Starting phenix.real_space_refine on Wed Jul 30 23:53:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6v5b_21051/07_2025/6v5b_21051.cif Found real_map, /net/cci-nas-00/data/ceres_data/6v5b_21051/07_2025/6v5b_21051.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6v5b_21051/07_2025/6v5b_21051.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6v5b_21051/07_2025/6v5b_21051.map" model { file = "/net/cci-nas-00/data/ceres_data/6v5b_21051/07_2025/6v5b_21051.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6v5b_21051/07_2025/6v5b_21051.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.012 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 7.01, per 1000 atoms: 0.56 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: 2.71 Conformation dependent library (CDL) restraints added in 1.3 seconds 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: 3.50 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: 4.02 Time building geometry restraints manager: 3.29 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: 0.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.420 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 32.370 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.610 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.024 0.003 TRP C 691 HIS 0.011 0.002 HIS A 774 PHE 0.020 0.003 PHE C 503 TYR 0.029 0.003 TYR C 609 ARG 0.005 0.001 ARG A1126 Details of bonding type rmsd hydrogen bonds : bond 0.18661 ( 487) hydrogen bonds : angle 7.72915 ( 1343) metal coordination : bond 0.42505 ( 3) covalent geometry : bond 0.00749 (12996) covalent geometry : angle 1.09866 (17897) *********************** 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 : 1.325 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: 0.6055 (t-100) cc_final: 0.5118 (t-100) REVERT: A 681 PHE cc_start: 0.8157 (m-80) cc_final: 0.7838 (m-80) REVERT: A 736 GLU cc_start: 0.8652 (mp0) cc_final: 0.8128 (mp0) REVERT: A 740 MET cc_start: 0.9050 (pmm) cc_final: 0.8569 (pmm) REVERT: A 815 LYS cc_start: 0.7664 (mmmt) cc_final: 0.7377 (mttp) REVERT: A 852 ILE cc_start: 0.8639 (tt) cc_final: 0.8413 (tp) REVERT: A 864 PRO cc_start: 0.9189 (Cg_exo) cc_final: 0.8960 (Cg_endo) REVERT: A 1012 LEU cc_start: 0.9150 (tp) cc_final: 0.8891 (tp) REVERT: A 1068 LEU cc_start: 0.9329 (tp) cc_final: 0.9042 (tp) REVERT: A 1081 TYR cc_start: 0.8634 (p90) cc_final: 0.8265 (p90) REVERT: A 1086 LEU cc_start: 0.9101 (mt) cc_final: 0.8675 (mt) REVERT: A 1090 GLU cc_start: 0.8921 (mp0) cc_final: 0.8630 (mp0) REVERT: A 1192 GLU cc_start: 0.8870 (tm-30) cc_final: 0.8234 (tm-30) REVERT: A 1208 ARG cc_start: 0.8326 (tpm170) cc_final: 0.8023 (tpp-160) REVERT: A 1261 PRO cc_start: 0.8808 (Cg_exo) cc_final: 0.8329 (Cg_endo) REVERT: A 1322 MET cc_start: 0.8971 (mtt) cc_final: 0.8401 (mmm) REVERT: C 617 LEU cc_start: 0.8798 (tp) cc_final: 0.8563 (mm) REVERT: C 681 LEU cc_start: 0.8210 (tp) cc_final: 0.7797 (mp) REVERT: C 691 TRP cc_start: 0.7902 (t-100) cc_final: 0.7414 (t60) REVERT: B 512 GLU cc_start: 0.8993 (mp0) cc_final: 0.8371 (mt-10) REVERT: B 535 CYS cc_start: 0.8888 (t) cc_final: 0.8531 (t) REVERT: B 553 TYR cc_start: 0.8353 (m-10) cc_final: 0.8075 (m-80) REVERT: B 573 LEU cc_start: 0.8885 (mm) cc_final: 0.8328 (tp) outliers start: 6 outliers final: 2 residues processed: 262 average time/residue: 0.2787 time to fit residues: 102.5806 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 : 1.256 ------------------------------------------------------------------------------- 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 117 optimal weight: 10.0000 chunk 105 optimal weight: 20.0000 chunk 58 optimal weight: 2.9990 chunk 35 optimal weight: 0.0060 chunk 71 optimal weight: 0.9990 chunk 56 optimal weight: 0.8980 chunk 108 optimal weight: 20.0000 chunk 42 optimal weight: 0.6980 chunk 66 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 126 optimal weight: 20.0000 overall best weight: 0.9200 ------------------------------------------------------------------------------- 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 680 HIS A 701 GLN A 888 GLN A 903 HIS A 947 ASN ** A1026 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1143 ASN ** A1170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1266 GLN C 495 GLN ** C 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 566 ASN C 599 ASN ** C 660 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 668 ASN C 678 GLN C 690 ASN C 736 GLN B 625 HIS ** B 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 674 GLN B 690 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.121683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.088677 restraints weight = 32542.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.091538 restraints weight = 16079.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.093378 restraints weight = 10240.232| |-----------------------------------------------------------------------------| r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.2292 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 : 0.690 9.947 17897 Z= 0.353 Chirality : 0.041 0.172 2009 Planarity : 0.005 0.056 2019 Dihedral : 17.109 94.659 2651 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.04 % Favored : 90.89 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.23 (0.21), residues: 1317 helix: -0.87 (0.20), residues: 585 sheet: -2.00 (0.60), residues: 77 loop : -3.50 (0.20), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 691 HIS 0.013 0.001 HIS C 625 PHE 0.014 0.001 PHE A 572 TYR 0.016 0.002 TYR A1303 ARG 0.005 0.001 ARG A1342 Details of bonding type rmsd hydrogen bonds : bond 0.04186 ( 487) hydrogen bonds : angle 4.97696 ( 1343) metal coordination : bond 0.02434 ( 3) covalent geometry : bond 0.00307 (12996) covalent geometry : angle 0.68950 (17897) *********************** 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 228 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 200 time to evaluate : 1.332 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: A 519 HIS cc_start: 0.7916 (t-90) cc_final: 0.7524 (t70) REVERT: A 544 ARG cc_start: 0.8306 (ttm-80) cc_final: 0.7925 (mtm-85) REVERT: A 545 THR cc_start: 0.8894 (t) cc_final: 0.8550 (p) REVERT: A 600 ILE cc_start: 0.9250 (mp) cc_final: 0.7992 (mt) REVERT: A 602 GLU cc_start: 0.8584 (mm-30) cc_final: 0.8288 (mp0) REVERT: A 659 LEU cc_start: 0.8135 (tp) cc_final: 0.7918 (tp) REVERT: A 736 GLU cc_start: 0.8552 (mp0) cc_final: 0.8162 (mp0) REVERT: A 740 MET cc_start: 0.8921 (pmm) cc_final: 0.8552 (pmm) REVERT: A 815 LYS cc_start: 0.7564 (mmmt) cc_final: 0.7221 (mttp) REVERT: A 848 TRP cc_start: 0.8640 (m100) cc_final: 0.7877 (m100) REVERT: A 852 ILE cc_start: 0.8835 (tt) cc_final: 0.8578 (tp) REVERT: A 908 MET cc_start: 0.6438 (mmp) cc_final: 0.6218 (mmt) REVERT: A 947 ASN cc_start: 0.9168 (OUTLIER) cc_final: 0.8806 (t0) REVERT: A 1068 LEU cc_start: 0.9331 (tp) cc_final: 0.9001 (tp) REVERT: A 1147 GLU cc_start: 0.8645 (pp20) cc_final: 0.8065 (pp20) REVERT: A 1155 GLN cc_start: 0.9123 (pp30) cc_final: 0.8504 (pp30) REVERT: A 1192 GLU cc_start: 0.8863 (tm-30) cc_final: 0.8249 (tm-30) REVERT: A 1303 TYR cc_start: 0.8144 (m-80) cc_final: 0.7886 (m-10) REVERT: C 520 MET cc_start: 0.7237 (mmm) cc_final: 0.6688 (tpt) REVERT: C 597 TYR cc_start: 0.9192 (m-80) cc_final: 0.8967 (m-80) REVERT: C 617 LEU cc_start: 0.9072 (tp) cc_final: 0.8811 (mm) REVERT: B 512 GLU cc_start: 0.9047 (mp0) cc_final: 0.8715 (mp0) REVERT: B 522 ARG cc_start: 0.7698 (mtt180) cc_final: 0.7364 (mmt180) REVERT: B 573 LEU cc_start: 0.8679 (mm) cc_final: 0.8437 (mp) REVERT: B 597 TYR cc_start: 0.7926 (m-10) cc_final: 0.7631 (m-80) REVERT: B 613 SER cc_start: 0.8307 (t) cc_final: 0.7913 (m) REVERT: B 630 ARG cc_start: 0.7848 (mmt180) cc_final: 0.7480 (mpt-90) REVERT: B 671 VAL cc_start: 0.7695 (OUTLIER) cc_final: 0.7288 (t) REVERT: B 697 MET cc_start: 0.7011 (mmt) cc_final: 0.6328 (mmm) outliers start: 28 outliers final: 14 residues processed: 222 average time/residue: 0.2419 time to fit residues: 78.9492 Evaluate side-chains 186 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 170 time to evaluate : 1.245 ------------------------------------------------------------------------------- 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 129 optimal weight: 7.9990 chunk 44 optimal weight: 0.7980 chunk 92 optimal weight: 9.9990 chunk 61 optimal weight: 4.9990 chunk 45 optimal weight: 4.9990 chunk 20 optimal weight: 4.9990 chunk 138 optimal weight: 6.9990 chunk 82 optimal weight: 0.9980 chunk 42 optimal weight: 0.7980 chunk 107 optimal weight: 1.9990 chunk 106 optimal weight: 5.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 614 ASN A 947 ASN ** A1026 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.124080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.087543 restraints weight = 32023.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.090661 restraints weight = 15375.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.092727 restraints weight = 9709.992| |-----------------------------------------------------------------------------| r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.2887 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= 0.178 Angle : 0.699 9.715 17897 Z= 0.353 Chirality : 0.041 0.161 2009 Planarity : 0.005 0.059 2019 Dihedral : 16.860 92.341 2651 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 13.64 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.64 % Favored : 90.28 % Rotamer: Outliers : 3.59 % Allowed : 20.27 % Favored : 76.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.16 % Twisted Proline : 1.54 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.63 (0.22), residues: 1317 helix: -0.14 (0.22), residues: 586 sheet: -2.40 (0.51), residues: 101 loop : -3.35 (0.21), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 523 HIS 0.007 0.001 HIS A 912 PHE 0.014 0.002 PHE A 572 TYR 0.036 0.002 TYR C 609 ARG 0.006 0.000 ARG A1273 Details of bonding type rmsd hydrogen bonds : bond 0.04096 ( 487) hydrogen bonds : angle 4.70374 ( 1343) metal coordination : bond 0.00657 ( 3) covalent geometry : bond 0.00390 (12996) covalent geometry : angle 0.69863 (17897) *********************** 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 218 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 175 time to evaluate : 1.264 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 417 HIS cc_start: 0.8990 (m90) cc_final: 0.8715 (t-170) REVERT: A 427 MET cc_start: 0.9297 (ppp) cc_final: 0.8950 (ppp) REVERT: A 519 HIS cc_start: 0.7778 (t-90) cc_final: 0.7081 (t-90) REVERT: A 544 ARG cc_start: 0.8497 (ttm-80) cc_final: 0.7833 (mtm-85) REVERT: A 600 ILE cc_start: 0.9254 (mp) cc_final: 0.9002 (mm) REVERT: A 635 MET cc_start: 0.8651 (tpp) cc_final: 0.8442 (ttm) REVERT: A 731 GLN cc_start: 0.8750 (OUTLIER) cc_final: 0.8488 (mp10) REVERT: A 736 GLU cc_start: 0.8643 (mp0) cc_final: 0.8231 (mp0) REVERT: A 740 MET cc_start: 0.8770 (pmm) cc_final: 0.8372 (pmm) REVERT: A 815 LYS cc_start: 0.7584 (mmmt) cc_final: 0.7193 (mttp) REVERT: A 852 ILE cc_start: 0.8566 (tt) cc_final: 0.8228 (tp) REVERT: A 1068 LEU cc_start: 0.9254 (tp) cc_final: 0.9030 (tp) REVERT: A 1155 GLN cc_start: 0.9189 (pp30) cc_final: 0.8376 (pp30) REVERT: A 1192 GLU cc_start: 0.9001 (tm-30) cc_final: 0.8330 (tm-30) REVERT: A 1273 ARG cc_start: 0.8597 (mmm160) cc_final: 0.8363 (mmm160) REVERT: A 1294 HIS cc_start: 0.7785 (m90) cc_final: 0.7470 (m90) REVERT: A 1303 TYR cc_start: 0.8506 (m-80) cc_final: 0.8226 (m-10) REVERT: A 1322 MET cc_start: 0.8885 (mtt) cc_final: 0.8233 (mmm) REVERT: C 520 MET cc_start: 0.7148 (mmm) cc_final: 0.6432 (tpp) REVERT: C 597 TYR cc_start: 0.9221 (m-80) cc_final: 0.8967 (m-80) REVERT: C 617 LEU cc_start: 0.9031 (tp) cc_final: 0.8399 (mt) REVERT: C 691 TRP cc_start: 0.7341 (t60) cc_final: 0.6282 (t-100) REVERT: B 512 GLU cc_start: 0.9090 (mp0) cc_final: 0.8219 (mt-10) REVERT: B 553 TYR cc_start: 0.7988 (m-80) cc_final: 0.7696 (m-80) REVERT: B 566 ASN cc_start: 0.9262 (m-40) cc_final: 0.8855 (m110) REVERT: B 573 LEU cc_start: 0.8799 (mm) cc_final: 0.8565 (mp) REVERT: B 597 TYR cc_start: 0.8017 (m-10) cc_final: 0.7756 (m-80) REVERT: B 613 SER cc_start: 0.8403 (t) cc_final: 0.8031 (m) REVERT: B 671 VAL cc_start: 0.7641 (t) cc_final: 0.7430 (t) REVERT: B 697 MET cc_start: 0.7115 (mmt) cc_final: 0.6336 (mmm) outliers start: 43 outliers final: 29 residues processed: 206 average time/residue: 0.2333 time to fit residues: 71.4393 Evaluate side-chains 193 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 163 time to evaluate : 1.263 ------------------------------------------------------------------------------- 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 699 MET Chi-restraints excluded: chain A residue 731 GLN Chi-restraints excluded: chain A residue 744 ASN Chi-restraints excluded: chain A residue 747 THR 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 1004 VAL 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 1252 PHE Chi-restraints excluded: chain A residue 1269 CYS Chi-restraints excluded: chain C residue 613 SER Chi-restraints excluded: chain C residue 680 ILE Chi-restraints excluded: chain B residue 522 ARG Chi-restraints excluded: chain B residue 546 VAL Chi-restraints excluded: chain B residue 624 LEU Chi-restraints excluded: chain B residue 685 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 27 optimal weight: 0.9990 chunk 30 optimal weight: 8.9990 chunk 84 optimal weight: 7.9990 chunk 31 optimal weight: 7.9990 chunk 134 optimal weight: 10.0000 chunk 8 optimal weight: 0.2980 chunk 54 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 chunk 103 optimal weight: 4.9990 chunk 135 optimal weight: 10.0000 chunk 87 optimal weight: 4.9990 overall best weight: 2.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 639 ASN A 781 GLN ** A1026 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1187 GLN ** A1256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 660 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 517 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.125490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.090193 restraints weight = 32661.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.093048 restraints weight = 15633.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.094909 restraints weight = 9760.702| |-----------------------------------------------------------------------------| r_work (final): 0.3557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.3500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 12999 Z= 0.204 Angle : 0.717 8.700 17897 Z= 0.363 Chirality : 0.042 0.171 2009 Planarity : 0.005 0.058 2019 Dihedral : 16.782 93.428 2651 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 14.09 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.79 % Favored : 90.13 % Rotamer: Outliers : 4.34 % Allowed : 22.94 % Favored : 72.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.38 (0.22), residues: 1317 helix: 0.16 (0.22), residues: 586 sheet: -2.43 (0.48), residues: 106 loop : -3.28 (0.21), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 523 HIS 0.006 0.001 HIS A 912 PHE 0.021 0.002 PHE B 580 TYR 0.029 0.002 TYR C 609 ARG 0.003 0.000 ARG A 829 Details of bonding type rmsd hydrogen bonds : bond 0.04095 ( 487) hydrogen bonds : angle 4.63658 ( 1343) metal coordination : bond 0.00548 ( 3) covalent geometry : bond 0.00448 (12996) covalent geometry : angle 0.71741 (17897) *********************** 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 218 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 166 time to evaluate : 1.395 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: A 544 ARG cc_start: 0.8506 (ttm-80) cc_final: 0.7974 (mtm-85) REVERT: A 635 MET cc_start: 0.8857 (tpp) cc_final: 0.8562 (tpp) REVERT: A 722 MET cc_start: 0.6501 (tpp) cc_final: 0.6293 (tpp) REVERT: A 723 LEU cc_start: 0.8563 (mp) cc_final: 0.8112 (mt) REVERT: A 731 GLN cc_start: 0.8837 (OUTLIER) cc_final: 0.8619 (mp10) REVERT: A 736 GLU cc_start: 0.8575 (mp0) cc_final: 0.8180 (mp0) REVERT: A 740 MET cc_start: 0.8683 (pmm) cc_final: 0.8289 (pmm) REVERT: A 815 LYS cc_start: 0.7674 (mmmt) cc_final: 0.7223 (mttp) REVERT: A 834 MET cc_start: 0.7084 (ptt) cc_final: 0.6854 (ptp) REVERT: A 852 ILE cc_start: 0.8450 (tt) cc_final: 0.8187 (tp) REVERT: A 1068 LEU cc_start: 0.9295 (tp) cc_final: 0.9094 (tp) REVERT: A 1155 GLN cc_start: 0.9037 (pp30) cc_final: 0.8212 (pp30) REVERT: A 1192 GLU cc_start: 0.9011 (tm-30) cc_final: 0.8302 (tm-30) REVERT: A 1244 CYS cc_start: 0.7379 (t) cc_final: 0.7156 (t) REVERT: A 1273 ARG cc_start: 0.8618 (mmm160) cc_final: 0.8375 (mmm160) REVERT: A 1334 PHE cc_start: 0.8048 (OUTLIER) cc_final: 0.7840 (p90) REVERT: C 512 GLU cc_start: 0.8994 (tp30) cc_final: 0.8250 (tp30) REVERT: C 520 MET cc_start: 0.7485 (mmm) cc_final: 0.6767 (tpp) REVERT: C 597 TYR cc_start: 0.9216 (m-80) cc_final: 0.8938 (m-80) REVERT: C 617 LEU cc_start: 0.9070 (tp) cc_final: 0.8497 (mt) REVERT: C 697 MET cc_start: 0.8559 (ppp) cc_final: 0.8341 (ppp) REVERT: B 512 GLU cc_start: 0.9212 (mp0) cc_final: 0.8918 (mp0) REVERT: B 522 ARG cc_start: 0.7676 (OUTLIER) cc_final: 0.7422 (mmt180) REVERT: B 553 TYR cc_start: 0.7824 (m-80) cc_final: 0.7283 (m-80) REVERT: B 566 ASN cc_start: 0.9285 (m-40) cc_final: 0.9085 (m110) REVERT: B 573 LEU cc_start: 0.8894 (mm) cc_final: 0.8643 (mp) REVERT: B 597 TYR cc_start: 0.8052 (m-10) cc_final: 0.7785 (m-10) REVERT: B 655 MET cc_start: 0.8001 (tmm) cc_final: 0.7721 (ppp) REVERT: B 665 TRP cc_start: 0.3366 (m-90) cc_final: 0.3025 (m-90) REVERT: B 671 VAL cc_start: 0.7666 (t) cc_final: 0.7455 (t) REVERT: B 697 MET cc_start: 0.7152 (mmt) cc_final: 0.6398 (mmt) outliers start: 52 outliers final: 33 residues processed: 207 average time/residue: 0.2166 time to fit residues: 67.8968 Evaluate side-chains 193 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 157 time to evaluate : 1.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 520 ASP Chi-restraints excluded: chain A residue 576 ILE Chi-restraints excluded: chain A residue 606 MET Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain A residue 645 LEU Chi-restraints excluded: chain A residue 688 PHE Chi-restraints excluded: chain A residue 699 MET Chi-restraints excluded: chain A residue 706 LEU Chi-restraints excluded: chain A residue 731 GLN Chi-restraints excluded: chain A residue 744 ASN Chi-restraints excluded: chain A residue 771 ILE Chi-restraints excluded: chain A residue 772 ILE Chi-restraints excluded: chain A residue 839 THR Chi-restraints excluded: chain A residue 840 VAL Chi-restraints excluded: chain A residue 916 SER Chi-restraints excluded: chain A residue 1004 VAL Chi-restraints excluded: chain A residue 1051 VAL Chi-restraints excluded: chain A residue 1130 LEU Chi-restraints excluded: chain A residue 1159 THR Chi-restraints excluded: chain A residue 1164 ILE Chi-restraints excluded: chain A residue 1190 VAL Chi-restraints excluded: chain A residue 1210 VAL Chi-restraints excluded: chain A residue 1252 PHE Chi-restraints excluded: chain A residue 1269 CYS Chi-restraints excluded: chain A residue 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 522 ARG Chi-restraints excluded: chain B residue 535 CYS 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 21 optimal weight: 2.9990 chunk 137 optimal weight: 10.0000 chunk 27 optimal weight: 7.9990 chunk 54 optimal weight: 6.9990 chunk 94 optimal weight: 30.0000 chunk 3 optimal weight: 7.9990 chunk 114 optimal weight: 0.0970 chunk 14 optimal weight: 2.9990 chunk 125 optimal weight: 6.9990 chunk 97 optimal weight: 20.0000 chunk 62 optimal weight: 0.9990 overall best weight: 2.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1026 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 660 HIS ** B 517 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.112015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.073230 restraints weight = 38992.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.076132 restraints weight = 19257.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.078017 restraints weight = 12441.974| |-----------------------------------------------------------------------------| r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.3983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 12999 Z= 0.223 Angle : 0.729 8.807 17897 Z= 0.368 Chirality : 0.043 0.180 2009 Planarity : 0.005 0.056 2019 Dihedral : 16.765 93.668 2651 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 14.87 Ramachandran Plot: Outliers : 0.08 % Allowed : 10.40 % Favored : 89.52 % Rotamer: Outliers : 4.67 % Allowed : 23.44 % Favored : 71.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.34 (0.23), residues: 1317 helix: 0.20 (0.22), residues: 590 sheet: -2.41 (0.51), residues: 100 loop : -3.28 (0.22), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 523 HIS 0.009 0.001 HIS B 685 PHE 0.025 0.002 PHE B 580 TYR 0.018 0.002 TYR B 698 ARG 0.003 0.000 ARG A 923 Details of bonding type rmsd hydrogen bonds : bond 0.04209 ( 487) hydrogen bonds : angle 4.64438 ( 1343) metal coordination : bond 0.00613 ( 3) covalent geometry : bond 0.00490 (12996) covalent geometry : angle 0.72899 (17897) *********************** 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 214 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 158 time to evaluate : 1.439 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 654 ARG cc_start: 0.8289 (mmt90) cc_final: 0.7847 (mpt180) REVERT: A 731 GLN cc_start: 0.8829 (OUTLIER) cc_final: 0.8597 (mp10) REVERT: A 736 GLU cc_start: 0.8562 (mp0) cc_final: 0.8186 (mp0) REVERT: A 740 MET cc_start: 0.8782 (pmm) cc_final: 0.8317 (pmm) REVERT: A 815 LYS cc_start: 0.7673 (mmmt) cc_final: 0.7241 (mttp) REVERT: A 852 ILE cc_start: 0.8443 (tt) cc_final: 0.8171 (tp) REVERT: A 1155 GLN cc_start: 0.9021 (pp30) cc_final: 0.8035 (pp30) REVERT: A 1192 GLU cc_start: 0.8991 (tm-30) cc_final: 0.8320 (tm-30) REVERT: A 1208 ARG cc_start: 0.8007 (tpp-160) cc_final: 0.7795 (tpp-160) REVERT: A 1244 CYS cc_start: 0.7421 (t) cc_final: 0.7196 (t) REVERT: A 1252 PHE cc_start: 0.8657 (OUTLIER) cc_final: 0.8254 (t80) REVERT: A 1256 GLN cc_start: 0.7327 (tt0) cc_final: 0.6938 (mt0) REVERT: A 1273 ARG cc_start: 0.8617 (mmm160) cc_final: 0.8373 (mmm160) REVERT: A 1294 HIS cc_start: 0.7710 (m90) cc_final: 0.7506 (m90) REVERT: C 520 MET cc_start: 0.7118 (mmm) cc_final: 0.6397 (tpp) REVERT: C 597 TYR cc_start: 0.9289 (m-80) cc_final: 0.9052 (m-80) REVERT: C 617 LEU cc_start: 0.8908 (tp) cc_final: 0.8562 (mm) REVERT: B 512 GLU cc_start: 0.9130 (mp0) cc_final: 0.8762 (mp0) REVERT: B 522 ARG cc_start: 0.7673 (OUTLIER) cc_final: 0.7184 (mmt180) REVERT: B 553 TYR cc_start: 0.7426 (m-80) cc_final: 0.6948 (m-80) REVERT: B 573 LEU cc_start: 0.8965 (mm) cc_final: 0.8746 (mp) REVERT: B 697 MET cc_start: 0.7147 (mmt) cc_final: 0.6899 (mmt) outliers start: 56 outliers final: 33 residues processed: 201 average time/residue: 0.2202 time to fit residues: 67.1789 Evaluate side-chains 188 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 152 time to evaluate : 1.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 417 HIS Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 576 ILE Chi-restraints excluded: chain A residue 606 MET Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain A residue 645 LEU Chi-restraints excluded: chain A residue 688 PHE Chi-restraints excluded: chain A residue 703 LEU Chi-restraints excluded: chain A residue 706 LEU Chi-restraints excluded: chain A residue 731 GLN Chi-restraints excluded: chain A residue 744 ASN Chi-restraints excluded: chain A residue 771 ILE Chi-restraints excluded: chain A residue 814 ASP Chi-restraints excluded: chain A residue 840 VAL Chi-restraints excluded: chain A residue 870 ILE Chi-restraints excluded: chain A residue 916 SER Chi-restraints excluded: chain A residue 942 ILE Chi-restraints excluded: chain A residue 962 ILE Chi-restraints excluded: chain A residue 1004 VAL Chi-restraints excluded: chain A residue 1051 VAL Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain A residue 1130 LEU Chi-restraints excluded: chain A residue 1159 THR Chi-restraints excluded: chain A residue 1174 LEU Chi-restraints excluded: chain A residue 1190 VAL Chi-restraints excluded: chain A residue 1210 VAL Chi-restraints excluded: chain A residue 1252 PHE Chi-restraints excluded: chain A residue 1269 CYS Chi-restraints excluded: chain C residue 639 ILE Chi-restraints excluded: chain C residue 680 ILE Chi-restraints excluded: chain B residue 522 ARG Chi-restraints excluded: chain B residue 535 CYS 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 107 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 135 optimal weight: 10.0000 chunk 45 optimal weight: 2.9990 chunk 29 optimal weight: 7.9990 chunk 121 optimal weight: 5.9990 chunk 138 optimal weight: 5.9990 chunk 114 optimal weight: 4.9990 chunk 27 optimal weight: 6.9990 chunk 124 optimal weight: 0.8980 chunk 88 optimal weight: 0.9980 overall best weight: 3.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 774 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1026 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1173 HIS ** A1336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 517 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 660 HIS B 736 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.110906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.072151 restraints weight = 39775.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.075018 restraints weight = 19562.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.076896 restraints weight = 12641.696| |-----------------------------------------------------------------------------| r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.4393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 12999 Z= 0.245 Angle : 0.761 10.152 17897 Z= 0.382 Chirality : 0.044 0.196 2009 Planarity : 0.005 0.049 2019 Dihedral : 16.766 93.436 2651 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 15.57 Ramachandran Plot: Outliers : 0.08 % Allowed : 10.63 % Favored : 89.29 % Rotamer: Outliers : 4.50 % Allowed : 24.44 % Favored : 71.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.28 (0.23), residues: 1317 helix: 0.28 (0.22), residues: 590 sheet: -2.34 (0.50), residues: 106 loop : -3.30 (0.22), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 523 HIS 0.006 0.001 HIS A1170 PHE 0.027 0.002 PHE B 580 TYR 0.018 0.002 TYR B 698 ARG 0.003 0.000 ARG A 829 Details of bonding type rmsd hydrogen bonds : bond 0.04325 ( 487) hydrogen bonds : angle 4.69981 ( 1343) metal coordination : bond 0.00754 ( 3) covalent geometry : bond 0.00537 (12996) covalent geometry : angle 0.76140 (17897) *********************** 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 212 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 158 time to evaluate : 1.363 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 635 MET cc_start: 0.8517 (tpp) cc_final: 0.8270 (ttt) REVERT: A 731 GLN cc_start: 0.8794 (OUTLIER) cc_final: 0.8505 (mm-40) REVERT: A 736 GLU cc_start: 0.8547 (mp0) cc_final: 0.8191 (mp0) REVERT: A 740 MET cc_start: 0.8697 (pmm) cc_final: 0.8245 (pmm) REVERT: A 815 LYS cc_start: 0.7663 (mmmt) cc_final: 0.7274 (mttp) REVERT: A 852 ILE cc_start: 0.8404 (OUTLIER) cc_final: 0.8153 (tp) REVERT: A 1192 GLU cc_start: 0.9032 (tm-30) cc_final: 0.8347 (tm-30) REVERT: A 1208 ARG cc_start: 0.8043 (tpp-160) cc_final: 0.7759 (tpp-160) REVERT: A 1244 CYS cc_start: 0.7378 (t) cc_final: 0.7154 (t) REVERT: A 1252 PHE cc_start: 0.8721 (OUTLIER) cc_final: 0.8256 (t80) REVERT: A 1256 GLN cc_start: 0.7460 (tt0) cc_final: 0.7094 (tt0) REVERT: C 597 TYR cc_start: 0.9260 (m-80) cc_final: 0.9020 (m-80) REVERT: C 617 LEU cc_start: 0.8855 (tp) cc_final: 0.8360 (mt) REVERT: C 737 GLU cc_start: 0.9069 (mm-30) cc_final: 0.8662 (mp0) REVERT: B 517 HIS cc_start: 0.8730 (OUTLIER) cc_final: 0.8484 (t70) REVERT: B 553 TYR cc_start: 0.7241 (m-80) cc_final: 0.6771 (m-80) REVERT: B 566 ASN cc_start: 0.9396 (m-40) cc_final: 0.9180 (m110) REVERT: B 649 GLN cc_start: 0.7009 (mp10) cc_final: 0.6415 (pm20) REVERT: B 694 LEU cc_start: 0.8211 (OUTLIER) cc_final: 0.7909 (mt) REVERT: B 697 MET cc_start: 0.7110 (mmt) cc_final: 0.6891 (mmt) outliers start: 54 outliers final: 41 residues processed: 198 average time/residue: 0.2313 time to fit residues: 69.0712 Evaluate side-chains 195 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 149 time to evaluate : 1.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 417 HIS Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 577 THR 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 662 TRP Chi-restraints excluded: chain A residue 688 PHE 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 814 ASP Chi-restraints excluded: chain A residue 840 VAL Chi-restraints excluded: chain A residue 852 ILE Chi-restraints excluded: chain A residue 870 ILE Chi-restraints excluded: chain A residue 916 SER Chi-restraints excluded: chain A residue 931 LYS Chi-restraints excluded: chain A residue 942 ILE Chi-restraints excluded: chain A residue 962 ILE Chi-restraints excluded: chain A residue 980 THR Chi-restraints excluded: chain A residue 987 LEU Chi-restraints excluded: chain A residue 1004 VAL Chi-restraints excluded: chain A residue 1051 VAL Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain A residue 1130 LEU Chi-restraints excluded: chain A residue 1159 THR Chi-restraints excluded: chain A residue 1164 ILE Chi-restraints excluded: chain A residue 1174 LEU Chi-restraints excluded: chain A residue 1190 VAL Chi-restraints excluded: chain A residue 1210 VAL Chi-restraints excluded: chain A residue 1252 PHE Chi-restraints excluded: chain A residue 1269 CYS Chi-restraints excluded: chain A residue 1270 LEU 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 517 HIS Chi-restraints excluded: chain B residue 535 CYS Chi-restraints excluded: chain B residue 546 VAL Chi-restraints excluded: chain B residue 624 LEU Chi-restraints excluded: chain B residue 668 ASN Chi-restraints excluded: chain B residue 685 HIS Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain B residue 698 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 108 optimal weight: 20.0000 chunk 88 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 105 optimal weight: 7.9990 chunk 110 optimal weight: 0.9980 chunk 119 optimal weight: 10.0000 chunk 27 optimal weight: 7.9990 chunk 125 optimal weight: 8.9990 chunk 36 optimal weight: 0.0370 chunk 77 optimal weight: 0.7980 chunk 73 optimal weight: 0.9990 overall best weight: 0.7662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 774 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1026 HIS ** A1170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 517 HIS ** B 517 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.116022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.081540 restraints weight = 35509.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.084580 restraints weight = 17108.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.086558 restraints weight = 10730.836| |-----------------------------------------------------------------------------| r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.4586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 12999 Z= 0.126 Angle : 0.680 10.413 17897 Z= 0.339 Chirality : 0.040 0.171 2009 Planarity : 0.004 0.055 2019 Dihedral : 16.539 90.970 2651 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.49 % Favored : 90.43 % Rotamer: Outliers : 3.50 % Allowed : 26.44 % Favored : 70.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.92 (0.23), residues: 1317 helix: 0.54 (0.22), residues: 590 sheet: -1.16 (0.66), residues: 67 loop : -3.19 (0.21), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 523 HIS 0.009 0.001 HIS C 517 PHE 0.032 0.001 PHE B 580 TYR 0.016 0.001 TYR B 597 ARG 0.006 0.000 ARG A1273 Details of bonding type rmsd hydrogen bonds : bond 0.03580 ( 487) hydrogen bonds : angle 4.27593 ( 1343) metal coordination : bond 0.00419 ( 3) covalent geometry : bond 0.00283 (12996) covalent geometry : angle 0.68029 (17897) *********************** 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 199 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 157 time to evaluate : 1.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 635 MET cc_start: 0.8565 (tpp) cc_final: 0.8278 (tpp) REVERT: A 688 PHE cc_start: 0.8314 (OUTLIER) cc_final: 0.7874 (t80) REVERT: A 731 GLN cc_start: 0.8783 (OUTLIER) cc_final: 0.8460 (mp10) REVERT: A 736 GLU cc_start: 0.8487 (mp0) cc_final: 0.8133 (mp0) REVERT: A 740 MET cc_start: 0.8818 (pmm) cc_final: 0.8168 (pmm) REVERT: A 815 LYS cc_start: 0.7674 (mmmt) cc_final: 0.7208 (mttp) REVERT: A 852 ILE cc_start: 0.8299 (OUTLIER) cc_final: 0.8016 (tp) REVERT: A 1035 ASP cc_start: 0.8507 (p0) cc_final: 0.7428 (m-30) REVERT: A 1040 MET cc_start: 0.9202 (tpp) cc_final: 0.8910 (mmt) REVERT: A 1118 PHE cc_start: 0.7623 (m-10) cc_final: 0.7281 (m-10) REVERT: A 1155 GLN cc_start: 0.8855 (pp30) cc_final: 0.7887 (pp30) REVERT: A 1192 GLU cc_start: 0.8995 (tm-30) cc_final: 0.8346 (tm-30) REVERT: A 1208 ARG cc_start: 0.7868 (tpp-160) cc_final: 0.7603 (tpp-160) REVERT: A 1252 PHE cc_start: 0.8597 (OUTLIER) cc_final: 0.8180 (t80) REVERT: A 1256 GLN cc_start: 0.7650 (tt0) cc_final: 0.7237 (mt0) REVERT: A 1273 ARG cc_start: 0.8513 (mmm160) cc_final: 0.8164 (mmm160) REVERT: C 517 HIS cc_start: 0.7603 (OUTLIER) cc_final: 0.7269 (t-170) REVERT: C 597 TYR cc_start: 0.9196 (m-80) cc_final: 0.8913 (m-80) REVERT: C 617 LEU cc_start: 0.8866 (tp) cc_final: 0.8530 (mt) REVERT: C 657 CYS cc_start: 0.4287 (OUTLIER) cc_final: 0.4018 (m) REVERT: B 512 GLU cc_start: 0.9329 (mp0) cc_final: 0.8545 (mt-10) REVERT: B 520 MET cc_start: 0.8431 (ptp) cc_final: 0.7905 (ptp) REVERT: B 553 TYR cc_start: 0.7165 (m-80) cc_final: 0.6783 (m-80) REVERT: B 566 ASN cc_start: 0.9286 (m-40) cc_final: 0.8824 (m110) REVERT: B 634 MET cc_start: 0.4856 (tmm) cc_final: 0.4633 (tpp) REVERT: B 649 GLN cc_start: 0.7335 (mp10) cc_final: 0.6730 (pm20) outliers start: 42 outliers final: 26 residues processed: 185 average time/residue: 0.2325 time to fit residues: 64.5047 Evaluate side-chains 184 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 152 time to evaluate : 1.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 417 HIS Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 591 VAL 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 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 840 VAL Chi-restraints excluded: chain A residue 852 ILE Chi-restraints excluded: chain A residue 931 LYS 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 1210 VAL Chi-restraints excluded: chain A residue 1252 PHE Chi-restraints excluded: chain A residue 1269 CYS Chi-restraints excluded: chain C residue 517 HIS Chi-restraints excluded: chain C residue 526 VAL Chi-restraints excluded: chain C residue 639 ILE Chi-restraints excluded: chain C residue 657 CYS Chi-restraints excluded: chain C residue 680 ILE Chi-restraints excluded: chain C residue 748 GLU Chi-restraints excluded: chain B residue 522 ARG Chi-restraints excluded: chain B residue 546 VAL Chi-restraints excluded: chain B residue 624 LEU Chi-restraints excluded: chain B residue 668 ASN Chi-restraints excluded: chain B residue 685 HIS Chi-restraints excluded: chain B residue 698 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 17 optimal weight: 0.9990 chunk 60 optimal weight: 4.9990 chunk 57 optimal weight: 4.9990 chunk 50 optimal weight: 1.9990 chunk 92 optimal weight: 6.9990 chunk 134 optimal weight: 10.0000 chunk 2 optimal weight: 9.9990 chunk 97 optimal weight: 9.9990 chunk 117 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 46 optimal weight: 4.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 774 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 517 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 521 GLN ** 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 = 0.3864 r_free = 0.3864 target = 0.111403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.072698 restraints weight = 39530.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.075559 restraints weight = 19521.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.077455 restraints weight = 12647.264| |-----------------------------------------------------------------------------| r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.4747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 12999 Z= 0.236 Angle : 0.771 9.519 17897 Z= 0.386 Chirality : 0.044 0.215 2009 Planarity : 0.005 0.072 2019 Dihedral : 16.605 91.040 2651 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 15.86 Ramachandran Plot: Outliers : 0.08 % Allowed : 10.63 % Favored : 89.29 % Rotamer: Outliers : 3.67 % Allowed : 25.85 % Favored : 70.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.96 (0.23), residues: 1317 helix: 0.55 (0.22), residues: 588 sheet: -2.13 (0.51), residues: 106 loop : -3.13 (0.22), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 691 HIS 0.016 0.002 HIS C 517 PHE 0.022 0.002 PHE B 580 TYR 0.019 0.002 TYR A1236 ARG 0.006 0.000 ARG A1273 Details of bonding type rmsd hydrogen bonds : bond 0.04306 ( 487) hydrogen bonds : angle 4.60178 ( 1343) metal coordination : bond 0.00680 ( 3) covalent geometry : bond 0.00519 (12996) covalent geometry : angle 0.77139 (17897) *********************** 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 199 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 155 time to evaluate : 1.430 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 635 MET cc_start: 0.8725 (tpp) cc_final: 0.8459 (tpp) REVERT: A 654 ARG cc_start: 0.8402 (mmt180) cc_final: 0.8187 (mmt90) REVERT: A 688 PHE cc_start: 0.8253 (OUTLIER) cc_final: 0.7797 (t80) REVERT: A 731 GLN cc_start: 0.8780 (OUTLIER) cc_final: 0.8484 (mm-40) REVERT: A 736 GLU cc_start: 0.8472 (mp0) cc_final: 0.8104 (mp0) REVERT: A 740 MET cc_start: 0.8807 (pmm) cc_final: 0.8293 (pmm) REVERT: A 815 LYS cc_start: 0.7694 (mmmt) cc_final: 0.7244 (mttp) REVERT: A 1155 GLN cc_start: 0.8919 (pp30) cc_final: 0.7951 (pp30) REVERT: A 1192 GLU cc_start: 0.8978 (tm-30) cc_final: 0.8401 (tm-30) REVERT: A 1208 ARG cc_start: 0.7900 (tpp-160) cc_final: 0.7581 (tpp-160) REVERT: A 1252 PHE cc_start: 0.8687 (OUTLIER) cc_final: 0.8241 (t80) REVERT: A 1273 ARG cc_start: 0.8687 (mmm160) cc_final: 0.8376 (mmm160) REVERT: C 520 MET cc_start: 0.6878 (mmm) cc_final: 0.6411 (tmm) REVERT: C 597 TYR cc_start: 0.9230 (m-80) cc_final: 0.8939 (m-80) REVERT: C 617 LEU cc_start: 0.8865 (tp) cc_final: 0.8363 (mp) REVERT: C 657 CYS cc_start: 0.4553 (OUTLIER) cc_final: 0.4269 (m) REVERT: C 737 GLU cc_start: 0.9049 (mm-30) cc_final: 0.8654 (mp0) REVERT: B 522 ARG cc_start: 0.7388 (OUTLIER) cc_final: 0.7005 (tpt90) REVERT: B 553 TYR cc_start: 0.6982 (m-80) cc_final: 0.6394 (m-80) REVERT: B 634 MET cc_start: 0.5168 (tmm) cc_final: 0.4864 (tpp) REVERT: B 649 GLN cc_start: 0.7097 (mp10) cc_final: 0.6588 (pm20) REVERT: B 665 TRP cc_start: 0.3752 (m-90) cc_final: 0.3401 (m-90) REVERT: B 697 MET cc_start: 0.7396 (mmt) cc_final: 0.6881 (mmp) outliers start: 44 outliers final: 32 residues processed: 185 average time/residue: 0.2162 time to fit residues: 60.7709 Evaluate side-chains 186 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 149 time to evaluate : 1.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 417 HIS 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 688 PHE Chi-restraints excluded: chain A residue 702 ILE 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 840 VAL Chi-restraints excluded: chain A residue 852 ILE Chi-restraints excluded: chain A residue 916 SER Chi-restraints excluded: chain A residue 931 LYS Chi-restraints excluded: chain A residue 942 ILE Chi-restraints excluded: chain A residue 980 THR Chi-restraints excluded: chain A residue 1004 VAL Chi-restraints excluded: chain A residue 1130 LEU Chi-restraints excluded: chain A residue 1159 THR Chi-restraints excluded: chain A residue 1164 ILE Chi-restraints excluded: chain A residue 1174 LEU Chi-restraints excluded: chain A residue 1210 VAL Chi-restraints excluded: chain A residue 1252 PHE Chi-restraints excluded: chain A residue 1269 CYS Chi-restraints excluded: chain A residue 1326 MET Chi-restraints excluded: chain C residue 526 VAL Chi-restraints excluded: chain C residue 639 ILE Chi-restraints excluded: chain C residue 657 CYS Chi-restraints excluded: chain C residue 680 ILE Chi-restraints excluded: chain C residue 748 GLU Chi-restraints excluded: chain B residue 522 ARG Chi-restraints excluded: chain B residue 546 VAL Chi-restraints excluded: chain B residue 624 LEU Chi-restraints excluded: chain B residue 668 ASN Chi-restraints excluded: chain B residue 685 HIS Chi-restraints excluded: chain B residue 698 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 117 optimal weight: 6.9990 chunk 81 optimal weight: 0.6980 chunk 23 optimal weight: 0.7980 chunk 78 optimal weight: 0.0020 chunk 129 optimal weight: 2.9990 chunk 96 optimal weight: 30.0000 chunk 31 optimal weight: 20.0000 chunk 91 optimal weight: 5.9990 chunk 124 optimal weight: 0.2980 chunk 12 optimal weight: 0.9990 chunk 62 optimal weight: 5.9990 overall best weight: 0.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 774 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 690 ASN ** B 517 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.116037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.081519 restraints weight = 35471.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.084543 restraints weight = 17049.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.086511 restraints weight = 10737.070| |-----------------------------------------------------------------------------| r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.4903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 12999 Z= 0.130 Angle : 0.714 10.878 17897 Z= 0.353 Chirality : 0.040 0.190 2009 Planarity : 0.004 0.067 2019 Dihedral : 16.479 88.224 2651 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.04 % Favored : 90.96 % Rotamer: Outliers : 2.50 % Allowed : 27.61 % Favored : 69.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.72 (0.23), residues: 1317 helix: 0.68 (0.22), residues: 586 sheet: -1.02 (0.64), residues: 74 loop : -3.04 (0.22), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 523 HIS 0.016 0.001 HIS C 517 PHE 0.024 0.001 PHE C 598 TYR 0.017 0.001 TYR B 621 ARG 0.005 0.000 ARG A1273 Details of bonding type rmsd hydrogen bonds : bond 0.03683 ( 487) hydrogen bonds : angle 4.32089 ( 1343) metal coordination : bond 0.00319 ( 3) covalent geometry : bond 0.00293 (12996) covalent geometry : angle 0.71423 (17897) *********************** 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 185 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 155 time to evaluate : 1.295 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 635 MET cc_start: 0.8675 (tpp) cc_final: 0.8386 (tpp) REVERT: A 654 ARG cc_start: 0.8387 (mmt180) cc_final: 0.7784 (mpt180) REVERT: A 688 PHE cc_start: 0.8334 (OUTLIER) cc_final: 0.7922 (t80) REVERT: A 731 GLN cc_start: 0.8804 (OUTLIER) cc_final: 0.8439 (mp10) REVERT: A 736 GLU cc_start: 0.8452 (mp0) cc_final: 0.8039 (mp0) REVERT: A 740 MET cc_start: 0.8844 (pmm) cc_final: 0.8274 (pmm) REVERT: A 815 LYS cc_start: 0.7656 (mmmt) cc_final: 0.7149 (mttp) REVERT: A 1019 ASP cc_start: 0.8609 (p0) cc_final: 0.8388 (t0) REVERT: A 1035 ASP cc_start: 0.8459 (p0) cc_final: 0.7359 (m-30) REVERT: A 1040 MET cc_start: 0.9200 (tpp) cc_final: 0.8884 (mmt) REVERT: A 1154 MET cc_start: 0.9395 (tpt) cc_final: 0.8695 (tpt) REVERT: A 1192 GLU cc_start: 0.9001 (tm-30) cc_final: 0.8380 (tm-30) REVERT: A 1196 MET cc_start: 0.8944 (mmp) cc_final: 0.8691 (mmp) REVERT: A 1208 ARG cc_start: 0.7843 (tpp-160) cc_final: 0.7555 (tpp-160) REVERT: A 1252 PHE cc_start: 0.8612 (OUTLIER) cc_final: 0.8188 (t80) REVERT: C 520 MET cc_start: 0.7124 (mmm) cc_final: 0.6697 (tmm) REVERT: C 597 TYR cc_start: 0.8943 (m-80) cc_final: 0.8665 (m-80) REVERT: C 617 LEU cc_start: 0.8984 (tp) cc_final: 0.8441 (mt) REVERT: C 657 CYS cc_start: 0.4563 (OUTLIER) cc_final: 0.4288 (m) REVERT: B 512 GLU cc_start: 0.9337 (mp0) cc_final: 0.8412 (mt-10) REVERT: B 520 MET cc_start: 0.8442 (ptp) cc_final: 0.8053 (ptp) REVERT: B 553 TYR cc_start: 0.7022 (m-80) cc_final: 0.6597 (m-80) REVERT: B 634 MET cc_start: 0.5674 (tmm) cc_final: 0.5423 (tpp) REVERT: B 655 MET cc_start: 0.8399 (ppp) cc_final: 0.7445 (pmm) REVERT: B 665 TRP cc_start: 0.3748 (m-90) cc_final: 0.3413 (m-90) REVERT: B 697 MET cc_start: 0.7465 (mmt) cc_final: 0.7244 (mmt) outliers start: 30 outliers final: 23 residues processed: 175 average time/residue: 0.2149 time to fit residues: 57.0192 Evaluate side-chains 172 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 145 time to evaluate : 1.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 417 HIS 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 688 PHE 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 840 VAL Chi-restraints excluded: chain A residue 852 ILE Chi-restraints excluded: chain A residue 916 SER 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 1210 VAL Chi-restraints excluded: chain A residue 1252 PHE Chi-restraints excluded: chain C residue 526 VAL Chi-restraints excluded: chain C residue 639 ILE Chi-restraints excluded: chain C residue 657 CYS Chi-restraints excluded: chain C residue 748 GLU Chi-restraints excluded: chain B residue 522 ARG Chi-restraints excluded: chain B residue 546 VAL Chi-restraints excluded: chain B residue 624 LEU Chi-restraints excluded: chain B residue 668 ASN Chi-restraints excluded: chain B residue 698 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 17 optimal weight: 2.9990 chunk 46 optimal weight: 0.8980 chunk 32 optimal weight: 8.9990 chunk 54 optimal weight: 0.0060 chunk 104 optimal weight: 30.0000 chunk 89 optimal weight: 7.9990 chunk 80 optimal weight: 0.3980 chunk 74 optimal weight: 7.9990 chunk 124 optimal weight: 0.7980 chunk 72 optimal weight: 0.8980 chunk 13 optimal weight: 0.2980 overall best weight: 0.4796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 663 ASN ** A 774 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1267 GLN ** A1336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 625 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 517 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.116561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.082296 restraints weight = 35401.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.085337 restraints weight = 17028.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.087326 restraints weight = 10672.600| |-----------------------------------------------------------------------------| r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.5049 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= 0.127 Angle : 0.706 11.107 17897 Z= 0.347 Chirality : 0.040 0.203 2009 Planarity : 0.004 0.062 2019 Dihedral : 16.356 86.653 2651 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.19 % Favored : 90.74 % Rotamer: Outliers : 2.42 % Allowed : 28.02 % Favored : 69.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.62 (0.24), residues: 1317 helix: 0.73 (0.22), residues: 583 sheet: -0.93 (0.65), residues: 74 loop : -2.94 (0.22), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 523 HIS 0.013 0.001 HIS C 517 PHE 0.016 0.001 PHE A1110 TYR 0.015 0.001 TYR B 621 ARG 0.012 0.000 ARG A1273 Details of bonding type rmsd hydrogen bonds : bond 0.03548 ( 487) hydrogen bonds : angle 4.23440 ( 1343) metal coordination : bond 0.00270 ( 3) covalent geometry : bond 0.00286 (12996) covalent geometry : angle 0.70565 (17897) ********************** 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 187 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 158 time to evaluate : 1.366 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: 0.7850 (t-90) cc_final: 0.7626 (t70) REVERT: A 635 MET cc_start: 0.8656 (tpp) cc_final: 0.8384 (tpp) REVERT: A 688 PHE cc_start: 0.8293 (OUTLIER) cc_final: 0.7922 (t80) REVERT: A 723 LEU cc_start: 0.8510 (mp) cc_final: 0.8053 (mt) REVERT: A 731 GLN cc_start: 0.8810 (OUTLIER) cc_final: 0.8472 (mp10) REVERT: A 736 GLU cc_start: 0.8434 (mp0) cc_final: 0.8003 (mp0) REVERT: A 740 MET cc_start: 0.8894 (pmm) cc_final: 0.8334 (pmm) REVERT: A 815 LYS cc_start: 0.7604 (mmmt) cc_final: 0.7165 (mttt) REVERT: A 1035 ASP cc_start: 0.8473 (p0) cc_final: 0.7387 (m-30) REVERT: A 1040 MET cc_start: 0.9184 (tpp) cc_final: 0.8860 (mmt) REVERT: A 1154 MET cc_start: 0.9395 (tpt) cc_final: 0.8793 (tpt) REVERT: A 1192 GLU cc_start: 0.8999 (tm-30) cc_final: 0.8347 (tm-30) REVERT: A 1208 ARG cc_start: 0.7869 (tpp-160) cc_final: 0.7582 (tpp-160) REVERT: A 1252 PHE cc_start: 0.8511 (OUTLIER) cc_final: 0.8150 (t80) REVERT: C 512 GLU cc_start: 0.8762 (tp30) cc_final: 0.7934 (tp30) REVERT: C 516 LEU cc_start: 0.9396 (tt) cc_final: 0.8656 (pp) REVERT: C 520 MET cc_start: 0.7163 (mmm) cc_final: 0.6670 (tmm) REVERT: C 597 TYR cc_start: 0.8975 (m-80) cc_final: 0.8653 (m-80) REVERT: C 617 LEU cc_start: 0.9073 (tp) cc_final: 0.8624 (mp) REVERT: C 621 TYR cc_start: 0.7562 (t80) cc_final: 0.7168 (t80) REVERT: C 625 HIS cc_start: 0.7337 (m-70) cc_final: 0.7014 (m-70) REVERT: C 657 CYS cc_start: 0.4352 (OUTLIER) cc_final: 0.4075 (m) REVERT: B 520 MET cc_start: 0.8367 (ptp) cc_final: 0.7902 (ptp) REVERT: B 553 TYR cc_start: 0.7033 (m-80) cc_final: 0.6621 (m-80) REVERT: B 621 TYR cc_start: 0.7796 (t80) cc_final: 0.7544 (t80) REVERT: B 634 MET cc_start: 0.6062 (tmm) cc_final: 0.5788 (tpp) REVERT: B 655 MET cc_start: 0.8506 (ppp) cc_final: 0.7511 (pmm) REVERT: B 665 TRP cc_start: 0.3628 (m-90) cc_final: 0.3329 (m-90) REVERT: B 697 MET cc_start: 0.7450 (mmt) cc_final: 0.7225 (mmt) outliers start: 29 outliers final: 22 residues processed: 177 average time/residue: 0.2181 time to fit residues: 58.3951 Evaluate side-chains 173 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 147 time to evaluate : 1.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 417 HIS Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 520 ASP Chi-restraints excluded: chain A residue 606 MET Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain A residue 645 LEU Chi-restraints excluded: chain A residue 663 ASN Chi-restraints excluded: chain A residue 688 PHE Chi-restraints excluded: chain A residue 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 916 SER Chi-restraints excluded: chain A residue 1130 LEU Chi-restraints excluded: chain A residue 1174 LEU Chi-restraints excluded: chain A residue 1210 VAL Chi-restraints excluded: chain A residue 1252 PHE Chi-restraints excluded: chain C residue 526 VAL Chi-restraints excluded: chain C residue 639 ILE Chi-restraints excluded: chain C residue 657 CYS Chi-restraints excluded: chain C residue 748 GLU Chi-restraints excluded: chain B residue 522 ARG Chi-restraints excluded: chain B residue 546 VAL Chi-restraints excluded: chain B residue 624 LEU Chi-restraints excluded: chain B residue 668 ASN Chi-restraints excluded: chain B residue 698 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 33 optimal weight: 0.8980 chunk 108 optimal weight: 10.0000 chunk 86 optimal weight: 2.9990 chunk 133 optimal weight: 6.9990 chunk 21 optimal weight: 0.4980 chunk 126 optimal weight: 0.3980 chunk 101 optimal weight: 2.9990 chunk 112 optimal weight: 10.0000 chunk 49 optimal weight: 3.9990 chunk 9 optimal weight: 0.0770 chunk 63 optimal weight: 0.8980 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 774 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 625 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 517 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 625 HIS ** B 674 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.120776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.082907 restraints weight = 36063.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.085907 restraints weight = 17404.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 63)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.087851 restraints weight = 10970.872| |-----------------------------------------------------------------------------| r_work (final): 0.3538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.5060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.155 12999 Z= 0.213 Angle : 0.918 59.164 17897 Z= 0.511 Chirality : 0.046 0.984 2009 Planarity : 0.005 0.075 2019 Dihedral : 16.357 86.645 2651 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 13.60 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.19 % Favored : 90.66 % Rotamer: Outliers : 2.59 % Allowed : 27.94 % Favored : 69.47 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.61 (0.24), residues: 1317 helix: 0.73 (0.22), residues: 583 sheet: -0.93 (0.65), residues: 74 loop : -2.92 (0.22), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 523 HIS 0.050 0.001 HIS A 933 PHE 0.016 0.001 PHE A1110 TYR 0.015 0.001 TYR B 597 ARG 0.011 0.000 ARG A1273 Details of bonding type rmsd hydrogen bonds : bond 0.03561 ( 487) hydrogen bonds : angle 4.23715 ( 1343) metal coordination : bond 0.00275 ( 3) covalent geometry : bond 0.00393 (12996) covalent geometry : angle 0.91816 (17897) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4420.54 seconds wall clock time: 77 minutes 31.35 seconds (4651.35 seconds total)