Starting phenix.real_space_refine on Sun May 3 14:57:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9h4m_51864/05_2026/9h4m_51864.cif Found real_map, /net/cci-nas-00/data/ceres_data/9h4m_51864/05_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_51864/05_2026/9h4m_51864.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9h4m_51864/05_2026/9h4m_51864.map" model { file = "/net/cci-nas-00/data/ceres_data/9h4m_51864/05_2026/9h4m_51864.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9h4m_51864/05_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-2.1rc2-6044/lib/python3.9/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: 3.48, per 1000 atoms: 0.26 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: 1.27 Conformation dependent library (CDL) restraints added in 589.7 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: 1.91 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: 3.50 Time building geometry restraints manager: 1.70 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=" N ASP A 672 " pdb=" CA ASP A 672 " ideal model delta sigma weight residual 1.459 1.492 -0.033 1.52e-02 4.33e+03 4.72e+00 bond pdb=" CA LYS A 536 " pdb=" C LYS A 536 " ideal model delta sigma weight residual 1.523 1.548 -0.025 1.19e-02 7.06e+03 4.35e+00 bond pdb=" N VAL A 713 " pdb=" CA VAL A 713 " ideal model delta sigma weight residual 1.461 1.482 -0.021 1.19e-02 7.06e+03 3.23e+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=" C PRO A 537 " pdb=" CA PRO A 537 " pdb=" CB PRO A 537 " ideal model delta sigma weight residual 111.56 118.30 -6.74 1.65e+00 3.67e-01 1.67e+01 angle pdb=" CB LYS A 880 " pdb=" CG LYS A 880 " pdb=" CD LYS A 880 " ideal model delta sigma weight residual 111.30 119.31 -8.01 2.30e+00 1.89e-01 1.21e+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: 2174 0.086 - 0.172: 79 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 2.46 2.24 0.22 2.00e-01 2.50e+01 1.20e+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 2.46 2.28 0.17 2.00e-01 2.50e+01 7.62e-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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.460 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: 16.510 Find NCS groups from input model: 0.050 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:1.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7167 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= 0.132 Angle : 0.797 72.872 19636 Z= 0.352 Chirality : 0.038 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 covalent geometry : bond 0.00304 (14123) covalent geometry : angle 0.79653 (19636) hydrogen bonds : bond 0.14961 ( 531) hydrogen bonds : angle 6.33210 ( 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 : 0.530 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: 0.1034 time to fit residues: 11.6031 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 : 0.451 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 794 GLN A 869 ASN A 990 ASN A1305 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.086701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.068032 restraints weight = 81885.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 68)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.069360 restraints weight = 51764.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.070095 restraints weight = 38206.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.070598 restraints weight = 32104.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.070835 restraints weight = 28809.836| |-----------------------------------------------------------------------------| r_work (final): 0.3887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7132 moved from start: 0.0797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 14123 Z= 0.125 Angle : 0.563 19.811 19636 Z= 0.293 Chirality : 0.037 0.292 2256 Planarity : 0.005 0.174 2021 Dihedral : 19.248 137.107 3270 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.49 % Favored : 95.43 % Rotamer: Outliers : 2.54 % Allowed : 20.51 % Favored : 76.95 % 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: -1.23 (0.22), residues: 1313 helix: 0.08 (0.21), residues: 597 sheet: -0.43 (0.58), residues: 77 loop : -1.75 (0.22), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 395 TYR 0.010 0.001 TYR A 136 PHE 0.008 0.001 PHE A1045 TRP 0.004 0.001 TRP A 464 HIS 0.003 0.001 HIS A 799 Details of bonding type rmsd covalent geometry : bond 0.00243 (14123) covalent geometry : angle 0.56279 (19636) hydrogen bonds : bond 0.04532 ( 531) hydrogen bonds : angle 5.10990 ( 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 99 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 69 time to evaluate : 0.456 Fit side-chains revert: symmetry clash REVERT: A 651 LEU cc_start: 0.9221 (OUTLIER) cc_final: 0.9010 (mt) REVERT: A 822 MET cc_start: 0.3074 (pmm) cc_final: 0.0931 (ppp) REVERT: A 1349 HIS cc_start: 0.6049 (m90) cc_final: 0.5682 (m170) outliers start: 30 outliers final: 8 residues processed: 92 average time/residue: 0.1002 time to fit residues: 14.7029 Evaluate side-chains 74 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 65 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 128 TYR Chi-restraints excluded: chain A residue 518 PHE Chi-restraints excluded: chain A residue 651 LEU 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: 0.8980 chunk 57 optimal weight: 2.9990 chunk 136 optimal weight: 0.9980 chunk 10 optimal weight: 0.0030 chunk 124 optimal weight: 2.9990 chunk 30 optimal weight: 6.9990 chunk 51 optimal weight: 1.9990 chunk 116 optimal weight: 4.9990 chunk 62 optimal weight: 3.9990 chunk 37 optimal weight: 10.0000 chunk 55 optimal weight: 2.9990 overall best weight: 1.3794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 354 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 = 0.4177 r_free = 0.4177 target = 0.086525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.067948 restraints weight = 81690.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 65)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.069161 restraints weight = 52808.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.069842 restraints weight = 39797.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 56)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.070308 restraints weight = 34022.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.070490 restraints weight = 30989.974| |-----------------------------------------------------------------------------| r_work (final): 0.3881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7100 moved from start: 0.1188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.079 14123 Z= 0.112 Angle : 0.527 11.369 19636 Z= 0.277 Chirality : 0.036 0.242 2256 Planarity : 0.005 0.135 2021 Dihedral : 19.192 138.486 3268 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.57 % Favored : 95.35 % Rotamer: Outliers : 2.88 % Allowed : 20.34 % Favored : 76.78 % 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: -1.11 (0.22), residues: 1313 helix: 0.15 (0.21), residues: 600 sheet: -0.68 (0.56), residues: 79 loop : -1.62 (0.23), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 832 TYR 0.015 0.001 TYR A 451 PHE 0.014 0.001 PHE A 98 TRP 0.003 0.001 TRP A 464 HIS 0.003 0.001 HIS A 641 Details of bonding type rmsd covalent geometry : bond 0.00243 (14123) covalent geometry : angle 0.52685 (19636) hydrogen bonds : bond 0.04085 ( 531) hydrogen bonds : angle 4.86509 ( 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 110 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 76 time to evaluate : 0.464 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 651 LEU cc_start: 0.9172 (OUTLIER) cc_final: 0.8934 (mt) REVERT: A 822 MET cc_start: 0.2942 (pmm) cc_final: 0.0813 (ppp) REVERT: A 828 LEU cc_start: -0.1391 (OUTLIER) cc_final: -0.1711 (mt) REVERT: A 1220 LEU cc_start: 0.6994 (OUTLIER) cc_final: 0.6359 (mt) outliers start: 34 outliers final: 12 residues processed: 101 average time/residue: 0.1078 time to fit residues: 16.6245 Evaluate side-chains 81 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 66 time to evaluate : 0.675 ------------------------------------------------------------------------------- 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 128 TYR Chi-restraints excluded: chain A residue 212 LEU 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 651 LEU Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 842 VAL Chi-restraints excluded: chain A residue 927 ILE Chi-restraints excluded: chain A residue 1220 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 87 optimal weight: 10.0000 chunk 25 optimal weight: 1.9990 chunk 123 optimal weight: 1.9990 chunk 4 optimal weight: 10.0000 chunk 89 optimal weight: 10.0000 chunk 5 optimal weight: 10.9990 chunk 32 optimal weight: 0.7980 chunk 57 optimal weight: 9.9990 chunk 99 optimal weight: 7.9990 chunk 19 optimal weight: 6.9990 chunk 55 optimal weight: 2.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 544 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 = 0.4126 r_free = 0.4126 target = 0.084437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.066030 restraints weight = 83220.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.067182 restraints weight = 51282.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 72)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.068049 restraints weight = 38250.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.068366 restraints weight = 31845.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.068639 restraints weight = 29036.658| |-----------------------------------------------------------------------------| r_work (final): 0.3828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7242 moved from start: 0.1717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 14123 Z= 0.168 Angle : 0.595 9.573 19636 Z= 0.313 Chirality : 0.038 0.228 2256 Planarity : 0.005 0.125 2021 Dihedral : 19.327 136.543 3268 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.64 % Favored : 94.29 % Rotamer: Outliers : 4.24 % Allowed : 21.27 % Favored : 74.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.19 (0.22), residues: 1313 helix: 0.07 (0.21), residues: 599 sheet: -0.60 (0.72), residues: 51 loop : -1.64 (0.22), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 395 TYR 0.014 0.002 TYR A 451 PHE 0.015 0.001 PHE A 704 TRP 0.004 0.001 TRP A 659 HIS 0.004 0.001 HIS A 167 Details of bonding type rmsd covalent geometry : bond 0.00363 (14123) covalent geometry : angle 0.59472 (19636) hydrogen bonds : bond 0.04693 ( 531) hydrogen bonds : angle 4.98836 ( 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 117 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 67 time to evaluate : 0.471 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 651 LEU cc_start: 0.9162 (OUTLIER) cc_final: 0.8930 (mt) REVERT: A 822 MET cc_start: 0.3145 (pmm) cc_final: 0.1128 (ppp) REVERT: A 1220 LEU cc_start: 0.7127 (OUTLIER) cc_final: 0.6455 (mt) outliers start: 50 outliers final: 32 residues processed: 106 average time/residue: 0.0965 time to fit residues: 16.4053 Evaluate side-chains 95 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 61 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 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 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 505 GLU Chi-restraints excluded: chain A residue 518 PHE Chi-restraints excluded: chain A residue 598 LEU Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain A residue 621 LEU Chi-restraints excluded: chain A residue 651 LEU Chi-restraints excluded: chain A residue 678 THR Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain A residue 842 VAL Chi-restraints excluded: chain A residue 857 LEU Chi-restraints excluded: chain A residue 866 LYS 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 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 1267 ASP Chi-restraints excluded: chain A residue 1314 THR Chi-restraints excluded: chain A residue 1362 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 18 optimal weight: 5.9990 chunk 57 optimal weight: 8.9990 chunk 44 optimal weight: 4.9990 chunk 35 optimal weight: 9.9990 chunk 54 optimal weight: 10.0000 chunk 95 optimal weight: 4.9990 chunk 133 optimal weight: 4.9990 chunk 17 optimal weight: 10.0000 chunk 110 optimal weight: 0.0870 chunk 131 optimal weight: 5.9990 chunk 36 optimal weight: 0.9990 overall best weight: 3.2166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 354 GLN A 698 HIS A 926 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.083538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.065025 restraints weight = 82944.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.066282 restraints weight = 52169.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.067107 restraints weight = 38492.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.067396 restraints weight = 32476.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.067700 restraints weight = 29803.320| |-----------------------------------------------------------------------------| r_work (final): 0.3815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7275 moved from start: 0.2096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 14123 Z= 0.173 Angle : 0.597 8.430 19636 Z= 0.314 Chirality : 0.039 0.235 2256 Planarity : 0.005 0.120 2021 Dihedral : 19.396 136.217 3268 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 12.60 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.26 % Favored : 94.67 % Rotamer: Outliers : 4.49 % Allowed : 21.78 % Favored : 73.73 % 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: -0.02 (0.21), residues: 599 sheet: -0.88 (0.63), residues: 65 loop : -1.66 (0.23), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 653 TYR 0.016 0.002 TYR A 451 PHE 0.016 0.001 PHE A 704 TRP 0.005 0.001 TRP A 476 HIS 0.004 0.001 HIS A 799 Details of bonding type rmsd covalent geometry : bond 0.00368 (14123) covalent geometry : angle 0.59682 (19636) hydrogen bonds : bond 0.04675 ( 531) hydrogen bonds : angle 5.01590 ( 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 116 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 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 212 LEU cc_start: 0.8472 (OUTLIER) cc_final: 0.8266 (pt) REVERT: A 651 LEU cc_start: 0.9151 (OUTLIER) cc_final: 0.8934 (mt) REVERT: A 822 MET cc_start: 0.3354 (pmm) cc_final: 0.1389 (ppp) REVERT: A 1220 LEU cc_start: 0.7112 (OUTLIER) cc_final: 0.6440 (mt) outliers start: 53 outliers final: 36 residues processed: 104 average time/residue: 0.0990 time to fit residues: 16.5711 Evaluate side-chains 97 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 58 time to evaluate : 0.438 ------------------------------------------------------------------------------- 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 199 ASN 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 389 LEU 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 619 ILE Chi-restraints excluded: chain A residue 621 LEU Chi-restraints excluded: chain A residue 651 LEU Chi-restraints excluded: chain A residue 678 THR Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain A residue 816 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 882 TYR Chi-restraints excluded: chain A residue 887 LEU Chi-restraints excluded: chain A residue 926 GLN Chi-restraints excluded: chain A residue 950 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 1299 ASP Chi-restraints excluded: chain A residue 1314 THR Chi-restraints excluded: chain A residue 1352 ILE Chi-restraints excluded: chain A residue 1362 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 88 optimal weight: 9.9990 chunk 8 optimal weight: 10.0000 chunk 95 optimal weight: 5.9990 chunk 130 optimal weight: 10.0000 chunk 55 optimal weight: 9.9990 chunk 78 optimal weight: 7.9990 chunk 82 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 123 optimal weight: 8.9990 chunk 2 optimal weight: 10.0000 chunk 23 optimal weight: 2.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 HIS ** A 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 402 GLN A 794 GLN A 805 GLN ** A 940 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.081078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.063143 restraints weight = 83988.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 65)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.064360 restraints weight = 53877.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.064874 restraints weight = 40222.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.065424 restraints weight = 34590.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 55)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.065568 restraints weight = 31463.074| |-----------------------------------------------------------------------------| r_work (final): 0.3748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7324 moved from start: 0.2683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 14123 Z= 0.272 Angle : 0.728 8.983 19636 Z= 0.382 Chirality : 0.043 0.299 2256 Planarity : 0.006 0.117 2021 Dihedral : 19.578 132.303 3268 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 16.83 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.63 % Favored : 93.30 % Rotamer: Outliers : 5.17 % Allowed : 22.46 % Favored : 72.37 % 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: -1.66 (0.22), residues: 1313 helix: -0.40 (0.20), residues: 600 sheet: -0.86 (0.59), residues: 64 loop : -1.80 (0.23), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 395 TYR 0.015 0.002 TYR A 812 PHE 0.032 0.002 PHE A 688 TRP 0.009 0.002 TRP A 659 HIS 0.006 0.002 HIS A 167 Details of bonding type rmsd covalent geometry : bond 0.00577 (14123) covalent geometry : angle 0.72847 (19636) hydrogen bonds : bond 0.05827 ( 531) hydrogen bonds : angle 5.41757 ( 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 119 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 58 time to evaluate : 0.458 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 212 LEU cc_start: 0.8555 (OUTLIER) cc_final: 0.8286 (pt) REVERT: A 651 LEU cc_start: 0.9125 (OUTLIER) cc_final: 0.8923 (mt) REVERT: A 822 MET cc_start: 0.3431 (pmm) cc_final: 0.1356 (ppp) REVERT: A 1220 LEU cc_start: 0.7199 (OUTLIER) cc_final: 0.6530 (mt) outliers start: 61 outliers final: 41 residues processed: 108 average time/residue: 0.1129 time to fit residues: 18.6847 Evaluate side-chains 103 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 59 time to evaluate : 0.469 ------------------------------------------------------------------------------- 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 393 LEU Chi-restraints excluded: chain A residue 409 SER Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain A residue 505 GLU Chi-restraints excluded: chain A residue 518 PHE Chi-restraints excluded: chain A residue 598 LEU Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain A residue 621 LEU Chi-restraints excluded: chain A residue 651 LEU Chi-restraints excluded: chain A residue 678 THR Chi-restraints excluded: chain A residue 741 VAL Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain A residue 816 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 887 LEU Chi-restraints excluded: chain A residue 892 ILE Chi-restraints excluded: chain A residue 895 ARG 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 1190 VAL 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 1267 ASP Chi-restraints excluded: chain A residue 1299 ASP Chi-restraints excluded: chain A residue 1314 THR Chi-restraints excluded: chain A residue 1352 ILE 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: 0.9990 chunk 57 optimal weight: 0.0050 chunk 110 optimal weight: 0.6980 chunk 88 optimal weight: 2.9990 chunk 93 optimal weight: 0.9980 chunk 69 optimal weight: 0.9990 chunk 112 optimal weight: 5.9990 chunk 129 optimal weight: 9.9990 chunk 6 optimal weight: 10.0000 chunk 53 optimal weight: 3.9990 chunk 130 optimal weight: 7.9990 overall best weight: 0.7398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 926 GLN A 940 ASN ** 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 = 0.4136 r_free = 0.4136 target = 0.085121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.066816 restraints weight = 81253.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 66)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.068234 restraints weight = 49640.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.069043 restraints weight = 36183.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.069292 restraints weight = 29972.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.069542 restraints weight = 26890.434| |-----------------------------------------------------------------------------| r_work (final): 0.3845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7171 moved from start: 0.2465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.076 14123 Z= 0.111 Angle : 0.569 8.642 19636 Z= 0.297 Chirality : 0.037 0.220 2256 Planarity : 0.004 0.109 2021 Dihedral : 19.269 139.710 3268 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.03 % Favored : 94.90 % Rotamer: Outliers : 3.14 % Allowed : 24.15 % Favored : 72.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.07 (0.23), residues: 1313 helix: 0.06 (0.21), residues: 605 sheet: -0.54 (0.64), residues: 63 loop : -1.48 (0.24), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 395 TYR 0.012 0.001 TYR A 451 PHE 0.022 0.001 PHE A 688 TRP 0.008 0.001 TRP A 476 HIS 0.004 0.001 HIS A 698 Details of bonding type rmsd covalent geometry : bond 0.00237 (14123) covalent geometry : angle 0.56905 (19636) hydrogen bonds : bond 0.04209 ( 531) hydrogen bonds : angle 4.87831 ( 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 109 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 72 time to evaluate : 0.458 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 212 LEU cc_start: 0.8523 (OUTLIER) cc_final: 0.8311 (pt) REVERT: A 651 LEU cc_start: 0.9056 (OUTLIER) cc_final: 0.8841 (mt) REVERT: A 822 MET cc_start: 0.3165 (pmm) cc_final: 0.1128 (ppp) outliers start: 37 outliers final: 28 residues processed: 100 average time/residue: 0.1076 time to fit residues: 16.4598 Evaluate side-chains 94 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 64 time to evaluate : 0.510 ------------------------------------------------------------------------------- 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 389 LEU Chi-restraints excluded: chain A residue 409 SER 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 651 LEU Chi-restraints excluded: chain A residue 678 THR Chi-restraints excluded: chain A residue 816 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 887 LEU Chi-restraints excluded: chain A residue 892 ILE Chi-restraints excluded: chain A residue 934 ILE 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 1352 ILE Chi-restraints excluded: chain A residue 1362 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 49 optimal weight: 5.9990 chunk 136 optimal weight: 0.9980 chunk 114 optimal weight: 9.9990 chunk 19 optimal weight: 7.9990 chunk 96 optimal weight: 3.9990 chunk 137 optimal weight: 0.0470 chunk 8 optimal weight: 10.0000 chunk 17 optimal weight: 8.9990 chunk 106 optimal weight: 7.9990 chunk 24 optimal weight: 10.0000 chunk 52 optimal weight: 6.9990 overall best weight: 3.6084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 265 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 = 0.4080 r_free = 0.4080 target = 0.082212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.063853 restraints weight = 82733.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.065082 restraints weight = 51679.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.065839 restraints weight = 38458.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.066154 restraints weight = 32454.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.066542 restraints weight = 29851.430| |-----------------------------------------------------------------------------| r_work (final): 0.3785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7305 moved from start: 0.2739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 14123 Z= 0.196 Angle : 0.639 9.128 19636 Z= 0.334 Chirality : 0.040 0.249 2256 Planarity : 0.005 0.106 2021 Dihedral : 19.392 135.762 3268 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 13.49 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.32 % Favored : 93.60 % Rotamer: Outliers : 3.90 % Allowed : 24.24 % Favored : 71.86 % 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: -1.26 (0.22), residues: 1313 helix: -0.12 (0.21), residues: 604 sheet: -0.72 (0.57), residues: 67 loop : -1.53 (0.24), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 395 TYR 0.012 0.002 TYR A 155 PHE 0.015 0.002 PHE A 704 TRP 0.006 0.002 TRP A 659 HIS 0.004 0.001 HIS A 167 Details of bonding type rmsd covalent geometry : bond 0.00418 (14123) covalent geometry : angle 0.63863 (19636) hydrogen bonds : bond 0.04896 ( 531) hydrogen bonds : angle 5.11268 ( 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 106 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 60 time to evaluate : 0.482 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 209 LYS cc_start: 0.4092 (OUTLIER) cc_final: 0.3847 (mppt) REVERT: A 212 LEU cc_start: 0.8550 (OUTLIER) cc_final: 0.8296 (pt) REVERT: A 651 LEU cc_start: 0.9114 (OUTLIER) cc_final: 0.8911 (mt) REVERT: A 822 MET cc_start: 0.3372 (pmm) cc_final: 0.1392 (ppp) outliers start: 46 outliers final: 34 residues processed: 95 average time/residue: 0.0985 time to fit residues: 14.9806 Evaluate side-chains 95 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 58 time to evaluate : 0.486 ------------------------------------------------------------------------------- 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 364 ASP Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 409 SER 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 651 LEU Chi-restraints excluded: chain A residue 678 THR Chi-restraints excluded: chain A residue 816 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 887 LEU Chi-restraints excluded: chain A residue 892 ILE Chi-restraints excluded: chain A residue 895 ARG Chi-restraints excluded: chain A residue 927 ILE Chi-restraints excluded: chain A residue 934 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 1299 ASP Chi-restraints excluded: chain A residue 1352 ILE Chi-restraints excluded: chain A residue 1362 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 103 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 110 optimal weight: 0.0060 chunk 7 optimal weight: 10.0000 chunk 29 optimal weight: 7.9990 chunk 18 optimal weight: 0.9980 chunk 46 optimal weight: 10.0000 chunk 127 optimal weight: 3.9990 chunk 43 optimal weight: 6.9990 chunk 14 optimal weight: 9.9990 chunk 42 optimal weight: 6.9990 overall best weight: 2.0002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 240 ASN A 255 ASN ** A 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1295 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.083699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.065488 restraints weight = 81428.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.066827 restraints weight = 50365.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.067598 restraints weight = 36825.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.067905 restraints weight = 30828.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.067976 restraints weight = 28143.273| |-----------------------------------------------------------------------------| r_work (final): 0.3812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7253 moved from start: 0.2746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 14123 Z= 0.130 Angle : 0.591 10.305 19636 Z= 0.307 Chirality : 0.038 0.266 2256 Planarity : 0.004 0.103 2021 Dihedral : 19.325 138.959 3268 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.26 % Favored : 94.67 % Rotamer: Outliers : 3.56 % Allowed : 24.58 % Favored : 71.86 % 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: -1.11 (0.23), residues: 1313 helix: -0.01 (0.21), residues: 604 sheet: -0.71 (0.67), residues: 53 loop : -1.42 (0.24), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 395 TYR 0.011 0.001 TYR A 451 PHE 0.009 0.001 PHE A 704 TRP 0.006 0.001 TRP A 476 HIS 0.003 0.001 HIS A 167 Details of bonding type rmsd covalent geometry : bond 0.00280 (14123) covalent geometry : angle 0.59141 (19636) hydrogen bonds : bond 0.04216 ( 531) hydrogen bonds : angle 4.94345 ( 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 103 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 61 time to evaluate : 0.472 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 209 LYS cc_start: 0.3970 (OUTLIER) cc_final: 0.3725 (mppt) REVERT: A 212 LEU cc_start: 0.8504 (OUTLIER) cc_final: 0.8247 (pt) REVERT: A 651 LEU cc_start: 0.9075 (OUTLIER) cc_final: 0.8865 (mt) REVERT: A 822 MET cc_start: 0.3363 (pmm) cc_final: 0.1413 (ppp) outliers start: 42 outliers final: 33 residues processed: 93 average time/residue: 0.1052 time to fit residues: 15.3692 Evaluate side-chains 96 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 60 time to evaluate : 0.481 ------------------------------------------------------------------------------- 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 364 ASP Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 409 SER 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 651 LEU Chi-restraints excluded: chain A residue 678 THR Chi-restraints excluded: chain A residue 816 LEU Chi-restraints excluded: chain A residue 842 VAL Chi-restraints excluded: chain A residue 854 ASN 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 887 LEU Chi-restraints excluded: chain A residue 892 ILE Chi-restraints excluded: chain A residue 895 ARG Chi-restraints excluded: chain A residue 934 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 1299 ASP Chi-restraints excluded: chain A residue 1352 ILE Chi-restraints excluded: chain A residue 1362 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 109 optimal weight: 0.1980 chunk 77 optimal weight: 0.9990 chunk 87 optimal weight: 6.9990 chunk 115 optimal weight: 5.9990 chunk 136 optimal weight: 0.8980 chunk 101 optimal weight: 0.6980 chunk 73 optimal weight: 8.9990 chunk 69 optimal weight: 4.9990 chunk 28 optimal weight: 7.9990 chunk 127 optimal weight: 8.9990 chunk 5 optimal weight: 10.0000 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.084385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.065992 restraints weight = 81639.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 68)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.067391 restraints weight = 50603.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.068001 restraints weight = 37076.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.068608 restraints weight = 31377.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.068822 restraints weight = 28153.141| |-----------------------------------------------------------------------------| r_work (final): 0.3830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7222 moved from start: 0.2810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 14123 Z= 0.121 Angle : 0.580 10.388 19636 Z= 0.302 Chirality : 0.038 0.260 2256 Planarity : 0.004 0.100 2021 Dihedral : 19.246 140.908 3268 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.79 % Favored : 94.14 % Rotamer: Outliers : 3.14 % Allowed : 25.08 % Favored : 71.78 % 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: -0.98 (0.23), residues: 1313 helix: 0.07 (0.21), residues: 605 sheet: -0.65 (0.55), residues: 78 loop : -1.33 (0.25), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 395 TYR 0.011 0.001 TYR A 451 PHE 0.008 0.001 PHE A1045 TRP 0.005 0.001 TRP A 464 HIS 0.003 0.001 HIS A 641 Details of bonding type rmsd covalent geometry : bond 0.00260 (14123) covalent geometry : angle 0.57954 (19636) hydrogen bonds : bond 0.04094 ( 531) hydrogen bonds : angle 4.88467 ( 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 104 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 67 time to evaluate : 0.483 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 209 LYS cc_start: 0.3906 (OUTLIER) cc_final: 0.3674 (mppt) REVERT: A 212 LEU cc_start: 0.8445 (OUTLIER) cc_final: 0.8182 (pt) REVERT: A 822 MET cc_start: 0.3257 (pmm) cc_final: 0.1098 (ppp) outliers start: 37 outliers final: 31 residues processed: 95 average time/residue: 0.1058 time to fit residues: 15.9418 Evaluate side-chains 97 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 64 time to evaluate : 0.461 ------------------------------------------------------------------------------- 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 389 LEU Chi-restraints excluded: chain A residue 409 SER 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 678 THR Chi-restraints excluded: chain A residue 816 LEU Chi-restraints excluded: chain A residue 842 VAL Chi-restraints excluded: chain A residue 849 ASP 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 887 LEU Chi-restraints excluded: chain A residue 892 ILE Chi-restraints excluded: chain A residue 895 ARG 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 1299 ASP Chi-restraints excluded: chain A residue 1352 ILE Chi-restraints excluded: chain A residue 1362 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 61 optimal weight: 10.0000 chunk 123 optimal weight: 3.9990 chunk 106 optimal weight: 2.9990 chunk 85 optimal weight: 0.9980 chunk 75 optimal weight: 8.9990 chunk 2 optimal weight: 10.0000 chunk 27 optimal weight: 9.9990 chunk 47 optimal weight: 0.9990 chunk 25 optimal weight: 0.8980 chunk 63 optimal weight: 5.9990 chunk 78 optimal weight: 0.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.084827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.066486 restraints weight = 82240.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.067831 restraints weight = 50599.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.068664 restraints weight = 36869.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.068934 restraints weight = 30831.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 66)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.069330 restraints weight = 28309.984| |-----------------------------------------------------------------------------| r_work (final): 0.3840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7200 moved from start: 0.2873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.072 14123 Z= 0.116 Angle : 0.575 11.196 19636 Z= 0.297 Chirality : 0.038 0.260 2256 Planarity : 0.004 0.097 2021 Dihedral : 19.187 142.691 3268 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.26 % Favored : 94.67 % Rotamer: Outliers : 2.88 % Allowed : 25.34 % Favored : 71.78 % 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: -0.88 (0.23), residues: 1313 helix: 0.19 (0.21), residues: 600 sheet: -0.11 (0.54), residues: 81 loop : -1.40 (0.25), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 395 TYR 0.011 0.001 TYR A 451 PHE 0.008 0.001 PHE A1045 TRP 0.005 0.001 TRP A 464 HIS 0.003 0.001 HIS A 641 Details of bonding type rmsd covalent geometry : bond 0.00250 (14123) covalent geometry : angle 0.57546 (19636) hydrogen bonds : bond 0.03958 ( 531) hydrogen bonds : angle 4.82352 ( 1438) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2961.12 seconds wall clock time: 51 minutes 52.37 seconds (3112.37 seconds total)