Starting phenix.real_space_refine on Thu Aug 6 06:46:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9h4m_51864/08_2026/9h4m_51864.cif Found real_map, /net/cci-nas-00/data/ceres_data/9h4m_51864/08_2026/9h4m_51864.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9h4m_51864/08_2026/9h4m_51864.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9h4m_51864/08_2026/9h4m_51864.map" model { file = "/net/cci-nas-00/data/ceres_data/9h4m_51864/08_2026/9h4m_51864.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9h4m_51864/08_2026/9h4m_51864.cif" } resolution = 3.8 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 132 5.49 5 S 21 5.16 5 C 8160 2.51 5 N 2379 2.21 5 O 2907 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 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: 13599 Number of models: 1 Model: "" Number of chains: 5 Chain: "B" Number of atoms: 2105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 2105 Classifications: {'RNA': 98} Modifications used: {'5*END': 1, 'rna2p_pur': 6, 'rna2p_pyr': 6, 'rna3p_pur': 55, 'rna3p_pyr': 31} Link IDs: {'rna2p': 11, 'rna3p': 86} Chain: "C" Number of atoms: 197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 197 Classifications: {'DNA': 10} Link IDs: {'rna3p': 9} Chain: "D" Number of atoms: 173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 173 Classifications: {'DNA': 8} Link IDs: {'rna3p': 7} Chain: "A" Number of atoms: 10784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1321, 10784 Classifications: {'peptide': 1321} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 35, 'TRANS': 1285} Chain breaks: 3 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "F" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 340 Classifications: {'DNA': 17} Link IDs: {'rna3p': 16} Time building chain proxies: 2.94, per 1000 atoms: 0.22 Number of scatterers: 13599 At special positions: 0 Unit cell: (113.05, 128.35, 134.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 21 16.00 P 132 15.00 O 2907 8.00 N 2379 7.00 C 8160 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: 1.19 Conformation dependent library (CDL) restraints added in 521.9 milliseconds 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2512 Finding SS restraints... Secondary structure from input PDB file: 61 helices and 10 sheets defined 50.0% alpha, 7.3% beta 37 base pairs and 78 stacking pairs defined. Time for finding SS restraints: 2.05 Creating SS restraints... Processing helix chain 'A' and resid 59 through 91 removed outlier: 3.527A pdb=" N ARG A 63 " --> pdb=" O ALA A 59 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N ASN A 88 " --> pdb=" O GLU A 84 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N GLU A 89 " --> pdb=" O ILE A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 103 removed outlier: 3.511A pdb=" N ARG A 100 " --> pdb=" O SER A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 132 Processing helix chain 'A' and resid 134 through 145 removed outlier: 3.633A pdb=" N LEU A 138 " --> pdb=" O THR A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 164 removed outlier: 3.583A pdb=" N ILE A 154 " --> pdb=" O ASP A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 196 removed outlier: 3.668A pdb=" N LEU A 195 " --> pdb=" O THR A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 214 Processing helix chain 'A' and resid 224 through 228 Processing helix chain 'A' and resid 236 through 246 removed outlier: 6.316A pdb=" N ILE A 242 " --> pdb=" O PHE A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 283 removed outlier: 4.263A pdb=" N GLN A 281 " --> pdb=" O ASN A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 304 Processing helix chain 'A' and resid 315 through 342 removed outlier: 3.626A pdb=" N ALA A 319 " --> pdb=" O ALA A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 345 No H-bonds generated for 'chain 'A' and resid 343 through 345' Processing helix chain 'A' and resid 346 through 353 removed outlier: 3.656A pdb=" N ASP A 353 " --> pdb=" O GLU A 349 " (cutoff:3.500A) 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 394 Processing helix chain 'A' and resid 404 through 408 removed outlier: 3.668A pdb=" N GLY A 408 " --> pdb=" O PHE A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 427 Processing helix chain 'A' and resid 436 through 446 Processing helix chain 'A' and resid 484 through 494 removed outlier: 3.565A pdb=" N ILE A 492 " --> pdb=" O ALA A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 525 removed outlier: 3.649A pdb=" N THR A 525 " --> pdb=" O TYR A 521 " (cutoff:3.500A) Processing helix chain 'A' and resid 541 through 553 Processing helix chain 'A' and resid 562 through 573 removed outlier: 3.931A pdb=" N GLU A 566 " --> pdb=" O LYS A 562 " (cutoff:3.500A) Processing helix chain 'A' and resid 591 through 602 Processing helix chain 'A' and resid 609 through 611 No H-bonds generated for 'chain 'A' and resid 609 through 611' Processing helix chain 'A' and resid 612 through 626 removed outlier: 3.595A pdb=" N PHE A 626 " --> pdb=" O THR A 622 " (cutoff:3.500A) Processing helix chain 'A' and resid 631 through 638 removed outlier: 4.417A pdb=" N THR A 638 " --> pdb=" O GLU A 634 " (cutoff:3.500A) Processing helix chain 'A' and resid 639 through 642 Processing helix chain 'A' and resid 644 through 652 removed outlier: 4.118A pdb=" N MET A 648 " --> pdb=" O ASP A 644 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LYS A 652 " --> pdb=" O MET A 648 " (cutoff:3.500A) Processing helix chain 'A' and resid 663 through 668 Processing helix chain 'A' and resid 678 through 686 Processing helix chain 'A' and resid 692 through 698 Processing helix chain 'A' and resid 703 through 715 removed outlier: 4.129A pdb=" N ILE A 708 " --> pdb=" O PHE A 704 " (cutoff:3.500A) Processing helix chain 'A' and resid 719 through 725 Processing helix chain 'A' and resid 730 through 750 removed outlier: 4.074A pdb=" N GLY A 736 " --> pdb=" O ALA A 732 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LYS A 749 " --> pdb=" O ASP A 745 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL A 750 " --> pdb=" O GLU A 746 " (cutoff:3.500A) Processing helix chain 'A' and resid 778 through 792 removed outlier: 4.078A pdb=" N LYS A 789 " --> pdb=" O GLU A 785 " (cutoff:3.500A) Processing helix chain 'A' and resid 794 through 799 Processing helix chain 'A' and resid 802 through 806 removed outlier: 3.723A pdb=" N LEU A 806 " --> pdb=" O ASN A 803 " (cutoff:3.500A) Processing helix chain 'A' and resid 808 through 813 Processing helix chain 'A' and resid 873 through 878 Processing helix chain 'A' and resid 879 through 890 Processing helix chain 'A' and resid 894 through 900 removed outlier: 3.514A pdb=" N ASP A 898 " --> pdb=" O GLN A 894 " (cutoff:3.500A) Processing helix chain 'A' and resid 901 through 904 Processing helix chain 'A' and resid 909 through 919 removed outlier: 3.796A pdb=" N ARG A 919 " --> pdb=" O GLY A 915 " (cutoff:3.500A) Processing helix chain 'A' and resid 928 through 940 Processing helix chain 'A' and resid 959 through 970 removed outlier: 4.065A pdb=" N VAL A 963 " --> pdb=" O LYS A 959 " (cutoff:3.500A) Processing helix chain 'A' and resid 980 through 1001 removed outlier: 4.124A pdb=" N ALA A 984 " --> pdb=" O ASN A 980 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ALA A 987 " --> pdb=" O HIS A 983 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N ILE A 998 " --> pdb=" O GLY A 994 " (cutoff:3.500A) Processing helix chain 'A' and resid 1002 through 1005 removed outlier: 4.285A pdb=" N GLU A1005 " --> pdb=" O PRO A1002 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1002 through 1005' Processing helix chain 'A' and resid 1043 through 1047 Processing helix chain 'A' and resid 1078 through 1088 Processing helix chain 'A' and resid 1127 through 1132 Processing helix chain 'A' and resid 1170 through 1177 Processing helix chain 'A' and resid 1177 through 1185 removed outlier: 3.562A pdb=" N PHE A1181 " --> pdb=" O ASN A1177 " (cutoff:3.500A) Processing helix chain 'A' and resid 1191 through 1195 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 1241 Processing helix chain 'A' and resid 1248 through 1262 removed outlier: 3.635A pdb=" N HIS A1262 " --> pdb=" O PHE A1258 " (cutoff:3.500A) Processing helix chain 'A' and resid 1264 through 1281 Processing helix chain 'A' and resid 1284 through 1297 Processing helix chain 'A' and resid 1301 through 1313 removed outlier: 3.607A pdb=" N PHE A1313 " --> pdb=" O ILE A1309 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 763 through 764 removed outlier: 7.254A pdb=" N ALA A 764 " --> pdb=" O LEU A 9 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N ILE A 11 " --> pdb=" O ALA A 764 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ILE A 759 " --> pdb=" O ILE A 956 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 763 through 764 removed outlier: 7.254A pdb=" N ALA A 764 " --> pdb=" O LEU A 9 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N ILE A 11 " --> pdb=" O ALA A 764 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ALA A 10 " --> pdb=" O GLY A 17 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N SER A 15 " --> pdb=" O GLY A 12 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 29 through 33 removed outlier: 3.666A pdb=" N LYS A 30 " --> pdb=" O LYS A 45 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 466 through 467 removed outlier: 3.845A pdb=" N THR A 466 " --> pdb=" O ASP A 483 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 838 through 839 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: 6.761A pdb=" N GLU A1064 " --> pdb=" O VAL A1073 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1156 through 1167 removed outlier: 3.762A pdb=" N LYS A1156 " --> pdb=" O LYS A1151 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LYS A1151 " --> pdb=" O LYS A1156 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N TYR A1141 " --> pdb=" O ILE A1166 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1219 through 1222 removed outlier: 6.335A pdb=" N GLU A1219 " --> pdb=" O ALA A1215 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N LEU A1203 " --> pdb=" O ILE A1348 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE A1348 " --> pdb=" O LEU A1203 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N THR A1346 " --> pdb=" O GLU A1205 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1324 through 1325 442 hydrogen bonds defined for protein. 1272 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 89 hydrogen bonds 166 hydrogen bond angles 0 basepair planarities 37 basepair parallelities 78 stacking parallelities Total time for adding SS restraints: 3.13 Time building geometry restraints manager: 1.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2520 1.33 - 1.45: 3977 1.45 - 1.57: 7324 1.57 - 1.69: 261 1.69 - 1.82: 41 Bond restraints: 14123 Sorted by residual: bond pdb=" C LYS A 536 " pdb=" N PRO A 537 " ideal model delta sigma weight residual 1.334 1.438 -0.104 2.34e-02 1.83e+03 1.98e+01 bond pdb=" CB PRO A 537 " pdb=" CG PRO A 537 " ideal model delta sigma weight residual 1.492 1.309 0.183 5.00e-02 4.00e+02 1.34e+01 bond pdb=" C3' DT F 25 " pdb=" C2' DT F 25 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.24e+01 bond pdb=" C3' DT F 35 " pdb=" C2' DT F 35 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.18e+01 bond pdb=" C2' DT F 21 " pdb=" C1' DT F 21 " ideal model delta sigma weight residual 1.518 1.548 -0.030 1.00e-02 1.00e+04 9.04e+00 ... (remaining 14118 not shown) Histogram of bond angle deviations from ideal: 0.00 - 14.57: 19634 14.57 - 29.15: 1 29.15 - 43.72: 0 43.72 - 58.30: 0 58.30 - 72.87: 1 Bond angle restraints: 19636 Sorted by residual: angle pdb=" C LYS A 536 " pdb=" N PRO A 537 " pdb=" CD PRO A 537 " ideal model delta sigma weight residual 125.00 52.13 72.87 4.10e+00 5.95e-02 3.16e+02 angle pdb=" CA PRO A 537 " pdb=" N PRO A 537 " pdb=" CD PRO A 537 " ideal model delta sigma weight residual 112.00 95.33 16.67 1.40e+00 5.10e-01 1.42e+02 angle pdb=" C LYS A 536 " pdb=" N PRO A 537 " pdb=" CA PRO A 537 " ideal model delta sigma weight residual 119.84 131.77 -11.93 1.25e+00 6.40e-01 9.10e+01 angle pdb=" C1' C B 70 " pdb=" N1 C B 70 " pdb=" C2 C B 70 " ideal model delta sigma weight residual 118.80 124.77 -5.97 1.10e+00 8.26e-01 2.94e+01 angle pdb=" N1 C B 70 " pdb=" C2 C B 70 " pdb=" O2 C B 70 " ideal model delta sigma weight residual 118.90 121.76 -2.86 6.00e-01 2.78e+00 2.28e+01 ... (remaining 19631 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.49: 7662 27.49 - 54.97: 734 54.97 - 82.46: 169 82.46 - 109.95: 12 109.95 - 137.43: 1 Dihedral angle restraints: 8578 sinusoidal: 4696 harmonic: 3882 Sorted by residual: dihedral pdb=" O4' C B 70 " pdb=" C1' C B 70 " pdb=" N1 C B 70 " pdb=" C2 C B 70 " ideal model delta sinusoidal sigma weight residual 200.00 62.57 137.43 1 1.50e+01 4.44e-03 7.41e+01 dihedral pdb=" O4' U B 56 " pdb=" C1' U B 56 " pdb=" N1 U B 56 " pdb=" C2 U B 56 " ideal model delta sinusoidal sigma weight residual -128.00 -25.19 -102.81 1 1.70e+01 3.46e-03 4.06e+01 dihedral pdb=" C PRO A 537 " pdb=" N PRO A 537 " pdb=" CA PRO A 537 " pdb=" CB PRO A 537 " ideal model delta harmonic sigma weight residual -120.70 -131.07 10.37 0 2.50e+00 1.60e-01 1.72e+01 ... (remaining 8575 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.086: 2072 0.086 - 0.172: 181 0.172 - 0.259: 2 0.259 - 0.345: 0 0.345 - 0.431: 1 Chirality restraints: 2256 Sorted by residual: chirality pdb=" CA PRO A 537 " pdb=" N PRO A 537 " pdb=" C PRO A 537 " pdb=" CB PRO A 537 " both_signs ideal model delta sigma weight residual False 2.72 2.29 0.43 2.00e-01 2.50e+01 4.65e+00 chirality pdb=" C1' A B 68 " pdb=" O4' A B 68 " pdb=" C2' A B 68 " pdb=" N9 A B 68 " both_signs ideal model delta sigma weight residual False 2.47 2.24 0.23 2.00e-01 2.50e+01 1.35e+00 chirality pdb=" C1' A B 65 " pdb=" O4' A B 65 " pdb=" C2' A B 65 " pdb=" N9 A B 65 " both_signs ideal model delta sigma weight residual False 2.47 2.28 0.19 2.00e-01 2.50e+01 8.83e-01 ... (remaining 2253 not shown) Planarity restraints: 2021 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A 536 " -0.218 5.00e-02 4.00e+02 2.04e-01 6.66e+01 pdb=" N PRO A 537 " 0.285 5.00e-02 4.00e+02 pdb=" CA PRO A 537 " -0.167 5.00e-02 4.00e+02 pdb=" CD PRO A 537 " 0.100 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA SER A 685 " 0.021 2.00e-02 2.50e+03 4.20e-02 1.76e+01 pdb=" C SER A 685 " -0.073 2.00e-02 2.50e+03 pdb=" O SER A 685 " 0.027 2.00e-02 2.50e+03 pdb=" N ASP A 686 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 536 " -0.020 2.00e-02 2.50e+03 3.96e-02 1.57e+01 pdb=" C LYS A 536 " 0.069 2.00e-02 2.50e+03 pdb=" O LYS A 536 " -0.026 2.00e-02 2.50e+03 pdb=" N PRO A 537 " -0.022 2.00e-02 2.50e+03 ... (remaining 2018 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.52: 124 2.52 - 3.11: 9979 3.11 - 3.71: 22599 3.71 - 4.30: 31148 4.30 - 4.90: 47995 Nonbonded interactions: 111845 Sorted by model distance: nonbonded pdb=" O LYS A 536 " pdb=" CD PRO A 537 " model vdw 1.919 2.752 nonbonded pdb=" O2' A B 69 " pdb=" O4' C B 70 " model vdw 2.188 3.040 nonbonded pdb=" OE1 GLN A 971 " pdb=" OH TYR A 973 " model vdw 2.189 3.040 nonbonded pdb=" O ALA A 149 " pdb=" OH TYR A 430 " model vdw 2.191 3.040 nonbonded pdb=" O LEU A 216 " pdb=" OG SER A 219 " model vdw 2.204 3.040 ... (remaining 111840 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.690 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: 0.280 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 15.400 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:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7060 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 : 0.003 0.183 14123 Z= 0.228 Angle : 0.861 72.872 19636 Z= 0.506 Chirality : 0.048 0.431 2256 Planarity : 0.006 0.204 2021 Dihedral : 20.023 137.433 6066 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 13.29 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.95 % Favored : 94.97 % Rotamer: Outliers : 0.25 % Allowed : 22.88 % Favored : 76.86 % 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: -1.38 (0.22), residues: 1313 helix: -0.05 (0.22), residues: 582 sheet: -0.44 (0.60), residues: 77 loop : -1.81 (0.22), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 905 TYR 0.009 0.001 TYR A 136 PHE 0.011 0.001 PHE A 518 TRP 0.006 0.001 TRP A 883 HIS 0.004 0.001 HIS A 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.23 (14123) covalent geometry : angle 0.86079 / 0.51 (19636) hydrogen bonds : bond 0.14961 / 16.09 ( 531) hydrogen bonds : angle 6.33210 / 8.45 ( 1438) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 67 time to evaluate : 0.350 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 448 ILE cc_start: 0.6545 (OUTLIER) cc_final: 0.6330 (tt) outliers start: 3 outliers final: 1 residues processed: 70 average time/residue: 0.0961 time to fit residues: 10.9084 Evaluate side-chains 66 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 64 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain A residue 842 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 9.9990 chunk 122 optimal weight: 0.0170 chunk 91 optimal weight: 9.9990 chunk 55 optimal weight: 7.9990 overall best weight: 1.3622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 794 GLN A 869 ASN ** A 940 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 990 ASN ** A1044 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.086927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.068226 restraints weight = 81630.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.069528 restraints weight = 51526.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.070355 restraints weight = 38279.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.070666 restraints weight = 32176.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.070830 restraints weight = 29327.467| |-----------------------------------------------------------------------------| r_work (final): 0.3884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7028 moved from start: 0.0690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.087 14123 Z= 0.121 Angle : 0.570 22.526 19636 Z= 0.309 Chirality : 0.038 0.284 2256 Planarity : 0.006 0.179 2021 Dihedral : 19.338 142.871 3270 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.42 % Favored : 95.51 % Rotamer: Outliers : 2.29 % Allowed : 20.59 % Favored : 77.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.28 (0.22), residues: 1313 helix: 0.03 (0.21), residues: 597 sheet: -0.70 (0.57), residues: 81 loop : -1.74 (0.22), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 395 TYR 0.011 0.001 TYR A 362 PHE 0.012 0.001 PHE A 290 TRP 0.005 0.001 TRP A 464 HIS 0.003 0.001 HIS A 799 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.12 (14123) covalent geometry : angle 0.57015 / 0.31 (19636) hydrogen bonds : bond 0.05129 / 5.38 ( 531) hydrogen bonds : angle 5.22974 / 6.92 ( 1438) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 70 time to evaluate : 0.475 Fit side-chains revert: symmetry clash REVERT: A 448 ILE cc_start: 0.6453 (OUTLIER) cc_final: 0.6204 (tt) REVERT: A 822 MET cc_start: 0.3247 (pmm) cc_final: 0.1175 (ppp) REVERT: A 1349 HIS cc_start: 0.6018 (m90) cc_final: 0.5653 (m170) outliers start: 27 outliers final: 9 residues processed: 91 average time/residue: 0.1047 time to fit residues: 14.9158 Evaluate side-chains 73 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 63 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 31 LYS Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 518 PHE Chi-restraints excluded: chain A residue 678 THR Chi-restraints excluded: chain A residue 842 VAL Chi-restraints excluded: chain A residue 997 LEU Chi-restraints excluded: chain A residue 1266 LEU Chi-restraints excluded: chain A residue 1314 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 48 optimal weight: 0.4980 chunk 57 optimal weight: 0.0040 chunk 136 optimal weight: 1.9990 chunk 10 optimal weight: 0.2980 chunk 124 optimal weight: 5.9990 chunk 30 optimal weight: 0.0570 chunk 51 optimal weight: 0.9990 chunk 116 optimal weight: 9.9990 chunk 62 optimal weight: 0.9990 chunk 37 optimal weight: 5.9990 chunk 55 optimal weight: 9.9990 overall best weight: 0.3712 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 354 GLN A 794 GLN ** A1044 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1305 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.087842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.069152 restraints weight = 81461.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.070528 restraints weight = 51423.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.071327 restraints weight = 37770.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.071697 restraints weight = 31364.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 59)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.072106 restraints weight = 28604.918| |-----------------------------------------------------------------------------| r_work (final): 0.3912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6974 moved from start: 0.1019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.107 14123 Z= 0.104 Angle : 0.518 12.738 19636 Z= 0.285 Chirality : 0.037 0.253 2256 Planarity : 0.005 0.150 2021 Dihedral : 19.253 146.435 3270 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.11 % Favored : 95.81 % Rotamer: Outliers : 2.54 % Allowed : 20.85 % Favored : 76.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.15 (0.22), residues: 1313 helix: 0.11 (0.21), residues: 599 sheet: -0.56 (0.56), residues: 79 loop : -1.66 (0.22), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 951 TYR 0.019 0.001 TYR A 451 PHE 0.014 0.001 PHE A 98 TRP 0.004 0.000 TRP A 464 HIS 0.003 0.001 HIS A 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00206 / 0.10 (14123) covalent geometry : angle 0.51765 / 0.29 (19636) hydrogen bonds : bond 0.04482 / 4.73 ( 531) hydrogen bonds : angle 4.94716 / 6.58 ( 1438) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 75 time to evaluate : 0.406 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 395 ARG cc_start: 0.7326 (mpp80) cc_final: 0.6689 (mtm-85) REVERT: A 822 MET cc_start: 0.3127 (pmm) cc_final: 0.0892 (ppp) outliers start: 30 outliers final: 13 residues processed: 98 average time/residue: 0.1063 time to fit residues: 15.9999 Evaluate side-chains 79 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 66 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 370 GLU Chi-restraints excluded: chain A residue 518 PHE Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 842 VAL Chi-restraints excluded: chain A residue 927 ILE Chi-restraints excluded: chain A residue 997 LEU Chi-restraints excluded: chain A residue 1257 LEU Chi-restraints excluded: chain A residue 1264 HIS Chi-restraints excluded: chain A residue 1266 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 87 optimal weight: 3.9990 chunk 25 optimal weight: 0.7980 chunk 123 optimal weight: 6.9990 chunk 4 optimal weight: 20.0000 chunk 89 optimal weight: 8.9990 chunk 5 optimal weight: 20.0000 chunk 32 optimal weight: 20.0000 chunk 57 optimal weight: 10.0000 chunk 99 optimal weight: 5.9990 chunk 19 optimal weight: 6.9990 chunk 55 optimal weight: 0.5980 overall best weight: 3.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 544 GLN A 794 GLN ** A 940 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1044 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 = 0.4134 r_free = 0.4134 target = 0.084495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.065871 restraints weight = 82707.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.067238 restraints weight = 52157.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.068054 restraints weight = 38476.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.068368 restraints weight = 32112.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 56)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.068746 restraints weight = 29311.565| |-----------------------------------------------------------------------------| r_work (final): 0.3832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7109 moved from start: 0.1389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.094 14123 Z= 0.193 Angle : 0.618 11.251 19636 Z= 0.337 Chirality : 0.040 0.245 2256 Planarity : 0.005 0.141 2021 Dihedral : 19.398 143.229 3268 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 12.64 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.56 % Favored : 94.36 % Rotamer: Outliers : 3.47 % Allowed : 21.27 % Favored : 75.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.29 (0.22), residues: 1313 helix: -0.04 (0.21), residues: 598 sheet: -0.30 (0.61), residues: 62 loop : -1.71 (0.22), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 765 TYR 0.021 0.002 TYR A 136 PHE 0.017 0.002 PHE A 704 TRP 0.006 0.002 TRP A 659 HIS 0.005 0.001 HIS A 985 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.19 (14123) covalent geometry : angle 0.61769 / 0.34 (19636) hydrogen bonds : bond 0.05150 / 5.46 ( 531) hydrogen bonds : angle 5.08328 / 6.80 ( 1438) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 67 time to evaluate : 0.529 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 212 LEU cc_start: 0.8389 (OUTLIER) cc_final: 0.8152 (pt) REVERT: A 395 ARG cc_start: 0.7584 (mpp80) cc_final: 0.7158 (mtm-85) REVERT: A 822 MET cc_start: 0.3071 (pmm) cc_final: 0.0901 (ppp) REVERT: A 1220 LEU cc_start: 0.7127 (OUTLIER) cc_final: 0.6480 (mt) outliers start: 41 outliers final: 24 residues processed: 98 average time/residue: 0.0853 time to fit residues: 13.6566 Evaluate side-chains 88 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 62 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 128 TYR Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 329 HIS Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 518 PHE Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain A residue 678 THR Chi-restraints excluded: chain A residue 735 LYS Chi-restraints excluded: chain A residue 842 VAL Chi-restraints excluded: chain A residue 847 LEU Chi-restraints excluded: chain A residue 892 ILE Chi-restraints excluded: chain A residue 927 ILE Chi-restraints excluded: chain A residue 997 LEU Chi-restraints excluded: chain A residue 1048 THR Chi-restraints excluded: chain A residue 1220 LEU Chi-restraints excluded: chain A residue 1236 LEU Chi-restraints excluded: chain A residue 1257 LEU Chi-restraints excluded: chain A residue 1264 HIS Chi-restraints excluded: chain A residue 1266 LEU Chi-restraints excluded: chain A residue 1314 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 18 optimal weight: 7.9990 chunk 57 optimal weight: 7.9990 chunk 44 optimal weight: 3.9990 chunk 35 optimal weight: 0.6980 chunk 54 optimal weight: 3.9990 chunk 95 optimal weight: 7.9990 chunk 133 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 110 optimal weight: 0.6980 chunk 131 optimal weight: 6.9990 chunk 36 optimal weight: 9.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 885 GLN ** A 940 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1044 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 = 0.4151 r_free = 0.4151 target = 0.085304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.066882 restraints weight = 81507.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.068171 restraints weight = 50171.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.069048 restraints weight = 36529.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.069342 restraints weight = 30432.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.069560 restraints weight = 27768.724| |-----------------------------------------------------------------------------| r_work (final): 0.3854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7034 moved from start: 0.1483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.092 14123 Z= 0.127 Angle : 0.551 12.134 19636 Z= 0.299 Chirality : 0.038 0.241 2256 Planarity : 0.005 0.132 2021 Dihedral : 19.388 145.726 3268 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.95 % Favored : 94.97 % Rotamer: Outliers : 3.64 % Allowed : 21.10 % Favored : 75.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.14 (0.22), residues: 1313 helix: 0.13 (0.21), residues: 594 sheet: -0.69 (0.62), residues: 65 loop : -1.61 (0.23), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 765 TYR 0.015 0.001 TYR A 451 PHE 0.010 0.001 PHE A 693 TRP 0.006 0.001 TRP A 476 HIS 0.004 0.001 HIS A 641 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.13 (14123) covalent geometry : angle 0.55127 / 0.30 (19636) hydrogen bonds : bond 0.04632 / 4.77 ( 531) hydrogen bonds : angle 4.96167 / 6.61 ( 1438) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 65 time to evaluate : 0.460 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 822 MET cc_start: 0.3019 (pmm) cc_final: 0.0941 (ppp) REVERT: A 828 LEU cc_start: -0.1168 (OUTLIER) cc_final: -0.1518 (mt) REVERT: A 1220 LEU cc_start: 0.7079 (OUTLIER) cc_final: 0.6449 (mt) outliers start: 43 outliers final: 26 residues processed: 97 average time/residue: 0.0862 time to fit residues: 13.5011 Evaluate side-chains 90 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 62 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 31 LYS Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 128 TYR Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 370 GLU Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 505 GLU Chi-restraints excluded: chain A residue 518 PHE Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain A residue 621 LEU Chi-restraints excluded: chain A residue 816 LEU Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 842 VAL Chi-restraints excluded: chain A residue 852 ILE Chi-restraints excluded: chain A residue 857 LEU Chi-restraints excluded: chain A residue 861 ASP Chi-restraints excluded: chain A residue 927 ILE Chi-restraints excluded: chain A residue 1220 LEU Chi-restraints excluded: chain A residue 1248 SER Chi-restraints excluded: chain A residue 1257 LEU Chi-restraints excluded: chain A residue 1264 HIS Chi-restraints excluded: chain A residue 1266 LEU Chi-restraints excluded: chain A residue 1267 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 88 optimal weight: 0.2980 chunk 8 optimal weight: 20.0000 chunk 95 optimal weight: 1.9990 chunk 130 optimal weight: 6.9990 chunk 55 optimal weight: 9.9990 chunk 78 optimal weight: 5.9990 chunk 82 optimal weight: 0.9980 chunk 0 optimal weight: 30.0000 chunk 123 optimal weight: 7.9990 chunk 2 optimal weight: 20.0000 chunk 23 optimal weight: 0.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 940 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 = 0.4149 r_free = 0.4149 target = 0.085257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.066751 restraints weight = 81255.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.068075 restraints weight = 49822.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.068697 restraints weight = 36580.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.069196 restraints weight = 30864.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 54)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.069471 restraints weight = 28061.514| |-----------------------------------------------------------------------------| r_work (final): 0.3851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7081 moved from start: 0.1612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.088 14123 Z= 0.125 Angle : 0.544 9.889 19636 Z= 0.295 Chirality : 0.038 0.241 2256 Planarity : 0.004 0.126 2021 Dihedral : 19.383 145.964 3268 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.33 % Favored : 94.59 % Rotamer: Outliers : 3.98 % Allowed : 21.27 % Favored : 74.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.05 (0.22), residues: 1313 helix: 0.18 (0.21), residues: 594 sheet: -0.40 (0.57), residues: 76 loop : -1.58 (0.23), residues: 643 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 653 TYR 0.015 0.001 TYR A 451 PHE 0.010 0.001 PHE A 704 TRP 0.006 0.001 TRP A 476 HIS 0.004 0.001 HIS A 641 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.12 (14123) covalent geometry : angle 0.54367 / 0.29 (19636) hydrogen bonds : bond 0.04511 / 4.64 ( 531) hydrogen bonds : angle 4.90591 / 6.54 ( 1438) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 65 time to evaluate : 0.391 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 MET cc_start: 0.7366 (tmm) cc_final: 0.7079 (tmm) REVERT: A 209 LYS cc_start: 0.4591 (OUTLIER) cc_final: 0.4331 (mppt) REVERT: A 212 LEU cc_start: 0.8403 (OUTLIER) cc_final: 0.8149 (pt) REVERT: A 395 ARG cc_start: 0.7550 (mpp80) cc_final: 0.7305 (mtm-85) REVERT: A 828 LEU cc_start: -0.1137 (OUTLIER) cc_final: -0.1448 (mt) outliers start: 47 outliers final: 35 residues processed: 102 average time/residue: 0.0961 time to fit residues: 15.5711 Evaluate side-chains 99 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 61 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 31 LYS Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 128 TYR Chi-restraints excluded: chain A residue 209 LYS Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 329 HIS Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 370 GLU Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 505 GLU Chi-restraints excluded: chain A residue 518 PHE Chi-restraints excluded: chain A residue 532 GLU Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain A residue 621 LEU Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain A residue 816 LEU Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 829 ASP Chi-restraints excluded: chain A residue 842 VAL Chi-restraints excluded: chain A residue 852 ILE Chi-restraints excluded: chain A residue 857 LEU Chi-restraints excluded: chain A residue 861 ASP Chi-restraints excluded: chain A residue 892 ILE Chi-restraints excluded: chain A residue 927 ILE Chi-restraints excluded: chain A residue 1048 THR Chi-restraints excluded: chain A residue 1236 LEU Chi-restraints excluded: chain A residue 1248 SER Chi-restraints excluded: chain A residue 1257 LEU Chi-restraints excluded: chain A residue 1264 HIS Chi-restraints excluded: chain A residue 1266 LEU Chi-restraints excluded: chain A residue 1267 ASP Chi-restraints excluded: chain A residue 1299 ASP Chi-restraints excluded: chain A residue 1314 THR Chi-restraints excluded: chain A residue 1362 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 60 optimal weight: 8.9990 chunk 57 optimal weight: 5.9990 chunk 110 optimal weight: 0.7980 chunk 88 optimal weight: 5.9990 chunk 93 optimal weight: 8.9990 chunk 69 optimal weight: 0.2980 chunk 112 optimal weight: 0.9990 chunk 129 optimal weight: 8.9990 chunk 6 optimal weight: 20.0000 chunk 53 optimal weight: 0.9990 chunk 130 optimal weight: 0.1980 overall best weight: 0.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 940 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.086533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.068040 restraints weight = 81673.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.069367 restraints weight = 50333.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.069906 restraints weight = 36786.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.070363 restraints weight = 31234.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 73)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.070813 restraints weight = 28218.429| |-----------------------------------------------------------------------------| r_work (final): 0.3886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7019 moved from start: 0.1706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.088 14123 Z= 0.101 Angle : 0.527 9.690 19636 Z= 0.284 Chirality : 0.037 0.240 2256 Planarity : 0.004 0.120 2021 Dihedral : 19.304 148.061 3268 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.81 % Favored : 96.12 % Rotamer: Outliers : 3.05 % Allowed : 22.63 % Favored : 74.32 % 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: -0.89 (0.22), residues: 1313 helix: 0.25 (0.21), residues: 596 sheet: -0.45 (0.57), residues: 78 loop : -1.42 (0.24), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 220 TYR 0.012 0.001 TYR A 451 PHE 0.010 0.001 PHE A 688 TRP 0.005 0.001 TRP A 476 HIS 0.005 0.001 HIS A 641 Details of bonding type rmsd/Z covalent geometry : bond 0.00199 / 0.10 (14123) covalent geometry : angle 0.52695 / 0.28 (19636) hydrogen bonds : bond 0.04186 / 4.31 ( 531) hydrogen bonds : angle 4.75388 / 6.37 ( 1438) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 70 time to evaluate : 0.532 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: A 90 MET cc_start: 0.7265 (tmm) cc_final: 0.6925 (tmm) REVERT: A 212 LEU cc_start: 0.8353 (OUTLIER) cc_final: 0.8114 (pt) REVERT: A 828 LEU cc_start: -0.1210 (OUTLIER) cc_final: -0.1519 (mt) outliers start: 36 outliers final: 23 residues processed: 98 average time/residue: 0.1011 time to fit residues: 15.5675 Evaluate side-chains 88 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 63 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 31 LYS Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 128 TYR Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 370 GLU Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 505 GLU Chi-restraints excluded: chain A residue 518 PHE Chi-restraints excluded: chain A residue 532 GLU Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 842 VAL Chi-restraints excluded: chain A residue 857 LEU Chi-restraints excluded: chain A residue 861 ASP Chi-restraints excluded: chain A residue 882 TYR Chi-restraints excluded: chain A residue 892 ILE Chi-restraints excluded: chain A residue 927 ILE Chi-restraints excluded: chain A residue 1248 SER Chi-restraints excluded: chain A residue 1257 LEU Chi-restraints excluded: chain A residue 1264 HIS Chi-restraints excluded: chain A residue 1266 LEU Chi-restraints excluded: chain A residue 1299 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 49 optimal weight: 0.7980 chunk 136 optimal weight: 5.9990 chunk 114 optimal weight: 6.9990 chunk 19 optimal weight: 5.9990 chunk 96 optimal weight: 7.9990 chunk 137 optimal weight: 5.9990 chunk 8 optimal weight: 20.0000 chunk 17 optimal weight: 10.0000 chunk 106 optimal weight: 10.0000 chunk 24 optimal weight: 7.9990 chunk 52 optimal weight: 0.7980 overall best weight: 3.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 650 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.083368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.065210 restraints weight = 82464.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 72)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.066406 restraints weight = 53581.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.067141 restraints weight = 40577.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.067420 restraints weight = 34355.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.067666 restraints weight = 31621.672| |-----------------------------------------------------------------------------| r_work (final): 0.3818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7101 moved from start: 0.1984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 14123 Z= 0.192 Angle : 0.621 8.869 19636 Z= 0.334 Chirality : 0.041 0.213 2256 Planarity : 0.005 0.118 2021 Dihedral : 19.420 143.313 3268 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 13.33 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.17 % Favored : 93.75 % Rotamer: Outliers : 3.56 % Allowed : 22.54 % Favored : 73.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.20 (0.22), residues: 1313 helix: -0.00 (0.21), residues: 603 sheet: -0.85 (0.72), residues: 51 loop : -1.55 (0.23), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 215 TYR 0.015 0.002 TYR A 136 PHE 0.019 0.002 PHE A 704 TRP 0.006 0.002 TRP A 659 HIS 0.010 0.002 HIS A1349 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.19 (14123) covalent geometry : angle 0.62084 / 0.33 (19636) hydrogen bonds : bond 0.05044 / 5.25 ( 531) hydrogen bonds : angle 5.00993 / 6.67 ( 1438) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 63 time to evaluate : 0.471 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 MET cc_start: 0.7325 (tmm) cc_final: 0.7095 (tmm) REVERT: A 212 LEU cc_start: 0.8432 (OUTLIER) cc_final: 0.8184 (pt) REVERT: A 747 LEU cc_start: 0.9136 (OUTLIER) cc_final: 0.8875 (pp) REVERT: A 822 MET cc_start: 0.3066 (pmm) cc_final: 0.0979 (ppp) REVERT: A 1220 LEU cc_start: 0.7160 (OUTLIER) cc_final: 0.6530 (mt) outliers start: 42 outliers final: 31 residues processed: 97 average time/residue: 0.0831 time to fit residues: 13.1126 Evaluate side-chains 93 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 59 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 31 LYS Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 128 TYR Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 370 GLU Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 505 GLU Chi-restraints excluded: chain A residue 518 PHE Chi-restraints excluded: chain A residue 560 THR Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain A residue 621 LEU Chi-restraints excluded: chain A residue 747 LEU Chi-restraints excluded: chain A residue 842 VAL Chi-restraints excluded: chain A residue 852 ILE Chi-restraints excluded: chain A residue 857 LEU Chi-restraints excluded: chain A residue 861 ASP Chi-restraints excluded: chain A residue 892 ILE Chi-restraints excluded: chain A residue 927 ILE Chi-restraints excluded: chain A residue 1048 THR Chi-restraints excluded: chain A residue 1220 LEU Chi-restraints excluded: chain A residue 1236 LEU Chi-restraints excluded: chain A residue 1248 SER Chi-restraints excluded: chain A residue 1257 LEU Chi-restraints excluded: chain A residue 1264 HIS Chi-restraints excluded: chain A residue 1266 LEU Chi-restraints excluded: chain A residue 1267 ASP Chi-restraints excluded: chain A residue 1299 ASP Chi-restraints excluded: chain A residue 1314 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 103 optimal weight: 0.9980 chunk 54 optimal weight: 0.0570 chunk 110 optimal weight: 0.6980 chunk 7 optimal weight: 30.0000 chunk 29 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 127 optimal weight: 2.9990 chunk 43 optimal weight: 0.9980 chunk 14 optimal weight: 4.9990 chunk 42 optimal weight: 5.9990 overall best weight: 0.9500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 228 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 = 0.4155 r_free = 0.4155 target = 0.085818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.067447 restraints weight = 80284.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 65)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.068911 restraints weight = 49230.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.069707 restraints weight = 35862.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.070049 restraints weight = 29721.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 54)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.070435 restraints weight = 27009.774| |-----------------------------------------------------------------------------| r_work (final): 0.3861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7002 moved from start: 0.1972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.083 14123 Z= 0.109 Angle : 0.548 9.352 19636 Z= 0.296 Chirality : 0.038 0.222 2256 Planarity : 0.004 0.114 2021 Dihedral : 19.332 147.668 3268 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.80 % Favored : 95.13 % Rotamer: Outliers : 2.88 % Allowed : 23.14 % Favored : 73.98 % 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: -0.97 (0.23), residues: 1313 helix: 0.14 (0.21), residues: 603 sheet: -0.44 (0.52), residues: 90 loop : -1.46 (0.24), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 395 TYR 0.011 0.001 TYR A 451 PHE 0.008 0.001 PHE A 688 TRP 0.005 0.001 TRP A 476 HIS 0.005 0.001 HIS A 641 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.11 (14123) covalent geometry : angle 0.54848 / 0.30 (19636) hydrogen bonds : bond 0.04331 / 4.40 ( 531) hydrogen bonds : angle 4.81234 / 6.45 ( 1438) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 65 time to evaluate : 0.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 MET cc_start: 0.7231 (tmm) cc_final: 0.7013 (tmm) REVERT: A 212 LEU cc_start: 0.8362 (OUTLIER) cc_final: 0.8078 (pt) REVERT: A 747 LEU cc_start: 0.9063 (OUTLIER) cc_final: 0.8808 (pp) REVERT: A 822 MET cc_start: 0.2835 (pmm) cc_final: 0.0591 (ppp) REVERT: A 1220 LEU cc_start: 0.7013 (OUTLIER) cc_final: 0.6379 (mt) outliers start: 34 outliers final: 28 residues processed: 91 average time/residue: 0.0989 time to fit residues: 14.4951 Evaluate side-chains 91 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 60 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 31 LYS Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 128 TYR Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 370 GLU Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 505 GLU Chi-restraints excluded: chain A residue 518 PHE Chi-restraints excluded: chain A residue 532 GLU Chi-restraints excluded: chain A residue 560 THR Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain A residue 621 LEU Chi-restraints excluded: chain A residue 747 LEU Chi-restraints excluded: chain A residue 842 VAL Chi-restraints excluded: chain A residue 857 LEU Chi-restraints excluded: chain A residue 861 ASP Chi-restraints excluded: chain A residue 882 TYR Chi-restraints excluded: chain A residue 892 ILE Chi-restraints excluded: chain A residue 927 ILE Chi-restraints excluded: chain A residue 950 ILE Chi-restraints excluded: chain A residue 1220 LEU Chi-restraints excluded: chain A residue 1248 SER Chi-restraints excluded: chain A residue 1257 LEU Chi-restraints excluded: chain A residue 1264 HIS Chi-restraints excluded: chain A residue 1266 LEU Chi-restraints excluded: chain A residue 1299 ASP Chi-restraints excluded: chain A residue 1314 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 109 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 chunk 87 optimal weight: 7.9990 chunk 115 optimal weight: 0.9980 chunk 136 optimal weight: 0.9990 chunk 101 optimal weight: 0.0970 chunk 73 optimal weight: 0.9990 chunk 69 optimal weight: 5.9990 chunk 28 optimal weight: 7.9990 chunk 127 optimal weight: 9.9990 chunk 5 optimal weight: 30.0000 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 228 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 = 0.4155 r_free = 0.4155 target = 0.085728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.067494 restraints weight = 80550.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.068749 restraints weight = 51256.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.069510 restraints weight = 38448.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.069791 restraints weight = 32340.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.070087 restraints weight = 29591.644| |-----------------------------------------------------------------------------| r_work (final): 0.3868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7039 moved from start: 0.2071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.082 14123 Z= 0.111 Angle : 0.541 9.394 19636 Z= 0.295 Chirality : 0.037 0.223 2256 Planarity : 0.004 0.110 2021 Dihedral : 19.224 146.716 3268 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.03 % Favored : 94.90 % Rotamer: Outliers : 2.80 % Allowed : 23.31 % Favored : 73.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.91 (0.23), residues: 1313 helix: 0.14 (0.21), residues: 606 sheet: -0.17 (0.58), residues: 76 loop : -1.39 (0.24), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 395 TYR 0.013 0.001 TYR A 451 PHE 0.012 0.001 PHE A 98 TRP 0.005 0.001 TRP A 464 HIS 0.005 0.001 HIS A 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.11 (14123) covalent geometry : angle 0.54073 / 0.30 (19636) hydrogen bonds : bond 0.04330 / 4.46 ( 531) hydrogen bonds : angle 4.78953 / 6.44 ( 1438) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 65 time to evaluate : 0.421 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 MET cc_start: 0.7273 (tmm) cc_final: 0.6976 (tmm) REVERT: A 212 LEU cc_start: 0.8330 (OUTLIER) cc_final: 0.8063 (pt) REVERT: A 747 LEU cc_start: 0.9067 (OUTLIER) cc_final: 0.8786 (pp) REVERT: A 1220 LEU cc_start: 0.7016 (OUTLIER) cc_final: 0.6363 (mt) outliers start: 33 outliers final: 28 residues processed: 92 average time/residue: 0.0849 time to fit residues: 13.0754 Evaluate side-chains 94 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 63 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 31 LYS Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 128 TYR Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 370 GLU Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 505 GLU Chi-restraints excluded: chain A residue 518 PHE Chi-restraints excluded: chain A residue 532 GLU Chi-restraints excluded: chain A residue 560 THR Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain A residue 621 LEU Chi-restraints excluded: chain A residue 747 LEU Chi-restraints excluded: chain A residue 842 VAL Chi-restraints excluded: chain A residue 857 LEU Chi-restraints excluded: chain A residue 861 ASP Chi-restraints excluded: chain A residue 882 TYR Chi-restraints excluded: chain A residue 892 ILE Chi-restraints excluded: chain A residue 927 ILE Chi-restraints excluded: chain A residue 950 ILE Chi-restraints excluded: chain A residue 1220 LEU Chi-restraints excluded: chain A residue 1248 SER Chi-restraints excluded: chain A residue 1257 LEU Chi-restraints excluded: chain A residue 1264 HIS Chi-restraints excluded: chain A residue 1266 LEU Chi-restraints excluded: chain A residue 1299 ASP Chi-restraints excluded: chain A residue 1314 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 61 optimal weight: 6.9990 chunk 123 optimal weight: 0.0980 chunk 106 optimal weight: 9.9990 chunk 85 optimal weight: 0.9980 chunk 75 optimal weight: 2.9990 chunk 2 optimal weight: 20.0000 chunk 27 optimal weight: 0.0670 chunk 47 optimal weight: 6.9990 chunk 25 optimal weight: 5.9990 chunk 63 optimal weight: 7.9990 chunk 78 optimal weight: 3.9990 overall best weight: 1.6322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 228 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 = 0.4152 r_free = 0.4152 target = 0.085567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.067071 restraints weight = 82337.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.068067 restraints weight = 51069.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.068981 restraints weight = 37792.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.069560 restraints weight = 32395.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.069731 restraints weight = 29121.686| |-----------------------------------------------------------------------------| r_work (final): 0.3865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7078 moved from start: 0.2147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.081 14123 Z= 0.115 Angle : 0.549 9.423 19636 Z= 0.296 Chirality : 0.039 0.430 2256 Planarity : 0.004 0.107 2021 Dihedral : 19.204 146.814 3268 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.80 % Favored : 95.13 % Rotamer: Outliers : 2.63 % Allowed : 23.90 % Favored : 73.47 % 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: -0.93 (0.23), residues: 1313 helix: 0.13 (0.21), residues: 607 sheet: -0.13 (0.53), residues: 88 loop : -1.43 (0.24), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 395 TYR 0.012 0.001 TYR A 451 PHE 0.009 0.001 PHE A 704 TRP 0.004 0.001 TRP A 464 HIS 0.004 0.001 HIS A 641 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.11 (14123) covalent geometry : angle 0.54870 / 0.30 (19636) hydrogen bonds : bond 0.04206 / 4.29 ( 531) hydrogen bonds : angle 4.80114 / 6.44 ( 1438) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2672.70 seconds wall clock time: 46 minutes 52.63 seconds (2812.63 seconds total)