Starting phenix.real_space_refine on Thu Aug 6 07:22:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sqh_40705/08_2026/8sqh_40705.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sqh_40705/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8sqh_40705/08_2026/8sqh_40705.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sqh_40705/08_2026/8sqh_40705.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8sqh_40705/08_2026/8sqh_40705.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sqh_40705/08_2026/8sqh_40705.map" } 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-2.2rc3-6140/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: 2.93, per 1000 atoms: 0.21 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: 1.16 Conformation dependent library (CDL) restraints added in 572.6 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: 1.68 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: 3.61 Time building geometry restraints manager: 1.55 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: 19804 2.94 - 5.88: 502 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=" C5' A B 12 " pdb=" C4' A B 12 " pdb=" O4' A B 12 " ideal model delta sigma weight residual 109.80 116.43 -6.63 9.00e-01 1.23e+00 5.43e+01 angle pdb=" O4' U B 64 " pdb=" C1' U B 64 " pdb=" N1 U B 64 " ideal model delta sigma weight residual 108.50 113.56 -5.06 7.00e-01 2.04e+00 5.22e+01 angle pdb=" C2' A B 8 " pdb=" C1' A B 8 " pdb=" N9 A B 8 " ideal model delta sigma weight residual 112.00 119.70 -7.70 1.10e+00 8.26e-01 4.90e+01 angle pdb=" C5' U B 64 " pdb=" C4' U B 64 " pdb=" O4' U B 64 " ideal model delta sigma weight residual 109.80 116.07 -6.27 9.00e-01 1.23e+00 4.86e+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: 2166 0.127 - 0.255: 152 0.255 - 0.382: 14 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: 3.450 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: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 15.230 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.200 ------------------------------------------------------------------------------- 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= 0.376 Angle : 1.170 14.698 20410 Z= 0.779 Chirality : 0.071 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 0.00580 / 0.38 (14660) covalent geometry : angle 1.17002 / 0.78 (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 : 0.411 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: 0.1218 time to fit residues: 9.3583 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 : 0.475 ------------------------------------------------------------------------------- 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 = 0.3078 r_free = 0.3078 target = 0.044486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2712 r_free = 0.2712 target = 0.033360 restraints weight = 92897.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2751 r_free = 0.2751 target = 0.034444 restraints weight = 45399.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2775 r_free = 0.2775 target = 0.035139 restraints weight = 29750.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.2789 r_free = 0.2789 target = 0.035594 restraints weight = 23007.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.035830 restraints weight = 19598.448| |-----------------------------------------------------------------------------| r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8685 moved from start: 0.1027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 14660 Z= 0.198 Angle : 0.657 8.940 20410 Z= 0.363 Chirality : 0.042 0.264 2337 Planarity : 0.004 0.048 2074 Dihedral : 19.495 152.801 3465 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.57 % Allowed : 14.72 % Favored : 83.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.25 (0.22), residues: 1333 helix: 0.16 (0.20), residues: 638 sheet: 0.13 (0.57), residues: 97 loop : -0.44 (0.25), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG A 535 TYR 0.024 0.001 TYR A 192 PHE 0.013 0.002 PHE A1046 TRP 0.018 0.001 TRP A1136 HIS 0.006 0.001 HIS A 799 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.20 (14660) covalent geometry : angle 0.65690 / 0.36 (20410) hydrogen bonds : bond 0.05232 / 3.44 ( 636) hydrogen bonds : angle 4.98773 / 3.57 ( 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 60 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 41 time to evaluate : 0.577 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 ILE cc_start: 0.8892 (OUTLIER) cc_final: 0.8683 (tt) REVERT: A 263 LYS cc_start: 0.7561 (OUTLIER) cc_final: 0.7348 (pptt) REVERT: A 974 LYS cc_start: 0.9183 (OUTLIER) cc_final: 0.8844 (ptmt) outliers start: 19 outliers final: 7 residues processed: 58 average time/residue: 0.1331 time to fit residues: 11.5742 Evaluate side-chains 48 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 38 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ILE 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 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: 0.0670 chunk 143 optimal weight: 20.0000 chunk 94 optimal weight: 0.5980 chunk 126 optimal weight: 5.9990 chunk 101 optimal weight: 3.9990 chunk 92 optimal weight: 1.9990 chunk 3 optimal weight: 0.0980 chunk 7 optimal weight: 3.9990 chunk 18 optimal weight: 9.9990 chunk 68 optimal weight: 2.9990 overall best weight: 1.1522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 202 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.044612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2735 r_free = 0.2735 target = 0.033700 restraints weight = 90308.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.2772 r_free = 0.2772 target = 0.034790 restraints weight = 42791.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.035519 restraints weight = 27688.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.2809 r_free = 0.2809 target = 0.035951 restraints weight = 21258.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.036201 restraints weight = 18131.884| |-----------------------------------------------------------------------------| r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8665 moved from start: 0.1335 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= 0.130 Angle : 0.573 9.963 20410 Z= 0.312 Chirality : 0.039 0.285 2337 Planarity : 0.003 0.048 2074 Dihedral : 19.398 153.161 3465 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 1.82 % Allowed : 13.98 % Favored : 84.20 % 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: 0.24 (0.23), residues: 1333 helix: 0.58 (0.20), residues: 642 sheet: 0.04 (0.51), residues: 106 loop : -0.15 (0.27), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 535 TYR 0.020 0.001 TYR A 192 PHE 0.009 0.001 PHE A1046 TRP 0.011 0.001 TRP A1136 HIS 0.006 0.001 HIS A 167 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.13 (14660) covalent geometry : angle 0.57311 / 0.31 (20410) hydrogen bonds : bond 0.04342 / 2.86 ( 636) hydrogen bonds : angle 4.52458 / 3.25 ( 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 62 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 40 time to evaluate : 0.495 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: 0.9656 (t80) cc_final: 0.9442 (t80) REVERT: A 585 ASP cc_start: 0.8241 (OUTLIER) cc_final: 0.8011 (p0) REVERT: A 647 VAL cc_start: 0.9370 (OUTLIER) cc_final: 0.9160 (m) REVERT: A 974 LYS cc_start: 0.9222 (OUTLIER) cc_final: 0.8892 (ptmt) REVERT: A 1304 GLU cc_start: 0.9190 (OUTLIER) cc_final: 0.8964 (pm20) outliers start: 22 outliers final: 9 residues processed: 58 average time/residue: 0.1399 time to fit residues: 12.1317 Evaluate side-chains 51 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 38 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 192 TYR Chi-restraints excluded: chain A residue 383 MET 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 1156 LYS Chi-restraints excluded: chain A residue 1194 LEU Chi-restraints excluded: chain A residue 1304 GLU 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: 3.9990 chunk 102 optimal weight: 8.9990 chunk 135 optimal weight: 10.0000 chunk 65 optimal weight: 4.9990 chunk 27 optimal weight: 10.0000 chunk 29 optimal weight: 6.9990 chunk 10 optimal weight: 3.9990 chunk 134 optimal weight: 9.9990 chunk 128 optimal weight: 0.8980 chunk 76 optimal weight: 0.9980 overall best weight: 2.9786 ------------------------------------------------------------------------------- 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 = 0.3001 r_free = 0.3001 target = 0.042591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2633 r_free = 0.2633 target = 0.031711 restraints weight = 93680.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2671 r_free = 0.2671 target = 0.032741 restraints weight = 44981.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.2694 r_free = 0.2694 target = 0.033418 restraints weight = 29288.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.2709 r_free = 0.2709 target = 0.033856 restraints weight = 22616.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2717 r_free = 0.2717 target = 0.034071 restraints weight = 19306.012| |-----------------------------------------------------------------------------| r_work (final): 0.2704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8707 moved from start: 0.1759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 14660 Z= 0.234 Angle : 0.612 10.247 20410 Z= 0.329 Chirality : 0.040 0.288 2337 Planarity : 0.004 0.049 2074 Dihedral : 19.405 155.370 3465 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.23 % Favored : 96.70 % Rotamer: Outliers : 2.15 % Allowed : 14.81 % Favored : 83.04 % 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: 0.37 (0.23), residues: 1333 helix: 0.70 (0.20), residues: 642 sheet: 0.18 (0.51), residues: 106 loop : -0.11 (0.27), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 220 TYR 0.018 0.002 TYR A 192 PHE 0.010 0.001 PHE A 375 TRP 0.012 0.001 TRP A1136 HIS 0.007 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00476 / 0.23 (14660) covalent geometry : angle 0.61249 / 0.33 (20410) hydrogen bonds : bond 0.04682 / 3.06 ( 636) hydrogen bonds : angle 4.49757 / 3.24 ( 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 65 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 39 time to evaluate : 0.507 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 196 PHE cc_start: 0.9678 (t80) cc_final: 0.9454 (t80) REVERT: A 585 ASP cc_start: 0.8356 (OUTLIER) cc_final: 0.8127 (p0) REVERT: A 763 MET cc_start: 0.9021 (mmm) cc_final: 0.8514 (tpt) REVERT: A 807 GLN cc_start: 0.9170 (mm-40) cc_final: 0.8792 (mp10) REVERT: A 974 LYS cc_start: 0.9236 (OUTLIER) cc_final: 0.8860 (ptmt) REVERT: A 1325 LYS cc_start: 0.9305 (ptmt) cc_final: 0.8969 (tttm) outliers start: 26 outliers final: 9 residues processed: 61 average time/residue: 0.1269 time to fit residues: 11.8918 Evaluate side-chains 50 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 39 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 TYR 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 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 1156 LYS Chi-restraints excluded: chain A residue 1194 LEU 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: 5.9990 chunk 131 optimal weight: 6.9990 chunk 145 optimal weight: 10.0000 chunk 111 optimal weight: 1.9990 chunk 122 optimal weight: 4.9990 chunk 30 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 108 optimal weight: 3.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- 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 = 0.2986 r_free = 0.2986 target = 0.041919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2616 r_free = 0.2616 target = 0.031120 restraints weight = 93974.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2654 r_free = 0.2654 target = 0.032144 restraints weight = 44772.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.2677 r_free = 0.2677 target = 0.032803 restraints weight = 29122.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.2691 r_free = 0.2691 target = 0.033234 restraints weight = 22477.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2699 r_free = 0.2699 target = 0.033440 restraints weight = 19239.925| |-----------------------------------------------------------------------------| r_work (final): 0.2686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8724 moved from start: 0.2107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 14660 Z= 0.227 Angle : 0.606 10.063 20410 Z= 0.326 Chirality : 0.040 0.299 2337 Planarity : 0.004 0.056 2074 Dihedral : 19.451 156.500 3465 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.68 % Favored : 96.25 % Rotamer: Outliers : 2.73 % Allowed : 14.97 % Favored : 82.30 % 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: 0.43 (0.23), residues: 1333 helix: 0.77 (0.20), residues: 644 sheet: 0.30 (0.52), residues: 106 loop : -0.14 (0.27), residues: 583 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 220 TYR 0.017 0.002 TYR A 192 PHE 0.012 0.002 PHE A 575 TRP 0.011 0.001 TRP A1136 HIS 0.011 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00463 / 0.23 (14660) covalent geometry : angle 0.60576 / 0.33 (20410) hydrogen bonds : bond 0.04462 / 2.89 ( 636) hydrogen bonds : angle 4.43655 / 3.20 ( 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 74 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 41 time to evaluate : 0.464 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 196 PHE cc_start: 0.9672 (t80) cc_final: 0.9439 (t80) REVERT: A 647 VAL cc_start: 0.9391 (OUTLIER) cc_final: 0.9188 (m) REVERT: A 763 MET cc_start: 0.9083 (mmm) cc_final: 0.8576 (tpt) REVERT: A 974 LYS cc_start: 0.9212 (OUTLIER) cc_final: 0.8824 (ptmt) outliers start: 33 outliers final: 18 residues processed: 70 average time/residue: 0.1232 time to fit residues: 13.0868 Evaluate side-chains 61 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 41 time to evaluate : 0.502 ------------------------------------------------------------------------------- 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 512 SER Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 647 VAL Chi-restraints excluded: chain A residue 648 MET 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 921 LEU Chi-restraints excluded: chain A residue 974 LYS Chi-restraints excluded: chain A residue 1006 SER Chi-restraints excluded: chain A residue 1015 VAL 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 13 optimal weight: 2.9990 chunk 58 optimal weight: 6.9990 chunk 125 optimal weight: 2.9990 chunk 16 optimal weight: 5.9990 chunk 97 optimal weight: 4.9990 chunk 98 optimal weight: 3.9990 chunk 30 optimal weight: 0.0370 chunk 25 optimal weight: 20.0000 chunk 21 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 overall best weight: 2.6066 ------------------------------------------------------------------------------- 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 = 0.2981 r_free = 0.2981 target = 0.041734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2615 r_free = 0.2615 target = 0.031026 restraints weight = 94213.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.2652 r_free = 0.2652 target = 0.032061 restraints weight = 44610.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2675 r_free = 0.2675 target = 0.032711 restraints weight = 28869.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.2689 r_free = 0.2689 target = 0.033125 restraints weight = 22421.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2696 r_free = 0.2696 target = 0.033311 restraints weight = 19181.296| |-----------------------------------------------------------------------------| r_work (final): 0.2683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8729 moved from start: 0.2341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 14660 Z= 0.205 Angle : 0.587 9.642 20410 Z= 0.315 Chirality : 0.039 0.308 2337 Planarity : 0.003 0.048 2074 Dihedral : 19.455 156.418 3465 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.60 % Favored : 96.32 % Rotamer: Outliers : 2.15 % Allowed : 15.22 % Favored : 82.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.23), residues: 1333 helix: 0.84 (0.20), residues: 638 sheet: 0.30 (0.52), residues: 106 loop : -0.11 (0.27), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 220 TYR 0.017 0.001 TYR A 155 PHE 0.011 0.001 PHE A 575 TRP 0.009 0.001 TRP A1136 HIS 0.008 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.20 (14660) covalent geometry : angle 0.58669 / 0.31 (20410) hydrogen bonds : bond 0.04392 / 2.85 ( 636) hydrogen bonds : angle 4.38241 / 3.16 ( 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 70 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 44 time to evaluate : 0.337 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: 0.9672 (t80) cc_final: 0.9450 (t80) REVERT: A 261 ASP cc_start: 0.0511 (OUTLIER) cc_final: -0.0672 (t0) REVERT: A 763 MET cc_start: 0.9017 (mmm) cc_final: 0.8493 (tpt) REVERT: A 807 GLN cc_start: 0.9093 (mm-40) cc_final: 0.8804 (mp10) REVERT: A 974 LYS cc_start: 0.9211 (OUTLIER) cc_final: 0.8784 (ptmt) outliers start: 26 outliers final: 19 residues processed: 67 average time/residue: 0.1088 time to fit residues: 10.9908 Evaluate side-chains 60 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 39 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 147 ASP Chi-restraints excluded: chain A residue 192 TYR 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 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 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 1014 LYS Chi-restraints excluded: chain A residue 1069 THR 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: 20.0000 chunk 47 optimal weight: 3.9990 chunk 7 optimal weight: 6.9990 chunk 141 optimal weight: 10.0000 chunk 21 optimal weight: 5.9990 chunk 70 optimal weight: 2.9990 chunk 109 optimal weight: 3.9990 chunk 22 optimal weight: 5.9990 chunk 95 optimal weight: 0.9990 chunk 51 optimal weight: 0.8980 chunk 36 optimal weight: 2.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 160 HIS A 194 GLN ** A 990 ASN ** 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 = 0.2985 r_free = 0.2985 target = 0.041769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2616 r_free = 0.2616 target = 0.031020 restraints weight = 94175.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2654 r_free = 0.2654 target = 0.032039 restraints weight = 44841.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.2676 r_free = 0.2676 target = 0.032702 restraints weight = 29253.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.2690 r_free = 0.2690 target = 0.033114 restraints weight = 22613.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2696 r_free = 0.2696 target = 0.033256 restraints weight = 19328.469| |-----------------------------------------------------------------------------| r_work (final): 0.2682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8734 moved from start: 0.2493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 14660 Z= 0.191 Angle : 0.568 8.470 20410 Z= 0.307 Chirality : 0.039 0.311 2337 Planarity : 0.003 0.048 2074 Dihedral : 19.457 156.238 3465 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.60 % Favored : 96.32 % Rotamer: Outliers : 1.99 % Allowed : 16.21 % 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: 0.56 (0.23), residues: 1333 helix: 0.93 (0.20), residues: 639 sheet: 0.37 (0.52), residues: 106 loop : -0.13 (0.27), residues: 588 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 0.010 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 0.00390 / 0.19 (14660) covalent geometry : angle 0.56802 / 0.31 (20410) hydrogen bonds : bond 0.04260 / 2.77 ( 636) hydrogen bonds : angle 4.33715 / 3.13 ( 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: 24 poor density : 39 time to evaluate : 0.482 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 196 PHE cc_start: 0.9676 (t80) cc_final: 0.9452 (t80) REVERT: A 261 ASP cc_start: 0.0575 (OUTLIER) cc_final: -0.0806 (t0) REVERT: A 647 VAL cc_start: 0.9369 (OUTLIER) cc_final: 0.9155 (m) REVERT: A 664 ARG cc_start: 0.9388 (OUTLIER) cc_final: 0.8999 (tmm-80) REVERT: A 763 MET cc_start: 0.9037 (mmm) cc_final: 0.8509 (tpt) REVERT: A 866 LYS cc_start: 0.7825 (OUTLIER) cc_final: 0.7255 (tmtt) REVERT: A 974 LYS cc_start: 0.9179 (OUTLIER) cc_final: 0.8766 (ptmt) REVERT: A 1089 MET cc_start: 0.9241 (ttm) cc_final: 0.8977 (ttt) outliers start: 24 outliers final: 16 residues processed: 62 average time/residue: 0.1107 time to fit residues: 10.1930 Evaluate side-chains 59 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 38 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 VAL 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 647 VAL 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 142 optimal weight: 20.0000 chunk 67 optimal weight: 4.9990 chunk 55 optimal weight: 4.9990 chunk 27 optimal weight: 0.9990 chunk 20 optimal weight: 9.9990 chunk 65 optimal weight: 2.9990 chunk 63 optimal weight: 0.7980 chunk 13 optimal weight: 0.8980 chunk 11 optimal weight: 6.9990 chunk 135 optimal weight: 10.0000 chunk 58 optimal weight: 0.9980 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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 = 0.3000 r_free = 0.3000 target = 0.042218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2633 r_free = 0.2633 target = 0.031463 restraints weight = 93503.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2672 r_free = 0.2672 target = 0.032504 restraints weight = 43964.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2694 r_free = 0.2694 target = 0.033167 restraints weight = 28485.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.2709 r_free = 0.2709 target = 0.033589 restraints weight = 22086.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.2718 r_free = 0.2718 target = 0.033829 restraints weight = 18867.774| |-----------------------------------------------------------------------------| r_work (final): 0.2705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8713 moved from start: 0.2526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14660 Z= 0.134 Angle : 0.543 7.627 20410 Z= 0.294 Chirality : 0.038 0.313 2337 Planarity : 0.003 0.046 2074 Dihedral : 19.441 155.071 3465 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.45 % Favored : 96.47 % Rotamer: Outliers : 1.82 % Allowed : 16.29 % Favored : 81.89 % 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: 1.03 (0.21), residues: 634 sheet: 0.44 (0.53), residues: 106 loop : -0.08 (0.27), residues: 593 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 221 TYR 0.017 0.001 TYR A 192 PHE 0.010 0.001 PHE A1105 TRP 0.006 0.001 TRP A1136 HIS 0.006 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.13 (14660) covalent geometry : angle 0.54299 / 0.29 (20410) hydrogen bonds : bond 0.03964 / 2.58 ( 636) hydrogen bonds : angle 4.24792 / 3.06 ( 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: 22 poor density : 40 time to evaluate : 0.475 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 196 PHE cc_start: 0.9669 (t80) cc_final: 0.9435 (t80) REVERT: A 261 ASP cc_start: 0.0597 (OUTLIER) cc_final: -0.0788 (t0) REVERT: A 664 ARG cc_start: 0.9390 (OUTLIER) cc_final: 0.9010 (tmm-80) REVERT: A 763 MET cc_start: 0.9043 (mmm) cc_final: 0.8536 (tpt) REVERT: A 804 THR cc_start: 0.9152 (OUTLIER) cc_final: 0.8283 (t) REVERT: A 807 GLN cc_start: 0.9081 (mm-40) cc_final: 0.8801 (mp10) REVERT: A 866 LYS cc_start: 0.7982 (OUTLIER) cc_final: 0.7441 (tmtt) REVERT: A 974 LYS cc_start: 0.9182 (OUTLIER) cc_final: 0.8754 (ptmt) outliers start: 22 outliers final: 15 residues processed: 61 average time/residue: 0.1217 time to fit residues: 11.0454 Evaluate side-chains 59 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 39 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 VAL 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 750 VAL Chi-restraints excluded: chain A residue 789 LYS Chi-restraints excluded: chain A residue 796 LEU Chi-restraints excluded: chain A residue 804 THR 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 1014 LYS 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: 0.8980 chunk 67 optimal weight: 1.9990 chunk 71 optimal weight: 8.9990 chunk 8 optimal weight: 5.9990 chunk 59 optimal weight: 10.0000 chunk 107 optimal weight: 10.0000 chunk 104 optimal weight: 5.9990 chunk 19 optimal weight: 6.9990 chunk 127 optimal weight: 2.9990 chunk 76 optimal weight: 5.9990 chunk 6 optimal weight: 8.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 160 HIS ** A 990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1261 GLN ** 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 = 0.2966 r_free = 0.2966 target = 0.041304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2596 r_free = 0.2596 target = 0.030649 restraints weight = 96224.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2634 r_free = 0.2634 target = 0.031625 restraints weight = 45965.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.2655 r_free = 0.2655 target = 0.032274 restraints weight = 30188.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2670 r_free = 0.2670 target = 0.032669 restraints weight = 23374.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.2678 r_free = 0.2678 target = 0.032926 restraints weight = 20071.663| |-----------------------------------------------------------------------------| r_work (final): 0.2660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8751 moved from start: 0.2792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 14660 Z= 0.271 Angle : 0.651 9.493 20410 Z= 0.341 Chirality : 0.041 0.326 2337 Planarity : 0.004 0.046 2074 Dihedral : 19.462 157.636 3465 Min Nonbonded Distance : 1.796 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.28 % Favored : 95.65 % Rotamer: Outliers : 1.99 % Allowed : 16.63 % Favored : 81.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.23), residues: 1333 helix: 0.91 (0.20), residues: 639 sheet: 0.24 (0.52), residues: 104 loop : -0.19 (0.27), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 220 TYR 0.019 0.002 TYR A 155 PHE 0.014 0.002 PHE A 375 TRP 0.011 0.002 TRP A1136 HIS 0.008 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00556 / 0.27 (14660) covalent geometry : angle 0.65104 / 0.34 (20410) hydrogen bonds : bond 0.04913 / 3.21 ( 636) hydrogen bonds : angle 4.44395 / 3.20 ( 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 64 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 40 time to evaluate : 0.312 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: 0.9676 (t80) cc_final: 0.9453 (t80) REVERT: A 218 LYS cc_start: 0.8853 (mmtt) cc_final: 0.8623 (mmmt) REVERT: A 261 ASP cc_start: 0.0529 (OUTLIER) cc_final: -0.0859 (t0) REVERT: A 534 MET cc_start: 0.8488 (pmm) cc_final: 0.8281 (pmm) REVERT: A 664 ARG cc_start: 0.9390 (OUTLIER) cc_final: 0.8933 (tmm-80) REVERT: A 763 MET cc_start: 0.9083 (mmm) cc_final: 0.8601 (tpt) REVERT: A 974 LYS cc_start: 0.9178 (OUTLIER) cc_final: 0.8597 (ptmt) outliers start: 24 outliers final: 17 residues processed: 63 average time/residue: 0.1199 time to fit residues: 11.2071 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 : 0.415 ------------------------------------------------------------------------------- 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 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 1014 LYS 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: 0.9990 chunk 139 optimal weight: 10.0000 chunk 57 optimal weight: 5.9990 chunk 115 optimal weight: 0.8980 chunk 4 optimal weight: 2.9990 chunk 141 optimal weight: 20.0000 chunk 2 optimal weight: 1.9990 chunk 30 optimal weight: 0.0040 chunk 63 optimal weight: 0.2980 chunk 138 optimal weight: 10.0000 chunk 41 optimal weight: 1.9990 overall best weight: 0.8396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 160 HIS A 990 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.042171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2641 r_free = 0.2641 target = 0.031557 restraints weight = 92877.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2678 r_free = 0.2678 target = 0.032603 restraints weight = 43123.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 63)----------------| | r_work = 0.2700 r_free = 0.2700 target = 0.033267 restraints weight = 27819.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2715 r_free = 0.2715 target = 0.033671 restraints weight = 21368.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2723 r_free = 0.2723 target = 0.033887 restraints weight = 18301.037| |-----------------------------------------------------------------------------| r_work (final): 0.2707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8715 moved from start: 0.2728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 14660 Z= 0.115 Angle : 0.547 8.664 20410 Z= 0.293 Chirality : 0.038 0.314 2337 Planarity : 0.003 0.045 2074 Dihedral : 19.481 155.068 3465 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.45 % Favored : 96.47 % Rotamer: Outliers : 1.57 % Allowed : 16.63 % 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: 0.74 (0.23), residues: 1333 helix: 1.12 (0.21), residues: 633 sheet: 0.40 (0.52), residues: 106 loop : -0.07 (0.27), 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 A 659 HIS 0.005 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.12 (14660) covalent geometry : angle 0.54714 / 0.29 (20410) hydrogen bonds : bond 0.03906 / 2.55 ( 636) hydrogen bonds : angle 4.20729 / 3.03 ( 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: 19 poor density : 41 time to evaluate : 0.400 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: 0.9665 (t80) cc_final: 0.9435 (t80) REVERT: A 261 ASP cc_start: 0.0494 (OUTLIER) cc_final: -0.0862 (t0) REVERT: A 294 LYS cc_start: 0.9249 (tmtt) cc_final: 0.8955 (tmtt) REVERT: A 664 ARG cc_start: 0.9383 (OUTLIER) cc_final: 0.8956 (tmm-80) REVERT: A 763 MET cc_start: 0.9065 (mmm) cc_final: 0.8590 (tpt) REVERT: A 807 GLN cc_start: 0.9035 (mm-40) cc_final: 0.8813 (mp10) REVERT: A 974 LYS cc_start: 0.9141 (OUTLIER) cc_final: 0.8703 (ptmt) outliers start: 19 outliers final: 14 residues processed: 60 average time/residue: 0.1104 time to fit residues: 9.8850 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 : 0.321 ------------------------------------------------------------------------------- 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 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 1014 LYS Chi-restraints excluded: chain A residue 1145 VAL Chi-restraints excluded: chain A residue 1156 LYS Chi-restraints excluded: chain A residue 1194 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 80 optimal weight: 0.7980 chunk 46 optimal weight: 4.9990 chunk 84 optimal weight: 0.9980 chunk 45 optimal weight: 0.0370 chunk 86 optimal weight: 0.7980 chunk 79 optimal weight: 4.9990 chunk 60 optimal weight: 5.9990 chunk 103 optimal weight: 0.7980 chunk 65 optimal weight: 0.0020 chunk 83 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 overall best weight: 0.4866 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.042901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2663 r_free = 0.2663 target = 0.032264 restraints weight = 91958.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2701 r_free = 0.2701 target = 0.033329 restraints weight = 43107.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.2723 r_free = 0.2723 target = 0.034009 restraints weight = 27680.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2738 r_free = 0.2738 target = 0.034408 restraints weight = 21239.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.2747 r_free = 0.2747 target = 0.034683 restraints weight = 18243.672| |-----------------------------------------------------------------------------| r_work (final): 0.2731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8693 moved from start: 0.2741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 14660 Z= 0.108 Angle : 0.530 8.523 20410 Z= 0.286 Chirality : 0.037 0.314 2337 Planarity : 0.003 0.043 2074 Dihedral : 19.403 152.832 3465 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.53 % Favored : 96.40 % Rotamer: Outliers : 0.99 % Allowed : 17.29 % 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: 0.84 (0.24), residues: 1333 helix: 1.20 (0.21), residues: 633 sheet: 0.49 (0.53), residues: 106 loop : -0.02 (0.27), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 535 TYR 0.016 0.001 TYR A 192 PHE 0.009 0.001 PHE A 575 TRP 0.006 0.001 TRP A 883 HIS 0.006 0.001 HIS A 167 Details of bonding type rmsd/Z covalent geometry : bond 0.00213 / 0.11 (14660) covalent geometry : angle 0.53000 / 0.29 (20410) hydrogen bonds : bond 0.03665 / 2.42 ( 636) hydrogen bonds : angle 4.11456 / 2.96 ( 1729) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2017.97 seconds wall clock time: 35 minutes 55.91 seconds (2155.91 seconds total)