Starting phenix.real_space_refine on Fri Jul 3 12:02:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9h4m_51864/07_2026/9h4m_51864.cif Found real_map, /net/cci-nas-00/data/ceres_data/9h4m_51864/07_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 { model { file = "/net/cci-nas-00/data/ceres_data/9h4m_51864/07_2026/9h4m_51864.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9h4m_51864/07_2026/9h4m_51864.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9h4m_51864/07_2026/9h4m_51864.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9h4m_51864/07_2026/9h4m_51864.map" } 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-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13599 Number of models: 1 Model: "" Number of chains: 5 Chain: "B" Number of atoms: 2105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 2105 Classifications: {'RNA': 98} Modifications used: {'5*END': 1, 'rna2p_pur': 6, 'rna2p_pyr': 6, 'rna3p_pur': 55, 'rna3p_pyr': 31} Link IDs: {'rna2p': 11, 'rna3p': 86} Chain: "C" Number of atoms: 197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 197 Classifications: {'DNA': 10} Link IDs: {'rna3p': 9} Chain: "D" Number of atoms: 173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 173 Classifications: {'DNA': 8} Link IDs: {'rna3p': 7} Chain: "A" Number of atoms: 10784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1321, 10784 Classifications: {'peptide': 1321} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 35, 'TRANS': 1285} Chain breaks: 3 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "F" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 340 Classifications: {'DNA': 17} Link IDs: {'rna3p': 16} Time building chain proxies: 2.99, per 1000 atoms: 0.22 Number of scatterers: 13599 At special positions: 0 Unit cell: (113.05, 128.35, 134.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 21 16.00 P 132 15.00 O 2907 8.00 N 2379 7.00 C 8160 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.00 Conformation dependent library (CDL) restraints added in 423.2 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: 1.75 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: 3.20 Time building geometry restraints manager: 1.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2520 1.33 - 1.45: 3977 1.45 - 1.57: 7324 1.57 - 1.69: 261 1.69 - 1.82: 41 Bond restraints: 14123 Sorted by residual: bond pdb=" C LYS A 536 " pdb=" N PRO A 537 " ideal model delta sigma weight residual 1.334 1.438 -0.104 2.34e-02 1.83e+03 1.98e+01 bond pdb=" CB PRO A 537 " pdb=" CG PRO A 537 " ideal model delta sigma weight residual 1.492 1.309 0.183 5.00e-02 4.00e+02 1.34e+01 bond pdb=" C3' DT F 25 " pdb=" C2' DT F 25 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.24e+01 bond pdb=" C3' DT F 35 " pdb=" C2' DT F 35 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.18e+01 bond pdb=" C2' DT F 21 " pdb=" C1' DT F 21 " ideal model delta sigma weight residual 1.518 1.548 -0.030 1.00e-02 1.00e+04 9.04e+00 ... (remaining 14118 not shown) Histogram of bond angle deviations from ideal: 0.00 - 14.57: 19634 14.57 - 29.15: 1 29.15 - 43.72: 0 43.72 - 58.30: 0 58.30 - 72.87: 1 Bond angle restraints: 19636 Sorted by residual: angle pdb=" C LYS A 536 " pdb=" N PRO A 537 " pdb=" CD PRO A 537 " ideal model delta sigma weight residual 125.00 52.13 72.87 4.10e+00 5.95e-02 3.16e+02 angle pdb=" CA PRO A 537 " pdb=" N PRO A 537 " pdb=" CD PRO A 537 " ideal model delta sigma weight residual 112.00 95.33 16.67 1.40e+00 5.10e-01 1.42e+02 angle pdb=" C LYS A 536 " pdb=" N PRO A 537 " pdb=" CA PRO A 537 " ideal model delta sigma weight residual 119.84 131.77 -11.93 1.25e+00 6.40e-01 9.10e+01 angle pdb=" C1' C B 70 " pdb=" N1 C B 70 " pdb=" C2 C B 70 " ideal model delta sigma weight residual 118.80 124.77 -5.97 1.10e+00 8.26e-01 2.94e+01 angle pdb=" N1 C B 70 " pdb=" C2 C B 70 " pdb=" O2 C B 70 " ideal model delta sigma weight residual 118.90 121.76 -2.86 6.00e-01 2.78e+00 2.28e+01 ... (remaining 19631 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.49: 7662 27.49 - 54.97: 734 54.97 - 82.46: 169 82.46 - 109.95: 12 109.95 - 137.43: 1 Dihedral angle restraints: 8578 sinusoidal: 4696 harmonic: 3882 Sorted by residual: dihedral pdb=" O4' C B 70 " pdb=" C1' C B 70 " pdb=" N1 C B 70 " pdb=" C2 C B 70 " ideal model delta sinusoidal sigma weight residual 200.00 62.57 137.43 1 1.50e+01 4.44e-03 7.41e+01 dihedral pdb=" O4' U B 56 " pdb=" C1' U B 56 " pdb=" N1 U B 56 " pdb=" C2 U B 56 " ideal model delta sinusoidal sigma weight residual -128.00 -25.19 -102.81 1 1.70e+01 3.46e-03 4.06e+01 dihedral pdb=" C PRO A 537 " pdb=" N PRO A 537 " pdb=" CA PRO A 537 " pdb=" CB PRO A 537 " ideal model delta harmonic sigma weight residual -120.70 -131.07 10.37 0 2.50e+00 1.60e-01 1.72e+01 ... (remaining 8575 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.086: 2165 0.086 - 0.172: 88 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.920 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: 0.020 Extract box with map and model: 0.270 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 14.980 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7060 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.183 14123 Z= 0.222 Angle : 0.814 72.872 19636 Z= 0.455 Chirality : 0.040 0.431 2256 Planarity : 0.006 0.204 2021 Dihedral : 20.023 137.433 6066 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 13.29 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.95 % Favored : 94.97 % Rotamer: Outliers : 0.25 % Allowed : 22.88 % Favored : 76.86 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.38 (0.22), residues: 1313 helix: -0.05 (0.22), residues: 582 sheet: -0.44 (0.60), residues: 77 loop : -1.81 (0.22), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 905 TYR 0.009 0.001 TYR A 136 PHE 0.011 0.001 PHE A 518 TRP 0.006 0.001 TRP A 883 HIS 0.004 0.001 HIS A 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.22 (14123) covalent geometry : angle 0.81393 / 0.45 (19636) hydrogen bonds : bond 0.14961 / 14.69 ( 531) hydrogen bonds : angle 6.33210 / 8.12 ( 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 : 0.495 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: 0.1028 time to fit residues: 11.6357 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 : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain A residue 842 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 9.9990 chunk 122 optimal weight: 0.0170 chunk 91 optimal weight: 9.9990 chunk 55 optimal weight: 7.9990 overall best weight: 1.3622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 794 GLN A 869 ASN ** A 940 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 990 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.086804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.068255 restraints weight = 81615.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 62)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.069577 restraints weight = 50743.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.070189 restraints weight = 37612.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.070672 restraints weight = 31776.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.070784 restraints weight = 29051.990| |-----------------------------------------------------------------------------| r_work (final): 0.3884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7031 moved from start: 0.0616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 14123 Z= 0.125 Angle : 0.578 25.673 19636 Z= 0.310 Chirality : 0.039 0.284 2256 Planarity : 0.006 0.187 2021 Dihedral : 19.370 140.108 3270 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.42 % Favored : 95.51 % Rotamer: Outliers : 2.12 % Allowed : 20.59 % Favored : 77.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.29 (0.22), residues: 1313 helix: 0.02 (0.21), residues: 597 sheet: -0.69 (0.57), residues: 81 loop : -1.75 (0.22), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 671 TYR 0.010 0.001 TYR A 362 PHE 0.011 0.001 PHE A 290 TRP 0.005 0.001 TRP A 464 HIS 0.003 0.001 HIS A 167 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.12 (14123) covalent geometry : angle 0.57808 / 0.31 (19636) hydrogen bonds : bond 0.05245 / 5.03 ( 531) hydrogen bonds : angle 5.27492 / 6.68 ( 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 94 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 69 time to evaluate : 0.400 Fit side-chains revert: symmetry clash REVERT: A 448 ILE cc_start: 0.6479 (OUTLIER) cc_final: 0.6235 (tt) REVERT: A 822 MET cc_start: 0.3304 (pmm) cc_final: 0.3013 (pmm) outliers start: 25 outliers final: 9 residues processed: 89 average time/residue: 0.1050 time to fit residues: 14.6208 Evaluate side-chains 73 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 63 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 31 LYS Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 518 PHE Chi-restraints excluded: chain A residue 678 THR Chi-restraints excluded: chain A residue 842 VAL Chi-restraints excluded: chain A residue 997 LEU Chi-restraints excluded: chain A residue 1266 LEU Chi-restraints excluded: chain A residue 1314 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 48 optimal weight: 0.9980 chunk 57 optimal weight: 0.5980 chunk 136 optimal weight: 2.9990 chunk 10 optimal weight: 0.0030 chunk 124 optimal weight: 6.9990 chunk 30 optimal weight: 9.9990 chunk 51 optimal weight: 1.9990 chunk 116 optimal weight: 2.9990 chunk 62 optimal weight: 0.0770 chunk 37 optimal weight: 2.9990 chunk 55 optimal weight: 10.0000 overall best weight: 0.7350 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 354 GLN A 794 GLN ** A1044 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1305 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.087259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.068713 restraints weight = 81588.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.069906 restraints weight = 50963.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 70)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.070753 restraints weight = 37996.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.071085 restraints weight = 31881.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.071390 restraints weight = 29030.006| |-----------------------------------------------------------------------------| r_work (final): 0.3904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7002 moved from start: 0.0971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.098 14123 Z= 0.105 Angle : 0.513 13.220 19636 Z= 0.284 Chirality : 0.037 0.230 2256 Planarity : 0.005 0.149 2021 Dihedral : 19.307 144.100 3270 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.04 % Favored : 95.89 % Rotamer: Outliers : 2.37 % Allowed : 21.27 % Favored : 76.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.14 (0.22), residues: 1313 helix: 0.13 (0.21), residues: 598 sheet: -0.56 (0.57), residues: 79 loop : -1.65 (0.22), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 765 TYR 0.018 0.001 TYR A 451 PHE 0.013 0.001 PHE A 98 TRP 0.004 0.001 TRP A 464 HIS 0.003 0.001 HIS A 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00207 / 0.10 (14123) covalent geometry : angle 0.51333 / 0.28 (19636) hydrogen bonds : bond 0.04447 / 4.26 ( 531) hydrogen bonds : angle 4.95100 / 6.29 ( 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 101 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 73 time to evaluate : 0.457 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 395 ARG cc_start: 0.7307 (mpp80) cc_final: 0.6933 (mtm-85) REVERT: A 822 MET cc_start: 0.3233 (pmm) cc_final: 0.1162 (ppp) outliers start: 28 outliers final: 12 residues processed: 95 average time/residue: 0.1041 time to fit residues: 15.2858 Evaluate side-chains 78 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 66 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 370 GLU Chi-restraints excluded: chain A residue 518 PHE Chi-restraints excluded: chain A residue 795 ILE Chi-restraints excluded: chain A residue 842 VAL Chi-restraints excluded: chain A residue 927 ILE Chi-restraints excluded: chain A residue 997 LEU Chi-restraints excluded: chain A residue 1264 HIS Chi-restraints excluded: chain A residue 1266 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 87 optimal weight: 9.9990 chunk 25 optimal weight: 5.9990 chunk 123 optimal weight: 4.9990 chunk 4 optimal weight: 20.0000 chunk 89 optimal weight: 6.9990 chunk 5 optimal weight: 20.0000 chunk 32 optimal weight: 1.9990 chunk 57 optimal weight: 9.9990 chunk 99 optimal weight: 4.9990 chunk 19 optimal weight: 8.9990 chunk 55 optimal weight: 6.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 544 GLN A 794 GLN ** A 940 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 = 0.4106 r_free = 0.4106 target = 0.083282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.065430 restraints weight = 83310.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.066385 restraints weight = 54436.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.067312 restraints weight = 40858.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.067508 restraints weight = 34792.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.067791 restraints weight = 31804.339| |-----------------------------------------------------------------------------| r_work (final): 0.3808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7115 moved from start: 0.1522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.091 14123 Z= 0.231 Angle : 0.667 12.041 19636 Z= 0.362 Chirality : 0.042 0.224 2256 Planarity : 0.006 0.142 2021 Dihedral : 19.537 139.907 3268 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 14.68 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.02 % Favored : 93.91 % Rotamer: Outliers : 4.58 % Allowed : 20.34 % Favored : 75.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.47 (0.22), residues: 1313 helix: -0.15 (0.21), residues: 598 sheet: -0.73 (0.70), residues: 51 loop : -1.79 (0.22), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 765 TYR 0.021 0.002 TYR A 136 PHE 0.022 0.002 PHE A 704 TRP 0.008 0.002 TRP A 659 HIS 0.006 0.002 HIS A 930 Details of bonding type rmsd/Z covalent geometry : bond 0.00474 / 0.23 (14123) covalent geometry : angle 0.66656 / 0.36 (19636) hydrogen bonds : bond 0.05634 / 5.48 ( 531) hydrogen bonds : angle 5.24997 / 6.65 ( 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 119 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 65 time to evaluate : 0.480 Fit side-chains revert: symmetry clash REVERT: A 212 LEU cc_start: 0.8450 (OUTLIER) cc_final: 0.8190 (pt) REVERT: A 395 ARG cc_start: 0.7539 (mpp80) cc_final: 0.7266 (mtm110) REVERT: A 822 MET cc_start: 0.3286 (pmm) cc_final: 0.1233 (ppp) REVERT: A 1220 LEU cc_start: 0.7145 (OUTLIER) cc_final: 0.6487 (mt) outliers start: 54 outliers final: 30 residues processed: 109 average time/residue: 0.0954 time to fit residues: 16.3033 Evaluate side-chains 94 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 62 time to evaluate : 0.506 ------------------------------------------------------------------------------- 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 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 619 ILE Chi-restraints excluded: chain A residue 621 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 847 LEU Chi-restraints excluded: chain A residue 852 ILE Chi-restraints excluded: chain A residue 857 LEU Chi-restraints excluded: chain A residue 892 ILE Chi-restraints excluded: chain A residue 927 ILE Chi-restraints excluded: chain A residue 997 LEU Chi-restraints excluded: chain A residue 1048 THR Chi-restraints excluded: chain A residue 1220 LEU Chi-restraints excluded: chain A residue 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 18 optimal weight: 2.9990 chunk 57 optimal weight: 4.9990 chunk 44 optimal weight: 0.8980 chunk 35 optimal weight: 5.9990 chunk 54 optimal weight: 1.9990 chunk 95 optimal weight: 3.9990 chunk 133 optimal weight: 5.9990 chunk 17 optimal weight: 4.9990 chunk 110 optimal weight: 0.3980 chunk 131 optimal weight: 9.9990 chunk 36 optimal weight: 10.0000 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 885 GLN A 926 GLN ** A 940 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.084555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.066047 restraints weight = 82513.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.067385 restraints weight = 50814.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.068214 restraints weight = 37273.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.068502 restraints weight = 30967.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 61)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.068878 restraints weight = 28533.154| |-----------------------------------------------------------------------------| r_work (final): 0.3835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7093 moved from start: 0.1548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.090 14123 Z= 0.132 Angle : 0.564 12.012 19636 Z= 0.306 Chirality : 0.039 0.235 2256 Planarity : 0.005 0.132 2021 Dihedral : 19.496 143.370 3268 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.03 % Favored : 94.90 % Rotamer: Outliers : 3.39 % Allowed : 21.78 % Favored : 74.83 % 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: -1.22 (0.22), residues: 1313 helix: 0.04 (0.21), residues: 599 sheet: -0.75 (0.63), residues: 65 loop : -1.64 (0.23), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 765 TYR 0.015 0.001 TYR A 451 PHE 0.011 0.001 PHE A 704 TRP 0.007 0.001 TRP A 476 HIS 0.004 0.001 HIS A 641 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.13 (14123) covalent geometry : angle 0.56389 / 0.31 (19636) hydrogen bonds : bond 0.04752 / 4.46 ( 531) hydrogen bonds : angle 5.05363 / 6.41 ( 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 107 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 67 time to evaluate : 0.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 822 MET cc_start: 0.2953 (pmm) cc_final: 0.0765 (ppp) REVERT: A 828 LEU cc_start: -0.1144 (OUTLIER) cc_final: -0.1491 (mt) REVERT: A 1220 LEU cc_start: 0.7100 (OUTLIER) cc_final: 0.6504 (mt) outliers start: 40 outliers final: 29 residues processed: 97 average time/residue: 0.0871 time to fit residues: 13.6650 Evaluate side-chains 91 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 60 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 128 TYR Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 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 518 PHE Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain A residue 621 LEU Chi-restraints excluded: chain A residue 741 VAL Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 829 ASP Chi-restraints excluded: chain A residue 842 VAL Chi-restraints excluded: chain A residue 861 ASP Chi-restraints excluded: chain A residue 892 ILE Chi-restraints excluded: chain A residue 927 ILE Chi-restraints excluded: chain A residue 997 LEU Chi-restraints excluded: chain A residue 1048 THR Chi-restraints excluded: chain A residue 1220 LEU Chi-restraints excluded: chain A residue 1236 LEU Chi-restraints excluded: chain A residue 1248 SER Chi-restraints excluded: chain A residue 1257 LEU Chi-restraints excluded: chain A residue 1264 HIS Chi-restraints excluded: chain A residue 1266 LEU Chi-restraints excluded: chain A residue 1267 ASP Chi-restraints excluded: chain A residue 1299 ASP Chi-restraints excluded: chain A residue 1314 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 88 optimal weight: 0.7980 chunk 8 optimal weight: 20.0000 chunk 95 optimal weight: 5.9990 chunk 130 optimal weight: 5.9990 chunk 55 optimal weight: 10.0000 chunk 78 optimal weight: 1.9990 chunk 82 optimal weight: 0.9990 chunk 0 optimal weight: 20.0000 chunk 123 optimal weight: 8.9990 chunk 2 optimal weight: 20.0000 chunk 23 optimal weight: 0.9980 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 940 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.084453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.066132 restraints weight = 81003.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.067186 restraints weight = 49951.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.068220 restraints weight = 36923.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.068520 restraints weight = 30834.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.068588 restraints weight = 28223.373| |-----------------------------------------------------------------------------| r_work (final): 0.3836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7113 moved from start: 0.1660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.087 14123 Z= 0.131 Angle : 0.560 10.277 19636 Z= 0.303 Chirality : 0.039 0.245 2256 Planarity : 0.005 0.124 2021 Dihedral : 19.481 144.014 3268 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.56 % Favored : 94.36 % Rotamer: Outliers : 3.73 % Allowed : 21.95 % Favored : 74.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.12 (0.22), residues: 1313 helix: 0.10 (0.21), residues: 599 sheet: -0.45 (0.56), residues: 76 loop : -1.61 (0.24), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 395 TYR 0.014 0.001 TYR A 451 PHE 0.011 0.001 PHE A 704 TRP 0.007 0.001 TRP A 476 HIS 0.004 0.001 HIS A 641 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.13 (14123) covalent geometry : angle 0.56021 / 0.30 (19636) hydrogen bonds : bond 0.04675 / 4.37 ( 531) hydrogen bonds : angle 4.99309 / 6.34 ( 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 106 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 62 time to evaluate : 0.502 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 212 LEU cc_start: 0.8414 (OUTLIER) cc_final: 0.8188 (pt) REVERT: A 822 MET cc_start: 0.3068 (pmm) cc_final: 0.0951 (ppp) REVERT: A 828 LEU cc_start: -0.1023 (OUTLIER) cc_final: -0.1379 (mt) REVERT: A 1220 LEU cc_start: 0.7101 (OUTLIER) cc_final: 0.6481 (mt) outliers start: 44 outliers final: 30 residues processed: 94 average time/residue: 0.1002 time to fit residues: 15.1056 Evaluate side-chains 92 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 59 time to evaluate : 0.534 ------------------------------------------------------------------------------- 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 370 GLU Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 395 ARG 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 741 VAL Chi-restraints excluded: chain A residue 816 LEU Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 829 ASP Chi-restraints excluded: chain A residue 842 VAL Chi-restraints excluded: chain A residue 857 LEU Chi-restraints excluded: chain A residue 861 ASP Chi-restraints excluded: chain A residue 892 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 1299 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 60 optimal weight: 8.9990 chunk 57 optimal weight: 4.9990 chunk 110 optimal weight: 0.1980 chunk 88 optimal weight: 4.9990 chunk 93 optimal weight: 2.9990 chunk 69 optimal weight: 0.3980 chunk 112 optimal weight: 8.9990 chunk 129 optimal weight: 10.0000 chunk 6 optimal weight: 20.0000 chunk 53 optimal weight: 2.9990 chunk 130 optimal weight: 0.9980 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 940 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.085232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.066844 restraints weight = 81398.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.068160 restraints weight = 49777.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 67)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.068976 restraints weight = 36496.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.069470 restraints weight = 30331.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.069620 restraints weight = 27238.074| |-----------------------------------------------------------------------------| r_work (final): 0.3852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7078 moved from start: 0.1741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.084 14123 Z= 0.113 Angle : 0.544 10.411 19636 Z= 0.293 Chirality : 0.038 0.218 2256 Planarity : 0.004 0.118 2021 Dihedral : 19.432 145.272 3268 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.72 % Favored : 95.20 % Rotamer: Outliers : 3.56 % Allowed : 22.03 % Favored : 74.41 % 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: -1.06 (0.22), residues: 1313 helix: 0.09 (0.21), residues: 605 sheet: -0.49 (0.57), residues: 78 loop : -1.51 (0.24), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 395 TYR 0.013 0.001 TYR A 451 PHE 0.009 0.001 PHE A 688 TRP 0.006 0.001 TRP A 476 HIS 0.004 0.001 HIS A 641 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.11 (14123) covalent geometry : angle 0.54356 / 0.29 (19636) hydrogen bonds : bond 0.04425 / 4.11 ( 531) hydrogen bonds : angle 4.88508 / 6.22 ( 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 105 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 63 time to evaluate : 0.510 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 212 LEU cc_start: 0.8375 (OUTLIER) cc_final: 0.8102 (pt) REVERT: A 822 MET cc_start: 0.3006 (pmm) cc_final: 0.0814 (ppp) REVERT: A 828 LEU cc_start: -0.1211 (OUTLIER) cc_final: -0.1542 (mt) outliers start: 42 outliers final: 32 residues processed: 97 average time/residue: 0.0988 time to fit residues: 15.4873 Evaluate side-chains 96 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 62 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 31 LYS Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 128 TYR Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 370 GLU Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 395 ARG 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 564 LEU 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 678 THR Chi-restraints excluded: chain A residue 816 LEU Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 829 ASP Chi-restraints excluded: chain A residue 842 VAL Chi-restraints excluded: chain A residue 857 LEU Chi-restraints excluded: chain A residue 861 ASP Chi-restraints excluded: chain A residue 892 ILE Chi-restraints excluded: chain A residue 950 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 1314 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 49 optimal weight: 2.9990 chunk 136 optimal weight: 0.8980 chunk 114 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 96 optimal weight: 8.9990 chunk 137 optimal weight: 9.9990 chunk 8 optimal weight: 20.0000 chunk 17 optimal weight: 7.9990 chunk 106 optimal weight: 8.9990 chunk 24 optimal weight: 7.9990 chunk 52 optimal weight: 1.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 940 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.084282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.066117 restraints weight = 80693.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 67)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.067457 restraints weight = 49780.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.068056 restraints weight = 36269.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 59)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.068643 restraints weight = 30628.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.068842 restraints weight = 27571.866| |-----------------------------------------------------------------------------| r_work (final): 0.3825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7123 moved from start: 0.1949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 14123 Z= 0.148 Angle : 0.566 9.015 19636 Z= 0.307 Chirality : 0.039 0.218 2256 Planarity : 0.005 0.115 2021 Dihedral : 19.461 143.386 3268 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.17 % Favored : 93.75 % Rotamer: Outliers : 3.81 % Allowed : 22.46 % 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: -1.11 (0.22), residues: 1313 helix: 0.06 (0.21), residues: 604 sheet: -0.50 (0.57), residues: 78 loop : -1.56 (0.24), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 653 TYR 0.014 0.001 TYR A 451 PHE 0.016 0.001 PHE A 704 TRP 0.004 0.001 TRP A 659 HIS 0.004 0.001 HIS A 641 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.15 (14123) covalent geometry : angle 0.56594 / 0.31 (19636) hydrogen bonds : bond 0.04710 / 4.36 ( 531) hydrogen bonds : angle 4.93471 / 6.28 ( 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: 45 poor density : 61 time to evaluate : 0.534 Fit side-chains revert: symmetry clash REVERT: A 212 LEU cc_start: 0.8432 (OUTLIER) cc_final: 0.8162 (pt) REVERT: A 822 MET cc_start: 0.3082 (pmm) cc_final: 0.0894 (ppp) REVERT: A 1220 LEU cc_start: 0.7134 (OUTLIER) cc_final: 0.6465 (mt) outliers start: 45 outliers final: 34 residues processed: 96 average time/residue: 0.1030 time to fit residues: 16.4780 Evaluate side-chains 93 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 57 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 31 LYS Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 128 TYR Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 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 560 THR Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain A residue 621 LEU Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain A residue 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 892 ILE Chi-restraints excluded: chain A residue 950 ILE Chi-restraints excluded: chain A residue 1048 THR Chi-restraints excluded: chain A residue 1220 LEU Chi-restraints excluded: chain A residue 1236 LEU Chi-restraints excluded: chain A residue 1248 SER Chi-restraints excluded: chain A residue 1257 LEU Chi-restraints excluded: chain A residue 1264 HIS Chi-restraints excluded: chain A residue 1266 LEU Chi-restraints excluded: chain A residue 1267 ASP Chi-restraints excluded: chain A residue 1299 ASP Chi-restraints excluded: chain A residue 1314 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 103 optimal weight: 0.7980 chunk 54 optimal weight: 7.9990 chunk 110 optimal weight: 1.9990 chunk 7 optimal weight: 20.0000 chunk 29 optimal weight: 8.9990 chunk 18 optimal weight: 3.9990 chunk 46 optimal weight: 0.9990 chunk 127 optimal weight: 9.9990 chunk 43 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 940 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.085254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.066972 restraints weight = 80952.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.068322 restraints weight = 49931.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.068886 restraints weight = 36689.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.069344 restraints weight = 31167.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.069424 restraints weight = 28183.865| |-----------------------------------------------------------------------------| r_work (final): 0.3853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7093 moved from start: 0.1978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.083 14123 Z= 0.107 Angle : 0.547 12.173 19636 Z= 0.294 Chirality : 0.038 0.219 2256 Planarity : 0.004 0.111 2021 Dihedral : 19.396 145.873 3268 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.95 % Favored : 94.97 % Rotamer: Outliers : 3.22 % Allowed : 23.14 % Favored : 73.64 % 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: -1.01 (0.23), residues: 1313 helix: 0.09 (0.21), residues: 609 sheet: -0.35 (0.52), residues: 90 loop : -1.48 (0.25), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 691 TYR 0.012 0.001 TYR A 451 PHE 0.008 0.001 PHE A 704 TRP 0.005 0.001 TRP A 476 HIS 0.005 0.001 HIS A 641 Details of bonding type rmsd/Z covalent geometry : bond 0.00219 / 0.11 (14123) covalent geometry : angle 0.54685 / 0.29 (19636) hydrogen bonds : bond 0.04316 / 3.93 ( 531) hydrogen bonds : angle 4.83746 / 6.19 ( 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 102 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 64 time to evaluate : 0.453 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 212 LEU cc_start: 0.8404 (OUTLIER) cc_final: 0.8139 (pt) REVERT: A 822 MET cc_start: 0.3220 (pmm) cc_final: 0.1229 (ppp) outliers start: 38 outliers final: 33 residues processed: 91 average time/residue: 0.0931 time to fit residues: 13.6861 Evaluate side-chains 92 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 58 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 31 LYS Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 128 TYR Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 505 GLU Chi-restraints excluded: chain A residue 518 PHE Chi-restraints excluded: chain A residue 560 THR Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain A residue 621 LEU Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain A residue 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 892 ILE Chi-restraints excluded: chain A residue 927 ILE Chi-restraints excluded: chain A residue 950 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 1299 ASP Chi-restraints excluded: chain A residue 1314 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 109 optimal weight: 8.9990 chunk 77 optimal weight: 5.9990 chunk 87 optimal weight: 6.9990 chunk 115 optimal weight: 6.9990 chunk 136 optimal weight: 0.7980 chunk 101 optimal weight: 6.9990 chunk 73 optimal weight: 0.0980 chunk 69 optimal weight: 3.9990 chunk 28 optimal weight: 5.9990 chunk 127 optimal weight: 0.9980 chunk 5 optimal weight: 20.0000 overall best weight: 2.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.4132 r_free = 0.4132 target = 0.084752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.066467 restraints weight = 81006.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 65)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.067822 restraints weight = 49461.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.068385 restraints weight = 36179.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.068868 restraints weight = 30760.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 65)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.069216 restraints weight = 28026.074| |-----------------------------------------------------------------------------| r_work (final): 0.3836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7102 moved from start: 0.2075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 14123 Z= 0.136 Angle : 0.565 11.193 19636 Z= 0.306 Chirality : 0.038 0.217 2256 Planarity : 0.004 0.107 2021 Dihedral : 19.396 144.600 3268 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.64 % Favored : 94.29 % Rotamer: Outliers : 2.97 % Allowed : 23.39 % Favored : 73.64 % 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: -1.03 (0.23), residues: 1313 helix: 0.09 (0.21), residues: 609 sheet: -0.43 (0.51), residues: 90 loop : -1.49 (0.25), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 395 TYR 0.013 0.001 TYR A 451 PHE 0.013 0.001 PHE A 704 TRP 0.005 0.001 TRP A 464 HIS 0.004 0.001 HIS A 641 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.14 (14123) covalent geometry : angle 0.56519 / 0.31 (19636) hydrogen bonds : bond 0.04488 / 4.15 ( 531) hydrogen bonds : angle 4.92943 / 6.33 ( 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 95 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 60 time to evaluate : 0.456 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 212 LEU cc_start: 0.8390 (OUTLIER) cc_final: 0.8124 (pt) REVERT: A 822 MET cc_start: 0.3029 (pmm) cc_final: 0.0823 (ppp) outliers start: 35 outliers final: 30 residues processed: 88 average time/residue: 0.0876 time to fit residues: 12.9383 Evaluate side-chains 91 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 60 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 31 LYS Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 128 TYR Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 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 564 LEU Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain A residue 621 LEU Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain A residue 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 892 ILE Chi-restraints excluded: chain A residue 950 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 1299 ASP Chi-restraints excluded: chain A residue 1314 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 61 optimal weight: 5.9990 chunk 123 optimal weight: 0.4980 chunk 106 optimal weight: 6.9990 chunk 85 optimal weight: 0.3980 chunk 75 optimal weight: 2.9990 chunk 2 optimal weight: 20.0000 chunk 27 optimal weight: 0.6980 chunk 47 optimal weight: 7.9990 chunk 25 optimal weight: 5.9990 chunk 63 optimal weight: 5.9990 chunk 78 optimal weight: 8.9990 overall best weight: 2.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.4132 r_free = 0.4132 target = 0.084586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.066192 restraints weight = 81425.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.067534 restraints weight = 50738.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.068372 restraints weight = 37125.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.068745 restraints weight = 31266.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 60)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.069087 restraints weight = 28436.315| |-----------------------------------------------------------------------------| r_work (final): 0.3840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7096 moved from start: 0.2207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 14123 Z= 0.125 Angle : 0.554 11.731 19636 Z= 0.301 Chirality : 0.038 0.213 2256 Planarity : 0.004 0.105 2021 Dihedral : 19.377 145.462 3268 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.03 % Favored : 94.90 % Rotamer: Outliers : 2.80 % Allowed : 23.73 % Favored : 73.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.98 (0.23), residues: 1313 helix: 0.10 (0.21), residues: 609 sheet: -0.36 (0.51), residues: 91 loop : -1.44 (0.25), residues: 613 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 691 TYR 0.011 0.001 TYR A 451 PHE 0.012 0.001 PHE A 704 TRP 0.005 0.001 TRP A 18 HIS 0.004 0.001 HIS A 641 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.12 (14123) covalent geometry : angle 0.55432 / 0.30 (19636) hydrogen bonds : bond 0.04359 / 3.98 ( 531) hydrogen bonds : angle 4.89051 / 6.31 ( 1438) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2805.91 seconds wall clock time: 49 minutes 14.80 seconds (2954.80 seconds total)