free = 0.2586 target = 0.028057 restraints weight = 85099.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2626 r_free = 0.2626 target = 0.029230 restraints weight = 42635.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2651 r_free = 0.2651 target = 0.029981 restraints weight = 28457.260| |-----------------------------------------------------------------------------| r_work (final): 0.2617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8880 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 : 0.005 0.049 12500 Z= 0.234 Angle : 0.624 10.093 17296 Z= 0.329 Chirality : 0.041 0.276 1930 Planarity : 0.003 0.032 1895 Dihedral : 20.035 179.770 2524 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 3.34 % Allowed : 19.31 % Favored : 77.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.25), residues: 1234 helix: 1.47 (0.21), residues: 619 sheet: -0.99 (0.45), residues: 121 loop : -0.00 (0.30), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 382 HIS 0.005 0.001 HIS A 754 PHE 0.013 0.001 PHE A1052 TYR 0.018 0.001 TYR A 61 ARG 0.005 0.000 ARG A 313 Details of bonding type rmsd hydrogen bonds : bond 0.04216 ( 607) hydrogen bonds : angle 4.46623 ( 1649) covalent geometry : bond 0.00488 (12500) covalent geometry : angle 0.62423 (17296) *********************** 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 88 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 51 time to evaluate : 1.716 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.9000 (tpp) cc_final: 0.8126 (tmm) REVERT: A 20 GLU cc_start: 0.8541 (tm-30) cc_final: 0.8122 (tm-30) REVERT: A 48 LYS cc_start: 0.9439 (pttm) cc_final: 0.9225 (ptpp) REVERT: A 165 PHE cc_start: 0.9018 (OUTLIER) cc_final: 0.8672 (t80) REVERT: A 271 THR cc_start: 0.8627 (OUTLIER) cc_final: 0.8283 (p) REVERT: A 507 MET cc_start: 0.9206 (ppp) cc_final: 0.8974 (ppp) REVERT: A 537 MET cc_start: 0.9300 (mmt) cc_final: 0.8565 (mmm) REVERT: A 604 MET cc_start: 0.9310 (mmm) cc_final: 0.8980 (mmm) REVERT: A 754 HIS cc_start: 0.8221 (OUTLIER) cc_final: 0.7854 (t-90) REVERT: A 786 GLU cc_start: 0.8683 (OUTLIER) cc_final: 0.8311 (mp0) REVERT: A 908 ASP cc_start: 0.7930 (t0) cc_final: 0.7662 (t0) REVERT: A 912 ARG cc_start: 0.8122 (tpm170) cc_final: 0.7846 (tpm170) REVERT: A 933 ASN cc_start: 0.8423 (OUTLIER) cc_final: 0.8097 (t0) REVERT: A 969 GLN cc_start: 0.8644 (OUTLIER) cc_final: 0.8327 (pp30) REVERT: A 1092 GLU cc_start: 0.9700 (OUTLIER) cc_final: 0.9337 (mp0) outliers start: 37 outliers final: 20 residues processed: 83 average time/residue: 0.3076 time to fit residues: 39.5545 Evaluate side-chains 76 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 49 time to evaluate : 1.708 ------------------------------------------------------------------------------- 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 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 467 LEU Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 622 HIS Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain A residue 703 GLN Chi-restraints excluded: chain A residue 752 LYS Chi-restraints excluded: chain A residue 754 HIS Chi-restraints excluded: chain A residue 786 GLU Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 933 ASN 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 1073 ILE Chi-restraints excluded: chain A residue 1088 ILE Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1182 LEU Chi-restraints excluded: chain A residue 1235 ASP Chi-restraints excluded: chain A residue 1307 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 57 optimal weight: 0.0770 chunk 6 optimal weight: 2.9990 chunk 75 optimal weight: 0.9990 chunk 109 optimal weight: 4.9990 chunk 129 optimal weight: 5.9990 chunk 12 optimal weight: 8.9990 chunk 99 optimal weight: 6.9990 chunk 16 optimal weight: 7.9990 chunk 22 optimal weight: 6.9990 chunk 102 optimal weight: 9.9990 chunk 110 optimal weight: 8.9990 overall best weight: 3.0146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 946 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.040024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2603 r_free = 0.2603 target = 0.028426 restraints weight = 84659.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.2643 r_free = 0.2643 target = 0.029623 restraints weight = 41950.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2668 r_free = 0.2668 target = 0.030386 restraints weight = 27667.805| |-----------------------------------------------------------------------------| r_work (final): 0.2634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8860 moved from start: 0.1916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 12500 Z= 0.194 Angle : 0.607 11.538 17296 Z= 0.317 Chirality : 0.040 0.157 1930 Planarity : 0.003 0.033 1895 Dihedral : 20.004 179.656 2524 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 3.43 % Allowed : 19.22 % Favored : 77.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.25), residues: 1234 helix: 1.53 (0.21), residues: 620 sheet: -0.99 (0.45), residues: 121 loop : 0.04 (0.30), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 382 HIS 0.005 0.001 HIS A 754 PHE 0.012 0.001 PHE A1052 TYR 0.017 0.001 TYR A 61 ARG 0.004 0.000 ARG A 313 Details of bonding type rmsd hydrogen bonds : bond 0.03840 ( 607) hydrogen bonds : angle 4.36078 ( 1649) covalent geometry : bond 0.00408 (12500) covalent geometry : angle 0.60718 (17296) *********************** 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 92 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 54 time to evaluate : 1.456 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.9027 (tpp) cc_final: 0.8100 (tmm) REVERT: A 20 GLU cc_start: 0.8560 (tm-30) cc_final: 0.8208 (tm-30) REVERT: A 145 GLN cc_start: 0.9308 (OUTLIER) cc_final: 0.9034 (mp10) REVERT: A 165 PHE cc_start: 0.8974 (OUTLIER) cc_final: 0.8588 (t80) REVERT: A 271 THR cc_start: 0.8561 (OUTLIER) cc_final: 0.8191 (p) REVERT: A 507 MET cc_start: 0.9215 (ppp) cc_final: 0.8962 (ppp) REVERT: A 604 MET cc_start: 0.9300 (mmm) cc_final: 0.8976 (mmm) REVERT: A 754 HIS cc_start: 0.8205 (OUTLIER) cc_final: 0.7775 (t-170) REVERT: A 786 GLU cc_start: 0.8661 (OUTLIER) cc_final: 0.8283 (mp0) REVERT: A 908 ASP cc_start: 0.7860 (t0) cc_final: 0.7497 (t0) REVERT: A 912 ARG cc_start: 0.8172 (tpm170) cc_final: 0.7970 (tpm170) REVERT: A 951 ARG cc_start: 0.9146 (tpp-160) cc_final: 0.8946 (tpp-160) REVERT: A 969 GLN cc_start: 0.8649 (OUTLIER) cc_final: 0.8310 (pp30) REVERT: A 1046 THR cc_start: 0.9203 (OUTLIER) cc_final: 0.8991 (p) REVERT: A 1092 GLU cc_start: 0.9718 (OUTLIER) cc_final: 0.9360 (mp0) outliers start: 38 outliers final: 22 residues processed: 85 average time/residue: 0.2884 time to fit residues: 36.7797 Evaluate side-chains 80 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 50 time to evaluate : 1.979 ------------------------------------------------------------------------------- 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 467 LEU Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 622 HIS Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain A residue 703 GLN Chi-restraints excluded: chain A residue 752 LYS Chi-restraints excluded: chain A residue 754 HIS Chi-restraints excluded: chain A residue 786 GLU Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 933 ASN 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 1073 ILE Chi-restraints excluded: chain A residue 1088 ILE Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1182 LEU Chi-restraints excluded: chain A residue 1235 ASP Chi-restraints excluded: chain A residue 1307 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 72 optimal weight: 8.9990 chunk 60 optimal weight: 10.0000 chunk 92 optimal weight: 3.9990 chunk 69 optimal weight: 7.9990 chunk 93 optimal weight: 0.3980 chunk 5 optimal weight: 0.9980 chunk 81 optimal weight: 8.9990 chunk 66 optimal weight: 3.9990 chunk 33 optimal weight: 5.9990 chunk 24 optimal weight: 0.0870 chunk 45 optimal weight: 10.0000 overall best weight: 1.8962 ------------------------------------------------------------------------------- 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 = 0.3049 r_free = 0.3049 target = 0.040604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2622 r_free = 0.2622 target = 0.028989 restraints weight = 83765.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2662 r_free = 0.2662 target = 0.030194 restraints weight = 42157.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2688 r_free = 0.2688 target = 0.030972 restraints weight = 28021.893| |-----------------------------------------------------------------------------| r_work (final): 0.2654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8844 moved from start: 0.2014 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= 0.147 Angle : 0.604 13.807 17296 Z= 0.311 Chirality : 0.039 0.162 1930 Planarity : 0.003 0.032 1895 Dihedral : 19.907 179.170 2524 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 3.34 % Allowed : 19.77 % Favored : 76.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.25), residues: 1234 helix: 1.60 (0.21), residues: 620 sheet: -0.90 (0.45), residues: 123 loop : 0.07 (0.30), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 382 HIS 0.005 0.001 HIS A 754 PHE 0.011 0.001 PHE A1052 TYR 0.015 0.001 TYR A 595 ARG 0.006 0.000 ARG A 313 Details of bonding type rmsd hydrogen bonds : bond 0.03592 ( 607) hydrogen bonds : angle 4.25013 ( 1649) covalent geometry : bond 0.00317 (12500) covalent geometry : angle 0.60403 (17296) *********************** 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 90 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 53 time to evaluate : 1.238 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.9042 (tpp) cc_final: 0.8075 (tmm) REVERT: A 20 GLU cc_start: 0.8554 (tm-30) cc_final: 0.8193 (tm-30) REVERT: A 145 GLN cc_start: 0.9336 (OUTLIER) cc_final: 0.9020 (mp10) REVERT: A 165 PHE cc_start: 0.8917 (OUTLIER) cc_final: 0.8517 (t80) REVERT: A 271 THR cc_start: 0.8592 (OUTLIER) cc_final: 0.8240 (p) REVERT: A 363 HIS cc_start: 0.9473 (OUTLIER) cc_final: 0.9084 (t70) REVERT: A 507 MET cc_start: 0.9200 (ppp) cc_final: 0.8940 (ppp) REVERT: A 604 MET cc_start: 0.9277 (mmm) cc_final: 0.8944 (mmm) REVERT: A 610 THR cc_start: 0.9701 (OUTLIER) cc_final: 0.9386 (p) REVERT: A 754 HIS cc_start: 0.8197 (OUTLIER) cc_final: 0.7822 (t-170) REVERT: A 786 GLU cc_start: 0.8584 (OUTLIER) cc_final: 0.8242 (mp0) REVERT: A 908 ASP cc_start: 0.7843 (t0) cc_final: 0.7458 (t0) REVERT: A 969 GLN cc_start: 0.8644 (OUTLIER) cc_final: 0.8287 (pp30) REVERT: A 1074 ASP cc_start: 0.9578 (OUTLIER) cc_final: 0.8792 (p0) REVERT: A 1092 GLU cc_start: 0.9724 (OUTLIER) cc_final: 0.9355 (mp0) REVERT: A 1194 ARG cc_start: 0.9529 (OUTLIER) cc_final: 0.8992 (mmm-85) outliers start: 37 outliers final: 22 residues processed: 83 average time/residue: 0.2627 time to fit residues: 32.4653 Evaluate side-chains 83 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 50 time to evaluate : 1.201 ------------------------------------------------------------------------------- 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 467 LEU Chi-restraints excluded: chain A residue 480 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 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 933 ASN 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 1073 ILE Chi-restraints excluded: chain A residue 1074 ASP Chi-restraints excluded: chain A residue 1088 ILE Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1182 LEU Chi-restraints excluded: chain A residue 1194 ARG Chi-restraints excluded: chain A residue 1235 ASP Chi-restraints excluded: chain A residue 1307 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 85 optimal weight: 10.0000 chunk 48 optimal weight: 10.0000 chunk 128 optimal weight: 5.9990 chunk 66 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 109 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 84 optimal weight: 9.9990 chunk 73 optimal weight: 10.0000 chunk 40 optimal weight: 6.9990 chunk 71 optimal weight: 0.5980 overall best weight: 3.3186 ------------------------------------------------------------------------------- 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 = 0.3032 r_free = 0.3032 target = 0.039990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2601 r_free = 0.2601 target = 0.028440 restraints weight = 85332.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2641 r_free = 0.2641 target = 0.029616 restraints weight = 42899.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2664 r_free = 0.2664 target = 0.030326 restraints weight = 28563.025| |-----------------------------------------------------------------------------| r_work (final): 0.2632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8866 moved from start: 0.2098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 12500 Z= 0.211 Angle : 0.632 13.911 17296 Z= 0.327 Chirality : 0.040 0.269 1930 Planarity : 0.003 0.044 1895 Dihedral : 19.899 177.690 2524 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 3.34 % Allowed : 20.76 % Favored : 75.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.25), residues: 1234 helix: 1.59 (0.21), residues: 620 sheet: -0.99 (0.46), residues: 121 loop : 0.06 (0.30), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 382 HIS 0.005 0.001 HIS A 754 PHE 0.013 0.001 PHE A1113 TYR 0.019 0.001 TYR A 61 ARG 0.005 0.000 ARG A 313 Details of bonding type rmsd hydrogen bonds : bond 0.03929 ( 607) hydrogen bonds : angle 4.32821 ( 1649) covalent geometry : bond 0.00444 (12500) covalent geometry : angle 0.63175 (17296) *********************** 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 89 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 52 time to evaluate : 1.239 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.9056 (tpp) cc_final: 0.8036 (tmm) REVERT: A 20 GLU cc_start: 0.8559 (tm-30) cc_final: 0.8248 (tm-30) REVERT: A 145 GLN cc_start: 0.9322 (OUTLIER) cc_final: 0.9048 (mp10) REVERT: A 165 PHE cc_start: 0.8995 (OUTLIER) cc_final: 0.8599 (t80) REVERT: A 271 THR cc_start: 0.8572 (OUTLIER) cc_final: 0.8210 (p) REVERT: A 363 HIS cc_start: 0.9459 (OUTLIER) cc_final: 0.9079 (t70) REVERT: A 507 MET cc_start: 0.9188 (ppp) cc_final: 0.8929 (ppp) REVERT: A 604 MET cc_start: 0.9299 (mmm) cc_final: 0.8966 (mmm) REVERT: A 610 THR cc_start: 0.9722 (OUTLIER) cc_final: 0.9416 (p) REVERT: A 754 HIS cc_start: 0.8263 (OUTLIER) cc_final: 0.7859 (t-170) REVERT: A 786 GLU cc_start: 0.8620 (OUTLIER) cc_final: 0.8274 (mp0) REVERT: A 908 ASP cc_start: 0.7994 (t0) cc_final: 0.7579 (t0) REVERT: A 912 ARG cc_start: 0.8032 (tpm170) cc_final: 0.7718 (tpm170) REVERT: A 933 ASN cc_start: 0.8596 (OUTLIER) cc_final: 0.8321 (t0) REVERT: A 969 GLN cc_start: 0.8633 (OUTLIER) cc_final: 0.8064 (pp30) REVERT: A 1046 THR cc_start: 0.9186 (OUTLIER) cc_final: 0.8974 (p) REVERT: A 1074 ASP cc_start: 0.9590 (OUTLIER) cc_final: 0.8733 (p0) REVERT: A 1092 GLU cc_start: 0.9728 (OUTLIER) cc_final: 0.9372 (mp0) REVERT: A 1194 ARG cc_start: 0.9524 (OUTLIER) cc_final: 0.8948 (mmm-85) outliers start: 37 outliers final: 21 residues processed: 83 average time/residue: 0.2549 time to fit residues: 31.5238 Evaluate side-chains 85 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 51 time to evaluate : 1.364 ------------------------------------------------------------------------------- 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 480 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 754 HIS Chi-restraints excluded: chain A residue 786 GLU Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 933 ASN Chi-restraints excluded: chain A residue 969 GLN Chi-restraints excluded: chain A residue 1004 THR Chi-restraints excluded: chain A residue 1018 MET Chi-restraints excluded: chain A residue 1046 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 1194 ARG Chi-restraints excluded: chain A residue 1235 ASP Chi-restraints excluded: chain A residue 1305 LEU Chi-restraints excluded: chain A residue 1307 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 11 optimal weight: 8.9990 chunk 46 optimal weight: 0.9980 chunk 78 optimal weight: 7.9990 chunk 42 optimal weight: 20.0000 chunk 50 optimal weight: 2.9990 chunk 105 optimal weight: 0.0370 chunk 102 optimal weight: 8.9990 chunk 3 optimal weight: 0.9980 chunk 59 optimal weight: 0.9980 chunk 91 optimal weight: 6.9990 chunk 123 optimal weight: 10.0000 overall best weight: 1.2060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 206 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.041018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2637 r_free = 0.2637 target = 0.029389 restraints weight = 83210.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2678 r_free = 0.2678 target = 0.030633 restraints weight = 40690.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.2703 r_free = 0.2703 target = 0.031435 restraints weight = 26610.613| |-----------------------------------------------------------------------------| r_work (final): 0.2672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8823 moved from start: 0.2195 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= 0.121 Angle : 0.609 14.555 17296 Z= 0.307 Chirality : 0.039 0.285 1930 Planarity : 0.003 0.032 1895 Dihedral : 19.773 178.144 2524 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.80 % Allowed : 21.21 % Favored : 75.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.25), residues: 1234 helix: 1.72 (0.21), residues: 620 sheet: -0.81 (0.46), residues: 123 loop : 0.13 (0.30), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 382 HIS 0.005 0.001 HIS A 754 PHE 0.010 0.001 PHE A1052 TYR 0.017 0.001 TYR A 595 ARG 0.005 0.000 ARG A 313 Details of bonding type rmsd hydrogen bonds : bond 0.03385 ( 607) hydrogen bonds : angle 4.14594 ( 1649) covalent geometry : bond 0.00266 (12500) covalent geometry : angle 0.60937 (17296) *********************** 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 : 1.288 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.9047 (tpp) cc_final: 0.8079 (tmm) REVERT: A 20 GLU cc_start: 0.8575 (tm-30) cc_final: 0.8163 (tm-30) REVERT: A 145 GLN cc_start: 0.9348 (OUTLIER) cc_final: 0.9068 (mp10) REVERT: A 165 PHE cc_start: 0.8906 (OUTLIER) cc_final: 0.8478 (t80) REVERT: A 271 THR cc_start: 0.8573 (OUTLIER) cc_final: 0.8213 (p) REVERT: A 363 HIS cc_start: 0.9474 (OUTLIER) cc_final: 0.9069 (t70) REVERT: A 507 MET cc_start: 0.9211 (ppp) cc_final: 0.8944 (ppp) REVERT: A 604 MET cc_start: 0.9263 (mmm) cc_final: 0.8909 (mmm) REVERT: A 786 GLU cc_start: 0.8496 (OUTLIER) cc_final: 0.8169 (mp0) REVERT: A 908 ASP cc_start: 0.7853 (t0) cc_final: 0.7457 (t0) REVERT: A 969 GLN cc_start: 0.8648 (OUTLIER) cc_final: 0.8027 (pp30) REVERT: A 1074 ASP cc_start: 0.9595 (OUTLIER) cc_final: 0.8739 (p0) outliers start: 31 outliers final: 17 residues processed: 77 average time/residue: 0.3201 time to fit residues: 36.4643 Evaluate side-chains 76 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 52 time to evaluate : 1.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ILE 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 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 752 LYS 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 1182 LEU Chi-restraints excluded: chain A residue 1235 ASP 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 121 optimal weight: 0.2980 chunk 0 optimal weight: 10.0000 chunk 70 optimal weight: 4.9990 chunk 33 optimal weight: 5.9990 chunk 23 optimal weight: 0.0770 chunk 82 optimal weight: 0.7980 chunk 119 optimal weight: 0.9980 chunk 36 optimal weight: 10.0000 chunk 11 optimal weight: 7.9990 chunk 104 optimal weight: 10.0000 chunk 5 optimal weight: 2.9990 overall best weight: 1.0340 ------------------------------------------------------------------------------- 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 = 0.3070 r_free = 0.3070 target = 0.041660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2652 r_free = 0.2652 target = 0.030120 restraints weight = 82092.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.2693 r_free = 0.2693 target = 0.031353 restraints weight = 40688.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2719 r_free = 0.2719 target = 0.032157 restraints weight = 26722.525| |-----------------------------------------------------------------------------| r_work (final): 0.2686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8816 moved from start: 0.2311 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= 0.120 Angle : 0.606 14.482 17296 Z= 0.304 Chirality : 0.039 0.236 1930 Planarity : 0.003 0.032 1895 Dihedral : 19.660 178.426 2524 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.25), residues: 1234 helix: 1.79 (0.22), residues: 613 sheet: -0.69 (0.46), residues: 123 loop : 0.17 (0.30), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 382 HIS 0.002 0.000 HIS A 618 PHE 0.011 0.001 PHE A1113 TYR 0.017 0.001 TYR A 595 ARG 0.003 0.000 ARG A 313 Details of bonding type rmsd hydrogen bonds : bond 0.03310 ( 607) hydrogen bonds : angle 4.09527 ( 1649) covalent geometry : bond 0.00263 (12500) covalent geometry : angle 0.60640 (17296) ********************** 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: 27 poor density : 53 time to evaluate : 1.365 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.9046 (tpp) cc_final: 0.8023 (tmm) REVERT: A 20 GLU cc_start: 0.8555 (tm-30) cc_final: 0.8138 (tm-30) REVERT: A 145 GLN cc_start: 0.9352 (OUTLIER) cc_final: 0.9093 (mp10) REVERT: A 165 PHE cc_start: 0.8928 (OUTLIER) cc_final: 0.8504 (t80) REVERT: A 271 THR cc_start: 0.8623 (OUTLIER) cc_final: 0.8284 (p) REVERT: A 363 HIS cc_start: 0.9473 (OUTLIER) cc_final: 0.9069 (t70) REVERT: A 507 MET cc_start: 0.9207 (ppp) cc_final: 0.8949 (ppp) REVERT: A 604 MET cc_start: 0.9283 (mmm) cc_final: 0.8919 (mmm) REVERT: A 786 GLU cc_start: 0.8425 (OUTLIER) cc_final: 0.8147 (mp0) REVERT: A 908 ASP cc_start: 0.7882 (t0) cc_final: 0.7437 (t0) REVERT: A 969 GLN cc_start: 0.8641 (OUTLIER) cc_final: 0.8041 (pp30) REVERT: A 1074 ASP cc_start: 0.9600 (OUTLIER) cc_final: 0.8686 (p0) REVERT: A 1092 GLU cc_start: 0.9716 (OUTLIER) cc_final: 0.9349 (mp0) outliers start: 27 outliers final: 17 residues processed: 76 average time/residue: 0.2804 time to fit residues: 32.3488 Evaluate side-chains 76 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 51 time to evaluate : 1.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ILE 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 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 752 LYS 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 1235 ASP 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 90 optimal weight: 7.9990 chunk 16 optimal weight: 2.9990 chunk 83 optimal weight: 4.9990 chunk 55 optimal weight: 6.9990 chunk 2 optimal weight: 7.9990 chunk 97 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 chunk 44 optimal weight: 5.9990 chunk 105 optimal weight: 5.9990 chunk 57 optimal weight: 10.0000 chunk 75 optimal weight: 6.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- 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 = 0.3036 r_free = 0.3036 target = 0.040270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2606 r_free = 0.2606 target = 0.028635 restraints weight = 85066.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2647 r_free = 0.2647 target = 0.029865 restraints weight = 42366.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2672 r_free = 0.2672 target = 0.030632 restraints weight = 28085.400| |-----------------------------------------------------------------------------| r_work (final): 0.2640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8864 moved from start: 0.2322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 12500 Z= 0.225 Angle : 0.652 13.034 17296 Z= 0.334 Chirality : 0.040 0.199 1930 Planarity : 0.003 0.033 1895 Dihedral : 19.757 176.720 2524 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 2.53 % Allowed : 21.48 % Favored : 75.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.25), residues: 1234 helix: 1.73 (0.21), residues: 618 sheet: -0.78 (0.47), residues: 121 loop : 0.12 (0.30), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 382 HIS 0.004 0.001 HIS A 191 PHE 0.012 0.001 PHE A1113 TYR 0.020 0.001 TYR A 61 ARG 0.008 0.000 ARG A 912 Details of bonding type rmsd hydrogen bonds : bond 0.03961 ( 607) hydrogen bonds : angle 4.23904 ( 1649) covalent geometry : bond 0.00470 (12500) covalent geometry : angle 0.65157 (17296) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3988.01 seconds wall clock time: 73 minutes 32.64 seconds (4412.64 seconds total)