Starting phenix.real_space_refine on Sat Sep 12 01:36:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6v5b_21051/09_2026/6v5b_21051.cif Found real_map, /net/cci-nas-00/data/ceres_data/6v5b_21051/09_2026/6v5b_21051.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6v5b_21051/09_2026/6v5b_21051.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6v5b_21051/09_2026/6v5b_21051.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6v5b_21051/09_2026/6v5b_21051.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6v5b_21051/09_2026/6v5b_21051.cif" model { file = "/net/cci-nas-00/data/ceres_data/6v5b_21051/09_2026/6v5b_21051.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6v5b_21051/09_2026/6v5b_21051.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.012 sd= 0.101 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: 7 Type Number sf(0) Gaussians Ca 1 9.91 5 Zn 2 6.06 5 P 78 5.49 5 S 70 5.16 5 C 7670 2.51 5 N 2216 2.21 5 O 2526 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12563 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 7419 Number of conformers: 1 Conformer: "" Number of residues, atoms: 908, 7419 Classifications: {'peptide': 908} Link IDs: {'CIS': 2, 'PTRANS': 49, 'TRANS': 856} Chain breaks: 1 Chain: "C" Number of atoms: 1750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1750 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 8, 'TRANS': 208} Chain breaks: 4 Chain: "B" Number of atoms: 1739 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1739 Classifications: {'peptide': 216} Link IDs: {'PTRANS': 8, 'TRANS': 207} Chain breaks: 4 Chain: "D" Number of atoms: 1652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 1652 Classifications: {'RNAv2': 78} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 2, 'rna3p_pur': 36, 'rna3p_pyr': 38} Link IDs: {'rna2p': 4, 'rna3p': 73} Chain breaks: 1 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 906 SG CYS A 561 50.511 93.376 40.445 1.00172.12 S ATOM 1864 SG CYS A 676 47.059 93.016 41.817 1.00178.36 S Time building chain proxies: 2.87, per 1000 atoms: 0.23 Number of scatterers: 12563 At special positions: 0 Unit cell: (92.22, 114.48, 167.48, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 Ca 1 19.99 S 70 16.00 P 78 15.00 O 2526 8.00 N 2216 7.00 C 7670 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.00 Conformation dependent library (CDL) restraints added in 640.5 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1401 " pdb="ZN ZN A1401 " - pdb=" NE2 HIS A 609 " pdb="ZN ZN A1401 " - pdb=" SG CYS A 561 " pdb="ZN ZN A1401 " - pdb=" SG CYS A 676 " 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2540 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 7 sheets defined 45.8% alpha, 8.3% beta 27 base pairs and 41 stacking pairs defined. Time for finding SS restraints: 1.48 Creating SS restraints... Processing helix chain 'A' and resid 425 through 429 removed outlier: 4.067A pdb=" N GLN A 429 " --> pdb=" O PRO A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 442 through 449 Processing helix chain 'A' and resid 503 through 512 removed outlier: 3.700A pdb=" N ILE A 508 " --> pdb=" O VAL A 504 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N LYS A 509 " --> pdb=" O ILE A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 642 through 655 Processing helix chain 'A' and resid 698 through 709 removed outlier: 3.635A pdb=" N ILE A 702 " --> pdb=" O SER A 698 " (cutoff:3.500A) Processing helix chain 'A' and resid 719 through 723 removed outlier: 3.558A pdb=" N LEU A 723 " --> pdb=" O ALA A 720 " (cutoff:3.500A) Processing helix chain 'A' and resid 728 through 736 Processing helix chain 'A' and resid 787 through 805 removed outlier: 3.692A pdb=" N LEU A 793 " --> pdb=" O GLN A 789 " (cutoff:3.500A) Processing helix chain 'A' and resid 814 through 829 removed outlier: 3.751A pdb=" N ARG A 829 " --> pdb=" O LEU A 825 " (cutoff:3.500A) Processing helix chain 'A' and resid 855 through 876 Proline residue: A 864 - end of helix Processing helix chain 'A' and resid 877 through 884 removed outlier: 3.920A pdb=" N LYS A 881 " --> pdb=" O MET A 877 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N LEU A 882 " --> pdb=" O HIS A 878 " (cutoff:3.500A) Processing helix chain 'A' and resid 890 through 897 removed outlier: 3.545A pdb=" N LEU A 895 " --> pdb=" O CYS A 891 " (cutoff:3.500A) Processing helix chain 'A' and resid 909 through 920 Processing helix chain 'A' and resid 944 through 950 Processing helix chain 'A' and resid 965 through 986 removed outlier: 3.839A pdb=" N ALA A 974 " --> pdb=" O PHE A 970 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N GLU A 977 " --> pdb=" O ASP A 973 " (cutoff:3.500A) Processing helix chain 'A' and resid 992 through 1004 removed outlier: 3.732A pdb=" N ILE A1003 " --> pdb=" O TYR A 999 " (cutoff:3.500A) Processing helix chain 'A' and resid 1005 through 1015 removed outlier: 3.562A pdb=" N LYS A1015 " --> pdb=" O MET A1011 " (cutoff:3.500A) Processing helix chain 'A' and resid 1016 through 1021 removed outlier: 5.973A pdb=" N ASP A1019 " --> pdb=" O LEU A1016 " (cutoff:3.500A) Processing helix chain 'A' and resid 1033 through 1055 Processing helix chain 'A' and resid 1056 through 1069 removed outlier: 3.707A pdb=" N ARG A1066 " --> pdb=" O GLN A1062 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N PHE A1069 " --> pdb=" O GLY A1065 " (cutoff:3.500A) Processing helix chain 'A' and resid 1071 through 1080 Processing helix chain 'A' and resid 1084 through 1089 Processing helix chain 'A' and resid 1104 through 1115 removed outlier: 3.851A pdb=" N GLU A1109 " --> pdb=" O GLN A1105 " (cutoff:3.500A) Processing helix chain 'A' and resid 1120 through 1128 removed outlier: 3.931A pdb=" N LEU A1124 " --> pdb=" O HIS A1120 " (cutoff:3.500A) Processing helix chain 'A' and resid 1145 through 1166 removed outlier: 3.724A pdb=" N LEU A1149 " --> pdb=" O ARG A1145 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N SER A1152 " --> pdb=" O PHE A1148 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N GLN A1155 " --> pdb=" O ASP A1151 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N THR A1159 " --> pdb=" O GLN A1155 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILE A1164 " --> pdb=" O GLU A1160 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N PHE A1166 " --> pdb=" O LEU A1162 " (cutoff:3.500A) Processing helix chain 'A' and resid 1170 through 1182 Processing helix chain 'A' and resid 1185 through 1195 removed outlier: 3.585A pdb=" N VAL A1190 " --> pdb=" O THR A1186 " (cutoff:3.500A) Processing helix chain 'A' and resid 1196 through 1200 Processing helix chain 'A' and resid 1213 through 1232 removed outlier: 3.578A pdb=" N ASP A1219 " --> pdb=" O LYS A1215 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEU A1220 " --> pdb=" O THR A1216 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU A1221 " --> pdb=" O LEU A1217 " (cutoff:3.500A) Processing helix chain 'A' and resid 1233 through 1245 removed outlier: 4.303A pdb=" N VAL A1237 " --> pdb=" O ASP A1233 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL A1243 " --> pdb=" O THR A1239 " (cutoff:3.500A) Processing helix chain 'A' and resid 1248 through 1256 removed outlier: 4.521A pdb=" N LEU A1254 " --> pdb=" O LYS A1250 " (cutoff:3.500A) Processing helix chain 'A' and resid 1262 through 1270 removed outlier: 3.648A pdb=" N LEU A1270 " --> pdb=" O GLN A1266 " (cutoff:3.500A) Processing helix chain 'A' and resid 1316 through 1332 Processing helix chain 'A' and resid 1335 through 1348 removed outlier: 3.835A pdb=" N ARG A1346 " --> pdb=" O ARG A1342 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LYS A1347 " --> pdb=" O PHE A1343 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N TYR A1348 " --> pdb=" O ILE A1344 " (cutoff:3.500A) Processing helix chain 'A' and resid 1349 through 1356 removed outlier: 4.180A pdb=" N LYS A1353 " --> pdb=" O ARG A1349 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ARG A1356 " --> pdb=" O LEU A1352 " (cutoff:3.500A) Processing helix chain 'C' and resid 511 through 521 removed outlier: 3.504A pdb=" N ILE C 515 " --> pdb=" O SER C 511 " (cutoff:3.500A) Processing helix chain 'C' and resid 560 through 577 Processing helix chain 'C' and resid 607 through 615 removed outlier: 3.771A pdb=" N LEU C 611 " --> pdb=" O ARG C 607 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N SER C 613 " --> pdb=" O TYR C 609 " (cutoff:3.500A) Processing helix chain 'C' and resid 619 through 629 Processing helix chain 'C' and resid 668 through 685 Processing helix chain 'C' and resid 691 through 699 Processing helix chain 'C' and resid 729 through 750 Processing helix chain 'B' and resid 511 through 523 removed outlier: 3.756A pdb=" N ILE B 515 " --> pdb=" O SER B 511 " (cutoff:3.500A) Processing helix chain 'B' and resid 560 through 575 Processing helix chain 'B' and resid 596 through 600 removed outlier: 4.163A pdb=" N ASN B 599 " --> pdb=" O GLU B 596 " (cutoff:3.500A) Processing helix chain 'B' and resid 605 through 609 removed outlier: 3.858A pdb=" N VAL B 608 " --> pdb=" O ASP B 605 " (cutoff:3.500A) Processing helix chain 'B' and resid 619 through 629 Processing helix chain 'B' and resid 668 through 685 Processing helix chain 'B' and resid 692 through 699 Processing helix chain 'B' and resid 728 through 745 removed outlier: 3.661A pdb=" N LEU B 732 " --> pdb=" O ASN B 728 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYS B 734 " --> pdb=" O HIS B 730 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 591 through 594 removed outlier: 12.398A pdb=" N GLU A 602 " --> pdb=" O VAL A 578 " (cutoff:3.500A) removed outlier: 8.166A pdb=" N VAL A 578 " --> pdb=" O GLU A 602 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N PHE A 604 " --> pdb=" O ILE A 576 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N CYS A 618 " --> pdb=" O ILE A 629 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 591 through 594 removed outlier: 5.373A pdb=" N PHE A 601 " --> pdb=" O VAL A 686 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N VAL A 686 " --> pdb=" O PHE A 601 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N GLY A 603 " --> pdb=" O ARG A 684 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1284 through 1290 removed outlier: 5.087A pdb=" N TYR A1284 " --> pdb=" O TYR A1303 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N TYR A1303 " --> pdb=" O TYR A1284 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N THR A1286 " --> pdb=" O ALA A1301 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ALA A1301 " --> pdb=" O THR A1286 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N VAL A1290 " --> pdb=" O THR A1297 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N TYR A1298 " --> pdb=" O LYS A1313 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N LYS A1313 " --> pdb=" O TYR A1298 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N VAL A1300 " --> pdb=" O CYS A1311 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N CYS A1311 " --> pdb=" O VAL A1300 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N VAL A1302 " --> pdb=" O ILE A1309 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 532 through 534 Processing sheet with id=AA5, first strand: chain 'C' and resid 652 through 653 Processing sheet with id=AA6, first strand: chain 'B' and resid 529 through 534 removed outlier: 3.699A pdb=" N VAL B 546 " --> pdb=" O GLY B 554 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N GLY B 554 " --> pdb=" O VAL B 546 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N ILE B 548 " --> pdb=" O THR B 552 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N THR B 552 " --> pdb=" O ILE B 548 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 651 through 657 removed outlier: 4.096A pdb=" N TYR B 653 " --> pdb=" O GLY B 664 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLY B 664 " --> pdb=" O TYR B 653 " (cutoff:3.500A) 426 hydrogen bonds defined for protein. 1221 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 65 hydrogen bonds 122 hydrogen bond angles 0 basepair planarities 27 basepair parallelities 41 stacking parallelities Total time for adding SS restraints: 2.49 Time building geometry restraints manager: 1.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3013 1.33 - 1.45: 3085 1.45 - 1.57: 6631 1.57 - 1.69: 157 1.69 - 1.82: 110 Bond restraints: 12996 Sorted by residual: bond pdb=" N TYR B 609 " pdb=" CA TYR B 609 " ideal model delta sigma weight residual 1.454 1.533 -0.079 1.34e-02 5.57e+03 3.51e+01 bond pdb=" CB TYR B 609 " pdb=" CG TYR B 609 " ideal model delta sigma weight residual 1.512 1.600 -0.088 2.20e-02 2.07e+03 1.60e+01 bond pdb=" N GLU B 610 " pdb=" CA GLU B 610 " ideal model delta sigma weight residual 1.457 1.509 -0.051 1.29e-02 6.01e+03 1.58e+01 bond pdb=" CA GLU B 610 " pdb=" C GLU B 610 " ideal model delta sigma weight residual 1.523 1.472 0.051 1.34e-02 5.57e+03 1.46e+01 bond pdb=" CA TYR C 609 " pdb=" C TYR C 609 " ideal model delta sigma weight residual 1.523 1.477 0.046 1.34e-02 5.57e+03 1.19e+01 ... (remaining 12991 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.10: 17439 3.10 - 6.20: 410 6.20 - 9.31: 37 9.31 - 12.41: 7 12.41 - 15.51: 4 Bond angle restraints: 17897 Sorted by residual: angle pdb=" CA GLU B 610 " pdb=" C GLU B 610 " pdb=" N LEU B 611 " ideal model delta sigma weight residual 116.84 103.81 13.03 1.71e+00 3.42e-01 5.81e+01 angle pdb=" N GLU B 610 " pdb=" CA GLU B 610 " pdb=" C GLU B 610 " ideal model delta sigma weight residual 110.80 95.29 15.51 2.13e+00 2.20e-01 5.30e+01 angle pdb=" O VAL B 608 " pdb=" C VAL B 608 " pdb=" N TYR B 609 " ideal model delta sigma weight residual 121.80 113.97 7.83 1.13e+00 7.83e-01 4.80e+01 angle pdb=" N ASP A1029 " pdb=" CA ASP A1029 " pdb=" CB ASP A1029 " ideal model delta sigma weight residual 114.17 106.61 7.56 1.14e+00 7.69e-01 4.39e+01 angle pdb=" CA VAL B 608 " pdb=" C VAL B 608 " pdb=" N TYR B 609 " ideal model delta sigma weight residual 117.69 125.24 -7.55 1.27e+00 6.20e-01 3.53e+01 ... (remaining 17892 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 6553 17.96 - 35.92: 863 35.92 - 53.88: 225 53.88 - 71.84: 67 71.84 - 89.80: 17 Dihedral angle restraints: 7725 sinusoidal: 3807 harmonic: 3918 Sorted by residual: dihedral pdb=" C4' C D 100 " pdb=" C3' C D 100 " pdb=" C2' C D 100 " pdb=" C1' C D 100 " ideal model delta sinusoidal sigma weight residual 36.34 -37.97 74.32 1 3.10e+00 1.04e-01 7.29e+02 dihedral pdb=" C4' A D 8 " pdb=" C3' A D 8 " pdb=" C2' A D 8 " pdb=" C1' A D 8 " ideal model delta sinusoidal sigma weight residual 36.34 -37.27 73.62 1 3.10e+00 1.04e-01 7.17e+02 dihedral pdb=" C4' C D 41 " pdb=" C3' C D 41 " pdb=" C2' C D 41 " pdb=" C1' C D 41 " ideal model delta sinusoidal sigma weight residual 36.35 -37.25 73.60 1 3.10e+00 1.04e-01 7.17e+02 ... (remaining 7722 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1428 0.057 - 0.113: 393 0.113 - 0.170: 87 0.170 - 0.226: 71 0.226 - 0.283: 30 Chirality restraints: 2009 Sorted by residual: chirality pdb=" C2' A D 8 " pdb=" C3' A D 8 " pdb=" O2' A D 8 " pdb=" C1' A D 8 " both_signs ideal model delta sigma weight residual False -2.79 -2.51 -0.28 2.00e-01 2.50e+01 2.00e+00 chirality pdb=" C2' C D 100 " pdb=" C3' C D 100 " pdb=" O2' C D 100 " pdb=" C1' C D 100 " both_signs ideal model delta sigma weight residual False -2.79 -2.51 -0.28 2.00e-01 2.50e+01 1.99e+00 chirality pdb=" CB ILE A 656 " pdb=" CA ILE A 656 " pdb=" CG1 ILE A 656 " pdb=" CG2 ILE A 656 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.28 2.00e-01 2.50e+01 1.96e+00 ... (remaining 2006 not shown) Planarity restraints: 2019 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL C 608 " -0.028 2.00e-02 2.50e+03 5.47e-02 2.99e+01 pdb=" C VAL C 608 " 0.095 2.00e-02 2.50e+03 pdb=" O VAL C 608 " -0.034 2.00e-02 2.50e+03 pdb=" N TYR C 609 " -0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A 714 " -0.053 5.00e-02 4.00e+02 7.93e-02 1.01e+01 pdb=" N PRO A 715 " 0.137 5.00e-02 4.00e+02 pdb=" CA PRO A 715 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO A 715 " -0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A1246 " -0.052 5.00e-02 4.00e+02 7.79e-02 9.71e+00 pdb=" N PRO A1247 " 0.135 5.00e-02 4.00e+02 pdb=" CA PRO A1247 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO A1247 " -0.044 5.00e-02 4.00e+02 ... (remaining 2016 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.56: 168 2.56 - 3.14: 9356 3.14 - 3.73: 21723 3.73 - 4.31: 26961 4.31 - 4.90: 40927 Nonbonded interactions: 99135 Sorted by model distance: nonbonded pdb=" N GLU B 610 " pdb=" N LEU B 611 " model vdw 1.972 2.560 nonbonded pdb=" CE2 TYR C 609 " pdb=" OE1 GLN C 674 " model vdw 2.078 3.340 nonbonded pdb=" OG SER A 539 " pdb="ZN ZN A1402 " model vdw 2.147 2.230 nonbonded pdb=" N ALA A 542 " pdb="ZN ZN A1402 " model vdw 2.179 2.310 nonbonded pdb=" O VAL A 435 " pdb=" OG1 THR A 565 " model vdw 2.224 3.040 ... (remaining 99130 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' selection = (chain 'C' and resid 493 through 749) } 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.250 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 16.070 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 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 : 0.010 0.690 12999 Z= 0.429 Angle : 1.134 15.509 17897 Z= 0.605 Chirality : 0.071 0.283 2009 Planarity : 0.008 0.079 2019 Dihedral : 17.493 89.805 5185 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.15 % Allowed : 11.69 % Favored : 88.15 % Rotamer: Outliers : 0.50 % Allowed : 11.76 % Favored : 87.74 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.16 % Twisted Proline : 3.08 % Twisted General : 0.24 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.89 (0.17), residues: 1317 helix: -2.70 (0.15), residues: 563 sheet: -3.42 (0.44), residues: 99 loop : -3.78 (0.20), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A1126 TYR 0.029 0.003 TYR C 609 PHE 0.020 0.003 PHE C 503 TRP 0.024 0.003 TRP C 691 HIS 0.011 0.002 HIS A 774 Details of bonding type rmsd/Z covalent geometry : bond 0.00754 / 0.37 (12996) covalent geometry : angle 1.13389 / 0.61 (17897) hydrogen bonds : bond 0.18661 / 12.37 ( 487) hydrogen bonds : angle 7.72915 / 5.31 ( 1343) metal coordination : bond 0.42505 / 16.59 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 257 time to evaluate : 0.474 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 456 GLN cc_start: 0.8523 (tp-100) cc_final: 0.7950 (pm20) REVERT: A 544 ARG cc_start: 0.8203 (ttm-80) cc_final: 0.7634 (mtm-85) REVERT: A 600 ILE cc_start: 0.9116 (mp) cc_final: 0.8764 (mt) REVERT: A 602 GLU cc_start: 0.8828 (mm-30) cc_final: 0.8611 (mm-30) REVERT: A 646 GLU cc_start: 0.9052 (tp30) cc_final: 0.8761 (tt0) REVERT: A 659 LEU cc_start: 0.8153 (tp) cc_final: 0.7069 (tp) REVERT: A 662 TRP cc_start: 0.6054 (t-100) cc_final: 0.5118 (t-100) REVERT: A 681 PHE cc_start: 0.8157 (m-80) cc_final: 0.7838 (m-80) REVERT: A 736 GLU cc_start: 0.8652 (mp0) cc_final: 0.8128 (mp0) REVERT: A 740 MET cc_start: 0.9050 (pmm) cc_final: 0.8569 (pmm) REVERT: A 815 LYS cc_start: 0.7664 (mmmt) cc_final: 0.7377 (mttp) REVERT: A 852 ILE cc_start: 0.8639 (tt) cc_final: 0.8413 (tp) REVERT: A 864 PRO cc_start: 0.9189 (Cg_exo) cc_final: 0.8960 (Cg_endo) REVERT: A 1012 LEU cc_start: 0.9150 (tp) cc_final: 0.8891 (tp) REVERT: A 1068 LEU cc_start: 0.9329 (tp) cc_final: 0.9042 (tp) REVERT: A 1081 TYR cc_start: 0.8634 (p90) cc_final: 0.8265 (p90) REVERT: A 1086 LEU cc_start: 0.9101 (mt) cc_final: 0.8675 (mt) REVERT: A 1090 GLU cc_start: 0.8921 (mp0) cc_final: 0.8630 (mp0) REVERT: A 1192 GLU cc_start: 0.8870 (tm-30) cc_final: 0.8234 (tm-30) REVERT: A 1208 ARG cc_start: 0.8326 (tpm170) cc_final: 0.8023 (tpp-160) REVERT: A 1261 PRO cc_start: 0.8808 (Cg_exo) cc_final: 0.8329 (Cg_endo) REVERT: A 1322 MET cc_start: 0.8971 (mtt) cc_final: 0.8401 (mmm) REVERT: C 617 LEU cc_start: 0.8798 (tp) cc_final: 0.8563 (mm) REVERT: C 681 LEU cc_start: 0.8210 (tp) cc_final: 0.7797 (mp) REVERT: C 691 TRP cc_start: 0.7902 (t-100) cc_final: 0.7414 (t60) REVERT: B 512 GLU cc_start: 0.8993 (mp0) cc_final: 0.8371 (mt-10) REVERT: B 535 CYS cc_start: 0.8888 (t) cc_final: 0.8531 (t) REVERT: B 553 TYR cc_start: 0.8353 (m-10) cc_final: 0.8075 (m-80) REVERT: B 573 LEU cc_start: 0.8885 (mm) cc_final: 0.8328 (tp) outliers start: 6 outliers final: 2 residues processed: 262 average time/residue: 0.1227 time to fit residues: 45.6476 Evaluate side-chains 185 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 183 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 612 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 98 optimal weight: 0.0570 chunk 107 optimal weight: 20.0000 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 0.0030 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 8.9990 chunk 91 optimal weight: 20.0000 chunk 55 optimal weight: 3.9990 overall best weight: 0.9512 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 583 ASN A 609 HIS A 614 ASN A 680 HIS A 701 GLN A 888 GLN A 903 HIS A 947 ASN ** A1026 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1143 ASN ** A1170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1266 GLN C 495 GLN ** C 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 566 ASN C 599 ASN ** C 660 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 668 ASN C 678 GLN C 690 ASN C 736 GLN B 625 HIS ** B 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 674 GLN B 690 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.124877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.088533 restraints weight = 31818.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.091720 restraints weight = 15401.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.093730 restraints weight = 9730.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.095160 restraints weight = 7274.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.096055 restraints weight = 5977.021| |-----------------------------------------------------------------------------| r_work (final): 0.3608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.2231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 12999 Z= 0.157 Angle : 0.834 12.685 17897 Z= 0.389 Chirality : 0.062 1.597 2009 Planarity : 0.006 0.058 2019 Dihedral : 13.097 143.614 2395 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.42 % Favored : 90.51 % Rotamer: Outliers : 2.17 % Allowed : 18.52 % Favored : 79.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.16 % Twisted Proline : 1.54 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.30 (0.21), residues: 1317 helix: -0.92 (0.20), residues: 589 sheet: -2.06 (0.59), residues: 78 loop : -3.56 (0.20), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 753 TYR 0.014 0.002 TYR A1303 PHE 0.014 0.001 PHE A 572 TRP 0.019 0.002 TRP C 691 HIS 0.009 0.001 HIS C 625 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.16 (12996) covalent geometry : angle 0.83414 / 0.39 (17897) hydrogen bonds : bond 0.04558 / 2.90 ( 487) hydrogen bonds : angle 5.08187 / 3.56 ( 1343) metal coordination : bond 0.01300 / 0.59 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 200 time to evaluate : 0.455 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 519 HIS cc_start: 0.7861 (t-90) cc_final: 0.7325 (t70) REVERT: A 544 ARG cc_start: 0.8388 (ttm-80) cc_final: 0.7823 (mtm-85) REVERT: A 545 THR cc_start: 0.8953 (t) cc_final: 0.8659 (p) REVERT: A 600 ILE cc_start: 0.9181 (mp) cc_final: 0.8004 (mt) REVERT: A 602 GLU cc_start: 0.8788 (mm-30) cc_final: 0.8306 (mp0) REVERT: A 646 GLU cc_start: 0.9080 (tp30) cc_final: 0.8749 (tt0) REVERT: A 659 LEU cc_start: 0.8037 (tp) cc_final: 0.7744 (tp) REVERT: A 736 GLU cc_start: 0.8633 (mp0) cc_final: 0.8199 (mp0) REVERT: A 740 MET cc_start: 0.8968 (pmm) cc_final: 0.8577 (pmm) REVERT: A 815 LYS cc_start: 0.7542 (mmmt) cc_final: 0.7185 (mttp) REVERT: A 848 TRP cc_start: 0.8599 (m100) cc_final: 0.7784 (m100) REVERT: A 852 ILE cc_start: 0.8738 (tt) cc_final: 0.8404 (tp) REVERT: A 908 MET cc_start: 0.6491 (mmp) cc_final: 0.6118 (mmt) REVERT: A 918 SER cc_start: 0.9338 (p) cc_final: 0.9127 (p) REVERT: A 947 ASN cc_start: 0.9256 (OUTLIER) cc_final: 0.8869 (t0) REVERT: A 1068 LEU cc_start: 0.9429 (tp) cc_final: 0.9036 (tp) REVERT: A 1081 TYR cc_start: 0.8752 (p90) cc_final: 0.8509 (p90) REVERT: A 1147 GLU cc_start: 0.8728 (pp20) cc_final: 0.8181 (pp20) REVERT: A 1155 GLN cc_start: 0.9156 (pp30) cc_final: 0.8453 (pp30) REVERT: A 1192 GLU cc_start: 0.8963 (tm-30) cc_final: 0.8312 (tm-30) REVERT: A 1196 MET cc_start: 0.8728 (mmm) cc_final: 0.8477 (mmm) REVERT: A 1208 ARG cc_start: 0.8345 (tpm170) cc_final: 0.8105 (tpp-160) REVERT: A 1259 ASN cc_start: 0.7080 (t0) cc_final: 0.6864 (t0) REVERT: A 1303 TYR cc_start: 0.8271 (m-80) cc_final: 0.8066 (m-10) REVERT: C 520 MET cc_start: 0.6958 (mmm) cc_final: 0.6381 (tpt) REVERT: C 597 TYR cc_start: 0.9219 (m-80) cc_final: 0.8998 (m-80) REVERT: C 617 LEU cc_start: 0.9054 (tp) cc_final: 0.8789 (mm) REVERT: B 512 GLU cc_start: 0.8999 (mp0) cc_final: 0.8717 (mp0) REVERT: B 522 ARG cc_start: 0.7867 (mtt180) cc_final: 0.7471 (mmt180) REVERT: B 535 CYS cc_start: 0.8732 (t) cc_final: 0.8459 (t) REVERT: B 597 TYR cc_start: 0.7916 (m-10) cc_final: 0.7627 (m-10) REVERT: B 613 SER cc_start: 0.8252 (t) cc_final: 0.7853 (m) REVERT: B 671 VAL cc_start: 0.7698 (OUTLIER) cc_final: 0.7374 (t) REVERT: B 697 MET cc_start: 0.6940 (mmt) cc_final: 0.6304 (mmt) outliers start: 26 outliers final: 13 residues processed: 220 average time/residue: 0.1051 time to fit residues: 34.6142 Evaluate side-chains 192 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 177 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 576 ILE Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain A residue 645 LEU Chi-restraints excluded: chain A residue 744 ASN Chi-restraints excluded: chain A residue 771 ILE Chi-restraints excluded: chain A residue 855 ASP Chi-restraints excluded: chain A residue 947 ASN Chi-restraints excluded: chain A residue 1051 VAL Chi-restraints excluded: chain A residue 1210 VAL Chi-restraints excluded: chain A residue 1220 LEU Chi-restraints excluded: chain A residue 1223 SER Chi-restraints excluded: chain A residue 1269 CYS Chi-restraints excluded: chain B residue 624 LEU Chi-restraints excluded: chain B residue 671 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 35 optimal weight: 0.0570 chunk 68 optimal weight: 6.9990 chunk 112 optimal weight: 2.9990 chunk 58 optimal weight: 4.9990 chunk 47 optimal weight: 0.9980 chunk 100 optimal weight: 9.9990 chunk 122 optimal weight: 5.9990 chunk 30 optimal weight: 10.0000 chunk 69 optimal weight: 2.9990 chunk 106 optimal weight: 3.9990 chunk 17 optimal weight: 0.8980 overall best weight: 1.5902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 903 HIS ** A1026 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1336 GLN A1340 GLN ** C 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 660 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.123924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.087569 restraints weight = 32280.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.090712 restraints weight = 15488.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.092782 restraints weight = 9767.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.094120 restraints weight = 7211.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.094985 restraints weight = 5955.295| |-----------------------------------------------------------------------------| r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.2915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 12999 Z= 0.172 Angle : 0.790 9.875 17897 Z= 0.369 Chirality : 0.049 0.455 2009 Planarity : 0.005 0.059 2019 Dihedral : 12.591 143.250 2395 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.02 % Favored : 89.98 % Rotamer: Outliers : 3.34 % Allowed : 20.02 % Favored : 76.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.16 % Twisted Proline : 1.54 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.66 (0.22), residues: 1317 helix: -0.14 (0.22), residues: 585 sheet: -2.51 (0.51), residues: 103 loop : -3.35 (0.21), residues: 629 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1273 TYR 0.028 0.002 TYR C 609 PHE 0.013 0.001 PHE A 572 TRP 0.026 0.002 TRP A 523 HIS 0.007 0.001 HIS A 934 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.17 (12996) covalent geometry : angle 0.79030 / 0.37 (17897) hydrogen bonds : bond 0.04090 / 2.60 ( 487) hydrogen bonds : angle 4.69895 / 3.29 ( 1343) metal coordination : bond 0.00605 / 0.24 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 181 time to evaluate : 0.466 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 417 HIS cc_start: 0.8937 (m90) cc_final: 0.8703 (t-170) REVERT: A 519 HIS cc_start: 0.7793 (t-90) cc_final: 0.7243 (t-90) REVERT: A 544 ARG cc_start: 0.8449 (ttm-80) cc_final: 0.7898 (mtm-85) REVERT: A 600 ILE cc_start: 0.9245 (mp) cc_final: 0.8942 (mm) REVERT: A 646 GLU cc_start: 0.9108 (tp30) cc_final: 0.8799 (tt0) REVERT: A 731 GLN cc_start: 0.8749 (OUTLIER) cc_final: 0.8534 (mp10) REVERT: A 736 GLU cc_start: 0.8632 (mp0) cc_final: 0.8224 (mp0) REVERT: A 740 MET cc_start: 0.8773 (pmm) cc_final: 0.8310 (pmm) REVERT: A 815 LYS cc_start: 0.7576 (mmmt) cc_final: 0.7139 (mttp) REVERT: A 852 ILE cc_start: 0.8549 (tt) cc_final: 0.8188 (tp) REVERT: A 918 SER cc_start: 0.9404 (p) cc_final: 0.9192 (p) REVERT: A 1068 LEU cc_start: 0.9246 (tp) cc_final: 0.9031 (tp) REVERT: A 1155 GLN cc_start: 0.9150 (pp30) cc_final: 0.8331 (pp30) REVERT: A 1192 GLU cc_start: 0.8985 (tm-30) cc_final: 0.8315 (tm-30) REVERT: A 1196 MET cc_start: 0.8630 (mmm) cc_final: 0.8406 (mmm) REVERT: A 1208 ARG cc_start: 0.8363 (tpm170) cc_final: 0.8073 (tpp-160) REVERT: A 1241 MET cc_start: 0.8920 (tpp) cc_final: 0.8149 (mmt) REVERT: A 1273 ARG cc_start: 0.8542 (mmm160) cc_final: 0.8305 (mmm160) REVERT: A 1303 TYR cc_start: 0.8470 (m-80) cc_final: 0.8187 (m-10) REVERT: A 1322 MET cc_start: 0.8946 (mtt) cc_final: 0.8307 (mmm) REVERT: C 512 GLU cc_start: 0.8924 (tp30) cc_final: 0.8155 (tp30) REVERT: C 516 LEU cc_start: 0.9381 (tt) cc_final: 0.9153 (tt) REVERT: C 520 MET cc_start: 0.7148 (mmm) cc_final: 0.6430 (tpp) REVERT: C 597 TYR cc_start: 0.9210 (m-80) cc_final: 0.8954 (m-80) REVERT: C 617 LEU cc_start: 0.9067 (tp) cc_final: 0.8682 (mm) REVERT: C 681 LEU cc_start: 0.8191 (tp) cc_final: 0.7560 (mp) REVERT: C 691 TRP cc_start: 0.7466 (t60) cc_final: 0.6411 (t60) REVERT: B 512 GLU cc_start: 0.8971 (mp0) cc_final: 0.8135 (mt-10) REVERT: B 522 ARG cc_start: 0.7785 (OUTLIER) cc_final: 0.7574 (mmt180) REVERT: B 535 CYS cc_start: 0.8647 (t) cc_final: 0.8347 (t) REVERT: B 553 TYR cc_start: 0.8021 (m-80) cc_final: 0.7220 (m-80) REVERT: B 566 ASN cc_start: 0.9242 (m-40) cc_final: 0.8820 (m110) REVERT: B 597 TYR cc_start: 0.8027 (m-10) cc_final: 0.7762 (m-80) REVERT: B 613 SER cc_start: 0.8394 (t) cc_final: 0.8035 (m) REVERT: B 655 MET cc_start: 0.7899 (tmm) cc_final: 0.7470 (ppp) REVERT: B 671 VAL cc_start: 0.7634 (t) cc_final: 0.7419 (t) REVERT: B 697 MET cc_start: 0.7007 (mmt) cc_final: 0.6461 (mmt) outliers start: 40 outliers final: 23 residues processed: 208 average time/residue: 0.0978 time to fit residues: 30.9462 Evaluate side-chains 192 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 167 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 520 ASP Chi-restraints excluded: chain A residue 576 ILE Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain A residue 645 LEU Chi-restraints excluded: chain A residue 731 GLN Chi-restraints excluded: chain A residue 744 ASN Chi-restraints excluded: chain A residue 771 ILE Chi-restraints excluded: chain A residue 772 ILE Chi-restraints excluded: chain A residue 814 ASP Chi-restraints excluded: chain A residue 839 THR Chi-restraints excluded: chain A residue 855 ASP Chi-restraints excluded: chain A residue 916 SER Chi-restraints excluded: chain A residue 1130 LEU Chi-restraints excluded: chain A residue 1210 VAL Chi-restraints excluded: chain A residue 1220 LEU Chi-restraints excluded: chain A residue 1223 SER Chi-restraints excluded: chain A residue 1252 PHE Chi-restraints excluded: chain A residue 1269 CYS Chi-restraints excluded: chain C residue 613 SER Chi-restraints excluded: chain C residue 680 ILE Chi-restraints excluded: chain B residue 522 ARG Chi-restraints excluded: chain B residue 546 VAL Chi-restraints excluded: chain B residue 624 LEU Chi-restraints excluded: chain B residue 685 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 18 optimal weight: 1.9990 chunk 46 optimal weight: 5.9990 chunk 10 optimal weight: 6.9990 chunk 43 optimal weight: 3.9990 chunk 11 optimal weight: 10.0000 chunk 35 optimal weight: 4.9990 chunk 67 optimal weight: 4.9990 chunk 103 optimal weight: 0.9980 chunk 26 optimal weight: 0.0270 chunk 95 optimal weight: 9.9990 chunk 21 optimal weight: 3.9990 overall best weight: 2.2044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 639 ASN A 781 GLN A 903 HIS ** A1026 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1187 GLN ** A1256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1340 GLN ** C 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 660 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.116259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.082825 restraints weight = 33443.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.085523 restraints weight = 17116.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.087255 restraints weight = 11136.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.088390 restraints weight = 8483.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.089054 restraints weight = 7082.829| |-----------------------------------------------------------------------------| r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.3510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 12999 Z= 0.198 Angle : 0.800 8.846 17897 Z= 0.374 Chirality : 0.049 0.226 2009 Planarity : 0.005 0.057 2019 Dihedral : 12.473 139.143 2395 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 12.98 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.64 % Favored : 90.28 % Rotamer: Outliers : 4.17 % Allowed : 22.35 % Favored : 73.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.33 (0.23), residues: 1317 helix: 0.17 (0.22), residues: 584 sheet: -2.40 (0.49), residues: 106 loop : -3.20 (0.22), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 517 TYR 0.029 0.002 TYR C 609 PHE 0.018 0.002 PHE B 580 TRP 0.016 0.002 TRP A 523 HIS 0.006 0.001 HIS A 912 Details of bonding type rmsd/Z covalent geometry : bond 0.00434 / 0.20 (12996) covalent geometry : angle 0.80031 / 0.37 (17897) hydrogen bonds : bond 0.04204 / 2.66 ( 487) hydrogen bonds : angle 4.61016 / 3.22 ( 1343) metal coordination : bond 0.00559 / 0.21 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 174 time to evaluate : 0.480 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 544 ARG cc_start: 0.8299 (ttm-80) cc_final: 0.8043 (mtm-85) REVERT: A 635 MET cc_start: 0.8687 (ttm) cc_final: 0.8323 (ptm) REVERT: A 731 GLN cc_start: 0.8928 (OUTLIER) cc_final: 0.8705 (mp10) REVERT: A 736 GLU cc_start: 0.8493 (mp0) cc_final: 0.8107 (mp0) REVERT: A 740 MET cc_start: 0.8782 (pmm) cc_final: 0.8438 (pmm) REVERT: A 815 LYS cc_start: 0.7766 (mmmt) cc_final: 0.7327 (mttp) REVERT: A 852 ILE cc_start: 0.8593 (tt) cc_final: 0.8379 (tp) REVERT: A 1155 GLN cc_start: 0.9016 (pp30) cc_final: 0.8215 (pp30) REVERT: A 1192 GLU cc_start: 0.8877 (tm-30) cc_final: 0.8195 (tm-30) REVERT: A 1208 ARG cc_start: 0.8161 (tpm170) cc_final: 0.7948 (tpp-160) REVERT: A 1334 PHE cc_start: 0.7936 (OUTLIER) cc_final: 0.7609 (p90) REVERT: C 512 GLU cc_start: 0.8921 (tp30) cc_final: 0.8194 (tp30) REVERT: C 516 LEU cc_start: 0.9388 (tt) cc_final: 0.9185 (tt) REVERT: C 520 MET cc_start: 0.7587 (mmm) cc_final: 0.6920 (tpp) REVERT: C 597 TYR cc_start: 0.9156 (m-80) cc_final: 0.8881 (m-80) REVERT: C 617 LEU cc_start: 0.9083 (tp) cc_final: 0.8520 (mt) REVERT: B 512 GLU cc_start: 0.9086 (mp0) cc_final: 0.8861 (mp0) REVERT: B 520 MET cc_start: 0.8230 (ptp) cc_final: 0.8029 (ptp) REVERT: B 522 ARG cc_start: 0.7661 (mtt180) cc_final: 0.7276 (mmt180) REVERT: B 535 CYS cc_start: 0.8714 (t) cc_final: 0.8429 (t) REVERT: B 553 TYR cc_start: 0.7817 (m-80) cc_final: 0.7456 (m-80) REVERT: B 566 ASN cc_start: 0.9281 (m-40) cc_final: 0.9038 (m110) REVERT: B 597 TYR cc_start: 0.8067 (m-10) cc_final: 0.7768 (m-10) REVERT: B 665 TRP cc_start: 0.3502 (m-90) cc_final: 0.3213 (m-90) REVERT: B 671 VAL cc_start: 0.7618 (t) cc_final: 0.7391 (t) REVERT: B 697 MET cc_start: 0.7080 (mmt) cc_final: 0.6389 (mmt) outliers start: 50 outliers final: 32 residues processed: 214 average time/residue: 0.0962 time to fit residues: 31.1456 Evaluate side-chains 187 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 153 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 520 ASP Chi-restraints excluded: chain A residue 576 ILE Chi-restraints excluded: chain A residue 606 MET Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain A residue 645 LEU Chi-restraints excluded: chain A residue 688 PHE Chi-restraints excluded: chain A residue 699 MET Chi-restraints excluded: chain A residue 706 LEU Chi-restraints excluded: chain A residue 731 GLN Chi-restraints excluded: chain A residue 744 ASN Chi-restraints excluded: chain A residue 771 ILE Chi-restraints excluded: chain A residue 772 ILE Chi-restraints excluded: chain A residue 839 THR Chi-restraints excluded: chain A residue 840 VAL Chi-restraints excluded: chain A residue 870 ILE Chi-restraints excluded: chain A residue 916 SER Chi-restraints excluded: chain A residue 1004 VAL Chi-restraints excluded: chain A residue 1051 VAL Chi-restraints excluded: chain A residue 1130 LEU Chi-restraints excluded: chain A residue 1159 THR Chi-restraints excluded: chain A residue 1190 VAL Chi-restraints excluded: chain A residue 1210 VAL Chi-restraints excluded: chain A residue 1220 LEU Chi-restraints excluded: chain A residue 1252 PHE Chi-restraints excluded: chain A residue 1269 CYS Chi-restraints excluded: chain A residue 1334 PHE Chi-restraints excluded: chain C residue 613 SER Chi-restraints excluded: chain C residue 639 ILE Chi-restraints excluded: chain C residue 680 ILE Chi-restraints excluded: chain B residue 546 VAL Chi-restraints excluded: chain B residue 624 LEU Chi-restraints excluded: chain B residue 668 ASN Chi-restraints excluded: chain B residue 685 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 45 optimal weight: 3.9990 chunk 129 optimal weight: 10.0000 chunk 41 optimal weight: 0.5980 chunk 105 optimal weight: 0.0980 chunk 22 optimal weight: 4.9990 chunk 26 optimal weight: 10.0000 chunk 130 optimal weight: 7.9990 chunk 119 optimal weight: 9.9990 chunk 25 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 9 optimal weight: 0.4980 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 417 HIS ** A1026 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1173 HIS ** C 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 622 GLN ** 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 = 0.4187 r_free = 0.4187 target = 0.123226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.090312 restraints weight = 33014.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.093263 restraints weight = 15343.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.095157 restraints weight = 9385.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.096315 restraints weight = 6831.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 57)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.097204 restraints weight = 5576.538| |-----------------------------------------------------------------------------| r_work (final): 0.3684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.3935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 12999 Z= 0.163 Angle : 0.766 9.547 17897 Z= 0.357 Chirality : 0.047 0.228 2009 Planarity : 0.004 0.055 2019 Dihedral : 12.302 139.313 2395 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.79 % Favored : 90.21 % Rotamer: Outliers : 3.92 % Allowed : 23.52 % Favored : 72.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.14 (0.23), residues: 1317 helix: 0.37 (0.22), residues: 585 sheet: -2.50 (0.48), residues: 109 loop : -3.12 (0.22), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A1273 TYR 0.014 0.002 TYR B 698 PHE 0.024 0.001 PHE B 580 TRP 0.015 0.001 TRP A 523 HIS 0.010 0.001 HIS A 417 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.16 (12996) covalent geometry : angle 0.76556 / 0.36 (17897) hydrogen bonds : bond 0.03900 / 2.47 ( 487) hydrogen bonds : angle 4.43275 / 3.11 ( 1343) metal coordination : bond 0.00432 / 0.16 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 162 time to evaluate : 0.453 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 544 ARG cc_start: 0.8462 (ttm-80) cc_final: 0.7971 (mtm-85) REVERT: A 731 GLN cc_start: 0.8841 (OUTLIER) cc_final: 0.8532 (mp10) REVERT: A 736 GLU cc_start: 0.8553 (mp0) cc_final: 0.8153 (mp0) REVERT: A 740 MET cc_start: 0.8747 (pmm) cc_final: 0.8297 (pmm) REVERT: A 815 LYS cc_start: 0.7641 (mmmt) cc_final: 0.7169 (mttp) REVERT: A 852 ILE cc_start: 0.8399 (tt) cc_final: 0.8079 (tp) REVERT: A 1155 GLN cc_start: 0.8895 (pp30) cc_final: 0.8039 (pp30) REVERT: A 1192 GLU cc_start: 0.8996 (tm-30) cc_final: 0.8196 (tm-30) REVERT: A 1208 ARG cc_start: 0.8217 (tpm170) cc_final: 0.7933 (tpp-160) REVERT: A 1241 MET cc_start: 0.9106 (tpt) cc_final: 0.8736 (tpt) REVERT: C 520 MET cc_start: 0.7501 (mmm) cc_final: 0.6708 (tpp) REVERT: C 597 TYR cc_start: 0.9133 (m-80) cc_final: 0.8871 (m-80) REVERT: C 617 LEU cc_start: 0.9050 (tp) cc_final: 0.8783 (mm) REVERT: B 512 GLU cc_start: 0.9138 (mp0) cc_final: 0.8826 (mp0) REVERT: B 522 ARG cc_start: 0.7593 (OUTLIER) cc_final: 0.7234 (tpt90) REVERT: B 535 CYS cc_start: 0.8591 (t) cc_final: 0.8185 (t) REVERT: B 553 TYR cc_start: 0.7619 (m-80) cc_final: 0.7251 (m-80) REVERT: B 597 TYR cc_start: 0.8091 (m-10) cc_final: 0.7821 (m-10) REVERT: B 634 MET cc_start: 0.5387 (tmm) cc_final: 0.5117 (tpp) REVERT: B 649 GLN cc_start: 0.7433 (mp10) cc_final: 0.6701 (pm20) REVERT: B 655 MET cc_start: 0.7926 (tmm) cc_final: 0.7696 (ppp) REVERT: B 671 VAL cc_start: 0.7663 (t) cc_final: 0.7443 (t) REVERT: B 697 MET cc_start: 0.7093 (mmt) cc_final: 0.6863 (mmt) outliers start: 47 outliers final: 27 residues processed: 197 average time/residue: 0.0975 time to fit residues: 29.4716 Evaluate side-chains 188 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 159 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 520 ASP Chi-restraints excluded: chain A residue 606 MET Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain A residue 645 LEU Chi-restraints excluded: chain A residue 688 PHE Chi-restraints excluded: chain A residue 699 MET Chi-restraints excluded: chain A residue 706 LEU Chi-restraints excluded: chain A residue 731 GLN Chi-restraints excluded: chain A residue 744 ASN Chi-restraints excluded: chain A residue 771 ILE Chi-restraints excluded: chain A residue 814 ASP Chi-restraints excluded: chain A residue 916 SER Chi-restraints excluded: chain A residue 1004 VAL Chi-restraints excluded: chain A residue 1051 VAL Chi-restraints excluded: chain A residue 1130 LEU Chi-restraints excluded: chain A residue 1159 THR Chi-restraints excluded: chain A residue 1174 LEU Chi-restraints excluded: chain A residue 1190 VAL Chi-restraints excluded: chain A residue 1210 VAL Chi-restraints excluded: chain A residue 1252 PHE Chi-restraints excluded: chain A residue 1269 CYS Chi-restraints excluded: chain C residue 639 ILE Chi-restraints excluded: chain C residue 680 ILE Chi-restraints excluded: chain B residue 522 ARG Chi-restraints excluded: chain B residue 546 VAL Chi-restraints excluded: chain B residue 624 LEU Chi-restraints excluded: chain B residue 668 ASN Chi-restraints excluded: chain B residue 685 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 121 optimal weight: 9.9990 chunk 102 optimal weight: 20.0000 chunk 19 optimal weight: 0.1980 chunk 34 optimal weight: 0.6980 chunk 133 optimal weight: 5.9990 chunk 20 optimal weight: 2.9990 chunk 99 optimal weight: 20.0000 chunk 91 optimal weight: 5.9990 chunk 51 optimal weight: 2.9990 chunk 86 optimal weight: 6.9990 chunk 52 optimal weight: 3.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 774 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1026 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 736 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.113517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.074825 restraints weight = 38929.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.077755 restraints weight = 18970.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.079667 restraints weight = 12217.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.080815 restraints weight = 9236.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 58)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.081636 restraints weight = 7796.453| |-----------------------------------------------------------------------------| r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.4203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 12999 Z= 0.190 Angle : 0.785 10.063 17897 Z= 0.365 Chirality : 0.048 0.232 2009 Planarity : 0.004 0.051 2019 Dihedral : 12.317 137.751 2395 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 13.51 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.95 % Favored : 89.98 % Rotamer: Outliers : 3.42 % Allowed : 24.85 % Favored : 71.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.00 (0.23), residues: 1317 helix: 0.50 (0.22), residues: 582 sheet: -2.45 (0.48), residues: 109 loop : -3.04 (0.22), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A1273 TYR 0.013 0.002 TYR A1229 PHE 0.027 0.002 PHE B 580 TRP 0.013 0.001 TRP A 523 HIS 0.008 0.001 HIS A 774 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.19 (12996) covalent geometry : angle 0.78505 / 0.37 (17897) hydrogen bonds : bond 0.04029 / 2.57 ( 487) hydrogen bonds : angle 4.46553 / 3.12 ( 1343) metal coordination : bond 0.00486 / 0.19 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 157 time to evaluate : 0.487 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 731 GLN cc_start: 0.8844 (OUTLIER) cc_final: 0.8538 (mp10) REVERT: A 736 GLU cc_start: 0.8531 (mp0) cc_final: 0.8152 (mp0) REVERT: A 740 MET cc_start: 0.8799 (pmm) cc_final: 0.8322 (pmm) REVERT: A 815 LYS cc_start: 0.7688 (mmmt) cc_final: 0.7202 (mttp) REVERT: A 852 ILE cc_start: 0.8379 (OUTLIER) cc_final: 0.8112 (tp) REVERT: A 1154 MET cc_start: 0.9400 (mmm) cc_final: 0.9194 (tpp) REVERT: A 1155 GLN cc_start: 0.8976 (pp30) cc_final: 0.8117 (pp30) REVERT: A 1192 GLU cc_start: 0.9008 (tm-30) cc_final: 0.8382 (tm-30) REVERT: A 1208 ARG cc_start: 0.8224 (tpm170) cc_final: 0.7898 (tpp-160) REVERT: C 520 MET cc_start: 0.7302 (mmm) cc_final: 0.6892 (tmm) REVERT: C 597 TYR cc_start: 0.9255 (m-80) cc_final: 0.8992 (m-80) REVERT: C 617 LEU cc_start: 0.8936 (tp) cc_final: 0.8607 (mm) REVERT: C 737 GLU cc_start: 0.8975 (mm-30) cc_final: 0.8517 (mp0) REVERT: B 535 CYS cc_start: 0.8645 (t) cc_final: 0.8208 (t) REVERT: B 553 TYR cc_start: 0.7381 (m-80) cc_final: 0.7033 (m-80) REVERT: B 634 MET cc_start: 0.5624 (tmm) cc_final: 0.5280 (tpp) REVERT: B 649 GLN cc_start: 0.7120 (mp10) cc_final: 0.6446 (pm20) REVERT: B 655 MET cc_start: 0.8151 (tmm) cc_final: 0.7940 (ppp) outliers start: 41 outliers final: 34 residues processed: 185 average time/residue: 0.0944 time to fit residues: 27.1432 Evaluate side-chains 189 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 153 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 520 ASP Chi-restraints excluded: chain A residue 606 MET Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain A residue 645 LEU Chi-restraints excluded: chain A residue 688 PHE Chi-restraints excluded: chain A residue 699 MET Chi-restraints excluded: chain A residue 706 LEU Chi-restraints excluded: chain A residue 731 GLN Chi-restraints excluded: chain A residue 744 ASN Chi-restraints excluded: chain A residue 771 ILE Chi-restraints excluded: chain A residue 852 ILE Chi-restraints excluded: chain A residue 916 SER Chi-restraints excluded: chain A residue 962 ILE Chi-restraints excluded: chain A residue 1004 VAL Chi-restraints excluded: chain A residue 1051 VAL Chi-restraints excluded: chain A residue 1130 LEU Chi-restraints excluded: chain A residue 1159 THR Chi-restraints excluded: chain A residue 1164 ILE Chi-restraints excluded: chain A residue 1174 LEU Chi-restraints excluded: chain A residue 1190 VAL Chi-restraints excluded: chain A residue 1210 VAL Chi-restraints excluded: chain A residue 1252 PHE Chi-restraints excluded: chain A residue 1256 GLN Chi-restraints excluded: chain A residue 1269 CYS Chi-restraints excluded: chain A residue 1270 LEU Chi-restraints excluded: chain A residue 1281 ILE Chi-restraints excluded: chain C residue 639 ILE Chi-restraints excluded: chain C residue 680 ILE Chi-restraints excluded: chain C residue 748 GLU Chi-restraints excluded: chain B residue 522 ARG Chi-restraints excluded: chain B residue 546 VAL Chi-restraints excluded: chain B residue 624 LEU Chi-restraints excluded: chain B residue 668 ASN Chi-restraints excluded: chain B residue 685 HIS Chi-restraints excluded: chain B residue 698 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 22 optimal weight: 4.9990 chunk 47 optimal weight: 2.9990 chunk 5 optimal weight: 6.9990 chunk 21 optimal weight: 2.9990 chunk 112 optimal weight: 0.4980 chunk 137 optimal weight: 7.9990 chunk 36 optimal weight: 0.9980 chunk 67 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 98 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 663 ASN ** A 774 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1026 HIS ** A1170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 517 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 622 GLN ** 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 = 0.3929 r_free = 0.3929 target = 0.115722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.077432 restraints weight = 38917.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.080520 restraints weight = 18564.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 60)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.082501 restraints weight = 11802.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.083748 restraints weight = 8850.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.084582 restraints weight = 7390.095| |-----------------------------------------------------------------------------| r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.4467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 12999 Z= 0.137 Angle : 0.737 10.243 17897 Z= 0.344 Chirality : 0.046 0.232 2009 Planarity : 0.004 0.051 2019 Dihedral : 12.093 139.048 2395 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.72 % Favored : 90.28 % Rotamer: Outliers : 3.67 % Allowed : 25.10 % Favored : 71.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.86 (0.23), residues: 1317 helix: 0.61 (0.23), residues: 584 sheet: -2.15 (0.51), residues: 107 loop : -3.02 (0.22), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A1273 TYR 0.013 0.001 TYR B 621 PHE 0.032 0.001 PHE B 580 TRP 0.013 0.001 TRP A 523 HIS 0.006 0.001 HIS A 774 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.14 (12996) covalent geometry : angle 0.73677 / 0.34 (17897) hydrogen bonds : bond 0.03648 / 2.34 ( 487) hydrogen bonds : angle 4.27763 / 3.02 ( 1343) metal coordination : bond 0.00294 / 0.11 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 161 time to evaluate : 0.458 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 635 MET cc_start: 0.8969 (ttp) cc_final: 0.8627 (ptm) REVERT: A 688 PHE cc_start: 0.8104 (OUTLIER) cc_final: 0.7692 (t80) REVERT: A 731 GLN cc_start: 0.8855 (OUTLIER) cc_final: 0.8568 (mp10) REVERT: A 736 GLU cc_start: 0.8506 (mp0) cc_final: 0.8141 (mp0) REVERT: A 740 MET cc_start: 0.8841 (pmm) cc_final: 0.8368 (pmm) REVERT: A 815 LYS cc_start: 0.7717 (mmmt) cc_final: 0.7200 (mttp) REVERT: A 852 ILE cc_start: 0.8295 (OUTLIER) cc_final: 0.7968 (tp) REVERT: A 1040 MET cc_start: 0.9194 (tpp) cc_final: 0.8783 (mmt) REVERT: A 1118 PHE cc_start: 0.7755 (m-10) cc_final: 0.7317 (m-10) REVERT: A 1154 MET cc_start: 0.9353 (mmm) cc_final: 0.8643 (tpt) REVERT: A 1155 GLN cc_start: 0.8916 (pp30) cc_final: 0.7923 (pp30) REVERT: A 1192 GLU cc_start: 0.8968 (tm-30) cc_final: 0.8298 (tm-30) REVERT: A 1208 ARG cc_start: 0.8180 (tpm170) cc_final: 0.7818 (tpp-160) REVERT: C 516 LEU cc_start: 0.9443 (tt) cc_final: 0.9064 (pp) REVERT: C 597 TYR cc_start: 0.9223 (m-80) cc_final: 0.8959 (m-80) REVERT: C 617 LEU cc_start: 0.8946 (tp) cc_final: 0.8335 (mt) REVERT: B 517 HIS cc_start: 0.8613 (OUTLIER) cc_final: 0.8403 (t-170) REVERT: B 535 CYS cc_start: 0.8618 (t) cc_final: 0.8177 (t) REVERT: B 553 TYR cc_start: 0.7211 (m-80) cc_final: 0.6766 (m-80) REVERT: B 634 MET cc_start: 0.5947 (tmm) cc_final: 0.5541 (tpp) REVERT: B 649 GLN cc_start: 0.7123 (mp10) cc_final: 0.6496 (pm20) REVERT: B 697 MET cc_start: 0.7233 (mmt) cc_final: 0.7014 (mmt) outliers start: 44 outliers final: 31 residues processed: 192 average time/residue: 0.0947 time to fit residues: 28.4543 Evaluate side-chains 192 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 157 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 520 ASP Chi-restraints excluded: chain A residue 606 MET Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain A residue 645 LEU Chi-restraints excluded: chain A residue 663 ASN Chi-restraints excluded: chain A residue 688 PHE Chi-restraints excluded: chain A residue 699 MET Chi-restraints excluded: chain A residue 706 LEU Chi-restraints excluded: chain A residue 731 GLN Chi-restraints excluded: chain A residue 744 ASN Chi-restraints excluded: chain A residue 771 ILE Chi-restraints excluded: chain A residue 772 ILE Chi-restraints excluded: chain A residue 852 ILE Chi-restraints excluded: chain A residue 916 SER Chi-restraints excluded: chain A residue 1004 VAL Chi-restraints excluded: chain A residue 1130 LEU Chi-restraints excluded: chain A residue 1159 THR Chi-restraints excluded: chain A residue 1164 ILE Chi-restraints excluded: chain A residue 1174 LEU Chi-restraints excluded: chain A residue 1190 VAL Chi-restraints excluded: chain A residue 1210 VAL Chi-restraints excluded: chain A residue 1252 PHE Chi-restraints excluded: chain A residue 1269 CYS Chi-restraints excluded: chain A residue 1281 ILE Chi-restraints excluded: chain C residue 526 VAL Chi-restraints excluded: chain C residue 639 ILE Chi-restraints excluded: chain C residue 748 GLU Chi-restraints excluded: chain B residue 517 HIS Chi-restraints excluded: chain B residue 522 ARG Chi-restraints excluded: chain B residue 546 VAL Chi-restraints excluded: chain B residue 624 LEU Chi-restraints excluded: chain B residue 668 ASN Chi-restraints excluded: chain B residue 685 HIS Chi-restraints excluded: chain B residue 698 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 112 optimal weight: 0.2980 chunk 72 optimal weight: 4.9990 chunk 103 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 chunk 64 optimal weight: 0.1980 chunk 96 optimal weight: 20.0000 chunk 135 optimal weight: 10.0000 chunk 101 optimal weight: 5.9990 chunk 82 optimal weight: 2.9990 chunk 126 optimal weight: 7.9990 chunk 116 optimal weight: 2.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 774 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 517 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.114771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.076558 restraints weight = 38607.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.079577 restraints weight = 18534.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.081551 restraints weight = 11846.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.082790 restraints weight = 8908.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 59)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.083577 restraints weight = 7458.702| |-----------------------------------------------------------------------------| r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.4614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 12999 Z= 0.155 Angle : 0.764 9.759 17897 Z= 0.359 Chirality : 0.047 0.238 2009 Planarity : 0.004 0.049 2019 Dihedral : 12.066 137.869 2395 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.64 % Favored : 90.36 % Rotamer: Outliers : 3.67 % Allowed : 25.02 % Favored : 71.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.67 (0.23), residues: 1317 helix: 0.69 (0.22), residues: 584 sheet: -1.50 (0.58), residues: 84 loop : -2.90 (0.22), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A1273 TYR 0.020 0.002 TYR A1236 PHE 0.024 0.001 PHE B 580 TRP 0.012 0.001 TRP A 523 HIS 0.012 0.001 HIS C 517 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.16 (12996) covalent geometry : angle 0.76389 / 0.36 (17897) hydrogen bonds : bond 0.03784 / 2.42 ( 487) hydrogen bonds : angle 4.29225 / 3.01 ( 1343) metal coordination : bond 0.00361 / 0.14 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 158 time to evaluate : 0.442 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 635 MET cc_start: 0.8920 (OUTLIER) cc_final: 0.8414 (ptm) REVERT: A 688 PHE cc_start: 0.8245 (OUTLIER) cc_final: 0.7827 (t80) REVERT: A 731 GLN cc_start: 0.8852 (OUTLIER) cc_final: 0.8495 (mp10) REVERT: A 736 GLU cc_start: 0.8489 (mp0) cc_final: 0.8117 (mp0) REVERT: A 740 MET cc_start: 0.8839 (pmm) cc_final: 0.8226 (pmm) REVERT: A 815 LYS cc_start: 0.7728 (mmmt) cc_final: 0.7269 (mttp) REVERT: A 850 THR cc_start: 0.8471 (OUTLIER) cc_final: 0.8247 (p) REVERT: A 852 ILE cc_start: 0.8263 (tt) cc_final: 0.7988 (tp) REVERT: A 1154 MET cc_start: 0.9399 (mmm) cc_final: 0.8614 (tpt) REVERT: A 1155 GLN cc_start: 0.8950 (pp30) cc_final: 0.8043 (pp30) REVERT: A 1192 GLU cc_start: 0.8973 (tm-30) cc_final: 0.8309 (tm-30) REVERT: A 1196 MET cc_start: 0.9061 (mmp) cc_final: 0.8840 (mmm) REVERT: A 1208 ARG cc_start: 0.8179 (tpm170) cc_final: 0.7807 (tpp-160) REVERT: C 516 LEU cc_start: 0.9429 (tt) cc_final: 0.8974 (pp) REVERT: C 520 MET cc_start: 0.7095 (mmm) cc_final: 0.6462 (tmm) REVERT: C 597 TYR cc_start: 0.9204 (m-80) cc_final: 0.8916 (m-80) REVERT: C 617 LEU cc_start: 0.8965 (tp) cc_final: 0.8384 (mt) REVERT: C 657 CYS cc_start: 0.4501 (OUTLIER) cc_final: 0.4162 (m) REVERT: B 517 HIS cc_start: 0.8667 (OUTLIER) cc_final: 0.8351 (t-170) REVERT: B 522 ARG cc_start: 0.7642 (OUTLIER) cc_final: 0.7092 (tpt90) REVERT: B 535 CYS cc_start: 0.8641 (t) cc_final: 0.8198 (t) REVERT: B 553 TYR cc_start: 0.7265 (m-80) cc_final: 0.6819 (m-80) REVERT: B 634 MET cc_start: 0.5991 (tmm) cc_final: 0.5618 (tpp) REVERT: B 649 GLN cc_start: 0.7218 (mp10) cc_final: 0.6548 (pm20) REVERT: B 697 MET cc_start: 0.7309 (mmt) cc_final: 0.7056 (mmt) outliers start: 44 outliers final: 30 residues processed: 188 average time/residue: 0.0911 time to fit residues: 26.8052 Evaluate side-chains 190 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 153 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 606 MET Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain A residue 635 MET Chi-restraints excluded: chain A residue 645 LEU Chi-restraints excluded: chain A residue 656 ILE Chi-restraints excluded: chain A residue 688 PHE Chi-restraints excluded: chain A residue 699 MET Chi-restraints excluded: chain A residue 706 LEU Chi-restraints excluded: chain A residue 731 GLN Chi-restraints excluded: chain A residue 744 ASN Chi-restraints excluded: chain A residue 771 ILE Chi-restraints excluded: chain A residue 772 ILE Chi-restraints excluded: chain A residue 850 THR Chi-restraints excluded: chain A residue 908 MET Chi-restraints excluded: chain A residue 916 SER Chi-restraints excluded: chain A residue 1004 VAL Chi-restraints excluded: chain A residue 1130 LEU Chi-restraints excluded: chain A residue 1159 THR Chi-restraints excluded: chain A residue 1164 ILE Chi-restraints excluded: chain A residue 1174 LEU Chi-restraints excluded: chain A residue 1190 VAL Chi-restraints excluded: chain A residue 1210 VAL Chi-restraints excluded: chain A residue 1252 PHE Chi-restraints excluded: chain A residue 1269 CYS Chi-restraints excluded: chain C residue 526 VAL Chi-restraints excluded: chain C residue 639 ILE Chi-restraints excluded: chain C residue 657 CYS Chi-restraints excluded: chain C residue 680 ILE Chi-restraints excluded: chain C residue 748 GLU Chi-restraints excluded: chain B residue 517 HIS Chi-restraints excluded: chain B residue 522 ARG Chi-restraints excluded: chain B residue 546 VAL Chi-restraints excluded: chain B residue 624 LEU Chi-restraints excluded: chain B residue 668 ASN Chi-restraints excluded: chain B residue 685 HIS Chi-restraints excluded: chain B residue 698 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 26 optimal weight: 0.0870 chunk 138 optimal weight: 4.9990 chunk 4 optimal weight: 0.1980 chunk 43 optimal weight: 0.6980 chunk 89 optimal weight: 6.9990 chunk 102 optimal weight: 7.9990 chunk 127 optimal weight: 6.9990 chunk 128 optimal weight: 0.0170 chunk 41 optimal weight: 0.5980 chunk 19 optimal weight: 2.9990 chunk 77 optimal weight: 0.9980 overall best weight: 0.3196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 774 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 625 HIS C 674 GLN B 517 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.122365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.084714 restraints weight = 35701.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.087805 restraints weight = 17180.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.089784 restraints weight = 10822.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.091081 restraints weight = 8022.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.091748 restraints weight = 6595.623| |-----------------------------------------------------------------------------| r_work (final): 0.3662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.4840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 12999 Z= 0.125 Angle : 0.736 10.961 17897 Z= 0.345 Chirality : 0.046 0.247 2009 Planarity : 0.004 0.053 2019 Dihedral : 11.826 140.000 2395 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.04 % Favored : 90.96 % Rotamer: Outliers : 2.75 % Allowed : 26.44 % Favored : 70.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.62 (0.23), residues: 1317 helix: 0.75 (0.23), residues: 577 sheet: -1.54 (0.58), residues: 87 loop : -2.86 (0.22), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A1273 TYR 0.017 0.001 TYR B 597 PHE 0.021 0.001 PHE A 448 TRP 0.013 0.001 TRP A 523 HIS 0.013 0.001 HIS C 517 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 (12996) covalent geometry : angle 0.73604 / 0.34 (17897) hydrogen bonds : bond 0.03489 / 2.24 ( 487) hydrogen bonds : angle 4.21006 / 2.98 ( 1343) metal coordination : bond 0.00234 / 0.10 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 170 time to evaluate : 0.460 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 635 MET cc_start: 0.8904 (OUTLIER) cc_final: 0.8385 (ptm) REVERT: A 731 GLN cc_start: 0.8786 (OUTLIER) cc_final: 0.8481 (mp10) REVERT: A 736 GLU cc_start: 0.8477 (mp0) cc_final: 0.8078 (mp0) REVERT: A 740 MET cc_start: 0.8850 (pmm) cc_final: 0.8194 (pmm) REVERT: A 815 LYS cc_start: 0.7628 (mmmt) cc_final: 0.7148 (mttp) REVERT: A 850 THR cc_start: 0.8245 (OUTLIER) cc_final: 0.8030 (p) REVERT: A 852 ILE cc_start: 0.8131 (tt) cc_final: 0.7837 (tp) REVERT: A 1040 MET cc_start: 0.9147 (tpp) cc_final: 0.8660 (mmt) REVERT: A 1154 MET cc_start: 0.9442 (mmm) cc_final: 0.8759 (tpt) REVERT: A 1155 GLN cc_start: 0.8780 (pp30) cc_final: 0.8041 (pp30) REVERT: A 1192 GLU cc_start: 0.9006 (tm-30) cc_final: 0.8350 (tm-30) REVERT: A 1196 MET cc_start: 0.8973 (mmp) cc_final: 0.8592 (mmm) REVERT: A 1208 ARG cc_start: 0.8141 (tpm170) cc_final: 0.7861 (tpp-160) REVERT: C 512 GLU cc_start: 0.8789 (tp30) cc_final: 0.7949 (tp30) REVERT: C 516 LEU cc_start: 0.9406 (tt) cc_final: 0.8721 (pp) REVERT: C 520 MET cc_start: 0.7013 (mmm) cc_final: 0.6324 (tmm) REVERT: C 597 TYR cc_start: 0.9203 (m-80) cc_final: 0.8911 (m-80) REVERT: C 617 LEU cc_start: 0.8930 (tp) cc_final: 0.8328 (mt) REVERT: C 621 TYR cc_start: 0.7497 (t80) cc_final: 0.6911 (t80) REVERT: C 625 HIS cc_start: 0.7642 (m-70) cc_final: 0.7395 (m90) REVERT: C 657 CYS cc_start: 0.4602 (OUTLIER) cc_final: 0.4294 (m) REVERT: B 522 ARG cc_start: 0.7871 (OUTLIER) cc_final: 0.7142 (tpt90) REVERT: B 535 CYS cc_start: 0.8571 (t) cc_final: 0.8127 (t) REVERT: B 553 TYR cc_start: 0.7203 (m-80) cc_final: 0.6803 (m-80) REVERT: B 621 TYR cc_start: 0.8213 (t80) cc_final: 0.8008 (t80) REVERT: B 634 MET cc_start: 0.6120 (tmm) cc_final: 0.5795 (tpp) REVERT: B 649 GLN cc_start: 0.7163 (mp10) cc_final: 0.6580 (pm20) REVERT: B 697 MET cc_start: 0.7274 (mmt) cc_final: 0.7000 (mmt) outliers start: 33 outliers final: 19 residues processed: 191 average time/residue: 0.0985 time to fit residues: 28.9693 Evaluate side-chains 177 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 153 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain A residue 635 MET Chi-restraints excluded: chain A residue 645 LEU Chi-restraints excluded: chain A residue 731 GLN Chi-restraints excluded: chain A residue 744 ASN Chi-restraints excluded: chain A residue 748 LYS Chi-restraints excluded: chain A residue 772 ILE Chi-restraints excluded: chain A residue 850 THR Chi-restraints excluded: chain A residue 908 MET Chi-restraints excluded: chain A residue 1130 LEU Chi-restraints excluded: chain A residue 1174 LEU Chi-restraints excluded: chain A residue 1190 VAL Chi-restraints excluded: chain A residue 1210 VAL Chi-restraints excluded: chain A residue 1252 PHE Chi-restraints excluded: chain C residue 526 VAL Chi-restraints excluded: chain C residue 657 CYS Chi-restraints excluded: chain C residue 680 ILE Chi-restraints excluded: chain C residue 748 GLU Chi-restraints excluded: chain B residue 522 ARG Chi-restraints excluded: chain B residue 546 VAL Chi-restraints excluded: chain B residue 624 LEU Chi-restraints excluded: chain B residue 668 ASN Chi-restraints excluded: chain B residue 698 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 93 optimal weight: 3.9990 chunk 115 optimal weight: 5.9990 chunk 136 optimal weight: 9.9990 chunk 65 optimal weight: 4.9990 chunk 71 optimal weight: 0.9990 chunk 40 optimal weight: 3.9990 chunk 85 optimal weight: 0.9980 chunk 62 optimal weight: 6.9990 chunk 126 optimal weight: 7.9990 chunk 123 optimal weight: 0.2980 chunk 49 optimal weight: 4.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 774 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1266 GLN A1267 GLN ** B 622 GLN ** 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 = 0.3910 r_free = 0.3910 target = 0.114328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.076342 restraints weight = 38874.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.079334 restraints weight = 18749.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.081275 restraints weight = 11954.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.082501 restraints weight = 8973.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.083251 restraints weight = 7493.255| |-----------------------------------------------------------------------------| r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.4922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 12999 Z= 0.185 Angle : 0.808 10.786 17897 Z= 0.381 Chirality : 0.047 0.253 2009 Planarity : 0.005 0.076 2019 Dihedral : 11.931 139.841 2395 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.72 % Favored : 90.28 % Rotamer: Outliers : 2.34 % Allowed : 27.19 % Favored : 70.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.55 (0.24), residues: 1317 helix: 0.76 (0.22), residues: 578 sheet: -1.61 (0.57), residues: 97 loop : -2.76 (0.23), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A1273 TYR 0.016 0.001 TYR A 784 PHE 0.017 0.001 PHE A1069 TRP 0.015 0.002 TRP A 523 HIS 0.009 0.001 HIS C 517 Details of bonding type rmsd/Z covalent geometry : bond 0.00413 / 0.19 (12996) covalent geometry : angle 0.80782 / 0.38 (17897) hydrogen bonds : bond 0.03922 / 2.50 ( 487) hydrogen bonds : angle 4.38501 / 3.06 ( 1343) metal coordination : bond 0.00468 / 0.19 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 152 time to evaluate : 0.474 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 635 MET cc_start: 0.8950 (OUTLIER) cc_final: 0.8435 (ptm) REVERT: A 731 GLN cc_start: 0.8825 (OUTLIER) cc_final: 0.8476 (mp10) REVERT: A 736 GLU cc_start: 0.8473 (mp0) cc_final: 0.8038 (mp0) REVERT: A 740 MET cc_start: 0.8845 (pmm) cc_final: 0.8213 (pmm) REVERT: A 815 LYS cc_start: 0.7720 (mmmt) cc_final: 0.7240 (mttp) REVERT: A 850 THR cc_start: 0.8394 (OUTLIER) cc_final: 0.8179 (p) REVERT: A 852 ILE cc_start: 0.8193 (tt) cc_final: 0.7889 (tp) REVERT: A 1022 MET cc_start: 0.8567 (tpp) cc_final: 0.8307 (tpp) REVERT: A 1155 GLN cc_start: 0.8969 (pp30) cc_final: 0.8126 (pp30) REVERT: A 1192 GLU cc_start: 0.9014 (tm-30) cc_final: 0.8339 (tm-30) REVERT: A 1208 ARG cc_start: 0.8110 (tpm170) cc_final: 0.7772 (tpp-160) REVERT: C 512 GLU cc_start: 0.8822 (tp30) cc_final: 0.8010 (tp30) REVERT: C 516 LEU cc_start: 0.9369 (tt) cc_final: 0.8772 (pp) REVERT: C 597 TYR cc_start: 0.9185 (m-80) cc_final: 0.8897 (m-80) REVERT: C 617 LEU cc_start: 0.8941 (tp) cc_final: 0.8422 (mt) REVERT: C 621 TYR cc_start: 0.7431 (t80) cc_final: 0.6856 (t80) REVERT: C 625 HIS cc_start: 0.7598 (m-70) cc_final: 0.7334 (m-70) REVERT: B 512 GLU cc_start: 0.9236 (mp0) cc_final: 0.8338 (mt-10) REVERT: B 522 ARG cc_start: 0.7845 (OUTLIER) cc_final: 0.7091 (tpt90) REVERT: B 535 CYS cc_start: 0.8687 (t) cc_final: 0.8203 (t) REVERT: B 553 TYR cc_start: 0.7235 (m-80) cc_final: 0.6749 (m-80) REVERT: B 634 MET cc_start: 0.6424 (tmm) cc_final: 0.5653 (mpp) REVERT: B 649 GLN cc_start: 0.7213 (mp10) cc_final: 0.6651 (pm20) REVERT: B 697 MET cc_start: 0.7355 (mmt) cc_final: 0.7064 (mmt) outliers start: 28 outliers final: 23 residues processed: 171 average time/residue: 0.0960 time to fit residues: 25.5675 Evaluate side-chains 173 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 146 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 520 ASP Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain A residue 635 MET Chi-restraints excluded: chain A residue 645 LEU Chi-restraints excluded: chain A residue 731 GLN Chi-restraints excluded: chain A residue 744 ASN Chi-restraints excluded: chain A residue 771 ILE Chi-restraints excluded: chain A residue 772 ILE Chi-restraints excluded: chain A residue 850 THR Chi-restraints excluded: chain A residue 908 MET Chi-restraints excluded: chain A residue 1130 LEU Chi-restraints excluded: chain A residue 1174 LEU Chi-restraints excluded: chain A residue 1190 VAL Chi-restraints excluded: chain A residue 1210 VAL Chi-restraints excluded: chain A residue 1252 PHE Chi-restraints excluded: chain A residue 1269 CYS Chi-restraints excluded: chain C residue 526 VAL Chi-restraints excluded: chain C residue 639 ILE Chi-restraints excluded: chain C residue 680 ILE Chi-restraints excluded: chain C residue 748 GLU Chi-restraints excluded: chain B residue 522 ARG Chi-restraints excluded: chain B residue 624 LEU Chi-restraints excluded: chain B residue 657 CYS Chi-restraints excluded: chain B residue 668 ASN Chi-restraints excluded: chain B residue 685 HIS Chi-restraints excluded: chain B residue 698 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 122 optimal weight: 1.9990 chunk 42 optimal weight: 0.6980 chunk 46 optimal weight: 3.9990 chunk 93 optimal weight: 5.9990 chunk 1 optimal weight: 6.9990 chunk 7 optimal weight: 4.9990 chunk 136 optimal weight: 10.0000 chunk 25 optimal weight: 1.9990 chunk 34 optimal weight: 0.5980 chunk 90 optimal weight: 20.0000 chunk 89 optimal weight: 0.7980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 774 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.116588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.081873 restraints weight = 36002.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.084916 restraints weight = 17365.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.086874 restraints weight = 10928.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 56)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.088149 restraints weight = 8131.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.088879 restraints weight = 6701.113| |-----------------------------------------------------------------------------| r_work (final): 0.3556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.5078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 12999 Z= 0.146 Angle : 0.783 11.111 17897 Z= 0.370 Chirality : 0.047 0.252 2009 Planarity : 0.005 0.074 2019 Dihedral : 11.847 140.417 2395 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.26 % Favored : 90.74 % Rotamer: Outliers : 2.42 % Allowed : 26.86 % Favored : 70.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.53 (0.23), residues: 1317 helix: 0.76 (0.22), residues: 577 sheet: -0.94 (0.68), residues: 68 loop : -2.78 (0.22), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A1273 TYR 0.019 0.001 TYR C 609 PHE 0.023 0.001 PHE A 448 TRP 0.015 0.001 TRP A 523 HIS 0.012 0.001 HIS C 517 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.15 (12996) covalent geometry : angle 0.78299 / 0.37 (17897) hydrogen bonds : bond 0.03691 / 2.36 ( 487) hydrogen bonds : angle 4.33642 / 3.04 ( 1343) metal coordination : bond 0.00316 / 0.12 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2489.21 seconds wall clock time: 43 minutes 55.76 seconds (2635.76 seconds total)