Starting phenix.real_space_refine on Fri Sep 11 19:54:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9s4u_54583/09_2026/9s4u_54583.cif Found real_map, /net/cci-nas-00/data/ceres_data/9s4u_54583/09_2026/9s4u_54583.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9s4u_54583/09_2026/9s4u_54583.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9s4u_54583/09_2026/9s4u_54583.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9s4u_54583/09_2026/9s4u_54583.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9s4u_54583/09_2026/9s4u_54583.map" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.011 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians P 5 5.49 5 Mg 1 5.21 5 S 60 5.16 5 Cl 2 4.86 5 C 7118 2.51 5 N 1784 2.21 5 O 1943 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10913 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 10560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1319, 10560 Classifications: {'peptide': 1319} Link IDs: {'PCIS': 1, 'PTRANS': 47, 'TRANS': 1270} Chain breaks: 8 Chain: "A" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Classifications: {'peptide': 1} Chain: "A" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 344 Unusual residues: {' MG': 1, '1YN': 1, 'ADP': 1, 'ATP': 1, 'ERG': 8} Classifications: {'undetermined': 12, 'water': 4} Link IDs: {None: 15} Time building chain proxies: 1.87, per 1000 atoms: 0.17 Number of scatterers: 10913 At special positions: 0 Unit cell: (85.176, 103.428, 150.579, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Cl 2 17.00 S 60 16.00 P 5 15.00 Mg 1 11.99 O 1943 8.00 N 1784 7.00 C 7118 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 711 " - pdb=" SG CYS A 731 " distance=2.03 Simple disulfide: pdb=" SG CYS A1399 " - pdb=" SG CYS A1443 " distance=2.03 Simple disulfide: pdb=" SG CYS A1415 " - pdb=" SG CYS A1440 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.68 Conformation dependent library (CDL) restraints added in 354.4 milliseconds 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2474 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 9 sheets defined 62.1% alpha, 7.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'A' and resid 31 through 51 removed outlier: 3.694A pdb=" N VAL A 35 " --> pdb=" O PHE A 31 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N SER A 51 " --> pdb=" O THR A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 100 Processing helix chain 'A' and resid 187 through 196 Processing helix chain 'A' and resid 216 through 224 Processing helix chain 'A' and resid 242 through 255 Processing helix chain 'A' and resid 265 through 280 Processing helix chain 'A' and resid 299 through 314 Processing helix chain 'A' and resid 329 through 347 Processing helix chain 'A' and resid 359 through 366 Processing helix chain 'A' and resid 384 through 394 removed outlier: 4.662A pdb=" N GLU A 388 " --> pdb=" O GLY A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 411 removed outlier: 4.092A pdb=" N THR A 411 " --> pdb=" O LEU A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 426 removed outlier: 3.578A pdb=" N ARG A 425 " --> pdb=" O ASP A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 443 Processing helix chain 'A' and resid 443 through 458 Processing helix chain 'A' and resid 489 through 508 Processing helix chain 'A' and resid 510 through 530 removed outlier: 3.856A pdb=" N ASN A 519 " --> pdb=" O MET A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 540 No H-bonds generated for 'chain 'A' and resid 538 through 540' Processing helix chain 'A' and resid 541 through 559 removed outlier: 3.600A pdb=" N ALA A 557 " --> pdb=" O VAL A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 570 removed outlier: 4.073A pdb=" N SER A 566 " --> pdb=" O LEU A 562 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 580 Processing helix chain 'A' and resid 584 through 615 Proline residue: A 598 - end of helix Processing helix chain 'A' and resid 620 through 648 Processing helix chain 'A' and resid 651 through 669 removed outlier: 4.108A pdb=" N VAL A 657 " --> pdb=" O SER A 653 " (cutoff:3.500A) Proline residue: A 658 - end of helix Processing helix chain 'A' and resid 680 through 682 No H-bonds generated for 'chain 'A' and resid 680 through 682' Processing helix chain 'A' and resid 683 through 690 Processing helix chain 'A' and resid 690 through 705 removed outlier: 3.783A pdb=" N TYR A 694 " --> pdb=" O ASN A 690 " (cutoff:3.500A) Processing helix chain 'A' and resid 718 through 722 removed outlier: 3.506A pdb=" N ASN A 722 " --> pdb=" O SER A 719 " (cutoff:3.500A) Processing helix chain 'A' and resid 725 through 729 Processing helix chain 'A' and resid 744 through 752 Processing helix chain 'A' and resid 756 through 759 Processing helix chain 'A' and resid 760 through 784 removed outlier: 4.302A pdb=" N PHE A 764 " --> pdb=" O LYS A 760 " (cutoff:3.500A) Processing helix chain 'A' and resid 798 through 803 removed outlier: 3.922A pdb=" N VAL A 802 " --> pdb=" O GLN A 799 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ARG A 803 " --> pdb=" O ASN A 800 " (cutoff:3.500A) Processing helix chain 'A' and resid 898 through 907 Processing helix chain 'A' and resid 948 through 961 Processing helix chain 'A' and resid 966 through 981 Processing helix chain 'A' and resid 983 through 987 removed outlier: 3.555A pdb=" N ALA A 987 " --> pdb=" O GLU A 984 " (cutoff:3.500A) Processing helix chain 'A' and resid 999 through 1014 removed outlier: 3.732A pdb=" N ALA A1014 " --> pdb=" O VAL A1010 " (cutoff:3.500A) Processing helix chain 'A' and resid 1030 through 1048 Processing helix chain 'A' and resid 1061 through 1066 removed outlier: 4.025A pdb=" N PHE A1066 " --> pdb=" O LEU A1062 " (cutoff:3.500A) Processing helix chain 'A' and resid 1085 through 1087 No H-bonds generated for 'chain 'A' and resid 1085 through 1087' Processing helix chain 'A' and resid 1088 through 1097 Processing helix chain 'A' and resid 1108 through 1118 Processing helix chain 'A' and resid 1128 through 1136 Processing helix chain 'A' and resid 1136 through 1153 Processing helix chain 'A' and resid 1154 through 1156 No H-bonds generated for 'chain 'A' and resid 1154 through 1156' Processing helix chain 'A' and resid 1171 through 1189 Processing helix chain 'A' and resid 1190 through 1212 removed outlier: 4.048A pdb=" N SER A1196 " --> pdb=" O ASP A1192 " (cutoff:3.500A) Processing helix chain 'A' and resid 1218 through 1233 Processing helix chain 'A' and resid 1235 through 1257 removed outlier: 3.821A pdb=" N LEU A1239 " --> pdb=" O ILE A1235 " (cutoff:3.500A) Proline residue: A1245 - end of helix Processing helix chain 'A' and resid 1265 through 1297 removed outlier: 3.589A pdb=" N GLU A1277 " --> pdb=" O GLN A1273 " (cutoff:3.500A) Proline residue: A1279 - end of helix removed outlier: 4.051A pdb=" N TYR A1294 " --> pdb=" O VAL A1290 " (cutoff:3.500A) Processing helix chain 'A' and resid 1297 through 1305 removed outlier: 4.137A pdb=" N ASN A1301 " --> pdb=" O GLY A1297 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA A1305 " --> pdb=" O ASN A1301 " (cutoff:3.500A) Processing helix chain 'A' and resid 1307 through 1337 removed outlier: 4.473A pdb=" N PHE A1336 " --> pdb=" O PHE A1332 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ASN A1337 " --> pdb=" O CYS A1333 " (cutoff:3.500A) Processing helix chain 'A' and resid 1339 through 1357 removed outlier: 3.544A pdb=" N ALA A1343 " --> pdb=" O VAL A1339 " (cutoff:3.500A) Processing helix chain 'A' and resid 1368 through 1370 No H-bonds generated for 'chain 'A' and resid 1368 through 1370' Processing helix chain 'A' and resid 1371 through 1378 Processing helix chain 'A' and resid 1378 through 1392 removed outlier: 4.371A pdb=" N TYR A1382 " --> pdb=" O SER A1378 " (cutoff:3.500A) Processing helix chain 'A' and resid 1414 through 1427 Proline residue: A1421 - end of helix Processing helix chain 'A' and resid 1447 through 1455 removed outlier: 3.829A pdb=" N PHE A1451 " --> pdb=" O HIS A1447 " (cutoff:3.500A) Processing helix chain 'A' and resid 1458 through 1460 No H-bonds generated for 'chain 'A' and resid 1458 through 1460' Processing helix chain 'A' and resid 1461 through 1489 removed outlier: 3.615A pdb=" N VAL A1489 " --> pdb=" O TRP A1485 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 170 through 172 removed outlier: 3.544A pdb=" N TYR A 116 " --> pdb=" O SER A 211 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 163 through 165 Processing sheet with id=AA3, first strand: chain 'A' and resid 228 through 232 removed outlier: 6.641A pdb=" N VAL A 229 " --> pdb=" O CYS A 320 " (cutoff:3.500A) removed outlier: 8.130A pdb=" N ASP A 322 " --> pdb=" O VAL A 229 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N ASN A 231 " --> pdb=" O ASP A 322 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N LEU A 178 " --> pdb=" O VAL A 353 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N LEU A 177 " --> pdb=" O LYS A 368 " (cutoff:3.500A) removed outlier: 7.979A pdb=" N CYS A 370 " --> pdb=" O LEU A 177 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N VAL A 179 " --> pdb=" O CYS A 370 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N LEU A 372 " --> pdb=" O VAL A 179 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N LEU A 181 " --> pdb=" O LEU A 372 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N VAL A 369 " --> pdb=" O PHE A 380 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N PHE A 380 " --> pdb=" O VAL A 369 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N VAL A 371 " --> pdb=" O ILE A 378 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 709 through 710 Processing sheet with id=AA5, first strand: chain 'A' and resid 714 through 715 Processing sheet with id=AA6, first strand: chain 'A' and resid 871 through 883 removed outlier: 6.036A pdb=" N ARG A 873 " --> pdb=" O ILE A 868 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N ILE A 868 " --> pdb=" O ARG A 873 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ILE A 875 " --> pdb=" O VAL A 866 " (cutoff:3.500A) removed outlier: 8.567A pdb=" N VAL A 866 " --> pdb=" O ILE A 875 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N ASN A 877 " --> pdb=" O TYR A 864 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N TYR A 864 " --> pdb=" O ASN A 877 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N GLY A 881 " --> pdb=" O ARG A 860 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N ARG A 860 " --> pdb=" O GLY A 881 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N VAL A 883 " --> pdb=" O HIS A 858 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N HIS A 858 " --> pdb=" O VAL A 883 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N LEU A 862 " --> pdb=" O THR A 916 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N THR A 916 " --> pdb=" O LEU A 862 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N TYR A 864 " --> pdb=" O VAL A 914 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N VAL A 914 " --> pdb=" O TYR A 864 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 934 through 937 removed outlier: 5.931A pdb=" N GLY A 935 " --> pdb=" O PHE A1021 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LYS A1077 " --> pdb=" O GLN A1073 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 992 through 993 Processing sheet with id=AA9, first strand: chain 'A' and resid 1430 through 1431 586 hydrogen bonds defined for protein. 1707 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: 1.99 Time building geometry restraints manager: 0.87 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: 3256 1.34 - 1.46: 1939 1.46 - 1.57: 5915 1.57 - 1.69: 8 1.69 - 1.81: 95 Bond restraints: 11213 Sorted by residual: bond pdb=" C23 1YN A1605 " pdb=" N20 1YN A1605 " ideal model delta sigma weight residual 1.413 1.386 0.027 2.00e-02 2.50e+03 1.83e+00 bond pdb=" CB ASP A 706 " pdb=" CG ASP A 706 " ideal model delta sigma weight residual 1.516 1.546 -0.030 2.50e-02 1.60e+03 1.48e+00 bond pdb=" C4 ADP A1604 " pdb=" C5 ADP A1604 " ideal model delta sigma weight residual 1.490 1.469 0.021 2.00e-02 2.50e+03 1.06e+00 bond pdb=" CA ASP A 706 " pdb=" CB ASP A 706 " ideal model delta sigma weight residual 1.530 1.547 -0.017 1.69e-02 3.50e+03 9.81e-01 bond pdb=" C02 1YN A1605 " pdb=" C03 1YN A1605 " ideal model delta sigma weight residual 1.531 1.512 0.019 2.00e-02 2.50e+03 9.36e-01 ... (remaining 11208 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.61: 15244 5.61 - 11.21: 14 11.21 - 16.82: 2 16.82 - 22.42: 1 22.42 - 28.03: 2 Bond angle restraints: 15263 Sorted by residual: angle pdb=" C19 ERG A1610 " pdb=" C10 ERG A1610 " pdb=" C9 ERG A1610 " ideal model delta sigma weight residual 111.82 83.79 28.03 3.00e+00 1.11e-01 8.73e+01 angle pdb=" C1 ERG A1610 " pdb=" C10 ERG A1610 " pdb=" C19 ERG A1610 " ideal model delta sigma weight residual 110.23 84.60 25.63 3.00e+00 1.11e-01 7.30e+01 angle pdb=" C19 ERG A1610 " pdb=" C10 ERG A1610 " pdb=" C5 ERG A1610 " ideal model delta sigma weight residual 105.59 84.62 20.97 3.00e+00 1.11e-01 4.89e+01 angle pdb=" C1 ERG A1610 " pdb=" C10 ERG A1610 " pdb=" C9 ERG A1610 " ideal model delta sigma weight residual 107.89 121.63 -13.74 3.00e+00 1.11e-01 2.10e+01 angle pdb=" CA LEU A1019 " pdb=" CB LEU A1019 " pdb=" CG LEU A1019 " ideal model delta sigma weight residual 116.30 129.72 -13.42 3.50e+00 8.16e-02 1.47e+01 ... (remaining 15258 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.86: 6738 34.86 - 69.73: 218 69.73 - 104.59: 33 104.59 - 139.45: 2 139.45 - 174.32: 5 Dihedral angle restraints: 6996 sinusoidal: 3142 harmonic: 3854 Sorted by residual: dihedral pdb=" CB CYS A1415 " pdb=" SG CYS A1415 " pdb=" SG CYS A1440 " pdb=" CB CYS A1440 " ideal model delta sinusoidal sigma weight residual 93.00 147.81 -54.81 1 1.00e+01 1.00e-02 4.07e+01 dihedral pdb=" C19 ERG A1610 " pdb=" C10 ERG A1610 " pdb=" C5 ERG A1610 " pdb=" C6 ERG A1610 " ideal model delta sinusoidal sigma weight residual 268.62 94.30 174.32 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C11 ERG A1610 " pdb=" C10 ERG A1610 " pdb=" C9 ERG A1610 " pdb=" C19 ERG A1610 " ideal model delta sinusoidal sigma weight residual 52.77 -120.04 172.81 1 3.00e+01 1.11e-03 2.12e+01 ... (remaining 6993 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.368: 1678 0.368 - 0.737: 0 0.737 - 1.105: 0 1.105 - 1.473: 0 1.473 - 1.841: 1 Chirality restraints: 1679 Sorted by residual: chirality pdb=" C10 ERG A1610 " pdb=" C1 ERG A1610 " pdb=" C5 ERG A1610 " pdb=" C9 ERG A1610 " both_signs ideal model delta sigma weight residual False -2.77 -0.93 -1.84 2.00e-01 2.50e+01 8.48e+01 chirality pdb=" C20 ERG A1606 " pdb=" C17 ERG A1606 " pdb=" C21 ERG A1606 " pdb=" C22 ERG A1606 " both_signs ideal model delta sigma weight residual False 2.58 2.36 0.22 2.00e-01 2.50e+01 1.22e+00 chirality pdb=" CA ASP A 706 " pdb=" N ASP A 706 " pdb=" C ASP A 706 " pdb=" CB ASP A 706 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.20e-01 ... (remaining 1676 not shown) Planarity restraints: 1867 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C03 1YN A1605 " 0.029 2.00e-02 2.50e+03 2.01e-02 8.08e+00 pdb=" C06 1YN A1605 " -0.005 2.00e-02 2.50e+03 pdb=" C09 1YN A1605 " -0.016 2.00e-02 2.50e+03 pdb=" C11 1YN A1605 " 0.036 2.00e-02 2.50e+03 pdb=" N05 1YN A1605 " 0.000 2.00e-02 2.50e+03 pdb=" N08 1YN A1605 " -0.013 2.00e-02 2.50e+03 pdb=" N10 1YN A1605 " -0.008 2.00e-02 2.50e+03 pdb=" O07 1YN A1605 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 706 " 0.010 2.00e-02 2.50e+03 1.96e-02 3.84e+00 pdb=" C ASP A 706 " -0.034 2.00e-02 2.50e+03 pdb=" O ASP A 706 " 0.013 2.00e-02 2.50e+03 pdb=" N ARG A 707 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY A 138 " 0.032 5.00e-02 4.00e+02 4.79e-02 3.67e+00 pdb=" N PRO A 139 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO A 139 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 139 " 0.027 5.00e-02 4.00e+02 ... (remaining 1864 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 69 2.54 - 3.13: 8473 3.13 - 3.72: 17362 3.72 - 4.31: 24590 4.31 - 4.90: 41185 Nonbonded interactions: 91679 Sorted by model distance: nonbonded pdb="MG MG A1603 " pdb=" O3B ADP A1604 " model vdw 1.953 2.170 nonbonded pdb=" OH TYR A 714 " pdb=" OD1 ASP A 741 " model vdw 2.148 3.040 nonbonded pdb=" O ILE A 263 " pdb=" OG1 THR A 267 " model vdw 2.217 3.040 nonbonded pdb=" O ALA A1268 " pdb=" OG SER A1272 " model vdw 2.227 3.040 nonbonded pdb=" OH TYR A 669 " pdb=" OG SER A 683 " model vdw 2.229 3.040 ... (remaining 91674 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 10.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.390 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 8.960 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:9.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 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 0.030 11216 Z= 0.135 Angle : 0.692 28.029 15269 Z= 0.314 Chirality : 0.061 1.841 1679 Planarity : 0.004 0.048 1867 Dihedral : 17.975 174.317 4513 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 2.46 % Allowed : 21.05 % Favored : 76.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.23), residues: 1301 helix: 1.25 (0.19), residues: 751 sheet: -0.62 (0.56), residues: 85 loop : -1.15 (0.28), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 578 TYR 0.010 0.001 TYR A1459 PHE 0.029 0.001 PHE A1298 TRP 0.018 0.001 TRP A 437 HIS 0.002 0.001 HIS A 759 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.14 (11213) covalent geometry : angle 0.69183 / 0.31 (15263) SS BOND : bond 0.00234 / 0.12 ( 3) SS BOND : angle 0.59934 / 0.35 ( 6) hydrogen bonds : bond 0.15082 / 10.06 ( 586) hydrogen bonds : angle 5.72238 / 4.10 ( 1707) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 136 time to evaluate : 0.420 Fit side-chains REVERT: A 392 LYS cc_start: 0.8173 (tttp) cc_final: 0.7592 (tmmt) REVERT: A 928 ASP cc_start: 0.7771 (t0) cc_final: 0.7530 (t0) REVERT: A 985 GLN cc_start: 0.8312 (tp40) cc_final: 0.8010 (tm-30) REVERT: A 1077 LYS cc_start: 0.8488 (mmtp) cc_final: 0.8206 (mppt) REVERT: A 1089 LYS cc_start: 0.8287 (tppt) cc_final: 0.8000 (tppp) REVERT: A 1135 ASN cc_start: 0.8124 (m-40) cc_final: 0.7822 (p0) REVERT: A 1459 TYR cc_start: 0.8707 (t80) cc_final: 0.8445 (t80) outliers start: 28 outliers final: 21 residues processed: 159 average time/residue: 0.4964 time to fit residues: 86.3828 Evaluate side-chains 145 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 124 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 ASN Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 299 SER Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 533 VAL Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 648 VAL Chi-restraints excluded: chain A residue 720 VAL Chi-restraints excluded: chain A residue 796 VAL Chi-restraints excluded: chain A residue 880 ASP Chi-restraints excluded: chain A residue 949 VAL Chi-restraints excluded: chain A residue 964 ASP Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 993 VAL Chi-restraints excluded: chain A residue 1019 LEU Chi-restraints excluded: chain A residue 1022 LEU Chi-restraints excluded: chain A residue 1061 ILE Chi-restraints excluded: chain A residue 1086 ASP Chi-restraints excluded: chain A residue 1173 LEU Chi-restraints excluded: chain A residue 1363 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 0.0770 chunk 122 optimal weight: 7.9990 chunk 91 optimal weight: 4.9990 chunk 55 optimal weight: 1.9990 overall best weight: 0.9340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 292 ASN A 419 ASN A 556 ASN A1108 ASN A1135 ASN ** A1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.158205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.130880 restraints weight = 12209.218| |-----------------------------------------------------------------------------| r_work (start): 0.3550 rms_B_bonded: 1.50 r_work: 0.3450 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3322 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.0803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11216 Z= 0.143 Angle : 0.691 28.053 15269 Z= 0.316 Chirality : 0.061 1.840 1679 Planarity : 0.004 0.049 1867 Dihedral : 13.843 174.051 2112 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.07 % Favored : 94.85 % Rotamer: Outliers : 4.21 % Allowed : 20.09 % Favored : 75.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.24), residues: 1301 helix: 1.57 (0.19), residues: 754 sheet: -0.66 (0.55), residues: 85 loop : -1.13 (0.29), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 578 TYR 0.012 0.001 TYR A 669 PHE 0.031 0.002 PHE A1298 TRP 0.017 0.001 TRP A 437 HIS 0.003 0.001 HIS A 759 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.14 (11213) covalent geometry : angle 0.69147 / 0.32 (15263) SS BOND : bond 0.00216 / 0.11 ( 3) SS BOND : angle 0.58007 / 0.33 ( 6) hydrogen bonds : bond 0.04957 / 3.23 ( 586) hydrogen bonds : angle 4.49488 / 3.23 ( 1707) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 139 time to evaluate : 0.342 Fit side-chains REVERT: A 392 LYS cc_start: 0.8163 (tttp) cc_final: 0.7427 (tmmt) REVERT: A 738 ARG cc_start: 0.8181 (OUTLIER) cc_final: 0.7957 (mtp180) REVERT: A 910 VAL cc_start: 0.7481 (OUTLIER) cc_final: 0.7183 (m) REVERT: A 912 MET cc_start: 0.8128 (ptt) cc_final: 0.7750 (ppp) REVERT: A 928 ASP cc_start: 0.7712 (t0) cc_final: 0.7449 (t0) REVERT: A 985 GLN cc_start: 0.8373 (tp40) cc_final: 0.7929 (tm-30) REVERT: A 1077 LYS cc_start: 0.8427 (mmtp) cc_final: 0.7967 (mppt) REVERT: A 1089 LYS cc_start: 0.8394 (tppt) cc_final: 0.8156 (tppp) REVERT: A 1135 ASN cc_start: 0.8130 (m110) cc_final: 0.7714 (p0) outliers start: 48 outliers final: 23 residues processed: 171 average time/residue: 0.4313 time to fit residues: 80.7492 Evaluate side-chains 151 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 126 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 403 THR Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 451 LYS Chi-restraints excluded: chain A residue 454 ASP Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 533 VAL Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 559 SER Chi-restraints excluded: chain A residue 738 ARG Chi-restraints excluded: chain A residue 910 VAL Chi-restraints excluded: chain A residue 949 VAL Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 993 VAL Chi-restraints excluded: chain A residue 1019 LEU Chi-restraints excluded: chain A residue 1061 ILE Chi-restraints excluded: chain A residue 1102 LYS Chi-restraints excluded: chain A residue 1178 LEU Chi-restraints excluded: chain A residue 1414 THR Chi-restraints excluded: chain A residue 1426 VAL Chi-restraints excluded: chain A residue 1428 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 45 optimal weight: 1.9990 chunk 100 optimal weight: 0.5980 chunk 121 optimal weight: 2.9990 chunk 125 optimal weight: 2.9990 chunk 51 optimal weight: 0.5980 chunk 57 optimal weight: 0.6980 chunk 94 optimal weight: 6.9990 chunk 123 optimal weight: 0.4980 chunk 92 optimal weight: 7.9990 chunk 110 optimal weight: 0.9990 chunk 75 optimal weight: 4.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 36 GLN A 292 ASN A 785 ASN ** A1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.159367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.132254 restraints weight = 12285.681| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 1.51 r_work: 0.3454 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3326 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.1023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 11216 Z= 0.123 Angle : 0.667 27.943 15269 Z= 0.302 Chirality : 0.061 1.846 1679 Planarity : 0.004 0.051 1867 Dihedral : 13.523 174.303 2095 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.53 % Favored : 95.31 % Rotamer: Outliers : 4.12 % Allowed : 20.61 % Favored : 75.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.82 (0.24), residues: 1301 helix: 1.68 (0.19), residues: 757 sheet: -0.68 (0.56), residues: 85 loop : -1.16 (0.29), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 441 TYR 0.012 0.001 TYR A 669 PHE 0.031 0.001 PHE A1298 TRP 0.018 0.001 TRP A 437 HIS 0.002 0.000 HIS A 759 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.12 (11213) covalent geometry : angle 0.66700 / 0.30 (15263) SS BOND : bond 0.00531 / 0.27 ( 3) SS BOND : angle 1.28032 / 0.76 ( 6) hydrogen bonds : bond 0.04408 / 2.89 ( 586) hydrogen bonds : angle 4.27166 / 3.07 ( 1707) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 136 time to evaluate : 0.262 Fit side-chains REVERT: A 392 LYS cc_start: 0.8163 (tttp) cc_final: 0.7411 (tmmt) REVERT: A 393 MET cc_start: 0.8022 (OUTLIER) cc_final: 0.6306 (tpp) REVERT: A 738 ARG cc_start: 0.8197 (OUTLIER) cc_final: 0.7942 (mtp180) REVERT: A 910 VAL cc_start: 0.7432 (OUTLIER) cc_final: 0.7189 (m) REVERT: A 912 MET cc_start: 0.8166 (ptt) cc_final: 0.7789 (ppp) REVERT: A 985 GLN cc_start: 0.8408 (tp40) cc_final: 0.7958 (tm-30) REVERT: A 1077 LYS cc_start: 0.8412 (mmtp) cc_final: 0.7912 (mppt) REVERT: A 1089 LYS cc_start: 0.8368 (tppt) cc_final: 0.8104 (tppp) REVERT: A 1135 ASN cc_start: 0.8153 (m110) cc_final: 0.7784 (p0) outliers start: 47 outliers final: 25 residues processed: 169 average time/residue: 0.4656 time to fit residues: 86.1093 Evaluate side-chains 158 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 130 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 393 MET Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 451 LYS Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 533 VAL Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 559 SER Chi-restraints excluded: chain A residue 648 VAL Chi-restraints excluded: chain A residue 679 ILE Chi-restraints excluded: chain A residue 738 ARG Chi-restraints excluded: chain A residue 796 VAL Chi-restraints excluded: chain A residue 910 VAL Chi-restraints excluded: chain A residue 915 ILE Chi-restraints excluded: chain A residue 949 VAL Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 993 VAL Chi-restraints excluded: chain A residue 1019 LEU Chi-restraints excluded: chain A residue 1061 ILE Chi-restraints excluded: chain A residue 1102 LYS Chi-restraints excluded: chain A residue 1381 THR Chi-restraints excluded: chain A residue 1414 THR Chi-restraints excluded: chain A residue 1426 VAL Chi-restraints excluded: chain A residue 1428 THR Chi-restraints excluded: chain A residue 1442 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 79 optimal weight: 1.9990 chunk 98 optimal weight: 6.9990 chunk 114 optimal weight: 4.9990 chunk 3 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 102 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 43 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 42 optimal weight: 0.6980 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 36 GLN A 284 HIS A 292 ASN A 616 ASN A1101 HIS A1127 GLN A1242 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.155298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.127906 restraints weight = 12351.566| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 1.50 r_work: 0.3392 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3265 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.1200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 11216 Z= 0.177 Angle : 0.709 28.270 15269 Z= 0.325 Chirality : 0.062 1.825 1679 Planarity : 0.004 0.051 1867 Dihedral : 13.440 173.698 2092 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.46 % Favored : 94.39 % Rotamer: Outliers : 5.18 % Allowed : 20.26 % Favored : 74.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.23), residues: 1301 helix: 1.52 (0.19), residues: 754 sheet: -0.77 (0.55), residues: 85 loop : -1.18 (0.29), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 441 TYR 0.016 0.002 TYR A 936 PHE 0.037 0.002 PHE A1298 TRP 0.021 0.001 TRP A 437 HIS 0.004 0.001 HIS A 759 Details of bonding type rmsd/Z covalent geometry : bond 0.00414 / 0.18 (11213) covalent geometry : angle 0.70922 / 0.32 (15263) SS BOND : bond 0.00592 / 0.30 ( 3) SS BOND : angle 0.71152 / 0.38 ( 6) hydrogen bonds : bond 0.05066 / 3.30 ( 586) hydrogen bonds : angle 4.29797 / 3.08 ( 1707) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 130 time to evaluate : 0.366 Fit side-chains REVERT: A 207 GLU cc_start: 0.7960 (OUTLIER) cc_final: 0.7140 (mp0) REVERT: A 392 LYS cc_start: 0.8162 (tttp) cc_final: 0.7397 (tmmt) REVERT: A 393 MET cc_start: 0.8073 (OUTLIER) cc_final: 0.6431 (tpp) REVERT: A 738 ARG cc_start: 0.8275 (OUTLIER) cc_final: 0.7959 (mtp180) REVERT: A 910 VAL cc_start: 0.7500 (OUTLIER) cc_final: 0.7215 (m) REVERT: A 928 ASP cc_start: 0.7744 (t0) cc_final: 0.7518 (t0) REVERT: A 940 GLN cc_start: 0.8275 (OUTLIER) cc_final: 0.8045 (mt0) REVERT: A 985 GLN cc_start: 0.8435 (tp40) cc_final: 0.7962 (tm-30) REVERT: A 1077 LYS cc_start: 0.8429 (mmtp) cc_final: 0.7932 (mppt) REVERT: A 1089 LYS cc_start: 0.8379 (tppt) cc_final: 0.8107 (tppp) REVERT: A 1135 ASN cc_start: 0.8189 (m110) cc_final: 0.7832 (p0) outliers start: 59 outliers final: 34 residues processed: 174 average time/residue: 0.4521 time to fit residues: 86.4375 Evaluate side-chains 162 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 123 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 134 ASN Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 393 MET Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 403 THR Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 451 LYS Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 533 VAL Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 559 SER Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 648 VAL Chi-restraints excluded: chain A residue 738 ARG Chi-restraints excluded: chain A residue 796 VAL Chi-restraints excluded: chain A residue 910 VAL Chi-restraints excluded: chain A residue 915 ILE Chi-restraints excluded: chain A residue 940 GLN Chi-restraints excluded: chain A residue 949 VAL Chi-restraints excluded: chain A residue 981 LEU Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 993 VAL Chi-restraints excluded: chain A residue 1061 ILE Chi-restraints excluded: chain A residue 1102 LYS Chi-restraints excluded: chain A residue 1142 VAL Chi-restraints excluded: chain A residue 1173 LEU Chi-restraints excluded: chain A residue 1178 LEU Chi-restraints excluded: chain A residue 1346 MET Chi-restraints excluded: chain A residue 1363 THR Chi-restraints excluded: chain A residue 1381 THR Chi-restraints excluded: chain A residue 1395 VAL Chi-restraints excluded: chain A residue 1426 VAL Chi-restraints excluded: chain A residue 1428 THR Chi-restraints excluded: chain A residue 1442 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 64 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 chunk 98 optimal weight: 0.4980 chunk 8 optimal weight: 4.9990 chunk 48 optimal weight: 0.9990 chunk 129 optimal weight: 1.9990 chunk 53 optimal weight: 0.7980 chunk 99 optimal weight: 3.9990 chunk 7 optimal weight: 0.7980 chunk 126 optimal weight: 5.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 36 GLN A1108 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.156782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.129531 restraints weight = 12341.898| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 1.51 r_work: 0.3414 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3286 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.1264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11216 Z= 0.143 Angle : 0.689 28.093 15269 Z= 0.312 Chirality : 0.061 1.836 1679 Planarity : 0.004 0.050 1867 Dihedral : 13.392 174.140 2090 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.15 % Favored : 94.70 % Rotamer: Outliers : 3.86 % Allowed : 21.75 % Favored : 74.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.23), residues: 1301 helix: 1.62 (0.19), residues: 755 sheet: -0.92 (0.55), residues: 86 loop : -1.15 (0.29), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 441 TYR 0.012 0.001 TYR A1459 PHE 0.036 0.002 PHE A1298 TRP 0.021 0.001 TRP A 437 HIS 0.003 0.001 HIS A 284 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.14 (11213) covalent geometry : angle 0.68879 / 0.31 (15263) SS BOND : bond 0.00268 / 0.14 ( 3) SS BOND : angle 0.58248 / 0.29 ( 6) hydrogen bonds : bond 0.04622 / 3.00 ( 586) hydrogen bonds : angle 4.19651 / 3.01 ( 1707) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 126 time to evaluate : 0.503 Fit side-chains REVERT: A 207 GLU cc_start: 0.7946 (OUTLIER) cc_final: 0.7163 (mp0) REVERT: A 392 LYS cc_start: 0.8152 (tttp) cc_final: 0.7395 (tmmt) REVERT: A 393 MET cc_start: 0.8014 (OUTLIER) cc_final: 0.6320 (tpp) REVERT: A 738 ARG cc_start: 0.8277 (OUTLIER) cc_final: 0.7951 (mtp180) REVERT: A 910 VAL cc_start: 0.7472 (OUTLIER) cc_final: 0.7201 (m) REVERT: A 940 GLN cc_start: 0.8246 (OUTLIER) cc_final: 0.8019 (mt0) REVERT: A 985 GLN cc_start: 0.8415 (tp40) cc_final: 0.7960 (tm-30) REVERT: A 1077 LYS cc_start: 0.8387 (mmtp) cc_final: 0.7961 (mppt) REVERT: A 1089 LYS cc_start: 0.8344 (tppt) cc_final: 0.8093 (tppp) REVERT: A 1135 ASN cc_start: 0.8196 (m110) cc_final: 0.7849 (p0) REVERT: A 1458 LYS cc_start: 0.7881 (mtpt) cc_final: 0.7657 (ttmm) outliers start: 44 outliers final: 29 residues processed: 160 average time/residue: 0.4921 time to fit residues: 86.3023 Evaluate side-chains 154 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 120 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 87 GLU Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 393 MET Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 403 THR Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 451 LYS Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 533 VAL Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 559 SER Chi-restraints excluded: chain A residue 648 VAL Chi-restraints excluded: chain A residue 738 ARG Chi-restraints excluded: chain A residue 796 VAL Chi-restraints excluded: chain A residue 910 VAL Chi-restraints excluded: chain A residue 915 ILE Chi-restraints excluded: chain A residue 940 GLN Chi-restraints excluded: chain A residue 949 VAL Chi-restraints excluded: chain A residue 981 LEU Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 993 VAL Chi-restraints excluded: chain A residue 1061 ILE Chi-restraints excluded: chain A residue 1173 LEU Chi-restraints excluded: chain A residue 1335 SER Chi-restraints excluded: chain A residue 1381 THR Chi-restraints excluded: chain A residue 1395 VAL Chi-restraints excluded: chain A residue 1426 VAL Chi-restraints excluded: chain A residue 1428 THR Chi-restraints excluded: chain A residue 1442 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 119 optimal weight: 0.6980 chunk 66 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 37 optimal weight: 5.9990 chunk 90 optimal weight: 4.9990 chunk 107 optimal weight: 0.8980 chunk 38 optimal weight: 0.7980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 36 GLN A 292 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.156837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.129587 restraints weight = 12338.248| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 1.50 r_work: 0.3399 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3276 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.1356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11216 Z= 0.145 Angle : 0.691 28.128 15269 Z= 0.313 Chirality : 0.061 1.834 1679 Planarity : 0.004 0.049 1867 Dihedral : 13.336 173.998 2090 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.30 % Favored : 94.54 % Rotamer: Outliers : 4.39 % Allowed : 21.67 % Favored : 73.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.24), residues: 1301 helix: 1.64 (0.19), residues: 757 sheet: -0.95 (0.54), residues: 85 loop : -1.23 (0.29), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 326 TYR 0.014 0.001 TYR A1459 PHE 0.036 0.002 PHE A1298 TRP 0.022 0.001 TRP A 437 HIS 0.004 0.001 HIS A 284 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.15 (11213) covalent geometry : angle 0.69085 / 0.31 (15263) SS BOND : bond 0.00252 / 0.13 ( 3) SS BOND : angle 0.59771 / 0.30 ( 6) hydrogen bonds : bond 0.04601 / 3.00 ( 586) hydrogen bonds : angle 4.17267 / 3.00 ( 1707) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 128 time to evaluate : 0.407 Fit side-chains REVERT: A 207 GLU cc_start: 0.7896 (OUTLIER) cc_final: 0.7132 (mp0) REVERT: A 392 LYS cc_start: 0.8152 (tttp) cc_final: 0.7424 (tmmt) REVERT: A 393 MET cc_start: 0.8030 (OUTLIER) cc_final: 0.6397 (tpp) REVERT: A 738 ARG cc_start: 0.8265 (OUTLIER) cc_final: 0.7933 (mtp180) REVERT: A 910 VAL cc_start: 0.7463 (OUTLIER) cc_final: 0.7185 (m) REVERT: A 940 GLN cc_start: 0.8253 (OUTLIER) cc_final: 0.8028 (mt0) REVERT: A 985 GLN cc_start: 0.8397 (tp40) cc_final: 0.7954 (tm-30) REVERT: A 1077 LYS cc_start: 0.8416 (mmtp) cc_final: 0.8016 (mppt) REVERT: A 1089 LYS cc_start: 0.8342 (tppt) cc_final: 0.8122 (tppp) REVERT: A 1135 ASN cc_start: 0.8182 (m110) cc_final: 0.7869 (p0) outliers start: 50 outliers final: 33 residues processed: 164 average time/residue: 0.4653 time to fit residues: 83.9672 Evaluate side-chains 162 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 124 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 87 GLU Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 393 MET Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 403 THR Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 451 LYS Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 533 VAL Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 559 SER Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 648 VAL Chi-restraints excluded: chain A residue 738 ARG Chi-restraints excluded: chain A residue 796 VAL Chi-restraints excluded: chain A residue 910 VAL Chi-restraints excluded: chain A residue 915 ILE Chi-restraints excluded: chain A residue 940 GLN Chi-restraints excluded: chain A residue 949 VAL Chi-restraints excluded: chain A residue 981 LEU Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 993 VAL Chi-restraints excluded: chain A residue 1061 ILE Chi-restraints excluded: chain A residue 1173 LEU Chi-restraints excluded: chain A residue 1178 LEU Chi-restraints excluded: chain A residue 1335 SER Chi-restraints excluded: chain A residue 1346 MET Chi-restraints excluded: chain A residue 1363 THR Chi-restraints excluded: chain A residue 1381 THR Chi-restraints excluded: chain A residue 1395 VAL Chi-restraints excluded: chain A residue 1426 VAL Chi-restraints excluded: chain A residue 1428 THR Chi-restraints excluded: chain A residue 1442 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 41 optimal weight: 4.9990 chunk 114 optimal weight: 4.9990 chunk 94 optimal weight: 0.9990 chunk 16 optimal weight: 0.8980 chunk 117 optimal weight: 0.9980 chunk 38 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 6 optimal weight: 8.9990 chunk 28 optimal weight: 0.4980 chunk 100 optimal weight: 0.0670 chunk 60 optimal weight: 2.9990 overall best weight: 0.6918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 36 GLN ** A 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.157012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.130270 restraints weight = 12236.280| |-----------------------------------------------------------------------------| r_work (start): 0.3556 rms_B_bonded: 1.51 r_work: 0.3452 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3323 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.1439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11216 Z= 0.124 Angle : 0.679 27.995 15269 Z= 0.306 Chirality : 0.061 1.843 1679 Planarity : 0.004 0.049 1867 Dihedral : 13.208 174.245 2090 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.07 % Favored : 94.77 % Rotamer: Outliers : 3.68 % Allowed : 22.72 % Favored : 73.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.84 (0.24), residues: 1301 helix: 1.75 (0.19), residues: 758 sheet: -1.00 (0.54), residues: 86 loop : -1.20 (0.29), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 441 TYR 0.012 0.001 TYR A1459 PHE 0.036 0.001 PHE A1298 TRP 0.021 0.001 TRP A 437 HIS 0.004 0.001 HIS A 271 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 (11213) covalent geometry : angle 0.67892 / 0.31 (15263) SS BOND : bond 0.00218 / 0.11 ( 3) SS BOND : angle 0.56139 / 0.27 ( 6) hydrogen bonds : bond 0.04228 / 2.75 ( 586) hydrogen bonds : angle 4.10164 / 2.94 ( 1707) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 122 time to evaluate : 0.413 Fit side-chains REVERT: A 207 GLU cc_start: 0.7944 (OUTLIER) cc_final: 0.7208 (mp0) REVERT: A 392 LYS cc_start: 0.8165 (tttp) cc_final: 0.7429 (tmmt) REVERT: A 393 MET cc_start: 0.7977 (OUTLIER) cc_final: 0.6234 (tpp) REVERT: A 738 ARG cc_start: 0.8263 (OUTLIER) cc_final: 0.7945 (mtp180) REVERT: A 910 VAL cc_start: 0.7431 (OUTLIER) cc_final: 0.7208 (m) REVERT: A 940 GLN cc_start: 0.8256 (OUTLIER) cc_final: 0.8033 (mt0) REVERT: A 985 GLN cc_start: 0.8366 (tp40) cc_final: 0.7922 (tm-30) REVERT: A 1077 LYS cc_start: 0.8424 (mmtp) cc_final: 0.8030 (mppt) REVERT: A 1089 LYS cc_start: 0.8317 (tppt) cc_final: 0.8112 (tppp) REVERT: A 1135 ASN cc_start: 0.8211 (m110) cc_final: 0.7890 (p0) outliers start: 42 outliers final: 29 residues processed: 152 average time/residue: 0.4592 time to fit residues: 76.3492 Evaluate side-chains 149 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 115 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 393 MET Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 403 THR Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 533 VAL Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 559 SER Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 648 VAL Chi-restraints excluded: chain A residue 679 ILE Chi-restraints excluded: chain A residue 738 ARG Chi-restraints excluded: chain A residue 796 VAL Chi-restraints excluded: chain A residue 910 VAL Chi-restraints excluded: chain A residue 915 ILE Chi-restraints excluded: chain A residue 940 GLN Chi-restraints excluded: chain A residue 949 VAL Chi-restraints excluded: chain A residue 981 LEU Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 993 VAL Chi-restraints excluded: chain A residue 1061 ILE Chi-restraints excluded: chain A residue 1172 VAL Chi-restraints excluded: chain A residue 1335 SER Chi-restraints excluded: chain A residue 1363 THR Chi-restraints excluded: chain A residue 1381 THR Chi-restraints excluded: chain A residue 1395 VAL Chi-restraints excluded: chain A residue 1426 VAL Chi-restraints excluded: chain A residue 1428 THR Chi-restraints excluded: chain A residue 1442 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 7 optimal weight: 7.9990 chunk 101 optimal weight: 3.9990 chunk 51 optimal weight: 0.7980 chunk 88 optimal weight: 5.9990 chunk 117 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 3 optimal weight: 5.9990 chunk 2 optimal weight: 0.9980 chunk 9 optimal weight: 0.8980 chunk 31 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 36 GLN A 357 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.158234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.131163 restraints weight = 12234.592| |-----------------------------------------------------------------------------| r_work (start): 0.3540 rms_B_bonded: 1.51 r_work: 0.3427 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3300 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.1499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11216 Z= 0.131 Angle : 0.684 28.046 15269 Z= 0.308 Chirality : 0.061 1.840 1679 Planarity : 0.004 0.049 1867 Dihedral : 13.139 174.123 2090 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.07 % Favored : 94.77 % Rotamer: Outliers : 4.47 % Allowed : 22.19 % Favored : 73.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.24), residues: 1301 helix: 1.77 (0.19), residues: 758 sheet: -1.00 (0.54), residues: 85 loop : -1.23 (0.29), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 441 TYR 0.012 0.001 TYR A 669 PHE 0.044 0.001 PHE A1298 TRP 0.026 0.001 TRP A 687 HIS 0.005 0.001 HIS A 284 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 (11213) covalent geometry : angle 0.68399 / 0.31 (15263) SS BOND : bond 0.00237 / 0.12 ( 3) SS BOND : angle 0.58427 / 0.29 ( 6) hydrogen bonds : bond 0.04303 / 2.80 ( 586) hydrogen bonds : angle 4.09479 / 2.93 ( 1707) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 118 time to evaluate : 0.477 Fit side-chains REVERT: A 207 GLU cc_start: 0.7957 (OUTLIER) cc_final: 0.7213 (mp0) REVERT: A 392 LYS cc_start: 0.8164 (tttp) cc_final: 0.7404 (tmmt) REVERT: A 393 MET cc_start: 0.7973 (OUTLIER) cc_final: 0.6235 (tpp) REVERT: A 652 LEU cc_start: 0.8061 (OUTLIER) cc_final: 0.7752 (tt) REVERT: A 656 MET cc_start: 0.7866 (mmp) cc_final: 0.7608 (mmt) REVERT: A 738 ARG cc_start: 0.8271 (OUTLIER) cc_final: 0.7938 (mtp180) REVERT: A 910 VAL cc_start: 0.7424 (OUTLIER) cc_final: 0.7218 (m) REVERT: A 940 GLN cc_start: 0.8289 (OUTLIER) cc_final: 0.8069 (mt0) REVERT: A 985 GLN cc_start: 0.8349 (tp40) cc_final: 0.7885 (tm-30) REVERT: A 1077 LYS cc_start: 0.8422 (mmtp) cc_final: 0.8037 (mppt) REVERT: A 1089 LYS cc_start: 0.8329 (tppt) cc_final: 0.8123 (tppp) REVERT: A 1135 ASN cc_start: 0.8243 (m110) cc_final: 0.7909 (p0) outliers start: 51 outliers final: 33 residues processed: 156 average time/residue: 0.4730 time to fit residues: 80.9536 Evaluate side-chains 155 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 116 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 87 GLU Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 393 MET Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 403 THR Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 533 VAL Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 559 SER Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 648 VAL Chi-restraints excluded: chain A residue 652 LEU Chi-restraints excluded: chain A residue 679 ILE Chi-restraints excluded: chain A residue 738 ARG Chi-restraints excluded: chain A residue 796 VAL Chi-restraints excluded: chain A residue 910 VAL Chi-restraints excluded: chain A residue 915 ILE Chi-restraints excluded: chain A residue 940 GLN Chi-restraints excluded: chain A residue 947 SER Chi-restraints excluded: chain A residue 949 VAL Chi-restraints excluded: chain A residue 981 LEU Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 993 VAL Chi-restraints excluded: chain A residue 1061 ILE Chi-restraints excluded: chain A residue 1172 VAL Chi-restraints excluded: chain A residue 1173 LEU Chi-restraints excluded: chain A residue 1178 LEU Chi-restraints excluded: chain A residue 1335 SER Chi-restraints excluded: chain A residue 1363 THR Chi-restraints excluded: chain A residue 1381 THR Chi-restraints excluded: chain A residue 1395 VAL Chi-restraints excluded: chain A residue 1426 VAL Chi-restraints excluded: chain A residue 1428 THR Chi-restraints excluded: chain A residue 1442 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 38 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 91 optimal weight: 0.0050 chunk 57 optimal weight: 0.9990 chunk 117 optimal weight: 3.9990 chunk 116 optimal weight: 0.6980 chunk 18 optimal weight: 4.9990 chunk 105 optimal weight: 1.9990 chunk 92 optimal weight: 0.8980 chunk 128 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 overall best weight: 0.6996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 36 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.157346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.130778 restraints weight = 12139.664| |-----------------------------------------------------------------------------| r_work (start): 0.3550 rms_B_bonded: 1.50 r_work: 0.3437 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3311 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.1559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11216 Z= 0.125 Angle : 0.682 27.988 15269 Z= 0.307 Chirality : 0.061 1.844 1679 Planarity : 0.004 0.049 1867 Dihedral : 13.035 174.229 2090 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.84 % Favored : 95.00 % Rotamer: Outliers : 3.51 % Allowed : 22.98 % Favored : 73.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.24), residues: 1301 helix: 1.81 (0.19), residues: 758 sheet: -1.06 (0.53), residues: 86 loop : -1.21 (0.29), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 676 TYR 0.011 0.001 TYR A 669 PHE 0.045 0.001 PHE A1298 TRP 0.028 0.001 TRP A 687 HIS 0.004 0.001 HIS A 284 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.13 (11213) covalent geometry : angle 0.68228 / 0.31 (15263) SS BOND : bond 0.00218 / 0.11 ( 3) SS BOND : angle 0.57420 / 0.28 ( 6) hydrogen bonds : bond 0.04171 / 2.72 ( 586) hydrogen bonds : angle 4.07123 / 2.91 ( 1707) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 126 time to evaluate : 0.329 Fit side-chains REVERT: A 207 GLU cc_start: 0.7944 (OUTLIER) cc_final: 0.7241 (mp0) REVERT: A 292 ASN cc_start: 0.7159 (t0) cc_final: 0.6829 (t0) REVERT: A 392 LYS cc_start: 0.8154 (tttp) cc_final: 0.7395 (tmmt) REVERT: A 393 MET cc_start: 0.7954 (OUTLIER) cc_final: 0.6210 (tpp) REVERT: A 652 LEU cc_start: 0.8019 (OUTLIER) cc_final: 0.7694 (tt) REVERT: A 656 MET cc_start: 0.7827 (mmp) cc_final: 0.7582 (mmt) REVERT: A 738 ARG cc_start: 0.8243 (OUTLIER) cc_final: 0.7914 (mtp180) REVERT: A 985 GLN cc_start: 0.8339 (tp40) cc_final: 0.7877 (tm-30) REVERT: A 1077 LYS cc_start: 0.8420 (mmtp) cc_final: 0.8026 (mppt) REVERT: A 1089 LYS cc_start: 0.8302 (tppt) cc_final: 0.8100 (tppp) REVERT: A 1135 ASN cc_start: 0.8247 (m110) cc_final: 0.7924 (p0) outliers start: 40 outliers final: 31 residues processed: 156 average time/residue: 0.4616 time to fit residues: 79.0616 Evaluate side-chains 152 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 117 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 87 GLU Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 393 MET Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 403 THR Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 533 VAL Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 559 SER Chi-restraints excluded: chain A residue 648 VAL Chi-restraints excluded: chain A residue 652 LEU Chi-restraints excluded: chain A residue 738 ARG Chi-restraints excluded: chain A residue 796 VAL Chi-restraints excluded: chain A residue 915 ILE Chi-restraints excluded: chain A residue 949 VAL Chi-restraints excluded: chain A residue 981 LEU Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 993 VAL Chi-restraints excluded: chain A residue 1061 ILE Chi-restraints excluded: chain A residue 1172 VAL Chi-restraints excluded: chain A residue 1173 LEU Chi-restraints excluded: chain A residue 1178 LEU Chi-restraints excluded: chain A residue 1335 SER Chi-restraints excluded: chain A residue 1363 THR Chi-restraints excluded: chain A residue 1381 THR Chi-restraints excluded: chain A residue 1395 VAL Chi-restraints excluded: chain A residue 1426 VAL Chi-restraints excluded: chain A residue 1428 THR Chi-restraints excluded: chain A residue 1442 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 61 optimal weight: 3.9990 chunk 70 optimal weight: 5.9990 chunk 85 optimal weight: 1.9990 chunk 109 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 chunk 107 optimal weight: 0.6980 chunk 93 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 124 optimal weight: 10.0000 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 36 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.154971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.127200 restraints weight = 12376.507| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 1.56 r_work: 0.3399 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3272 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.1575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 11216 Z= 0.184 Angle : 0.734 28.319 15269 Z= 0.337 Chirality : 0.063 1.822 1679 Planarity : 0.004 0.049 1867 Dihedral : 13.180 173.641 2090 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.46 % Favored : 94.39 % Rotamer: Outliers : 3.51 % Allowed : 22.98 % Favored : 73.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.60 (0.23), residues: 1301 helix: 1.55 (0.19), residues: 755 sheet: -0.93 (0.56), residues: 77 loop : -1.31 (0.29), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 676 TYR 0.015 0.002 TYR A 936 PHE 0.053 0.002 PHE A1298 TRP 0.040 0.002 TRP A 687 HIS 0.005 0.001 HIS A 284 Details of bonding type rmsd/Z covalent geometry : bond 0.00435 / 0.18 (11213) covalent geometry : angle 0.73428 / 0.34 (15263) SS BOND : bond 0.00316 / 0.16 ( 3) SS BOND : angle 0.68452 / 0.35 ( 6) hydrogen bonds : bond 0.05007 / 3.24 ( 586) hydrogen bonds : angle 4.24737 / 3.04 ( 1707) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 124 time to evaluate : 0.433 Fit side-chains REVERT: A 207 GLU cc_start: 0.7933 (OUTLIER) cc_final: 0.7151 (mp0) REVERT: A 392 LYS cc_start: 0.8161 (tttp) cc_final: 0.7426 (tmmt) REVERT: A 393 MET cc_start: 0.8034 (OUTLIER) cc_final: 0.6393 (tpp) REVERT: A 656 MET cc_start: 0.8033 (mmp) cc_final: 0.7790 (mmt) REVERT: A 738 ARG cc_start: 0.8286 (OUTLIER) cc_final: 0.7908 (mtp180) REVERT: A 940 GLN cc_start: 0.8268 (OUTLIER) cc_final: 0.8008 (mt0) REVERT: A 1077 LYS cc_start: 0.8445 (mmtp) cc_final: 0.8042 (mppt) REVERT: A 1089 LYS cc_start: 0.8329 (tppt) cc_final: 0.8126 (tppp) REVERT: A 1135 ASN cc_start: 0.8250 (m110) cc_final: 0.7957 (p0) outliers start: 40 outliers final: 33 residues processed: 157 average time/residue: 0.4894 time to fit residues: 84.1153 Evaluate side-chains 154 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 117 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 393 MET Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 403 THR Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 454 ASP Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 533 VAL Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 559 SER Chi-restraints excluded: chain A residue 648 VAL Chi-restraints excluded: chain A residue 679 ILE Chi-restraints excluded: chain A residue 738 ARG Chi-restraints excluded: chain A residue 796 VAL Chi-restraints excluded: chain A residue 915 ILE Chi-restraints excluded: chain A residue 940 GLN Chi-restraints excluded: chain A residue 947 SER Chi-restraints excluded: chain A residue 949 VAL Chi-restraints excluded: chain A residue 981 LEU Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 993 VAL Chi-restraints excluded: chain A residue 1061 ILE Chi-restraints excluded: chain A residue 1172 VAL Chi-restraints excluded: chain A residue 1173 LEU Chi-restraints excluded: chain A residue 1178 LEU Chi-restraints excluded: chain A residue 1335 SER Chi-restraints excluded: chain A residue 1363 THR Chi-restraints excluded: chain A residue 1381 THR Chi-restraints excluded: chain A residue 1395 VAL Chi-restraints excluded: chain A residue 1426 VAL Chi-restraints excluded: chain A residue 1428 THR Chi-restraints excluded: chain A residue 1442 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 89 optimal weight: 1.9990 chunk 66 optimal weight: 0.7980 chunk 19 optimal weight: 0.8980 chunk 40 optimal weight: 3.9990 chunk 4 optimal weight: 0.8980 chunk 130 optimal weight: 0.7980 chunk 82 optimal weight: 4.9990 chunk 119 optimal weight: 3.9990 chunk 116 optimal weight: 0.8980 chunk 101 optimal weight: 0.5980 chunk 61 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 36 GLN A 292 ASN A1108 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.156020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.129434 restraints weight = 12320.938| |-----------------------------------------------------------------------------| r_work (start): 0.3553 rms_B_bonded: 1.50 r_work: 0.3436 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3310 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.1613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11216 Z= 0.135 Angle : 0.709 28.055 15269 Z= 0.321 Chirality : 0.061 1.838 1679 Planarity : 0.004 0.049 1867 Dihedral : 13.035 174.207 2090 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.15 % Favored : 94.70 % Rotamer: Outliers : 3.25 % Allowed : 23.77 % Favored : 72.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.24), residues: 1301 helix: 1.69 (0.19), residues: 756 sheet: -1.10 (0.54), residues: 85 loop : -1.21 (0.29), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 441 TYR 0.012 0.001 TYR A1292 PHE 0.055 0.002 PHE A1298 TRP 0.037 0.001 TRP A 687 HIS 0.004 0.001 HIS A 284 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.14 (11213) covalent geometry : angle 0.70878 / 0.32 (15263) SS BOND : bond 0.00241 / 0.12 ( 3) SS BOND : angle 0.59223 / 0.29 ( 6) hydrogen bonds : bond 0.04424 / 2.88 ( 586) hydrogen bonds : angle 4.17140 / 2.98 ( 1707) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3401.49 seconds wall clock time: 58 minutes 54.31 seconds (3534.31 seconds total)