Starting phenix.real_space_refine on Wed Aug 5 17:11:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qh3_18397/08_2026/8qh3_18397.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qh3_18397/08_2026/8qh3_18397.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.81 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8qh3_18397/08_2026/8qh3_18397.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qh3_18397/08_2026/8qh3_18397.map" model { file = "/net/cci-nas-00/data/ceres_data/8qh3_18397/08_2026/8qh3_18397.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qh3_18397/08_2026/8qh3_18397.cif" } resolution = 2.81 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= 0.001 sd= 0.065 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: 6 Type Number sf(0) Gaussians P 11 5.49 5 Mg 1 5.21 5 S 58 5.16 5 C 6907 2.51 5 N 1815 2.21 5 O 2004 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10796 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 10556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1310, 10556 Classifications: {'peptide': 1310} Link IDs: {'PTRANS': 43, 'TRANS': 1266} Chain breaks: 5 Chain: "C" Number of atoms: 239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 239 Classifications: {'RNA': 11} Modifications used: {'rna2p_pur': 3, 'rna3p_pur': 5, 'rna3p_pyr': 3} Link IDs: {'rna2p': 2, 'rna3p': 8} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.30, per 1000 atoms: 0.21 Number of scatterers: 10796 At special positions: 0 Unit cell: (94.807, 99.841, 121.655, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 58 16.00 P 11 15.00 Mg 1 11.99 O 2004 8.00 N 1815 7.00 C 6907 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.92 Conformation dependent library (CDL) restraints added in 510.7 milliseconds 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2498 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 11 sheets defined 58.2% alpha, 11.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain 'A' and resid 239 through 251 removed outlier: 3.740A pdb=" N LEU A 243 " --> pdb=" O ASN A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 278 Processing helix chain 'A' and resid 279 through 281 No H-bonds generated for 'chain 'A' and resid 279 through 281' Processing helix chain 'A' and resid 306 through 322 Processing helix chain 'A' and resid 328 through 343 Processing helix chain 'A' and resid 345 through 352 Processing helix chain 'A' and resid 374 through 378 Processing helix chain 'A' and resid 379 through 390 Processing helix chain 'A' and resid 409 through 428 removed outlier: 3.564A pdb=" N GLN A 413 " --> pdb=" O SER A 409 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N SER A 414 " --> pdb=" O HIS A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 458 Processing helix chain 'A' and resid 463 through 468 Processing helix chain 'A' and resid 470 through 490 removed outlier: 3.616A pdb=" N HIS A 474 " --> pdb=" O THR A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 563 through 572 Processing helix chain 'A' and resid 572 through 593 Processing helix chain 'A' and resid 597 through 614 Processing helix chain 'A' and resid 616 through 634 removed outlier: 3.835A pdb=" N TYR A 628 " --> pdb=" O ASP A 624 " (cutoff:3.500A) Proline residue: A 631 - end of helix Processing helix chain 'A' and resid 639 through 648 Processing helix chain 'A' and resid 654 through 674 Processing helix chain 'A' and resid 712 through 726 removed outlier: 3.657A pdb=" N LEU A 716 " --> pdb=" O HIS A 712 " (cutoff:3.500A) Processing helix chain 'A' and resid 733 through 760 removed outlier: 3.725A pdb=" N ALA A 739 " --> pdb=" O MET A 735 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N HIS A 742 " --> pdb=" O GLU A 738 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N GLU A 744 " --> pdb=" O LYS A 740 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N THR A 745 " --> pdb=" O ILE A 741 " (cutoff:3.500A) Processing helix chain 'A' and resid 760 through 767 Processing helix chain 'A' and resid 769 through 776 Processing helix chain 'A' and resid 777 through 780 removed outlier: 3.644A pdb=" N ALA A 780 " --> pdb=" O ALA A 777 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 777 through 780' Processing helix chain 'A' and resid 786 through 802 removed outlier: 4.015A pdb=" N VAL A 800 " --> pdb=" O GLU A 796 " (cutoff:3.500A) Processing helix chain 'A' and resid 804 through 814 Processing helix chain 'A' and resid 824 through 828 Processing helix chain 'A' and resid 848 through 859 Processing helix chain 'A' and resid 864 through 872 Processing helix chain 'A' and resid 898 through 917 Processing helix chain 'A' and resid 929 through 946 removed outlier: 3.870A pdb=" N LEU A 933 " --> pdb=" O GLU A 929 " (cutoff:3.500A) Processing helix chain 'A' and resid 983 through 992 removed outlier: 4.044A pdb=" N ARG A 987 " --> pdb=" O ALA A 983 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N PHE A 988 " --> pdb=" O LYS A 984 " (cutoff:3.500A) Processing helix chain 'A' and resid 999 through 1012 Processing helix chain 'A' and resid 1020 through 1029 Processing helix chain 'A' and resid 1034 through 1042 Processing helix chain 'A' and resid 1061 through 1084 Processing helix chain 'A' and resid 1116 through 1126 Processing helix chain 'A' and resid 1128 through 1135 removed outlier: 3.553A pdb=" N ASN A1135 " --> pdb=" O PHE A1132 " (cutoff:3.500A) Processing helix chain 'A' and resid 1137 through 1153 removed outlier: 3.923A pdb=" N SER A1141 " --> pdb=" O GLU A1137 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLY A1153 " --> pdb=" O ILE A1149 " (cutoff:3.500A) Processing helix chain 'A' and resid 1185 through 1193 removed outlier: 3.943A pdb=" N LEU A1193 " --> pdb=" O LEU A1189 " (cutoff:3.500A) Processing helix chain 'A' and resid 1200 through 1218 Processing helix chain 'A' and resid 1221 through 1240 Processing helix chain 'A' and resid 1249 through 1253 Processing helix chain 'A' and resid 1262 through 1266 Processing helix chain 'A' and resid 1272 through 1279 Processing helix chain 'A' and resid 1282 through 1299 removed outlier: 3.543A pdb=" N LYS A1286 " --> pdb=" O GLY A1282 " (cutoff:3.500A) Processing helix chain 'A' and resid 1301 through 1321 Processing helix chain 'A' and resid 1354 through 1365 Processing helix chain 'A' and resid 1366 through 1370 Processing helix chain 'A' and resid 1375 through 1385 removed outlier: 3.717A pdb=" N ILE A1381 " --> pdb=" O ASP A1377 " (cutoff:3.500A) Processing helix chain 'A' and resid 1386 through 1388 No H-bonds generated for 'chain 'A' and resid 1386 through 1388' Processing helix chain 'A' and resid 1389 through 1396 Processing helix chain 'A' and resid 1400 through 1408 removed outlier: 4.196A pdb=" N GLN A1403 " --> pdb=" O SER A1400 " (cutoff:3.500A) Processing helix chain 'A' and resid 1425 through 1439 Processing helix chain 'A' and resid 1443 through 1457 Processing helix chain 'A' and resid 1460 through 1471 removed outlier: 3.561A pdb=" N TRP A1464 " --> pdb=" O LYS A1460 " (cutoff:3.500A) Processing helix chain 'A' and resid 1503 through 1512 Processing helix chain 'A' and resid 1514 through 1525 Processing helix chain 'A' and resid 1530 through 1546 removed outlier: 3.587A pdb=" N ASP A1540 " --> pdb=" O LYS A1536 " (cutoff:3.500A) Processing helix chain 'A' and resid 1552 through 1564 Proline residue: A1561 - end of helix removed outlier: 3.804A pdb=" N TYR A1564 " --> pdb=" O ALA A1560 " (cutoff:3.500A) Processing helix chain 'A' and resid 1581 through 1592 removed outlier: 3.926A pdb=" N CYS A1586 " --> pdb=" O ALA A1582 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ARG A1587 " --> pdb=" O GLU A1583 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 260 through 261 Processing sheet with id=AA2, first strand: chain 'A' and resid 260 through 261 removed outlier: 3.674A pdb=" N ASP A1099 " --> pdb=" O HIS A1096 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 499 through 503 Processing sheet with id=AA4, first strand: chain 'A' and resid 499 through 503 Processing sheet with id=AA5, first strand: chain 'A' and resid 701 through 702 Processing sheet with id=AA6, first strand: chain 'A' and resid 832 through 837 removed outlier: 5.365A pdb=" N SER A 844 " --> pdb=" O GLY A 835 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 893 through 897 removed outlier: 7.040A pdb=" N ALA A 877 " --> pdb=" O ASP A1016 " (cutoff:3.500A) removed outlier: 8.088A pdb=" N PHE A1018 " --> pdb=" O ALA A 877 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N ALA A 879 " --> pdb=" O PHE A1018 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1168 through 1171 Processing sheet with id=AA9, first strand: chain 'A' and resid 1417 through 1419 Processing sheet with id=AB1, first strand: chain 'A' and resid 1474 through 1479 removed outlier: 4.263A pdb=" N THR A1598 " --> pdb=" O ILE A1476 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 1485 through 1489 596 hydrogen bonds defined for protein. 1668 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: 1.94 Time building geometry restraints manager: 1.23 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: 3325 1.34 - 1.46: 2022 1.46 - 1.58: 5597 1.58 - 1.70: 21 1.70 - 1.82: 97 Bond restraints: 11062 Sorted by residual: bond pdb=" CE1 HIS A 957 " pdb=" NE2 HIS A 957 " ideal model delta sigma weight residual 1.321 1.361 -0.040 1.00e-02 1.00e+04 1.59e+01 bond pdb=" CA SER A 715 " pdb=" CB SER A 715 " ideal model delta sigma weight residual 1.529 1.482 0.047 1.55e-02 4.16e+03 9.05e+00 bond pdb=" N LYS A 876 " pdb=" CA LYS A 876 " ideal model delta sigma weight residual 1.454 1.488 -0.034 1.17e-02 7.31e+03 8.28e+00 bond pdb=" N ILE A 960 " pdb=" CA ILE A 960 " ideal model delta sigma weight residual 1.459 1.492 -0.033 1.19e-02 7.06e+03 7.60e+00 bond pdb=" N ILE A 952 " pdb=" CA ILE A 952 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.24e-02 6.50e+03 7.43e+00 ... (remaining 11057 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.69: 14672 1.69 - 3.38: 278 3.38 - 5.07: 38 5.07 - 6.76: 10 6.76 - 8.45: 3 Bond angle restraints: 15001 Sorted by residual: angle pdb=" C3' A C 2 " pdb=" O3' A C 2 " pdb=" P G C 3 " ideal model delta sigma weight residual 119.70 114.73 4.97 1.20e+00 6.94e-01 1.71e+01 angle pdb=" CA GLN A 875 " pdb=" C GLN A 875 " pdb=" O GLN A 875 " ideal model delta sigma weight residual 121.87 117.70 4.17 1.10e+00 8.26e-01 1.44e+01 angle pdb=" CA ASN A 956 " pdb=" C ASN A 956 " pdb=" O ASN A 956 " ideal model delta sigma weight residual 122.64 117.96 4.68 1.25e+00 6.40e-01 1.40e+01 angle pdb=" C1' U C 7 " pdb=" N1 U C 7 " pdb=" C2 U C 7 " ideal model delta sigma weight residual 117.70 121.96 -4.26 1.20e+00 6.94e-01 1.26e+01 angle pdb=" O5' A C 8 " pdb=" C5' A C 8 " pdb=" C4' A C 8 " ideal model delta sigma weight residual 109.40 112.15 -2.75 8.00e-01 1.56e+00 1.18e+01 ... (remaining 14996 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.79: 6258 29.79 - 59.59: 348 59.59 - 89.38: 30 89.38 - 119.18: 1 119.18 - 148.97: 1 Dihedral angle restraints: 6638 sinusoidal: 2780 harmonic: 3858 Sorted by residual: dihedral pdb=" O4' U C 7 " pdb=" C1' U C 7 " pdb=" N1 U C 7 " pdb=" C2 U C 7 " ideal model delta sinusoidal sigma weight residual 200.00 51.03 148.97 1 1.50e+01 4.44e-03 7.92e+01 dihedral pdb=" CA MET A1246 " pdb=" C MET A1246 " pdb=" N VAL A1247 " pdb=" CA VAL A1247 " ideal model delta harmonic sigma weight residual -180.00 -163.15 -16.85 0 5.00e+00 4.00e-02 1.14e+01 dihedral pdb=" CB GLU A1092 " pdb=" CG GLU A1092 " pdb=" CD GLU A1092 " pdb=" OE1 GLU A1092 " ideal model delta sinusoidal sigma weight residual 0.00 -89.86 89.86 1 3.00e+01 1.11e-03 1.06e+01 ... (remaining 6635 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.110: 1637 0.110 - 0.220: 37 0.220 - 0.331: 0 0.331 - 0.441: 0 0.441 - 0.551: 1 Chirality restraints: 1675 Sorted by residual: chirality pdb=" P A C 2 " pdb=" OP1 A C 2 " pdb=" OP2 A C 2 " pdb=" O5' A C 2 " both_signs ideal model delta sigma weight residual True 2.41 -2.96 -0.55 2.00e-01 2.50e+01 7.59e+00 chirality pdb=" CA ILE A 952 " pdb=" N ILE A 952 " pdb=" C ILE A 952 " pdb=" CB ILE A 952 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.22 2.00e-01 2.50e+01 1.18e+00 chirality pdb=" CA ILE A 960 " pdb=" N ILE A 960 " pdb=" C ILE A 960 " pdb=" CB ILE A 960 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.20 2.00e-01 2.50e+01 9.60e-01 ... (remaining 1672 not shown) Planarity restraints: 1848 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A1503 " 0.052 5.00e-02 4.00e+02 7.77e-02 9.66e+00 pdb=" N PRO A1504 " -0.134 5.00e-02 4.00e+02 pdb=" CA PRO A1504 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO A1504 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 961 " -0.272 9.50e-02 1.11e+02 1.22e-01 9.12e+00 pdb=" NE ARG A 961 " 0.017 2.00e-02 2.50e+03 pdb=" CZ ARG A 961 " 0.000 2.00e-02 2.50e+03 pdb=" NH1 ARG A 961 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A 961 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 904 " 0.266 9.50e-02 1.11e+02 1.19e-01 8.74e+00 pdb=" NE ARG A 904 " -0.016 2.00e-02 2.50e+03 pdb=" CZ ARG A 904 " -0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG A 904 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 904 " 0.009 2.00e-02 2.50e+03 ... (remaining 1845 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 100 2.61 - 3.18: 9243 3.18 - 3.76: 17605 3.76 - 4.33: 25326 4.33 - 4.90: 40832 Nonbonded interactions: 93106 Sorted by model distance: nonbonded pdb=" OD1 ASP A1099 " pdb="MG MG A2201 " model vdw 2.038 2.170 nonbonded pdb=" N GLU A1275 " pdb=" OE1 GLU A1275 " model vdw 2.188 3.120 nonbonded pdb=" OD2 ASP A 544 " pdb=" OG1 THR A 545 " model vdw 2.202 3.040 nonbonded pdb=" OH TYR A 855 " pdb=" OE1 GLU A 871 " model vdw 2.242 3.040 nonbonded pdb=" OH TYR A 302 " pdb=" OD2 ASP A 481 " model vdw 2.252 3.040 ... (remaining 93101 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 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: 2.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.220 Find NCS groups from input model: 0.060 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: 0.010 Load rotamer database and sin/cos tables:6.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 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 0.048 11062 Z= 0.182 Angle : 0.560 8.452 15001 Z= 0.330 Chirality : 0.043 0.551 1675 Planarity : 0.006 0.122 1848 Dihedral : 17.219 148.971 4140 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.16 % Allowed : 23.02 % Favored : 74.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.24), residues: 1298 helix: 1.11 (0.20), residues: 714 sheet: 0.26 (0.53), residues: 93 loop : -0.40 (0.29), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1405 TYR 0.014 0.001 TYR A 912 PHE 0.016 0.001 PHE A 894 TRP 0.013 0.002 TRP A 473 HIS 0.005 0.001 HIS A1413 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.18 (11062) covalent geometry : angle 0.56006 / 0.33 (15001) hydrogen bonds : bond 0.14059 / 9.51 ( 578) hydrogen bonds : angle 5.57755 / 3.93 ( 1668) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 201 time to evaluate : 0.412 Fit side-chains REVERT: A 280 GLN cc_start: 0.7655 (OUTLIER) cc_final: 0.7088 (mm110) outliers start: 25 outliers final: 8 residues processed: 220 average time/residue: 0.6211 time to fit residues: 147.1262 Evaluate side-chains 168 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 159 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 280 GLN Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 845 SER Chi-restraints excluded: chain A residue 847 VAL Chi-restraints excluded: chain A residue 1098 ASP Chi-restraints excluded: chain A residue 1229 VAL Chi-restraints excluded: chain A residue 1239 LEU Chi-restraints excluded: chain A residue 1247 VAL Chi-restraints excluded: chain A residue 1592 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 98 optimal weight: 0.5980 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 0.6980 chunk 55 optimal weight: 3.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 364 ASN A 592 GLN A 875 GLN A 936 GLN A1058 GLN A1078 GLN A1122 GLN A1268 ASN A1364 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.167867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.140139 restraints weight = 11643.733| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 0.98 r_work: 0.3251 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3150 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.2225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 11062 Z= 0.239 Angle : 0.663 8.913 15001 Z= 0.349 Chirality : 0.045 0.186 1675 Planarity : 0.005 0.062 1848 Dihedral : 9.513 151.758 1591 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 5.43 % Allowed : 19.48 % Favored : 75.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.23), residues: 1298 helix: 1.03 (0.20), residues: 721 sheet: 0.42 (0.51), residues: 93 loop : -0.78 (0.28), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 532 TYR 0.027 0.002 TYR A 912 PHE 0.023 0.002 PHE A 894 TRP 0.015 0.002 TRP A1338 HIS 0.007 0.001 HIS A 501 Details of bonding type rmsd/Z covalent geometry : bond 0.00553 / 0.24 (11062) covalent geometry : angle 0.66287 / 0.35 (15001) hydrogen bonds : bond 0.05727 / 3.75 ( 578) hydrogen bonds : angle 4.88670 / 3.42 ( 1668) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 168 time to evaluate : 0.443 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 253 ARG cc_start: 0.7822 (OUTLIER) cc_final: 0.7290 (mtm-85) REVERT: A 902 ARG cc_start: 0.7905 (OUTLIER) cc_final: 0.7519 (mmp-170) REVERT: A 1364 GLN cc_start: 0.7243 (OUTLIER) cc_final: 0.7019 (tt0) outliers start: 63 outliers final: 23 residues processed: 206 average time/residue: 0.5900 time to fit residues: 131.0729 Evaluate side-chains 175 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 149 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 ARG Chi-restraints excluded: chain A residue 358 GLN Chi-restraints excluded: chain A residue 411 ILE Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 666 SER Chi-restraints excluded: chain A residue 706 SER Chi-restraints excluded: chain A residue 734 ASN Chi-restraints excluded: chain A residue 743 LEU Chi-restraints excluded: chain A residue 845 SER Chi-restraints excluded: chain A residue 847 VAL Chi-restraints excluded: chain A residue 902 ARG Chi-restraints excluded: chain A residue 949 GLU Chi-restraints excluded: chain A residue 1098 ASP Chi-restraints excluded: chain A residue 1114 THR Chi-restraints excluded: chain A residue 1188 ILE Chi-restraints excluded: chain A residue 1204 ASP Chi-restraints excluded: chain A residue 1229 VAL Chi-restraints excluded: chain A residue 1239 LEU Chi-restraints excluded: chain A residue 1247 VAL Chi-restraints excluded: chain A residue 1259 THR Chi-restraints excluded: chain A residue 1281 ILE Chi-restraints excluded: chain A residue 1364 GLN Chi-restraints excluded: chain A residue 1408 MET Chi-restraints excluded: chain A residue 1415 LYS Chi-restraints excluded: chain A residue 1427 ARG Chi-restraints excluded: chain A residue 1457 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 46 optimal weight: 2.9990 chunk 73 optimal weight: 0.8980 chunk 74 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 chunk 59 optimal weight: 0.6980 chunk 119 optimal weight: 9.9990 chunk 22 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 936 GLN A1058 GLN A1122 GLN A1268 ASN ** A1413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.166778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.138802 restraints weight = 11732.132| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 1.16 r_work: 0.3225 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3118 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.2570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 11062 Z= 0.205 Angle : 0.585 7.895 15001 Z= 0.308 Chirality : 0.042 0.178 1675 Planarity : 0.004 0.051 1848 Dihedral : 9.407 151.883 1587 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 4.74 % Allowed : 20.43 % Favored : 74.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.23), residues: 1298 helix: 1.12 (0.20), residues: 721 sheet: 0.42 (0.50), residues: 93 loop : -0.76 (0.28), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 650 TYR 0.019 0.002 TYR A 912 PHE 0.018 0.002 PHE A1132 TRP 0.014 0.002 TRP A1338 HIS 0.007 0.001 HIS A1413 Details of bonding type rmsd/Z covalent geometry : bond 0.00473 / 0.21 (11062) covalent geometry : angle 0.58454 / 0.31 (15001) hydrogen bonds : bond 0.05362 / 3.49 ( 578) hydrogen bonds : angle 4.76384 / 3.32 ( 1668) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 155 time to evaluate : 0.503 Fit side-chains revert: symmetry clash REVERT: A 236 ILE cc_start: 0.8773 (OUTLIER) cc_final: 0.8440 (pt) REVERT: A 902 ARG cc_start: 0.7991 (OUTLIER) cc_final: 0.7599 (mmp-170) REVERT: A 1355 SER cc_start: 0.8396 (t) cc_final: 0.8102 (m) outliers start: 55 outliers final: 27 residues processed: 189 average time/residue: 0.5339 time to fit residues: 109.4826 Evaluate side-chains 182 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 153 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 358 GLN Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 523 SER Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 549 ASP Chi-restraints excluded: chain A residue 666 SER Chi-restraints excluded: chain A residue 706 SER Chi-restraints excluded: chain A residue 734 ASN Chi-restraints excluded: chain A residue 743 LEU Chi-restraints excluded: chain A residue 845 SER Chi-restraints excluded: chain A residue 847 VAL Chi-restraints excluded: chain A residue 902 ARG Chi-restraints excluded: chain A residue 949 GLU Chi-restraints excluded: chain A residue 955 SER Chi-restraints excluded: chain A residue 1098 ASP Chi-restraints excluded: chain A residue 1114 THR Chi-restraints excluded: chain A residue 1188 ILE Chi-restraints excluded: chain A residue 1204 ASP Chi-restraints excluded: chain A residue 1229 VAL Chi-restraints excluded: chain A residue 1239 LEU Chi-restraints excluded: chain A residue 1247 VAL Chi-restraints excluded: chain A residue 1259 THR Chi-restraints excluded: chain A residue 1281 ILE Chi-restraints excluded: chain A residue 1393 VAL Chi-restraints excluded: chain A residue 1404 LEU Chi-restraints excluded: chain A residue 1408 MET Chi-restraints excluded: chain A residue 1457 THR Chi-restraints excluded: chain A residue 1554 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 50 optimal weight: 0.9990 chunk 16 optimal weight: 5.9990 chunk 42 optimal weight: 2.9990 chunk 12 optimal weight: 0.1980 chunk 99 optimal weight: 0.9990 chunk 124 optimal weight: 9.9990 chunk 78 optimal weight: 0.5980 chunk 56 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 102 optimal weight: 4.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 430 ASN A 936 GLN A1058 GLN A1122 GLN A1268 ASN A1364 GLN ** A1413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.169047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.141917 restraints weight = 11702.830| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 1.07 r_work: 0.3245 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3139 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.2805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 11062 Z= 0.165 Angle : 0.543 8.167 15001 Z= 0.286 Chirality : 0.040 0.139 1675 Planarity : 0.004 0.049 1848 Dihedral : 9.286 151.959 1587 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 5.00 % Allowed : 19.91 % Favored : 75.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.24), residues: 1298 helix: 1.27 (0.20), residues: 722 sheet: 0.50 (0.50), residues: 93 loop : -0.73 (0.28), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 650 TYR 0.018 0.002 TYR A 912 PHE 0.020 0.002 PHE A 894 TRP 0.012 0.002 TRP A 473 HIS 0.008 0.001 HIS A1413 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.16 (11062) covalent geometry : angle 0.54284 / 0.29 (15001) hydrogen bonds : bond 0.04781 / 3.12 ( 578) hydrogen bonds : angle 4.63189 / 3.23 ( 1668) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 158 time to evaluate : 0.443 Fit side-chains revert: symmetry clash REVERT: A 236 ILE cc_start: 0.8744 (OUTLIER) cc_final: 0.8434 (pt) REVERT: A 902 ARG cc_start: 0.7959 (OUTLIER) cc_final: 0.7538 (mmp-170) REVERT: A 1022 LYS cc_start: 0.8901 (ttmm) cc_final: 0.8686 (tttp) REVERT: A 1355 SER cc_start: 0.8314 (t) cc_final: 0.8013 (m) outliers start: 58 outliers final: 26 residues processed: 194 average time/residue: 0.5404 time to fit residues: 113.6262 Evaluate side-chains 182 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 154 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 358 GLN Chi-restraints excluded: chain A residue 523 SER Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 549 ASP Chi-restraints excluded: chain A residue 666 SER Chi-restraints excluded: chain A residue 706 SER Chi-restraints excluded: chain A residue 719 GLU Chi-restraints excluded: chain A residue 743 LEU Chi-restraints excluded: chain A residue 845 SER Chi-restraints excluded: chain A residue 847 VAL Chi-restraints excluded: chain A residue 902 ARG Chi-restraints excluded: chain A residue 949 GLU Chi-restraints excluded: chain A residue 952 ILE Chi-restraints excluded: chain A residue 963 LYS Chi-restraints excluded: chain A residue 1098 ASP Chi-restraints excluded: chain A residue 1114 THR Chi-restraints excluded: chain A residue 1229 VAL Chi-restraints excluded: chain A residue 1239 LEU Chi-restraints excluded: chain A residue 1247 VAL Chi-restraints excluded: chain A residue 1259 THR Chi-restraints excluded: chain A residue 1281 ILE Chi-restraints excluded: chain A residue 1398 MET Chi-restraints excluded: chain A residue 1404 LEU Chi-restraints excluded: chain A residue 1408 MET Chi-restraints excluded: chain A residue 1457 THR Chi-restraints excluded: chain A residue 1481 VAL Chi-restraints excluded: chain A residue 1554 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 19 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 30 optimal weight: 2.9990 chunk 109 optimal weight: 2.9990 chunk 123 optimal weight: 0.9990 chunk 48 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 413 GLN A 430 ASN A 736 ASN A 936 GLN A1058 GLN A1122 GLN A1268 ASN A1434 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.165937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.138077 restraints weight = 11710.837| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 1.09 r_work: 0.3210 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3101 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.3011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 11062 Z= 0.236 Angle : 0.614 8.514 15001 Z= 0.323 Chirality : 0.043 0.198 1675 Planarity : 0.005 0.051 1848 Dihedral : 9.371 151.328 1587 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 4.83 % Allowed : 21.55 % Favored : 73.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.23), residues: 1298 helix: 1.13 (0.20), residues: 721 sheet: 0.44 (0.50), residues: 93 loop : -0.86 (0.28), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG A1427 TYR 0.024 0.002 TYR A 912 PHE 0.020 0.002 PHE A 894 TRP 0.015 0.002 TRP A1338 HIS 0.011 0.001 HIS A1413 Details of bonding type rmsd/Z covalent geometry : bond 0.00550 / 0.24 (11062) covalent geometry : angle 0.61350 / 0.32 (15001) hydrogen bonds : bond 0.05433 / 3.53 ( 578) hydrogen bonds : angle 4.77132 / 3.33 ( 1668) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 159 time to evaluate : 0.361 Fit side-chains revert: symmetry clash REVERT: A 236 ILE cc_start: 0.8779 (OUTLIER) cc_final: 0.8504 (pt) REVERT: A 902 ARG cc_start: 0.8028 (OUTLIER) cc_final: 0.7606 (mmp-170) REVERT: A 1022 LYS cc_start: 0.8960 (ttmm) cc_final: 0.8738 (tttp) REVERT: A 1196 LEU cc_start: 0.5397 (OUTLIER) cc_final: 0.5182 (tm) REVERT: A 1355 SER cc_start: 0.8346 (t) cc_final: 0.8038 (m) REVERT: A 1408 MET cc_start: 0.7242 (OUTLIER) cc_final: 0.7002 (ttt) outliers start: 56 outliers final: 29 residues processed: 197 average time/residue: 0.4866 time to fit residues: 103.9286 Evaluate side-chains 187 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 154 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 297 SER Chi-restraints excluded: chain A residue 358 GLN Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 523 SER Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 549 ASP Chi-restraints excluded: chain A residue 666 SER Chi-restraints excluded: chain A residue 706 SER Chi-restraints excluded: chain A residue 719 GLU Chi-restraints excluded: chain A residue 743 LEU Chi-restraints excluded: chain A residue 845 SER Chi-restraints excluded: chain A residue 847 VAL Chi-restraints excluded: chain A residue 864 SER Chi-restraints excluded: chain A residue 902 ARG Chi-restraints excluded: chain A residue 949 GLU Chi-restraints excluded: chain A residue 952 ILE Chi-restraints excluded: chain A residue 955 SER Chi-restraints excluded: chain A residue 1098 ASP Chi-restraints excluded: chain A residue 1114 THR Chi-restraints excluded: chain A residue 1188 ILE Chi-restraints excluded: chain A residue 1196 LEU Chi-restraints excluded: chain A residue 1229 VAL Chi-restraints excluded: chain A residue 1239 LEU Chi-restraints excluded: chain A residue 1247 VAL Chi-restraints excluded: chain A residue 1259 THR Chi-restraints excluded: chain A residue 1281 ILE Chi-restraints excluded: chain A residue 1398 MET Chi-restraints excluded: chain A residue 1408 MET Chi-restraints excluded: chain A residue 1457 THR Chi-restraints excluded: chain A residue 1481 VAL Chi-restraints excluded: chain A residue 1516 GLU Chi-restraints excluded: chain A residue 1554 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 48 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 73 optimal weight: 0.5980 chunk 4 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 98 optimal weight: 0.9990 chunk 131 optimal weight: 5.9990 overall best weight: 1.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 363 GLN A 430 ASN A 886 GLN A 936 GLN A1268 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.166529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.138820 restraints weight = 11680.793| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 1.12 r_work: 0.3224 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3117 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.3147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 11062 Z= 0.200 Angle : 0.579 8.295 15001 Z= 0.306 Chirality : 0.042 0.157 1675 Planarity : 0.004 0.050 1848 Dihedral : 9.322 150.822 1587 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.70 % Favored : 97.23 % Rotamer: Outliers : 4.05 % Allowed : 22.50 % Favored : 73.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.23), residues: 1298 helix: 1.15 (0.20), residues: 722 sheet: 0.43 (0.49), residues: 93 loop : -0.87 (0.27), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 650 TYR 0.021 0.002 TYR A 912 PHE 0.022 0.002 PHE A1132 TRP 0.014 0.002 TRP A1338 HIS 0.004 0.001 HIS A1130 Details of bonding type rmsd/Z covalent geometry : bond 0.00462 / 0.20 (11062) covalent geometry : angle 0.57948 / 0.31 (15001) hydrogen bonds : bond 0.05114 / 3.33 ( 578) hydrogen bonds : angle 4.70775 / 3.29 ( 1668) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 156 time to evaluate : 0.292 Fit side-chains revert: symmetry clash REVERT: A 236 ILE cc_start: 0.8796 (OUTLIER) cc_final: 0.8523 (pt) REVERT: A 461 LYS cc_start: 0.7650 (mptt) cc_final: 0.7404 (mptt) REVERT: A 902 ARG cc_start: 0.8036 (OUTLIER) cc_final: 0.7587 (mmp-170) REVERT: A 1022 LYS cc_start: 0.8928 (ttmm) cc_final: 0.8700 (tttp) REVERT: A 1033 LEU cc_start: 0.8757 (OUTLIER) cc_final: 0.8399 (mt) REVERT: A 1107 LEU cc_start: 0.8935 (OUTLIER) cc_final: 0.8697 (mm) REVERT: A 1196 LEU cc_start: 0.5386 (OUTLIER) cc_final: 0.5158 (tm) REVERT: A 1355 SER cc_start: 0.8352 (t) cc_final: 0.8026 (m) REVERT: A 1408 MET cc_start: 0.7275 (OUTLIER) cc_final: 0.7059 (ttt) outliers start: 47 outliers final: 25 residues processed: 188 average time/residue: 0.5365 time to fit residues: 109.3618 Evaluate side-chains 186 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 155 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 523 SER Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 549 ASP Chi-restraints excluded: chain A residue 666 SER Chi-restraints excluded: chain A residue 706 SER Chi-restraints excluded: chain A residue 719 GLU Chi-restraints excluded: chain A residue 734 ASN Chi-restraints excluded: chain A residue 743 LEU Chi-restraints excluded: chain A residue 845 SER Chi-restraints excluded: chain A residue 847 VAL Chi-restraints excluded: chain A residue 864 SER Chi-restraints excluded: chain A residue 902 ARG Chi-restraints excluded: chain A residue 949 GLU Chi-restraints excluded: chain A residue 952 ILE Chi-restraints excluded: chain A residue 955 SER Chi-restraints excluded: chain A residue 1033 LEU Chi-restraints excluded: chain A residue 1098 ASP Chi-restraints excluded: chain A residue 1107 LEU Chi-restraints excluded: chain A residue 1114 THR Chi-restraints excluded: chain A residue 1196 LEU Chi-restraints excluded: chain A residue 1229 VAL Chi-restraints excluded: chain A residue 1239 LEU Chi-restraints excluded: chain A residue 1259 THR Chi-restraints excluded: chain A residue 1281 ILE Chi-restraints excluded: chain A residue 1398 MET Chi-restraints excluded: chain A residue 1408 MET Chi-restraints excluded: chain A residue 1457 THR Chi-restraints excluded: chain A residue 1481 VAL Chi-restraints excluded: chain A residue 1516 GLU Chi-restraints excluded: chain A residue 1554 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 110 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 126 optimal weight: 0.5980 chunk 67 optimal weight: 8.9990 chunk 20 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 84 optimal weight: 0.3980 chunk 10 optimal weight: 0.7980 chunk 15 optimal weight: 0.8980 chunk 63 optimal weight: 2.9990 chunk 122 optimal weight: 0.0670 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 363 GLN A 430 ASN A 886 GLN A 936 GLN A1268 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.168293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.138622 restraints weight = 11674.655| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 1.16 r_work: 0.3223 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3112 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.3155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11062 Z= 0.127 Angle : 0.516 7.808 15001 Z= 0.274 Chirality : 0.039 0.139 1675 Planarity : 0.004 0.046 1848 Dihedral : 9.186 151.404 1586 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.31 % Favored : 97.61 % Rotamer: Outliers : 3.28 % Allowed : 22.93 % Favored : 73.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.23), residues: 1298 helix: 1.39 (0.20), residues: 722 sheet: 0.51 (0.49), residues: 93 loop : -0.78 (0.28), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 650 TYR 0.016 0.001 TYR A 912 PHE 0.024 0.001 PHE A1132 TRP 0.013 0.002 TRP A 473 HIS 0.004 0.001 HIS A1413 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.13 (11062) covalent geometry : angle 0.51644 / 0.27 (15001) hydrogen bonds : bond 0.04372 / 2.85 ( 578) hydrogen bonds : angle 4.55957 / 3.18 ( 1668) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 154 time to evaluate : 0.355 Fit side-chains revert: symmetry clash REVERT: A 236 ILE cc_start: 0.8793 (OUTLIER) cc_final: 0.8509 (pt) REVERT: A 902 ARG cc_start: 0.7983 (OUTLIER) cc_final: 0.7579 (mmp-170) REVERT: A 1196 LEU cc_start: 0.5514 (OUTLIER) cc_final: 0.5271 (tm) REVERT: A 1355 SER cc_start: 0.8332 (t) cc_final: 0.8014 (m) REVERT: A 1408 MET cc_start: 0.7240 (OUTLIER) cc_final: 0.7033 (ttt) outliers start: 38 outliers final: 21 residues processed: 181 average time/residue: 0.5665 time to fit residues: 111.6239 Evaluate side-chains 175 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 150 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 523 SER Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 549 ASP Chi-restraints excluded: chain A residue 666 SER Chi-restraints excluded: chain A residue 706 SER Chi-restraints excluded: chain A residue 743 LEU Chi-restraints excluded: chain A residue 847 VAL Chi-restraints excluded: chain A residue 902 ARG Chi-restraints excluded: chain A residue 949 GLU Chi-restraints excluded: chain A residue 952 ILE Chi-restraints excluded: chain A residue 955 SER Chi-restraints excluded: chain A residue 1098 ASP Chi-restraints excluded: chain A residue 1114 THR Chi-restraints excluded: chain A residue 1196 LEU Chi-restraints excluded: chain A residue 1229 VAL Chi-restraints excluded: chain A residue 1239 LEU Chi-restraints excluded: chain A residue 1247 VAL Chi-restraints excluded: chain A residue 1259 THR Chi-restraints excluded: chain A residue 1281 ILE Chi-restraints excluded: chain A residue 1398 MET Chi-restraints excluded: chain A residue 1408 MET Chi-restraints excluded: chain A residue 1457 THR Chi-restraints excluded: chain A residue 1481 VAL Chi-restraints excluded: chain A residue 1554 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 110 optimal weight: 1.9990 chunk 38 optimal weight: 0.5980 chunk 126 optimal weight: 0.9990 chunk 58 optimal weight: 0.6980 chunk 3 optimal weight: 2.9990 chunk 17 optimal weight: 5.9990 chunk 103 optimal weight: 1.9990 chunk 105 optimal weight: 0.9980 chunk 46 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 109 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 734 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 886 GLN A 936 GLN A1268 ASN ** A1413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1482 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.167665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.139575 restraints weight = 11603.593| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 1.22 r_work: 0.3228 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3121 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.3250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11062 Z= 0.175 Angle : 0.558 8.052 15001 Z= 0.296 Chirality : 0.041 0.137 1675 Planarity : 0.004 0.046 1848 Dihedral : 9.187 151.237 1585 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.62 % Favored : 97.30 % Rotamer: Outliers : 2.84 % Allowed : 23.88 % Favored : 73.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.23), residues: 1298 helix: 1.32 (0.20), residues: 722 sheet: 0.53 (0.49), residues: 93 loop : -0.79 (0.28), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 892 TYR 0.019 0.002 TYR A 912 PHE 0.019 0.002 PHE A 894 TRP 0.012 0.002 TRP A 473 HIS 0.005 0.001 HIS A1413 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.17 (11062) covalent geometry : angle 0.55796 / 0.30 (15001) hydrogen bonds : bond 0.04803 / 3.12 ( 578) hydrogen bonds : angle 4.57283 / 3.19 ( 1668) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 154 time to evaluate : 0.415 Fit side-chains revert: symmetry clash REVERT: A 236 ILE cc_start: 0.8814 (OUTLIER) cc_final: 0.8550 (pt) REVERT: A 461 LYS cc_start: 0.7591 (mptt) cc_final: 0.7379 (mptt) REVERT: A 902 ARG cc_start: 0.7981 (OUTLIER) cc_final: 0.7562 (mmp-170) REVERT: A 1033 LEU cc_start: 0.8746 (OUTLIER) cc_final: 0.8418 (mt) REVERT: A 1107 LEU cc_start: 0.8939 (OUTLIER) cc_final: 0.8708 (mm) REVERT: A 1196 LEU cc_start: 0.5450 (OUTLIER) cc_final: 0.5212 (tm) REVERT: A 1402 LEU cc_start: 0.5001 (mt) cc_final: 0.4698 (mt) REVERT: A 1408 MET cc_start: 0.7249 (OUTLIER) cc_final: 0.6964 (ttp) outliers start: 33 outliers final: 22 residues processed: 179 average time/residue: 0.5643 time to fit residues: 109.4942 Evaluate side-chains 182 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 154 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 358 GLN Chi-restraints excluded: chain A residue 523 SER Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 549 ASP Chi-restraints excluded: chain A residue 666 SER Chi-restraints excluded: chain A residue 706 SER Chi-restraints excluded: chain A residue 743 LEU Chi-restraints excluded: chain A residue 847 VAL Chi-restraints excluded: chain A residue 902 ARG Chi-restraints excluded: chain A residue 949 GLU Chi-restraints excluded: chain A residue 952 ILE Chi-restraints excluded: chain A residue 955 SER Chi-restraints excluded: chain A residue 1033 LEU Chi-restraints excluded: chain A residue 1098 ASP Chi-restraints excluded: chain A residue 1107 LEU Chi-restraints excluded: chain A residue 1114 THR Chi-restraints excluded: chain A residue 1196 LEU Chi-restraints excluded: chain A residue 1239 LEU Chi-restraints excluded: chain A residue 1247 VAL Chi-restraints excluded: chain A residue 1259 THR Chi-restraints excluded: chain A residue 1281 ILE Chi-restraints excluded: chain A residue 1398 MET Chi-restraints excluded: chain A residue 1408 MET Chi-restraints excluded: chain A residue 1457 THR Chi-restraints excluded: chain A residue 1481 VAL Chi-restraints excluded: chain A residue 1516 GLU Chi-restraints excluded: chain A residue 1554 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 80 optimal weight: 0.8980 chunk 130 optimal weight: 6.9990 chunk 118 optimal weight: 0.8980 chunk 35 optimal weight: 2.9990 chunk 16 optimal weight: 4.9990 chunk 83 optimal weight: 0.0570 chunk 26 optimal weight: 0.9990 chunk 42 optimal weight: 0.5980 chunk 31 optimal weight: 0.9980 chunk 129 optimal weight: 0.6980 chunk 45 optimal weight: 0.8980 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 363 GLN A 456 GLN ** A 734 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 886 GLN A 936 GLN A1268 ASN ** A1413 HIS ** 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 = 0.3783 r_free = 0.3783 target = 0.169094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.142095 restraints weight = 11608.405| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 1.06 r_work: 0.3264 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3155 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.3257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11062 Z= 0.130 Angle : 0.519 7.693 15001 Z= 0.275 Chirality : 0.039 0.137 1675 Planarity : 0.004 0.044 1848 Dihedral : 9.087 151.637 1584 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.31 % Favored : 97.61 % Rotamer: Outliers : 3.36 % Allowed : 23.62 % Favored : 73.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.23), residues: 1298 helix: 1.44 (0.20), residues: 722 sheet: 0.55 (0.50), residues: 93 loop : -0.72 (0.28), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 650 TYR 0.015 0.001 TYR A 912 PHE 0.018 0.001 PHE A 894 TRP 0.013 0.002 TRP A 473 HIS 0.003 0.001 HIS A1413 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 (11062) covalent geometry : angle 0.51918 / 0.27 (15001) hydrogen bonds : bond 0.04308 / 2.80 ( 578) hydrogen bonds : angle 4.46878 / 3.13 ( 1668) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 149 time to evaluate : 0.429 Fit side-chains revert: symmetry clash REVERT: A 236 ILE cc_start: 0.8800 (OUTLIER) cc_final: 0.8516 (pt) REVERT: A 886 GLN cc_start: 0.8837 (OUTLIER) cc_final: 0.8633 (pt0) REVERT: A 902 ARG cc_start: 0.7946 (OUTLIER) cc_final: 0.7528 (mmp-170) REVERT: A 1033 LEU cc_start: 0.8735 (OUTLIER) cc_final: 0.8404 (mt) REVERT: A 1196 LEU cc_start: 0.5368 (OUTLIER) cc_final: 0.5126 (tm) REVERT: A 1316 LYS cc_start: 0.8128 (ttpp) cc_final: 0.7728 (ptmm) REVERT: A 1408 MET cc_start: 0.7212 (OUTLIER) cc_final: 0.6958 (ttp) outliers start: 39 outliers final: 22 residues processed: 177 average time/residue: 0.5882 time to fit residues: 112.6780 Evaluate side-chains 178 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 150 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 358 GLN Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 523 SER Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 549 ASP Chi-restraints excluded: chain A residue 706 SER Chi-restraints excluded: chain A residue 743 LEU Chi-restraints excluded: chain A residue 847 VAL Chi-restraints excluded: chain A residue 886 GLN Chi-restraints excluded: chain A residue 902 ARG Chi-restraints excluded: chain A residue 949 GLU Chi-restraints excluded: chain A residue 952 ILE Chi-restraints excluded: chain A residue 955 SER Chi-restraints excluded: chain A residue 1033 LEU Chi-restraints excluded: chain A residue 1098 ASP Chi-restraints excluded: chain A residue 1114 THR Chi-restraints excluded: chain A residue 1196 LEU Chi-restraints excluded: chain A residue 1229 VAL Chi-restraints excluded: chain A residue 1239 LEU Chi-restraints excluded: chain A residue 1247 VAL Chi-restraints excluded: chain A residue 1259 THR Chi-restraints excluded: chain A residue 1281 ILE Chi-restraints excluded: chain A residue 1398 MET Chi-restraints excluded: chain A residue 1408 MET Chi-restraints excluded: chain A residue 1457 THR Chi-restraints excluded: chain A residue 1481 VAL Chi-restraints excluded: chain A residue 1554 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 122 optimal weight: 2.9990 chunk 84 optimal weight: 0.9990 chunk 71 optimal weight: 2.9990 chunk 110 optimal weight: 0.9980 chunk 103 optimal weight: 1.9990 chunk 123 optimal weight: 0.9980 chunk 112 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 118 optimal weight: 0.8980 chunk 41 optimal weight: 0.9990 chunk 124 optimal weight: 9.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 280 GLN A 363 GLN A 430 ASN ** A 734 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 886 GLN A 936 GLN ** A1413 HIS ** 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 = 0.3773 r_free = 0.3773 target = 0.168163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.141086 restraints weight = 11643.018| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 0.94 r_work: 0.3273 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3166 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.3307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 11062 Z= 0.165 Angle : 0.551 7.603 15001 Z= 0.291 Chirality : 0.041 0.136 1675 Planarity : 0.004 0.045 1848 Dihedral : 9.091 151.533 1584 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.77 % Favored : 97.15 % Rotamer: Outliers : 3.10 % Allowed : 23.71 % Favored : 73.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.23), residues: 1298 helix: 1.37 (0.20), residues: 718 sheet: 0.57 (0.50), residues: 93 loop : -0.80 (0.28), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 892 TYR 0.018 0.002 TYR A 912 PHE 0.018 0.002 PHE A 894 TRP 0.011 0.002 TRP A 976 HIS 0.005 0.001 HIS A1413 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.17 (11062) covalent geometry : angle 0.55089 / 0.29 (15001) hydrogen bonds : bond 0.04597 / 2.99 ( 578) hydrogen bonds : angle 4.51302 / 3.16 ( 1668) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 150 time to evaluate : 0.422 Fit side-chains revert: symmetry clash REVERT: A 236 ILE cc_start: 0.8801 (OUTLIER) cc_final: 0.8518 (pt) REVERT: A 461 LYS cc_start: 0.7525 (mptt) cc_final: 0.7280 (mptt) REVERT: A 902 ARG cc_start: 0.7919 (OUTLIER) cc_final: 0.7485 (mmp-170) REVERT: A 1033 LEU cc_start: 0.8706 (OUTLIER) cc_final: 0.8368 (mt) REVERT: A 1107 LEU cc_start: 0.8897 (OUTLIER) cc_final: 0.8671 (mm) REVERT: A 1196 LEU cc_start: 0.5540 (OUTLIER) cc_final: 0.5303 (tm) REVERT: A 1316 LYS cc_start: 0.8134 (ttpp) cc_final: 0.7757 (ptmm) REVERT: A 1402 LEU cc_start: 0.4944 (mt) cc_final: 0.4627 (mt) REVERT: A 1408 MET cc_start: 0.7196 (OUTLIER) cc_final: 0.6932 (ttp) outliers start: 36 outliers final: 23 residues processed: 178 average time/residue: 0.5778 time to fit residues: 111.7223 Evaluate side-chains 179 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 150 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 358 GLN Chi-restraints excluded: chain A residue 523 SER Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 549 ASP Chi-restraints excluded: chain A residue 666 SER Chi-restraints excluded: chain A residue 706 SER Chi-restraints excluded: chain A residue 743 LEU Chi-restraints excluded: chain A residue 847 VAL Chi-restraints excluded: chain A residue 902 ARG Chi-restraints excluded: chain A residue 917 LYS Chi-restraints excluded: chain A residue 949 GLU Chi-restraints excluded: chain A residue 952 ILE Chi-restraints excluded: chain A residue 955 SER Chi-restraints excluded: chain A residue 1033 LEU Chi-restraints excluded: chain A residue 1098 ASP Chi-restraints excluded: chain A residue 1107 LEU Chi-restraints excluded: chain A residue 1114 THR Chi-restraints excluded: chain A residue 1196 LEU Chi-restraints excluded: chain A residue 1229 VAL Chi-restraints excluded: chain A residue 1239 LEU Chi-restraints excluded: chain A residue 1247 VAL Chi-restraints excluded: chain A residue 1259 THR Chi-restraints excluded: chain A residue 1281 ILE Chi-restraints excluded: chain A residue 1398 MET Chi-restraints excluded: chain A residue 1408 MET Chi-restraints excluded: chain A residue 1457 THR Chi-restraints excluded: chain A residue 1481 VAL Chi-restraints excluded: chain A residue 1554 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 27 optimal weight: 0.6980 chunk 129 optimal weight: 0.0030 chunk 17 optimal weight: 4.9990 chunk 34 optimal weight: 0.0010 chunk 81 optimal weight: 1.9990 chunk 28 optimal weight: 0.5980 chunk 117 optimal weight: 5.9990 chunk 15 optimal weight: 3.9990 chunk 67 optimal weight: 4.9990 chunk 50 optimal weight: 0.7980 chunk 29 optimal weight: 0.9980 overall best weight: 0.4196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 280 GLN A 886 GLN A 936 GLN ** A1413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.171857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.145410 restraints weight = 11717.024| |-----------------------------------------------------------------------------| r_work (start): 0.3499 rms_B_bonded: 1.03 r_work: 0.3294 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3188 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.3314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11062 Z= 0.118 Angle : 0.510 7.239 15001 Z= 0.270 Chirality : 0.038 0.135 1675 Planarity : 0.004 0.043 1848 Dihedral : 9.019 152.236 1584 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.39 % Favored : 97.53 % Rotamer: Outliers : 2.33 % Allowed : 24.57 % Favored : 73.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.89 (0.23), residues: 1298 helix: 1.50 (0.20), residues: 717 sheet: 0.59 (0.50), residues: 93 loop : -0.75 (0.28), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 650 TYR 0.015 0.001 TYR A 912 PHE 0.016 0.001 PHE A 894 TRP 0.013 0.001 TRP A 473 HIS 0.006 0.001 HIS A1413 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.12 (11062) covalent geometry : angle 0.50981 / 0.27 (15001) hydrogen bonds : bond 0.04074 / 2.66 ( 578) hydrogen bonds : angle 4.39836 / 3.08 ( 1668) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3896.24 seconds wall clock time: 67 minutes 19.84 seconds (4039.84 seconds total)