Starting phenix.real_space_refine on Fri Jul 3 12:32:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sqh_40705/07_2026/8sqh_40705.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sqh_40705/07_2026/8sqh_40705.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.69 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8sqh_40705/07_2026/8sqh_40705.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sqh_40705/07_2026/8sqh_40705.map" model { file = "/net/cci-nas-00/data/ceres_data/8sqh_40705/07_2026/8sqh_40705.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sqh_40705/07_2026/8sqh_40705.cif" } resolution = 3.69 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.025 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 146 5.49 5 Mg 4 5.21 5 S 22 5.16 5 C 8430 2.51 5 N 2476 2.21 5 O 3023 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14101 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 11002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1341, 11002 Classifications: {'peptide': 1341} Link IDs: {'PTRANS': 36, 'TRANS': 1304} Chain breaks: 3 Chain: "B" Number of atoms: 2100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 2100 Classifications: {'RNA': 98} Modifications used: {'5*END': 1, 'rna2p_pur': 7, 'rna2p_pyr': 5, 'rna3p_pur': 52, 'rna3p_pyr': 34} Link IDs: {'rna2p': 11, 'rna3p': 86} Chain: "C" Number of atoms: 269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 269 Classifications: {'DNA': 13} Link IDs: {'rna3p': 12} Chain: "D" Number of atoms: 342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 342 Classifications: {'DNA': 17} Link IDs: {'rna3p': 16} Chain breaks: 1 Chain: "c" Number of atoms: 384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 384 Classifications: {'DNA': 19} Link IDs: {'rna3p': 18} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.27, per 1000 atoms: 0.16 Number of scatterers: 14101 At special positions: 0 Unit cell: (85.54, 119.38, 130.66, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 22 16.00 P 146 15.00 Mg 4 11.99 O 3023 8.00 N 2476 7.00 C 8430 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: 0.97 Conformation dependent library (CDL) restraints added in 474.6 milliseconds 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2554 Finding SS restraints... Secondary structure from input PDB file: 67 helices and 11 sheets defined 53.8% alpha, 10.0% beta 54 base pairs and 82 stacking pairs defined. Time for finding SS restraints: 1.62 Creating SS restraints... Processing helix chain 'A' and resid 59 through 94 removed outlier: 4.997A pdb=" N ASN A 88 " --> pdb=" O GLU A 84 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N GLU A 89 " --> pdb=" O ILE A 85 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N LYS A 92 " --> pdb=" O ASN A 88 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N VAL A 93 " --> pdb=" O GLU A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 103 Processing helix chain 'A' and resid 121 through 132 Processing helix chain 'A' and resid 134 through 145 removed outlier: 3.568A pdb=" N LEU A 138 " --> pdb=" O THR A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 164 Processing helix chain 'A' and resid 181 through 183 No H-bonds generated for 'chain 'A' and resid 181 through 183' Processing helix chain 'A' and resid 184 through 196 Processing helix chain 'A' and resid 208 through 213 Processing helix chain 'A' and resid 217 through 229 removed outlier: 4.607A pdb=" N GLU A 223 " --> pdb=" O SER A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 306 Processing helix chain 'A' and resid 315 through 343 Processing helix chain 'A' and resid 346 through 352 Processing helix chain 'A' and resid 358 through 364 Processing helix chain 'A' and resid 368 through 383 Proline residue: A 378 - end of helix Processing helix chain 'A' and resid 386 through 395 Processing helix chain 'A' and resid 404 through 410 removed outlier: 3.510A pdb=" N GLY A 408 " --> pdb=" O PHE A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 427 removed outlier: 4.371A pdb=" N HIS A 415 " --> pdb=" O PRO A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 436 removed outlier: 3.807A pdb=" N LYS A 434 " --> pdb=" O TYR A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 446 Processing helix chain 'A' and resid 483 through 494 removed outlier: 3.738A pdb=" N ILE A 492 " --> pdb=" O ALA A 488 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ARG A 494 " --> pdb=" O SER A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 525 Processing helix chain 'A' and resid 541 through 552 Processing helix chain 'A' and resid 553 through 556 removed outlier: 3.623A pdb=" N ASN A 556 " --> pdb=" O PHE A 553 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 553 through 556' Processing helix chain 'A' and resid 560 through 568 Processing helix chain 'A' and resid 591 through 602 Processing helix chain 'A' and resid 603 through 609 Processing helix chain 'A' and resid 612 through 626 removed outlier: 3.600A pdb=" N LEU A 616 " --> pdb=" O ASN A 612 " (cutoff:3.500A) Processing helix chain 'A' and resid 628 through 637 Processing helix chain 'A' and resid 638 through 642 removed outlier: 4.397A pdb=" N HIS A 641 " --> pdb=" O THR A 638 " (cutoff:3.500A) Processing helix chain 'A' and resid 644 through 652 Processing helix chain 'A' and resid 663 through 668 removed outlier: 3.550A pdb=" N ILE A 667 " --> pdb=" O SER A 663 " (cutoff:3.500A) Processing helix chain 'A' and resid 678 through 685 Processing helix chain 'A' and resid 692 through 699 Processing helix chain 'A' and resid 703 through 712 removed outlier: 3.844A pdb=" N ASP A 707 " --> pdb=" O THR A 703 " (cutoff:3.500A) Processing helix chain 'A' and resid 719 through 726 Processing helix chain 'A' and resid 730 through 751 removed outlier: 4.354A pdb=" N LYS A 734 " --> pdb=" O SER A 730 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N LYS A 735 " --> pdb=" O PRO A 731 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N GLY A 736 " --> pdb=" O ALA A 732 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N MET A 751 " --> pdb=" O LEU A 747 " (cutoff:3.500A) Processing helix chain 'A' and resid 769 through 777 Processing helix chain 'A' and resid 779 through 792 removed outlier: 3.603A pdb=" N ARG A 783 " --> pdb=" O GLU A 779 " (cutoff:3.500A) Processing helix chain 'A' and resid 794 through 799 Processing helix chain 'A' and resid 802 through 807 removed outlier: 3.717A pdb=" N GLN A 805 " --> pdb=" O GLU A 802 " (cutoff:3.500A) Processing helix chain 'A' and resid 808 through 817 Processing helix chain 'A' and resid 851 through 853 No H-bonds generated for 'chain 'A' and resid 851 through 853' Processing helix chain 'A' and resid 859 through 866 Processing helix chain 'A' and resid 872 through 888 removed outlier: 5.679A pdb=" N ASN A 881 " --> pdb=" O LYS A 877 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N TYR A 882 " --> pdb=" O LYS A 878 " (cutoff:3.500A) Processing helix chain 'A' and resid 893 through 901 Processing helix chain 'A' and resid 902 through 906 Processing helix chain 'A' and resid 909 through 913 Processing helix chain 'A' and resid 917 through 940 removed outlier: 4.142A pdb=" N LEU A 921 " --> pdb=" O ILE A 917 " (cutoff:3.500A) Processing helix chain 'A' and resid 960 through 970 Processing helix chain 'A' and resid 980 through 1001 removed outlier: 4.398A pdb=" N ALA A 984 " --> pdb=" O ASN A 980 " (cutoff:3.500A) Processing helix chain 'A' and resid 1004 through 1009 removed outlier: 3.652A pdb=" N PHE A1008 " --> pdb=" O LEU A1004 " (cutoff:3.500A) Processing helix chain 'A' and resid 1030 through 1042 Processing helix chain 'A' and resid 1043 through 1047 Processing helix chain 'A' and resid 1077 through 1088 Processing helix chain 'A' and resid 1127 through 1132 Processing helix chain 'A' and resid 1168 through 1177 removed outlier: 4.377A pdb=" N SER A1172 " --> pdb=" O ILE A1168 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N SER A1173 " --> pdb=" O MET A1169 " (cutoff:3.500A) Processing helix chain 'A' and resid 1177 through 1185 Processing helix chain 'A' and resid 1191 through 1195 removed outlier: 3.519A pdb=" N LEU A1194 " --> pdb=" O LYS A1191 " (cutoff:3.500A) Processing helix chain 'A' and resid 1207 through 1209 No H-bonds generated for 'chain 'A' and resid 1207 through 1209' Processing helix chain 'A' and resid 1229 through 1240 Processing helix chain 'A' and resid 1248 through 1262 Processing helix chain 'A' and resid 1264 through 1281 Processing helix chain 'A' and resid 1283 through 1298 Processing helix chain 'A' and resid 1301 through 1313 Processing helix chain 'A' and resid 1314 through 1316 No H-bonds generated for 'chain 'A' and resid 1314 through 1316' Processing helix chain 'A' and resid 1340 through 1344 removed outlier: 4.148A pdb=" N ASP A1344 " --> pdb=" O GLU A1341 " (cutoff:3.500A) Processing helix chain 'A' and resid 1363 through 1365 No H-bonds generated for 'chain 'A' and resid 1363 through 1365' Processing sheet with id=AA1, first strand: chain 'A' and resid 954 through 959 removed outlier: 6.290A pdb=" N ILE A 759 " --> pdb=" O ILE A 956 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N LEU A 958 " --> pdb=" O ILE A 759 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N ILE A 761 " --> pdb=" O LEU A 958 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ILE A 7 " --> pdb=" O VAL A 760 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N GLU A 762 " --> pdb=" O ILE A 7 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N LEU A 9 " --> pdb=" O GLU A 762 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 46 removed outlier: 4.587A pdb=" N GLU A1357 " --> pdb=" O LYS A 33 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N LEU A1203 " --> pdb=" O ILE A1348 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N SER A1202 " --> pdb=" O LEU A1214 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N GLN A1219 " --> pdb=" O ALA A1215 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 252 through 253 removed outlier: 3.904A pdb=" N PHE A 252 " --> pdb=" O LEU A 264 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 538 through 539 Processing sheet with id=AA5, first strand: chain 'A' and resid 837 through 840 Processing sheet with id=AA6, first strand: chain 'A' and resid 1049 through 1051 Processing sheet with id=AA7, first strand: chain 'A' and resid 1063 through 1065 removed outlier: 3.702A pdb=" N TRP A1074 " --> pdb=" O GLU A1064 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1120 through 1121 Processing sheet with id=AA9, first strand: chain 'A' and resid 1156 through 1167 Processing sheet with id=AB1, first strand: chain 'A' and resid 1156 through 1167 removed outlier: 3.752A pdb=" N ILE A1196 " --> pdb=" O LEU A1144 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 1324 through 1326 515 hydrogen bonds defined for protein. 1467 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 133 hydrogen bonds 262 hydrogen bond angles 0 basepair planarities 54 basepair parallelities 82 stacking parallelities Total time for adding SS restraints: 3.09 Time building geometry restraints manager: 1.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3719 1.34 - 1.46: 3699 1.46 - 1.58: 6914 1.58 - 1.70: 286 1.70 - 1.82: 42 Bond restraints: 14660 Sorted by residual: bond pdb=" C1' DC c 6 " pdb=" N1 DC c 6 " ideal model delta sigma weight residual 1.468 1.550 -0.082 1.40e-02 5.10e+03 3.43e+01 bond pdb=" C1' DC c 13 " pdb=" N1 DC c 13 " ideal model delta sigma weight residual 1.468 1.539 -0.071 1.40e-02 5.10e+03 2.60e+01 bond pdb=" C1' DC D 34 " pdb=" N1 DC D 34 " ideal model delta sigma weight residual 1.468 1.536 -0.068 1.40e-02 5.10e+03 2.33e+01 bond pdb=" C1' DT c 11 " pdb=" N1 DT c 11 " ideal model delta sigma weight residual 1.468 1.534 -0.066 1.40e-02 5.10e+03 2.23e+01 bond pdb=" C3' DA C 14 " pdb=" C2' DA C 14 " ideal model delta sigma weight residual 1.516 1.548 -0.032 8.00e-03 1.56e+04 1.62e+01 ... (remaining 14655 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.94: 19819 2.94 - 5.88: 487 5.88 - 8.82: 79 8.82 - 11.76: 18 11.76 - 14.70: 7 Bond angle restraints: 20410 Sorted by residual: angle pdb=" O4' DG D 35 " pdb=" C1' DG D 35 " pdb=" N9 DG D 35 " ideal model delta sigma weight residual 108.00 114.04 -6.04 7.00e-01 2.04e+00 7.44e+01 angle pdb=" O2 U B 64 " pdb=" C2 U B 64 " pdb=" N3 U B 64 " ideal model delta sigma weight residual 122.20 117.39 4.81 7.00e-01 2.04e+00 4.73e+01 angle pdb=" N1 U B 64 " pdb=" C2 U B 64 " pdb=" O2 U B 64 " ideal model delta sigma weight residual 122.80 127.27 -4.47 7.00e-01 2.04e+00 4.07e+01 angle pdb=" O4' DC D 36 " pdb=" C4' DC D 36 " pdb=" C3' DC D 36 " ideal model delta sigma weight residual 106.00 102.41 3.59 6.00e-01 2.78e+00 3.57e+01 angle pdb=" O5' DA C 14 " pdb=" C5' DA C 14 " pdb=" C4' DA C 14 " ideal model delta sigma weight residual 109.40 114.07 -4.67 8.00e-01 1.56e+00 3.41e+01 ... (remaining 20405 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.86: 8202 29.86 - 59.71: 571 59.71 - 89.57: 115 89.57 - 119.42: 3 119.42 - 149.28: 2 Dihedral angle restraints: 8893 sinusoidal: 4949 harmonic: 3944 Sorted by residual: dihedral pdb=" CA SER A1106 " pdb=" C SER A1106 " pdb=" N LYS A1107 " pdb=" CA LYS A1107 " ideal model delta harmonic sigma weight residual 180.00 152.05 27.95 0 5.00e+00 4.00e-02 3.13e+01 dihedral pdb=" CA ASP A 837 " pdb=" C ASP A 837 " pdb=" N VAL A 838 " pdb=" CA VAL A 838 " ideal model delta harmonic sigma weight residual 180.00 152.89 27.11 0 5.00e+00 4.00e-02 2.94e+01 dihedral pdb=" CA LYS A 526 " pdb=" C LYS A 526 " pdb=" N VAL A 527 " pdb=" CA VAL A 527 " ideal model delta harmonic sigma weight residual 180.00 153.40 26.60 0 5.00e+00 4.00e-02 2.83e+01 ... (remaining 8890 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.127: 2228 0.127 - 0.255: 91 0.255 - 0.382: 13 0.382 - 0.510: 1 0.510 - 0.637: 4 Chirality restraints: 2337 Sorted by residual: chirality pdb=" C3' A B 12 " pdb=" C4' A B 12 " pdb=" O3' A B 12 " pdb=" C2' A B 12 " both_signs ideal model delta sigma weight residual False -2.48 -1.84 -0.64 2.00e-01 2.50e+01 1.01e+01 chirality pdb=" C4' A B 12 " pdb=" C5' A B 12 " pdb=" O4' A B 12 " pdb=" C3' A B 12 " both_signs ideal model delta sigma weight residual False -2.50 -1.86 -0.63 2.00e-01 2.50e+01 1.01e+01 chirality pdb=" C3' G B 11 " pdb=" C4' G B 11 " pdb=" O3' G B 11 " pdb=" C2' G B 11 " both_signs ideal model delta sigma weight residual False -2.48 -1.89 -0.59 2.00e-01 2.50e+01 8.57e+00 ... (remaining 2334 not shown) Planarity restraints: 2074 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DG D 41 " -0.063 2.00e-02 2.50e+03 2.90e-02 2.53e+01 pdb=" N9 DG D 41 " 0.075 2.00e-02 2.50e+03 pdb=" C8 DG D 41 " -0.004 2.00e-02 2.50e+03 pdb=" N7 DG D 41 " -0.002 2.00e-02 2.50e+03 pdb=" C5 DG D 41 " -0.002 2.00e-02 2.50e+03 pdb=" C6 DG D 41 " -0.006 2.00e-02 2.50e+03 pdb=" O6 DG D 41 " -0.015 2.00e-02 2.50e+03 pdb=" N1 DG D 41 " -0.004 2.00e-02 2.50e+03 pdb=" C2 DG D 41 " 0.001 2.00e-02 2.50e+03 pdb=" N2 DG D 41 " 0.002 2.00e-02 2.50e+03 pdb=" N3 DG D 41 " 0.004 2.00e-02 2.50e+03 pdb=" C4 DG D 41 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G B 1 " 0.040 2.00e-02 2.50e+03 2.88e-02 2.49e+01 pdb=" N9 G B 1 " -0.084 2.00e-02 2.50e+03 pdb=" C8 G B 1 " 0.005 2.00e-02 2.50e+03 pdb=" N7 G B 1 " 0.005 2.00e-02 2.50e+03 pdb=" C5 G B 1 " 0.002 2.00e-02 2.50e+03 pdb=" C6 G B 1 " 0.008 2.00e-02 2.50e+03 pdb=" O6 G B 1 " 0.001 2.00e-02 2.50e+03 pdb=" N1 G B 1 " -0.003 2.00e-02 2.50e+03 pdb=" C2 G B 1 " -0.002 2.00e-02 2.50e+03 pdb=" N2 G B 1 " -0.004 2.00e-02 2.50e+03 pdb=" N3 G B 1 " -0.002 2.00e-02 2.50e+03 pdb=" C4 G B 1 " 0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT c 11 " 0.026 2.00e-02 2.50e+03 2.94e-02 2.16e+01 pdb=" N1 DT c 11 " -0.074 2.00e-02 2.50e+03 pdb=" C2 DT c 11 " 0.047 2.00e-02 2.50e+03 pdb=" O2 DT c 11 " -0.007 2.00e-02 2.50e+03 pdb=" N3 DT c 11 " -0.006 2.00e-02 2.50e+03 pdb=" C4 DT c 11 " -0.001 2.00e-02 2.50e+03 pdb=" O4 DT c 11 " -0.003 2.00e-02 2.50e+03 pdb=" C5 DT c 11 " 0.005 2.00e-02 2.50e+03 pdb=" C7 DT c 11 " 0.007 2.00e-02 2.50e+03 pdb=" C6 DT c 11 " 0.006 2.00e-02 2.50e+03 ... (remaining 2071 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 79 2.54 - 3.13: 10533 3.13 - 3.72: 24467 3.72 - 4.31: 32720 4.31 - 4.90: 50396 Nonbonded interactions: 118195 Sorted by model distance: nonbonded pdb=" OD2 ASP A 10 " pdb="MG MG A1402 " model vdw 1.955 2.170 nonbonded pdb=" OP1 DC D 34 " pdb="MG MG A1401 " model vdw 2.015 2.170 nonbonded pdb=" ND1 HIS A 983 " pdb="MG MG A1402 " model vdw 2.040 2.250 nonbonded pdb=" OE1 GLU A 762 " pdb="MG MG A1401 " model vdw 2.045 2.170 nonbonded pdb=" OP2 A B 65 " pdb="MG MG B 101 " model vdw 2.062 2.170 ... (remaining 118190 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: 4.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.180 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 13.620 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:0.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 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 0.096 14660 Z= 0.366 Angle : 1.137 14.698 20410 Z= 0.733 Chirality : 0.065 0.637 2337 Planarity : 0.008 0.083 2074 Dihedral : 19.150 149.280 6339 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 0.17 % Allowed : 17.78 % Favored : 82.05 % Cbeta Deviations : 0.08 % 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: -1.51 (0.21), residues: 1333 helix: -1.07 (0.18), residues: 629 sheet: -0.29 (0.64), residues: 80 loop : -0.86 (0.23), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.039 0.003 ARG A 220 TYR 0.033 0.004 TYR A 192 PHE 0.033 0.002 PHE A1046 TRP 0.031 0.003 TRP A1136 HIS 0.010 0.002 HIS A 167 Details of bonding type rmsd/Z covalent geometry : bond 0.00577 / 0.37 (14660) covalent geometry : angle 1.13688 / 0.73 (20410) hydrogen bonds : bond 0.13845 / 9.04 ( 636) hydrogen bonds : angle 6.07353 / 4.32 ( 1729) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 49 time to evaluate : 0.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1325 LYS cc_start: 0.9228 (ptmt) cc_final: 0.8750 (ttpp) outliers start: 2 outliers final: 1 residues processed: 51 average time/residue: 0.1275 time to fit residues: 9.6948 Evaluate side-chains 42 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 41 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 921 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 175 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.044448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2713 r_free = 0.2713 target = 0.033346 restraints weight = 92949.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.2749 r_free = 0.2749 target = 0.034414 restraints weight = 45352.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2772 r_free = 0.2772 target = 0.035017 restraints weight = 29648.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.2787 r_free = 0.2787 target = 0.035510 restraints weight = 23313.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2796 r_free = 0.2796 target = 0.035772 restraints weight = 19891.827| |-----------------------------------------------------------------------------| r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 moved from start: 0.1077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 14660 Z= 0.197 Angle : 0.648 8.909 20410 Z= 0.360 Chirality : 0.041 0.220 2337 Planarity : 0.004 0.048 2074 Dihedral : 19.569 154.965 3465 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 1.82 % Allowed : 14.56 % Favored : 83.62 % 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: -0.23 (0.23), residues: 1333 helix: 0.18 (0.20), residues: 638 sheet: 0.13 (0.57), residues: 97 loop : -0.42 (0.26), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 535 TYR 0.024 0.002 TYR A 192 PHE 0.013 0.002 PHE A1046 TRP 0.019 0.001 TRP A1136 HIS 0.006 0.001 HIS A 799 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.20 (14660) covalent geometry : angle 0.64803 / 0.36 (20410) hydrogen bonds : bond 0.05170 / 3.41 ( 636) hydrogen bonds : angle 4.95738 / 3.55 ( 1729) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 42 time to evaluate : 0.476 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 ILE cc_start: 0.8890 (OUTLIER) cc_final: 0.8682 (tt) REVERT: A 263 LYS cc_start: 0.7604 (OUTLIER) cc_final: 0.7392 (pptt) REVERT: A 974 LYS cc_start: 0.9210 (OUTLIER) cc_final: 0.8847 (ptmt) REVERT: A 1325 LYS cc_start: 0.9308 (ptmt) cc_final: 0.9097 (tttp) outliers start: 22 outliers final: 9 residues processed: 62 average time/residue: 0.1186 time to fit residues: 11.1077 Evaluate side-chains 49 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 37 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 192 TYR Chi-restraints excluded: chain A residue 263 LYS Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 837 ASP Chi-restraints excluded: chain A residue 921 LEU Chi-restraints excluded: chain A residue 974 LYS Chi-restraints excluded: chain A residue 1156 LYS Chi-restraints excluded: chain A residue 1194 LEU Chi-restraints excluded: chain A residue 1328 ASP Chi-restraints excluded: chain A residue 1342 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 62 optimal weight: 3.9990 chunk 77 optimal weight: 0.4980 chunk 143 optimal weight: 20.0000 chunk 94 optimal weight: 0.0570 chunk 126 optimal weight: 5.9990 chunk 101 optimal weight: 2.9990 chunk 92 optimal weight: 3.9990 chunk 3 optimal weight: 5.9990 chunk 7 optimal weight: 6.9990 chunk 18 optimal weight: 9.9990 chunk 68 optimal weight: 1.9990 overall best weight: 1.9104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 121 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 = 0.3068 r_free = 0.3068 target = 0.044067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2703 r_free = 0.2703 target = 0.032961 restraints weight = 92872.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.2740 r_free = 0.2740 target = 0.034029 restraints weight = 44775.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2764 r_free = 0.2764 target = 0.034680 restraints weight = 29387.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2779 r_free = 0.2779 target = 0.035145 restraints weight = 22943.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2786 r_free = 0.2786 target = 0.035339 restraints weight = 19600.052| |-----------------------------------------------------------------------------| r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8700 moved from start: 0.1413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14660 Z= 0.169 Angle : 0.578 9.199 20410 Z= 0.319 Chirality : 0.039 0.189 2337 Planarity : 0.003 0.048 2074 Dihedral : 19.512 155.547 3465 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 1.90 % Allowed : 14.06 % Favored : 84.04 % 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: 0.18 (0.23), residues: 1333 helix: 0.50 (0.20), residues: 643 sheet: 0.03 (0.51), residues: 106 loop : -0.14 (0.27), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1171 TYR 0.020 0.001 TYR A 192 PHE 0.009 0.001 PHE A1046 TRP 0.013 0.001 TRP A1136 HIS 0.006 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.17 (14660) covalent geometry : angle 0.57824 / 0.32 (20410) hydrogen bonds : bond 0.04573 / 2.98 ( 636) hydrogen bonds : angle 4.58277 / 3.29 ( 1729) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 40 time to evaluate : 0.501 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 196 PHE cc_start: 0.9684 (t80) cc_final: 0.9472 (t80) REVERT: A 263 LYS cc_start: 0.7708 (OUTLIER) cc_final: 0.7507 (pptt) REVERT: A 585 ASP cc_start: 0.8216 (OUTLIER) cc_final: 0.7966 (p0) REVERT: A 647 VAL cc_start: 0.9361 (OUTLIER) cc_final: 0.9148 (m) REVERT: A 974 LYS cc_start: 0.9237 (OUTLIER) cc_final: 0.8881 (ptmt) outliers start: 23 outliers final: 11 residues processed: 59 average time/residue: 0.1121 time to fit residues: 9.9370 Evaluate side-chains 53 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 38 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 TYR Chi-restraints excluded: chain A residue 263 LYS Chi-restraints excluded: chain A residue 383 MET Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 585 ASP Chi-restraints excluded: chain A residue 647 VAL Chi-restraints excluded: chain A residue 648 MET Chi-restraints excluded: chain A residue 837 ASP Chi-restraints excluded: chain A residue 847 LEU Chi-restraints excluded: chain A residue 921 LEU Chi-restraints excluded: chain A residue 974 LYS Chi-restraints excluded: chain A residue 1006 SER Chi-restraints excluded: chain A residue 1156 LYS Chi-restraints excluded: chain A residue 1194 LEU Chi-restraints excluded: chain A residue 1328 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 129 optimal weight: 5.9990 chunk 72 optimal weight: 0.6980 chunk 102 optimal weight: 6.9990 chunk 135 optimal weight: 10.0000 chunk 65 optimal weight: 7.9990 chunk 27 optimal weight: 10.0000 chunk 29 optimal weight: 7.9990 chunk 10 optimal weight: 3.9990 chunk 134 optimal weight: 10.0000 chunk 128 optimal weight: 0.9990 chunk 76 optimal weight: 1.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 202 ASN ** A 990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.042374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2628 r_free = 0.2628 target = 0.031587 restraints weight = 93866.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.2666 r_free = 0.2666 target = 0.032625 restraints weight = 44542.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.2687 r_free = 0.2687 target = 0.033290 restraints weight = 28856.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2702 r_free = 0.2702 target = 0.033696 restraints weight = 22332.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2711 r_free = 0.2711 target = 0.033963 restraints weight = 19204.130| |-----------------------------------------------------------------------------| r_work (final): 0.2699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8714 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 0.043 14660 Z= 0.219 Angle : 0.595 7.380 20410 Z= 0.324 Chirality : 0.039 0.193 2337 Planarity : 0.004 0.054 2074 Dihedral : 19.519 157.394 3465 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.23 % Favored : 96.70 % Rotamer: Outliers : 2.56 % Allowed : 14.14 % Favored : 83.29 % 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: 0.37 (0.23), residues: 1333 helix: 0.68 (0.20), residues: 648 sheet: 0.21 (0.52), residues: 106 loop : -0.10 (0.27), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 220 TYR 0.018 0.002 TYR A 192 PHE 0.010 0.002 PHE A 375 TRP 0.013 0.001 TRP A1136 HIS 0.010 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00448 / 0.22 (14660) covalent geometry : angle 0.59512 / 0.32 (20410) hydrogen bonds : bond 0.04619 / 3.02 ( 636) hydrogen bonds : angle 4.47119 / 3.23 ( 1729) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 40 time to evaluate : 0.316 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 196 PHE cc_start: 0.9668 (t80) cc_final: 0.9431 (t80) REVERT: A 263 LYS cc_start: 0.7548 (OUTLIER) cc_final: 0.7326 (pptt) REVERT: A 585 ASP cc_start: 0.8390 (OUTLIER) cc_final: 0.8159 (p0) REVERT: A 974 LYS cc_start: 0.9230 (OUTLIER) cc_final: 0.8826 (ptmt) REVERT: A 1325 LYS cc_start: 0.9309 (ptmt) cc_final: 0.8965 (tttm) outliers start: 31 outliers final: 14 residues processed: 67 average time/residue: 0.1126 time to fit residues: 11.4096 Evaluate side-chains 54 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 37 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 ASP Chi-restraints excluded: chain A residue 192 TYR Chi-restraints excluded: chain A residue 263 LYS Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 585 ASP Chi-restraints excluded: chain A residue 648 MET Chi-restraints excluded: chain A residue 697 ILE Chi-restraints excluded: chain A residue 796 LEU Chi-restraints excluded: chain A residue 837 ASP Chi-restraints excluded: chain A residue 847 LEU Chi-restraints excluded: chain A residue 921 LEU Chi-restraints excluded: chain A residue 974 LYS Chi-restraints excluded: chain A residue 1006 SER Chi-restraints excluded: chain A residue 1156 LYS Chi-restraints excluded: chain A residue 1194 LEU Chi-restraints excluded: chain A residue 1236 LEU Chi-restraints excluded: chain A residue 1328 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 107 optimal weight: 4.9990 chunk 39 optimal weight: 7.9990 chunk 40 optimal weight: 1.9990 chunk 131 optimal weight: 6.9990 chunk 145 optimal weight: 10.0000 chunk 111 optimal weight: 1.9990 chunk 122 optimal weight: 6.9990 chunk 30 optimal weight: 0.6980 chunk 91 optimal weight: 0.9980 chunk 18 optimal weight: 5.9990 chunk 108 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 990 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 = 0.3009 r_free = 0.3009 target = 0.042668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2644 r_free = 0.2644 target = 0.031854 restraints weight = 91831.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.2682 r_free = 0.2682 target = 0.032931 restraints weight = 43466.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.2704 r_free = 0.2704 target = 0.033605 restraints weight = 27941.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.2719 r_free = 0.2719 target = 0.034023 restraints weight = 21509.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 58)----------------| | r_work = 0.2727 r_free = 0.2727 target = 0.034286 restraints weight = 18418.223| |-----------------------------------------------------------------------------| r_work (final): 0.2715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8694 moved from start: 0.1993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 14660 Z= 0.145 Angle : 0.537 9.183 20410 Z= 0.296 Chirality : 0.037 0.183 2337 Planarity : 0.003 0.047 2074 Dihedral : 19.504 156.517 3465 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.23 % Favored : 96.70 % Rotamer: Outliers : 2.15 % Allowed : 15.47 % Favored : 82.38 % 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: 0.62 (0.23), residues: 1333 helix: 0.92 (0.20), residues: 638 sheet: 0.38 (0.52), residues: 106 loop : -0.01 (0.27), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 220 TYR 0.017 0.001 TYR A 192 PHE 0.009 0.001 PHE A 575 TRP 0.008 0.001 TRP A1136 HIS 0.008 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.15 (14660) covalent geometry : angle 0.53713 / 0.30 (20410) hydrogen bonds : bond 0.04084 / 2.66 ( 636) hydrogen bonds : angle 4.31977 / 3.12 ( 1729) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 40 time to evaluate : 0.410 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 196 PHE cc_start: 0.9654 (t80) cc_final: 0.9439 (t80) REVERT: A 585 ASP cc_start: 0.8428 (OUTLIER) cc_final: 0.8192 (p0) REVERT: A 807 GLN cc_start: 0.9184 (mm-40) cc_final: 0.8784 (mp10) REVERT: A 866 LYS cc_start: 0.7757 (OUTLIER) cc_final: 0.7235 (tttm) REVERT: A 974 LYS cc_start: 0.9218 (OUTLIER) cc_final: 0.8814 (ptmt) REVERT: A 1089 MET cc_start: 0.9211 (ttm) cc_final: 0.8892 (ttp) REVERT: A 1325 LYS cc_start: 0.9295 (ptmt) cc_final: 0.9028 (tttm) outliers start: 26 outliers final: 15 residues processed: 63 average time/residue: 0.1065 time to fit residues: 10.2158 Evaluate side-chains 56 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 38 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 TYR Chi-restraints excluded: chain A residue 512 SER Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 585 ASP Chi-restraints excluded: chain A residue 697 ILE Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain A residue 791 LEU Chi-restraints excluded: chain A residue 796 LEU Chi-restraints excluded: chain A residue 837 ASP Chi-restraints excluded: chain A residue 847 LEU Chi-restraints excluded: chain A residue 866 LYS Chi-restraints excluded: chain A residue 921 LEU Chi-restraints excluded: chain A residue 974 LYS Chi-restraints excluded: chain A residue 1006 SER Chi-restraints excluded: chain A residue 1145 VAL Chi-restraints excluded: chain A residue 1156 LYS Chi-restraints excluded: chain A residue 1194 LEU Chi-restraints excluded: chain A residue 1360 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 13 optimal weight: 4.9990 chunk 58 optimal weight: 4.9990 chunk 125 optimal weight: 2.9990 chunk 16 optimal weight: 5.9990 chunk 97 optimal weight: 8.9990 chunk 98 optimal weight: 0.9980 chunk 30 optimal weight: 9.9990 chunk 25 optimal weight: 20.0000 chunk 21 optimal weight: 5.9990 chunk 11 optimal weight: 5.9990 chunk 68 optimal weight: 4.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 342 GLN ** A 990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.041282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2597 r_free = 0.2597 target = 0.030565 restraints weight = 95250.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.2634 r_free = 0.2634 target = 0.031557 restraints weight = 45966.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.2657 r_free = 0.2657 target = 0.032234 restraints weight = 30034.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.2670 r_free = 0.2670 target = 0.032630 restraints weight = 23185.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2676 r_free = 0.2676 target = 0.032790 restraints weight = 19871.248| |-----------------------------------------------------------------------------| r_work (final): 0.2661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8749 moved from start: 0.2452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 14660 Z= 0.280 Angle : 0.645 9.471 20410 Z= 0.345 Chirality : 0.040 0.176 2337 Planarity : 0.004 0.048 2074 Dihedral : 19.544 159.444 3465 Min Nonbonded Distance : 1.793 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.90 % Favored : 96.02 % Rotamer: Outliers : 2.40 % Allowed : 15.14 % Favored : 82.46 % 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: 0.30 (0.23), residues: 1333 helix: 0.71 (0.20), residues: 644 sheet: 0.24 (0.52), residues: 104 loop : -0.27 (0.26), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 951 TYR 0.019 0.002 TYR A 155 PHE 0.015 0.002 PHE A 375 TRP 0.012 0.002 TRP A1136 HIS 0.009 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00572 / 0.28 (14660) covalent geometry : angle 0.64521 / 0.35 (20410) hydrogen bonds : bond 0.05122 / 3.35 ( 636) hydrogen bonds : angle 4.51459 / 3.25 ( 1729) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 40 time to evaluate : 0.506 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 196 PHE cc_start: 0.9678 (t80) cc_final: 0.9451 (t80) REVERT: A 218 LYS cc_start: 0.8907 (mmtt) cc_final: 0.8676 (mmmt) REVERT: A 261 ASP cc_start: 0.0634 (OUTLIER) cc_final: -0.0703 (t0) REVERT: A 664 ARG cc_start: 0.9378 (OUTLIER) cc_final: 0.9005 (tmm-80) REVERT: A 974 LYS cc_start: 0.9223 (OUTLIER) cc_final: 0.8771 (ptmt) REVERT: A 1006 SER cc_start: 0.8997 (OUTLIER) cc_final: 0.8646 (t) REVERT: A 1325 LYS cc_start: 0.9329 (ptmt) cc_final: 0.9053 (tttt) outliers start: 29 outliers final: 16 residues processed: 67 average time/residue: 0.1227 time to fit residues: 12.2133 Evaluate side-chains 60 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 40 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 ASP Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 512 SER Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 664 ARG Chi-restraints excluded: chain A residue 697 ILE Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain A residue 789 LYS Chi-restraints excluded: chain A residue 796 LEU Chi-restraints excluded: chain A residue 847 LEU Chi-restraints excluded: chain A residue 866 LYS Chi-restraints excluded: chain A residue 921 LEU Chi-restraints excluded: chain A residue 974 LYS Chi-restraints excluded: chain A residue 1006 SER Chi-restraints excluded: chain A residue 1069 THR Chi-restraints excluded: chain A residue 1145 VAL Chi-restraints excluded: chain A residue 1156 LYS Chi-restraints excluded: chain A residue 1194 LEU Chi-restraints excluded: chain A residue 1236 LEU Chi-restraints excluded: chain A residue 1360 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 137 optimal weight: 10.0000 chunk 47 optimal weight: 4.9990 chunk 7 optimal weight: 5.9990 chunk 141 optimal weight: 10.0000 chunk 21 optimal weight: 3.9990 chunk 70 optimal weight: 0.6980 chunk 109 optimal weight: 4.9990 chunk 22 optimal weight: 9.9990 chunk 95 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 990 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 = 0.2984 r_free = 0.2984 target = 0.041748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2613 r_free = 0.2613 target = 0.031008 restraints weight = 93670.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.2652 r_free = 0.2652 target = 0.032035 restraints weight = 44674.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.2674 r_free = 0.2674 target = 0.032695 restraints weight = 28926.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2689 r_free = 0.2689 target = 0.033092 restraints weight = 22328.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.2697 r_free = 0.2697 target = 0.033352 restraints weight = 19226.475| |-----------------------------------------------------------------------------| r_work (final): 0.2683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8731 moved from start: 0.2475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 14660 Z= 0.177 Angle : 0.554 6.961 20410 Z= 0.303 Chirality : 0.038 0.227 2337 Planarity : 0.003 0.047 2074 Dihedral : 19.563 158.398 3465 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.38 % Favored : 96.55 % Rotamer: Outliers : 1.82 % Allowed : 16.13 % Favored : 82.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.48 (0.23), residues: 1333 helix: 0.89 (0.20), residues: 638 sheet: 0.27 (0.52), residues: 106 loop : -0.19 (0.26), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 220 TYR 0.017 0.001 TYR A 155 PHE 0.011 0.001 PHE A 575 TRP 0.007 0.001 TRP A1136 HIS 0.007 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.18 (14660) covalent geometry : angle 0.55434 / 0.30 (20410) hydrogen bonds : bond 0.04293 / 2.79 ( 636) hydrogen bonds : angle 4.35388 / 3.14 ( 1729) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 41 time to evaluate : 0.391 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 196 PHE cc_start: 0.9664 (t80) cc_final: 0.9440 (t80) REVERT: A 261 ASP cc_start: 0.0599 (OUTLIER) cc_final: -0.0803 (t0) REVERT: A 866 LYS cc_start: 0.7802 (OUTLIER) cc_final: 0.7239 (tmtt) REVERT: A 974 LYS cc_start: 0.9185 (OUTLIER) cc_final: 0.8770 (ptmt) REVERT: A 1006 SER cc_start: 0.9008 (OUTLIER) cc_final: 0.8630 (t) outliers start: 22 outliers final: 13 residues processed: 62 average time/residue: 0.1075 time to fit residues: 10.1696 Evaluate side-chains 55 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 38 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 ASP Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 512 SER Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 697 ILE Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain A residue 796 LEU Chi-restraints excluded: chain A residue 837 ASP Chi-restraints excluded: chain A residue 847 LEU Chi-restraints excluded: chain A residue 866 LYS Chi-restraints excluded: chain A residue 921 LEU Chi-restraints excluded: chain A residue 974 LYS Chi-restraints excluded: chain A residue 1006 SER Chi-restraints excluded: chain A residue 1145 VAL Chi-restraints excluded: chain A residue 1156 LYS Chi-restraints excluded: chain A residue 1194 LEU Chi-restraints excluded: chain A residue 1360 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 142 optimal weight: 10.0000 chunk 67 optimal weight: 0.4980 chunk 55 optimal weight: 0.8980 chunk 27 optimal weight: 10.0000 chunk 20 optimal weight: 20.0000 chunk 65 optimal weight: 0.9980 chunk 63 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 chunk 11 optimal weight: 6.9990 chunk 135 optimal weight: 10.0000 chunk 58 optimal weight: 4.9990 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 194 GLN ** A 990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.042228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2637 r_free = 0.2637 target = 0.031601 restraints weight = 92419.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.2674 r_free = 0.2674 target = 0.032643 restraints weight = 43231.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2698 r_free = 0.2698 target = 0.033305 restraints weight = 27828.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.2711 r_free = 0.2711 target = 0.033661 restraints weight = 21426.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.2719 r_free = 0.2719 target = 0.033964 restraints weight = 18676.724| |-----------------------------------------------------------------------------| r_work (final): 0.2704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8710 moved from start: 0.2534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14660 Z= 0.133 Angle : 0.524 6.912 20410 Z= 0.288 Chirality : 0.037 0.185 2337 Planarity : 0.003 0.046 2074 Dihedral : 19.501 156.334 3465 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.45 % Favored : 96.47 % Rotamer: Outliers : 1.74 % Allowed : 15.88 % Favored : 82.38 % 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: 0.67 (0.23), residues: 1333 helix: 1.07 (0.21), residues: 633 sheet: 0.37 (0.52), residues: 106 loop : -0.12 (0.26), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 220 TYR 0.016 0.001 TYR A 155 PHE 0.009 0.001 PHE A 575 TRP 0.005 0.001 TRP A1136 HIS 0.006 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.13 (14660) covalent geometry : angle 0.52351 / 0.29 (20410) hydrogen bonds : bond 0.03866 / 2.53 ( 636) hydrogen bonds : angle 4.22255 / 3.05 ( 1729) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 41 time to evaluate : 0.428 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 196 PHE cc_start: 0.9661 (t80) cc_final: 0.9432 (t80) REVERT: A 261 ASP cc_start: 0.0412 (OUTLIER) cc_final: -0.1008 (t0) REVERT: A 294 LYS cc_start: 0.9198 (tmtt) cc_final: 0.8893 (tmtt) REVERT: A 664 ARG cc_start: 0.9383 (OUTLIER) cc_final: 0.8981 (tmm-80) REVERT: A 763 MET cc_start: 0.8839 (mmm) cc_final: 0.7920 (tpt) REVERT: A 807 GLN cc_start: 0.9066 (mm-40) cc_final: 0.8819 (mp10) REVERT: A 866 LYS cc_start: 0.8079 (OUTLIER) cc_final: 0.7505 (tmtt) REVERT: A 974 LYS cc_start: 0.9179 (OUTLIER) cc_final: 0.8753 (ptmt) REVERT: A 1089 MET cc_start: 0.9182 (ttm) cc_final: 0.8786 (ttp) REVERT: A 1325 LYS cc_start: 0.9317 (ptmt) cc_final: 0.9083 (tttm) outliers start: 21 outliers final: 12 residues processed: 61 average time/residue: 0.1181 time to fit residues: 10.6915 Evaluate side-chains 55 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 39 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 ASP Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 512 SER Chi-restraints excluded: chain A residue 664 ARG Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain A residue 796 LEU Chi-restraints excluded: chain A residue 837 ASP Chi-restraints excluded: chain A residue 847 LEU Chi-restraints excluded: chain A residue 866 LYS Chi-restraints excluded: chain A residue 921 LEU Chi-restraints excluded: chain A residue 974 LYS Chi-restraints excluded: chain A residue 1006 SER Chi-restraints excluded: chain A residue 1145 VAL Chi-restraints excluded: chain A residue 1156 LYS Chi-restraints excluded: chain A residue 1194 LEU Chi-restraints excluded: chain A residue 1360 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 118 optimal weight: 6.9990 chunk 67 optimal weight: 4.9990 chunk 71 optimal weight: 6.9990 chunk 8 optimal weight: 5.9990 chunk 59 optimal weight: 6.9990 chunk 107 optimal weight: 10.0000 chunk 104 optimal weight: 0.4980 chunk 19 optimal weight: 6.9990 chunk 127 optimal weight: 0.2980 chunk 76 optimal weight: 7.9990 chunk 6 optimal weight: 8.9990 overall best weight: 3.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1261 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 = 0.2960 r_free = 0.2960 target = 0.041012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2589 r_free = 0.2589 target = 0.030373 restraints weight = 96234.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.2627 r_free = 0.2627 target = 0.031373 restraints weight = 45900.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.2649 r_free = 0.2649 target = 0.032015 restraints weight = 29805.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2663 r_free = 0.2663 target = 0.032395 restraints weight = 23084.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2672 r_free = 0.2672 target = 0.032655 restraints weight = 19947.054| |-----------------------------------------------------------------------------| r_work (final): 0.2658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8756 moved from start: 0.2811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 14660 Z= 0.291 Angle : 0.644 6.898 20410 Z= 0.344 Chirality : 0.040 0.182 2337 Planarity : 0.004 0.046 2074 Dihedral : 19.538 159.262 3465 Min Nonbonded Distance : 1.790 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.28 % Favored : 95.65 % Rotamer: Outliers : 1.74 % Allowed : 16.54 % Favored : 81.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.23), residues: 1333 helix: 0.85 (0.20), residues: 645 sheet: -0.03 (0.47), residues: 127 loop : -0.20 (0.27), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 976 TYR 0.019 0.002 TYR A 155 PHE 0.014 0.002 PHE A 375 TRP 0.012 0.002 TRP A1136 HIS 0.008 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00601 / 0.29 (14660) covalent geometry : angle 0.64447 / 0.34 (20410) hydrogen bonds : bond 0.04952 / 3.25 ( 636) hydrogen bonds : angle 4.44635 / 3.21 ( 1729) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 41 time to evaluate : 0.419 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 196 PHE cc_start: 0.9680 (t80) cc_final: 0.9458 (t80) REVERT: A 261 ASP cc_start: 0.0414 (OUTLIER) cc_final: -0.0916 (t0) REVERT: A 265 GLN cc_start: 0.7623 (tt0) cc_final: 0.7366 (mt0) REVERT: A 664 ARG cc_start: 0.9392 (OUTLIER) cc_final: 0.8963 (tmm-80) REVERT: A 974 LYS cc_start: 0.9051 (OUTLIER) cc_final: 0.8614 (ptmt) REVERT: A 1006 SER cc_start: 0.9084 (OUTLIER) cc_final: 0.8737 (t) REVERT: A 1089 MET cc_start: 0.9224 (ttm) cc_final: 0.8937 (ttp) outliers start: 21 outliers final: 14 residues processed: 61 average time/residue: 0.1382 time to fit residues: 12.4668 Evaluate side-chains 59 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 41 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 ASP Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 512 SER Chi-restraints excluded: chain A residue 664 ARG Chi-restraints excluded: chain A residue 697 ILE Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain A residue 789 LYS Chi-restraints excluded: chain A residue 796 LEU Chi-restraints excluded: chain A residue 837 ASP Chi-restraints excluded: chain A residue 847 LEU Chi-restraints excluded: chain A residue 921 LEU Chi-restraints excluded: chain A residue 974 LYS Chi-restraints excluded: chain A residue 1006 SER Chi-restraints excluded: chain A residue 1145 VAL Chi-restraints excluded: chain A residue 1156 LYS Chi-restraints excluded: chain A residue 1194 LEU Chi-restraints excluded: chain A residue 1360 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 79 optimal weight: 0.7980 chunk 139 optimal weight: 10.0000 chunk 57 optimal weight: 3.9990 chunk 115 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 141 optimal weight: 10.0000 chunk 2 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 63 optimal weight: 4.9990 chunk 138 optimal weight: 10.0000 chunk 41 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 990 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 = 0.2986 r_free = 0.2986 target = 0.041760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2618 r_free = 0.2618 target = 0.031076 restraints weight = 94080.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2656 r_free = 0.2656 target = 0.032102 restraints weight = 44367.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2679 r_free = 0.2679 target = 0.032766 restraints weight = 28707.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.2694 r_free = 0.2694 target = 0.033172 restraints weight = 22182.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2702 r_free = 0.2702 target = 0.033373 restraints weight = 19031.008| |-----------------------------------------------------------------------------| r_work (final): 0.2689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8733 moved from start: 0.2774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14660 Z= 0.146 Angle : 0.544 7.456 20410 Z= 0.297 Chirality : 0.037 0.183 2337 Planarity : 0.003 0.046 2074 Dihedral : 19.563 157.702 3465 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.45 % Favored : 96.47 % Rotamer: Outliers : 1.65 % Allowed : 16.29 % Favored : 82.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.23), residues: 1333 helix: 1.02 (0.21), residues: 635 sheet: 0.32 (0.52), residues: 106 loop : -0.21 (0.26), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 220 TYR 0.017 0.001 TYR A 192 PHE 0.010 0.001 PHE A 575 TRP 0.006 0.001 TRP A 659 HIS 0.007 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.15 (14660) covalent geometry : angle 0.54414 / 0.30 (20410) hydrogen bonds : bond 0.04027 / 2.63 ( 636) hydrogen bonds : angle 4.25682 / 3.07 ( 1729) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 40 time to evaluate : 0.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 196 PHE cc_start: 0.9679 (t80) cc_final: 0.9456 (t80) REVERT: A 261 ASP cc_start: 0.0461 (OUTLIER) cc_final: -0.0851 (t0) REVERT: A 265 GLN cc_start: 0.7607 (tt0) cc_final: 0.7373 (mt0) REVERT: A 294 LYS cc_start: 0.9257 (tmtt) cc_final: 0.8974 (tmtt) REVERT: A 664 ARG cc_start: 0.9386 (OUTLIER) cc_final: 0.8995 (tmm-80) REVERT: A 763 MET cc_start: 0.8851 (mmm) cc_final: 0.7909 (tpt) REVERT: A 974 LYS cc_start: 0.9090 (OUTLIER) cc_final: 0.8599 (ptmt) REVERT: A 1089 MET cc_start: 0.9215 (ttm) cc_final: 0.8863 (ttp) REVERT: A 1325 LYS cc_start: 0.9334 (ptmt) cc_final: 0.9119 (tttm) outliers start: 20 outliers final: 14 residues processed: 60 average time/residue: 0.1358 time to fit residues: 12.1022 Evaluate side-chains 56 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 39 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 ASP Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 512 SER Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 664 ARG Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain A residue 796 LEU Chi-restraints excluded: chain A residue 837 ASP Chi-restraints excluded: chain A residue 847 LEU Chi-restraints excluded: chain A residue 921 LEU Chi-restraints excluded: chain A residue 974 LYS Chi-restraints excluded: chain A residue 1006 SER Chi-restraints excluded: chain A residue 1145 VAL Chi-restraints excluded: chain A residue 1156 LYS Chi-restraints excluded: chain A residue 1194 LEU Chi-restraints excluded: chain A residue 1360 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 80 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 84 optimal weight: 0.8980 chunk 45 optimal weight: 0.7980 chunk 86 optimal weight: 5.9990 chunk 79 optimal weight: 1.9990 chunk 60 optimal weight: 4.9990 chunk 103 optimal weight: 7.9990 chunk 65 optimal weight: 0.9980 chunk 83 optimal weight: 3.9990 chunk 50 optimal weight: 0.8980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 807 GLN ** A 990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.042023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2629 r_free = 0.2629 target = 0.031357 restraints weight = 93466.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.2667 r_free = 0.2667 target = 0.032399 restraints weight = 44030.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 60)----------------| | r_work = 0.2690 r_free = 0.2690 target = 0.033071 restraints weight = 28451.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2706 r_free = 0.2706 target = 0.033474 restraints weight = 21918.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.2715 r_free = 0.2715 target = 0.033749 restraints weight = 18809.990| |-----------------------------------------------------------------------------| r_work (final): 0.2701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8718 moved from start: 0.2793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14660 Z= 0.126 Angle : 0.533 7.498 20410 Z= 0.290 Chirality : 0.037 0.192 2337 Planarity : 0.003 0.045 2074 Dihedral : 19.519 156.303 3465 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.75 % Favored : 96.17 % Rotamer: Outliers : 1.49 % Allowed : 16.71 % Favored : 81.80 % 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: 0.73 (0.23), residues: 1333 helix: 1.15 (0.21), residues: 633 sheet: 0.41 (0.53), residues: 106 loop : -0.12 (0.26), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 220 TYR 0.017 0.001 TYR A 192 PHE 0.010 0.001 PHE A 575 TRP 0.006 0.001 TRP A1136 HIS 0.006 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.13 (14660) covalent geometry : angle 0.53295 / 0.29 (20410) hydrogen bonds : bond 0.03893 / 2.55 ( 636) hydrogen bonds : angle 4.17541 / 3.01 ( 1729) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1964.38 seconds wall clock time: 34 minutes 58.83 seconds (2098.83 seconds total)