Starting phenix.real_space_refine on Thu Jul 31 21:21:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sny_40642/07_2025/8sny_40642.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sny_40642/07_2025/8sny_40642.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.41 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8sny_40642/07_2025/8sny_40642.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sny_40642/07_2025/8sny_40642.map" model { file = "/net/cci-nas-00/data/ceres_data/8sny_40642/07_2025/8sny_40642.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sny_40642/07_2025/8sny_40642.cif" } resolution = 3.41 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.005 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 8 5.49 5 S 75 5.16 5 C 8733 2.51 5 N 2333 2.21 5 O 2595 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 13744 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 11317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1388, 11317 Classifications: {'peptide': 1388} Link IDs: {'PTRANS': 47, 'TRANS': 1340} Chain breaks: 3 Chain: "B" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 444 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 1, 'TRANS': 56} Chain: "C" Number of atoms: 439 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 439 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 1, 'TRANS': 55} Chain: "D" Number of atoms: 496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 496 Classifications: {'peptide': 63} Link IDs: {'TRANS': 62} Chain breaks: 1 Chain: "E" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 885 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 2, 'TRANS': 111} Chain: "T" Number of atoms: 163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 163 Classifications: {'RNA': 8} Modifications used: {'rna2p_pyr': 2, 'rna3p_pur': 1, 'rna3p_pyr': 5} Link IDs: {'rna2p': 2, 'rna3p': 5} Time building chain proxies: 8.33, per 1000 atoms: 0.61 Number of scatterers: 13744 At special positions: 0 Unit cell: (123.786, 108.974, 108.974, 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 75 16.00 P 8 15.00 O 2595 8.00 N 2333 7.00 C 8733 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: 3.65 Conformation dependent library (CDL) restraints added in 1.8 seconds 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3218 Finding SS restraints... Secondary structure from input PDB file: 77 helices and 8 sheets defined 62.8% alpha, 3.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.50 Creating SS restraints... Processing helix chain 'A' and resid 24 through 37 Processing helix chain 'A' and resid 44 through 53 removed outlier: 3.725A pdb=" N LEU A 48 " --> pdb=" O ASP A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 64 removed outlier: 3.679A pdb=" N LEU A 64 " --> pdb=" O ASN A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 76 Processing helix chain 'A' and resid 83 through 93 Processing helix chain 'A' and resid 98 through 132 removed outlier: 3.813A pdb=" N VAL A 122 " --> pdb=" O GLU A 118 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LYS A 123 " --> pdb=" O ILE A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 197 Processing helix chain 'A' and resid 201 through 228 Processing helix chain 'A' and resid 265 through 296 removed outlier: 3.782A pdb=" N LEU A 295 " --> pdb=" O CYS A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 325 Processing helix chain 'A' and resid 328 through 333 Processing helix chain 'A' and resid 334 through 348 Processing helix chain 'A' and resid 349 through 380 removed outlier: 3.535A pdb=" N CYS A 380 " --> pdb=" O LEU A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 395 removed outlier: 3.966A pdb=" N ILE A 393 " --> pdb=" O SER A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 413 removed outlier: 3.766A pdb=" N LEU A 400 " --> pdb=" O ARG A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 422 Processing helix chain 'A' and resid 424 through 429 removed outlier: 3.935A pdb=" N PHE A 429 " --> pdb=" O LEU A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 448 Processing helix chain 'A' and resid 455 through 478 Processing helix chain 'A' and resid 490 through 499 Processing helix chain 'A' and resid 509 through 518 removed outlier: 4.449A pdb=" N GLY A 518 " --> pdb=" O ILE A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 532 through 537 Processing helix chain 'A' and resid 545 through 553 removed outlier: 3.583A pdb=" N ILE A 549 " --> pdb=" O LYS A 546 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N TRP A 550 " --> pdb=" O ASN A 547 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 571 removed outlier: 4.399A pdb=" N LEU A 571 " --> pdb=" O GLU A 567 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 588 Processing helix chain 'A' and resid 595 through 604 removed outlier: 3.776A pdb=" N ASN A 599 " --> pdb=" O CYS A 595 " (cutoff:3.500A) Processing helix chain 'A' and resid 633 through 651 Processing helix chain 'A' and resid 652 through 659 Proline residue: A 656 - end of helix removed outlier: 3.777A pdb=" N LEU A 659 " --> pdb=" O PRO A 656 " (cutoff:3.500A) Processing helix chain 'A' and resid 667 through 676 Processing helix chain 'A' and resid 703 through 708 removed outlier: 3.959A pdb=" N PHE A 708 " --> pdb=" O ASN A 705 " (cutoff:3.500A) Processing helix chain 'A' and resid 709 through 724 removed outlier: 4.718A pdb=" N ILE A 715 " --> pdb=" O GLU A 711 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N CYS A 716 " --> pdb=" O THR A 712 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N VAL A 719 " --> pdb=" O ILE A 715 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU A 720 " --> pdb=" O CYS A 716 " (cutoff:3.500A) Processing helix chain 'A' and resid 732 through 737 Processing helix chain 'A' and resid 781 through 801 Processing helix chain 'A' and resid 832 through 852 Processing helix chain 'A' and resid 882 through 887 Processing helix chain 'A' and resid 900 through 919 removed outlier: 3.743A pdb=" N GLU A 914 " --> pdb=" O SER A 910 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N LEU A 915 " --> pdb=" O LEU A 911 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N GLU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 921 through 939 Processing helix chain 'A' and resid 940 through 944 Processing helix chain 'A' and resid 949 through 966 Processing helix chain 'A' and resid 970 through 981 Processing helix chain 'A' and resid 982 through 986 removed outlier: 3.538A pdb=" N PHE A 985 " --> pdb=" O PRO A 982 " (cutoff:3.500A) Processing helix chain 'A' and resid 993 through 997 Processing helix chain 'A' and resid 1003 through 1020 removed outlier: 4.300A pdb=" N GLU A1007 " --> pdb=" O ASP A1003 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N TYR A1018 " --> pdb=" O PHE A1014 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N TYR A1019 " --> pdb=" O ILE A1015 " (cutoff:3.500A) Processing helix chain 'A' and resid 1034 through 1045 Processing helix chain 'A' and resid 1052 through 1060 Processing helix chain 'A' and resid 1072 through 1087 removed outlier: 3.719A pdb=" N ILE A1076 " --> pdb=" O ILE A1072 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N LEU A1079 " --> pdb=" O GLU A1075 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N ALA A1080 " --> pdb=" O ILE A1076 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N THR A1087 " --> pdb=" O GLU A1083 " (cutoff:3.500A) Processing helix chain 'A' and resid 1090 through 1099 Processing helix chain 'A' and resid 1099 through 1110 Processing helix chain 'A' and resid 1118 through 1129 Processing helix chain 'A' and resid 1130 through 1143 removed outlier: 3.861A pdb=" N ALA A1134 " --> pdb=" O PRO A1130 " (cutoff:3.500A) Processing helix chain 'A' and resid 1159 through 1174 Processing helix chain 'A' and resid 1175 through 1180 Processing helix chain 'A' and resid 1198 through 1212 Processing helix chain 'A' and resid 1223 through 1228 Processing helix chain 'A' and resid 1282 through 1299 Processing helix chain 'A' and resid 1304 through 1317 Processing helix chain 'A' and resid 1320 through 1326 removed outlier: 4.256A pdb=" N LYS A1326 " --> pdb=" O GLU A1322 " (cutoff:3.500A) Processing helix chain 'A' and resid 1356 through 1359 Processing helix chain 'A' and resid 1365 through 1375 Processing helix chain 'A' and resid 1384 through 1404 removed outlier: 3.514A pdb=" N CYS A1388 " --> pdb=" O VAL A1384 " (cutoff:3.500A) Processing helix chain 'A' and resid 1415 through 1419 Processing helix chain 'A' and resid 1432 through 1443 Processing helix chain 'A' and resid 1452 through 1457 Processing helix chain 'A' and resid 1458 through 1461 removed outlier: 3.952A pdb=" N LEU A1461 " --> pdb=" O GLU A1458 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1458 through 1461' Processing helix chain 'B' and resid 131 through 156 Processing helix chain 'B' and resid 157 through 165 removed outlier: 3.570A pdb=" N ALA B 162 " --> pdb=" O GLY B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 172 Processing helix chain 'B' and resid 174 through 187 Processing helix chain 'C' and resid 129 through 157 removed outlier: 4.798A pdb=" N GLU C 140 " --> pdb=" O ASP C 136 " (cutoff:3.500A) Processing helix chain 'C' and resid 162 through 183 Processing helix chain 'D' and resid 129 through 158 Processing helix chain 'D' and resid 171 through 200 removed outlier: 3.570A pdb=" N MET D 195 " --> pdb=" O ARG D 191 " (cutoff:3.500A) Processing helix chain 'E' and resid 129 through 151 removed outlier: 4.050A pdb=" N ARG E 137 " --> pdb=" O ALA E 133 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N ILE E 138 " --> pdb=" O ARG E 134 " (cutoff:3.500A) Processing helix chain 'E' and resid 174 through 183 Processing helix chain 'E' and resid 191 through 200 Processing helix chain 'E' and resid 203 through 210 Processing helix chain 'E' and resid 217 through 229 Processing sheet with id=AA1, first strand: chain 'A' and resid 11 through 12 Processing sheet with id=AA2, first strand: chain 'A' and resid 80 through 81 removed outlier: 6.319A pdb=" N LYS A 80 " --> pdb=" O ILE A 261 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA4, first strand: chain 'A' and resid 629 through 631 removed outlier: 6.543A pdb=" N VAL A 614 " --> pdb=" O ILE A 743 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 691 through 694 Processing sheet with id=AA6, first strand: chain 'A' and resid 812 through 815 Processing sheet with id=AA7, first strand: chain 'A' and resid 873 through 875 removed outlier: 3.845A pdb=" N ILE A 873 " --> pdb=" O TYR A 880 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1361 through 1364 750 hydrogen bonds defined for protein. 2178 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.05 Time building geometry restraints manager: 4.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 2265 1.31 - 1.44: 3591 1.44 - 1.56: 8000 1.56 - 1.69: 15 1.69 - 1.81: 127 Bond restraints: 13998 Sorted by residual: bond pdb=" CA PHE A 704 " pdb=" C PHE A 704 " ideal model delta sigma weight residual 1.523 1.458 0.065 1.30e-02 5.92e+03 2.50e+01 bond pdb=" CA MET A 631 " pdb=" C MET A 631 " ideal model delta sigma weight residual 1.524 1.462 0.062 1.24e-02 6.50e+03 2.50e+01 bond pdb=" CA LYS A1145 " pdb=" C LYS A1145 " ideal model delta sigma weight residual 1.524 1.471 0.052 1.26e-02 6.30e+03 1.73e+01 bond pdb=" CA LEU A 673 " pdb=" C LEU A 673 " ideal model delta sigma weight residual 1.522 1.463 0.058 1.40e-02 5.10e+03 1.73e+01 bond pdb=" CA GLN A 913 " pdb=" C GLN A 913 " ideal model delta sigma weight residual 1.524 1.471 0.053 1.29e-02 6.01e+03 1.66e+01 ... (remaining 13993 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.43: 18717 2.43 - 4.85: 197 4.85 - 7.28: 22 7.28 - 9.71: 7 9.71 - 12.14: 3 Bond angle restraints: 18946 Sorted by residual: angle pdb=" N LEU A 667 " pdb=" CA LEU A 667 " pdb=" C LEU A 667 " ideal model delta sigma weight residual 111.02 98.88 12.14 1.22e+00 6.72e-01 9.90e+01 angle pdb=" N ALA A 675 " pdb=" CA ALA A 675 " pdb=" C ALA A 675 " ideal model delta sigma weight residual 111.07 102.61 8.46 1.07e+00 8.73e-01 6.25e+01 angle pdb=" N LEU A 673 " pdb=" CA LEU A 673 " pdb=" C LEU A 673 " ideal model delta sigma weight residual 112.90 103.68 9.22 1.31e+00 5.83e-01 4.95e+01 angle pdb=" N LYS A1025 " pdb=" CA LYS A1025 " pdb=" C LYS A1025 " ideal model delta sigma weight residual 114.04 105.99 8.05 1.24e+00 6.50e-01 4.21e+01 angle pdb=" C PHE A 704 " pdb=" CA PHE A 704 " pdb=" CB PHE A 704 " ideal model delta sigma weight residual 110.79 100.65 10.14 1.66e+00 3.63e-01 3.73e+01 ... (remaining 18941 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.83: 7570 17.83 - 35.66: 811 35.66 - 53.49: 153 53.49 - 71.32: 36 71.32 - 89.15: 14 Dihedral angle restraints: 8584 sinusoidal: 3627 harmonic: 4957 Sorted by residual: dihedral pdb=" C PHE A 704 " pdb=" N PHE A 704 " pdb=" CA PHE A 704 " pdb=" CB PHE A 704 " ideal model delta harmonic sigma weight residual -122.60 -108.68 -13.92 0 2.50e+00 1.60e-01 3.10e+01 dihedral pdb=" N PHE A 704 " pdb=" C PHE A 704 " pdb=" CA PHE A 704 " pdb=" CB PHE A 704 " ideal model delta harmonic sigma weight residual 122.80 112.96 9.84 0 2.50e+00 1.60e-01 1.55e+01 dihedral pdb=" CA GLN A 874 " pdb=" C GLN A 874 " pdb=" N HIS A 875 " pdb=" CA HIS A 875 " ideal model delta harmonic sigma weight residual 180.00 161.75 18.25 0 5.00e+00 4.00e-02 1.33e+01 ... (remaining 8581 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1847 0.055 - 0.110: 310 0.110 - 0.166: 35 0.166 - 0.221: 7 0.221 - 0.276: 2 Chirality restraints: 2201 Sorted by residual: chirality pdb=" CG LEU A 671 " pdb=" CB LEU A 671 " pdb=" CD1 LEU A 671 " pdb=" CD2 LEU A 671 " both_signs ideal model delta sigma weight residual False -2.59 -2.31 -0.28 2.00e-01 2.50e+01 1.91e+00 chirality pdb=" CA LEU A 422 " pdb=" N LEU A 422 " pdb=" C LEU A 422 " pdb=" CB LEU A 422 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.24 2.00e-01 2.50e+01 1.38e+00 chirality pdb=" CB THR A 93 " pdb=" CA THR A 93 " pdb=" OG1 THR A 93 " pdb=" CG2 THR A 93 " both_signs ideal model delta sigma weight residual False 2.55 2.36 0.20 2.00e-01 2.50e+01 9.54e-01 ... (remaining 2198 not shown) Planarity restraints: 2361 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA A 707 " 0.011 2.00e-02 2.50e+03 2.20e-02 4.86e+00 pdb=" C ALA A 707 " -0.038 2.00e-02 2.50e+03 pdb=" O ALA A 707 " 0.014 2.00e-02 2.50e+03 pdb=" N PHE A 708 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN A 53 " 0.033 5.00e-02 4.00e+02 4.94e-02 3.91e+00 pdb=" N PRO A 54 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO A 54 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 54 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A 83 " -0.032 5.00e-02 4.00e+02 4.86e-02 3.79e+00 pdb=" N PRO A 84 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO A 84 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 84 " -0.027 5.00e-02 4.00e+02 ... (remaining 2358 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.53: 116 2.53 - 3.12: 10875 3.12 - 3.71: 22625 3.71 - 4.31: 31221 4.31 - 4.90: 52711 Nonbonded interactions: 117548 Sorted by model distance: nonbonded pdb=" O ASN A 991 " pdb=" ND2 ASN A 991 " model vdw 1.932 3.120 nonbonded pdb=" O CYS A 251 " pdb=" OG1 THR A 264 " model vdw 2.216 3.040 nonbonded pdb=" OD1 ASP D 136 " pdb=" NH1 ARG E 134 " model vdw 2.242 3.120 nonbonded pdb=" NH2 ARG A 588 " pdb=" O LEU A1151 " model vdw 2.256 3.120 nonbonded pdb=" O VAL A1399 " pdb=" OG1 THR A1403 " model vdw 2.271 3.040 ... (remaining 117543 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 Found NCS groups: ncs_group { reference = (chain 'B' and resid 130 through 184) selection = (chain 'C' and resid 130 through 184) } 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=0.20 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.590 Check model and map are aligned: 0.100 Set scattering table: 0.140 Process input model: 33.860 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 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 : 0.004 0.065 13998 Z= 0.226 Angle : 0.625 12.136 18946 Z= 0.350 Chirality : 0.042 0.276 2201 Planarity : 0.004 0.049 2361 Dihedral : 15.353 89.155 5366 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 13.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 0.33 % Allowed : 0.85 % Favored : 98.83 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.21), residues: 1662 helix: 1.75 (0.17), residues: 955 sheet: -1.69 (0.55), residues: 72 loop : -0.86 (0.25), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 480 HIS 0.019 0.001 HIS C 150 PHE 0.024 0.001 PHE A 704 TYR 0.021 0.001 TYR A1356 ARG 0.009 0.000 ARG C 167 Details of bonding type rmsd hydrogen bonds : bond 0.10348 ( 750) hydrogen bonds : angle 5.07754 ( 2178) covalent geometry : bond 0.00362 (13998) covalent geometry : angle 0.62492 (18946) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 309 time to evaluate : 1.566 Fit side-chains REVERT: A 669 LYS cc_start: 0.7851 (OUTLIER) cc_final: 0.7588 (pttp) REVERT: A 824 MET cc_start: 0.6091 (tmm) cc_final: 0.5831 (tmm) REVERT: A 1023 ASP cc_start: 0.6407 (m-30) cc_final: 0.6169 (t0) REVERT: B 152 LEU cc_start: 0.9017 (tp) cc_final: 0.8600 (tt) REVERT: C 140 GLU cc_start: 0.7632 (mp0) cc_final: 0.6963 (mp0) REVERT: C 177 MET cc_start: 0.8371 (tpp) cc_final: 0.8031 (tpp) REVERT: D 177 MET cc_start: 0.7450 (ppp) cc_final: 0.6904 (ppp) REVERT: D 178 ILE cc_start: 0.7151 (mm) cc_final: 0.6830 (mm) REVERT: E 145 ILE cc_start: 0.7918 (mt) cc_final: 0.7545 (mt) outliers start: 5 outliers final: 2 residues processed: 313 average time/residue: 0.2455 time to fit residues: 115.2741 Evaluate side-chains 241 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 238 time to evaluate : 1.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 669 LYS Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain A residue 674 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 139 optimal weight: 1.9990 chunk 125 optimal weight: 2.9990 chunk 69 optimal weight: 5.9990 chunk 42 optimal weight: 3.9990 chunk 84 optimal weight: 4.9990 chunk 66 optimal weight: 0.9980 chunk 129 optimal weight: 7.9990 chunk 50 optimal weight: 4.9990 chunk 78 optimal weight: 3.9990 chunk 96 optimal weight: 10.0000 chunk 149 optimal weight: 3.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 HIS ** A 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 248 GLN ** A 831 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 895 ASN ** A 991 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1149 ASN ** C 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.119843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.099745 restraints weight = 25031.458| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 2.14 r_work: 0.3076 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3076 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3076 r_free = 0.3076 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3076 r_free = 0.3076 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3076 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.1326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 13998 Z= 0.194 Angle : 0.577 8.076 18946 Z= 0.300 Chirality : 0.043 0.170 2201 Planarity : 0.004 0.045 2361 Dihedral : 7.740 73.530 1966 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 1.76 % Allowed : 11.18 % Favored : 87.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.21), residues: 1662 helix: 1.58 (0.17), residues: 971 sheet: -1.64 (0.59), residues: 61 loop : -0.88 (0.26), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 932 HIS 0.018 0.001 HIS C 150 PHE 0.023 0.002 PHE A 629 TYR 0.020 0.002 TYR A1356 ARG 0.005 0.001 ARG C 182 Details of bonding type rmsd hydrogen bonds : bond 0.03923 ( 750) hydrogen bonds : angle 4.54576 ( 2178) covalent geometry : bond 0.00456 (13998) covalent geometry : angle 0.57680 (18946) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 251 time to evaluate : 1.646 Fit side-chains REVERT: A 565 TYR cc_start: 0.8710 (t80) cc_final: 0.8351 (t80) REVERT: A 669 LYS cc_start: 0.7964 (mtmt) cc_final: 0.7484 (pttm) REVERT: A 1308 PHE cc_start: 0.7852 (t80) cc_final: 0.7644 (t80) REVERT: B 152 LEU cc_start: 0.9158 (tp) cc_final: 0.8745 (tt) REVERT: C 140 GLU cc_start: 0.8029 (mp0) cc_final: 0.7374 (mp0) REVERT: D 131 ILE cc_start: 0.6029 (mp) cc_final: 0.5750 (mp) REVERT: D 136 ASP cc_start: 0.7207 (m-30) cc_final: 0.6831 (t0) REVERT: D 177 MET cc_start: 0.7626 (ppp) cc_final: 0.7333 (ppp) REVERT: E 195 MET cc_start: 0.7474 (mtp) cc_final: 0.7145 (mtt) outliers start: 27 outliers final: 12 residues processed: 263 average time/residue: 0.2511 time to fit residues: 99.3986 Evaluate side-chains 238 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 226 time to evaluate : 1.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 674 LYS Chi-restraints excluded: chain A residue 835 LEU Chi-restraints excluded: chain A residue 851 ILE Chi-restraints excluded: chain A residue 895 ASN Chi-restraints excluded: chain A residue 948 ASN Chi-restraints excluded: chain A residue 972 ASP Chi-restraints excluded: chain A residue 1342 VAL Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 156 SER Chi-restraints excluded: chain E residue 175 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 119 optimal weight: 10.0000 chunk 2 optimal weight: 6.9990 chunk 55 optimal weight: 0.9980 chunk 90 optimal weight: 0.7980 chunk 67 optimal weight: 0.1980 chunk 91 optimal weight: 2.9990 chunk 86 optimal weight: 3.9990 chunk 136 optimal weight: 1.9990 chunk 148 optimal weight: 9.9990 chunk 35 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 248 GLN ** A 813 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 895 ASN ** A 991 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 150 HIS ** 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 = 0.3512 r_free = 0.3512 target = 0.121179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.101317 restraints weight = 25114.464| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 2.15 r_work: 0.3099 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3100 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3100 r_free = 0.3100 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3100 r_free = 0.3100 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3100 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.1447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13998 Z= 0.124 Angle : 0.511 7.807 18946 Z= 0.268 Chirality : 0.040 0.142 2201 Planarity : 0.004 0.051 2361 Dihedral : 7.589 73.397 1960 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 1.89 % Allowed : 14.17 % Favored : 83.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.21), residues: 1662 helix: 1.79 (0.16), residues: 954 sheet: -1.76 (0.55), residues: 69 loop : -0.72 (0.26), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 932 HIS 0.014 0.001 HIS C 150 PHE 0.026 0.001 PHE A 87 TYR 0.015 0.001 TYR A 221 ARG 0.006 0.000 ARG C 182 Details of bonding type rmsd hydrogen bonds : bond 0.03527 ( 750) hydrogen bonds : angle 4.38244 ( 2178) covalent geometry : bond 0.00284 (13998) covalent geometry : angle 0.51093 (18946) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 259 time to evaluate : 1.678 Fit side-chains REVERT: A 360 MET cc_start: 0.8012 (tpp) cc_final: 0.7811 (tpp) REVERT: A 440 MET cc_start: 0.8699 (mtp) cc_final: 0.8473 (mtm) REVERT: A 565 TYR cc_start: 0.8733 (t80) cc_final: 0.8350 (t80) REVERT: A 669 LYS cc_start: 0.8070 (mtmt) cc_final: 0.7533 (pttm) REVERT: A 989 ASP cc_start: 0.8303 (t0) cc_final: 0.8022 (t0) REVERT: A 1135 GLU cc_start: 0.8479 (tt0) cc_final: 0.8239 (tt0) REVERT: A 1372 LEU cc_start: 0.8119 (mm) cc_final: 0.7875 (mp) REVERT: A 1376 TYR cc_start: 0.7315 (m-80) cc_final: 0.6941 (m-80) REVERT: B 152 LEU cc_start: 0.9142 (tp) cc_final: 0.8700 (tt) REVERT: C 140 GLU cc_start: 0.8141 (mp0) cc_final: 0.7563 (mp0) REVERT: C 152 LEU cc_start: 0.8945 (mt) cc_final: 0.8723 (mp) REVERT: D 131 ILE cc_start: 0.6024 (mp) cc_final: 0.5724 (mp) REVERT: D 136 ASP cc_start: 0.7204 (m-30) cc_final: 0.6818 (t0) REVERT: E 220 SER cc_start: 0.8946 (m) cc_final: 0.8561 (m) outliers start: 29 outliers final: 19 residues processed: 273 average time/residue: 0.2976 time to fit residues: 123.7903 Evaluate side-chains 247 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 228 time to evaluate : 1.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 616 LEU Chi-restraints excluded: chain A residue 674 LYS Chi-restraints excluded: chain A residue 815 ILE Chi-restraints excluded: chain A residue 835 LEU Chi-restraints excluded: chain A residue 836 LEU Chi-restraints excluded: chain A residue 840 SER Chi-restraints excluded: chain A residue 851 ILE Chi-restraints excluded: chain A residue 972 ASP Chi-restraints excluded: chain A residue 1342 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain D residue 149 LEU Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 156 SER Chi-restraints excluded: chain E residue 175 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 123 optimal weight: 0.7980 chunk 102 optimal weight: 9.9990 chunk 103 optimal weight: 9.9990 chunk 133 optimal weight: 10.0000 chunk 153 optimal weight: 6.9990 chunk 142 optimal weight: 10.0000 chunk 114 optimal weight: 0.1980 chunk 33 optimal weight: 0.0060 chunk 148 optimal weight: 10.0000 chunk 86 optimal weight: 6.9990 chunk 90 optimal weight: 4.9990 overall best weight: 2.6000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 547 ASN ** A 813 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 831 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 895 ASN ** A 991 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 150 HIS ** 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 = 0.3475 r_free = 0.3475 target = 0.118763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.098544 restraints weight = 25065.571| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 2.13 r_work: 0.3057 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2927 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2929 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2929 r_free = 0.2929 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2929 r_free = 0.2929 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2929 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.1744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13998 Z= 0.175 Angle : 0.539 7.764 18946 Z= 0.283 Chirality : 0.041 0.150 2201 Planarity : 0.004 0.049 2361 Dihedral : 7.633 73.396 1960 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.67 % Allowed : 16.97 % Favored : 80.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.21), residues: 1662 helix: 1.62 (0.16), residues: 959 sheet: -1.59 (0.57), residues: 61 loop : -0.75 (0.25), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 932 HIS 0.014 0.001 HIS C 150 PHE 0.026 0.002 PHE A 87 TYR 0.014 0.001 TYR A 221 ARG 0.004 0.000 ARG C 182 Details of bonding type rmsd hydrogen bonds : bond 0.03703 ( 750) hydrogen bonds : angle 4.44067 ( 2178) covalent geometry : bond 0.00414 (13998) covalent geometry : angle 0.53887 (18946) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 241 time to evaluate : 1.766 Fit side-chains revert: symmetry clash REVERT: A 360 MET cc_start: 0.8151 (tpp) cc_final: 0.7830 (tpp) REVERT: A 483 LEU cc_start: 0.8710 (OUTLIER) cc_final: 0.7990 (pp) REVERT: A 565 TYR cc_start: 0.8853 (t80) cc_final: 0.8545 (t80) REVERT: A 669 LYS cc_start: 0.8164 (mtmt) cc_final: 0.7504 (pttm) REVERT: A 989 ASP cc_start: 0.8517 (t0) cc_final: 0.8223 (t0) REVERT: A 1135 GLU cc_start: 0.8768 (tt0) cc_final: 0.8482 (tt0) REVERT: A 1372 LEU cc_start: 0.8148 (mm) cc_final: 0.7898 (mp) REVERT: B 152 LEU cc_start: 0.9234 (tp) cc_final: 0.8842 (tt) REVERT: C 140 GLU cc_start: 0.8234 (mp0) cc_final: 0.7740 (mp0) REVERT: D 131 ILE cc_start: 0.6116 (mp) cc_final: 0.5758 (mp) REVERT: D 136 ASP cc_start: 0.7307 (m-30) cc_final: 0.6877 (t0) REVERT: E 220 SER cc_start: 0.9112 (m) cc_final: 0.8855 (m) outliers start: 41 outliers final: 32 residues processed: 261 average time/residue: 0.3219 time to fit residues: 128.6342 Evaluate side-chains 261 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 228 time to evaluate : 1.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain A residue 616 LEU Chi-restraints excluded: chain A residue 617 THR Chi-restraints excluded: chain A residue 674 LYS Chi-restraints excluded: chain A residue 745 THR Chi-restraints excluded: chain A residue 763 VAL Chi-restraints excluded: chain A residue 815 ILE Chi-restraints excluded: chain A residue 835 LEU Chi-restraints excluded: chain A residue 836 LEU Chi-restraints excluded: chain A residue 840 SER Chi-restraints excluded: chain A residue 851 ILE Chi-restraints excluded: chain A residue 921 SER Chi-restraints excluded: chain A residue 948 ASN Chi-restraints excluded: chain A residue 971 ILE Chi-restraints excluded: chain A residue 972 ASP Chi-restraints excluded: chain A residue 1023 ASP Chi-restraints excluded: chain A residue 1242 ILE Chi-restraints excluded: chain A residue 1342 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 156 SER Chi-restraints excluded: chain E residue 171 VAL Chi-restraints excluded: chain E residue 175 GLU Chi-restraints excluded: chain E residue 178 ILE Chi-restraints excluded: chain E residue 239 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 100 optimal weight: 5.9990 chunk 118 optimal weight: 0.6980 chunk 101 optimal weight: 0.9980 chunk 160 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 90 optimal weight: 0.9980 chunk 4 optimal weight: 0.9990 chunk 35 optimal weight: 3.9990 chunk 64 optimal weight: 0.9980 chunk 104 optimal weight: 5.9990 chunk 62 optimal weight: 10.0000 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 248 GLN A 853 HIS ** A 991 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 = 0.3512 r_free = 0.3512 target = 0.121176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.101345 restraints weight = 24966.702| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 2.15 r_work: 0.3111 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3106 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3106 r_free = 0.3106 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3106 r_free = 0.3106 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3106 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.1773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 13998 Z= 0.109 Angle : 0.499 8.974 18946 Z= 0.261 Chirality : 0.039 0.157 2201 Planarity : 0.003 0.053 2361 Dihedral : 7.491 73.360 1960 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.34 % Allowed : 18.86 % Favored : 78.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.21), residues: 1662 helix: 1.73 (0.16), residues: 965 sheet: -1.52 (0.56), residues: 61 loop : -0.67 (0.25), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 932 HIS 0.015 0.001 HIS C 150 PHE 0.015 0.001 PHE A 629 TYR 0.013 0.001 TYR A 221 ARG 0.006 0.000 ARG C 167 Details of bonding type rmsd hydrogen bonds : bond 0.03379 ( 750) hydrogen bonds : angle 4.29713 ( 2178) covalent geometry : bond 0.00242 (13998) covalent geometry : angle 0.49869 (18946) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 270 time to evaluate : 1.604 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 34 TYR cc_start: 0.8309 (t80) cc_final: 0.8082 (t80) REVERT: A 92 MET cc_start: 0.8292 (OUTLIER) cc_final: 0.7986 (mmp) REVERT: A 131 LEU cc_start: 0.9236 (OUTLIER) cc_final: 0.8590 (mp) REVERT: A 340 MET cc_start: 0.8636 (tpt) cc_final: 0.8159 (tpt) REVERT: A 483 LEU cc_start: 0.8547 (OUTLIER) cc_final: 0.7835 (pp) REVERT: A 565 TYR cc_start: 0.8861 (t80) cc_final: 0.8398 (t80) REVERT: A 669 LYS cc_start: 0.8054 (mtmt) cc_final: 0.7433 (pttm) REVERT: A 989 ASP cc_start: 0.8292 (t0) cc_final: 0.8023 (t0) REVERT: A 1026 ASP cc_start: 0.7600 (OUTLIER) cc_final: 0.7187 (p0) REVERT: A 1135 GLU cc_start: 0.8480 (tt0) cc_final: 0.8199 (tt0) REVERT: A 1422 MET cc_start: 0.7422 (ptt) cc_final: 0.7134 (ptt) REVERT: B 134 ARG cc_start: 0.7450 (ptm160) cc_final: 0.6677 (mtp-110) REVERT: B 152 LEU cc_start: 0.9128 (tp) cc_final: 0.8749 (tt) REVERT: C 140 GLU cc_start: 0.8082 (mp0) cc_final: 0.7677 (mp0) REVERT: D 131 ILE cc_start: 0.6062 (mp) cc_final: 0.5725 (mp) REVERT: D 136 ASP cc_start: 0.7225 (m-30) cc_final: 0.6801 (t0) REVERT: E 136 ASP cc_start: 0.7381 (OUTLIER) cc_final: 0.7101 (t0) outliers start: 36 outliers final: 24 residues processed: 289 average time/residue: 0.2896 time to fit residues: 128.6623 Evaluate side-chains 271 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 242 time to evaluate : 2.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 92 MET Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 487 ILE Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain A residue 616 LEU Chi-restraints excluded: chain A residue 617 THR Chi-restraints excluded: chain A residue 674 LYS Chi-restraints excluded: chain A residue 737 ILE Chi-restraints excluded: chain A residue 835 LEU Chi-restraints excluded: chain A residue 851 ILE Chi-restraints excluded: chain A residue 921 SER Chi-restraints excluded: chain A residue 948 ASN Chi-restraints excluded: chain A residue 972 ASP Chi-restraints excluded: chain A residue 983 MET Chi-restraints excluded: chain A residue 1026 ASP Chi-restraints excluded: chain A residue 1072 ILE Chi-restraints excluded: chain A residue 1342 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain E residue 136 ASP Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 239 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 16 optimal weight: 5.9990 chunk 91 optimal weight: 0.9990 chunk 8 optimal weight: 0.7980 chunk 66 optimal weight: 1.9990 chunk 142 optimal weight: 9.9990 chunk 17 optimal weight: 9.9990 chunk 151 optimal weight: 0.8980 chunk 72 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 115 optimal weight: 10.0000 chunk 144 optimal weight: 0.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 853 HIS ** A 991 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.121814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.102082 restraints weight = 25129.090| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 2.13 r_work: 0.3112 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3113 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3113 r_free = 0.3113 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3113 r_free = 0.3113 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3113 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.1853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13998 Z= 0.115 Angle : 0.509 7.750 18946 Z= 0.264 Chirality : 0.040 0.203 2201 Planarity : 0.003 0.053 2361 Dihedral : 7.433 73.333 1960 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 3.12 % Allowed : 19.51 % Favored : 77.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.21), residues: 1662 helix: 1.78 (0.16), residues: 965 sheet: -1.43 (0.55), residues: 61 loop : -0.66 (0.25), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 932 HIS 0.014 0.001 HIS C 150 PHE 0.024 0.001 PHE A 629 TYR 0.018 0.001 TYR A 266 ARG 0.007 0.000 ARG C 167 Details of bonding type rmsd hydrogen bonds : bond 0.03377 ( 750) hydrogen bonds : angle 4.29884 ( 2178) covalent geometry : bond 0.00261 (13998) covalent geometry : angle 0.50874 (18946) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 249 time to evaluate : 1.675 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 34 TYR cc_start: 0.8260 (t80) cc_final: 0.8046 (t80) REVERT: A 92 MET cc_start: 0.8290 (OUTLIER) cc_final: 0.7998 (mmp) REVERT: A 131 LEU cc_start: 0.9121 (OUTLIER) cc_final: 0.8505 (mp) REVERT: A 483 LEU cc_start: 0.8573 (OUTLIER) cc_final: 0.7860 (pp) REVERT: A 565 TYR cc_start: 0.8857 (t80) cc_final: 0.8375 (t80) REVERT: A 979 MET cc_start: 0.8892 (mmm) cc_final: 0.8617 (mmp) REVERT: A 989 ASP cc_start: 0.8273 (t0) cc_final: 0.8071 (t0) REVERT: A 1026 ASP cc_start: 0.7608 (OUTLIER) cc_final: 0.7165 (p0) REVERT: A 1135 GLU cc_start: 0.8461 (tt0) cc_final: 0.8183 (tt0) REVERT: B 152 LEU cc_start: 0.9121 (tp) cc_final: 0.8723 (tt) REVERT: C 140 GLU cc_start: 0.8110 (mp0) cc_final: 0.7844 (mp0) REVERT: D 131 ILE cc_start: 0.6204 (mp) cc_final: 0.5788 (mp) outliers start: 48 outliers final: 34 residues processed: 278 average time/residue: 0.2378 time to fit residues: 100.7265 Evaluate side-chains 271 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 233 time to evaluate : 1.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 92 MET Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 487 ILE Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain A residue 617 THR Chi-restraints excluded: chain A residue 674 LYS Chi-restraints excluded: chain A residue 745 THR Chi-restraints excluded: chain A residue 835 LEU Chi-restraints excluded: chain A residue 836 LEU Chi-restraints excluded: chain A residue 851 ILE Chi-restraints excluded: chain A residue 921 SER Chi-restraints excluded: chain A residue 948 ASN Chi-restraints excluded: chain A residue 971 ILE Chi-restraints excluded: chain A residue 972 ASP Chi-restraints excluded: chain A residue 983 MET Chi-restraints excluded: chain A residue 1026 ASP Chi-restraints excluded: chain A residue 1072 ILE Chi-restraints excluded: chain A residue 1242 ILE Chi-restraints excluded: chain A residue 1248 VAL Chi-restraints excluded: chain A residue 1342 VAL Chi-restraints excluded: chain A residue 1413 ILE Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 156 SER Chi-restraints excluded: chain E residue 171 VAL Chi-restraints excluded: chain E residue 175 GLU Chi-restraints excluded: chain E residue 176 GLU Chi-restraints excluded: chain E residue 220 SER Chi-restraints excluded: chain E residue 239 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 128 optimal weight: 5.9990 chunk 44 optimal weight: 6.9990 chunk 54 optimal weight: 3.9990 chunk 16 optimal weight: 5.9990 chunk 75 optimal weight: 5.9990 chunk 32 optimal weight: 9.9990 chunk 38 optimal weight: 0.9990 chunk 62 optimal weight: 9.9990 chunk 111 optimal weight: 20.0000 chunk 133 optimal weight: 3.9990 chunk 3 optimal weight: 6.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 734 HIS ** A 813 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 991 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.115861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.095598 restraints weight = 25314.565| |-----------------------------------------------------------------------------| r_work (start): 0.3122 rms_B_bonded: 2.12 r_work: 0.3012 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2883 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2885 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2885 r_free = 0.2885 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2885 r_free = 0.2885 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2885 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.2216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 13998 Z= 0.256 Angle : 0.624 8.445 18946 Z= 0.324 Chirality : 0.044 0.182 2201 Planarity : 0.004 0.046 2361 Dihedral : 7.758 73.522 1960 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 3.19 % Allowed : 20.68 % Favored : 76.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.20), residues: 1662 helix: 1.37 (0.16), residues: 958 sheet: -1.64 (0.54), residues: 61 loop : -0.87 (0.25), residues: 643 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 932 HIS 0.017 0.001 HIS C 150 PHE 0.018 0.002 PHE A 629 TYR 0.015 0.002 TYR A 221 ARG 0.006 0.001 ARG C 167 Details of bonding type rmsd hydrogen bonds : bond 0.04120 ( 750) hydrogen bonds : angle 4.64262 ( 2178) covalent geometry : bond 0.00603 (13998) covalent geometry : angle 0.62417 (18946) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 231 time to evaluate : 2.532 Fit side-chains revert: symmetry clash REVERT: A 131 LEU cc_start: 0.9209 (OUTLIER) cc_final: 0.8629 (mp) REVERT: A 483 LEU cc_start: 0.8776 (OUTLIER) cc_final: 0.8025 (pp) REVERT: A 565 TYR cc_start: 0.8926 (t80) cc_final: 0.8388 (t80) REVERT: A 586 TYR cc_start: 0.8326 (m-80) cc_final: 0.7890 (m-10) REVERT: A 875 HIS cc_start: 0.7782 (OUTLIER) cc_final: 0.7119 (p90) REVERT: A 954 ASP cc_start: 0.8578 (m-30) cc_final: 0.8124 (m-30) REVERT: A 1135 GLU cc_start: 0.8815 (tt0) cc_final: 0.8456 (tt0) REVERT: B 152 LEU cc_start: 0.9262 (tp) cc_final: 0.8884 (tt) REVERT: C 140 GLU cc_start: 0.8254 (mp0) cc_final: 0.7985 (mp0) REVERT: D 131 ILE cc_start: 0.6132 (mp) cc_final: 0.5747 (mp) outliers start: 49 outliers final: 35 residues processed: 261 average time/residue: 0.3662 time to fit residues: 147.6752 Evaluate side-chains 255 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 217 time to evaluate : 3.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain A residue 616 LEU Chi-restraints excluded: chain A residue 617 THR Chi-restraints excluded: chain A residue 674 LYS Chi-restraints excluded: chain A residue 737 ILE Chi-restraints excluded: chain A residue 745 THR Chi-restraints excluded: chain A residue 782 GLN Chi-restraints excluded: chain A residue 815 ILE Chi-restraints excluded: chain A residue 835 LEU Chi-restraints excluded: chain A residue 836 LEU Chi-restraints excluded: chain A residue 851 ILE Chi-restraints excluded: chain A residue 875 HIS Chi-restraints excluded: chain A residue 921 SER Chi-restraints excluded: chain A residue 955 ILE Chi-restraints excluded: chain A residue 971 ILE Chi-restraints excluded: chain A residue 972 ASP Chi-restraints excluded: chain A residue 983 MET Chi-restraints excluded: chain A residue 1023 ASP Chi-restraints excluded: chain A residue 1242 ILE Chi-restraints excluded: chain A residue 1248 VAL Chi-restraints excluded: chain A residue 1342 VAL Chi-restraints excluded: chain A residue 1413 ILE Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 156 SER Chi-restraints excluded: chain E residue 171 VAL Chi-restraints excluded: chain E residue 175 GLU Chi-restraints excluded: chain E residue 220 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 46 optimal weight: 0.6980 chunk 53 optimal weight: 0.8980 chunk 4 optimal weight: 0.9980 chunk 147 optimal weight: 5.9990 chunk 37 optimal weight: 1.9990 chunk 60 optimal weight: 10.0000 chunk 159 optimal weight: 20.0000 chunk 1 optimal weight: 0.4980 chunk 150 optimal weight: 7.9990 chunk 45 optimal weight: 1.9990 chunk 113 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 248 GLN A 734 HIS A 761 ASN ** A 813 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 853 HIS ** A 991 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.120744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.100596 restraints weight = 25045.093| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 2.13 r_work: 0.3089 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3090 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3090 r_free = 0.3090 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3090 r_free = 0.3090 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3090 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.2066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13998 Z= 0.114 Angle : 0.526 8.417 18946 Z= 0.273 Chirality : 0.040 0.174 2201 Planarity : 0.003 0.050 2361 Dihedral : 7.557 73.344 1960 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.60 % Allowed : 21.78 % Favored : 75.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.21), residues: 1662 helix: 1.62 (0.16), residues: 964 sheet: -1.50 (0.55), residues: 61 loop : -0.76 (0.25), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 932 HIS 0.016 0.001 HIS C 150 PHE 0.024 0.001 PHE A 629 TYR 0.014 0.001 TYR A 221 ARG 0.007 0.000 ARG C 167 Details of bonding type rmsd hydrogen bonds : bond 0.03447 ( 750) hydrogen bonds : angle 4.38491 ( 2178) covalent geometry : bond 0.00252 (13998) covalent geometry : angle 0.52555 (18946) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 241 time to evaluate : 1.645 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 131 LEU cc_start: 0.9049 (OUTLIER) cc_final: 0.8584 (mp) REVERT: A 360 MET cc_start: 0.7874 (tpp) cc_final: 0.7568 (tpp) REVERT: A 483 LEU cc_start: 0.8599 (OUTLIER) cc_final: 0.7910 (pp) REVERT: A 565 TYR cc_start: 0.8853 (t80) cc_final: 0.8318 (t80) REVERT: A 824 MET cc_start: 0.6156 (OUTLIER) cc_final: 0.5723 (tmm) REVERT: A 875 HIS cc_start: 0.7558 (OUTLIER) cc_final: 0.6731 (p90) REVERT: A 979 MET cc_start: 0.8902 (mmm) cc_final: 0.8667 (mmp) REVERT: A 1135 GLU cc_start: 0.8491 (tt0) cc_final: 0.8176 (tt0) REVERT: B 134 ARG cc_start: 0.7434 (ptm160) cc_final: 0.6868 (mtp-110) REVERT: B 152 LEU cc_start: 0.9140 (tp) cc_final: 0.8762 (tt) REVERT: C 140 GLU cc_start: 0.8102 (mp0) cc_final: 0.7880 (mp0) REVERT: D 131 ILE cc_start: 0.6150 (mp) cc_final: 0.5762 (mp) outliers start: 40 outliers final: 28 residues processed: 265 average time/residue: 0.2581 time to fit residues: 104.8001 Evaluate side-chains 258 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 226 time to evaluate : 1.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain A residue 674 LYS Chi-restraints excluded: chain A residue 737 ILE Chi-restraints excluded: chain A residue 745 THR Chi-restraints excluded: chain A residue 824 MET Chi-restraints excluded: chain A residue 835 LEU Chi-restraints excluded: chain A residue 851 ILE Chi-restraints excluded: chain A residue 875 HIS Chi-restraints excluded: chain A residue 921 SER Chi-restraints excluded: chain A residue 972 ASP Chi-restraints excluded: chain A residue 983 MET Chi-restraints excluded: chain A residue 1242 ILE Chi-restraints excluded: chain A residue 1342 VAL Chi-restraints excluded: chain A residue 1413 ILE Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 156 SER Chi-restraints excluded: chain E residue 171 VAL Chi-restraints excluded: chain E residue 175 GLU Chi-restraints excluded: chain E residue 214 VAL Chi-restraints excluded: chain E residue 220 SER Chi-restraints excluded: chain E residue 239 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 117 optimal weight: 1.9990 chunk 52 optimal weight: 7.9990 chunk 67 optimal weight: 8.9990 chunk 87 optimal weight: 2.9990 chunk 130 optimal weight: 10.0000 chunk 136 optimal weight: 7.9990 chunk 146 optimal weight: 20.0000 chunk 9 optimal weight: 9.9990 chunk 14 optimal weight: 0.8980 chunk 82 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 813 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 991 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 = 0.3469 r_free = 0.3469 target = 0.118472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.098494 restraints weight = 24935.679| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 2.10 r_work: 0.3049 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2920 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2924 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2924 r_free = 0.2924 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2924 r_free = 0.2924 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2924 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.2174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13998 Z= 0.176 Angle : 0.569 8.192 18946 Z= 0.296 Chirality : 0.042 0.196 2201 Planarity : 0.004 0.046 2361 Dihedral : 7.626 73.428 1960 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 2.80 % Allowed : 22.04 % Favored : 75.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.21), residues: 1662 helix: 1.50 (0.16), residues: 965 sheet: -1.49 (0.55), residues: 61 loop : -0.78 (0.25), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 932 HIS 0.017 0.001 HIS C 150 PHE 0.024 0.002 PHE A 629 TYR 0.019 0.001 TYR A 746 ARG 0.009 0.000 ARG C 167 Details of bonding type rmsd hydrogen bonds : bond 0.03718 ( 750) hydrogen bonds : angle 4.46901 ( 2178) covalent geometry : bond 0.00417 (13998) covalent geometry : angle 0.56870 (18946) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 225 time to evaluate : 1.711 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 131 LEU cc_start: 0.9149 (OUTLIER) cc_final: 0.8569 (mp) REVERT: A 376 LEU cc_start: 0.9421 (OUTLIER) cc_final: 0.9154 (mm) REVERT: A 459 SER cc_start: 0.9141 (t) cc_final: 0.8910 (t) REVERT: A 483 LEU cc_start: 0.8738 (OUTLIER) cc_final: 0.7987 (pp) REVERT: A 565 TYR cc_start: 0.8942 (t80) cc_final: 0.8439 (t80) REVERT: A 875 HIS cc_start: 0.7819 (OUTLIER) cc_final: 0.6933 (p90) REVERT: A 1135 GLU cc_start: 0.8791 (tt0) cc_final: 0.8428 (tt0) REVERT: A 1309 MET cc_start: 0.7824 (mmt) cc_final: 0.7524 (mmt) REVERT: A 1422 MET cc_start: 0.7818 (ptt) cc_final: 0.7511 (ptt) REVERT: B 134 ARG cc_start: 0.7716 (ptm160) cc_final: 0.6878 (mtp-110) REVERT: B 152 LEU cc_start: 0.9229 (tp) cc_final: 0.8819 (tt) REVERT: C 140 GLU cc_start: 0.8208 (mp0) cc_final: 0.7971 (mp0) REVERT: D 131 ILE cc_start: 0.6191 (mp) cc_final: 0.5771 (mp) REVERT: E 136 ASP cc_start: 0.7434 (OUTLIER) cc_final: 0.7162 (t0) outliers start: 43 outliers final: 34 residues processed: 252 average time/residue: 0.2472 time to fit residues: 94.2678 Evaluate side-chains 260 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 221 time to evaluate : 1.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 600 CYS Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain A residue 617 THR Chi-restraints excluded: chain A residue 674 LYS Chi-restraints excluded: chain A residue 737 ILE Chi-restraints excluded: chain A residue 745 THR Chi-restraints excluded: chain A residue 835 LEU Chi-restraints excluded: chain A residue 836 LEU Chi-restraints excluded: chain A residue 851 ILE Chi-restraints excluded: chain A residue 875 HIS Chi-restraints excluded: chain A residue 921 SER Chi-restraints excluded: chain A residue 971 ILE Chi-restraints excluded: chain A residue 972 ASP Chi-restraints excluded: chain A residue 983 MET Chi-restraints excluded: chain A residue 1242 ILE Chi-restraints excluded: chain A residue 1248 VAL Chi-restraints excluded: chain A residue 1342 VAL Chi-restraints excluded: chain A residue 1413 ILE Chi-restraints excluded: chain A residue 1419 ILE Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain E residue 136 ASP Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 156 SER Chi-restraints excluded: chain E residue 171 VAL Chi-restraints excluded: chain E residue 175 GLU Chi-restraints excluded: chain E residue 214 VAL Chi-restraints excluded: chain E residue 220 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 8 optimal weight: 3.9990 chunk 48 optimal weight: 0.9980 chunk 59 optimal weight: 0.0670 chunk 123 optimal weight: 4.9990 chunk 43 optimal weight: 0.6980 chunk 132 optimal weight: 1.9990 chunk 110 optimal weight: 2.9990 chunk 111 optimal weight: 0.5980 chunk 96 optimal weight: 1.9990 chunk 75 optimal weight: 10.0000 chunk 4 optimal weight: 0.9990 overall best weight: 0.6720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 640 GLN ** A 813 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 853 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 874 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.122200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.101987 restraints weight = 25002.973| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 2.14 r_work: 0.3111 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3110 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3110 r_free = 0.3110 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3110 r_free = 0.3110 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3110 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.2109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 13998 Z= 0.109 Angle : 0.531 9.769 18946 Z= 0.275 Chirality : 0.040 0.195 2201 Planarity : 0.003 0.053 2361 Dihedral : 7.414 73.352 1960 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.47 % Allowed : 21.91 % Favored : 75.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.21), residues: 1662 helix: 1.72 (0.16), residues: 962 sheet: -1.36 (0.55), residues: 69 loop : -0.76 (0.25), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 932 HIS 0.016 0.001 HIS C 150 PHE 0.024 0.001 PHE A 629 TYR 0.024 0.001 TYR A 746 ARG 0.008 0.000 ARG C 167 Details of bonding type rmsd hydrogen bonds : bond 0.03366 ( 750) hydrogen bonds : angle 4.33957 ( 2178) covalent geometry : bond 0.00242 (13998) covalent geometry : angle 0.53137 (18946) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 248 time to evaluate : 1.513 Fit side-chains revert: symmetry clash REVERT: A 131 LEU cc_start: 0.9045 (OUTLIER) cc_final: 0.8561 (mp) REVERT: A 360 MET cc_start: 0.7867 (tpp) cc_final: 0.7600 (tpp) REVERT: A 483 LEU cc_start: 0.8602 (OUTLIER) cc_final: 0.7884 (pp) REVERT: A 565 TYR cc_start: 0.8835 (t80) cc_final: 0.8309 (t80) REVERT: A 875 HIS cc_start: 0.7577 (OUTLIER) cc_final: 0.6557 (p90) REVERT: A 979 MET cc_start: 0.8888 (mmm) cc_final: 0.8673 (mmp) REVERT: A 1135 GLU cc_start: 0.8494 (tt0) cc_final: 0.8206 (tt0) REVERT: A 1372 LEU cc_start: 0.8272 (mt) cc_final: 0.8048 (mp) REVERT: A 1396 MET cc_start: 0.8974 (tpp) cc_final: 0.8443 (mtp) REVERT: C 177 MET cc_start: 0.8284 (tpp) cc_final: 0.8047 (tpp) REVERT: D 131 ILE cc_start: 0.6227 (mp) cc_final: 0.5856 (mp) outliers start: 38 outliers final: 29 residues processed: 271 average time/residue: 0.2381 time to fit residues: 97.1224 Evaluate side-chains 268 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 236 time to evaluate : 1.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 600 CYS Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain A residue 617 THR Chi-restraints excluded: chain A residue 674 LYS Chi-restraints excluded: chain A residue 737 ILE Chi-restraints excluded: chain A residue 745 THR Chi-restraints excluded: chain A residue 835 LEU Chi-restraints excluded: chain A residue 851 ILE Chi-restraints excluded: chain A residue 875 HIS Chi-restraints excluded: chain A residue 921 SER Chi-restraints excluded: chain A residue 971 ILE Chi-restraints excluded: chain A residue 1173 ILE Chi-restraints excluded: chain A residue 1342 VAL Chi-restraints excluded: chain A residue 1413 ILE Chi-restraints excluded: chain A residue 1419 ILE Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 171 VAL Chi-restraints excluded: chain E residue 175 GLU Chi-restraints excluded: chain E residue 214 VAL Chi-restraints excluded: chain E residue 220 SER Chi-restraints excluded: chain E residue 239 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 74 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 chunk 140 optimal weight: 0.7980 chunk 110 optimal weight: 7.9990 chunk 96 optimal weight: 10.0000 chunk 22 optimal weight: 4.9990 chunk 60 optimal weight: 10.0000 chunk 67 optimal weight: 0.9980 chunk 131 optimal weight: 4.9990 chunk 56 optimal weight: 9.9990 chunk 27 optimal weight: 5.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 813 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 831 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 853 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 991 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 = 0.3475 r_free = 0.3475 target = 0.118871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.098809 restraints weight = 25277.839| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 2.12 r_work: 0.3061 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2933 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2933 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2933 r_free = 0.2933 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2933 r_free = 0.2933 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2933 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.2193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13998 Z= 0.168 Angle : 0.569 8.375 18946 Z= 0.299 Chirality : 0.042 0.268 2201 Planarity : 0.004 0.050 2361 Dihedral : 7.538 73.412 1960 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.34 % Allowed : 22.24 % Favored : 75.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.21), residues: 1662 helix: 1.55 (0.16), residues: 967 sheet: -1.27 (0.56), residues: 61 loop : -0.76 (0.25), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 932 HIS 0.016 0.001 HIS C 150 PHE 0.017 0.002 PHE A 629 TYR 0.018 0.001 TYR A 746 ARG 0.009 0.000 ARG C 167 Details of bonding type rmsd hydrogen bonds : bond 0.03667 ( 750) hydrogen bonds : angle 4.42546 ( 2178) covalent geometry : bond 0.00396 (13998) covalent geometry : angle 0.56931 (18946) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7138.65 seconds wall clock time: 131 minutes 19.14 seconds (7879.14 seconds total)