Starting phenix.real_space_refine on Fri Jan 17 23:18:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8v3l_42949/01_2025/8v3l_42949.cif Found real_map, /net/cci-nas-00/data/ceres_data/8v3l_42949/01_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8v3l_42949/01_2025/8v3l_42949.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8v3l_42949/01_2025/8v3l_42949.map" model { file = "/net/cci-nas-00/data/ceres_data/8v3l_42949/01_2025/8v3l_42949.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8v3l_42949/01_2025/8v3l_42949.cif" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.010 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/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: 9.41, per 1000 atoms: 0.83 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: 2.93 Conformation dependent library (CDL) restraints added in 1.5 seconds 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: 1.41 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: 4.20 Time building geometry restraints manager: 3.32 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: 13.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.460 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 30.800 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.040 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:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.260 ------------------------------------------------------------------------------- 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= 0.170 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (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 TRP 0.038 0.002 TRP A 999 HIS 0.002 0.001 HIS A1082 PHE 0.039 0.002 PHE A 790 TYR 0.015 0.001 TYR A 197 ARG 0.013 0.001 ARG A 883 *********************** 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 : 1.405 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: 0.2941 time to fit residues: 135.6544 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 : 1.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 113 optimal weight: 9.9990 chunk 102 optimal weight: 0.9980 chunk 56 optimal weight: 2.9990 chunk 34 optimal weight: 6.9990 chunk 69 optimal weight: 8.9990 chunk 54 optimal weight: 4.9990 chunk 105 optimal weight: 7.9990 chunk 40 optimal weight: 8.9990 chunk 64 optimal weight: 10.0000 chunk 78 optimal weight: 10.0000 chunk 122 optimal weight: 0.6980 overall best weight: 3.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 166 GLN A 323 GLN A 348 GLN A 666 GLN A 980 GLN A1190 ASN A1253 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 = 0.4192 r_free = 0.4192 target = 0.153703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.130688 restraints weight = 29934.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.134869 restraints weight = 19527.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.137778 restraints weight = 13859.515| |-----------------------------------------------------------------------------| r_work (final): 0.3990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6663 moved from start: 0.2150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 11500 Z= 0.247 Angle : 0.622 10.831 15436 Z= 0.345 Chirality : 0.043 0.161 1666 Planarity : 0.005 0.084 1973 Dihedral : 4.697 22.160 1464 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.45 % Favored : 96.40 % Rotamer: Outliers : 0.32 % Allowed : 4.10 % Favored : 95.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.23), residues: 1335 helix: 1.23 (0.17), residues: 885 sheet: -0.32 (1.28), residues: 17 loop : 0.05 (0.31), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A1069 HIS 0.006 0.001 HIS A 193 PHE 0.029 0.002 PHE A 156 TYR 0.015 0.002 TYRA1 28 ARG 0.007 0.001 ARG A 58 *********************** 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 348 residues out of total 1249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 344 time to evaluate : 1.384 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 152 VAL cc_start: 0.8518 (t) cc_final: 0.8288 (p) REVERT: A 162 GLN cc_start: 0.8371 (tm-30) cc_final: 0.7167 (tm-30) REVERT: A 166 GLN cc_start: 0.8291 (mt0) cc_final: 0.7676 (mm-40) REVERT: A 197 TYR cc_start: 0.7137 (t80) cc_final: 0.6901 (t80) REVERT: A 306 PHE cc_start: 0.8605 (m-80) cc_final: 0.7991 (m-80) REVERT: A 309 LYS cc_start: 0.8857 (mtmm) cc_final: 0.8430 (mttt) REVERT: A 310 ARG cc_start: 0.8708 (mpt180) cc_final: 0.8140 (mmt90) REVERT: A 314 TRP cc_start: 0.8785 (t60) cc_final: 0.8202 (t60) REVERT: A 347 LYS cc_start: 0.8946 (mttt) cc_final: 0.8520 (mttt) REVERT: A 349 PHE cc_start: 0.8288 (t80) cc_final: 0.7895 (t80) REVERT: A 355 LYS cc_start: 0.7273 (mtmt) cc_final: 0.6814 (ptpp) REVERT: A 362 GLU cc_start: 0.8345 (tt0) cc_final: 0.7347 (tp30) REVERT: A 395 HIS cc_start: 0.7769 (m-70) cc_final: 0.7272 (m170) REVERT: A 398 TYR cc_start: 0.8207 (t80) cc_final: 0.7803 (t80) REVERT: A 417 MET cc_start: 0.7843 (mtp) cc_final: 0.7631 (mtp) REVERT: A 437 LYS cc_start: 0.8613 (mttt) cc_final: 0.8411 (mmmm) REVERT: A 469 SER cc_start: 0.8495 (t) cc_final: 0.8234 (p) REVERT: A 503 ASN cc_start: 0.8488 (m-40) cc_final: 0.8271 (m-40) REVERT: A 505 ILE cc_start: 0.9229 (mt) cc_final: 0.8914 (tp) REVERT: A 507 GLU cc_start: 0.8477 (mt-10) cc_final: 0.7980 (mt-10) REVERT: A 529 LEU cc_start: 0.8209 (mt) cc_final: 0.7910 (pp) REVERT: A 548 LEU cc_start: 0.8607 (mt) cc_final: 0.8194 (mt) REVERT: A 596 LYS cc_start: 0.8829 (mmpt) cc_final: 0.8601 (mmmt) REVERT: A 627 GLN cc_start: 0.8618 (tp40) cc_final: 0.8324 (tm-30) REVERT: A 652 LEU cc_start: 0.8559 (mt) cc_final: 0.8222 (mt) REVERT: A 725 ARG cc_start: 0.8161 (mtt180) cc_final: 0.7891 (mtp180) REVERT: A 750 LEU cc_start: 0.8548 (mt) cc_final: 0.8191 (mm) REVERT: A 777 MET cc_start: 0.7961 (mtm) cc_final: 0.7653 (mtm) REVERT: A 813 GLU cc_start: 0.7780 (mp0) cc_final: 0.6991 (mp0) REVERT: A 815 GLU cc_start: 0.7943 (tt0) cc_final: 0.7509 (tt0) REVERT: A 816 MET cc_start: 0.8738 (mtm) cc_final: 0.8400 (mtm) REVERT: A 818 PHE cc_start: 0.8195 (m-80) cc_final: 0.7840 (m-80) REVERT: A 819 ARG cc_start: 0.8049 (mtp-110) cc_final: 0.7690 (mtp-110) REVERT: A 822 GLN cc_start: 0.8647 (mt0) cc_final: 0.8196 (mt0) REVERT: A 823 TRP cc_start: 0.7788 (t60) cc_final: 0.7454 (t60) REVERT: A 825 LYS cc_start: 0.8563 (mmmt) cc_final: 0.8359 (mmmt) REVERT: A 826 LYS cc_start: 0.8522 (mtmt) cc_final: 0.8042 (ttpt) REVERT: A 858 CYS cc_start: 0.7419 (m) cc_final: 0.7038 (m) REVERT: A 927 GLN cc_start: 0.8490 (tp-100) cc_final: 0.7776 (tm-30) REVERT: A 944 PHE cc_start: 0.8080 (t80) cc_final: 0.7655 (t80) REVERT: A 945 ASP cc_start: 0.7346 (t70) cc_final: 0.7134 (t0) REVERT: A 958 HIS cc_start: 0.8365 (m90) cc_final: 0.7087 (m90) REVERT: A 964 GLN cc_start: 0.8960 (tp-100) cc_final: 0.8696 (tp40) REVERT: A 976 GLU cc_start: 0.8489 (pm20) cc_final: 0.8199 (pm20) REVERT: A 979 MET cc_start: 0.8114 (mtm) cc_final: 0.7529 (mtm) REVERT: A 985 ASP cc_start: 0.8822 (t0) cc_final: 0.8486 (t0) REVERT: A 989 HIS cc_start: 0.7908 (m90) cc_final: 0.7404 (m90) REVERT: A 998 ASP cc_start: 0.8645 (m-30) cc_final: 0.7830 (m-30) REVERT: A 1012 MET cc_start: 0.8624 (ttt) cc_final: 0.8255 (ttt) REVERT: A 1033 PHE cc_start: 0.8387 (t80) cc_final: 0.8149 (t80) REVERT: A 1034 PHE cc_start: 0.8563 (m-80) cc_final: 0.7994 (m-80) REVERT: A 1050 LYS cc_start: 0.9314 (tttt) cc_final: 0.8785 (ptmm) REVERT: A 1053 ASN cc_start: 0.7399 (m110) cc_final: 0.6986 (m110) REVERT: A 1055 ILE cc_start: 0.8337 (mt) cc_final: 0.7894 (tp) REVERT: A 1064 ASP cc_start: 0.8514 (m-30) cc_final: 0.8303 (m-30) REVERT: A 1068 LEU cc_start: 0.9232 (mt) cc_final: 0.8975 (mm) REVERT: A 1071 TYR cc_start: 0.7408 (t80) cc_final: 0.7201 (t80) REVERT: A 1163 ARG cc_start: 0.8888 (ptm160) cc_final: 0.8219 (ptp-110) REVERT: A 1165 LEU cc_start: 0.7983 (mt) cc_final: 0.7706 (mt) REVERT: A 1167 ARG cc_start: 0.8441 (mtt180) cc_final: 0.7901 (mtt180) REVERT: A 1177 LEU cc_start: 0.8579 (mt) cc_final: 0.8348 (pp) REVERT: A 1208 GLU cc_start: 0.7357 (mp0) cc_final: 0.7106 (mp0) REVERT: A 1214 ASN cc_start: 0.8457 (m110) cc_final: 0.8238 (m110) REVERT: A 1238 LYS cc_start: 0.8296 (mtmm) cc_final: 0.7786 (mttt) REVERT: A 1288 LYS cc_start: 0.8093 (tptt) cc_final: 0.7835 (tppt) REVERT: A 1304 LYS cc_start: 0.8061 (ptpt) cc_final: 0.7726 (pptt) REVERT: A 1306 LEU cc_start: 0.8324 (mt) cc_final: 0.8037 (mt) REVERT: A 1314 LYS cc_start: 0.8322 (mmtt) cc_final: 0.7808 (mmtt) REVERT: A 1324 MET cc_start: 0.8013 (mmp) cc_final: 0.7591 (mmp) REVERT: A 1327 PHE cc_start: 0.8525 (m-80) cc_final: 0.8296 (m-80) REVERT: A 1329 LYS cc_start: 0.8394 (mttp) cc_final: 0.7815 (mppt) REVERT: A 1435 GLU cc_start: 0.8197 (tt0) cc_final: 0.7735 (tt0) REVERT: A 1438 LYS cc_start: 0.8161 (mttt) cc_final: 0.7630 (mmtm) REVERT: A 1440 ILE cc_start: 0.8127 (mt) cc_final: 0.7847 (pt) REVERT: A 1470 LYS cc_start: 0.8584 (pttp) cc_final: 0.8326 (pttp) REVERT: A1 22 LYS cc_start: 0.7835 (ptmm) cc_final: 0.7483 (ptmm) REVERT: A1 29 TYR cc_start: 0.6477 (m-10) cc_final: 0.6251 (m-80) REVERT: A1 52 LYS cc_start: 0.8749 (tttt) cc_final: 0.8281 (tttt) REVERT: A1 121 LEU cc_start: 0.8304 (mt) cc_final: 0.8002 (mt) REVERT: A1 123 PHE cc_start: 0.8355 (p90) cc_final: 0.8033 (p90) outliers start: 4 outliers final: 2 residues processed: 346 average time/residue: 0.2997 time to fit residues: 138.4968 Evaluate side-chains 313 residues out of total 1249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 311 time to evaluate : 1.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 31 optimal weight: 10.0000 chunk 12 optimal weight: 3.9990 chunk 55 optimal weight: 7.9990 chunk 108 optimal weight: 0.9980 chunk 78 optimal weight: 9.9990 chunk 62 optimal weight: 10.0000 chunk 112 optimal weight: 10.0000 chunk 19 optimal weight: 0.0980 chunk 7 optimal weight: 0.0970 chunk 100 optimal weight: 2.9990 chunk 97 optimal weight: 9.9990 overall best weight: 1.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 348 GLN A1010 HIS A1190 ASN A1320 GLN ** A1 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.156256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.132879 restraints weight = 29997.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.137123 restraints weight = 19557.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.140179 restraints weight = 13951.226| |-----------------------------------------------------------------------------| r_work (final): 0.4025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6619 moved from start: 0.2642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11500 Z= 0.171 Angle : 0.560 9.477 15436 Z= 0.305 Chirality : 0.042 0.161 1666 Planarity : 0.004 0.051 1973 Dihedral : 4.481 21.424 1464 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.15 % Allowed : 2.55 % Favored : 97.30 % Rotamer: Outliers : 0.24 % Allowed : 1.93 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.23), residues: 1335 helix: 1.28 (0.18), residues: 889 sheet: -0.36 (1.03), residues: 27 loop : 0.05 (0.32), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 314 HIS 0.010 0.001 HIS A1010 PHE 0.025 0.001 PHE A 156 TYR 0.016 0.001 TYR A 547 ARG 0.005 0.001 ARG A 168 *********************** 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 343 residues out of total 1249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 340 time to evaluate : 1.306 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: symmetry clash revert: symmetry clash REVERT: A 152 VAL cc_start: 0.8506 (t) cc_final: 0.8274 (p) REVERT: A 169 GLN cc_start: 0.7703 (mm-40) cc_final: 0.7228 (pp30) REVERT: A 201 ASN cc_start: 0.7251 (m-40) cc_final: 0.6153 (m-40) REVERT: A 306 PHE cc_start: 0.8820 (m-80) cc_final: 0.7983 (m-80) REVERT: A 309 LYS cc_start: 0.8855 (mtmm) cc_final: 0.8340 (mttt) REVERT: A 310 ARG cc_start: 0.8680 (mpt90) cc_final: 0.8079 (mmt90) REVERT: A 324 ASP cc_start: 0.6634 (t0) cc_final: 0.6359 (t0) REVERT: A 347 LYS cc_start: 0.8911 (mttt) cc_final: 0.8456 (mttt) REVERT: A 349 PHE cc_start: 0.8269 (t80) cc_final: 0.7884 (t80) REVERT: A 362 GLU cc_start: 0.8280 (tt0) cc_final: 0.7421 (tp30) REVERT: A 395 HIS cc_start: 0.7899 (m-70) cc_final: 0.7409 (m170) REVERT: A 398 TYR cc_start: 0.8351 (t80) cc_final: 0.7986 (t80) REVERT: A 469 SER cc_start: 0.8377 (t) cc_final: 0.8160 (p) REVERT: A 505 ILE cc_start: 0.9213 (mt) cc_final: 0.8912 (tp) REVERT: A 507 GLU cc_start: 0.8424 (mt-10) cc_final: 0.7872 (mt-10) REVERT: A 525 PHE cc_start: 0.7458 (t80) cc_final: 0.7062 (t80) REVERT: A 529 LEU cc_start: 0.8219 (mt) cc_final: 0.8005 (mt) REVERT: A 548 LEU cc_start: 0.8603 (mt) cc_final: 0.8168 (mt) REVERT: A 557 ASP cc_start: 0.7816 (t0) cc_final: 0.7042 (t0) REVERT: A 559 TYR cc_start: 0.8655 (m-80) cc_final: 0.8286 (m-80) REVERT: A 560 ASN cc_start: 0.8481 (t0) cc_final: 0.8084 (m110) REVERT: A 596 LYS cc_start: 0.8792 (mmpt) cc_final: 0.8558 (mmmt) REVERT: A 627 GLN cc_start: 0.8789 (tp40) cc_final: 0.8357 (tm-30) REVERT: A 652 LEU cc_start: 0.8538 (mt) cc_final: 0.8203 (mt) REVERT: A 777 MET cc_start: 0.7965 (mtm) cc_final: 0.7624 (mtm) REVERT: A 784 MET cc_start: 0.7408 (mpp) cc_final: 0.7172 (mtm) REVERT: A 813 GLU cc_start: 0.7729 (mp0) cc_final: 0.7020 (mp0) REVERT: A 815 GLU cc_start: 0.8050 (tt0) cc_final: 0.7564 (pt0) REVERT: A 816 MET cc_start: 0.8645 (mtm) cc_final: 0.8333 (mtm) REVERT: A 818 PHE cc_start: 0.8187 (m-80) cc_final: 0.7890 (m-80) REVERT: A 819 ARG cc_start: 0.8058 (mtp-110) cc_final: 0.7639 (mtp-110) REVERT: A 822 GLN cc_start: 0.8596 (mt0) cc_final: 0.8093 (mt0) REVERT: A 826 LYS cc_start: 0.8502 (mtmt) cc_final: 0.7964 (ttpt) REVERT: A 858 CYS cc_start: 0.7246 (m) cc_final: 0.6829 (m) REVERT: A 944 PHE cc_start: 0.8039 (t80) cc_final: 0.7588 (t80) REVERT: A 958 HIS cc_start: 0.7686 (m90) cc_final: 0.7331 (m90) REVERT: A 961 LYS cc_start: 0.9047 (tmtt) cc_final: 0.8401 (tptp) REVERT: A 964 GLN cc_start: 0.9009 (tp-100) cc_final: 0.8711 (tp40) REVERT: A 976 GLU cc_start: 0.8526 (pm20) cc_final: 0.8069 (pm20) REVERT: A 979 MET cc_start: 0.7986 (mtm) cc_final: 0.7461 (mtm) REVERT: A 982 LEU cc_start: 0.7859 (tp) cc_final: 0.7547 (tp) REVERT: A 985 ASP cc_start: 0.8718 (t0) cc_final: 0.8491 (t0) REVERT: A 989 HIS cc_start: 0.7912 (m90) cc_final: 0.7294 (m90) REVERT: A 998 ASP cc_start: 0.8612 (m-30) cc_final: 0.7839 (m-30) REVERT: A 1014 GLU cc_start: 0.7828 (OUTLIER) cc_final: 0.7495 (pm20) REVERT: A 1015 GLU cc_start: 0.7572 (tm-30) cc_final: 0.7238 (tm-30) REVERT: A 1034 PHE cc_start: 0.8544 (m-80) cc_final: 0.7834 (m-80) REVERT: A 1050 LYS cc_start: 0.9309 (tttt) cc_final: 0.8749 (ptmm) REVERT: A 1053 ASN cc_start: 0.7476 (m110) cc_final: 0.6965 (m110) REVERT: A 1055 ILE cc_start: 0.8256 (mt) cc_final: 0.7792 (tp) REVERT: A 1064 ASP cc_start: 0.8444 (m-30) cc_final: 0.8182 (m-30) REVERT: A 1068 LEU cc_start: 0.9201 (mt) cc_final: 0.8921 (mt) REVERT: A 1163 ARG cc_start: 0.8845 (ttm110) cc_final: 0.8634 (mtp-110) REVERT: A 1165 LEU cc_start: 0.7970 (mt) cc_final: 0.7646 (mt) REVERT: A 1177 LEU cc_start: 0.8571 (mt) cc_final: 0.8331 (pp) REVERT: A 1188 ILE cc_start: 0.7935 (pt) cc_final: 0.7413 (pt) REVERT: A 1192 GLU cc_start: 0.7503 (pm20) cc_final: 0.7114 (pt0) REVERT: A 1201 ASN cc_start: 0.6241 (t0) cc_final: 0.5914 (p0) REVERT: A 1208 GLU cc_start: 0.7321 (mp0) cc_final: 0.6940 (mp0) REVERT: A 1214 ASN cc_start: 0.8395 (m110) cc_final: 0.8145 (m110) REVERT: A 1230 PHE cc_start: 0.7198 (t80) cc_final: 0.6767 (t80) REVERT: A 1242 GLN cc_start: 0.8539 (tp-100) cc_final: 0.8060 (tp-100) REVERT: A 1245 ILE cc_start: 0.7812 (OUTLIER) cc_final: 0.7605 (mp) REVERT: A 1285 PHE cc_start: 0.7920 (t80) cc_final: 0.7664 (t80) REVERT: A 1288 LYS cc_start: 0.8065 (tptt) cc_final: 0.7681 (tppt) REVERT: A 1292 LEU cc_start: 0.8242 (mt) cc_final: 0.7889 (mt) REVERT: A 1304 LYS cc_start: 0.8060 (ptpt) cc_final: 0.7657 (pptt) REVERT: A 1306 LEU cc_start: 0.8256 (mt) cc_final: 0.7986 (mt) REVERT: A 1309 TYR cc_start: 0.8107 (t80) cc_final: 0.7857 (t80) REVERT: A 1314 LYS cc_start: 0.8422 (mmtt) cc_final: 0.8073 (mmtt) REVERT: A 1324 MET cc_start: 0.7788 (mmp) cc_final: 0.7182 (mmp) REVERT: A 1327 PHE cc_start: 0.8454 (m-80) cc_final: 0.8191 (m-80) REVERT: A 1434 LYS cc_start: 0.2349 (mttt) cc_final: 0.1796 (tppt) REVERT: A 1435 GLU cc_start: 0.8274 (tt0) cc_final: 0.7916 (tt0) REVERT: A 1440 ILE cc_start: 0.8081 (mt) cc_final: 0.7777 (pt) REVERT: A1 29 TYR cc_start: 0.6553 (m-10) cc_final: 0.6327 (m-80) REVERT: A1 52 LYS cc_start: 0.8725 (tttt) cc_final: 0.8259 (tttt) REVERT: A1 121 LEU cc_start: 0.8346 (mt) cc_final: 0.8046 (mt) REVERT: A1 123 PHE cc_start: 0.8316 (p90) cc_final: 0.8075 (p90) REVERT: A1 173 LYS cc_start: 0.8215 (mptt) cc_final: 0.7667 (mptt) outliers start: 3 outliers final: 1 residues processed: 342 average time/residue: 0.3158 time to fit residues: 145.1967 Evaluate side-chains 317 residues out of total 1249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 314 time to evaluate : 1.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 112 optimal weight: 10.0000 chunk 125 optimal weight: 30.0000 chunk 39 optimal weight: 6.9990 chunk 30 optimal weight: 7.9990 chunk 63 optimal weight: 8.9990 chunk 41 optimal weight: 4.9990 chunk 88 optimal weight: 0.0770 chunk 76 optimal weight: 8.9990 chunk 48 optimal weight: 9.9990 chunk 78 optimal weight: 0.7980 chunk 96 optimal weight: 0.6980 overall best weight: 2.7142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 452 GLN A 814 ASN A 915 ASN A1190 ASN ** A1 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.153852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.130733 restraints weight = 29715.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.134942 restraints weight = 19347.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.137900 restraints weight = 13777.408| |-----------------------------------------------------------------------------| r_work (final): 0.3992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6679 moved from start: 0.3192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11500 Z= 0.217 Angle : 0.584 9.623 15436 Z= 0.322 Chirality : 0.042 0.153 1666 Planarity : 0.004 0.049 1973 Dihedral : 4.657 27.081 1464 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.30 % Favored : 96.55 % Rotamer: Outliers : 0.24 % Allowed : 2.81 % Favored : 96.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.23), residues: 1335 helix: 1.14 (0.17), residues: 889 sheet: -0.31 (1.08), residues: 27 loop : -0.03 (0.32), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 921 HIS 0.004 0.001 HIS A 193 PHE 0.040 0.002 PHE A 790 TYR 0.016 0.002 TYR A 674 ARG 0.010 0.000 ARG A 168 *********************** 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 346 residues out of total 1249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 343 time to evaluate : 1.336 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: symmetry clash revert: symmetry clash REVERT: A 19 PHE cc_start: 0.8144 (m-80) cc_final: 0.7848 (t80) REVERT: A 119 HIS cc_start: 0.7483 (t70) cc_final: 0.7170 (t70) REVERT: A 152 VAL cc_start: 0.8500 (t) cc_final: 0.8235 (p) REVERT: A 197 TYR cc_start: 0.7251 (t80) cc_final: 0.6840 (t80) REVERT: A 306 PHE cc_start: 0.8811 (m-80) cc_final: 0.8106 (m-80) REVERT: A 309 LYS cc_start: 0.8868 (mtmm) cc_final: 0.8561 (mttt) REVERT: A 310 ARG cc_start: 0.8675 (mpt90) cc_final: 0.8187 (mmt90) REVERT: A 324 ASP cc_start: 0.6748 (t0) cc_final: 0.6472 (t0) REVERT: A 347 LYS cc_start: 0.8915 (mttt) cc_final: 0.8546 (mttt) REVERT: A 349 PHE cc_start: 0.8297 (t80) cc_final: 0.7902 (t80) REVERT: A 362 GLU cc_start: 0.8262 (tt0) cc_final: 0.7418 (tp30) REVERT: A 395 HIS cc_start: 0.8178 (m-70) cc_final: 0.7955 (m170) REVERT: A 398 TYR cc_start: 0.8363 (t80) cc_final: 0.7993 (t80) REVERT: A 469 SER cc_start: 0.8437 (t) cc_final: 0.8184 (p) REVERT: A 505 ILE cc_start: 0.9266 (mt) cc_final: 0.8933 (tp) REVERT: A 507 GLU cc_start: 0.8453 (mt-10) cc_final: 0.7929 (mt-10) REVERT: A 525 PHE cc_start: 0.7477 (t80) cc_final: 0.7050 (t80) REVERT: A 529 LEU cc_start: 0.8360 (mt) cc_final: 0.8085 (mt) REVERT: A 548 LEU cc_start: 0.8621 (mt) cc_final: 0.8211 (mt) REVERT: A 557 ASP cc_start: 0.7869 (t0) cc_final: 0.7326 (t0) REVERT: A 560 ASN cc_start: 0.8572 (t0) cc_final: 0.8153 (m110) REVERT: A 596 LYS cc_start: 0.8829 (mmpt) cc_final: 0.8581 (mmmt) REVERT: A 627 GLN cc_start: 0.8756 (tp40) cc_final: 0.8329 (tm-30) REVERT: A 652 LEU cc_start: 0.8556 (mt) cc_final: 0.8200 (mt) REVERT: A 662 GLU cc_start: 0.7230 (mm-30) cc_final: 0.6988 (mm-30) REVERT: A 672 TYR cc_start: 0.7645 (p90) cc_final: 0.7154 (p90) REVERT: A 725 ARG cc_start: 0.7818 (mmm160) cc_final: 0.7479 (mmm-85) REVERT: A 728 MET cc_start: 0.7792 (mtp) cc_final: 0.7588 (mtp) REVERT: A 777 MET cc_start: 0.7943 (mtm) cc_final: 0.7627 (mtm) REVERT: A 784 MET cc_start: 0.7579 (mpp) cc_final: 0.7138 (mtm) REVERT: A 813 GLU cc_start: 0.7798 (mp0) cc_final: 0.7225 (mp0) REVERT: A 815 GLU cc_start: 0.8102 (tt0) cc_final: 0.7708 (tt0) REVERT: A 816 MET cc_start: 0.8721 (mtm) cc_final: 0.8451 (mtm) REVERT: A 818 PHE cc_start: 0.8280 (m-80) cc_final: 0.8019 (m-80) REVERT: A 819 ARG cc_start: 0.8049 (mtp-110) cc_final: 0.7642 (mtp-110) REVERT: A 821 ARG cc_start: 0.8291 (mtt-85) cc_final: 0.8074 (mtt180) REVERT: A 822 GLN cc_start: 0.8554 (mt0) cc_final: 0.8187 (mt0) REVERT: A 826 LYS cc_start: 0.8551 (mtmt) cc_final: 0.8101 (ttmt) REVERT: A 849 ASP cc_start: 0.8359 (m-30) cc_final: 0.8038 (m-30) REVERT: A 858 CYS cc_start: 0.7581 (m) cc_final: 0.7147 (m) REVERT: A 914 ASP cc_start: 0.7396 (p0) cc_final: 0.7148 (p0) REVERT: A 927 GLN cc_start: 0.8440 (tp-100) cc_final: 0.8045 (tm-30) REVERT: A 944 PHE cc_start: 0.8223 (t80) cc_final: 0.7812 (t80) REVERT: A 945 ASP cc_start: 0.7213 (t70) cc_final: 0.6947 (t0) REVERT: A 958 HIS cc_start: 0.7667 (m90) cc_final: 0.7299 (m90) REVERT: A 961 LYS cc_start: 0.9039 (tmtt) cc_final: 0.8334 (tptp) REVERT: A 964 GLN cc_start: 0.9028 (tp-100) cc_final: 0.8697 (tp40) REVERT: A 979 MET cc_start: 0.8168 (mtm) cc_final: 0.7664 (mtm) REVERT: A 982 LEU cc_start: 0.7954 (tp) cc_final: 0.7610 (tp) REVERT: A 985 ASP cc_start: 0.8927 (t0) cc_final: 0.8593 (t0) REVERT: A 989 HIS cc_start: 0.7925 (m90) cc_final: 0.7137 (m90) REVERT: A 998 ASP cc_start: 0.8630 (m-30) cc_final: 0.7962 (m-30) REVERT: A 1015 GLU cc_start: 0.7609 (tm-30) cc_final: 0.7374 (tm-30) REVERT: A 1033 PHE cc_start: 0.8482 (t80) cc_final: 0.8243 (t80) REVERT: A 1034 PHE cc_start: 0.8572 (m-80) cc_final: 0.7882 (m-80) REVERT: A 1053 ASN cc_start: 0.7485 (m110) cc_final: 0.6983 (m110) REVERT: A 1055 ILE cc_start: 0.8357 (mt) cc_final: 0.7892 (tp) REVERT: A 1061 ILE cc_start: 0.8670 (pt) cc_final: 0.8416 (pt) REVERT: A 1064 ASP cc_start: 0.8444 (m-30) cc_final: 0.8043 (m-30) REVERT: A 1068 LEU cc_start: 0.9198 (mt) cc_final: 0.8929 (mt) REVERT: A 1165 LEU cc_start: 0.8014 (mt) cc_final: 0.7742 (mt) REVERT: A 1177 LEU cc_start: 0.8611 (mt) cc_final: 0.8378 (pp) REVERT: A 1188 ILE cc_start: 0.7895 (pt) cc_final: 0.7582 (pt) REVERT: A 1201 ASN cc_start: 0.6064 (t0) cc_final: 0.5808 (p0) REVERT: A 1208 GLU cc_start: 0.7344 (mp0) cc_final: 0.6913 (mp0) REVERT: A 1214 ASN cc_start: 0.8428 (m110) cc_final: 0.8131 (m110) REVERT: A 1223 ASN cc_start: 0.8022 (p0) cc_final: 0.7564 (p0) REVERT: A 1225 LYS cc_start: 0.8597 (mmpt) cc_final: 0.8319 (mmmt) REVERT: A 1242 GLN cc_start: 0.8560 (tp-100) cc_final: 0.8065 (tp-100) REVERT: A 1245 ILE cc_start: 0.7841 (OUTLIER) cc_final: 0.7620 (mp) REVERT: A 1285 PHE cc_start: 0.7998 (t80) cc_final: 0.7762 (t80) REVERT: A 1292 LEU cc_start: 0.8372 (mt) cc_final: 0.8052 (mt) REVERT: A 1304 LYS cc_start: 0.8137 (ptpt) cc_final: 0.7733 (pptt) REVERT: A 1306 LEU cc_start: 0.8334 (mt) cc_final: 0.8044 (mt) REVERT: A 1309 TYR cc_start: 0.8220 (t80) cc_final: 0.8005 (t80) REVERT: A 1313 LYS cc_start: 0.7580 (tttt) cc_final: 0.7143 (ptmm) REVERT: A 1314 LYS cc_start: 0.8371 (mmtt) cc_final: 0.7968 (mmtt) REVERT: A 1324 MET cc_start: 0.7826 (mmp) cc_final: 0.7241 (mmp) REVERT: A 1325 ASP cc_start: 0.7817 (m-30) cc_final: 0.7602 (m-30) REVERT: A 1327 PHE cc_start: 0.8454 (m-80) cc_final: 0.8189 (m-80) REVERT: A 1329 LYS cc_start: 0.8329 (mttp) cc_final: 0.7778 (mppt) REVERT: A 1434 LYS cc_start: 0.2357 (mttt) cc_final: 0.1582 (tppt) REVERT: A 1435 GLU cc_start: 0.8354 (tt0) cc_final: 0.7857 (tt0) REVERT: A 1438 LYS cc_start: 0.8148 (mttt) cc_final: 0.7612 (mmtm) REVERT: A 1440 ILE cc_start: 0.8149 (mt) cc_final: 0.7869 (pt) REVERT: A1 22 LYS cc_start: 0.7972 (ptmm) cc_final: 0.7505 (ptmm) REVERT: A1 29 TYR cc_start: 0.6475 (m-10) cc_final: 0.6170 (m-80) REVERT: A1 52 LYS cc_start: 0.8740 (tttt) cc_final: 0.8284 (tttt) REVERT: A1 78 ASP cc_start: 0.8954 (p0) cc_final: 0.8753 (p0) REVERT: A1 121 LEU cc_start: 0.8495 (mt) cc_final: 0.8198 (mt) REVERT: A1 127 LEU cc_start: 0.8036 (mt) cc_final: 0.7721 (mt) REVERT: A1 173 LYS cc_start: 0.8126 (mptt) cc_final: 0.7629 (mptt) outliers start: 3 outliers final: 1 residues processed: 346 average time/residue: 0.3181 time to fit residues: 147.3644 Evaluate side-chains 306 residues out of total 1249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 304 time to evaluate : 1.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 65 optimal weight: 9.9990 chunk 25 optimal weight: 10.0000 chunk 27 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 chunk 86 optimal weight: 3.9990 chunk 6 optimal weight: 6.9990 chunk 2 optimal weight: 0.0670 chunk 83 optimal weight: 8.9990 chunk 13 optimal weight: 0.3980 chunk 85 optimal weight: 1.9990 chunk 111 optimal weight: 10.0000 overall best weight: 1.8924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 56 GLN ** A 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 516 ASN A1010 HIS A1190 ASN A1223 ASN A1461 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.154705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.131584 restraints weight = 29374.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.135848 restraints weight = 19086.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.138808 restraints weight = 13511.262| |-----------------------------------------------------------------------------| r_work (final): 0.4007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6655 moved from start: 0.3515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 11500 Z= 0.183 Angle : 0.558 9.120 15436 Z= 0.303 Chirality : 0.042 0.187 1666 Planarity : 0.004 0.048 1973 Dihedral : 4.537 24.306 1464 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.15 % Allowed : 2.77 % Favored : 97.08 % Rotamer: Outliers : 0.32 % Allowed : 1.77 % Favored : 97.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.23), residues: 1335 helix: 1.20 (0.18), residues: 885 sheet: -0.36 (1.04), residues: 27 loop : -0.06 (0.32), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 385 HIS 0.006 0.001 HIS A1010 PHE 0.040 0.002 PHE A 790 TYR 0.017 0.001 TYR A 680 ARG 0.012 0.000 ARG A 168 *********************** 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 341 residues out of total 1249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 337 time to evaluate : 1.272 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: symmetry clash REVERT: A 55 ARG cc_start: 0.8417 (ttt180) cc_final: 0.7888 (ttt180) REVERT: A 119 HIS cc_start: 0.7556 (t70) cc_final: 0.7327 (t-90) REVERT: A 152 VAL cc_start: 0.8510 (t) cc_final: 0.8249 (p) REVERT: A 197 TYR cc_start: 0.7156 (t80) cc_final: 0.6925 (t80) REVERT: A 201 ASN cc_start: 0.7313 (m-40) cc_final: 0.6235 (m-40) REVERT: A 306 PHE cc_start: 0.8783 (m-80) cc_final: 0.8091 (m-80) REVERT: A 309 LYS cc_start: 0.8878 (mtmm) cc_final: 0.8554 (mttt) REVERT: A 310 ARG cc_start: 0.8609 (mpt90) cc_final: 0.8177 (mmt90) REVERT: A 324 ASP cc_start: 0.6822 (t0) cc_final: 0.6525 (t0) REVERT: A 347 LYS cc_start: 0.8925 (mttt) cc_final: 0.8527 (mttt) REVERT: A 349 PHE cc_start: 0.8217 (t80) cc_final: 0.7824 (t80) REVERT: A 362 GLU cc_start: 0.8245 (tt0) cc_final: 0.7393 (tp30) REVERT: A 382 TYR cc_start: 0.6142 (t80) cc_final: 0.5859 (t80) REVERT: A 386 ARG cc_start: 0.8496 (ptp90) cc_final: 0.7889 (ttp-110) REVERT: A 395 HIS cc_start: 0.8146 (m-70) cc_final: 0.7926 (m170) REVERT: A 398 TYR cc_start: 0.8178 (t80) cc_final: 0.7854 (t80) REVERT: A 431 LEU cc_start: 0.8402 (tp) cc_final: 0.8150 (tp) REVERT: A 505 ILE cc_start: 0.9205 (mt) cc_final: 0.8879 (tp) REVERT: A 507 GLU cc_start: 0.8478 (mt-10) cc_final: 0.7950 (mt-10) REVERT: A 525 PHE cc_start: 0.7255 (t80) cc_final: 0.6972 (t80) REVERT: A 529 LEU cc_start: 0.8335 (mt) cc_final: 0.8119 (mt) REVERT: A 548 LEU cc_start: 0.8685 (mt) cc_final: 0.8276 (mt) REVERT: A 560 ASN cc_start: 0.8543 (t0) cc_final: 0.8281 (m110) REVERT: A 596 LYS cc_start: 0.8770 (mmpt) cc_final: 0.8509 (mmmt) REVERT: A 627 GLN cc_start: 0.8736 (tp40) cc_final: 0.8330 (tm-30) REVERT: A 652 LEU cc_start: 0.8552 (mt) cc_final: 0.8183 (mt) REVERT: A 662 GLU cc_start: 0.7116 (mm-30) cc_final: 0.6796 (mm-30) REVERT: A 672 TYR cc_start: 0.7666 (p90) cc_final: 0.7012 (p90) REVERT: A 725 ARG cc_start: 0.7742 (mmm160) cc_final: 0.7468 (mmm-85) REVERT: A 746 GLN cc_start: 0.7994 (mp-120) cc_final: 0.7697 (mp10) REVERT: A 758 ASN cc_start: 0.8609 (m-40) cc_final: 0.8173 (m-40) REVERT: A 777 MET cc_start: 0.8144 (mtm) cc_final: 0.7695 (mtm) REVERT: A 784 MET cc_start: 0.7640 (mpp) cc_final: 0.6908 (mtt) REVERT: A 815 GLU cc_start: 0.8318 (tt0) cc_final: 0.7919 (pt0) REVERT: A 818 PHE cc_start: 0.8267 (m-80) cc_final: 0.7998 (m-80) REVERT: A 819 ARG cc_start: 0.8036 (mtp-110) cc_final: 0.7595 (mtp-110) REVERT: A 822 GLN cc_start: 0.8578 (mt0) cc_final: 0.8146 (mt0) REVERT: A 825 LYS cc_start: 0.8607 (mmmt) cc_final: 0.8142 (mmmt) REVERT: A 826 LYS cc_start: 0.8604 (mtmt) cc_final: 0.8104 (ttmt) REVERT: A 847 ASN cc_start: 0.7664 (p0) cc_final: 0.7392 (p0) REVERT: A 849 ASP cc_start: 0.8336 (m-30) cc_final: 0.8038 (m-30) REVERT: A 856 LYS cc_start: 0.8096 (pttm) cc_final: 0.7317 (tppt) REVERT: A 858 CYS cc_start: 0.7454 (m) cc_final: 0.6994 (m) REVERT: A 908 MET cc_start: 0.7285 (mpp) cc_final: 0.6724 (ptp) REVERT: A 914 ASP cc_start: 0.7287 (p0) cc_final: 0.7054 (p0) REVERT: A 927 GLN cc_start: 0.8350 (tp-100) cc_final: 0.8002 (tm-30) REVERT: A 945 ASP cc_start: 0.7189 (t70) cc_final: 0.6987 (t0) REVERT: A 958 HIS cc_start: 0.7702 (m90) cc_final: 0.7370 (m90) REVERT: A 961 LYS cc_start: 0.9009 (tmtt) cc_final: 0.8325 (tptp) REVERT: A 964 GLN cc_start: 0.9037 (tp-100) cc_final: 0.8691 (tp40) REVERT: A 979 MET cc_start: 0.8119 (mtm) cc_final: 0.7607 (mtm) REVERT: A 982 LEU cc_start: 0.7889 (tp) cc_final: 0.7548 (tp) REVERT: A 985 ASP cc_start: 0.8813 (t0) cc_final: 0.8472 (t0) REVERT: A 989 HIS cc_start: 0.7868 (m90) cc_final: 0.7082 (m90) REVERT: A 998 ASP cc_start: 0.8658 (m-30) cc_final: 0.8264 (m-30) REVERT: A 1012 MET cc_start: 0.8536 (ttt) cc_final: 0.8068 (ttt) REVERT: A 1034 PHE cc_start: 0.8549 (m-80) cc_final: 0.7796 (m-80) REVERT: A 1053 ASN cc_start: 0.7562 (m110) cc_final: 0.7084 (m110) REVERT: A 1055 ILE cc_start: 0.8310 (mt) cc_final: 0.7839 (tp) REVERT: A 1064 ASP cc_start: 0.8464 (m-30) cc_final: 0.8129 (m-30) REVERT: A 1068 LEU cc_start: 0.9203 (mt) cc_final: 0.8921 (mt) REVERT: A 1165 LEU cc_start: 0.8033 (mt) cc_final: 0.7768 (mt) REVERT: A 1167 ARG cc_start: 0.8377 (mtt180) cc_final: 0.8150 (mtt180) REVERT: A 1177 LEU cc_start: 0.8604 (mt) cc_final: 0.8352 (pp) REVERT: A 1201 ASN cc_start: 0.6083 (t0) cc_final: 0.5813 (p0) REVERT: A 1208 GLU cc_start: 0.7585 (mp0) cc_final: 0.6987 (mp0) REVERT: A 1242 GLN cc_start: 0.8556 (tp-100) cc_final: 0.8231 (tp-100) REVERT: A 1285 PHE cc_start: 0.7904 (t80) cc_final: 0.7699 (t80) REVERT: A 1304 LYS cc_start: 0.8147 (ptpt) cc_final: 0.7771 (pptt) REVERT: A 1306 LEU cc_start: 0.8292 (mt) cc_final: 0.7995 (mt) REVERT: A 1313 LYS cc_start: 0.7785 (tttt) cc_final: 0.7367 (ptmm) REVERT: A 1314 LYS cc_start: 0.8448 (mmtt) cc_final: 0.8111 (mmtt) REVERT: A 1324 MET cc_start: 0.7726 (mmp) cc_final: 0.7139 (mmp) REVERT: A 1327 PHE cc_start: 0.8394 (m-80) cc_final: 0.8136 (m-80) REVERT: A 1329 LYS cc_start: 0.8341 (mttp) cc_final: 0.7768 (mppt) REVERT: A 1434 LYS cc_start: 0.2295 (mttt) cc_final: 0.1999 (mmmm) REVERT: A 1435 GLU cc_start: 0.8357 (tt0) cc_final: 0.8019 (tt0) REVERT: A1 22 LYS cc_start: 0.8070 (ptmm) cc_final: 0.7689 (ptmm) REVERT: A1 52 LYS cc_start: 0.8736 (tttt) cc_final: 0.8278 (tttt) REVERT: A1 78 ASP cc_start: 0.8967 (p0) cc_final: 0.8743 (p0) REVERT: A1 121 LEU cc_start: 0.8569 (mt) cc_final: 0.8250 (mt) REVERT: A1 127 LEU cc_start: 0.7887 (mt) cc_final: 0.7578 (mt) REVERT: A1 173 LYS cc_start: 0.8075 (mptt) cc_final: 0.7579 (mptt) outliers start: 4 outliers final: 1 residues processed: 337 average time/residue: 0.3133 time to fit residues: 140.3251 Evaluate side-chains 312 residues out of total 1249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 311 time to evaluate : 1.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 58 optimal weight: 9.9990 chunk 19 optimal weight: 0.8980 chunk 98 optimal weight: 0.7980 chunk 68 optimal weight: 7.9990 chunk 7 optimal weight: 6.9990 chunk 57 optimal weight: 0.3980 chunk 16 optimal weight: 8.9990 chunk 73 optimal weight: 0.7980 chunk 8 optimal weight: 0.9980 chunk 84 optimal weight: 5.9990 chunk 111 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 56 GLN A 119 HIS A 670 ASN A1190 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.156626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.133925 restraints weight = 29702.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.138134 restraints weight = 19103.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.141105 restraints weight = 13485.621| |-----------------------------------------------------------------------------| r_work (final): 0.4044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6615 moved from start: 0.3670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 11500 Z= 0.155 Angle : 0.543 9.306 15436 Z= 0.293 Chirality : 0.041 0.154 1666 Planarity : 0.004 0.095 1973 Dihedral : 4.369 21.285 1464 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.15 % Allowed : 2.55 % Favored : 97.30 % Rotamer: Outliers : 0.00 % Allowed : 1.53 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.23), residues: 1335 helix: 1.27 (0.18), residues: 887 sheet: -0.49 (0.99), residues: 27 loop : -0.02 (0.32), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 314 HIS 0.004 0.001 HIS A1010 PHE 0.033 0.001 PHE A 790 TYR 0.014 0.001 TYR A 680 ARG 0.011 0.000 ARG A 168 *********************** 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 340 residues out of total 1249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 340 time to evaluate : 1.328 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 56 GLN cc_start: 0.8362 (mm110) cc_final: 0.7906 (tp-100) REVERT: A 119 HIS cc_start: 0.7232 (t-90) cc_final: 0.6930 (t-90) REVERT: A 152 VAL cc_start: 0.8512 (t) cc_final: 0.8266 (p) REVERT: A 177 ILE cc_start: 0.7800 (mt) cc_final: 0.7586 (mt) REVERT: A 197 TYR cc_start: 0.7146 (t80) cc_final: 0.6906 (t80) REVERT: A 201 ASN cc_start: 0.7279 (m-40) cc_final: 0.6209 (m-40) REVERT: A 306 PHE cc_start: 0.8788 (m-80) cc_final: 0.8337 (m-80) REVERT: A 309 LYS cc_start: 0.8784 (mtmm) cc_final: 0.8517 (mttt) REVERT: A 310 ARG cc_start: 0.8677 (mpt90) cc_final: 0.8163 (mmt90) REVERT: A 324 ASP cc_start: 0.6982 (t0) cc_final: 0.6688 (t0) REVERT: A 329 MET cc_start: 0.8233 (ptm) cc_final: 0.7968 (ptm) REVERT: A 347 LYS cc_start: 0.8903 (mttt) cc_final: 0.8501 (mttt) REVERT: A 349 PHE cc_start: 0.8374 (t80) cc_final: 0.7868 (t80) REVERT: A 362 GLU cc_start: 0.8218 (tt0) cc_final: 0.7337 (tp30) REVERT: A 386 ARG cc_start: 0.8361 (ptp90) cc_final: 0.7702 (ttp80) REVERT: A 395 HIS cc_start: 0.8103 (m-70) cc_final: 0.7887 (m170) REVERT: A 398 TYR cc_start: 0.8311 (t80) cc_final: 0.7990 (t80) REVERT: A 431 LEU cc_start: 0.8333 (tp) cc_final: 0.8103 (tp) REVERT: A 505 ILE cc_start: 0.9189 (mt) cc_final: 0.8848 (tp) REVERT: A 507 GLU cc_start: 0.8470 (mt-10) cc_final: 0.7951 (mt-10) REVERT: A 525 PHE cc_start: 0.7242 (t80) cc_final: 0.6970 (t80) REVERT: A 548 LEU cc_start: 0.8695 (mt) cc_final: 0.8295 (mt) REVERT: A 560 ASN cc_start: 0.8479 (t0) cc_final: 0.8199 (m110) REVERT: A 596 LYS cc_start: 0.8661 (mmpt) cc_final: 0.8377 (mmmt) REVERT: A 627 GLN cc_start: 0.8723 (tp40) cc_final: 0.8318 (tm-30) REVERT: A 662 GLU cc_start: 0.7093 (mm-30) cc_final: 0.6785 (mm-30) REVERT: A 672 TYR cc_start: 0.7654 (p90) cc_final: 0.6997 (p90) REVERT: A 725 ARG cc_start: 0.7831 (mmm160) cc_final: 0.7446 (mmm-85) REVERT: A 750 LEU cc_start: 0.8572 (mt) cc_final: 0.8268 (mm) REVERT: A 758 ASN cc_start: 0.8479 (m-40) cc_final: 0.8083 (m-40) REVERT: A 777 MET cc_start: 0.8108 (mtm) cc_final: 0.7620 (mtm) REVERT: A 784 MET cc_start: 0.7614 (mpp) cc_final: 0.6804 (mtt) REVERT: A 813 GLU cc_start: 0.7608 (mp0) cc_final: 0.7041 (mp0) REVERT: A 815 GLU cc_start: 0.8185 (tt0) cc_final: 0.7833 (tt0) REVERT: A 819 ARG cc_start: 0.7989 (mtp-110) cc_final: 0.7577 (mtp-110) REVERT: A 822 GLN cc_start: 0.8524 (mt0) cc_final: 0.8218 (mt0) REVERT: A 825 LYS cc_start: 0.8348 (mmmt) cc_final: 0.7905 (mmmt) REVERT: A 826 LYS cc_start: 0.8581 (mtmt) cc_final: 0.8098 (ttmt) REVERT: A 849 ASP cc_start: 0.8288 (m-30) cc_final: 0.7956 (m-30) REVERT: A 858 CYS cc_start: 0.7387 (m) cc_final: 0.6902 (m) REVERT: A 908 MET cc_start: 0.7190 (mpp) cc_final: 0.6678 (ptp) REVERT: A 914 ASP cc_start: 0.6959 (p0) cc_final: 0.6675 (p0) REVERT: A 927 GLN cc_start: 0.8381 (tp-100) cc_final: 0.8025 (tm-30) REVERT: A 955 LEU cc_start: 0.8017 (mt) cc_final: 0.7524 (tp) REVERT: A 958 HIS cc_start: 0.7806 (m90) cc_final: 0.7421 (m90) REVERT: A 961 LYS cc_start: 0.8984 (tmtt) cc_final: 0.8319 (tptp) REVERT: A 964 GLN cc_start: 0.9024 (tp-100) cc_final: 0.8665 (tp40) REVERT: A 979 MET cc_start: 0.7958 (mtm) cc_final: 0.7424 (mtm) REVERT: A 985 ASP cc_start: 0.8736 (t0) cc_final: 0.8244 (m-30) REVERT: A 989 HIS cc_start: 0.7704 (m90) cc_final: 0.6872 (m90) REVERT: A 998 ASP cc_start: 0.8658 (m-30) cc_final: 0.8218 (m-30) REVERT: A 1012 MET cc_start: 0.8500 (ttt) cc_final: 0.8060 (ttt) REVERT: A 1028 GLU cc_start: 0.8006 (tm-30) cc_final: 0.7294 (pp20) REVERT: A 1032 GLU cc_start: 0.8066 (tt0) cc_final: 0.7488 (mt-10) REVERT: A 1033 PHE cc_start: 0.8484 (t80) cc_final: 0.8255 (t80) REVERT: A 1034 PHE cc_start: 0.8508 (m-80) cc_final: 0.7722 (m-80) REVERT: A 1053 ASN cc_start: 0.7472 (m110) cc_final: 0.7060 (m110) REVERT: A 1055 ILE cc_start: 0.8177 (mt) cc_final: 0.7788 (tp) REVERT: A 1064 ASP cc_start: 0.8428 (m-30) cc_final: 0.8202 (m-30) REVERT: A 1068 LEU cc_start: 0.9189 (mt) cc_final: 0.8915 (mt) REVERT: A 1165 LEU cc_start: 0.8009 (mt) cc_final: 0.7730 (mt) REVERT: A 1177 LEU cc_start: 0.8602 (mt) cc_final: 0.8351 (pp) REVERT: A 1201 ASN cc_start: 0.6060 (t0) cc_final: 0.5761 (p0) REVERT: A 1208 GLU cc_start: 0.7562 (mp0) cc_final: 0.6878 (mp0) REVERT: A 1225 LYS cc_start: 0.8568 (mmpt) cc_final: 0.8304 (mmmt) REVERT: A 1242 GLN cc_start: 0.8556 (tp-100) cc_final: 0.8214 (tp-100) REVERT: A 1285 PHE cc_start: 0.7867 (t80) cc_final: 0.7660 (t80) REVERT: A 1292 LEU cc_start: 0.8323 (mt) cc_final: 0.8008 (mt) REVERT: A 1304 LYS cc_start: 0.8177 (ptpt) cc_final: 0.7790 (pptt) REVERT: A 1306 LEU cc_start: 0.8263 (mt) cc_final: 0.7900 (mt) REVERT: A 1313 LYS cc_start: 0.7765 (tttt) cc_final: 0.7352 (ptmm) REVERT: A 1314 LYS cc_start: 0.8489 (mmtt) cc_final: 0.8025 (mmtt) REVERT: A 1324 MET cc_start: 0.7461 (mmp) cc_final: 0.6967 (mmp) REVERT: A 1325 ASP cc_start: 0.7596 (m-30) cc_final: 0.7263 (m-30) REVERT: A 1327 PHE cc_start: 0.8257 (m-80) cc_final: 0.8025 (m-80) REVERT: A 1434 LYS cc_start: 0.2450 (mttt) cc_final: 0.1766 (mmmm) REVERT: A 1435 GLU cc_start: 0.8269 (tt0) cc_final: 0.7755 (tt0) REVERT: A 1438 LYS cc_start: 0.8045 (mttt) cc_final: 0.7525 (mmtm) REVERT: A1 22 LYS cc_start: 0.8079 (ptmm) cc_final: 0.7813 (ptmm) REVERT: A1 52 LYS cc_start: 0.8711 (tttt) cc_final: 0.8257 (tttt) REVERT: A1 78 ASP cc_start: 0.8933 (p0) cc_final: 0.8704 (p0) REVERT: A1 121 LEU cc_start: 0.8581 (mt) cc_final: 0.8260 (mt) REVERT: A1 127 LEU cc_start: 0.7779 (mt) cc_final: 0.7467 (mt) REVERT: A1 141 LEU cc_start: 0.8471 (mt) cc_final: 0.8263 (mt) REVERT: A1 173 LYS cc_start: 0.7897 (mptt) cc_final: 0.7498 (mptt) outliers start: 0 outliers final: 0 residues processed: 340 average time/residue: 0.3106 time to fit residues: 141.0347 Evaluate side-chains 310 residues out of total 1249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 310 time to evaluate : 1.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 94 optimal weight: 5.9990 chunk 46 optimal weight: 2.9990 chunk 14 optimal weight: 4.9990 chunk 26 optimal weight: 8.9990 chunk 33 optimal weight: 0.9980 chunk 104 optimal weight: 1.9990 chunk 80 optimal weight: 9.9990 chunk 32 optimal weight: 7.9990 chunk 7 optimal weight: 4.9990 chunk 82 optimal weight: 0.7980 chunk 62 optimal weight: 3.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1010 HIS A1190 ASN ** A1223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1499 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.154441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.131102 restraints weight = 30270.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.135469 restraints weight = 19546.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.138515 restraints weight = 13856.805| |-----------------------------------------------------------------------------| r_work (final): 0.3998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6687 moved from start: 0.3999 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= 0.199 Angle : 0.590 9.003 15436 Z= 0.316 Chirality : 0.042 0.212 1666 Planarity : 0.004 0.059 1973 Dihedral : 4.475 27.803 1464 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.37 % Favored : 96.48 % Rotamer: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.23), residues: 1335 helix: 1.22 (0.18), residues: 885 sheet: -0.46 (1.00), residues: 27 loop : -0.04 (0.32), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 314 HIS 0.004 0.001 HIS A1010 PHE 0.030 0.001 PHE A 790 TYR 0.017 0.001 TYR A 680 ARG 0.013 0.001 ARG A 168 *********************** 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: 0 poor density : 337 time to evaluate : 1.198 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 119 HIS cc_start: 0.7402 (t-90) cc_final: 0.7193 (t-90) REVERT: A 152 VAL cc_start: 0.8582 (t) cc_final: 0.8319 (p) REVERT: A 177 ILE cc_start: 0.7860 (mt) cc_final: 0.7651 (mt) REVERT: A 197 TYR cc_start: 0.7210 (t80) cc_final: 0.6921 (t80) REVERT: A 306 PHE cc_start: 0.8779 (m-80) cc_final: 0.8211 (m-80) REVERT: A 309 LYS cc_start: 0.8779 (mtmm) cc_final: 0.8565 (mttt) REVERT: A 310 ARG cc_start: 0.8698 (mpt90) cc_final: 0.8387 (mmt90) REVERT: A 324 ASP cc_start: 0.6980 (t0) cc_final: 0.6684 (t0) REVERT: A 329 MET cc_start: 0.8324 (ptm) cc_final: 0.8078 (ptm) REVERT: A 349 PHE cc_start: 0.8429 (t80) cc_final: 0.7901 (t80) REVERT: A 362 GLU cc_start: 0.8230 (tt0) cc_final: 0.7372 (tp30) REVERT: A 386 ARG cc_start: 0.8474 (ptp90) cc_final: 0.7677 (ttp80) REVERT: A 398 TYR cc_start: 0.8283 (t80) cc_final: 0.7964 (t80) REVERT: A 431 LEU cc_start: 0.8373 (tp) cc_final: 0.8113 (tp) REVERT: A 503 ASN cc_start: 0.8559 (m110) cc_final: 0.8270 (m110) REVERT: A 505 ILE cc_start: 0.9310 (mt) cc_final: 0.8972 (tp) REVERT: A 507 GLU cc_start: 0.8518 (mt-10) cc_final: 0.7991 (mt-10) REVERT: A 548 LEU cc_start: 0.8709 (mt) cc_final: 0.8304 (mt) REVERT: A 560 ASN cc_start: 0.8544 (t0) cc_final: 0.8341 (m110) REVERT: A 567 ARG cc_start: 0.6482 (tpm170) cc_final: 0.5940 (tpm170) REVERT: A 596 LYS cc_start: 0.8691 (mmpt) cc_final: 0.8418 (mmmt) REVERT: A 627 GLN cc_start: 0.8723 (tp40) cc_final: 0.8315 (tm-30) REVERT: A 662 GLU cc_start: 0.7217 (mm-30) cc_final: 0.6783 (mm-30) REVERT: A 672 TYR cc_start: 0.7853 (p90) cc_final: 0.7113 (p90) REVERT: A 725 ARG cc_start: 0.7732 (mmm160) cc_final: 0.7453 (mmm-85) REVERT: A 746 GLN cc_start: 0.7955 (mp-120) cc_final: 0.7653 (mp10) REVERT: A 750 LEU cc_start: 0.8564 (mt) cc_final: 0.8308 (mm) REVERT: A 758 ASN cc_start: 0.8545 (m-40) cc_final: 0.8167 (m-40) REVERT: A 773 PHE cc_start: 0.8064 (t80) cc_final: 0.7493 (t80) REVERT: A 777 MET cc_start: 0.8284 (mtm) cc_final: 0.7106 (mtm) REVERT: A 784 MET cc_start: 0.7662 (mpp) cc_final: 0.6823 (mtt) REVERT: A 813 GLU cc_start: 0.7717 (mp0) cc_final: 0.7207 (mp0) REVERT: A 815 GLU cc_start: 0.8301 (tt0) cc_final: 0.7954 (tt0) REVERT: A 819 ARG cc_start: 0.8084 (mtp-110) cc_final: 0.7613 (mtp-110) REVERT: A 822 GLN cc_start: 0.8558 (mt0) cc_final: 0.8087 (mt0) REVERT: A 825 LYS cc_start: 0.8547 (mmmt) cc_final: 0.7962 (mmmt) REVERT: A 826 LYS cc_start: 0.8663 (mtmt) cc_final: 0.8175 (ttmt) REVERT: A 849 ASP cc_start: 0.8332 (m-30) cc_final: 0.8075 (m-30) REVERT: A 855 LEU cc_start: 0.7515 (mt) cc_final: 0.7157 (mt) REVERT: A 858 CYS cc_start: 0.7586 (m) cc_final: 0.7125 (m) REVERT: A 888 PHE cc_start: 0.6875 (t80) cc_final: 0.6501 (t80) REVERT: A 908 MET cc_start: 0.7220 (mpp) cc_final: 0.6893 (ptp) REVERT: A 914 ASP cc_start: 0.6906 (p0) cc_final: 0.6527 (p0) REVERT: A 927 GLN cc_start: 0.8315 (tp-100) cc_final: 0.7990 (tm-30) REVERT: A 958 HIS cc_start: 0.7834 (m90) cc_final: 0.7557 (m90) REVERT: A 961 LYS cc_start: 0.9000 (tmtt) cc_final: 0.8349 (tptp) REVERT: A 964 GLN cc_start: 0.9083 (tp-100) cc_final: 0.8740 (tp40) REVERT: A 979 MET cc_start: 0.8109 (mtm) cc_final: 0.7603 (mtm) REVERT: A 985 ASP cc_start: 0.8866 (t0) cc_final: 0.8286 (m-30) REVERT: A 989 HIS cc_start: 0.7909 (m90) cc_final: 0.7204 (m90) REVERT: A 998 ASP cc_start: 0.8697 (m-30) cc_final: 0.8100 (m-30) REVERT: A 1011 GLN cc_start: 0.8602 (tm-30) cc_final: 0.8224 (tp40) REVERT: A 1014 GLU cc_start: 0.8119 (pm20) cc_final: 0.7463 (pm20) REVERT: A 1028 GLU cc_start: 0.8084 (tm-30) cc_final: 0.7459 (tm-30) REVERT: A 1032 GLU cc_start: 0.8119 (tt0) cc_final: 0.7495 (tt0) REVERT: A 1033 PHE cc_start: 0.8550 (t80) cc_final: 0.8250 (t80) REVERT: A 1034 PHE cc_start: 0.8560 (m-80) cc_final: 0.7772 (m-80) REVERT: A 1053 ASN cc_start: 0.7541 (m110) cc_final: 0.7110 (m110) REVERT: A 1055 ILE cc_start: 0.8335 (mt) cc_final: 0.7933 (tp) REVERT: A 1058 LYS cc_start: 0.8401 (tppt) cc_final: 0.7978 (tppt) REVERT: A 1064 ASP cc_start: 0.8539 (m-30) cc_final: 0.8263 (m-30) REVERT: A 1068 LEU cc_start: 0.9188 (mt) cc_final: 0.8929 (mt) REVERT: A 1165 LEU cc_start: 0.8065 (mt) cc_final: 0.7782 (mt) REVERT: A 1177 LEU cc_start: 0.8647 (mt) cc_final: 0.8399 (pp) REVERT: A 1201 ASN cc_start: 0.6152 (t0) cc_final: 0.5829 (p0) REVERT: A 1208 GLU cc_start: 0.7590 (mp0) cc_final: 0.6876 (mp0) REVERT: A 1242 GLN cc_start: 0.8545 (tp-100) cc_final: 0.8250 (tp-100) REVERT: A 1304 LYS cc_start: 0.8147 (ptpt) cc_final: 0.7790 (pptt) REVERT: A 1306 LEU cc_start: 0.8184 (mt) cc_final: 0.7913 (mt) REVERT: A 1313 LYS cc_start: 0.7746 (tttt) cc_final: 0.7364 (ptmm) REVERT: A 1314 LYS cc_start: 0.8474 (mmtt) cc_final: 0.8008 (mmtt) REVERT: A 1324 MET cc_start: 0.7642 (mmp) cc_final: 0.7144 (mmp) REVERT: A 1325 ASP cc_start: 0.7823 (m-30) cc_final: 0.7253 (p0) REVERT: A 1327 PHE cc_start: 0.8343 (m-80) cc_final: 0.8124 (m-80) REVERT: A 1329 LYS cc_start: 0.8329 (mttp) cc_final: 0.7773 (mppt) REVERT: A 1434 LYS cc_start: 0.2233 (mttt) cc_final: 0.1776 (mmmm) REVERT: A 1435 GLU cc_start: 0.8285 (tt0) cc_final: 0.7838 (tt0) REVERT: A 1438 LYS cc_start: 0.8122 (mttt) cc_final: 0.7640 (mmtm) REVERT: A 1513 GLU cc_start: 0.8048 (pp20) cc_final: 0.7676 (pp20) REVERT: A1 22 LYS cc_start: 0.8125 (ptmm) cc_final: 0.7887 (ptmm) REVERT: A1 52 LYS cc_start: 0.8746 (tttt) cc_final: 0.8290 (tttt) REVERT: A1 78 ASP cc_start: 0.8975 (p0) cc_final: 0.8726 (p0) REVERT: A1 121 LEU cc_start: 0.8573 (mt) cc_final: 0.8242 (mt) REVERT: A1 141 LEU cc_start: 0.8527 (mt) cc_final: 0.8285 (mt) REVERT: A1 147 PHE cc_start: 0.6047 (m-80) cc_final: 0.5796 (m-10) REVERT: A1 173 LYS cc_start: 0.7862 (mptt) cc_final: 0.7415 (mptt) outliers start: 0 outliers final: 0 residues processed: 337 average time/residue: 0.3147 time to fit residues: 142.0162 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 : 1.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 96 optimal weight: 0.3980 chunk 94 optimal weight: 8.9990 chunk 79 optimal weight: 2.9990 chunk 109 optimal weight: 6.9990 chunk 85 optimal weight: 1.9990 chunk 68 optimal weight: 0.9980 chunk 24 optimal weight: 8.9990 chunk 65 optimal weight: 6.9990 chunk 11 optimal weight: 0.2980 chunk 48 optimal weight: 10.0000 chunk 113 optimal weight: 2.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1190 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.155755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.133003 restraints weight = 29588.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.137210 restraints weight = 18911.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.140098 restraints weight = 13326.465| |-----------------------------------------------------------------------------| r_work (final): 0.4021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6647 moved from start: 0.4158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11500 Z= 0.165 Angle : 0.565 9.139 15436 Z= 0.303 Chirality : 0.041 0.195 1666 Planarity : 0.005 0.156 1973 Dihedral : 4.443 23.526 1464 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.00 % Favored : 96.85 % Rotamer: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.23), residues: 1335 helix: 1.22 (0.18), residues: 884 sheet: -0.57 (0.98), residues: 27 loop : -0.04 (0.32), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 314 HIS 0.002 0.001 HIS A 119 PHE 0.033 0.002 PHE A 19 TYR 0.019 0.001 TYR A 382 ARG 0.013 0.001 ARG A 168 *********************** 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 338 residues out of total 1249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 338 time to evaluate : 1.414 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 55 ARG cc_start: 0.8370 (ttt180) cc_final: 0.7822 (ttt180) REVERT: A 152 VAL cc_start: 0.8558 (t) cc_final: 0.8278 (p) REVERT: A 197 TYR cc_start: 0.7171 (t80) cc_final: 0.6877 (t80) REVERT: A 306 PHE cc_start: 0.8733 (m-80) cc_final: 0.8211 (m-80) REVERT: A 309 LYS cc_start: 0.8751 (mtmm) cc_final: 0.8483 (mttt) REVERT: A 310 ARG cc_start: 0.8608 (mpt90) cc_final: 0.8359 (mmt90) REVERT: A 324 ASP cc_start: 0.6987 (t0) cc_final: 0.6686 (t0) REVERT: A 329 MET cc_start: 0.8338 (ptm) cc_final: 0.8095 (ptm) REVERT: A 349 PHE cc_start: 0.8426 (t80) cc_final: 0.7900 (t80) REVERT: A 362 GLU cc_start: 0.8206 (tt0) cc_final: 0.7345 (tp30) REVERT: A 386 ARG cc_start: 0.8306 (ptp90) cc_final: 0.7833 (ttp-110) REVERT: A 398 TYR cc_start: 0.8204 (t80) cc_final: 0.7935 (t80) REVERT: A 505 ILE cc_start: 0.9230 (mt) cc_final: 0.8861 (tp) REVERT: A 507 GLU cc_start: 0.8498 (mt-10) cc_final: 0.8046 (mt-10) REVERT: A 525 PHE cc_start: 0.7363 (t80) cc_final: 0.6930 (t80) REVERT: A 548 LEU cc_start: 0.8706 (mt) cc_final: 0.8320 (mt) REVERT: A 560 ASN cc_start: 0.8462 (t0) cc_final: 0.8253 (m110) REVERT: A 596 LYS cc_start: 0.8746 (mmpt) cc_final: 0.8475 (mmmt) REVERT: A 627 GLN cc_start: 0.8708 (tp40) cc_final: 0.8311 (tm-30) REVERT: A 662 GLU cc_start: 0.7314 (mm-30) cc_final: 0.6884 (mm-30) REVERT: A 672 TYR cc_start: 0.7804 (p90) cc_final: 0.7136 (p90) REVERT: A 680 TYR cc_start: 0.5466 (m-10) cc_final: 0.5184 (m-10) REVERT: A 725 ARG cc_start: 0.7775 (mmm160) cc_final: 0.7423 (mmm160) REVERT: A 746 GLN cc_start: 0.7973 (mp-120) cc_final: 0.7691 (mp10) REVERT: A 750 LEU cc_start: 0.8564 (mt) cc_final: 0.8284 (mm) REVERT: A 758 ASN cc_start: 0.8575 (m-40) cc_final: 0.8176 (m-40) REVERT: A 773 PHE cc_start: 0.8048 (t80) cc_final: 0.7673 (t80) REVERT: A 777 MET cc_start: 0.8223 (mtm) cc_final: 0.7068 (mtm) REVERT: A 784 MET cc_start: 0.7687 (mpp) cc_final: 0.6767 (mtt) REVERT: A 813 GLU cc_start: 0.7906 (mp0) cc_final: 0.7176 (mp0) REVERT: A 815 GLU cc_start: 0.8234 (tt0) cc_final: 0.7874 (tt0) REVERT: A 816 MET cc_start: 0.8867 (mtp) cc_final: 0.8404 (mtm) REVERT: A 819 ARG cc_start: 0.8015 (mtp-110) cc_final: 0.7514 (mtp-110) REVERT: A 822 GLN cc_start: 0.8452 (mt0) cc_final: 0.8072 (mt0) REVERT: A 826 LYS cc_start: 0.8525 (mtmt) cc_final: 0.8134 (ptmt) REVERT: A 849 ASP cc_start: 0.8271 (m-30) cc_final: 0.7940 (m-30) REVERT: A 855 LEU cc_start: 0.7308 (mt) cc_final: 0.7029 (mt) REVERT: A 858 CYS cc_start: 0.7513 (m) cc_final: 0.7122 (m) REVERT: A 888 PHE cc_start: 0.6987 (t80) cc_final: 0.6566 (t80) REVERT: A 908 MET cc_start: 0.7335 (mpp) cc_final: 0.6831 (ptp) REVERT: A 914 ASP cc_start: 0.6895 (p0) cc_final: 0.6529 (p0) REVERT: A 927 GLN cc_start: 0.8413 (tp-100) cc_final: 0.7938 (tm-30) REVERT: A 958 HIS cc_start: 0.7773 (m90) cc_final: 0.7505 (m90) REVERT: A 961 LYS cc_start: 0.8982 (tmtt) cc_final: 0.8534 (tmtt) REVERT: A 964 GLN cc_start: 0.9072 (tp-100) cc_final: 0.8729 (tp40) REVERT: A 978 LEU cc_start: 0.8860 (mm) cc_final: 0.8660 (mm) REVERT: A 979 MET cc_start: 0.8114 (mtm) cc_final: 0.7624 (mtm) REVERT: A 985 ASP cc_start: 0.8847 (t0) cc_final: 0.8502 (t0) REVERT: A 989 HIS cc_start: 0.7722 (m90) cc_final: 0.6848 (m90) REVERT: A 998 ASP cc_start: 0.8652 (m-30) cc_final: 0.8239 (m-30) REVERT: A 1010 HIS cc_start: 0.8351 (t70) cc_final: 0.8073 (t-170) REVERT: A 1012 MET cc_start: 0.8643 (ttt) cc_final: 0.8188 (ttt) REVERT: A 1028 GLU cc_start: 0.8031 (tm-30) cc_final: 0.7375 (tm-30) REVERT: A 1032 GLU cc_start: 0.8081 (tt0) cc_final: 0.7468 (tt0) REVERT: A 1033 PHE cc_start: 0.8517 (t80) cc_final: 0.8317 (t80) REVERT: A 1034 PHE cc_start: 0.8505 (m-80) cc_final: 0.7716 (m-80) REVERT: A 1053 ASN cc_start: 0.7507 (m110) cc_final: 0.7106 (m110) REVERT: A 1055 ILE cc_start: 0.8258 (mt) cc_final: 0.7826 (tp) REVERT: A 1058 LYS cc_start: 0.8315 (tppt) cc_final: 0.7967 (tppt) REVERT: A 1064 ASP cc_start: 0.8534 (m-30) cc_final: 0.8283 (m-30) REVERT: A 1068 LEU cc_start: 0.9178 (mt) cc_final: 0.8931 (mt) REVERT: A 1165 LEU cc_start: 0.8057 (mt) cc_final: 0.7793 (mt) REVERT: A 1177 LEU cc_start: 0.8654 (mt) cc_final: 0.8409 (pp) REVERT: A 1201 ASN cc_start: 0.6127 (t0) cc_final: 0.5844 (p0) REVERT: A 1208 GLU cc_start: 0.7592 (mp0) cc_final: 0.6860 (mp0) REVERT: A 1225 LYS cc_start: 0.8667 (mmpt) cc_final: 0.8407 (mmmt) REVERT: A 1242 GLN cc_start: 0.8252 (tp-100) cc_final: 0.7858 (tp-100) REVERT: A 1285 PHE cc_start: 0.7849 (t80) cc_final: 0.7630 (t80) REVERT: A 1288 LYS cc_start: 0.8072 (tptt) cc_final: 0.7775 (tppt) REVERT: A 1304 LYS cc_start: 0.8146 (ptpt) cc_final: 0.7808 (pptt) REVERT: A 1306 LEU cc_start: 0.8148 (mt) cc_final: 0.7876 (mt) REVERT: A 1313 LYS cc_start: 0.7680 (tttt) cc_final: 0.7312 (ptmm) REVERT: A 1314 LYS cc_start: 0.8445 (mmtt) cc_final: 0.7976 (mmtt) REVERT: A 1324 MET cc_start: 0.7465 (mmp) cc_final: 0.7022 (mmp) REVERT: A 1329 LYS cc_start: 0.8319 (mttp) cc_final: 0.7756 (mppt) REVERT: A 1434 LYS cc_start: 0.2214 (mttt) cc_final: 0.1997 (mmmm) REVERT: A 1435 GLU cc_start: 0.8284 (tt0) cc_final: 0.7925 (tt0) REVERT: A 1513 GLU cc_start: 0.7977 (pp20) cc_final: 0.7615 (pp20) REVERT: A1 22 LYS cc_start: 0.8045 (ptmm) cc_final: 0.7785 (ptmm) REVERT: A1 52 LYS cc_start: 0.8724 (tttt) cc_final: 0.8274 (tttt) REVERT: A1 78 ASP cc_start: 0.8952 (p0) cc_final: 0.8696 (p0) REVERT: A1 121 LEU cc_start: 0.8597 (mt) cc_final: 0.8270 (mt) REVERT: A1 141 LEU cc_start: 0.8536 (mt) cc_final: 0.8306 (mt) REVERT: A1 147 PHE cc_start: 0.5940 (m-80) cc_final: 0.5663 (m-10) REVERT: A1 173 LYS cc_start: 0.7711 (mptt) cc_final: 0.7333 (mptt) outliers start: 0 outliers final: 0 residues processed: 338 average time/residue: 0.2956 time to fit residues: 133.8297 Evaluate side-chains 301 residues out of total 1249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 301 time to evaluate : 1.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 84 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 24 optimal weight: 3.9990 chunk 2 optimal weight: 0.1980 chunk 64 optimal weight: 20.0000 chunk 115 optimal weight: 20.0000 chunk 67 optimal weight: 0.0970 chunk 92 optimal weight: 0.6980 chunk 72 optimal weight: 5.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 56 GLN ** A 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 980 GLN A1011 GLN A1190 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.156776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.133585 restraints weight = 29847.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.137850 restraints weight = 19393.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.140771 restraints weight = 13782.584| |-----------------------------------------------------------------------------| r_work (final): 0.4031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6636 moved from start: 0.4307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.058 11500 Z= 0.159 Angle : 0.561 9.133 15436 Z= 0.300 Chirality : 0.041 0.178 1666 Planarity : 0.005 0.110 1973 Dihedral : 4.269 22.505 1464 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.15 % Allowed : 2.92 % Favored : 96.93 % Rotamer: Outliers : 0.08 % Allowed : 0.48 % Favored : 99.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.24), residues: 1335 helix: 1.27 (0.18), residues: 878 sheet: -0.60 (0.98), residues: 27 loop : 0.09 (0.32), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 314 HIS 0.002 0.000 HIS A1082 PHE 0.031 0.001 PHE A 790 TYR 0.015 0.001 TYR A 382 ARG 0.014 0.001 ARG A 168 *********************** 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 333 residues out of total 1249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 332 time to evaluate : 1.281 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 55 ARG cc_start: 0.8337 (ttt180) cc_final: 0.7921 (ttt180) REVERT: A 119 HIS cc_start: 0.7304 (t-90) cc_final: 0.7087 (t-90) REVERT: A 152 VAL cc_start: 0.8665 (t) cc_final: 0.8417 (p) REVERT: A 197 TYR cc_start: 0.7176 (t80) cc_final: 0.6931 (t80) REVERT: A 201 ASN cc_start: 0.7299 (m-40) cc_final: 0.6244 (m-40) REVERT: A 306 PHE cc_start: 0.8739 (m-80) cc_final: 0.8155 (m-80) REVERT: A 309 LYS cc_start: 0.8765 (mtmm) cc_final: 0.8476 (mttt) REVERT: A 310 ARG cc_start: 0.8589 (mpt90) cc_final: 0.8316 (mmt90) REVERT: A 324 ASP cc_start: 0.6949 (t0) cc_final: 0.6644 (t0) REVERT: A 329 MET cc_start: 0.8361 (ptm) cc_final: 0.8128 (ptm) REVERT: A 349 PHE cc_start: 0.8487 (t80) cc_final: 0.7938 (t80) REVERT: A 362 GLU cc_start: 0.8277 (tt0) cc_final: 0.7411 (tp30) REVERT: A 386 ARG cc_start: 0.8266 (ptp90) cc_final: 0.7714 (ttp-110) REVERT: A 398 TYR cc_start: 0.8212 (t80) cc_final: 0.8002 (t80) REVERT: A 503 ASN cc_start: 0.8504 (m110) cc_final: 0.8265 (m110) REVERT: A 505 ILE cc_start: 0.9240 (mt) cc_final: 0.8896 (tp) REVERT: A 507 GLU cc_start: 0.8489 (mt-10) cc_final: 0.8021 (mt-10) REVERT: A 525 PHE cc_start: 0.7394 (t80) cc_final: 0.6951 (t80) REVERT: A 548 LEU cc_start: 0.8700 (mt) cc_final: 0.8307 (mt) REVERT: A 596 LYS cc_start: 0.8737 (mmpt) cc_final: 0.8442 (mmmt) REVERT: A 627 GLN cc_start: 0.8711 (tp40) cc_final: 0.8302 (tm-30) REVERT: A 662 GLU cc_start: 0.7329 (mm-30) cc_final: 0.6874 (mm-30) REVERT: A 672 TYR cc_start: 0.7873 (p90) cc_final: 0.7185 (p90) REVERT: A 746 GLN cc_start: 0.7956 (mp-120) cc_final: 0.7667 (mp10) REVERT: A 750 LEU cc_start: 0.8637 (mt) cc_final: 0.8393 (mm) REVERT: A 758 ASN cc_start: 0.8519 (m-40) cc_final: 0.8151 (m-40) REVERT: A 773 PHE cc_start: 0.7927 (t80) cc_final: 0.7281 (t80) REVERT: A 777 MET cc_start: 0.8209 (mtm) cc_final: 0.7260 (mtm) REVERT: A 784 MET cc_start: 0.7651 (mpp) cc_final: 0.6704 (mtt) REVERT: A 813 GLU cc_start: 0.7837 (mp0) cc_final: 0.7547 (mp0) REVERT: A 815 GLU cc_start: 0.8238 (tt0) cc_final: 0.7894 (tt0) REVERT: A 816 MET cc_start: 0.8821 (mtp) cc_final: 0.8439 (mtm) REVERT: A 819 ARG cc_start: 0.7987 (mtp-110) cc_final: 0.7466 (mtp-110) REVERT: A 822 GLN cc_start: 0.8427 (mt0) cc_final: 0.7995 (mt0) REVERT: A 825 LYS cc_start: 0.8429 (mmmt) cc_final: 0.8103 (mmmt) REVERT: A 826 LYS cc_start: 0.8540 (mtmt) cc_final: 0.8016 (ttmt) REVERT: A 833 ASP cc_start: 0.8025 (m-30) cc_final: 0.7795 (m-30) REVERT: A 849 ASP cc_start: 0.8171 (m-30) cc_final: 0.7919 (m-30) REVERT: A 855 LEU cc_start: 0.7260 (mt) cc_final: 0.7026 (mt) REVERT: A 856 LYS cc_start: 0.8020 (pttm) cc_final: 0.7251 (tppt) REVERT: A 858 CYS cc_start: 0.7425 (m) cc_final: 0.7022 (m) REVERT: A 888 PHE cc_start: 0.7015 (t80) cc_final: 0.6564 (t80) REVERT: A 908 MET cc_start: 0.7426 (mpp) cc_final: 0.6866 (ptp) REVERT: A 914 ASP cc_start: 0.6779 (p0) cc_final: 0.6348 (p0) REVERT: A 921 TRP cc_start: 0.7378 (p-90) cc_final: 0.7170 (p-90) REVERT: A 927 GLN cc_start: 0.8451 (tp-100) cc_final: 0.8050 (tm-30) REVERT: A 931 LEU cc_start: 0.6963 (mt) cc_final: 0.6743 (mt) REVERT: A 958 HIS cc_start: 0.7772 (m90) cc_final: 0.7508 (m90) REVERT: A 961 LYS cc_start: 0.8990 (tmtt) cc_final: 0.8541 (tmtt) REVERT: A 964 GLN cc_start: 0.9029 (tp-100) cc_final: 0.8690 (tp40) REVERT: A 979 MET cc_start: 0.7803 (mtm) cc_final: 0.7358 (mtm) REVERT: A 982 LEU cc_start: 0.7948 (tp) cc_final: 0.7745 (tp) REVERT: A 985 ASP cc_start: 0.8816 (t0) cc_final: 0.8239 (m-30) REVERT: A 989 HIS cc_start: 0.7739 (m90) cc_final: 0.6848 (m90) REVERT: A 998 ASP cc_start: 0.8669 (m-30) cc_final: 0.8246 (m-30) REVERT: A 1009 GLU cc_start: 0.8576 (mt-10) cc_final: 0.8007 (mt-10) REVERT: A 1010 HIS cc_start: 0.8335 (t70) cc_final: 0.7926 (t-170) REVERT: A 1011 GLN cc_start: 0.8463 (tm130) cc_final: 0.8183 (tp40) REVERT: A 1014 GLU cc_start: 0.8175 (pm20) cc_final: 0.7674 (pm20) REVERT: A 1028 GLU cc_start: 0.7953 (tm-30) cc_final: 0.7368 (tm-30) REVERT: A 1032 GLU cc_start: 0.8016 (tt0) cc_final: 0.7417 (tt0) REVERT: A 1034 PHE cc_start: 0.8485 (m-80) cc_final: 0.7658 (m-80) REVERT: A 1044 GLU cc_start: 0.7705 (mt-10) cc_final: 0.6968 (mt-10) REVERT: A 1053 ASN cc_start: 0.7412 (m110) cc_final: 0.7017 (m110) REVERT: A 1055 ILE cc_start: 0.8219 (mt) cc_final: 0.7796 (tp) REVERT: A 1058 LYS cc_start: 0.8301 (tppt) cc_final: 0.7901 (tppt) REVERT: A 1064 ASP cc_start: 0.8560 (m-30) cc_final: 0.8319 (m-30) REVERT: A 1068 LEU cc_start: 0.9157 (mt) cc_final: 0.8930 (mt) REVERT: A 1088 PHE cc_start: 0.8108 (m-10) cc_final: 0.7858 (m-10) REVERT: A 1167 ARG cc_start: 0.8363 (mtt180) cc_final: 0.7835 (mtt180) REVERT: A 1177 LEU cc_start: 0.8715 (mt) cc_final: 0.8494 (pp) REVERT: A 1201 ASN cc_start: 0.6139 (t0) cc_final: 0.5833 (p0) REVERT: A 1208 GLU cc_start: 0.7629 (mp0) cc_final: 0.6944 (mp0) REVERT: A 1225 LYS cc_start: 0.8668 (mmpt) cc_final: 0.8398 (mmmt) REVERT: A 1242 GLN cc_start: 0.8242 (tp-100) cc_final: 0.7809 (tp-100) REVERT: A 1288 LYS cc_start: 0.8082 (tptt) cc_final: 0.7796 (tppt) REVERT: A 1304 LYS cc_start: 0.8086 (ptpt) cc_final: 0.7724 (pptt) REVERT: A 1306 LEU cc_start: 0.8117 (mt) cc_final: 0.7872 (mt) REVERT: A 1313 LYS cc_start: 0.7698 (tttt) cc_final: 0.7294 (ptmm) REVERT: A 1314 LYS cc_start: 0.8499 (mmtt) cc_final: 0.8010 (mmtt) REVERT: A 1324 MET cc_start: 0.7346 (mmp) cc_final: 0.6972 (mmp) REVERT: A 1327 PHE cc_start: 0.8165 (m-80) cc_final: 0.7965 (m-80) REVERT: A 1329 LYS cc_start: 0.8291 (mttp) cc_final: 0.7759 (mppt) REVERT: A 1434 LYS cc_start: 0.2306 (mttt) cc_final: 0.2086 (mmmm) REVERT: A 1435 GLU cc_start: 0.8275 (tt0) cc_final: 0.7930 (tt0) REVERT: A 1436 PHE cc_start: 0.8387 (t80) cc_final: 0.8044 (t80) REVERT: A 1450 LEU cc_start: 0.7954 (mt) cc_final: 0.7750 (pp) REVERT: A 1513 GLU cc_start: 0.7997 (pp20) cc_final: 0.7630 (pp20) REVERT: A1 22 LYS cc_start: 0.8010 (ptmm) cc_final: 0.7768 (ptmm) REVERT: A1 52 LYS cc_start: 0.8719 (tttt) cc_final: 0.8263 (tttt) REVERT: A1 78 ASP cc_start: 0.8931 (p0) cc_final: 0.8672 (p0) REVERT: A1 121 LEU cc_start: 0.8591 (mt) cc_final: 0.8333 (mt) REVERT: A1 141 LEU cc_start: 0.8509 (mt) cc_final: 0.8291 (mt) REVERT: A1 147 PHE cc_start: 0.5822 (m-80) cc_final: 0.5598 (m-10) REVERT: A1 173 LYS cc_start: 0.7702 (mptt) cc_final: 0.7289 (mptt) outliers start: 1 outliers final: 0 residues processed: 333 average time/residue: 0.3036 time to fit residues: 134.9766 Evaluate side-chains 297 residues out of total 1249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 297 time to evaluate : 1.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 101 optimal weight: 7.9990 chunk 78 optimal weight: 7.9990 chunk 63 optimal weight: 6.9990 chunk 48 optimal weight: 10.0000 chunk 93 optimal weight: 10.0000 chunk 104 optimal weight: 8.9990 chunk 17 optimal weight: 0.8980 chunk 57 optimal weight: 1.9990 chunk 116 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 56 GLN ** A 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 942 HIS A1190 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.154045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.130873 restraints weight = 29811.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.135113 restraints weight = 19390.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.138088 restraints weight = 13818.067| |-----------------------------------------------------------------------------| r_work (final): 0.3995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6704 moved from start: 0.4575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 11500 Z= 0.206 Angle : 0.596 8.694 15436 Z= 0.325 Chirality : 0.043 0.212 1666 Planarity : 0.005 0.100 1973 Dihedral : 4.390 21.775 1464 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.37 % Favored : 96.48 % Rotamer: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.24), residues: 1335 helix: 1.13 (0.18), residues: 879 sheet: -0.48 (1.03), residues: 27 loop : 0.01 (0.33), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.089 0.003 TRP A1069 HIS 0.005 0.001 HIS A 193 PHE 0.025 0.002 PHE A 790 TYR 0.016 0.001 TYR A 680 ARG 0.015 0.001 ARG A 168 ********************** 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 332 residues out of total 1249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 332 time to evaluate : 1.226 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 56 GLN cc_start: 0.8399 (mm110) cc_final: 0.8059 (tp-100) REVERT: A 119 HIS cc_start: 0.7345 (t-90) cc_final: 0.7115 (t-90) REVERT: A 197 TYR cc_start: 0.7311 (t80) cc_final: 0.7038 (t80) REVERT: A 201 ASN cc_start: 0.7374 (m-40) cc_final: 0.6555 (m-40) REVERT: A 207 LYS cc_start: 0.7328 (pptt) cc_final: 0.6934 (pptt) REVERT: A 306 PHE cc_start: 0.8768 (m-80) cc_final: 0.8151 (m-80) REVERT: A 309 LYS cc_start: 0.8746 (mtmm) cc_final: 0.8526 (mttt) REVERT: A 310 ARG cc_start: 0.8605 (mpt90) cc_final: 0.8373 (mmt90) REVERT: A 324 ASP cc_start: 0.7035 (t0) cc_final: 0.6729 (t0) REVERT: A 329 MET cc_start: 0.8368 (ptm) cc_final: 0.8120 (ptm) REVERT: A 349 PHE cc_start: 0.8531 (t80) cc_final: 0.7958 (t80) REVERT: A 362 GLU cc_start: 0.8287 (tt0) cc_final: 0.7417 (tp30) REVERT: A 382 TYR cc_start: 0.6208 (t80) cc_final: 0.5928 (t80) REVERT: A 386 ARG cc_start: 0.8385 (ptp90) cc_final: 0.7727 (ttp-110) REVERT: A 395 HIS cc_start: 0.8358 (m-70) cc_final: 0.8119 (m-70) REVERT: A 398 TYR cc_start: 0.8273 (t80) cc_final: 0.7985 (t80) REVERT: A 492 ILE cc_start: 0.6791 (mm) cc_final: 0.6577 (mt) REVERT: A 505 ILE cc_start: 0.9264 (mt) cc_final: 0.8916 (tp) REVERT: A 507 GLU cc_start: 0.8544 (mt-10) cc_final: 0.8094 (mt-10) REVERT: A 548 LEU cc_start: 0.8676 (mt) cc_final: 0.8319 (mt) REVERT: A 560 ASN cc_start: 0.8867 (m110) cc_final: 0.8420 (m110) REVERT: A 596 LYS cc_start: 0.8754 (mmpt) cc_final: 0.8466 (mmmt) REVERT: A 627 GLN cc_start: 0.8735 (tp40) cc_final: 0.8324 (tm-30) REVERT: A 662 GLU cc_start: 0.7361 (mm-30) cc_final: 0.6930 (mm-30) REVERT: A 672 TYR cc_start: 0.7938 (p90) cc_final: 0.7317 (p90) REVERT: A 725 ARG cc_start: 0.7669 (mmm160) cc_final: 0.7468 (mmm-85) REVERT: A 758 ASN cc_start: 0.8623 (m-40) cc_final: 0.8226 (m-40) REVERT: A 773 PHE cc_start: 0.7976 (t80) cc_final: 0.7280 (t80) REVERT: A 777 MET cc_start: 0.8300 (mtm) cc_final: 0.7357 (mtm) REVERT: A 784 MET cc_start: 0.7649 (mpp) cc_final: 0.6730 (mtt) REVERT: A 813 GLU cc_start: 0.7961 (mp0) cc_final: 0.7286 (mp0) REVERT: A 815 GLU cc_start: 0.8290 (tt0) cc_final: 0.7965 (tt0) REVERT: A 816 MET cc_start: 0.8928 (mtp) cc_final: 0.8584 (mtm) REVERT: A 819 ARG cc_start: 0.8079 (mtp-110) cc_final: 0.7557 (mtp-110) REVERT: A 822 GLN cc_start: 0.8501 (mt0) cc_final: 0.8073 (mt0) REVERT: A 823 TRP cc_start: 0.7683 (t60) cc_final: 0.7385 (t60) REVERT: A 825 LYS cc_start: 0.8518 (mmmt) cc_final: 0.8250 (mmmt) REVERT: A 826 LYS cc_start: 0.8624 (mtmt) cc_final: 0.8178 (ttmt) REVERT: A 855 LEU cc_start: 0.7573 (mt) cc_final: 0.7182 (mt) REVERT: A 858 CYS cc_start: 0.7759 (m) cc_final: 0.7470 (m) REVERT: A 908 MET cc_start: 0.7337 (mpp) cc_final: 0.6930 (ptp) REVERT: A 914 ASP cc_start: 0.6990 (p0) cc_final: 0.6640 (p0) REVERT: A 961 LYS cc_start: 0.9003 (tmtt) cc_final: 0.8499 (tmtt) REVERT: A 964 GLN cc_start: 0.9090 (tp-100) cc_final: 0.8791 (tp-100) REVERT: A 965 ASP cc_start: 0.8218 (p0) cc_final: 0.7923 (p0) REVERT: A 979 MET cc_start: 0.8157 (mtm) cc_final: 0.7684 (mtm) REVERT: A 985 ASP cc_start: 0.8804 (t0) cc_final: 0.8277 (m-30) REVERT: A 989 HIS cc_start: 0.7936 (m90) cc_final: 0.7178 (m90) REVERT: A 998 ASP cc_start: 0.8726 (m-30) cc_final: 0.8094 (m-30) REVERT: A 1010 HIS cc_start: 0.8326 (t70) cc_final: 0.7959 (t-170) REVERT: A 1033 PHE cc_start: 0.8643 (t80) cc_final: 0.8416 (t80) REVERT: A 1034 PHE cc_start: 0.8491 (m-80) cc_final: 0.7992 (m-80) REVERT: A 1053 ASN cc_start: 0.7673 (m110) cc_final: 0.7212 (m110) REVERT: A 1055 ILE cc_start: 0.8396 (mt) cc_final: 0.8000 (tp) REVERT: A 1058 LYS cc_start: 0.8297 (tppt) cc_final: 0.7701 (tppt) REVERT: A 1064 ASP cc_start: 0.8577 (m-30) cc_final: 0.8263 (m-30) REVERT: A 1068 LEU cc_start: 0.9124 (mt) cc_final: 0.8907 (mt) REVERT: A 1069 TRP cc_start: 0.6938 (t-100) cc_final: 0.6469 (t-100) REVERT: A 1165 LEU cc_start: 0.8054 (mt) cc_final: 0.7793 (mt) REVERT: A 1167 ARG cc_start: 0.8369 (mtt180) cc_final: 0.7814 (mtt180) REVERT: A 1177 LEU cc_start: 0.8677 (mt) cc_final: 0.8467 (pp) REVERT: A 1183 ASN cc_start: 0.5956 (m-40) cc_final: 0.5699 (m-40) REVERT: A 1201 ASN cc_start: 0.6190 (t0) cc_final: 0.5938 (p0) REVERT: A 1208 GLU cc_start: 0.7621 (mp0) cc_final: 0.6898 (mp0) REVERT: A 1225 LYS cc_start: 0.8698 (mmpt) cc_final: 0.8417 (mmmt) REVERT: A 1242 GLN cc_start: 0.8352 (tp-100) cc_final: 0.7961 (tp-100) REVERT: A 1285 PHE cc_start: 0.8188 (t80) cc_final: 0.7957 (t80) REVERT: A 1288 LYS cc_start: 0.8126 (tptt) cc_final: 0.7845 (tppt) REVERT: A 1304 LYS cc_start: 0.8162 (ptpt) cc_final: 0.7739 (pptt) REVERT: A 1313 LYS cc_start: 0.7700 (tttt) cc_final: 0.7299 (ptmm) REVERT: A 1314 LYS cc_start: 0.8472 (mmtt) cc_final: 0.7973 (mmtt) REVERT: A 1324 MET cc_start: 0.7635 (mmp) cc_final: 0.7231 (mmp) REVERT: A 1329 LYS cc_start: 0.8386 (mttp) cc_final: 0.7850 (mppt) REVERT: A 1434 LYS cc_start: 0.2288 (mttt) cc_final: 0.2049 (mmmm) REVERT: A 1435 GLU cc_start: 0.8353 (tt0) cc_final: 0.8054 (tt0) REVERT: A 1436 PHE cc_start: 0.8371 (t80) cc_final: 0.8018 (t80) REVERT: A1 22 LYS cc_start: 0.8055 (ptmm) cc_final: 0.7842 (ptmm) REVERT: A1 52 LYS cc_start: 0.8737 (tttt) cc_final: 0.8302 (tttt) REVERT: A1 78 ASP cc_start: 0.8974 (p0) cc_final: 0.8719 (p0) REVERT: A1 121 LEU cc_start: 0.8674 (mt) cc_final: 0.8389 (mt) REVERT: A1 141 LEU cc_start: 0.8541 (mt) cc_final: 0.8304 (mt) REVERT: A1 147 PHE cc_start: 0.5888 (m-80) cc_final: 0.5688 (m-10) REVERT: A1 168 PRO cc_start: 0.7566 (Cg_exo) cc_final: 0.7363 (Cg_endo) REVERT: A1 173 LYS cc_start: 0.7771 (mptt) cc_final: 0.7379 (mptt) outliers start: 0 outliers final: 0 residues processed: 332 average time/residue: 0.3008 time to fit residues: 134.8154 Evaluate side-chains 304 residues out of total 1249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 304 time to evaluate : 1.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 89 optimal weight: 3.9990 chunk 59 optimal weight: 0.0570 chunk 111 optimal weight: 7.9990 chunk 57 optimal weight: 3.9990 chunk 3 optimal weight: 5.9990 chunk 121 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 85 optimal weight: 0.9990 chunk 84 optimal weight: 0.9990 chunk 17 optimal weight: 0.0670 chunk 5 optimal weight: 3.9990 overall best weight: 0.8242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 169 GLN ** A 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1036 GLN A1190 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.157125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.133866 restraints weight = 29992.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.138082 restraints weight = 19550.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.141078 restraints weight = 13975.600| |-----------------------------------------------------------------------------| r_work (final): 0.4031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6645 moved from start: 0.4664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 11500 Z= 0.159 Angle : 0.572 8.150 15436 Z= 0.308 Chirality : 0.042 0.178 1666 Planarity : 0.004 0.071 1973 Dihedral : 4.235 21.832 1464 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.15 % Allowed : 2.55 % Favored : 97.30 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.24), residues: 1335 helix: 1.25 (0.18), residues: 874 sheet: -0.48 (1.00), residues: 27 loop : 0.04 (0.33), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.002 TRP A1069 HIS 0.004 0.001 HIS A 67 PHE 0.044 0.001 PHE A 156 TYR 0.017 0.001 TYR A 52 ARG 0.004 0.000 ARGA1 156 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4300.80 seconds wall clock time: 79 minutes 44.51 seconds (4784.51 seconds total)