Starting phenix.real_space_refine on Sat Aug 23 10:21:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8v3l_42949/08_2025/8v3l_42949.cif Found real_map, /net/cci-nas-00/data/ceres_data/8v3l_42949/08_2025/8v3l_42949.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8v3l_42949/08_2025/8v3l_42949.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8v3l_42949/08_2025/8v3l_42949.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8v3l_42949/08_2025/8v3l_42949.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8v3l_42949/08_2025/8v3l_42949.map" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.010 sd= 0.067 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: 4 Type Number sf(0) Gaussians S 40 5.16 5 C 7248 2.51 5 N 1915 2.21 5 O 2079 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11282 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 10120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1218, 10120 Classifications: {'peptide': 1218} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 26, 'TRANS': 1191} Chain breaks: 8 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "A1" Number of atoms: 1162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1162 Classifications: {'peptide': 141} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 135} Chain breaks: 2 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'GLU:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 13 Time building chain proxies: 3.15, per 1000 atoms: 0.28 Number of scatterers: 11282 At special positions: 0 Unit cell: (171.25, 112.34, 167.14, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 40 16.00 O 2079 8.00 N 1915 7.00 C 7248 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.79 Conformation dependent library (CDL) restraints added in 499.8 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2670 Ramachandran restraints generated. 1335 Oldfield, 0 Emsley, 1335 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2604 Finding SS restraints... Secondary structure from input PDB file: 79 helices and 5 sheets defined 68.9% alpha, 3.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.51 Creating SS restraints... Processing helix chain 'A' and resid 6 through 25 Processing helix chain 'A' and resid 40 through 60 Processing helix chain 'A' and resid 137 through 146 Processing helix chain 'A' and resid 148 through 170 Processing helix chain 'A' and resid 195 through 202 Processing helix chain 'A' and resid 204 through 208 removed outlier: 3.663A pdb=" N LYS A 207 " --> pdb=" O GLY A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 217 Processing helix chain 'A' and resid 304 through 318 Processing helix chain 'A' and resid 321 through 335 Processing helix chain 'A' and resid 345 through 356 Processing helix chain 'A' and resid 361 through 373 Processing helix chain 'A' and resid 381 through 389 Processing helix chain 'A' and resid 394 through 407 Processing helix chain 'A' and resid 409 through 418 Processing helix chain 'A' and resid 427 through 439 Processing helix chain 'A' and resid 443 through 456 Processing helix chain 'A' and resid 462 through 471 Processing helix chain 'A' and resid 483 through 499 Processing helix chain 'A' and resid 503 through 513 Processing helix chain 'A' and resid 521 through 532 Processing helix chain 'A' and resid 537 through 547 removed outlier: 3.537A pdb=" N ARG A 546 " --> pdb=" O ASN A 542 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N TYR A 547 " --> pdb=" O ARG A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 558 through 567 Processing helix chain 'A' and resid 580 through 595 removed outlier: 4.007A pdb=" N LYS A 595 " --> pdb=" O PHE A 591 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 608 Processing helix chain 'A' and resid 625 through 636 Processing helix chain 'A' and resid 641 through 653 removed outlier: 4.179A pdb=" N GLU A 651 " --> pdb=" O PHE A 647 " (cutoff:3.500A) Processing helix chain 'A' and resid 661 through 671 Processing helix chain 'A' and resid 672 through 675 Processing helix chain 'A' and resid 713 through 732 Processing helix chain 'A' and resid 734 through 743 removed outlier: 3.624A pdb=" N ASP A 743 " --> pdb=" O PHE A 739 " (cutoff:3.500A) Processing helix chain 'A' and resid 751 through 760 removed outlier: 4.063A pdb=" N ARG A 760 " --> pdb=" O SER A 756 " (cutoff:3.500A) Processing helix chain 'A' and resid 766 through 778 Processing helix chain 'A' and resid 786 through 795 Processing helix chain 'A' and resid 810 through 828 removed outlier: 3.688A pdb=" N ASN A 814 " --> pdb=" O PHE A 810 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LYS A 825 " --> pdb=" O ARG A 821 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LYS A 826 " --> pdb=" O GLN A 822 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N GLU A 827 " --> pdb=" O TRP A 823 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N GLY A 828 " --> pdb=" O PHE A 824 " (cutoff:3.500A) Processing helix chain 'A' and resid 830 through 837 Processing helix chain 'A' and resid 847 through 858 Processing helix chain 'A' and resid 862 through 866 Processing helix chain 'A' and resid 867 through 879 Processing helix chain 'A' and resid 887 through 897 Processing helix chain 'A' and resid 898 through 903 removed outlier: 4.149A pdb=" N TYR A 901 " --> pdb=" O ASP A 898 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N GLY A 902 " --> pdb=" O PHE A 899 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N MET A 903 " --> pdb=" O GLY A 900 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 898 through 903' Processing helix chain 'A' and resid 904 through 909 Processing helix chain 'A' and resid 920 through 937 Processing helix chain 'A' and resid 939 through 949 Processing helix chain 'A' and resid 955 through 967 Processing helix chain 'A' and resid 975 through 987 Processing helix chain 'A' and resid 995 through 1004 Processing helix chain 'A' and resid 1007 through 1024 Processing helix chain 'A' and resid 1026 through 1035 Processing helix chain 'A' and resid 1044 through 1056 Processing helix chain 'A' and resid 1061 through 1074 Processing helix chain 'A' and resid 1080 through 1088 Processing helix chain 'A' and resid 1150 through 1166 Processing helix chain 'A' and resid 1172 through 1180 Processing helix chain 'A' and resid 1189 through 1201 Processing helix chain 'A' and resid 1205 through 1216 Processing helix chain 'A' and resid 1224 through 1231 Processing helix chain 'A' and resid 1234 through 1244 removed outlier: 3.941A pdb=" N SER A1244 " --> pdb=" O ILE A1240 " (cutoff:3.500A) Processing helix chain 'A' and resid 1244 through 1258 Processing helix chain 'A' and resid 1261 through 1270 Processing helix chain 'A' and resid 1278 through 1294 removed outlier: 3.525A pdb=" N PHE A1282 " --> pdb=" O ASP A1278 " (cutoff:3.500A) Processing helix chain 'A' and resid 1299 through 1311 Processing helix chain 'A' and resid 1319 through 1328 Processing helix chain 'A' and resid 1423 through 1433 removed outlier: 3.503A pdb=" N LYS A1432 " --> pdb=" O GLY A1428 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N THR A1433 " --> pdb=" O GLU A1429 " (cutoff:3.500A) Processing helix chain 'A' and resid 1433 through 1446 removed outlier: 3.964A pdb=" N ASP A1437 " --> pdb=" O THR A1433 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ASN A1446 " --> pdb=" O SER A1442 " (cutoff:3.500A) Processing helix chain 'A' and resid 1446 through 1460 Processing helix chain 'A' and resid 1465 through 1480 removed outlier: 3.520A pdb=" N ALA A1469 " --> pdb=" O THR A1465 " (cutoff:3.500A) Processing helix chain 'A' and resid 1485 through 1487 No H-bonds generated for 'chain 'A' and resid 1485 through 1487' Processing helix chain 'A' and resid 1488 through 1494 removed outlier: 4.135A pdb=" N ILE A1492 " --> pdb=" O SER A1488 " (cutoff:3.500A) Processing helix chain 'A' and resid 1503 through 1520 removed outlier: 3.710A pdb=" N LEU A1507 " --> pdb=" O ASP A1503 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N SER A1520 " --> pdb=" O LYS A1516 " (cutoff:3.500A) Processing helix chain 'A1' and resid 13 through 21 Processing helix chain 'A1' and resid 22 through 26 removed outlier: 3.644A pdb=" N ILEA1 26 " --> pdb=" O PROA1 23 " (cutoff:3.500A) Processing helix chain 'A1' and resid 31 through 36 Processing helix chain 'A1' and resid 37 through 54 Processing helix chain 'A1' and resid 78 through 91 removed outlier: 3.655A pdb=" N GLUA1 83 " --> pdb=" O PHEA1 79 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLUA1 84 " --> pdb=" O GLNA1 80 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N META1 85 " --> pdb=" O LYSA1 81 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N SERA1 89 " --> pdb=" O META1 85 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILEA1 91 " --> pdb=" O ARGA1 87 " (cutoff:3.500A) Processing helix chain 'A1' and resid 121 through 125 Processing helix chain 'A1' and resid 128 through 140 removed outlier: 3.737A pdb=" N TRPA1 138 " --> pdb=" O PHEA1 134 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILEA1 139 " --> pdb=" O ILEA1 135 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLUA1 140 " --> pdb=" O ASPA1 136 " (cutoff:3.500A) Processing helix chain 'A1' and resid 144 through 146 No H-bonds generated for 'chain 'A1' and resid 144 through 146' Processing helix chain 'A1' and resid 147 through 164 removed outlier: 3.938A pdb=" N VALA1 151 " --> pdb=" O PHEA1 147 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ALAA1 164 " --> pdb=" O SERA1 160 " (cutoff:3.500A) Processing helix chain 'A1' and resid 172 through 177 Processing sheet with id=AA1, first strand: chain 'A' and resid 96 through 100 removed outlier: 5.817A pdb=" N GLY A 62 " --> pdb=" O THR A 134 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 119 through 122 removed outlier: 3.945A pdb=" N ALA A 190 " --> pdb=" O LYS A 111 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N VAL A 192 " --> pdb=" O GLY A 113 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N PHE A 115 " --> pdb=" O VAL A 192 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N PHE A 194 " --> pdb=" O PHE A 115 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 519 through 520 Processing sheet with id=AA4, first strand: chain 'A' and resid 1187 through 1188 Processing sheet with id=AA5, first strand: chain 'A' and resid 1497 through 1498 626 hydrogen bonds defined for protein. 1833 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.09 Time building geometry restraints manager: 1.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3642 1.34 - 1.46: 2421 1.46 - 1.58: 5368 1.58 - 1.70: 0 1.70 - 1.82: 69 Bond restraints: 11500 Sorted by residual: bond pdb=" C ASP A 695 " pdb=" O ASP A 695 " ideal model delta sigma weight residual 1.235 1.227 0.008 4.70e-03 4.53e+04 2.81e+00 bond pdb=" CG1 ILE A1286 " pdb=" CD1 ILE A1286 " ideal model delta sigma weight residual 1.513 1.460 0.053 3.90e-02 6.57e+02 1.83e+00 bond pdb=" CA ILE A 599 " pdb=" CB ILE A 599 " ideal model delta sigma weight residual 1.539 1.532 0.007 5.40e-03 3.43e+04 1.67e+00 bond pdb=" CB GLN A1242 " pdb=" CG GLN A1242 " ideal model delta sigma weight residual 1.520 1.557 -0.037 3.00e-02 1.11e+03 1.52e+00 bond pdb=" CB LYS A1247 " pdb=" CG LYS A1247 " ideal model delta sigma weight residual 1.520 1.554 -0.034 3.00e-02 1.11e+03 1.28e+00 ... (remaining 11495 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.19: 15217 2.19 - 4.38: 180 4.38 - 6.57: 30 6.57 - 8.76: 6 8.76 - 10.95: 3 Bond angle restraints: 15436 Sorted by residual: angle pdb=" C SERA1 93 " pdb=" CA SERA1 93 " pdb=" CB SERA1 93 " ideal model delta sigma weight residual 116.54 109.99 6.55 1.15e+00 7.56e-01 3.25e+01 angle pdb=" N THR A 698 " pdb=" CA THR A 698 " pdb=" C THR A 698 " ideal model delta sigma weight residual 114.75 107.84 6.91 1.26e+00 6.30e-01 3.01e+01 angle pdb=" C ILE A 496 " pdb=" N MET A 497 " pdb=" CA MET A 497 " ideal model delta sigma weight residual 121.94 112.70 9.24 2.00e+00 2.50e-01 2.13e+01 angle pdb=" N GLU A1014 " pdb=" CA GLU A1014 " pdb=" CB GLU A1014 " ideal model delta sigma weight residual 110.28 116.65 -6.37 1.55e+00 4.16e-01 1.69e+01 angle pdb=" C PHEA1 147 " pdb=" N GLNA1 148 " pdb=" CA GLNA1 148 " ideal model delta sigma weight residual 122.26 115.99 6.27 1.59e+00 3.96e-01 1.56e+01 ... (remaining 15431 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.70: 6389 16.70 - 33.39: 519 33.39 - 50.08: 66 50.08 - 66.78: 11 66.78 - 83.47: 5 Dihedral angle restraints: 6990 sinusoidal: 2994 harmonic: 3996 Sorted by residual: dihedral pdb=" CA PRO A1299 " pdb=" C PRO A1299 " pdb=" N TYR A1300 " pdb=" CA TYR A1300 " ideal model delta harmonic sigma weight residual -180.00 -158.77 -21.23 0 5.00e+00 4.00e-02 1.80e+01 dihedral pdb=" CA MET A 685 " pdb=" C MET A 685 " pdb=" N THR A 686 " pdb=" CA THR A 686 " ideal model delta harmonic sigma weight residual 180.00 161.03 18.97 0 5.00e+00 4.00e-02 1.44e+01 dihedral pdb=" CA LEU A 706 " pdb=" C LEU A 706 " pdb=" N TYR A 707 " pdb=" CA TYR A 707 " ideal model delta harmonic sigma weight residual 180.00 162.74 17.26 0 5.00e+00 4.00e-02 1.19e+01 ... (remaining 6987 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1221 0.041 - 0.083: 344 0.083 - 0.124: 89 0.124 - 0.165: 11 0.165 - 0.206: 1 Chirality restraints: 1666 Sorted by residual: chirality pdb=" CG LEU A 706 " pdb=" CB LEU A 706 " pdb=" CD1 LEU A 706 " pdb=" CD2 LEU A 706 " both_signs ideal model delta sigma weight residual False -2.59 -2.38 -0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" CA GLU A1014 " pdb=" N GLU A1014 " pdb=" C GLU A1014 " pdb=" CB GLU A1014 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.16 2.00e-01 2.50e+01 6.01e-01 chirality pdb=" CA VAL A 95 " pdb=" N VAL A 95 " pdb=" C VAL A 95 " pdb=" CB VAL A 95 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.48e-01 ... (remaining 1663 not shown) Planarity restraints: 1973 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 883 " 0.210 9.50e-02 1.11e+02 9.45e-02 6.00e+00 pdb=" NE ARG A 883 " -0.017 2.00e-02 2.50e+03 pdb=" CZ ARG A 883 " 0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG A 883 " -0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG A 883 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A1447 " 0.220 9.50e-02 1.11e+02 9.88e-02 5.99e+00 pdb=" NE ARG A1447 " -0.013 2.00e-02 2.50e+03 pdb=" CZ ARG A1447 " -0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG A1447 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG A1447 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 790 " 0.014 2.00e-02 2.50e+03 1.77e-02 5.51e+00 pdb=" CG PHE A 790 " -0.039 2.00e-02 2.50e+03 pdb=" CD1 PHE A 790 " 0.019 2.00e-02 2.50e+03 pdb=" CD2 PHE A 790 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE A 790 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE A 790 " 0.006 2.00e-02 2.50e+03 pdb=" CZ PHE A 790 " 0.001 2.00e-02 2.50e+03 ... (remaining 1970 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1221 2.75 - 3.29: 11704 3.29 - 3.82: 18312 3.82 - 4.36: 21109 4.36 - 4.90: 34902 Nonbonded interactions: 87248 Sorted by model distance: nonbonded pdb=" O ILE A1443 " pdb=" NH2 ARG A1447 " model vdw 2.209 3.120 nonbonded pdb=" O THR A 782 " pdb=" OG SER A 984 " model vdw 2.210 3.040 nonbonded pdb=" OG SERA1 119 " pdb=" OD2 ASPA1 136 " model vdw 2.223 3.040 nonbonded pdb=" N GLUA1 149 " pdb=" OE1 GLUA1 149 " model vdw 2.225 3.120 nonbonded pdb=" OG1 THRA1 92 " pdb=" O TYRA1 95 " model vdw 2.241 3.040 ... (remaining 87243 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 10.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.210 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 11.980 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6516 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 11500 Z= 0.128 Angle : 0.628 10.946 15436 Z= 0.355 Chirality : 0.041 0.206 1666 Planarity : 0.005 0.099 1973 Dihedral : 12.021 83.475 4386 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.15 % Allowed : 2.70 % Favored : 97.15 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.47 (0.23), residues: 1335 helix: 1.46 (0.18), residues: 862 sheet: -0.31 (0.86), residues: 27 loop : 0.25 (0.31), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 883 TYR 0.015 0.001 TYR A 197 PHE 0.039 0.002 PHE A 790 TRP 0.038 0.002 TRP A 999 HIS 0.002 0.001 HIS A1082 Details of bonding type rmsd covalent geometry : bond 0.00267 (11500) covalent geometry : angle 0.62843 (15436) hydrogen bonds : bond 0.16120 ( 626) hydrogen bonds : angle 5.66133 ( 1833) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2670 Ramachandran restraints generated. 1335 Oldfield, 0 Emsley, 1335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2670 Ramachandran restraints generated. 1335 Oldfield, 0 Emsley, 1335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 1249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 342 time to evaluate : 0.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 VAL cc_start: 0.8713 (t) cc_final: 0.8243 (m) REVERT: A 309 LYS cc_start: 0.8856 (mtmm) cc_final: 0.8293 (mttt) REVERT: A 311 LEU cc_start: 0.9143 (tp) cc_final: 0.8932 (pp) REVERT: A 329 MET cc_start: 0.8024 (ptt) cc_final: 0.7579 (ptt) REVERT: A 347 LYS cc_start: 0.8942 (mttt) cc_final: 0.8487 (mttt) REVERT: A 349 PHE cc_start: 0.8175 (t80) cc_final: 0.7768 (t80) REVERT: A 356 MET cc_start: 0.6744 (mtm) cc_final: 0.6307 (mtm) REVERT: A 362 GLU cc_start: 0.8344 (tt0) cc_final: 0.7561 (tp30) REVERT: A 386 ARG cc_start: 0.8558 (ptp90) cc_final: 0.7693 (ptp90) REVERT: A 395 HIS cc_start: 0.7630 (m-70) cc_final: 0.7329 (m-70) REVERT: A 398 TYR cc_start: 0.8229 (t80) cc_final: 0.7786 (t80) REVERT: A 503 ASN cc_start: 0.8311 (m-40) cc_final: 0.8087 (m-40) REVERT: A 505 ILE cc_start: 0.9178 (mt) cc_final: 0.8889 (tp) REVERT: A 507 GLU cc_start: 0.8295 (mt-10) cc_final: 0.7783 (mt-10) REVERT: A 539 LYS cc_start: 0.8476 (mttt) cc_final: 0.8194 (mttt) REVERT: A 548 LEU cc_start: 0.8567 (mt) cc_final: 0.8130 (mt) REVERT: A 559 TYR cc_start: 0.8608 (m-80) cc_final: 0.8342 (m-80) REVERT: A 604 LYS cc_start: 0.8984 (tmmt) cc_final: 0.8622 (mmtm) REVERT: A 662 GLU cc_start: 0.7589 (tt0) cc_final: 0.7262 (tt0) REVERT: A 716 LYS cc_start: 0.8439 (ptpp) cc_final: 0.8137 (pttm) REVERT: A 746 GLN cc_start: 0.8014 (mp-120) cc_final: 0.7734 (mp10) REVERT: A 750 LEU cc_start: 0.8491 (mt) cc_final: 0.8120 (mm) REVERT: A 777 MET cc_start: 0.7806 (mtm) cc_final: 0.7529 (mtm) REVERT: A 786 ASP cc_start: 0.8006 (p0) cc_final: 0.7770 (p0) REVERT: A 813 GLU cc_start: 0.7733 (mp0) cc_final: 0.7048 (mp0) REVERT: A 815 GLU cc_start: 0.8182 (tt0) cc_final: 0.7776 (tt0) REVERT: A 818 PHE cc_start: 0.8182 (m-80) cc_final: 0.7581 (m-80) REVERT: A 822 GLN cc_start: 0.8543 (mt0) cc_final: 0.8189 (mt0) REVERT: A 826 LYS cc_start: 0.8439 (mtmt) cc_final: 0.7916 (ttpt) REVERT: A 856 LYS cc_start: 0.7949 (pttm) cc_final: 0.7476 (tppt) REVERT: A 888 PHE cc_start: 0.7057 (t80) cc_final: 0.6819 (t80) REVERT: A 908 MET cc_start: 0.7579 (mtm) cc_final: 0.7043 (ptp) REVERT: A 944 PHE cc_start: 0.7722 (t80) cc_final: 0.7318 (t80) REVERT: A 958 HIS cc_start: 0.8300 (m90) cc_final: 0.7825 (m90) REVERT: A 961 LYS cc_start: 0.9117 (tmtt) cc_final: 0.8443 (tptp) REVERT: A 965 ASP cc_start: 0.8216 (p0) cc_final: 0.7959 (p0) REVERT: A 979 MET cc_start: 0.8112 (mtm) cc_final: 0.7624 (mtm) REVERT: A 989 HIS cc_start: 0.7842 (m90) cc_final: 0.7516 (m90) REVERT: A 998 ASP cc_start: 0.8710 (m-30) cc_final: 0.8093 (m-30) REVERT: A 1033 PHE cc_start: 0.8409 (t80) cc_final: 0.8178 (t80) REVERT: A 1034 PHE cc_start: 0.8463 (m-80) cc_final: 0.8048 (m-80) REVERT: A 1050 LYS cc_start: 0.9326 (tttt) cc_final: 0.8798 (ptmm) REVERT: A 1053 ASN cc_start: 0.7311 (m110) cc_final: 0.6945 (m110) REVERT: A 1055 ILE cc_start: 0.8175 (mt) cc_final: 0.7664 (tp) REVERT: A 1068 LEU cc_start: 0.9252 (mt) cc_final: 0.8948 (mm) REVERT: A 1165 LEU cc_start: 0.7862 (mt) cc_final: 0.7513 (mt) REVERT: A 1282 PHE cc_start: 0.8764 (t80) cc_final: 0.8243 (t80) REVERT: A 1288 LYS cc_start: 0.8105 (tptt) cc_final: 0.7888 (tppt) REVERT: A 1292 LEU cc_start: 0.8122 (mt) cc_final: 0.7826 (mt) REVERT: A 1304 LYS cc_start: 0.7954 (ptpt) cc_final: 0.7555 (pptt) REVERT: A 1306 LEU cc_start: 0.8223 (mt) cc_final: 0.7898 (mt) REVERT: A 1314 LYS cc_start: 0.8223 (mmtt) cc_final: 0.7704 (mmtm) REVERT: A 1324 MET cc_start: 0.8058 (mmp) cc_final: 0.7589 (mmp) REVERT: A 1327 PHE cc_start: 0.8379 (m-80) cc_final: 0.8179 (m-10) REVERT: A 1435 GLU cc_start: 0.8244 (tt0) cc_final: 0.7941 (tt0) REVERT: A 1440 ILE cc_start: 0.7706 (mt) cc_final: 0.7300 (mm) REVERT: A 1470 LYS cc_start: 0.8379 (pttp) cc_final: 0.8003 (pttp) REVERT: A1 29 TYR cc_start: 0.6492 (m-10) cc_final: 0.6257 (m-80) REVERT: A1 52 LYS cc_start: 0.8788 (tttt) cc_final: 0.8328 (tttt) REVERT: A1 120 ASP cc_start: 0.8100 (m-30) cc_final: 0.7842 (m-30) REVERT: A1 121 LEU cc_start: 0.8407 (mt) cc_final: 0.7997 (mt) REVERT: A1 149 GLU cc_start: 0.6975 (mp0) cc_final: 0.6720 (mp0) outliers start: 0 outliers final: 0 residues processed: 342 average time/residue: 0.1189 time to fit residues: 54.9811 Evaluate side-chains 303 residues out of total 1249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 303 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 0.8980 chunk 55 optimal weight: 0.7980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 20 ASN A 166 GLN A 323 GLN A 348 GLN A 666 GLN A 980 GLN A1190 ASN A1320 GLN ** A1 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.162625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.139082 restraints weight = 30138.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.143314 restraints weight = 19696.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.146359 restraints weight = 14084.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.148600 restraints weight = 10658.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.150240 restraints weight = 8455.006| |-----------------------------------------------------------------------------| r_work (final): 0.4104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6489 moved from start: 0.1755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11500 Z= 0.127 Angle : 0.556 10.826 15436 Z= 0.305 Chirality : 0.041 0.147 1666 Planarity : 0.005 0.082 1973 Dihedral : 4.360 21.894 1464 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.15 % Allowed : 2.47 % Favored : 97.38 % Rotamer: Outliers : 0.24 % Allowed : 2.17 % Favored : 97.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.53 (0.24), residues: 1335 helix: 1.49 (0.18), residues: 892 sheet: -0.05 (1.33), residues: 17 loop : 0.19 (0.32), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 883 TYR 0.012 0.001 TYR A 197 PHE 0.027 0.002 PHE A 156 TRP 0.014 0.002 TRP A 999 HIS 0.002 0.001 HIS A 193 Details of bonding type rmsd covalent geometry : bond 0.00261 (11500) covalent geometry : angle 0.55631 (15436) hydrogen bonds : bond 0.04264 ( 626) hydrogen bonds : angle 4.58023 ( 1833) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2670 Ramachandran restraints generated. 1335 Oldfield, 0 Emsley, 1335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2670 Ramachandran restraints generated. 1335 Oldfield, 0 Emsley, 1335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 1249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 331 time to evaluate : 0.393 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 162 GLN cc_start: 0.8314 (tm-30) cc_final: 0.7972 (tm-30) REVERT: A 197 TYR cc_start: 0.7298 (t80) cc_final: 0.7081 (t80) REVERT: A 309 LYS cc_start: 0.8797 (mtmm) cc_final: 0.8321 (mttt) REVERT: A 347 LYS cc_start: 0.8949 (mttt) cc_final: 0.8520 (mttt) REVERT: A 349 PHE cc_start: 0.8252 (t80) cc_final: 0.7893 (t80) REVERT: A 355 LYS cc_start: 0.7102 (mtmt) cc_final: 0.6751 (pttt) REVERT: A 362 GLU cc_start: 0.8284 (tt0) cc_final: 0.7290 (tp30) REVERT: A 386 ARG cc_start: 0.8509 (ptp90) cc_final: 0.7970 (ttp-110) REVERT: A 395 HIS cc_start: 0.7668 (m-70) cc_final: 0.7190 (m170) REVERT: A 398 TYR cc_start: 0.8244 (t80) cc_final: 0.7916 (t80) REVERT: A 417 MET cc_start: 0.7683 (mtp) cc_final: 0.7420 (mtp) REVERT: A 437 LYS cc_start: 0.8343 (mttt) cc_final: 0.8080 (mmmm) REVERT: A 469 SER cc_start: 0.8521 (t) cc_final: 0.8273 (p) REVERT: A 505 ILE cc_start: 0.9215 (mt) cc_final: 0.8913 (tp) REVERT: A 507 GLU cc_start: 0.8389 (mt-10) cc_final: 0.7880 (mt-10) REVERT: A 539 LYS cc_start: 0.8398 (mttt) cc_final: 0.8167 (mttt) REVERT: A 548 LEU cc_start: 0.8612 (mt) cc_final: 0.8203 (mt) REVERT: A 596 LYS cc_start: 0.8723 (mmpt) cc_final: 0.8495 (mmmt) REVERT: A 627 GLN cc_start: 0.8655 (tp40) cc_final: 0.8413 (tp-100) REVERT: A 652 LEU cc_start: 0.8456 (mt) cc_final: 0.8100 (mt) REVERT: A 725 ARG cc_start: 0.8068 (mtt180) cc_final: 0.7789 (mtp180) REVERT: A 750 LEU cc_start: 0.8434 (mt) cc_final: 0.8101 (mm) REVERT: A 777 MET cc_start: 0.7845 (mtm) cc_final: 0.7444 (mtm) REVERT: A 813 GLU cc_start: 0.7659 (mp0) cc_final: 0.6909 (mp0) REVERT: A 815 GLU cc_start: 0.8017 (tt0) cc_final: 0.7396 (pt0) REVERT: A 818 PHE cc_start: 0.8099 (m-80) cc_final: 0.7758 (m-80) REVERT: A 819 ARG cc_start: 0.7936 (mtp-110) cc_final: 0.7537 (mtp-110) REVERT: A 822 GLN cc_start: 0.8622 (mt0) cc_final: 0.8138 (mt0) REVERT: A 823 TRP cc_start: 0.7864 (t60) cc_final: 0.7505 (t60) REVERT: A 826 LYS cc_start: 0.8466 (mtmt) cc_final: 0.7980 (ttpt) REVERT: A 908 MET cc_start: 0.7745 (mtm) cc_final: 0.7179 (mtm) REVERT: A 927 GLN cc_start: 0.8270 (tp-100) cc_final: 0.7617 (tm-30) REVERT: A 944 PHE cc_start: 0.7779 (t80) cc_final: 0.7312 (t80) REVERT: A 955 LEU cc_start: 0.8103 (mt) cc_final: 0.7266 (tp) REVERT: A 958 HIS cc_start: 0.8338 (m90) cc_final: 0.6992 (m90) REVERT: A 961 LYS cc_start: 0.9142 (tmtt) cc_final: 0.8398 (tptp) REVERT: A 964 GLN cc_start: 0.8976 (tp-100) cc_final: 0.8636 (tp-100) REVERT: A 965 ASP cc_start: 0.8186 (p0) cc_final: 0.7826 (p0) REVERT: A 976 GLU cc_start: 0.8525 (pm20) cc_final: 0.8021 (pm20) REVERT: A 979 MET cc_start: 0.7972 (mtm) cc_final: 0.7374 (mtm) REVERT: A 985 ASP cc_start: 0.8818 (t0) cc_final: 0.8461 (t0) REVERT: A 989 HIS cc_start: 0.7791 (m90) cc_final: 0.7431 (m90) REVERT: A 998 ASP cc_start: 0.8610 (m-30) cc_final: 0.7812 (m-30) REVERT: A 1012 MET cc_start: 0.8518 (ttt) cc_final: 0.8146 (ttt) REVERT: A 1033 PHE cc_start: 0.8371 (t80) cc_final: 0.8123 (t80) REVERT: A 1034 PHE cc_start: 0.8406 (m-80) cc_final: 0.7863 (m-80) REVERT: A 1050 LYS cc_start: 0.9294 (tttt) cc_final: 0.8739 (ptmm) REVERT: A 1053 ASN cc_start: 0.7296 (m110) cc_final: 0.6925 (m110) REVERT: A 1055 ILE cc_start: 0.8083 (mt) cc_final: 0.7662 (tp) REVERT: A 1068 LEU cc_start: 0.9215 (mt) cc_final: 0.8870 (mm) REVERT: A 1165 LEU cc_start: 0.7956 (mt) cc_final: 0.7660 (mt) REVERT: A 1167 ARG cc_start: 0.8320 (mtt180) cc_final: 0.8091 (mtt180) REVERT: A 1188 ILE cc_start: 0.7839 (pt) cc_final: 0.7403 (pt) REVERT: A 1192 GLU cc_start: 0.7324 (pm20) cc_final: 0.7097 (pt0) REVERT: A 1223 ASN cc_start: 0.6758 (t0) cc_final: 0.6551 (t0) REVERT: A 1225 LYS cc_start: 0.8046 (mmpt) cc_final: 0.7807 (mmmt) REVERT: A 1238 LYS cc_start: 0.8189 (mtmm) cc_final: 0.7804 (mttt) REVERT: A 1282 PHE cc_start: 0.8804 (t80) cc_final: 0.8315 (t80) REVERT: A 1288 LYS cc_start: 0.8002 (tptt) cc_final: 0.7793 (tppt) REVERT: A 1304 LYS cc_start: 0.7937 (ptpt) cc_final: 0.7608 (pptt) REVERT: A 1306 LEU cc_start: 0.8107 (mt) cc_final: 0.7817 (mt) REVERT: A 1314 LYS cc_start: 0.8278 (mmtt) cc_final: 0.7812 (mmtp) REVERT: A 1324 MET cc_start: 0.7779 (mmp) cc_final: 0.7343 (mmp) REVERT: A 1327 PHE cc_start: 0.8307 (m-80) cc_final: 0.8091 (m-80) REVERT: A 1435 GLU cc_start: 0.8133 (tt0) cc_final: 0.7784 (tt0) REVERT: A 1440 ILE cc_start: 0.7808 (mt) cc_final: 0.7515 (pt) REVERT: A1 29 TYR cc_start: 0.6290 (m-10) cc_final: 0.6068 (m-80) REVERT: A1 52 LYS cc_start: 0.8736 (tttt) cc_final: 0.8265 (tttt) REVERT: A1 120 ASP cc_start: 0.8026 (m-30) cc_final: 0.7818 (m-30) REVERT: A1 121 LEU cc_start: 0.8263 (mt) cc_final: 0.7960 (mt) REVERT: A1 123 PHE cc_start: 0.8199 (p90) cc_final: 0.7838 (p90) outliers start: 3 outliers final: 1 residues processed: 333 average time/residue: 0.1203 time to fit residues: 53.9832 Evaluate side-chains 298 residues out of total 1249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 297 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 46 optimal weight: 5.9990 chunk 89 optimal weight: 10.0000 chunk 21 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 chunk 93 optimal weight: 9.9990 chunk 92 optimal weight: 3.9990 chunk 51 optimal weight: 5.9990 chunk 9 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 131 optimal weight: 0.0070 chunk 24 optimal weight: 5.9990 overall best weight: 1.8006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1010 HIS A1190 ASN A1320 GLN A1 159 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.157491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.133874 restraints weight = 30215.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.138113 restraints weight = 19906.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.141080 restraints weight = 14277.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.143270 restraints weight = 10872.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.144874 restraints weight = 8662.500| |-----------------------------------------------------------------------------| r_work (final): 0.4078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6544 moved from start: 0.2370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 11500 Z= 0.136 Angle : 0.536 8.741 15436 Z= 0.296 Chirality : 0.041 0.160 1666 Planarity : 0.004 0.047 1973 Dihedral : 4.367 21.863 1464 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.15 % Allowed : 2.77 % Favored : 97.08 % Rotamer: Outliers : 0.24 % Allowed : 2.73 % Favored : 97.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.46 (0.24), residues: 1335 helix: 1.43 (0.18), residues: 887 sheet: -0.61 (0.96), residues: 27 loop : 0.24 (0.33), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 936 TYR 0.013 0.001 TYRA1 176 PHE 0.025 0.002 PHE A 156 TRP 0.047 0.002 TRP A1069 HIS 0.005 0.001 HIS A1010 Details of bonding type rmsd covalent geometry : bond 0.00272 (11500) covalent geometry : angle 0.53604 (15436) hydrogen bonds : bond 0.03788 ( 626) hydrogen bonds : angle 4.46426 ( 1833) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2670 Ramachandran restraints generated. 1335 Oldfield, 0 Emsley, 1335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2670 Ramachandran restraints generated. 1335 Oldfield, 0 Emsley, 1335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 1249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 327 time to evaluate : 0.429 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: A 162 GLN cc_start: 0.8372 (tm-30) cc_final: 0.8067 (tm-30) REVERT: A 177 ILE cc_start: 0.7660 (mt) cc_final: 0.7448 (mt) REVERT: A 306 PHE cc_start: 0.8679 (m-80) cc_final: 0.7939 (m-80) REVERT: A 309 LYS cc_start: 0.8827 (mtmm) cc_final: 0.8414 (mttt) REVERT: A 310 ARG cc_start: 0.8752 (mpt90) cc_final: 0.8250 (mmt90) REVERT: A 324 ASP cc_start: 0.6579 (t0) cc_final: 0.6310 (t0) REVERT: A 347 LYS cc_start: 0.8917 (mttt) cc_final: 0.8471 (mttt) REVERT: A 349 PHE cc_start: 0.8250 (t80) cc_final: 0.7901 (t80) REVERT: A 362 GLU cc_start: 0.8285 (tt0) cc_final: 0.7424 (tp30) REVERT: A 382 TYR cc_start: 0.6087 (t80) cc_final: 0.5654 (t80) REVERT: A 386 ARG cc_start: 0.8490 (ptp90) cc_final: 0.8041 (ttp-110) REVERT: A 395 HIS cc_start: 0.7827 (m-70) cc_final: 0.7292 (m170) REVERT: A 398 TYR cc_start: 0.8289 (t80) cc_final: 0.7964 (t80) REVERT: A 505 ILE cc_start: 0.9229 (mt) cc_final: 0.8961 (tp) REVERT: A 507 GLU cc_start: 0.8392 (mt-10) cc_final: 0.7831 (mt-10) REVERT: A 548 LEU cc_start: 0.8612 (mt) cc_final: 0.8176 (mt) REVERT: A 560 ASN cc_start: 0.8521 (t0) cc_final: 0.8193 (m110) REVERT: A 596 LYS cc_start: 0.8827 (mmpt) cc_final: 0.8569 (mmmt) REVERT: A 627 GLN cc_start: 0.8637 (tp40) cc_final: 0.8317 (tm-30) REVERT: A 652 LEU cc_start: 0.8489 (mt) cc_final: 0.8145 (mt) REVERT: A 662 GLU cc_start: 0.7645 (mt-10) cc_final: 0.6819 (mm-30) REVERT: A 750 LEU cc_start: 0.8471 (mt) cc_final: 0.8145 (mm) REVERT: A 777 MET cc_start: 0.7893 (mtm) cc_final: 0.7543 (mtm) REVERT: A 791 LEU cc_start: 0.8538 (mt) cc_final: 0.8336 (pp) REVERT: A 813 GLU cc_start: 0.7705 (mp0) cc_final: 0.7075 (mp0) REVERT: A 815 GLU cc_start: 0.8303 (tt0) cc_final: 0.7962 (tt0) REVERT: A 818 PHE cc_start: 0.8192 (m-80) cc_final: 0.7858 (m-80) REVERT: A 819 ARG cc_start: 0.7972 (mtp-110) cc_final: 0.7549 (mtp-110) REVERT: A 822 GLN cc_start: 0.8588 (mt0) cc_final: 0.8108 (mt0) REVERT: A 823 TRP cc_start: 0.7664 (t60) cc_final: 0.7336 (t60) REVERT: A 826 LYS cc_start: 0.8471 (mtmt) cc_final: 0.8056 (ptmt) REVERT: A 847 ASN cc_start: 0.7714 (p0) cc_final: 0.7475 (p0) REVERT: A 856 LYS cc_start: 0.7973 (pttm) cc_final: 0.7490 (tppt) REVERT: A 875 PHE cc_start: 0.7680 (t80) cc_final: 0.7455 (t80) REVERT: A 927 GLN cc_start: 0.8217 (tp-100) cc_final: 0.8011 (tp-100) REVERT: A 944 PHE cc_start: 0.7952 (t80) cc_final: 0.7079 (t80) REVERT: A 955 LEU cc_start: 0.8010 (mt) cc_final: 0.7423 (tp) REVERT: A 958 HIS cc_start: 0.7575 (m90) cc_final: 0.7135 (m90) REVERT: A 961 LYS cc_start: 0.9133 (tmtt) cc_final: 0.8563 (tptp) REVERT: A 964 GLN cc_start: 0.8994 (tp-100) cc_final: 0.8681 (tp40) REVERT: A 976 GLU cc_start: 0.8562 (pm20) cc_final: 0.8061 (pm20) REVERT: A 979 MET cc_start: 0.7903 (mtm) cc_final: 0.7297 (mtm) REVERT: A 985 ASP cc_start: 0.8731 (t0) cc_final: 0.8293 (m-30) REVERT: A 989 HIS cc_start: 0.7830 (m90) cc_final: 0.7260 (m90) REVERT: A 998 ASP cc_start: 0.8615 (m-30) cc_final: 0.7805 (m-30) REVERT: A 1012 MET cc_start: 0.8611 (ttt) cc_final: 0.8201 (ttt) REVERT: A 1033 PHE cc_start: 0.8249 (t80) cc_final: 0.8041 (t80) REVERT: A 1034 PHE cc_start: 0.8508 (m-80) cc_final: 0.7900 (m-80) REVERT: A 1050 LYS cc_start: 0.9284 (tttt) cc_final: 0.8775 (ptmm) REVERT: A 1053 ASN cc_start: 0.7443 (m110) cc_final: 0.7066 (m110) REVERT: A 1055 ILE cc_start: 0.8213 (mt) cc_final: 0.7748 (tp) REVERT: A 1064 ASP cc_start: 0.8366 (m-30) cc_final: 0.8047 (m-30) REVERT: A 1165 LEU cc_start: 0.7932 (mt) cc_final: 0.7617 (mt) REVERT: A 1167 ARG cc_start: 0.8294 (mtt180) cc_final: 0.7700 (mtt180) REVERT: A 1177 LEU cc_start: 0.8518 (mt) cc_final: 0.8270 (pp) REVERT: A 1188 ILE cc_start: 0.7912 (pt) cc_final: 0.7345 (pt) REVERT: A 1192 GLU cc_start: 0.7524 (pm20) cc_final: 0.7160 (pt0) REVERT: A 1201 ASN cc_start: 0.6241 (t0) cc_final: 0.5906 (p0) REVERT: A 1214 ASN cc_start: 0.8369 (m110) cc_final: 0.8125 (m110) REVERT: A 1242 GLN cc_start: 0.8553 (tp-100) cc_final: 0.8092 (tp-100) REVERT: A 1245 ILE cc_start: 0.7730 (OUTLIER) cc_final: 0.7525 (mp) REVERT: A 1285 PHE cc_start: 0.7924 (t80) cc_final: 0.7667 (t80) REVERT: A 1304 LYS cc_start: 0.7997 (ptpt) cc_final: 0.7652 (pptt) REVERT: A 1306 LEU cc_start: 0.8128 (mt) cc_final: 0.7889 (mt) REVERT: A 1314 LYS cc_start: 0.8386 (mmtt) cc_final: 0.7755 (mmtt) REVERT: A 1324 MET cc_start: 0.7639 (mmp) cc_final: 0.7248 (mmp) REVERT: A 1327 PHE cc_start: 0.8286 (m-80) cc_final: 0.8070 (m-80) REVERT: A 1435 GLU cc_start: 0.8121 (tt0) cc_final: 0.7763 (tt0) REVERT: A 1440 ILE cc_start: 0.7834 (mt) cc_final: 0.7520 (pt) REVERT: A1 52 LYS cc_start: 0.8737 (tttt) cc_final: 0.8277 (tttt) REVERT: A1 121 LEU cc_start: 0.8237 (mt) cc_final: 0.7956 (mt) REVERT: A1 123 PHE cc_start: 0.8245 (p90) cc_final: 0.7915 (p90) REVERT: A1 173 LYS cc_start: 0.8227 (mptt) cc_final: 0.7580 (mptt) outliers start: 3 outliers final: 1 residues processed: 329 average time/residue: 0.1109 time to fit residues: 49.1478 Evaluate side-chains 307 residues out of total 1249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 305 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 122 optimal weight: 4.9990 chunk 116 optimal weight: 0.9990 chunk 71 optimal weight: 0.7980 chunk 130 optimal weight: 5.9990 chunk 21 optimal weight: 0.9990 chunk 22 optimal weight: 0.8980 chunk 41 optimal weight: 0.6980 chunk 30 optimal weight: 5.9990 chunk 27 optimal weight: 0.6980 chunk 11 optimal weight: 5.9990 chunk 103 optimal weight: 7.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1190 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.159509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.135644 restraints weight = 30440.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.139906 restraints weight = 20058.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.142894 restraints weight = 14401.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.145112 restraints weight = 10978.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.146809 restraints weight = 8750.297| |-----------------------------------------------------------------------------| r_work (final): 0.4107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6503 moved from start: 0.2718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 11500 Z= 0.106 Angle : 0.526 7.479 15436 Z= 0.285 Chirality : 0.041 0.189 1666 Planarity : 0.004 0.046 1973 Dihedral : 4.352 23.762 1464 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.15 % Allowed : 2.10 % Favored : 97.75 % Rotamer: Outliers : 0.08 % Allowed : 2.09 % Favored : 97.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.52 (0.24), residues: 1335 helix: 1.46 (0.18), residues: 887 sheet: -0.84 (0.89), residues: 27 loop : 0.34 (0.33), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 168 TYR 0.014 0.001 TYR A 547 PHE 0.039 0.001 PHE A 790 TRP 0.021 0.002 TRP A 314 HIS 0.002 0.001 HIS A 119 Details of bonding type rmsd covalent geometry : bond 0.00224 (11500) covalent geometry : angle 0.52597 (15436) hydrogen bonds : bond 0.03434 ( 626) hydrogen bonds : angle 4.27452 ( 1833) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2670 Ramachandran restraints generated. 1335 Oldfield, 0 Emsley, 1335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2670 Ramachandran restraints generated. 1335 Oldfield, 0 Emsley, 1335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 1249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 327 time to evaluate : 0.417 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 PHE cc_start: 0.8033 (m-80) cc_final: 0.7765 (t80) REVERT: A 162 GLN cc_start: 0.8369 (tm-30) cc_final: 0.8043 (tm-30) REVERT: A 168 ARG cc_start: 0.8898 (ttm110) cc_final: 0.8456 (ttm110) REVERT: A 177 ILE cc_start: 0.7622 (mt) cc_final: 0.7406 (mt) REVERT: A 197 TYR cc_start: 0.7195 (t80) cc_final: 0.6971 (t80) REVERT: A 306 PHE cc_start: 0.8702 (m-80) cc_final: 0.8001 (m-80) REVERT: A 309 LYS cc_start: 0.8772 (mtmm) cc_final: 0.8521 (mttt) REVERT: A 310 ARG cc_start: 0.8696 (mpt90) cc_final: 0.8181 (mmt90) REVERT: A 324 ASP cc_start: 0.6595 (t0) cc_final: 0.6330 (t0) REVERT: A 347 LYS cc_start: 0.8893 (mttt) cc_final: 0.8534 (mttt) REVERT: A 348 GLN cc_start: 0.8639 (mp10) cc_final: 0.8425 (mp10) REVERT: A 349 PHE cc_start: 0.8230 (t80) cc_final: 0.7867 (t80) REVERT: A 382 TYR cc_start: 0.6103 (t80) cc_final: 0.5561 (t80) REVERT: A 386 ARG cc_start: 0.8610 (ptp90) cc_final: 0.8137 (ttp-110) REVERT: A 395 HIS cc_start: 0.7912 (m-70) cc_final: 0.7387 (m170) REVERT: A 398 TYR cc_start: 0.8296 (t80) cc_final: 0.8044 (t80) REVERT: A 492 ILE cc_start: 0.6698 (mm) cc_final: 0.6472 (mt) REVERT: A 503 ASN cc_start: 0.8465 (m-40) cc_final: 0.8263 (m-40) REVERT: A 505 ILE cc_start: 0.9257 (mt) cc_final: 0.8938 (tp) REVERT: A 507 GLU cc_start: 0.8359 (mt-10) cc_final: 0.7812 (mt-10) REVERT: A 525 PHE cc_start: 0.7345 (t80) cc_final: 0.7108 (t80) REVERT: A 548 LEU cc_start: 0.8670 (mt) cc_final: 0.8251 (mt) REVERT: A 560 ASN cc_start: 0.8470 (t0) cc_final: 0.8156 (m110) REVERT: A 627 GLN cc_start: 0.8686 (tp40) cc_final: 0.8262 (tm-30) REVERT: A 652 LEU cc_start: 0.8485 (mt) cc_final: 0.8168 (mt) REVERT: A 662 GLU cc_start: 0.7630 (mt-10) cc_final: 0.6822 (mm-30) REVERT: A 746 GLN cc_start: 0.7938 (mp-120) cc_final: 0.7637 (mp10) REVERT: A 750 LEU cc_start: 0.8405 (mt) cc_final: 0.8130 (mm) REVERT: A 758 ASN cc_start: 0.8320 (m-40) cc_final: 0.8060 (m-40) REVERT: A 777 MET cc_start: 0.7835 (mtm) cc_final: 0.7529 (mtm) REVERT: A 784 MET cc_start: 0.7325 (mpp) cc_final: 0.6992 (mtm) REVERT: A 813 GLU cc_start: 0.7627 (mp0) cc_final: 0.6988 (mp0) REVERT: A 815 GLU cc_start: 0.8196 (tt0) cc_final: 0.7745 (pt0) REVERT: A 818 PHE cc_start: 0.8211 (m-80) cc_final: 0.7889 (m-80) REVERT: A 819 ARG cc_start: 0.7981 (mtp-110) cc_final: 0.7555 (mtp-110) REVERT: A 822 GLN cc_start: 0.8541 (mt0) cc_final: 0.8040 (mt0) REVERT: A 826 LYS cc_start: 0.8497 (mtmt) cc_final: 0.8117 (ptmt) REVERT: A 847 ASN cc_start: 0.7705 (p0) cc_final: 0.7419 (p0) REVERT: A 852 GLU cc_start: 0.7974 (pt0) cc_final: 0.7657 (pt0) REVERT: A 856 LYS cc_start: 0.7931 (pttm) cc_final: 0.7463 (tppt) REVERT: A 914 ASP cc_start: 0.7287 (p0) cc_final: 0.7015 (p0) REVERT: A 927 GLN cc_start: 0.8175 (tp-100) cc_final: 0.7889 (tp-100) REVERT: A 944 PHE cc_start: 0.7970 (t80) cc_final: 0.7495 (t80) REVERT: A 955 LEU cc_start: 0.8082 (mt) cc_final: 0.7492 (tp) REVERT: A 958 HIS cc_start: 0.7544 (m90) cc_final: 0.7203 (m90) REVERT: A 961 LYS cc_start: 0.9102 (tmtt) cc_final: 0.8489 (tptp) REVERT: A 964 GLN cc_start: 0.9002 (tp-100) cc_final: 0.8608 (tp40) REVERT: A 976 GLU cc_start: 0.8605 (pm20) cc_final: 0.8059 (pm20) REVERT: A 979 MET cc_start: 0.7837 (mtm) cc_final: 0.7260 (mtm) REVERT: A 982 LEU cc_start: 0.7802 (tp) cc_final: 0.7586 (tp) REVERT: A 985 ASP cc_start: 0.8761 (t0) cc_final: 0.8313 (m-30) REVERT: A 989 HIS cc_start: 0.7790 (m90) cc_final: 0.7229 (m90) REVERT: A 998 ASP cc_start: 0.8611 (m-30) cc_final: 0.7928 (m-30) REVERT: A 1010 HIS cc_start: 0.8215 (t-90) cc_final: 0.7997 (t-170) REVERT: A 1015 GLU cc_start: 0.7755 (tm-30) cc_final: 0.7511 (tm-30) REVERT: A 1034 PHE cc_start: 0.8420 (m-80) cc_final: 0.7709 (m-80) REVERT: A 1050 LYS cc_start: 0.9288 (tttt) cc_final: 0.8691 (ptmm) REVERT: A 1053 ASN cc_start: 0.7439 (m110) cc_final: 0.6943 (m110) REVERT: A 1055 ILE cc_start: 0.8133 (mt) cc_final: 0.7723 (tp) REVERT: A 1064 ASP cc_start: 0.8260 (m-30) cc_final: 0.7959 (m-30) REVERT: A 1165 LEU cc_start: 0.7899 (mt) cc_final: 0.7581 (mt) REVERT: A 1177 LEU cc_start: 0.8550 (mt) cc_final: 0.8294 (pp) REVERT: A 1188 ILE cc_start: 0.7779 (pt) cc_final: 0.7189 (pt) REVERT: A 1192 GLU cc_start: 0.7512 (pm20) cc_final: 0.7216 (pt0) REVERT: A 1201 ASN cc_start: 0.5967 (t0) cc_final: 0.5667 (p0) REVERT: A 1214 ASN cc_start: 0.8337 (m110) cc_final: 0.8086 (m110) REVERT: A 1223 ASN cc_start: 0.8153 (p0) cc_final: 0.7705 (p0) REVERT: A 1225 LYS cc_start: 0.8214 (mmpt) cc_final: 0.7943 (mmmt) REVERT: A 1226 GLN cc_start: 0.7590 (pm20) cc_final: 0.6912 (pp30) REVERT: A 1242 GLN cc_start: 0.8521 (tp-100) cc_final: 0.8172 (tp-100) REVERT: A 1260 LEU cc_start: 0.7913 (tp) cc_final: 0.7626 (tp) REVERT: A 1285 PHE cc_start: 0.7918 (t80) cc_final: 0.7649 (t80) REVERT: A 1304 LYS cc_start: 0.7973 (ptpt) cc_final: 0.7603 (pptt) REVERT: A 1306 LEU cc_start: 0.8058 (mt) cc_final: 0.7811 (mt) REVERT: A 1314 LYS cc_start: 0.8381 (mmtt) cc_final: 0.8026 (mmtt) REVERT: A 1324 MET cc_start: 0.7470 (mmp) cc_final: 0.7112 (mmp) REVERT: A 1327 PHE cc_start: 0.8300 (m-80) cc_final: 0.8007 (m-80) REVERT: A 1435 GLU cc_start: 0.8105 (tt0) cc_final: 0.7718 (tt0) REVERT: A 1440 ILE cc_start: 0.7848 (mt) cc_final: 0.7571 (pt) REVERT: A 1472 ILE cc_start: 0.8371 (mt) cc_final: 0.7941 (mp) REVERT: A 1473 ILE cc_start: 0.8495 (pt) cc_final: 0.7919 (pt) REVERT: A 1476 MET cc_start: 0.7833 (mtp) cc_final: 0.7401 (mtp) REVERT: A1 22 LYS cc_start: 0.7652 (ptmm) cc_final: 0.7431 (ptmm) REVERT: A1 52 LYS cc_start: 0.8731 (tttt) cc_final: 0.8269 (tttt) REVERT: A1 121 LEU cc_start: 0.8294 (mt) cc_final: 0.8033 (mt) REVERT: A1 123 PHE cc_start: 0.8015 (p90) cc_final: 0.7740 (p90) outliers start: 1 outliers final: 1 residues processed: 328 average time/residue: 0.1054 time to fit residues: 47.1023 Evaluate side-chains 296 residues out of total 1249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 295 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 50 optimal weight: 0.8980 chunk 3 optimal weight: 4.9990 chunk 126 optimal weight: 4.9990 chunk 66 optimal weight: 0.8980 chunk 114 optimal weight: 0.8980 chunk 60 optimal weight: 7.9990 chunk 43 optimal weight: 7.9990 chunk 110 optimal weight: 3.9990 chunk 12 optimal weight: 0.9990 chunk 21 optimal weight: 5.9990 chunk 53 optimal weight: 3.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1190 ASN A1223 ASN A1499 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.157845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.134611 restraints weight = 29484.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.138799 restraints weight = 19347.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.141732 restraints weight = 13804.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.143913 restraints weight = 10479.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.145539 restraints weight = 8318.185| |-----------------------------------------------------------------------------| r_work (final): 0.4089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6537 moved from start: 0.2995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 11500 Z= 0.120 Angle : 0.516 7.161 15436 Z= 0.284 Chirality : 0.041 0.169 1666 Planarity : 0.004 0.044 1973 Dihedral : 4.313 22.066 1464 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.15 % Allowed : 2.70 % Favored : 97.15 % Rotamer: Outliers : 0.08 % Allowed : 2.09 % Favored : 97.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.50 (0.24), residues: 1335 helix: 1.46 (0.18), residues: 887 sheet: -0.69 (0.92), residues: 27 loop : 0.27 (0.33), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 449 TYR 0.011 0.001 TYR A 197 PHE 0.034 0.001 PHE A 790 TRP 0.046 0.003 TRP A1069 HIS 0.003 0.001 HIS A 193 Details of bonding type rmsd covalent geometry : bond 0.00254 (11500) covalent geometry : angle 0.51572 (15436) hydrogen bonds : bond 0.03435 ( 626) hydrogen bonds : angle 4.28087 ( 1833) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2670 Ramachandran restraints generated. 1335 Oldfield, 0 Emsley, 1335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2670 Ramachandran restraints generated. 1335 Oldfield, 0 Emsley, 1335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 1249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 326 time to evaluate : 0.410 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 19 PHE cc_start: 0.8007 (m-80) cc_final: 0.7801 (t80) REVERT: A 162 GLN cc_start: 0.8369 (tm-30) cc_final: 0.7935 (tm-30) REVERT: A 177 ILE cc_start: 0.7750 (mt) cc_final: 0.7531 (mt) REVERT: A 306 PHE cc_start: 0.8753 (m-80) cc_final: 0.8033 (m-80) REVERT: A 309 LYS cc_start: 0.8826 (mtmm) cc_final: 0.8541 (mttt) REVERT: A 310 ARG cc_start: 0.8638 (mpt90) cc_final: 0.8207 (mmt90) REVERT: A 324 ASP cc_start: 0.6798 (t0) cc_final: 0.6503 (t0) REVERT: A 347 LYS cc_start: 0.8891 (mttt) cc_final: 0.8532 (mttt) REVERT: A 348 GLN cc_start: 0.8570 (mp10) cc_final: 0.8308 (mp10) REVERT: A 349 PHE cc_start: 0.8164 (t80) cc_final: 0.7814 (t80) REVERT: A 362 GLU cc_start: 0.8245 (tt0) cc_final: 0.7392 (tp30) REVERT: A 382 TYR cc_start: 0.6230 (t80) cc_final: 0.5636 (t80) REVERT: A 386 ARG cc_start: 0.8532 (ptp90) cc_final: 0.8096 (ttp-110) REVERT: A 395 HIS cc_start: 0.8158 (m-70) cc_final: 0.7615 (m170) REVERT: A 398 TYR cc_start: 0.8378 (t80) cc_final: 0.8114 (t80) REVERT: A 503 ASN cc_start: 0.8501 (m-40) cc_final: 0.8288 (m110) REVERT: A 505 ILE cc_start: 0.9248 (mt) cc_final: 0.8945 (tp) REVERT: A 507 GLU cc_start: 0.8382 (mt-10) cc_final: 0.7842 (mt-10) REVERT: A 548 LEU cc_start: 0.8683 (mt) cc_final: 0.8286 (mt) REVERT: A 560 ASN cc_start: 0.8476 (t0) cc_final: 0.8150 (m110) REVERT: A 627 GLN cc_start: 0.8742 (tp40) cc_final: 0.8443 (tp-100) REVERT: A 652 LEU cc_start: 0.8484 (mt) cc_final: 0.8135 (mt) REVERT: A 662 GLU cc_start: 0.7589 (mt-10) cc_final: 0.6810 (mm-30) REVERT: A 672 TYR cc_start: 0.7483 (p90) cc_final: 0.7123 (p90) REVERT: A 758 ASN cc_start: 0.8422 (m-40) cc_final: 0.8151 (m-40) REVERT: A 777 MET cc_start: 0.7912 (mtm) cc_final: 0.7588 (mtm) REVERT: A 784 MET cc_start: 0.7393 (mpp) cc_final: 0.7148 (mtm) REVERT: A 815 GLU cc_start: 0.8223 (tt0) cc_final: 0.7755 (pt0) REVERT: A 816 MET cc_start: 0.8693 (mtm) cc_final: 0.8391 (mtm) REVERT: A 818 PHE cc_start: 0.8202 (m-80) cc_final: 0.7950 (m-80) REVERT: A 819 ARG cc_start: 0.8005 (mtp-110) cc_final: 0.7597 (mtp-110) REVERT: A 822 GLN cc_start: 0.8547 (mt0) cc_final: 0.8067 (mt0) REVERT: A 825 LYS cc_start: 0.8586 (mmmt) cc_final: 0.8322 (mmmt) REVERT: A 826 LYS cc_start: 0.8558 (mtmt) cc_final: 0.8082 (ttmt) REVERT: A 847 ASN cc_start: 0.7712 (p0) cc_final: 0.7372 (p0) REVERT: A 852 GLU cc_start: 0.8010 (pt0) cc_final: 0.7686 (pt0) REVERT: A 856 LYS cc_start: 0.8026 (pttm) cc_final: 0.7508 (tppt) REVERT: A 858 CYS cc_start: 0.7512 (m) cc_final: 0.7153 (m) REVERT: A 914 ASP cc_start: 0.7316 (p0) cc_final: 0.7087 (p0) REVERT: A 927 GLN cc_start: 0.8198 (tp-100) cc_final: 0.7683 (tm-30) REVERT: A 944 PHE cc_start: 0.8047 (t80) cc_final: 0.7574 (t80) REVERT: A 955 LEU cc_start: 0.7990 (mt) cc_final: 0.7584 (tp) REVERT: A 958 HIS cc_start: 0.7574 (m90) cc_final: 0.7196 (m90) REVERT: A 961 LYS cc_start: 0.9087 (tmtt) cc_final: 0.8516 (tptp) REVERT: A 964 GLN cc_start: 0.9002 (tp-100) cc_final: 0.8622 (tp40) REVERT: A 976 GLU cc_start: 0.8596 (pm20) cc_final: 0.8085 (pm20) REVERT: A 979 MET cc_start: 0.7857 (mtm) cc_final: 0.7278 (mtm) REVERT: A 982 LEU cc_start: 0.7825 (tp) cc_final: 0.7607 (tp) REVERT: A 985 ASP cc_start: 0.8759 (t0) cc_final: 0.8302 (m-30) REVERT: A 989 HIS cc_start: 0.7761 (m90) cc_final: 0.7226 (m90) REVERT: A 998 ASP cc_start: 0.8570 (m-30) cc_final: 0.7872 (m-30) REVERT: A 1010 HIS cc_start: 0.8233 (t-90) cc_final: 0.8031 (t-170) REVERT: A 1015 GLU cc_start: 0.7804 (tm-30) cc_final: 0.7583 (tm-30) REVERT: A 1034 PHE cc_start: 0.8455 (m-80) cc_final: 0.7730 (m-80) REVERT: A 1050 LYS cc_start: 0.9266 (tttt) cc_final: 0.8482 (tppt) REVERT: A 1053 ASN cc_start: 0.7527 (m110) cc_final: 0.7189 (m110) REVERT: A 1055 ILE cc_start: 0.8260 (mt) cc_final: 0.7807 (tp) REVERT: A 1165 LEU cc_start: 0.7886 (mt) cc_final: 0.7637 (mt) REVERT: A 1177 LEU cc_start: 0.8647 (mt) cc_final: 0.8400 (pp) REVERT: A 1201 ASN cc_start: 0.5980 (t0) cc_final: 0.5696 (p0) REVERT: A 1208 GLU cc_start: 0.8065 (mp0) cc_final: 0.7367 (mp0) REVERT: A 1214 ASN cc_start: 0.8355 (m110) cc_final: 0.8087 (m110) REVERT: A 1223 ASN cc_start: 0.8252 (OUTLIER) cc_final: 0.7941 (p0) REVERT: A 1267 ARG cc_start: 0.8416 (mmt180) cc_final: 0.8209 (mmt180) REVERT: A 1285 PHE cc_start: 0.8000 (t80) cc_final: 0.7779 (t80) REVERT: A 1304 LYS cc_start: 0.8032 (ptpt) cc_final: 0.7753 (pptt) REVERT: A 1306 LEU cc_start: 0.8075 (mt) cc_final: 0.7830 (mt) REVERT: A 1309 TYR cc_start: 0.8014 (t80) cc_final: 0.7751 (t80) REVERT: A 1314 LYS cc_start: 0.8425 (mmtt) cc_final: 0.7733 (mmmt) REVERT: A 1324 MET cc_start: 0.7501 (mmp) cc_final: 0.7132 (mmp) REVERT: A 1327 PHE cc_start: 0.8289 (m-80) cc_final: 0.8026 (m-80) REVERT: A 1434 LYS cc_start: 0.2484 (mttt) cc_final: 0.1927 (mmmm) REVERT: A 1435 GLU cc_start: 0.8159 (tt0) cc_final: 0.7849 (tt0) REVERT: A 1436 PHE cc_start: 0.8262 (t80) cc_final: 0.8058 (t80) REVERT: A 1440 ILE cc_start: 0.8079 (mt) cc_final: 0.7818 (pt) REVERT: A 1472 ILE cc_start: 0.8385 (mt) cc_final: 0.7966 (mp) REVERT: A 1473 ILE cc_start: 0.8741 (pt) cc_final: 0.8278 (pt) REVERT: A 1476 MET cc_start: 0.7727 (mtp) cc_final: 0.7354 (mtp) REVERT: A1 22 LYS cc_start: 0.7717 (ptmm) cc_final: 0.7449 (ptmm) REVERT: A1 52 LYS cc_start: 0.8741 (tttt) cc_final: 0.8287 (tttt) REVERT: A1 121 LEU cc_start: 0.8385 (mt) cc_final: 0.8089 (mt) REVERT: A1 123 PHE cc_start: 0.8183 (p90) cc_final: 0.7960 (p90) REVERT: A1 127 LEU cc_start: 0.7733 (mt) cc_final: 0.7420 (mt) outliers start: 1 outliers final: 0 residues processed: 326 average time/residue: 0.1164 time to fit residues: 51.6741 Evaluate side-chains 304 residues out of total 1249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 303 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 75 optimal weight: 0.0060 chunk 68 optimal weight: 0.9980 chunk 55 optimal weight: 6.9990 chunk 60 optimal weight: 6.9990 chunk 45 optimal weight: 10.0000 chunk 98 optimal weight: 2.9990 chunk 85 optimal weight: 6.9990 chunk 10 optimal weight: 7.9990 chunk 34 optimal weight: 5.9990 chunk 79 optimal weight: 3.9990 chunk 6 optimal weight: 8.9990 overall best weight: 2.8002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1223 ASN A1253 ASN A1461 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.155253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.131450 restraints weight = 30273.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.135718 restraints weight = 19875.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.138781 restraints weight = 14193.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.140970 restraints weight = 10770.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.142610 restraints weight = 8571.285| |-----------------------------------------------------------------------------| r_work (final): 0.4053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6610 moved from start: 0.3330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 11500 Z= 0.169 Angle : 0.551 8.416 15436 Z= 0.304 Chirality : 0.042 0.146 1666 Planarity : 0.004 0.055 1973 Dihedral : 4.442 21.297 1464 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.07 % Favored : 96.78 % Rotamer: Outliers : 0.16 % Allowed : 2.01 % Favored : 97.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.28 (0.23), residues: 1335 helix: 1.33 (0.18), residues: 888 sheet: -0.76 (0.96), residues: 27 loop : 0.09 (0.32), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 168 TYR 0.014 0.001 TYR A 197 PHE 0.030 0.002 PHE A 790 TRP 0.037 0.002 TRP A1069 HIS 0.006 0.001 HIS A 193 Details of bonding type rmsd covalent geometry : bond 0.00341 (11500) covalent geometry : angle 0.55074 (15436) hydrogen bonds : bond 0.03684 ( 626) hydrogen bonds : angle 4.42331 ( 1833) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2670 Ramachandran restraints generated. 1335 Oldfield, 0 Emsley, 1335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2670 Ramachandran restraints generated. 1335 Oldfield, 0 Emsley, 1335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 1249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 336 time to evaluate : 0.417 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 119 HIS cc_start: 0.7604 (t70) cc_final: 0.7400 (t-90) REVERT: A 162 GLN cc_start: 0.8377 (tm-30) cc_final: 0.7930 (tm-30) REVERT: A 177 ILE cc_start: 0.7778 (mt) cc_final: 0.7568 (mt) REVERT: A 201 ASN cc_start: 0.7319 (m-40) cc_final: 0.6504 (m110) REVERT: A 306 PHE cc_start: 0.8849 (m-80) cc_final: 0.8340 (m-80) REVERT: A 309 LYS cc_start: 0.8820 (mtmm) cc_final: 0.8519 (mttt) REVERT: A 310 ARG cc_start: 0.8847 (mpt90) cc_final: 0.8248 (mmt90) REVERT: A 324 ASP cc_start: 0.6826 (t0) cc_final: 0.6529 (t0) REVERT: A 347 LYS cc_start: 0.8897 (mttt) cc_final: 0.8512 (mttt) REVERT: A 348 GLN cc_start: 0.8586 (mp10) cc_final: 0.8280 (mp10) REVERT: A 349 PHE cc_start: 0.8287 (t80) cc_final: 0.7892 (t80) REVERT: A 362 GLU cc_start: 0.8244 (tt0) cc_final: 0.7412 (tp30) REVERT: A 386 ARG cc_start: 0.8525 (ptp90) cc_final: 0.8094 (ttp-110) REVERT: A 395 HIS cc_start: 0.8265 (m-70) cc_final: 0.7909 (m170) REVERT: A 398 TYR cc_start: 0.8427 (t80) cc_final: 0.8103 (t80) REVERT: A 503 ASN cc_start: 0.8533 (m-40) cc_final: 0.8310 (m-40) REVERT: A 505 ILE cc_start: 0.9277 (mt) cc_final: 0.8975 (tp) REVERT: A 507 GLU cc_start: 0.8441 (mt-10) cc_final: 0.7905 (mt-10) REVERT: A 548 LEU cc_start: 0.8685 (mt) cc_final: 0.8305 (mt) REVERT: A 560 ASN cc_start: 0.8545 (t0) cc_final: 0.8203 (m-40) REVERT: A 627 GLN cc_start: 0.8701 (tp40) cc_final: 0.8350 (tm-30) REVERT: A 662 GLU cc_start: 0.7626 (mt-10) cc_final: 0.6797 (mm-30) REVERT: A 672 TYR cc_start: 0.7374 (p90) cc_final: 0.6883 (p90) REVERT: A 739 PHE cc_start: 0.7912 (m-10) cc_final: 0.7601 (m-10) REVERT: A 746 GLN cc_start: 0.7955 (mp-120) cc_final: 0.7687 (mp10) REVERT: A 750 LEU cc_start: 0.8466 (mt) cc_final: 0.8114 (mm) REVERT: A 777 MET cc_start: 0.8050 (mtm) cc_final: 0.7609 (mtm) REVERT: A 784 MET cc_start: 0.7464 (mpp) cc_final: 0.7105 (mtm) REVERT: A 813 GLU cc_start: 0.7712 (mp0) cc_final: 0.7439 (mp0) REVERT: A 815 GLU cc_start: 0.8298 (tt0) cc_final: 0.7952 (tt0) REVERT: A 816 MET cc_start: 0.8744 (mtm) cc_final: 0.8495 (mtm) REVERT: A 818 PHE cc_start: 0.8332 (m-80) cc_final: 0.8060 (m-80) REVERT: A 819 ARG cc_start: 0.8106 (mtp-110) cc_final: 0.7664 (mtp-110) REVERT: A 822 GLN cc_start: 0.8605 (mt0) cc_final: 0.8138 (mt0) REVERT: A 826 LYS cc_start: 0.8628 (mtmt) cc_final: 0.8161 (ttmt) REVERT: A 833 ASP cc_start: 0.8065 (m-30) cc_final: 0.6387 (m-30) REVERT: A 836 ARG cc_start: 0.8063 (mtt180) cc_final: 0.7815 (mtt180) REVERT: A 847 ASN cc_start: 0.7719 (p0) cc_final: 0.7448 (p0) REVERT: A 852 GLU cc_start: 0.8091 (pt0) cc_final: 0.7783 (pt0) REVERT: A 856 LYS cc_start: 0.8129 (pttm) cc_final: 0.7569 (tppt) REVERT: A 858 CYS cc_start: 0.7578 (m) cc_final: 0.7118 (m) REVERT: A 883 ARG cc_start: 0.6941 (mtm110) cc_final: 0.5969 (ptm-80) REVERT: A 914 ASP cc_start: 0.7390 (p0) cc_final: 0.7184 (p0) REVERT: A 927 GLN cc_start: 0.8312 (tp-100) cc_final: 0.8028 (tp40) REVERT: A 944 PHE cc_start: 0.8102 (t80) cc_final: 0.7636 (t80) REVERT: A 958 HIS cc_start: 0.7712 (m90) cc_final: 0.7320 (m90) REVERT: A 961 LYS cc_start: 0.9090 (tmtt) cc_final: 0.8532 (tptp) REVERT: A 964 GLN cc_start: 0.9032 (tp-100) cc_final: 0.8681 (tp40) REVERT: A 976 GLU cc_start: 0.8640 (pm20) cc_final: 0.8166 (pm20) REVERT: A 979 MET cc_start: 0.7968 (mtm) cc_final: 0.7427 (mtm) REVERT: A 982 LEU cc_start: 0.7893 (tp) cc_final: 0.7588 (tp) REVERT: A 985 ASP cc_start: 0.8855 (t0) cc_final: 0.8518 (t0) REVERT: A 989 HIS cc_start: 0.7846 (m90) cc_final: 0.7108 (m90) REVERT: A 998 ASP cc_start: 0.8652 (m-30) cc_final: 0.7992 (m-30) REVERT: A 1009 GLU cc_start: 0.8599 (mt-10) cc_final: 0.8038 (mt-10) REVERT: A 1010 HIS cc_start: 0.8293 (t-90) cc_final: 0.8091 (t-170) REVERT: A 1011 GLN cc_start: 0.8459 (tm-30) cc_final: 0.8259 (tm-30) REVERT: A 1028 GLU cc_start: 0.8285 (tm-30) cc_final: 0.7907 (tm-30) REVERT: A 1034 PHE cc_start: 0.8575 (m-80) cc_final: 0.7822 (m-80) REVERT: A 1049 ASN cc_start: 0.8454 (m-40) cc_final: 0.8042 (m110) REVERT: A 1050 LYS cc_start: 0.9289 (tttt) cc_final: 0.8446 (tppt) REVERT: A 1053 ASN cc_start: 0.7577 (m110) cc_final: 0.7180 (m110) REVERT: A 1054 SER cc_start: 0.7884 (t) cc_final: 0.7446 (p) REVERT: A 1055 ILE cc_start: 0.8399 (mt) cc_final: 0.7787 (tp) REVERT: A 1165 LEU cc_start: 0.7988 (mt) cc_final: 0.7728 (mt) REVERT: A 1177 LEU cc_start: 0.8662 (mt) cc_final: 0.8399 (pp) REVERT: A 1201 ASN cc_start: 0.6056 (t0) cc_final: 0.5785 (p0) REVERT: A 1208 GLU cc_start: 0.8234 (mp0) cc_final: 0.7290 (mp0) REVERT: A 1223 ASN cc_start: 0.8192 (OUTLIER) cc_final: 0.7868 (p0) REVERT: A 1225 LYS cc_start: 0.8358 (mmpt) cc_final: 0.8067 (mmmt) REVERT: A 1226 GLN cc_start: 0.7699 (pm20) cc_final: 0.6962 (pp30) REVERT: A 1267 ARG cc_start: 0.8463 (mmt180) cc_final: 0.8222 (mmt180) REVERT: A 1292 LEU cc_start: 0.8293 (mt) cc_final: 0.7955 (mt) REVERT: A 1304 LYS cc_start: 0.8074 (ptpt) cc_final: 0.7800 (pptt) REVERT: A 1306 LEU cc_start: 0.8216 (mt) cc_final: 0.7822 (mt) REVERT: A 1314 LYS cc_start: 0.8420 (mmtt) cc_final: 0.7937 (mmtt) REVERT: A 1324 MET cc_start: 0.7656 (mmp) cc_final: 0.7053 (mmp) REVERT: A 1327 PHE cc_start: 0.8345 (m-80) cc_final: 0.8086 (m-80) REVERT: A 1329 LYS cc_start: 0.8295 (mmtt) cc_final: 0.7609 (mppt) REVERT: A 1434 LYS cc_start: 0.2515 (mttt) cc_final: 0.1933 (mmmm) REVERT: A 1435 GLU cc_start: 0.8199 (tt0) cc_final: 0.7882 (tt0) REVERT: A 1436 PHE cc_start: 0.8369 (t80) cc_final: 0.8105 (t80) REVERT: A 1472 ILE cc_start: 0.8437 (mt) cc_final: 0.8024 (mp) REVERT: A 1473 ILE cc_start: 0.8815 (pt) cc_final: 0.8452 (pt) REVERT: A 1476 MET cc_start: 0.7924 (mtp) cc_final: 0.7538 (mtp) REVERT: A1 22 LYS cc_start: 0.7929 (ptmm) cc_final: 0.7621 (ptmm) REVERT: A1 52 LYS cc_start: 0.8757 (tttt) cc_final: 0.8305 (tttt) REVERT: A1 121 LEU cc_start: 0.8432 (mt) cc_final: 0.8117 (mt) REVERT: A1 127 LEU cc_start: 0.7751 (mt) cc_final: 0.7435 (mt) REVERT: A1 147 PHE cc_start: 0.5980 (m-80) cc_final: 0.5705 (m-10) outliers start: 2 outliers final: 0 residues processed: 336 average time/residue: 0.1233 time to fit residues: 55.9846 Evaluate side-chains 315 residues out of total 1249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 314 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 5 optimal weight: 9.9990 chunk 70 optimal weight: 4.9990 chunk 95 optimal weight: 6.9990 chunk 131 optimal weight: 0.8980 chunk 114 optimal weight: 10.0000 chunk 115 optimal weight: 5.9990 chunk 72 optimal weight: 5.9990 chunk 44 optimal weight: 2.9990 chunk 85 optimal weight: 6.9990 chunk 11 optimal weight: 8.9990 chunk 127 optimal weight: 0.0370 overall best weight: 2.9864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 GLN A 670 ASN A 814 ASN ** A1022 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1223 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.153262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.129870 restraints weight = 29983.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.134160 restraints weight = 19532.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.137115 restraints weight = 13897.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.139287 restraints weight = 10556.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.140891 restraints weight = 8395.088| |-----------------------------------------------------------------------------| r_work (final): 0.4028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6659 moved from start: 0.3873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 11500 Z= 0.177 Angle : 0.586 7.871 15436 Z= 0.322 Chirality : 0.043 0.155 1666 Planarity : 0.004 0.056 1973 Dihedral : 4.584 18.694 1464 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.37 % Favored : 96.48 % Rotamer: Outliers : 0.16 % Allowed : 1.20 % Favored : 98.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.97 (0.23), residues: 1335 helix: 1.10 (0.17), residues: 888 sheet: -0.63 (1.01), residues: 27 loop : -0.07 (0.32), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 168 TYR 0.017 0.002 TYR A 674 PHE 0.031 0.002 PHE A 790 TRP 0.036 0.003 TRP A1069 HIS 0.005 0.001 HIS A 193 Details of bonding type rmsd covalent geometry : bond 0.00352 (11500) covalent geometry : angle 0.58609 (15436) hydrogen bonds : bond 0.03937 ( 626) hydrogen bonds : angle 4.56832 ( 1833) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2670 Ramachandran restraints generated. 1335 Oldfield, 0 Emsley, 1335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2670 Ramachandran restraints generated. 1335 Oldfield, 0 Emsley, 1335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 1249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 335 time to evaluate : 0.404 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: A 55 ARG cc_start: 0.8434 (ttt180) cc_final: 0.8022 (ttt180) REVERT: A 119 HIS cc_start: 0.7722 (t70) cc_final: 0.7452 (t-90) REVERT: A 162 GLN cc_start: 0.8265 (tm-30) cc_final: 0.7806 (tm-30) REVERT: A 177 ILE cc_start: 0.7831 (mt) cc_final: 0.7616 (mt) REVERT: A 201 ASN cc_start: 0.7320 (m-40) cc_final: 0.6737 (m110) REVERT: A 306 PHE cc_start: 0.8890 (m-80) cc_final: 0.8245 (m-80) REVERT: A 309 LYS cc_start: 0.8822 (mtmm) cc_final: 0.8375 (mttt) REVERT: A 310 ARG cc_start: 0.8712 (mpt90) cc_final: 0.8341 (mmt90) REVERT: A 312 LYS cc_start: 0.8909 (mmmt) cc_final: 0.8582 (pttm) REVERT: A 324 ASP cc_start: 0.6907 (t0) cc_final: 0.6614 (t0) REVERT: A 329 MET cc_start: 0.8216 (ptm) cc_final: 0.7904 (ptm) REVERT: A 348 GLN cc_start: 0.8587 (mp10) cc_final: 0.8284 (mp10) REVERT: A 349 PHE cc_start: 0.8338 (t80) cc_final: 0.7874 (t80) REVERT: A 362 GLU cc_start: 0.8256 (tt0) cc_final: 0.7405 (tp30) REVERT: A 382 TYR cc_start: 0.6357 (t80) cc_final: 0.5722 (t80) REVERT: A 386 ARG cc_start: 0.8411 (ptp90) cc_final: 0.7979 (ttm110) REVERT: A 395 HIS cc_start: 0.8415 (m-70) cc_final: 0.8006 (m170) REVERT: A 398 TYR cc_start: 0.8361 (t80) cc_final: 0.7962 (t80) REVERT: A 431 LEU cc_start: 0.8409 (tp) cc_final: 0.8174 (tp) REVERT: A 503 ASN cc_start: 0.8562 (m-40) cc_final: 0.8315 (m-40) REVERT: A 505 ILE cc_start: 0.9261 (mt) cc_final: 0.8947 (tp) REVERT: A 507 GLU cc_start: 0.8461 (mt-10) cc_final: 0.7937 (mt-10) REVERT: A 548 LEU cc_start: 0.8691 (mt) cc_final: 0.8347 (mt) REVERT: A 560 ASN cc_start: 0.8637 (t0) cc_final: 0.8279 (m110) REVERT: A 627 GLN cc_start: 0.8781 (tp40) cc_final: 0.8359 (tm-30) REVERT: A 652 LEU cc_start: 0.8520 (mt) cc_final: 0.8314 (mt) REVERT: A 662 GLU cc_start: 0.7643 (mt-10) cc_final: 0.7008 (mm-30) REVERT: A 672 TYR cc_start: 0.7692 (p90) cc_final: 0.7203 (p90) REVERT: A 695 ASP cc_start: 0.8132 (m-30) cc_final: 0.7917 (m-30) REVERT: A 777 MET cc_start: 0.8092 (mtm) cc_final: 0.7632 (mtm) REVERT: A 813 GLU cc_start: 0.7716 (mp0) cc_final: 0.7230 (mp0) REVERT: A 815 GLU cc_start: 0.8370 (tt0) cc_final: 0.8030 (tt0) REVERT: A 816 MET cc_start: 0.8700 (mtm) cc_final: 0.8440 (mtm) REVERT: A 819 ARG cc_start: 0.8098 (mtp-110) cc_final: 0.7686 (mtp-110) REVERT: A 822 GLN cc_start: 0.8542 (mt0) cc_final: 0.8132 (mt0) REVERT: A 826 LYS cc_start: 0.8697 (mtmt) cc_final: 0.8245 (ttmt) REVERT: A 847 ASN cc_start: 0.7651 (p0) cc_final: 0.7408 (p0) REVERT: A 852 GLU cc_start: 0.8115 (pt0) cc_final: 0.7700 (pt0) REVERT: A 856 LYS cc_start: 0.8176 (pttm) cc_final: 0.7527 (tppt) REVERT: A 858 CYS cc_start: 0.7746 (m) cc_final: 0.7410 (m) REVERT: A 874 LEU cc_start: 0.9271 (tp) cc_final: 0.9014 (pp) REVERT: A 914 ASP cc_start: 0.7422 (p0) cc_final: 0.7208 (p0) REVERT: A 927 GLN cc_start: 0.8421 (tp-100) cc_final: 0.7980 (tm-30) REVERT: A 945 ASP cc_start: 0.7276 (t70) cc_final: 0.7021 (t0) REVERT: A 958 HIS cc_start: 0.7668 (m90) cc_final: 0.7285 (m90) REVERT: A 961 LYS cc_start: 0.9080 (tmtt) cc_final: 0.8520 (tptp) REVERT: A 964 GLN cc_start: 0.9026 (tp-100) cc_final: 0.8693 (tp40) REVERT: A 976 GLU cc_start: 0.8566 (pm20) cc_final: 0.8280 (pm20) REVERT: A 978 LEU cc_start: 0.8936 (mm) cc_final: 0.8694 (mm) REVERT: A 979 MET cc_start: 0.8153 (mtm) cc_final: 0.7634 (mtm) REVERT: A 985 ASP cc_start: 0.8909 (t0) cc_final: 0.8582 (t0) REVERT: A 989 HIS cc_start: 0.7834 (m90) cc_final: 0.7155 (m90) REVERT: A 998 ASP cc_start: 0.8765 (m-30) cc_final: 0.8158 (m-30) REVERT: A 1009 GLU cc_start: 0.8600 (mt-10) cc_final: 0.8007 (mt-10) REVERT: A 1011 GLN cc_start: 0.8400 (tm-30) cc_final: 0.8191 (tm-30) REVERT: A 1012 MET cc_start: 0.8180 (ttp) cc_final: 0.7750 (ttp) REVERT: A 1033 PHE cc_start: 0.8505 (t80) cc_final: 0.8282 (t80) REVERT: A 1034 PHE cc_start: 0.8558 (m-80) cc_final: 0.7782 (m-80) REVERT: A 1044 GLU cc_start: 0.7739 (mt-10) cc_final: 0.7165 (pm20) REVERT: A 1053 ASN cc_start: 0.7726 (m110) cc_final: 0.7292 (m110) REVERT: A 1054 SER cc_start: 0.7987 (t) cc_final: 0.7603 (p) REVERT: A 1055 ILE cc_start: 0.8452 (mt) cc_final: 0.7823 (tp) REVERT: A 1177 LEU cc_start: 0.8672 (mt) cc_final: 0.8396 (pp) REVERT: A 1201 ASN cc_start: 0.6118 (t0) cc_final: 0.5858 (p0) REVERT: A 1208 GLU cc_start: 0.8150 (mp0) cc_final: 0.7173 (mp0) REVERT: A 1242 GLN cc_start: 0.8679 (tp-100) cc_final: 0.8146 (tp40) REVERT: A 1285 PHE cc_start: 0.7784 (t80) cc_final: 0.7452 (t80) REVERT: A 1304 LYS cc_start: 0.8079 (ptpt) cc_final: 0.7805 (pptt) REVERT: A 1306 LEU cc_start: 0.8314 (mt) cc_final: 0.7976 (mt) REVERT: A 1314 LYS cc_start: 0.8496 (mmtt) cc_final: 0.8080 (mmtt) REVERT: A 1324 MET cc_start: 0.7748 (mmp) cc_final: 0.7098 (mmp) REVERT: A 1325 ASP cc_start: 0.7780 (m-30) cc_final: 0.7559 (m-30) REVERT: A 1329 LYS cc_start: 0.8408 (mmtt) cc_final: 0.7616 (mppt) REVERT: A 1434 LYS cc_start: 0.2375 (mttt) cc_final: 0.1685 (mmmm) REVERT: A 1435 GLU cc_start: 0.8239 (tt0) cc_final: 0.7848 (tt0) REVERT: A 1438 LYS cc_start: 0.8117 (mttt) cc_final: 0.7606 (mmmm) REVERT: A 1513 GLU cc_start: 0.7997 (pp20) cc_final: 0.7734 (pp20) REVERT: A1 22 LYS cc_start: 0.8085 (ptmm) cc_final: 0.7821 (ptmm) REVERT: A1 52 LYS cc_start: 0.8770 (tttt) cc_final: 0.8338 (tttt) REVERT: A1 121 LEU cc_start: 0.8540 (mt) cc_final: 0.8226 (mt) REVERT: A1 127 LEU cc_start: 0.7809 (mt) cc_final: 0.7515 (mt) REVERT: A1 141 LEU cc_start: 0.8511 (mt) cc_final: 0.8274 (mt) REVERT: A1 147 PHE cc_start: 0.5856 (m-80) cc_final: 0.5630 (m-10) outliers start: 2 outliers final: 0 residues processed: 337 average time/residue: 0.1181 time to fit residues: 54.0515 Evaluate side-chains 308 residues out of total 1249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 308 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 97 optimal weight: 2.9990 chunk 58 optimal weight: 4.9990 chunk 28 optimal weight: 0.9980 chunk 96 optimal weight: 6.9990 chunk 45 optimal weight: 3.9990 chunk 54 optimal weight: 0.0030 chunk 60 optimal weight: 6.9990 chunk 20 optimal weight: 9.9990 chunk 126 optimal weight: 0.9990 chunk 88 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 overall best weight: 1.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 942 HIS A1010 HIS ** A1022 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1223 ASN A1461 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.155052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.131787 restraints weight = 29678.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.136064 restraints weight = 19224.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.139100 restraints weight = 13629.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.141265 restraints weight = 10296.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.142823 restraints weight = 8155.086| |-----------------------------------------------------------------------------| r_work (final): 0.4054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6619 moved from start: 0.4044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 11500 Z= 0.129 Angle : 0.567 9.934 15436 Z= 0.305 Chirality : 0.042 0.241 1666 Planarity : 0.004 0.061 1973 Dihedral : 4.487 19.373 1464 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.15 % Favored : 96.70 % Rotamer: Outliers : 0.24 % Allowed : 1.29 % Favored : 98.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.08 (0.23), residues: 1335 helix: 1.22 (0.17), residues: 888 sheet: -0.85 (0.98), residues: 27 loop : -0.08 (0.32), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 168 TYR 0.015 0.001 TYR A 197 PHE 0.031 0.001 PHE A 591 TRP 0.027 0.002 TRP A 314 HIS 0.009 0.001 HIS A1010 Details of bonding type rmsd covalent geometry : bond 0.00281 (11500) covalent geometry : angle 0.56709 (15436) hydrogen bonds : bond 0.03509 ( 626) hydrogen bonds : angle 4.40679 ( 1833) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2670 Ramachandran restraints generated. 1335 Oldfield, 0 Emsley, 1335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2670 Ramachandran restraints generated. 1335 Oldfield, 0 Emsley, 1335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 1249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 329 time to evaluate : 0.412 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: A 119 HIS cc_start: 0.7523 (t70) cc_final: 0.7289 (t-90) REVERT: A 162 GLN cc_start: 0.8282 (tm-30) cc_final: 0.7842 (tm-30) REVERT: A 201 ASN cc_start: 0.7254 (m-40) cc_final: 0.6742 (m110) REVERT: A 207 LYS cc_start: 0.7834 (tmtt) cc_final: 0.7628 (tmtt) REVERT: A 306 PHE cc_start: 0.8806 (m-80) cc_final: 0.8225 (m-80) REVERT: A 309 LYS cc_start: 0.8685 (mtmm) cc_final: 0.8278 (mttt) REVERT: A 310 ARG cc_start: 0.8633 (mpt90) cc_final: 0.8331 (mmt90) REVERT: A 312 LYS cc_start: 0.8812 (mmmt) cc_final: 0.8492 (pttm) REVERT: A 324 ASP cc_start: 0.6906 (t0) cc_final: 0.6613 (t0) REVERT: A 329 MET cc_start: 0.8215 (ptm) cc_final: 0.7875 (ptm) REVERT: A 349 PHE cc_start: 0.8333 (t80) cc_final: 0.7854 (t80) REVERT: A 362 GLU cc_start: 0.8236 (tt0) cc_final: 0.7379 (tp30) REVERT: A 386 ARG cc_start: 0.8343 (ptp90) cc_final: 0.7894 (ttp-110) REVERT: A 395 HIS cc_start: 0.8368 (m-70) cc_final: 0.8029 (m170) REVERT: A 398 TYR cc_start: 0.8346 (t80) cc_final: 0.8004 (t80) REVERT: A 431 LEU cc_start: 0.8340 (tp) cc_final: 0.8124 (tp) REVERT: A 503 ASN cc_start: 0.8518 (m-40) cc_final: 0.8285 (m-40) REVERT: A 505 ILE cc_start: 0.9252 (mt) cc_final: 0.8904 (tp) REVERT: A 507 GLU cc_start: 0.8443 (mt-10) cc_final: 0.7934 (mt-10) REVERT: A 548 LEU cc_start: 0.8701 (mt) cc_final: 0.8345 (mt) REVERT: A 560 ASN cc_start: 0.8575 (t0) cc_final: 0.8271 (m110) REVERT: A 567 ARG cc_start: 0.6862 (tpm170) cc_final: 0.6640 (tpm170) REVERT: A 627 GLN cc_start: 0.8780 (tp40) cc_final: 0.8305 (tm-30) REVERT: A 652 LEU cc_start: 0.8497 (mt) cc_final: 0.8291 (mt) REVERT: A 662 GLU cc_start: 0.7608 (mt-10) cc_final: 0.6930 (mm-30) REVERT: A 672 TYR cc_start: 0.7602 (p90) cc_final: 0.7107 (p90) REVERT: A 746 GLN cc_start: 0.7946 (mp-120) cc_final: 0.7636 (mp10) REVERT: A 758 ASN cc_start: 0.8643 (m-40) cc_final: 0.8188 (m-40) REVERT: A 777 MET cc_start: 0.8127 (mtm) cc_final: 0.7645 (mtm) REVERT: A 784 MET cc_start: 0.7753 (mpp) cc_final: 0.6903 (mtt) REVERT: A 791 LEU cc_start: 0.8538 (mt) cc_final: 0.8273 (pp) REVERT: A 813 GLU cc_start: 0.7811 (mp0) cc_final: 0.7166 (mp0) REVERT: A 815 GLU cc_start: 0.8269 (tt0) cc_final: 0.7970 (tt0) REVERT: A 819 ARG cc_start: 0.8113 (mtp-110) cc_final: 0.7627 (mtp-110) REVERT: A 822 GLN cc_start: 0.8474 (mt0) cc_final: 0.8077 (mt0) REVERT: A 826 LYS cc_start: 0.8731 (mtmt) cc_final: 0.8187 (ttmt) REVERT: A 847 ASN cc_start: 0.7624 (p0) cc_final: 0.7380 (p0) REVERT: A 858 CYS cc_start: 0.7602 (m) cc_final: 0.7262 (m) REVERT: A 874 LEU cc_start: 0.9296 (tp) cc_final: 0.9031 (pp) REVERT: A 927 GLN cc_start: 0.8440 (tp-100) cc_final: 0.7968 (tp-100) REVERT: A 958 HIS cc_start: 0.7663 (m90) cc_final: 0.7288 (m90) REVERT: A 961 LYS cc_start: 0.9055 (tmtt) cc_final: 0.8563 (tptp) REVERT: A 964 GLN cc_start: 0.9011 (tp-100) cc_final: 0.8663 (tp40) REVERT: A 976 GLU cc_start: 0.8529 (pm20) cc_final: 0.8227 (pm20) REVERT: A 978 LEU cc_start: 0.8924 (mm) cc_final: 0.8714 (mm) REVERT: A 979 MET cc_start: 0.8083 (mtm) cc_final: 0.7573 (mtm) REVERT: A 982 LEU cc_start: 0.7959 (tp) cc_final: 0.7641 (tp) REVERT: A 985 ASP cc_start: 0.8903 (t0) cc_final: 0.8558 (t0) REVERT: A 989 HIS cc_start: 0.7620 (m90) cc_final: 0.6759 (m90) REVERT: A 998 ASP cc_start: 0.8706 (m-30) cc_final: 0.8308 (m-30) REVERT: A 1009 GLU cc_start: 0.8633 (mt-10) cc_final: 0.8017 (mt-10) REVERT: A 1011 GLN cc_start: 0.8414 (tm-30) cc_final: 0.8150 (tm-30) REVERT: A 1012 MET cc_start: 0.8231 (ttp) cc_final: 0.8026 (ttp) REVERT: A 1032 GLU cc_start: 0.8046 (tt0) cc_final: 0.7533 (tt0) REVERT: A 1033 PHE cc_start: 0.8450 (t80) cc_final: 0.8190 (t80) REVERT: A 1034 PHE cc_start: 0.8533 (m-80) cc_final: 0.7755 (m-80) REVERT: A 1044 GLU cc_start: 0.7712 (mt-10) cc_final: 0.7184 (pm20) REVERT: A 1053 ASN cc_start: 0.7598 (m110) cc_final: 0.7165 (m110) REVERT: A 1054 SER cc_start: 0.7632 (t) cc_final: 0.7278 (p) REVERT: A 1055 ILE cc_start: 0.8378 (mt) cc_final: 0.7787 (tp) REVERT: A 1165 LEU cc_start: 0.8023 (mt) cc_final: 0.7725 (mt) REVERT: A 1177 LEU cc_start: 0.8681 (mt) cc_final: 0.8398 (pp) REVERT: A 1201 ASN cc_start: 0.6088 (t0) cc_final: 0.5821 (p0) REVERT: A 1208 GLU cc_start: 0.8158 (mp0) cc_final: 0.7268 (mp0) REVERT: A 1225 LYS cc_start: 0.8630 (mmpt) cc_final: 0.8330 (mmmt) REVERT: A 1242 GLN cc_start: 0.8652 (tp-100) cc_final: 0.8253 (tp-100) REVERT: A 1285 PHE cc_start: 0.7704 (t80) cc_final: 0.7396 (t80) REVERT: A 1304 LYS cc_start: 0.8018 (ptpt) cc_final: 0.7690 (pptt) REVERT: A 1306 LEU cc_start: 0.8195 (mt) cc_final: 0.7916 (mt) REVERT: A 1314 LYS cc_start: 0.8501 (mmtt) cc_final: 0.7980 (mmtt) REVERT: A 1324 MET cc_start: 0.7576 (mmp) cc_final: 0.7046 (mmp) REVERT: A 1329 LYS cc_start: 0.8411 (mmtt) cc_final: 0.7700 (mppt) REVERT: A 1434 LYS cc_start: 0.2292 (mttt) cc_final: 0.1812 (tppt) REVERT: A 1435 GLU cc_start: 0.8162 (tt0) cc_final: 0.7635 (tt0) REVERT: A 1436 PHE cc_start: 0.8347 (t80) cc_final: 0.8023 (t80) REVERT: A 1438 LYS cc_start: 0.8114 (mttt) cc_final: 0.7616 (mmtm) REVERT: A 1473 ILE cc_start: 0.9044 (mt) cc_final: 0.8648 (mt) REVERT: A 1476 MET cc_start: 0.8103 (mtp) cc_final: 0.7644 (mtp) REVERT: A 1513 GLU cc_start: 0.7953 (pp20) cc_final: 0.7678 (pp20) REVERT: A1 22 LYS cc_start: 0.8078 (ptmm) cc_final: 0.7862 (ptmm) REVERT: A1 52 LYS cc_start: 0.8755 (tttt) cc_final: 0.8324 (tttt) REVERT: A1 121 LEU cc_start: 0.8591 (mt) cc_final: 0.8262 (mt) REVERT: A1 127 LEU cc_start: 0.7757 (mt) cc_final: 0.7442 (mt) REVERT: A1 141 LEU cc_start: 0.8539 (mt) cc_final: 0.8310 (mt) outliers start: 3 outliers final: 0 residues processed: 330 average time/residue: 0.1180 time to fit residues: 52.4086 Evaluate side-chains 302 residues out of total 1249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 302 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 128 optimal weight: 0.8980 chunk 31 optimal weight: 8.9990 chunk 107 optimal weight: 4.9990 chunk 74 optimal weight: 8.9990 chunk 60 optimal weight: 7.9990 chunk 45 optimal weight: 2.9990 chunk 65 optimal weight: 0.0970 chunk 4 optimal weight: 0.1980 chunk 83 optimal weight: 0.9990 chunk 46 optimal weight: 3.9990 chunk 71 optimal weight: 6.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 980 GLN A1223 ASN A1253 ASN A1461 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.156796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.133566 restraints weight = 29406.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.137830 restraints weight = 19207.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.140830 restraints weight = 13700.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.143003 restraints weight = 10374.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.144608 restraints weight = 8236.817| |-----------------------------------------------------------------------------| r_work (final): 0.4078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6592 moved from start: 0.4179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.088 11500 Z= 0.123 Angle : 0.576 10.483 15436 Z= 0.310 Chirality : 0.042 0.208 1666 Planarity : 0.005 0.114 1973 Dihedral : 4.419 18.563 1464 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.07 % Favored : 96.85 % Rotamer: Outliers : 0.24 % Allowed : 0.48 % Favored : 99.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.08 (0.23), residues: 1335 helix: 1.19 (0.18), residues: 887 sheet: -0.78 (0.95), residues: 27 loop : -0.02 (0.32), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.026 0.001 ARG A1243 TYR 0.014 0.001 TYR A 197 PHE 0.027 0.002 PHE A 842 TRP 0.025 0.002 TRP A 314 HIS 0.002 0.001 HIS A 193 Details of bonding type rmsd covalent geometry : bond 0.00279 (11500) covalent geometry : angle 0.57605 (15436) hydrogen bonds : bond 0.03416 ( 626) hydrogen bonds : angle 4.38572 ( 1833) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2670 Ramachandran restraints generated. 1335 Oldfield, 0 Emsley, 1335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2670 Ramachandran restraints generated. 1335 Oldfield, 0 Emsley, 1335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 1249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 322 time to evaluate : 0.427 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 162 GLN cc_start: 0.8214 (tm-30) cc_final: 0.7761 (tm-30) REVERT: A 201 ASN cc_start: 0.7252 (m-40) cc_final: 0.6721 (m110) REVERT: A 207 LYS cc_start: 0.7815 (tmtt) cc_final: 0.7610 (tmtt) REVERT: A 306 PHE cc_start: 0.8810 (m-80) cc_final: 0.8218 (m-80) REVERT: A 309 LYS cc_start: 0.8672 (mtmm) cc_final: 0.8432 (mttt) REVERT: A 310 ARG cc_start: 0.8608 (mpt90) cc_final: 0.8248 (mmt90) REVERT: A 311 LEU cc_start: 0.9220 (tp) cc_final: 0.8958 (tp) REVERT: A 324 ASP cc_start: 0.6884 (t0) cc_final: 0.6611 (t0) REVERT: A 329 MET cc_start: 0.8220 (ptm) cc_final: 0.7851 (ptm) REVERT: A 349 PHE cc_start: 0.8341 (t80) cc_final: 0.7858 (t80) REVERT: A 362 GLU cc_start: 0.8236 (tt0) cc_final: 0.7380 (tp30) REVERT: A 386 ARG cc_start: 0.8310 (ptp90) cc_final: 0.7888 (ttp-110) REVERT: A 395 HIS cc_start: 0.8382 (m-70) cc_final: 0.7988 (m170) REVERT: A 398 TYR cc_start: 0.8308 (t80) cc_final: 0.8040 (t80) REVERT: A 431 LEU cc_start: 0.8313 (tp) cc_final: 0.8098 (tp) REVERT: A 503 ASN cc_start: 0.8503 (m-40) cc_final: 0.8286 (m-40) REVERT: A 505 ILE cc_start: 0.9242 (mt) cc_final: 0.8887 (tp) REVERT: A 507 GLU cc_start: 0.8435 (mt-10) cc_final: 0.7910 (mt-10) REVERT: A 548 LEU cc_start: 0.8705 (mt) cc_final: 0.8372 (mt) REVERT: A 560 ASN cc_start: 0.8503 (t0) cc_final: 0.8218 (m110) REVERT: A 596 LYS cc_start: 0.8746 (mmpt) cc_final: 0.8527 (mmmt) REVERT: A 627 GLN cc_start: 0.8765 (tp40) cc_final: 0.8291 (tm-30) REVERT: A 662 GLU cc_start: 0.7605 (mt-10) cc_final: 0.6928 (mm-30) REVERT: A 672 TYR cc_start: 0.7574 (p90) cc_final: 0.7134 (p90) REVERT: A 746 GLN cc_start: 0.7946 (mp-120) cc_final: 0.7655 (mp10) REVERT: A 758 ASN cc_start: 0.8506 (m-40) cc_final: 0.8167 (m-40) REVERT: A 773 PHE cc_start: 0.7992 (t80) cc_final: 0.7168 (t80) REVERT: A 777 MET cc_start: 0.8172 (mtm) cc_final: 0.7339 (mtm) REVERT: A 784 MET cc_start: 0.7741 (mpp) cc_final: 0.6890 (mtt) REVERT: A 791 LEU cc_start: 0.8550 (mt) cc_final: 0.8282 (pp) REVERT: A 813 GLU cc_start: 0.7713 (mp0) cc_final: 0.7168 (mp0) REVERT: A 815 GLU cc_start: 0.8264 (tt0) cc_final: 0.7890 (tt0) REVERT: A 818 PHE cc_start: 0.8269 (m-80) cc_final: 0.7980 (m-80) REVERT: A 819 ARG cc_start: 0.8078 (mtp-110) cc_final: 0.7591 (mtp-110) REVERT: A 822 GLN cc_start: 0.8420 (mt0) cc_final: 0.8130 (mt0) REVERT: A 826 LYS cc_start: 0.8577 (mtmt) cc_final: 0.8090 (ttmt) REVERT: A 833 ASP cc_start: 0.8079 (m-30) cc_final: 0.6351 (m-30) REVERT: A 836 ARG cc_start: 0.8137 (mtt180) cc_final: 0.7787 (mtt180) REVERT: A 856 LYS cc_start: 0.8181 (pttm) cc_final: 0.7519 (tppt) REVERT: A 858 CYS cc_start: 0.7605 (m) cc_final: 0.7160 (m) REVERT: A 914 ASP cc_start: 0.6992 (p0) cc_final: 0.6749 (p0) REVERT: A 927 GLN cc_start: 0.8452 (tp-100) cc_final: 0.7684 (tp40) REVERT: A 958 HIS cc_start: 0.7598 (m90) cc_final: 0.7313 (m90) REVERT: A 961 LYS cc_start: 0.9088 (tmtt) cc_final: 0.8580 (tptp) REVERT: A 964 GLN cc_start: 0.9003 (tp-100) cc_final: 0.8640 (tp40) REVERT: A 976 GLU cc_start: 0.8531 (pm20) cc_final: 0.8228 (pm20) REVERT: A 979 MET cc_start: 0.7966 (mtm) cc_final: 0.7456 (mtm) REVERT: A 982 LEU cc_start: 0.7943 (tp) cc_final: 0.7602 (tp) REVERT: A 985 ASP cc_start: 0.8849 (t0) cc_final: 0.8524 (t0) REVERT: A 989 HIS cc_start: 0.7649 (m90) cc_final: 0.6977 (m90) REVERT: A 998 ASP cc_start: 0.8715 (m-30) cc_final: 0.8191 (m-30) REVERT: A 1009 GLU cc_start: 0.8569 (mt-10) cc_final: 0.7994 (mt-10) REVERT: A 1011 GLN cc_start: 0.8413 (tm-30) cc_final: 0.8174 (tm-30) REVERT: A 1012 MET cc_start: 0.8239 (ttp) cc_final: 0.7887 (ttp) REVERT: A 1028 GLU cc_start: 0.8136 (tm-30) cc_final: 0.7313 (tm-30) REVERT: A 1032 GLU cc_start: 0.7991 (tt0) cc_final: 0.7466 (tt0) REVERT: A 1033 PHE cc_start: 0.8463 (t80) cc_final: 0.8223 (t80) REVERT: A 1034 PHE cc_start: 0.8526 (m-80) cc_final: 0.7728 (m-80) REVERT: A 1044 GLU cc_start: 0.7699 (mt-10) cc_final: 0.7117 (mt-10) REVERT: A 1053 ASN cc_start: 0.7636 (m110) cc_final: 0.7185 (m110) REVERT: A 1055 ILE cc_start: 0.8333 (mt) cc_final: 0.7920 (tp) REVERT: A 1061 ILE cc_start: 0.8485 (pt) cc_final: 0.8169 (pt) REVERT: A 1177 LEU cc_start: 0.8726 (mt) cc_final: 0.8421 (pp) REVERT: A 1201 ASN cc_start: 0.6103 (t0) cc_final: 0.5823 (p0) REVERT: A 1208 GLU cc_start: 0.8207 (mp0) cc_final: 0.7471 (mp0) REVERT: A 1223 ASN cc_start: 0.8053 (OUTLIER) cc_final: 0.7732 (p0) REVERT: A 1225 LYS cc_start: 0.8690 (mmpt) cc_final: 0.8234 (mmmt) REVERT: A 1226 GLN cc_start: 0.7984 (pm20) cc_final: 0.7199 (pp30) REVERT: A 1230 PHE cc_start: 0.7207 (t80) cc_final: 0.6743 (t80) REVERT: A 1242 GLN cc_start: 0.8665 (tp-100) cc_final: 0.8226 (tp40) REVERT: A 1285 PHE cc_start: 0.7700 (t80) cc_final: 0.7407 (t80) REVERT: A 1304 LYS cc_start: 0.7997 (ptpt) cc_final: 0.7651 (pptt) REVERT: A 1306 LEU cc_start: 0.8158 (mt) cc_final: 0.7793 (mt) REVERT: A 1314 LYS cc_start: 0.8522 (mmtt) cc_final: 0.7998 (mmtt) REVERT: A 1324 MET cc_start: 0.7488 (mmp) cc_final: 0.6961 (mmp) REVERT: A 1329 LYS cc_start: 0.8437 (mmtt) cc_final: 0.7698 (mppt) REVERT: A 1435 GLU cc_start: 0.8143 (tt0) cc_final: 0.7796 (tt0) REVERT: A 1472 ILE cc_start: 0.8397 (mt) cc_final: 0.8051 (mp) REVERT: A 1473 ILE cc_start: 0.9078 (mt) cc_final: 0.8742 (mt) REVERT: A 1476 MET cc_start: 0.7876 (mtp) cc_final: 0.7406 (mtp) REVERT: A 1499 ASN cc_start: 0.7397 (t0) cc_final: 0.6809 (m-40) REVERT: A 1510 VAL cc_start: 0.8172 (m) cc_final: 0.7656 (p) REVERT: A 1513 GLU cc_start: 0.7942 (pp20) cc_final: 0.7562 (pp20) REVERT: A1 22 LYS cc_start: 0.8089 (ptmm) cc_final: 0.7881 (ptmm) REVERT: A1 52 LYS cc_start: 0.8749 (tttt) cc_final: 0.8318 (tttt) REVERT: A1 121 LEU cc_start: 0.8590 (mt) cc_final: 0.8263 (mt) REVERT: A1 127 LEU cc_start: 0.7692 (mt) cc_final: 0.7388 (mt) REVERT: A1 156 ARG cc_start: 0.8164 (tmt170) cc_final: 0.7468 (tmm160) outliers start: 3 outliers final: 0 residues processed: 324 average time/residue: 0.1230 time to fit residues: 53.8927 Evaluate side-chains 298 residues out of total 1249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 297 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 11 optimal weight: 9.9990 chunk 22 optimal weight: 0.7980 chunk 77 optimal weight: 8.9990 chunk 72 optimal weight: 0.7980 chunk 129 optimal weight: 0.9990 chunk 90 optimal weight: 1.9990 chunk 54 optimal weight: 0.0980 chunk 134 optimal weight: 0.9990 chunk 6 optimal weight: 5.9990 chunk 21 optimal weight: 4.9990 chunk 75 optimal weight: 4.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 GLN A1010 HIS A1223 ASN A1461 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.157406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.134028 restraints weight = 29902.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.138245 restraints weight = 19653.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.141225 restraints weight = 14099.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.143447 restraints weight = 10717.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.145108 restraints weight = 8506.082| |-----------------------------------------------------------------------------| r_work (final): 0.4084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6578 moved from start: 0.4315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 11500 Z= 0.114 Angle : 0.580 10.730 15436 Z= 0.305 Chirality : 0.042 0.216 1666 Planarity : 0.004 0.089 1973 Dihedral : 4.254 18.390 1464 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.55 % Favored : 97.38 % Rotamer: Outliers : 0.24 % Allowed : 0.48 % Favored : 99.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.21 (0.24), residues: 1335 helix: 1.28 (0.18), residues: 887 sheet: -0.80 (0.92), residues: 27 loop : 0.06 (0.33), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG A1243 TYR 0.014 0.001 TYR A 197 PHE 0.029 0.001 PHE A 790 TRP 0.020 0.002 TRP A 314 HIS 0.009 0.001 HIS A1010 Details of bonding type rmsd covalent geometry : bond 0.00254 (11500) covalent geometry : angle 0.57952 (15436) hydrogen bonds : bond 0.03262 ( 626) hydrogen bonds : angle 4.31010 ( 1833) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2670 Ramachandran restraints generated. 1335 Oldfield, 0 Emsley, 1335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2670 Ramachandran restraints generated. 1335 Oldfield, 0 Emsley, 1335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 1249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 317 time to evaluate : 0.442 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 HIS cc_start: 0.7439 (t-90) cc_final: 0.7173 (t-90) REVERT: A 162 GLN cc_start: 0.8205 (tm-30) cc_final: 0.7764 (tm-30) REVERT: A 177 ILE cc_start: 0.7868 (mt) cc_final: 0.7647 (mt) REVERT: A 197 TYR cc_start: 0.7332 (t80) cc_final: 0.6983 (t80) REVERT: A 207 LYS cc_start: 0.7754 (tmtt) cc_final: 0.7535 (tmtt) REVERT: A 306 PHE cc_start: 0.8771 (m-80) cc_final: 0.8211 (m-80) REVERT: A 309 LYS cc_start: 0.8660 (mtmm) cc_final: 0.8385 (mttt) REVERT: A 310 ARG cc_start: 0.8503 (mpt90) cc_final: 0.8169 (mmt90) REVERT: A 324 ASP cc_start: 0.6858 (t0) cc_final: 0.6573 (t0) REVERT: A 329 MET cc_start: 0.8220 (ptm) cc_final: 0.7892 (ptm) REVERT: A 349 PHE cc_start: 0.8346 (t80) cc_final: 0.7851 (t80) REVERT: A 362 GLU cc_start: 0.8290 (tt0) cc_final: 0.7433 (tp30) REVERT: A 386 ARG cc_start: 0.8268 (ptp90) cc_final: 0.7830 (ttp-110) REVERT: A 395 HIS cc_start: 0.8385 (m-70) cc_final: 0.8012 (m170) REVERT: A 398 TYR cc_start: 0.8317 (t80) cc_final: 0.8070 (t80) REVERT: A 505 ILE cc_start: 0.9232 (mt) cc_final: 0.8887 (tp) REVERT: A 507 GLU cc_start: 0.8425 (mt-10) cc_final: 0.8001 (mt-10) REVERT: A 548 LEU cc_start: 0.8709 (mt) cc_final: 0.8368 (mt) REVERT: A 560 ASN cc_start: 0.8406 (t0) cc_final: 0.8202 (m110) REVERT: A 596 LYS cc_start: 0.8641 (mmpt) cc_final: 0.8427 (mmmt) REVERT: A 627 GLN cc_start: 0.8813 (tp40) cc_final: 0.8319 (tm-30) REVERT: A 662 GLU cc_start: 0.7571 (mt-10) cc_final: 0.6882 (mm-30) REVERT: A 672 TYR cc_start: 0.7603 (p90) cc_final: 0.7203 (p90) REVERT: A 758 ASN cc_start: 0.8333 (m-40) cc_final: 0.8070 (m-40) REVERT: A 773 PHE cc_start: 0.8021 (t80) cc_final: 0.7415 (t80) REVERT: A 777 MET cc_start: 0.8142 (mtm) cc_final: 0.7348 (mtm) REVERT: A 784 MET cc_start: 0.7748 (mpp) cc_final: 0.6849 (mtt) REVERT: A 791 LEU cc_start: 0.8493 (mt) cc_final: 0.8154 (pp) REVERT: A 795 ARG cc_start: 0.8013 (tpm170) cc_final: 0.7775 (tpm170) REVERT: A 813 GLU cc_start: 0.7714 (mp0) cc_final: 0.7475 (mp0) REVERT: A 815 GLU cc_start: 0.8214 (tt0) cc_final: 0.7811 (tt0) REVERT: A 818 PHE cc_start: 0.8188 (m-80) cc_final: 0.7432 (m-80) REVERT: A 819 ARG cc_start: 0.8007 (mtp-110) cc_final: 0.7481 (mtp-110) REVERT: A 822 GLN cc_start: 0.8466 (mt0) cc_final: 0.8041 (mt0) REVERT: A 826 LYS cc_start: 0.8576 (mtmt) cc_final: 0.8034 (ttmt) REVERT: A 833 ASP cc_start: 0.8047 (m-30) cc_final: 0.7759 (m-30) REVERT: A 856 LYS cc_start: 0.8201 (pttm) cc_final: 0.7406 (tppt) REVERT: A 858 CYS cc_start: 0.7666 (m) cc_final: 0.7337 (m) REVERT: A 891 TRP cc_start: 0.8483 (t60) cc_final: 0.7061 (t60) REVERT: A 914 ASP cc_start: 0.6869 (p0) cc_final: 0.6604 (p0) REVERT: A 927 GLN cc_start: 0.8391 (tp-100) cc_final: 0.7704 (tp40) REVERT: A 944 PHE cc_start: 0.8232 (t80) cc_final: 0.7781 (t80) REVERT: A 958 HIS cc_start: 0.7535 (m90) cc_final: 0.7286 (m90) REVERT: A 961 LYS cc_start: 0.9084 (tmtt) cc_final: 0.8600 (tptp) REVERT: A 964 GLN cc_start: 0.8983 (tp-100) cc_final: 0.8614 (tp40) REVERT: A 976 GLU cc_start: 0.8542 (pm20) cc_final: 0.8247 (pm20) REVERT: A 979 MET cc_start: 0.7930 (mtm) cc_final: 0.7414 (mtm) REVERT: A 982 LEU cc_start: 0.7901 (tp) cc_final: 0.7634 (tp) REVERT: A 985 ASP cc_start: 0.8792 (t0) cc_final: 0.8457 (t0) REVERT: A 989 HIS cc_start: 0.7622 (m90) cc_final: 0.6919 (m90) REVERT: A 998 ASP cc_start: 0.8705 (m-30) cc_final: 0.8161 (m-30) REVERT: A 1009 GLU cc_start: 0.8607 (mt-10) cc_final: 0.8038 (mt-10) REVERT: A 1012 MET cc_start: 0.8344 (ttp) cc_final: 0.7923 (ttp) REVERT: A 1032 GLU cc_start: 0.7956 (tt0) cc_final: 0.7447 (tt0) REVERT: A 1033 PHE cc_start: 0.8438 (t80) cc_final: 0.8207 (t80) REVERT: A 1034 PHE cc_start: 0.8469 (m-80) cc_final: 0.7674 (m-80) REVERT: A 1044 GLU cc_start: 0.7668 (mt-10) cc_final: 0.7064 (mt-10) REVERT: A 1053 ASN cc_start: 0.7598 (m110) cc_final: 0.7138 (m110) REVERT: A 1055 ILE cc_start: 0.8277 (mt) cc_final: 0.7891 (tp) REVERT: A 1061 ILE cc_start: 0.8489 (pt) cc_final: 0.8201 (pt) REVERT: A 1064 ASP cc_start: 0.8238 (m-30) cc_final: 0.7969 (m-30) REVERT: A 1174 LYS cc_start: 0.8269 (mppt) cc_final: 0.7634 (mptt) REVERT: A 1177 LEU cc_start: 0.8740 (mt) cc_final: 0.8472 (pp) REVERT: A 1201 ASN cc_start: 0.6086 (t0) cc_final: 0.5785 (p0) REVERT: A 1208 GLU cc_start: 0.8160 (mp0) cc_final: 0.7429 (mp0) REVERT: A 1225 LYS cc_start: 0.8682 (mmpt) cc_final: 0.8377 (mmmt) REVERT: A 1230 PHE cc_start: 0.7107 (t80) cc_final: 0.6615 (t80) REVERT: A 1242 GLN cc_start: 0.8652 (tp-100) cc_final: 0.8193 (tp-100) REVERT: A 1254 GLN cc_start: 0.8420 (mp10) cc_final: 0.7865 (mp10) REVERT: A 1285 PHE cc_start: 0.7695 (t80) cc_final: 0.7412 (t80) REVERT: A 1304 LYS cc_start: 0.7996 (ptpt) cc_final: 0.7647 (pptt) REVERT: A 1306 LEU cc_start: 0.8121 (mt) cc_final: 0.7860 (mt) REVERT: A 1324 MET cc_start: 0.7412 (mmp) cc_final: 0.6913 (mmp) REVERT: A 1327 PHE cc_start: 0.8091 (m-80) cc_final: 0.7749 (m-80) REVERT: A 1329 LYS cc_start: 0.8418 (mmtt) cc_final: 0.7690 (mppt) REVERT: A 1435 GLU cc_start: 0.8103 (tt0) cc_final: 0.7754 (tt0) REVERT: A 1499 ASN cc_start: 0.7315 (t0) cc_final: 0.6629 (m-40) REVERT: A 1510 VAL cc_start: 0.8134 (m) cc_final: 0.7628 (p) REVERT: A 1513 GLU cc_start: 0.7926 (pp20) cc_final: 0.7542 (pp20) REVERT: A1 22 LYS cc_start: 0.8073 (ptmm) cc_final: 0.7871 (ptmm) REVERT: A1 52 LYS cc_start: 0.8749 (tttt) cc_final: 0.8313 (tttt) REVERT: A1 121 LEU cc_start: 0.8600 (mt) cc_final: 0.8356 (mt) REVERT: A1 127 LEU cc_start: 0.7623 (mt) cc_final: 0.7312 (mt) REVERT: A1 156 ARG cc_start: 0.8117 (tmt170) cc_final: 0.7467 (tmm160) outliers start: 3 outliers final: 0 residues processed: 318 average time/residue: 0.1165 time to fit residues: 50.5966 Evaluate side-chains 288 residues out of total 1249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 288 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 37 optimal weight: 0.9990 chunk 84 optimal weight: 9.9990 chunk 28 optimal weight: 6.9990 chunk 61 optimal weight: 5.9990 chunk 63 optimal weight: 4.9990 chunk 106 optimal weight: 0.7980 chunk 39 optimal weight: 0.8980 chunk 2 optimal weight: 0.0470 chunk 126 optimal weight: 1.9990 chunk 32 optimal weight: 0.0070 chunk 6 optimal weight: 6.9990 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1022 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1023 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1223 ASN A1461 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.158628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.134739 restraints weight = 29918.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.138954 restraints weight = 19774.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.142005 restraints weight = 14242.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.144205 restraints weight = 10881.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.145748 restraints weight = 8675.764| |-----------------------------------------------------------------------------| r_work (final): 0.4091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6564 moved from start: 0.4423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 11500 Z= 0.115 Angle : 0.577 11.183 15436 Z= 0.308 Chirality : 0.042 0.201 1666 Planarity : 0.004 0.073 1973 Dihedral : 4.224 18.383 1464 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.47 % Favored : 97.45 % Rotamer: Outliers : 0.16 % Allowed : 0.24 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.22 (0.24), residues: 1335 helix: 1.29 (0.18), residues: 882 sheet: -0.93 (0.90), residues: 27 loop : 0.09 (0.33), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A1243 TYR 0.013 0.001 TYR A 197 PHE 0.029 0.001 PHE A 790 TRP 0.058 0.002 TRP A1069 HIS 0.002 0.000 HIS A1010 Details of bonding type rmsd covalent geometry : bond 0.00262 (11500) covalent geometry : angle 0.57741 (15436) hydrogen bonds : bond 0.03272 ( 626) hydrogen bonds : angle 4.32728 ( 1833) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2229.50 seconds wall clock time: 39 minutes 17.80 seconds (2357.80 seconds total)