Starting phenix.real_space_refine on Wed Mar 4 10:24:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6v5b_21051/03_2026/6v5b_21051.cif Found real_map, /net/cci-nas-00/data/ceres_data/6v5b_21051/03_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 { model { file = "/net/cci-nas-00/data/ceres_data/6v5b_21051/03_2026/6v5b_21051.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6v5b_21051/03_2026/6v5b_21051.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6v5b_21051/03_2026/6v5b_21051.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6v5b_21051/03_2026/6v5b_21051.map" } 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-dev-5986/lib/python3.9/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: {'RNA': 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: 2.79, per 1000 atoms: 0.22 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: 0.96 Conformation dependent library (CDL) restraints added in 528.5 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: 1.74 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: 2.33 Time building geometry restraints manager: 1.32 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: 17489 3.10 - 6.20: 360 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 - 18.64: 6790 18.64 - 37.28: 859 37.28 - 55.92: 202 55.92 - 74.57: 117 74.57 - 93.21: 13 Dihedral angle restraints: 7981 sinusoidal: 4063 harmonic: 3918 Sorted by residual: dihedral pdb=" CA GLY A 941 " pdb=" C GLY A 941 " pdb=" N ILE A 942 " pdb=" CA ILE A 942 " ideal model delta harmonic sigma weight residual 180.00 133.87 46.13 0 5.00e+00 4.00e-02 8.51e+01 dihedral pdb=" CA VAL A 714 " pdb=" C VAL A 714 " pdb=" N PRO A 715 " pdb=" CA PRO A 715 " ideal model delta harmonic sigma weight residual 180.00 136.29 43.71 0 5.00e+00 4.00e-02 7.64e+01 dihedral pdb=" CA LYS A 748 " pdb=" C LYS A 748 " pdb=" N PRO A 749 " pdb=" CA PRO A 749 " ideal model delta harmonic sigma weight residual -180.00 -147.40 -32.60 0 5.00e+00 4.00e-02 4.25e+01 ... (remaining 7978 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 1502 0.056 - 0.112: 397 0.112 - 0.168: 82 0.168 - 0.224: 21 0.224 - 0.280: 7 Chirality restraints: 2009 Sorted by residual: 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 chirality pdb=" P U D 89 " pdb=" OP1 U D 89 " pdb=" OP2 U D 89 " pdb=" O5' U D 89 " both_signs ideal model delta sigma weight residual True 2.41 -2.17 0.24 2.00e-01 2.50e+01 1.41e+00 chirality pdb=" CA TYR B 609 " pdb=" N TYR B 609 " pdb=" C TYR B 609 " pdb=" CB TYR B 609 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.39e+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: 1.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 15.180 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 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= 0.430 Angle : 1.099 15.509 17897 Z= 0.605 Chirality : 0.057 0.280 2009 Planarity : 0.008 0.079 2019 Dihedral : 18.495 93.207 5441 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 covalent geometry : bond 0.00749 (12996) covalent geometry : angle 1.09866 (17897) hydrogen bonds : bond 0.18661 ( 487) hydrogen bonds : angle 7.72915 ( 1343) metal coordination : bond 0.42505 ( 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 : 0.433 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: 0.7794 (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: 0.1145 time to fit residues: 42.2447 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 : 0.377 ------------------------------------------------------------------------------- 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: 6.9990 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... Flipped N/Q/H residues before XYZ refinement: 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 631 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: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.121530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.088270 restraints weight = 32643.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.091204 restraints weight = 15784.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.093105 restraints weight = 9940.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.094242 restraints weight = 7369.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.095071 restraints weight = 6116.425| |-----------------------------------------------------------------------------| r_work (final): 0.3574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.2219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 12999 Z= 0.145 Angle : 0.697 9.857 17897 Z= 0.357 Chirality : 0.041 0.163 2009 Planarity : 0.005 0.057 2019 Dihedral : 17.132 94.621 2651 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.26 % Favored : 90.66 % Rotamer: Outliers : 2.34 % Allowed : 18.35 % 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: -3.28 (0.21), residues: 1317 helix: -0.91 (0.20), residues: 587 sheet: -2.06 (0.59), residues: 78 loop : -3.54 (0.20), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 961 TYR 0.015 0.002 TYR A1303 PHE 0.014 0.001 PHE A 572 TRP 0.020 0.002 TRP C 691 HIS 0.011 0.001 HIS C 625 Details of bonding type rmsd covalent geometry : bond 0.00314 (12996) covalent geometry : angle 0.69686 (17897) hydrogen bonds : bond 0.04408 ( 487) hydrogen bonds : angle 5.04223 ( 1343) metal coordination : bond 0.01455 ( 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: 28 poor density : 198 time to evaluate : 0.395 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: 0.7963 (t-90) cc_final: 0.7487 (t70) REVERT: A 544 ARG cc_start: 0.8223 (ttm-80) cc_final: 0.7970 (mmt180) REVERT: A 545 THR cc_start: 0.8855 (t) cc_final: 0.8497 (p) REVERT: A 600 ILE cc_start: 0.9254 (mp) cc_final: 0.7961 (mt) REVERT: A 602 GLU cc_start: 0.8507 (mm-30) cc_final: 0.8211 (mp0) REVERT: A 736 GLU cc_start: 0.8517 (mp0) cc_final: 0.8123 (mp0) REVERT: A 740 MET cc_start: 0.8981 (pmm) cc_final: 0.8678 (pmm) REVERT: A 815 LYS cc_start: 0.7612 (mmmt) cc_final: 0.7235 (mttp) REVERT: A 848 TRP cc_start: 0.8628 (m100) cc_final: 0.7865 (m100) REVERT: A 852 ILE cc_start: 0.8844 (tt) cc_final: 0.8590 (tp) REVERT: A 908 MET cc_start: 0.6501 (mmp) cc_final: 0.6287 (mmt) REVERT: A 947 ASN cc_start: 0.9145 (OUTLIER) cc_final: 0.8768 (t0) REVERT: A 1068 LEU cc_start: 0.9318 (tp) cc_final: 0.8999 (tp) REVERT: A 1147 GLU cc_start: 0.8589 (pp20) cc_final: 0.8025 (pp20) REVERT: A 1155 GLN cc_start: 0.9134 (pp30) cc_final: 0.8474 (pp30) REVERT: A 1192 GLU cc_start: 0.8802 (tm-30) cc_final: 0.8224 (tm-30) REVERT: A 1303 TYR cc_start: 0.8036 (m-80) cc_final: 0.7818 (m-10) REVERT: C 520 MET cc_start: 0.7133 (mmm) cc_final: 0.6545 (tpt) REVERT: C 597 TYR cc_start: 0.9141 (m-80) cc_final: 0.8926 (m-80) REVERT: C 617 LEU cc_start: 0.9088 (tp) cc_final: 0.8837 (mm) REVERT: B 512 GLU cc_start: 0.9044 (mp0) cc_final: 0.8739 (mp0) REVERT: B 522 ARG cc_start: 0.7661 (mtt180) cc_final: 0.7324 (mmt180) REVERT: B 597 TYR cc_start: 0.7940 (m-10) cc_final: 0.7612 (m-80) REVERT: B 613 SER cc_start: 0.8301 (t) cc_final: 0.7906 (m) REVERT: B 671 VAL cc_start: 0.7716 (OUTLIER) cc_final: 0.7295 (t) REVERT: B 697 MET cc_start: 0.6995 (mmt) cc_final: 0.6356 (mmt) outliers start: 28 outliers final: 14 residues processed: 220 average time/residue: 0.0927 time to fit residues: 30.3177 Evaluate side-chains 190 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 174 time to evaluate : 0.417 ------------------------------------------------------------------------------- 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 839 THR 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: 0.9990 chunk 68 optimal weight: 7.9990 chunk 112 optimal weight: 6.9990 chunk 58 optimal weight: 4.9990 chunk 47 optimal weight: 3.9990 chunk 100 optimal weight: 9.9990 chunk 122 optimal weight: 5.9990 chunk 30 optimal weight: 2.9990 chunk 69 optimal weight: 0.7980 chunk 106 optimal weight: 10.0000 chunk 17 optimal weight: 0.9980 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 947 ASN ** A1026 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1173 HIS A1336 GLN A1340 GLN ** C 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 622 GLN ** C 660 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.125074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.085172 restraints weight = 33725.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.088328 restraints weight = 16496.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.090401 restraints weight = 10540.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.091779 restraints weight = 7883.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.092626 restraints weight = 6529.982| |-----------------------------------------------------------------------------| r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 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= 0.180 Angle : 0.705 9.819 17897 Z= 0.356 Chirality : 0.041 0.160 2009 Planarity : 0.005 0.058 2019 Dihedral : 16.875 92.644 2651 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 13.47 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.72 % Favored : 90.21 % Rotamer: Outliers : 3.42 % Allowed : 20.18 % Favored : 76.40 % 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: -2.65 (0.22), residues: 1317 helix: -0.13 (0.22), residues: 585 sheet: -2.46 (0.51), residues: 101 loop : -3.37 (0.21), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1273 TYR 0.031 0.002 TYR C 609 PHE 0.015 0.002 PHE A 681 TRP 0.026 0.002 TRP A 523 HIS 0.007 0.001 HIS A 912 Details of bonding type rmsd covalent geometry : bond 0.00394 (12996) covalent geometry : angle 0.70487 (17897) hydrogen bonds : bond 0.04144 ( 487) hydrogen bonds : angle 4.72819 ( 1343) metal coordination : bond 0.00660 ( 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 217 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 176 time to evaluate : 0.447 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: 0.8980 (m90) cc_final: 0.8713 (t-170) REVERT: A 427 MET cc_start: 0.9297 (ppp) cc_final: 0.8953 (ppp) REVERT: A 519 HIS cc_start: 0.7769 (t-90) cc_final: 0.7179 (t-90) REVERT: A 544 ARG cc_start: 0.8468 (ttm-80) cc_final: 0.7839 (mtm-85) REVERT: A 600 ILE cc_start: 0.9262 (mp) cc_final: 0.8970 (mm) REVERT: A 635 MET cc_start: 0.8658 (tpp) cc_final: 0.8442 (ttm) REVERT: A 695 GLU cc_start: 0.7225 (mm-30) cc_final: 0.6763 (tp30) REVERT: A 731 GLN cc_start: 0.8759 (OUTLIER) cc_final: 0.8493 (mp10) REVERT: A 736 GLU cc_start: 0.8650 (mp0) cc_final: 0.8228 (mp0) REVERT: A 740 MET cc_start: 0.8765 (pmm) cc_final: 0.8351 (pmm) REVERT: A 815 LYS cc_start: 0.7605 (mmmt) cc_final: 0.7165 (mttp) REVERT: A 852 ILE cc_start: 0.8531 (tt) cc_final: 0.8195 (tp) REVERT: A 1068 LEU cc_start: 0.9256 (tp) cc_final: 0.9044 (tp) REVERT: A 1155 GLN cc_start: 0.9191 (pp30) cc_final: 0.8349 (pp30) REVERT: A 1192 GLU cc_start: 0.8978 (tm-30) cc_final: 0.8294 (tm-30) REVERT: A 1241 MET cc_start: 0.8958 (tpp) cc_final: 0.8584 (mmt) REVERT: A 1273 ARG cc_start: 0.8570 (mmm160) cc_final: 0.8339 (mmm160) REVERT: A 1303 TYR cc_start: 0.8489 (m-80) cc_final: 0.8199 (m-10) REVERT: A 1322 MET cc_start: 0.8894 (mtt) cc_final: 0.8359 (mmm) REVERT: C 512 GLU cc_start: 0.8905 (tp30) cc_final: 0.8155 (tp30) REVERT: C 516 LEU cc_start: 0.9386 (tt) cc_final: 0.9162 (tt) REVERT: C 520 MET cc_start: 0.7114 (mmm) cc_final: 0.6410 (tpp) REVERT: C 597 TYR cc_start: 0.9230 (m-80) cc_final: 0.8975 (m-80) REVERT: C 617 LEU cc_start: 0.9000 (tp) cc_final: 0.8366 (mt) REVERT: C 691 TRP cc_start: 0.7403 (t60) cc_final: 0.6379 (t-100) REVERT: B 553 TYR cc_start: 0.7971 (m-80) cc_final: 0.7111 (m-80) REVERT: B 566 ASN cc_start: 0.9243 (m-40) cc_final: 0.9039 (m110) REVERT: B 597 TYR cc_start: 0.8009 (m-10) cc_final: 0.7754 (m-80) REVERT: B 613 SER cc_start: 0.8381 (t) cc_final: 0.8008 (m) REVERT: B 671 VAL cc_start: 0.7618 (t) cc_final: 0.7408 (t) REVERT: B 697 MET cc_start: 0.7028 (mmt) cc_final: 0.6503 (mmt) outliers start: 41 outliers final: 26 residues processed: 206 average time/residue: 0.1014 time to fit residues: 31.3475 Evaluate side-chains 187 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 160 time to evaluate : 0.386 ------------------------------------------------------------------------------- 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 870 ILE Chi-restraints excluded: chain A residue 916 SER Chi-restraints excluded: chain A residue 1051 VAL Chi-restraints excluded: chain A residue 1130 LEU 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 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 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: 4.9990 chunk 46 optimal weight: 5.9990 chunk 10 optimal weight: 5.9990 chunk 43 optimal weight: 2.9990 chunk 11 optimal weight: 9.9990 chunk 35 optimal weight: 0.3980 chunk 67 optimal weight: 4.9990 chunk 103 optimal weight: 0.0980 chunk 26 optimal weight: 0.0270 chunk 95 optimal weight: 5.9990 chunk 21 optimal weight: 0.0770 overall best weight: 0.7198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 639 ASN A 663 ASN ** A1026 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1256 GLN ** C 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 660 HIS ** B 517 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 622 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.120503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.087900 restraints weight = 33080.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.090651 restraints weight = 17103.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 61)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.092424 restraints weight = 11152.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.093548 restraints weight = 8435.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.094223 restraints weight = 7068.489| |-----------------------------------------------------------------------------| r_work (final): 0.3578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.3393 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= 0.122 Angle : 0.653 9.567 17897 Z= 0.325 Chirality : 0.039 0.166 2009 Planarity : 0.004 0.057 2019 Dihedral : 16.643 92.284 2651 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.64 % Favored : 90.28 % Rotamer: Outliers : 3.92 % Allowed : 22.10 % Favored : 73.98 % 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: -2.19 (0.23), residues: 1317 helix: 0.26 (0.22), residues: 584 sheet: -2.11 (0.55), residues: 86 loop : -3.15 (0.21), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 753 TYR 0.032 0.001 TYR C 609 PHE 0.016 0.001 PHE B 580 TRP 0.017 0.001 TRP A 523 HIS 0.004 0.001 HIS A 912 Details of bonding type rmsd covalent geometry : bond 0.00272 (12996) covalent geometry : angle 0.65316 (17897) hydrogen bonds : bond 0.03500 ( 487) hydrogen bonds : angle 4.41586 ( 1343) metal coordination : bond 0.00484 ( 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 233 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 186 time to evaluate : 0.467 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 544 ARG cc_start: 0.8297 (ttm-80) cc_final: 0.8031 (mtm-85) REVERT: A 722 MET cc_start: 0.6450 (tpp) cc_final: 0.6151 (tpp) REVERT: A 731 GLN cc_start: 0.8869 (OUTLIER) cc_final: 0.8664 (mp10) REVERT: A 736 GLU cc_start: 0.8482 (mp0) cc_final: 0.8099 (mp0) REVERT: A 740 MET cc_start: 0.8855 (pmm) cc_final: 0.8481 (pmm) REVERT: A 815 LYS cc_start: 0.7653 (mmmt) cc_final: 0.7191 (mttp) REVERT: A 852 ILE cc_start: 0.8600 (tt) cc_final: 0.8359 (tp) REVERT: A 1155 GLN cc_start: 0.9033 (pp30) cc_final: 0.8167 (pp30) REVERT: A 1192 GLU cc_start: 0.8868 (tm-30) cc_final: 0.8239 (tm-30) REVERT: A 1257 ASP cc_start: 0.5750 (p0) cc_final: 0.4967 (p0) REVERT: A 1303 TYR cc_start: 0.8200 (m-80) cc_final: 0.7930 (m-10) REVERT: A 1322 MET cc_start: 0.8670 (mtt) cc_final: 0.8278 (mmm) REVERT: A 1334 PHE cc_start: 0.7585 (OUTLIER) cc_final: 0.6915 (p90) REVERT: C 512 GLU cc_start: 0.8900 (tp30) cc_final: 0.8135 (tp30) REVERT: C 516 LEU cc_start: 0.9373 (tt) cc_final: 0.9157 (tt) REVERT: C 520 MET cc_start: 0.7642 (mmm) cc_final: 0.6920 (tpp) REVERT: C 597 TYR cc_start: 0.9173 (m-80) cc_final: 0.8874 (m-80) REVERT: C 617 LEU cc_start: 0.9090 (tp) cc_final: 0.8831 (mm) REVERT: B 512 GLU cc_start: 0.9335 (mp0) cc_final: 0.8303 (pm20) REVERT: B 522 ARG cc_start: 0.6717 (mmt180) cc_final: 0.5663 (mmt180) REVERT: B 553 TYR cc_start: 0.7728 (m-80) cc_final: 0.7351 (m-80) REVERT: B 597 TYR cc_start: 0.8117 (m-10) cc_final: 0.7816 (m-80) REVERT: B 613 SER cc_start: 0.8370 (t) cc_final: 0.8098 (m) REVERT: B 634 MET cc_start: 0.4974 (tmm) cc_final: 0.4771 (tpp) REVERT: B 655 MET cc_start: 0.7882 (tmm) cc_final: 0.7554 (ppp) REVERT: B 671 VAL cc_start: 0.7633 (t) cc_final: 0.7401 (t) REVERT: B 697 MET cc_start: 0.7017 (mmt) cc_final: 0.6668 (mmt) outliers start: 47 outliers final: 28 residues processed: 219 average time/residue: 0.0937 time to fit residues: 31.2857 Evaluate side-chains 194 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 164 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 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 839 THR Chi-restraints excluded: chain A residue 855 ASP 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 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: 1.9990 chunk 129 optimal weight: 10.0000 chunk 41 optimal weight: 0.4980 chunk 105 optimal weight: 0.5980 chunk 22 optimal weight: 7.9990 chunk 26 optimal weight: 8.9990 chunk 130 optimal weight: 2.9990 chunk 119 optimal weight: 0.0020 chunk 25 optimal weight: 2.9990 chunk 44 optimal weight: 0.0970 chunk 9 optimal weight: 0.0980 overall best weight: 0.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 417 HIS ** A1170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1187 GLN A1264 GLN ** C 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 517 HIS ** B 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.127571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.092209 restraints weight = 32076.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.095515 restraints weight = 15115.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.097732 restraints weight = 9405.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.099196 restraints weight = 6845.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.099964 restraints weight = 5554.528| |-----------------------------------------------------------------------------| r_work (final): 0.3597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.3757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 12999 Z= 0.117 Angle : 0.637 9.329 17897 Z= 0.318 Chirality : 0.039 0.166 2009 Planarity : 0.004 0.053 2019 Dihedral : 16.462 91.886 2651 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.42 % Favored : 90.51 % Rotamer: Outliers : 3.34 % Allowed : 23.94 % Favored : 72.73 % 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: -1.96 (0.23), residues: 1317 helix: 0.43 (0.23), residues: 586 sheet: -1.88 (0.56), residues: 89 loop : -3.02 (0.22), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A1273 TYR 0.020 0.001 TYR A1236 PHE 0.025 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 covalent geometry : bond 0.00257 (12996) covalent geometry : angle 0.63725 (17897) hydrogen bonds : bond 0.03325 ( 487) hydrogen bonds : angle 4.28459 ( 1343) metal coordination : bond 0.00325 ( 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 224 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 184 time to evaluate : 0.418 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 526 ASP cc_start: 0.8360 (OUTLIER) cc_final: 0.8157 (m-30) REVERT: A 544 ARG cc_start: 0.8433 (ttm-80) cc_final: 0.7740 (mtm-85) REVERT: A 545 THR cc_start: 0.8951 (t) cc_final: 0.8701 (p) REVERT: A 577 THR cc_start: 0.7903 (m) cc_final: 0.7314 (p) REVERT: A 600 ILE cc_start: 0.9200 (mp) cc_final: 0.8934 (mm) REVERT: A 602 GLU cc_start: 0.8754 (mm-30) cc_final: 0.8546 (mm-30) REVERT: A 736 GLU cc_start: 0.8549 (mp0) cc_final: 0.8118 (mp0) REVERT: A 740 MET cc_start: 0.8813 (pmm) cc_final: 0.8390 (pmm) REVERT: A 747 THR cc_start: 0.7312 (t) cc_final: 0.6936 (t) REVERT: A 758 ASP cc_start: 0.7586 (OUTLIER) cc_final: 0.6191 (t70) REVERT: A 815 LYS cc_start: 0.7558 (mmmt) cc_final: 0.7062 (mttp) REVERT: A 852 ILE cc_start: 0.8497 (tt) cc_final: 0.8203 (tp) REVERT: A 1035 ASP cc_start: 0.8488 (p0) cc_final: 0.7218 (m-30) REVERT: A 1126 ARG cc_start: 0.7245 (ttt180) cc_final: 0.7001 (tpt-90) REVERT: A 1155 GLN cc_start: 0.8898 (pp30) cc_final: 0.8229 (pp30) REVERT: A 1192 GLU cc_start: 0.8986 (tm-30) cc_final: 0.8283 (tm-30) REVERT: A 1334 PHE cc_start: 0.7657 (OUTLIER) cc_final: 0.6989 (p90) REVERT: C 512 GLU cc_start: 0.8922 (tp30) cc_final: 0.8125 (tp30) REVERT: C 516 LEU cc_start: 0.9392 (tt) cc_final: 0.9105 (tt) REVERT: C 520 MET cc_start: 0.7548 (mmm) cc_final: 0.6834 (tpp) REVERT: C 597 TYR cc_start: 0.9185 (m-80) cc_final: 0.8904 (m-80) REVERT: C 617 LEU cc_start: 0.9040 (tp) cc_final: 0.8474 (mt) REVERT: C 621 TYR cc_start: 0.7599 (t80) cc_final: 0.7278 (t80) REVERT: B 522 ARG cc_start: 0.6449 (mmt180) cc_final: 0.5870 (mmt180) REVERT: B 597 TYR cc_start: 0.8113 (m-10) cc_final: 0.7863 (m-80) REVERT: B 613 SER cc_start: 0.8321 (t) cc_final: 0.8008 (m) REVERT: B 634 MET cc_start: 0.5218 (tmm) cc_final: 0.4972 (tpp) REVERT: B 649 GLN cc_start: 0.7382 (mp10) cc_final: 0.6678 (pm20) REVERT: B 665 TRP cc_start: 0.3324 (m-90) cc_final: 0.3035 (m-90) outliers start: 40 outliers final: 24 residues processed: 211 average time/residue: 0.0894 time to fit residues: 28.8294 Evaluate side-chains 197 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 170 time to evaluate : 0.419 ------------------------------------------------------------------------------- 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 526 ASP 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 744 ASN Chi-restraints excluded: chain A residue 758 ASP Chi-restraints excluded: chain A residue 771 ILE Chi-restraints excluded: chain A residue 772 ILE Chi-restraints excluded: chain A residue 803 LEU Chi-restraints excluded: chain A residue 855 ASP Chi-restraints excluded: chain A residue 1130 LEU Chi-restraints excluded: chain A residue 1159 THR Chi-restraints excluded: chain A residue 1210 VAL Chi-restraints excluded: chain A residue 1252 PHE Chi-restraints excluded: chain A residue 1281 ILE Chi-restraints excluded: chain A residue 1334 PHE Chi-restraints excluded: chain C residue 608 VAL 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 121 optimal weight: 8.9990 chunk 102 optimal weight: 10.0000 chunk 19 optimal weight: 0.9980 chunk 34 optimal weight: 0.8980 chunk 133 optimal weight: 6.9990 chunk 20 optimal weight: 1.9990 chunk 99 optimal weight: 9.9990 chunk 91 optimal weight: 8.9990 chunk 51 optimal weight: 1.9990 chunk 86 optimal weight: 0.9990 chunk 52 optimal weight: 3.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 731 GLN ** A1026 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1340 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.124332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.088521 restraints weight = 32546.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.091651 restraints weight = 15755.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.093692 restraints weight = 9996.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.095018 restraints weight = 7454.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.095725 restraints weight = 6167.475| |-----------------------------------------------------------------------------| r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.3990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12999 Z= 0.144 Angle : 0.661 9.592 17897 Z= 0.330 Chirality : 0.040 0.162 2009 Planarity : 0.004 0.050 2019 Dihedral : 16.373 91.795 2651 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.26 % Favored : 90.74 % Rotamer: Outliers : 3.09 % Allowed : 25.19 % Favored : 71.73 % 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: -1.88 (0.23), residues: 1317 helix: 0.51 (0.22), residues: 588 sheet: -1.95 (0.52), residues: 99 loop : -2.99 (0.22), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A1273 TYR 0.025 0.002 TYR C 609 PHE 0.025 0.002 PHE A1118 TRP 0.013 0.001 TRP A 523 HIS 0.005 0.001 HIS A 912 Details of bonding type rmsd covalent geometry : bond 0.00322 (12996) covalent geometry : angle 0.66086 (17897) hydrogen bonds : bond 0.03503 ( 487) hydrogen bonds : angle 4.26558 ( 1343) metal coordination : bond 0.00331 ( 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 204 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 167 time to evaluate : 0.444 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 736 GLU cc_start: 0.8543 (mp0) cc_final: 0.8129 (mp0) REVERT: A 740 MET cc_start: 0.8824 (pmm) cc_final: 0.8405 (pmm) REVERT: A 758 ASP cc_start: 0.7520 (t70) cc_final: 0.6034 (t70) REVERT: A 815 LYS cc_start: 0.7652 (mmmt) cc_final: 0.7193 (mttp) REVERT: A 852 ILE cc_start: 0.8336 (tt) cc_final: 0.8012 (tp) REVERT: A 861 MET cc_start: 0.9056 (mmt) cc_final: 0.8713 (mmm) REVERT: A 1126 ARG cc_start: 0.7499 (ttt180) cc_final: 0.7260 (tpt-90) REVERT: A 1192 GLU cc_start: 0.8971 (tm-30) cc_final: 0.8181 (tm-30) REVERT: A 1196 MET cc_start: 0.8992 (mmp) cc_final: 0.8759 (mmm) REVERT: A 1241 MET cc_start: 0.9343 (tpp) cc_final: 0.9084 (tpt) REVERT: A 1244 CYS cc_start: 0.7392 (t) cc_final: 0.7144 (t) REVERT: A 1278 GLU cc_start: 0.8267 (tp30) cc_final: 0.7790 (tt0) REVERT: A 1334 PHE cc_start: 0.7899 (OUTLIER) cc_final: 0.7435 (p90) REVERT: C 512 GLU cc_start: 0.8951 (tp30) cc_final: 0.8163 (tp30) REVERT: C 516 LEU cc_start: 0.9369 (tt) cc_final: 0.9108 (tt) REVERT: C 520 MET cc_start: 0.7566 (mmm) cc_final: 0.6812 (tpp) REVERT: C 597 TYR cc_start: 0.9164 (m-80) cc_final: 0.8890 (m-80) REVERT: C 617 LEU cc_start: 0.8976 (tp) cc_final: 0.8753 (mm) REVERT: B 512 GLU cc_start: 0.9359 (mp0) cc_final: 0.8681 (pm20) REVERT: B 522 ARG cc_start: 0.6459 (mmt180) cc_final: 0.5623 (mmt180) REVERT: B 566 ASN cc_start: 0.9219 (m-40) cc_final: 0.8827 (m110) REVERT: B 597 TYR cc_start: 0.8161 (m-10) cc_final: 0.7915 (m-10) REVERT: B 628 LEU cc_start: 0.8603 (tp) cc_final: 0.8386 (tp) REVERT: B 634 MET cc_start: 0.5870 (tmm) cc_final: 0.5613 (tpp) REVERT: B 649 GLN cc_start: 0.7426 (mp10) cc_final: 0.6738 (pm20) REVERT: B 671 VAL cc_start: 0.7637 (t) cc_final: 0.7420 (t) outliers start: 37 outliers final: 26 residues processed: 194 average time/residue: 0.0801 time to fit residues: 24.0971 Evaluate side-chains 188 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 161 time to evaluate : 0.356 ------------------------------------------------------------------------------- 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 744 ASN Chi-restraints excluded: chain A residue 771 ILE Chi-restraints excluded: chain A residue 772 ILE Chi-restraints excluded: chain A residue 855 ASP 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 1190 VAL Chi-restraints excluded: chain A residue 1210 VAL Chi-restraints excluded: chain A residue 1252 PHE Chi-restraints excluded: chain A residue 1334 PHE Chi-restraints excluded: chain C residue 608 VAL 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 C residue 748 GLU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 22 optimal weight: 0.5980 chunk 47 optimal weight: 1.9990 chunk 5 optimal weight: 8.9990 chunk 21 optimal weight: 0.0170 chunk 112 optimal weight: 6.9990 chunk 137 optimal weight: 10.0000 chunk 36 optimal weight: 0.9980 chunk 67 optimal weight: 5.9990 chunk 57 optimal weight: 3.9990 chunk 98 optimal weight: 0.0020 chunk 18 optimal weight: 1.9990 overall best weight: 0.7228 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 622 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.134599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.093045 restraints weight = 33338.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.096322 restraints weight = 15969.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.098480 restraints weight = 10088.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.099838 restraints weight = 7480.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.100797 restraints weight = 6191.776| |-----------------------------------------------------------------------------| r_work (final): 0.3578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.4198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12999 Z= 0.119 Angle : 0.648 11.378 17897 Z= 0.319 Chirality : 0.039 0.166 2009 Planarity : 0.004 0.049 2019 Dihedral : 16.322 90.991 2651 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.49 % Favored : 90.51 % Rotamer: Outliers : 2.92 % Allowed : 25.60 % Favored : 71.48 % 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: -1.75 (0.23), residues: 1317 helix: 0.61 (0.23), residues: 585 sheet: -1.73 (0.56), residues: 87 loop : -2.92 (0.22), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A1273 TYR 0.028 0.001 TYR C 609 PHE 0.013 0.001 PHE A1069 TRP 0.012 0.001 TRP A 523 HIS 0.006 0.001 HIS A 774 Details of bonding type rmsd covalent geometry : bond 0.00267 (12996) covalent geometry : angle 0.64783 (17897) hydrogen bonds : bond 0.03281 ( 487) hydrogen bonds : angle 4.14595 ( 1343) metal coordination : bond 0.00282 ( 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 202 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 167 time to evaluate : 0.408 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 519 HIS cc_start: 0.7914 (t-90) cc_final: 0.7408 (t70) REVERT: A 577 THR cc_start: 0.7939 (m) cc_final: 0.7381 (p) REVERT: A 636 MET cc_start: 0.8902 (tmm) cc_final: 0.8412 (tmm) REVERT: A 736 GLU cc_start: 0.8536 (mp0) cc_final: 0.8141 (mp0) REVERT: A 740 MET cc_start: 0.8866 (pmm) cc_final: 0.8435 (pmm) REVERT: A 758 ASP cc_start: 0.7339 (OUTLIER) cc_final: 0.6510 (t70) REVERT: A 815 LYS cc_start: 0.7650 (mmmt) cc_final: 0.7175 (mttp) REVERT: A 852 ILE cc_start: 0.8329 (tt) cc_final: 0.8024 (tp) REVERT: A 861 MET cc_start: 0.9034 (mmt) cc_final: 0.8737 (mmm) REVERT: A 1019 ASP cc_start: 0.8512 (p0) cc_final: 0.8030 (t0) REVERT: A 1035 ASP cc_start: 0.8383 (p0) cc_final: 0.7113 (m-30) REVERT: A 1045 GLU cc_start: 0.8520 (OUTLIER) cc_final: 0.8292 (mt-10) REVERT: A 1192 GLU cc_start: 0.8968 (tm-30) cc_final: 0.8292 (tm-30) REVERT: A 1196 MET cc_start: 0.8946 (mmp) cc_final: 0.8711 (mmm) REVERT: A 1208 ARG cc_start: 0.7989 (tpp-160) cc_final: 0.7728 (tpp-160) REVERT: A 1241 MET cc_start: 0.9254 (tpp) cc_final: 0.9010 (tpt) REVERT: A 1244 CYS cc_start: 0.7234 (t) cc_final: 0.6991 (t) REVERT: A 1334 PHE cc_start: 0.7785 (OUTLIER) cc_final: 0.7301 (p90) REVERT: C 512 GLU cc_start: 0.8922 (tp30) cc_final: 0.8140 (tp30) REVERT: C 516 LEU cc_start: 0.9384 (tt) cc_final: 0.9133 (tt) REVERT: C 520 MET cc_start: 0.7562 (mmm) cc_final: 0.6804 (tpp) REVERT: C 597 TYR cc_start: 0.9153 (m-80) cc_final: 0.8884 (m-80) REVERT: B 522 ARG cc_start: 0.6323 (mmt180) cc_final: 0.5590 (mmt180) REVERT: B 597 TYR cc_start: 0.8120 (m-10) cc_final: 0.7891 (m-80) REVERT: B 628 LEU cc_start: 0.8573 (tp) cc_final: 0.8320 (tp) REVERT: B 634 MET cc_start: 0.5903 (tmm) cc_final: 0.5624 (tpp) REVERT: B 649 GLN cc_start: 0.7397 (mp10) cc_final: 0.6730 (pm20) REVERT: B 697 MET cc_start: 0.7369 (mmt) cc_final: 0.6710 (mmt) outliers start: 35 outliers final: 23 residues processed: 188 average time/residue: 0.0946 time to fit residues: 27.2235 Evaluate side-chains 188 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 162 time to evaluate : 0.367 ------------------------------------------------------------------------------- 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 686 VAL Chi-restraints excluded: chain A residue 688 PHE Chi-restraints excluded: chain A residue 699 MET Chi-restraints excluded: chain A residue 744 ASN Chi-restraints excluded: chain A residue 758 ASP Chi-restraints excluded: chain A residue 771 ILE Chi-restraints excluded: chain A residue 908 MET Chi-restraints excluded: chain A residue 1045 GLU Chi-restraints excluded: chain A residue 1130 LEU Chi-restraints excluded: chain A residue 1159 THR Chi-restraints excluded: chain A residue 1210 VAL Chi-restraints excluded: chain A residue 1252 PHE Chi-restraints excluded: chain A residue 1334 PHE Chi-restraints excluded: chain C residue 608 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 112 optimal weight: 4.9990 chunk 72 optimal weight: 4.9990 chunk 103 optimal weight: 9.9990 chunk 11 optimal weight: 10.0000 chunk 64 optimal weight: 0.0670 chunk 96 optimal weight: 0.9980 chunk 135 optimal weight: 10.0000 chunk 101 optimal weight: 10.0000 chunk 82 optimal weight: 5.9990 chunk 126 optimal weight: 6.9990 chunk 116 optimal weight: 6.9990 overall best weight: 3.4124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 964 HIS A 965 ASN ** A1026 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1340 GLN ** C 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 631 ASN ** B 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 660 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.111723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.073108 restraints weight = 38903.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.075979 restraints weight = 19150.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.077820 restraints weight = 12353.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.079022 restraints weight = 9393.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.079690 restraints weight = 7881.307| |-----------------------------------------------------------------------------| r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.4449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 12999 Z= 0.268 Angle : 0.802 11.073 17897 Z= 0.402 Chirality : 0.045 0.202 2009 Planarity : 0.005 0.044 2019 Dihedral : 16.498 91.616 2651 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 16.07 Ramachandran Plot: Outliers : 0.08 % Allowed : 10.10 % Favored : 89.83 % 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: -1.95 (0.23), residues: 1317 helix: 0.46 (0.22), residues: 589 sheet: -2.19 (0.50), residues: 109 loop : -3.01 (0.22), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A1273 TYR 0.027 0.002 TYR C 609 PHE 0.026 0.002 PHE A1069 TRP 0.014 0.002 TRP A 662 HIS 0.009 0.002 HIS A1170 Details of bonding type rmsd covalent geometry : bond 0.00582 (12996) covalent geometry : angle 0.80208 (17897) hydrogen bonds : bond 0.04482 ( 487) hydrogen bonds : angle 4.62062 ( 1343) metal coordination : bond 0.00796 ( 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 200 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 156 time to evaluate : 0.441 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 548 ARG cc_start: 0.8539 (ttt-90) cc_final: 0.8138 (ttt-90) REVERT: A 682 MET cc_start: 0.8408 (tpp) cc_final: 0.8086 (tpp) REVERT: A 736 GLU cc_start: 0.8540 (mp0) cc_final: 0.8183 (mp0) REVERT: A 740 MET cc_start: 0.8797 (pmm) cc_final: 0.8106 (pmm) REVERT: A 815 LYS cc_start: 0.7726 (mmmt) cc_final: 0.7279 (mttp) REVERT: A 850 THR cc_start: 0.8649 (OUTLIER) cc_final: 0.8264 (p) REVERT: A 852 ILE cc_start: 0.8373 (OUTLIER) cc_final: 0.8140 (tp) REVERT: A 861 MET cc_start: 0.9054 (mmt) cc_final: 0.8812 (mmm) REVERT: A 1192 GLU cc_start: 0.9040 (tm-30) cc_final: 0.8379 (tm-30) REVERT: A 1196 MET cc_start: 0.9126 (mmp) cc_final: 0.8828 (mmm) REVERT: A 1208 ARG cc_start: 0.7978 (tpp-160) cc_final: 0.7732 (tpp-160) REVERT: A 1244 CYS cc_start: 0.7537 (t) cc_final: 0.7331 (t) REVERT: C 512 GLU cc_start: 0.8950 (tp30) cc_final: 0.8232 (tp30) REVERT: C 516 LEU cc_start: 0.9358 (tt) cc_final: 0.9157 (tt) REVERT: C 520 MET cc_start: 0.7383 (mmm) cc_final: 0.6944 (tmm) REVERT: C 597 TYR cc_start: 0.9220 (m-80) cc_final: 0.8899 (m-80) REVERT: B 634 MET cc_start: 0.6128 (tmm) cc_final: 0.5747 (tpp) REVERT: B 649 GLN cc_start: 0.7213 (mp10) cc_final: 0.6586 (pm20) REVERT: B 671 VAL cc_start: 0.7599 (t) cc_final: 0.7398 (t) REVERT: B 697 MET cc_start: 0.7330 (mmt) cc_final: 0.6987 (mmt) outliers start: 44 outliers final: 29 residues processed: 184 average time/residue: 0.0878 time to fit residues: 25.3148 Evaluate side-chains 183 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 152 time to evaluate : 0.363 ------------------------------------------------------------------------------- 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 645 LEU Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain A residue 688 PHE Chi-restraints excluded: chain A residue 699 MET Chi-restraints excluded: chain A residue 744 ASN Chi-restraints excluded: chain A residue 771 ILE Chi-restraints excluded: chain A residue 850 THR Chi-restraints excluded: chain A residue 852 ILE Chi-restraints excluded: chain A residue 908 MET Chi-restraints excluded: chain A residue 942 ILE Chi-restraints excluded: chain A residue 949 MET Chi-restraints excluded: chain A residue 965 ASN 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 C residue 608 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 535 CYS 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 26 optimal weight: 0.6980 chunk 138 optimal weight: 5.9990 chunk 4 optimal weight: 8.9990 chunk 43 optimal weight: 1.9990 chunk 89 optimal weight: 0.6980 chunk 102 optimal weight: 3.9990 chunk 127 optimal weight: 7.9990 chunk 128 optimal weight: 0.0170 chunk 41 optimal weight: 0.6980 chunk 19 optimal weight: 6.9990 chunk 77 optimal weight: 0.9980 overall best weight: 0.6218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.116311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.080600 restraints weight = 35532.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.083630 restraints weight = 17476.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.085638 restraints weight = 11165.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.086934 restraints weight = 8335.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.087666 restraints weight = 6909.691| |-----------------------------------------------------------------------------| r_work (final): 0.3557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.4618 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= 0.127 Angle : 0.698 11.113 17897 Z= 0.345 Chirality : 0.040 0.171 2009 Planarity : 0.004 0.055 2019 Dihedral : 16.390 89.296 2651 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.11 % Favored : 90.89 % Rotamer: Outliers : 2.34 % Allowed : 27.11 % Favored : 70.56 % 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: -1.74 (0.23), residues: 1317 helix: 0.68 (0.22), residues: 580 sheet: -1.63 (0.59), residues: 82 loop : -2.97 (0.22), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A1273 TYR 0.027 0.001 TYR C 609 PHE 0.015 0.001 PHE A1069 TRP 0.012 0.001 TRP A 523 HIS 0.008 0.001 HIS B 685 Details of bonding type rmsd covalent geometry : bond 0.00282 (12996) covalent geometry : angle 0.69792 (17897) hydrogen bonds : bond 0.03624 ( 487) hydrogen bonds : angle 4.27154 ( 1343) metal coordination : bond 0.00323 ( 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 188 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 160 time to evaluate : 0.393 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: A 519 HIS cc_start: 0.7715 (t-90) cc_final: 0.7319 (t-90) REVERT: A 688 PHE cc_start: 0.8100 (OUTLIER) cc_final: 0.7747 (t80) REVERT: A 723 LEU cc_start: 0.8469 (mp) cc_final: 0.8058 (mt) REVERT: A 736 GLU cc_start: 0.8524 (mp0) cc_final: 0.8115 (mp0) REVERT: A 740 MET cc_start: 0.8743 (pmm) cc_final: 0.8015 (pmm) REVERT: A 815 LYS cc_start: 0.7539 (mmmt) cc_final: 0.7049 (mttp) REVERT: A 850 THR cc_start: 0.8248 (OUTLIER) cc_final: 0.7972 (p) REVERT: A 852 ILE cc_start: 0.8089 (tt) cc_final: 0.7725 (tp) REVERT: A 861 MET cc_start: 0.8930 (mmt) cc_final: 0.8713 (mmm) REVERT: A 949 MET cc_start: 0.8411 (OUTLIER) cc_final: 0.8196 (tmm) REVERT: A 1019 ASP cc_start: 0.8532 (p0) cc_final: 0.8062 (t0) REVERT: A 1192 GLU cc_start: 0.9023 (tm-30) cc_final: 0.8387 (tm-30) REVERT: A 1196 MET cc_start: 0.9024 (mmp) cc_final: 0.8629 (mmm) REVERT: A 1208 ARG cc_start: 0.7969 (tpp-160) cc_final: 0.7738 (tpp-160) REVERT: A 1244 CYS cc_start: 0.7340 (t) cc_final: 0.7096 (t) REVERT: C 512 GLU cc_start: 0.8842 (tp30) cc_final: 0.8109 (tp30) REVERT: C 516 LEU cc_start: 0.9350 (tt) cc_final: 0.9135 (tt) REVERT: C 520 MET cc_start: 0.7290 (mmm) cc_final: 0.6856 (tmm) REVERT: C 597 TYR cc_start: 0.9211 (m-80) cc_final: 0.8898 (m-80) REVERT: B 512 GLU cc_start: 0.9140 (mp0) cc_final: 0.8226 (mt-10) REVERT: B 634 MET cc_start: 0.6173 (tmm) cc_final: 0.5913 (tpp) REVERT: B 649 GLN cc_start: 0.7175 (mp10) cc_final: 0.6553 (pm20) outliers start: 28 outliers final: 22 residues processed: 175 average time/residue: 0.0846 time to fit residues: 23.0263 Evaluate side-chains 178 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 153 time to evaluate : 0.418 ------------------------------------------------------------------------------- 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 645 LEU Chi-restraints excluded: chain A residue 688 PHE Chi-restraints excluded: chain A residue 699 MET Chi-restraints excluded: chain A residue 744 ASN Chi-restraints excluded: chain A residue 771 ILE Chi-restraints excluded: chain A residue 850 THR Chi-restraints excluded: chain A residue 908 MET Chi-restraints excluded: chain A residue 949 MET 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 1326 MET Chi-restraints excluded: chain C residue 608 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 624 LEU 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 93 optimal weight: 5.9990 chunk 115 optimal weight: 0.0470 chunk 136 optimal weight: 10.0000 chunk 65 optimal weight: 9.9990 chunk 71 optimal weight: 2.9990 chunk 40 optimal weight: 4.9990 chunk 85 optimal weight: 4.9990 chunk 62 optimal weight: 0.0980 chunk 126 optimal weight: 0.0000 chunk 123 optimal weight: 0.0050 chunk 49 optimal weight: 4.9990 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1267 GLN C 690 ASN ** B 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 668 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.116516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.082016 restraints weight = 35552.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.085080 restraints weight = 17218.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.087102 restraints weight = 10852.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.088398 restraints weight = 8019.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.089126 restraints weight = 6600.008| |-----------------------------------------------------------------------------| r_work (final): 0.3579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.4818 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= 0.125 Angle : 0.686 10.381 17897 Z= 0.341 Chirality : 0.040 0.167 2009 Planarity : 0.004 0.050 2019 Dihedral : 16.318 87.753 2651 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.11 % Favored : 90.81 % Rotamer: Outliers : 2.42 % Allowed : 26.94 % Favored : 70.64 % 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: -1.66 (0.23), residues: 1317 helix: 0.71 (0.22), residues: 579 sheet: -1.85 (0.59), residues: 79 loop : -2.84 (0.22), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A1273 TYR 0.022 0.001 TYR C 609 PHE 0.023 0.001 PHE A 448 TRP 0.014 0.001 TRP A 523 HIS 0.010 0.001 HIS A 933 Details of bonding type rmsd covalent geometry : bond 0.00280 (12996) covalent geometry : angle 0.68632 (17897) hydrogen bonds : bond 0.03504 ( 487) hydrogen bonds : angle 4.18530 ( 1343) metal coordination : bond 0.00244 ( 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 191 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 162 time to evaluate : 0.434 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 519 HIS cc_start: 0.7780 (t-90) cc_final: 0.7365 (t-90) REVERT: A 688 PHE cc_start: 0.8149 (OUTLIER) cc_final: 0.7798 (t80) REVERT: A 723 LEU cc_start: 0.8474 (mp) cc_final: 0.8049 (mt) REVERT: A 736 GLU cc_start: 0.8503 (mp0) cc_final: 0.8078 (mp0) REVERT: A 740 MET cc_start: 0.8807 (pmm) cc_final: 0.8089 (pmm) REVERT: A 815 LYS cc_start: 0.7580 (mmmt) cc_final: 0.7119 (mttp) REVERT: A 850 THR cc_start: 0.8130 (OUTLIER) cc_final: 0.7903 (p) REVERT: A 852 ILE cc_start: 0.8035 (tt) cc_final: 0.7672 (tp) REVERT: A 861 MET cc_start: 0.8995 (mmt) cc_final: 0.8770 (mmm) REVERT: A 939 LYS cc_start: 0.5727 (tptt) cc_final: 0.5443 (tptp) REVERT: A 949 MET cc_start: 0.8435 (OUTLIER) cc_final: 0.8051 (tmm) REVERT: A 1019 ASP cc_start: 0.8381 (p0) cc_final: 0.7946 (t0) REVERT: A 1035 ASP cc_start: 0.8600 (p0) cc_final: 0.7417 (m-30) REVERT: A 1192 GLU cc_start: 0.9010 (tm-30) cc_final: 0.8394 (tm-30) REVERT: A 1196 MET cc_start: 0.9026 (mmp) cc_final: 0.8503 (mmm) REVERT: A 1208 ARG cc_start: 0.7942 (tpp-160) cc_final: 0.7721 (tpp-160) REVERT: A 1244 CYS cc_start: 0.7321 (t) cc_final: 0.7075 (t) REVERT: C 512 GLU cc_start: 0.8832 (tp30) cc_final: 0.8062 (tp30) REVERT: C 516 LEU cc_start: 0.9426 (tt) cc_final: 0.9161 (tt) REVERT: C 520 MET cc_start: 0.7084 (mmm) cc_final: 0.6530 (tmm) REVERT: C 597 TYR cc_start: 0.9095 (m-80) cc_final: 0.8761 (m-80) REVERT: B 621 TYR cc_start: 0.8058 (t80) cc_final: 0.7793 (t80) REVERT: B 649 GLN cc_start: 0.7218 (mp10) cc_final: 0.6683 (pm20) REVERT: B 668 ASN cc_start: 0.8335 (OUTLIER) cc_final: 0.7449 (p0) REVERT: B 671 VAL cc_start: 0.7432 (t) cc_final: 0.7163 (t) outliers start: 29 outliers final: 19 residues processed: 177 average time/residue: 0.0913 time to fit residues: 24.5326 Evaluate side-chains 175 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 152 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 592 ILE 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 744 ASN Chi-restraints excluded: chain A residue 771 ILE Chi-restraints excluded: chain A residue 850 THR Chi-restraints excluded: chain A residue 908 MET Chi-restraints excluded: chain A residue 949 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 608 VAL Chi-restraints excluded: chain C residue 639 ILE Chi-restraints excluded: chain C residue 748 GLU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 122 optimal weight: 9.9990 chunk 42 optimal weight: 1.9990 chunk 46 optimal weight: 4.9990 chunk 93 optimal weight: 30.0000 chunk 1 optimal weight: 0.0020 chunk 7 optimal weight: 5.9990 chunk 136 optimal weight: 9.9990 chunk 25 optimal weight: 4.9990 chunk 34 optimal weight: 0.7980 chunk 90 optimal weight: 20.0000 chunk 89 optimal weight: 8.9990 overall best weight: 2.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1267 GLN ** B 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 625 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.117617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.082122 restraints weight = 36252.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.085147 restraints weight = 17761.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.087099 restraints weight = 11288.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 58)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.088409 restraints weight = 8445.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.089180 restraints weight = 6990.809| |-----------------------------------------------------------------------------| r_work (final): 0.3571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.4818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.187 12999 Z= 0.254 Angle : 0.908 59.190 17897 Z= 0.507 Chirality : 0.043 0.530 2009 Planarity : 0.004 0.050 2019 Dihedral : 16.319 87.748 2651 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 14.63 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.26 % Favored : 90.66 % Rotamer: Outliers : 2.09 % Allowed : 27.36 % Favored : 70.56 % Cbeta Deviations : 0.08 % 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: -1.66 (0.23), residues: 1317 helix: 0.72 (0.23), residues: 579 sheet: -1.84 (0.59), residues: 79 loop : -2.84 (0.22), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A1273 TYR 0.021 0.001 TYR C 609 PHE 0.024 0.001 PHE C 598 TRP 0.040 0.002 TRP C 691 HIS 0.041 0.001 HIS A 933 Details of bonding type rmsd covalent geometry : bond 0.00498 (12996) covalent geometry : angle 0.90799 (17897) hydrogen bonds : bond 0.03538 ( 487) hydrogen bonds : angle 4.18664 ( 1343) metal coordination : bond 0.00360 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2304.51 seconds wall clock time: 40 minutes 34.92 seconds (2434.92 seconds total)