Starting phenix.real_space_refine on Sat Jul 4 13:16:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8p1n_17355/07_2026/8p1n_17355.cif Found real_map, /net/cci-nas-00/data/ceres_data/8p1n_17355/07_2026/8p1n_17355.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.79 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8p1n_17355/07_2026/8p1n_17355.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8p1n_17355/07_2026/8p1n_17355.map" model { file = "/net/cci-nas-00/data/ceres_data/8p1n_17355/07_2026/8p1n_17355.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8p1n_17355/07_2026/8p1n_17355.cif" } resolution = 2.79 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= 0.054 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 5 5.49 5 S 56 5.16 5 C 6718 2.51 5 N 1760 2.21 5 O 1931 1.98 5 H 10405 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 20875 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 20765 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1287, 20765 Classifications: {'peptide': 1287} Link IDs: {'PTRANS': 42, 'TRANS': 1244} Chain breaks: 5 Chain: "B" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 110 Classifications: {'RNA': 5} Modifications used: {'rna3p_pur': 4, 'rna3p_pyr': 1} Link IDs: {'rna3p': 4} Time building chain proxies: 3.33, per 1000 atoms: 0.16 Number of scatterers: 20875 At special positions: 0 Unit cell: (88.54, 103.452, 123.024, 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 56 16.00 P 5 15.00 O 1931 8.00 N 1760 7.00 C 6718 6.00 H 10405 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.04 Conformation dependent library (CDL) restraints added in 581.8 milliseconds 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2456 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 12 sheets defined 57.3% alpha, 9.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.53 Creating SS restraints... Processing helix chain 'A' and resid 239 through 252 removed outlier: 4.085A pdb=" N LEU A 243 " --> pdb=" O ASN A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 279 removed outlier: 3.934A pdb=" N CYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) 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 354 Processing helix chain 'A' and resid 355 through 359 removed outlier: 3.536A pdb=" N PHE A 359 " --> pdb=" O ARG A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 391 removed outlier: 3.773A pdb=" N MET A 385 " --> pdb=" O GLU A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 416 removed outlier: 3.558A pdb=" N SER A 416 " --> pdb=" O VAL A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 427 removed outlier: 3.975A pdb=" N LYS A 422 " --> pdb=" O SER A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 458 removed outlier: 3.751A pdb=" N ASN A 457 " --> pdb=" O LYS A 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 463 Processing helix chain 'A' and resid 463 through 468 Processing helix chain 'A' and resid 470 through 489 removed outlier: 3.699A pdb=" N HIS A 474 " --> pdb=" O THR A 470 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N HIS A 477 " --> pdb=" O TRP A 473 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 541 No H-bonds generated for 'chain 'A' and resid 539 through 541' Processing helix chain 'A' and resid 563 through 571 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: 3.522A pdb=" N ARG A 627 " --> pdb=" O PHE A 623 " (cutoff:3.500A) removed outlier: 3.967A 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 656 through 673 removed outlier: 3.715A pdb=" N TYR A 662 " --> pdb=" O VAL A 658 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER A 666 " --> pdb=" O TYR A 662 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLN A 673 " --> pdb=" O VAL A 669 " (cutoff:3.500A) Processing helix chain 'A' and resid 712 through 725 removed outlier: 3.875A pdb=" N LEU A 716 " --> pdb=" O HIS A 712 " (cutoff:3.500A) Processing helix chain 'A' and resid 733 through 767 removed outlier: 3.956A pdb=" N HIS A 742 " --> pdb=" O GLU A 738 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLU A 744 " --> pdb=" O LYS A 740 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N THR A 745 " --> pdb=" O ILE A 741 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N GLU A 761 " --> pdb=" O GLU A 757 " (cutoff:3.500A) removed outlier: 9.357A pdb=" N SER A 762 " --> pdb=" O LYS A 758 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N LEU A 763 " --> pdb=" O TYR A 759 " (cutoff:3.500A) Processing helix chain 'A' and resid 769 through 777 Processing helix chain 'A' and resid 786 through 802 removed outlier: 3.854A 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 858 Processing helix chain 'A' and resid 864 through 872 removed outlier: 3.721A pdb=" N GLU A 871 " --> pdb=" O LYS A 867 " (cutoff:3.500A) Processing helix chain 'A' and resid 898 through 917 Processing helix chain 'A' and resid 929 through 947 removed outlier: 4.225A pdb=" N LEU A 933 " --> pdb=" O GLU A 929 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 992 removed outlier: 4.002A pdb=" N ARG A 986 " --> pdb=" O SER A 982 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ARG A 987 " --> pdb=" O ALA A 983 " (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 1061 through 1084 removed outlier: 3.547A pdb=" N LEU A1067 " --> pdb=" O LYS A1063 " (cutoff:3.500A) Processing helix chain 'A' and resid 1113 through 1126 removed outlier: 3.604A pdb=" N LEU A1118 " --> pdb=" O THR A1114 " (cutoff:3.500A) Processing helix chain 'A' and resid 1128 through 1135 removed outlier: 4.050A pdb=" N ASN A1135 " --> pdb=" O PHE A1132 " (cutoff:3.500A) Processing helix chain 'A' and resid 1137 through 1153 removed outlier: 3.883A pdb=" N SER A1141 " --> pdb=" O GLU A1137 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLY A1153 " --> pdb=" O ILE A1149 " (cutoff:3.500A) Processing helix chain 'A' and resid 1185 through 1192 Processing helix chain 'A' and resid 1200 through 1218 Processing helix chain 'A' and resid 1223 through 1240 Processing helix chain 'A' and resid 1249 through 1254 removed outlier: 4.062A pdb=" N TYR A1253 " --> pdb=" O HIS A1249 " (cutoff:3.500A) Processing helix chain 'A' and resid 1262 through 1266 Processing helix chain 'A' and resid 1272 through 1277 Processing helix chain 'A' and resid 1282 through 1300 removed outlier: 4.057A pdb=" N LYS A1286 " --> pdb=" O GLY A1282 " (cutoff:3.500A) Processing helix chain 'A' and resid 1301 through 1318 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 1387 Processing helix chain 'A' and resid 1389 through 1397 Processing helix chain 'A' and resid 1401 through 1412 removed outlier: 4.770A pdb=" N GLN A1409 " --> pdb=" O ARG A1405 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N ALA A1410 " --> pdb=" O PHE A1406 " (cutoff:3.500A) Processing helix chain 'A' and resid 1425 through 1439 Processing helix chain 'A' and resid 1443 through 1454 Processing helix chain 'A' and resid 1502 through 1511 removed outlier: 3.662A pdb=" N PHE A1511 " --> pdb=" O ILE A1507 " (cutoff:3.500A) Processing helix chain 'A' and resid 1514 through 1524 Processing helix chain 'A' and resid 1527 through 1529 No H-bonds generated for 'chain 'A' and resid 1527 through 1529' Processing helix chain 'A' and resid 1530 through 1544 Processing helix chain 'A' and resid 1555 through 1564 Proline residue: A1561 - end of helix removed outlier: 3.650A pdb=" N TYR A1564 " --> pdb=" O ALA A1560 " (cutoff:3.500A) Processing helix chain 'A' and resid 1581 through 1592 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 284 through 285 Processing sheet with id=AA3, first strand: chain 'A' and resid 296 through 297 Processing sheet with id=AA4, first strand: chain 'A' and resid 499 through 503 removed outlier: 5.010A pdb=" N THR A 529 " --> pdb=" O SER A 557 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 499 through 503 Processing sheet with id=AA6, first strand: chain 'A' and resid 701 through 702 Processing sheet with id=AA7, first strand: chain 'A' and resid 832 through 837 removed outlier: 5.378A pdb=" N SER A 844 " --> pdb=" O GLY A 835 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 893 through 897 removed outlier: 4.275A pdb=" N ALA A 877 " --> pdb=" O LYS A1014 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N ILE A 881 " --> pdb=" O PHE A1018 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 949 through 953 Processing sheet with id=AB1, first strand: chain 'A' and resid 1169 through 1171 Processing sheet with id=AB2, first strand: chain 'A' and resid 1417 through 1419 Processing sheet with id=AB3, first strand: chain 'A' and resid 1486 through 1490 removed outlier: 4.116A pdb=" N ARG A1570 " --> pdb=" O PHE A1490 " (cutoff:3.500A) 556 hydrogen bonds defined for protein. 1584 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.58 Time building geometry restraints manager: 2.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 10388 1.03 - 1.23: 61 1.23 - 1.43: 4502 1.43 - 1.62: 6071 1.62 - 1.82: 95 Bond restraints: 21117 Sorted by residual: bond pdb=" CG1 ILE A 790 " pdb=" CD1 ILE A 790 " ideal model delta sigma weight residual 1.513 1.462 0.051 3.90e-02 6.57e+02 1.68e+00 bond pdb=" N ASN A 956 " pdb=" CA ASN A 956 " ideal model delta sigma weight residual 1.457 1.471 -0.014 1.29e-02 6.01e+03 1.13e+00 bond pdb=" C ILE A1037 " pdb=" O ILE A1037 " ideal model delta sigma weight residual 1.241 1.228 0.013 1.25e-02 6.40e+03 1.04e+00 bond pdb=" CA ASN A 956 " pdb=" CB ASN A 956 " ideal model delta sigma weight residual 1.530 1.515 0.015 1.69e-02 3.50e+03 8.18e-01 bond pdb=" C VAL A 633 " pdb=" O VAL A 633 " ideal model delta sigma weight residual 1.241 1.230 0.011 1.25e-02 6.40e+03 7.07e-01 ... (remaining 21112 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.16: 38118 7.16 - 14.32: 0 14.32 - 21.47: 0 21.47 - 28.63: 0 28.63 - 35.79: 3 Bond angle restraints: 38121 Sorted by residual: angle pdb=" C SER A 970 " pdb=" CA SER A 970 " pdb=" HA SER A 970 " ideal model delta sigma weight residual 109.00 73.21 35.79 3.00e+00 1.11e-01 1.42e+02 angle pdb=" N SER A 970 " pdb=" CA SER A 970 " pdb=" HA SER A 970 " ideal model delta sigma weight residual 110.00 75.72 34.28 3.00e+00 1.11e-01 1.31e+02 angle pdb=" CB SER A 970 " pdb=" CA SER A 970 " pdb=" HA SER A 970 " ideal model delta sigma weight residual 109.00 74.88 34.12 3.00e+00 1.11e-01 1.29e+02 angle pdb=" N TYR A 659 " pdb=" CA TYR A 659 " pdb=" C TYR A 659 " ideal model delta sigma weight residual 112.68 108.53 4.15 1.33e+00 5.65e-01 9.74e+00 angle pdb=" N ILE A1037 " pdb=" CA ILE A1037 " pdb=" C ILE A1037 " ideal model delta sigma weight residual 113.47 110.42 3.05 1.01e+00 9.80e-01 9.11e+00 ... (remaining 38116 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 9185 17.95 - 35.91: 589 35.91 - 53.86: 127 53.86 - 71.81: 34 71.81 - 89.77: 5 Dihedral angle restraints: 9940 sinusoidal: 5372 harmonic: 4568 Sorted by residual: dihedral pdb=" CA ARG A 650 " pdb=" C ARG A 650 " pdb=" N PRO A 651 " pdb=" CA PRO A 651 " ideal model delta harmonic sigma weight residual 180.00 162.07 17.93 0 5.00e+00 4.00e-02 1.29e+01 dihedral pdb=" C SER A 970 " pdb=" N SER A 970 " pdb=" CA SER A 970 " pdb=" CB SER A 970 " ideal model delta harmonic sigma weight residual -122.60 -131.35 8.75 0 2.50e+00 1.60e-01 1.22e+01 dihedral pdb=" CA ASP A 544 " pdb=" CB ASP A 544 " pdb=" CG ASP A 544 " pdb=" OD1 ASP A 544 " ideal model delta sinusoidal sigma weight residual -30.00 -88.01 58.01 1 2.00e+01 2.50e-03 1.13e+01 ... (remaining 9937 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 1485 0.064 - 0.128: 125 0.128 - 0.192: 7 0.192 - 0.256: 0 0.256 - 0.320: 1 Chirality restraints: 1618 Sorted by residual: chirality pdb=" CA SER A 970 " pdb=" N SER A 970 " pdb=" C SER A 970 " pdb=" CB SER A 970 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.55e+00 chirality pdb=" CA ILE A 896 " pdb=" N ILE A 896 " pdb=" C ILE A 896 " pdb=" CB ILE A 896 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.58e-01 chirality pdb=" CA ILE A1183 " pdb=" N ILE A1183 " pdb=" C ILE A1183 " pdb=" CB ILE A1183 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.10e-01 ... (remaining 1615 not shown) Planarity restraints: 3045 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A1034 " -0.033 5.00e-02 4.00e+02 5.00e-02 4.01e+00 pdb=" N PRO A1035 " 0.087 5.00e-02 4.00e+02 pdb=" CA PRO A1035 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A1035 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLY A1245 " 0.010 2.00e-02 2.50e+03 1.96e-02 3.84e+00 pdb=" C GLY A1245 " -0.034 2.00e-02 2.50e+03 pdb=" O GLY A1245 " 0.013 2.00e-02 2.50e+03 pdb=" N MET A1246 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA A1560 " -0.023 5.00e-02 4.00e+02 3.52e-02 1.98e+00 pdb=" N PRO A1561 " 0.061 5.00e-02 4.00e+02 pdb=" CA PRO A1561 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO A1561 " -0.020 5.00e-02 4.00e+02 ... (remaining 3042 not shown) Histogram of nonbonded interaction distances: 1.50 - 2.12: 369 2.12 - 2.74: 37750 2.74 - 3.36: 61051 3.36 - 3.98: 78858 3.98 - 4.60: 126281 Nonbonded interactions: 304309 Sorted by model distance: nonbonded pdb=" OD1 ASN A 625 " pdb="HH21 ARG A 650 " model vdw 1.497 2.450 nonbonded pdb="HH22 ARG A 650 " pdb=" OE1 GLU A 889 " model vdw 1.571 2.450 nonbonded pdb=" O GLN A 875 " pdb="HH22 ARG A 904 " model vdw 1.573 2.450 nonbonded pdb=" O ASP A 972 " pdb=" H SER A1158 " model vdw 1.578 2.450 nonbonded pdb=" OD2 ASP A 539 " pdb="HD22 ASN A 542 " model vdw 1.594 2.450 ... (remaining 304304 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.920 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: 0.090 Extract box with map and model: 0.360 Check model and map are aligned: 0.080 Set scattering table: 0.040 Process input model: 18.840 Find NCS groups from input model: 0.090 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:6.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7424 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 0.051 10712 Z= 0.126 Angle : 0.523 5.571 14495 Z= 0.309 Chirality : 0.037 0.320 1618 Planarity : 0.003 0.050 1806 Dihedral : 12.882 89.767 3987 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.92 % Favored : 96.00 % Rotamer: Outliers : 0.00 % Allowed : 0.09 % Favored : 99.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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 (0.24), residues: 1275 helix: 0.41 (0.20), residues: 688 sheet: -0.36 (0.51), residues: 90 loop : -1.36 (0.28), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 650 TYR 0.014 0.001 TYR A 912 PHE 0.014 0.001 PHE A 585 TRP 0.010 0.001 TRP A 748 HIS 0.005 0.001 HIS A 732 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.13 (10712) covalent geometry : angle 0.52254 / 0.31 (14495) hydrogen bonds : bond 0.14761 / 9.77 ( 546) hydrogen bonds : angle 6.71997 / 4.69 ( 1584) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 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: 0 poor density : 183 time to evaluate : 0.553 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 233 MET cc_start: 0.8831 (mtp) cc_final: 0.8607 (mtp) REVERT: A 836 GLN cc_start: 0.8044 (mp10) cc_final: 0.7560 (mp10) REVERT: A 1257 LYS cc_start: 0.7303 (mtmt) cc_final: 0.6226 (mptt) REVERT: A 1348 GLU cc_start: 0.7243 (mt-10) cc_final: 0.6395 (mp0) REVERT: A 1408 MET cc_start: 0.6672 (tpp) cc_final: 0.6459 (mmm) REVERT: A 1448 ASP cc_start: 0.6457 (m-30) cc_final: 0.6137 (m-30) outliers start: 0 outliers final: 0 residues processed: 183 average time/residue: 1.1095 time to fit residues: 220.7059 Evaluate side-chains 147 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 147 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 7.9990 chunk 91 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1039 GLN A1125 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.146969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.119450 restraints weight = 36036.911| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 1.93 r_work: 0.3348 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3252 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7433 moved from start: 0.1006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 10712 Z= 0.232 Angle : 0.561 5.956 14495 Z= 0.300 Chirality : 0.040 0.322 1618 Planarity : 0.004 0.047 1806 Dihedral : 6.256 63.932 1468 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.02 % Favored : 94.90 % Rotamer: Outliers : 1.58 % Allowed : 6.93 % Favored : 91.49 % 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: -0.58 (0.23), residues: 1275 helix: 0.46 (0.20), residues: 699 sheet: -0.50 (0.49), residues: 94 loop : -1.56 (0.28), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 904 TYR 0.015 0.002 TYR A 912 PHE 0.017 0.002 PHE A 585 TRP 0.011 0.002 TRP A 771 HIS 0.006 0.001 HIS A 732 Details of bonding type rmsd/Z covalent geometry : bond 0.00559 / 0.23 (10712) covalent geometry : angle 0.56126 / 0.30 (14495) hydrogen bonds : bond 0.05169 / 3.41 ( 546) hydrogen bonds : angle 5.14771 / 3.67 ( 1584) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 144 time to evaluate : 0.583 Fit side-chains revert: symmetry clash REVERT: A 594 GLN cc_start: 0.7840 (OUTLIER) cc_final: 0.7392 (pt0) REVERT: A 1030 MET cc_start: 0.7215 (ttp) cc_final: 0.6488 (mtm) REVERT: A 1036 HIS cc_start: 0.7303 (m-70) cc_final: 0.6790 (t-170) REVERT: A 1246 MET cc_start: 0.6801 (mtm) cc_final: 0.6530 (ttm) REVERT: A 1257 LYS cc_start: 0.7075 (mtmt) cc_final: 0.5895 (mptt) REVERT: A 1348 GLU cc_start: 0.7430 (mt-10) cc_final: 0.6217 (mp0) REVERT: A 1448 ASP cc_start: 0.6272 (m-30) cc_final: 0.6006 (m-30) REVERT: A 1451 GLN cc_start: 0.7416 (OUTLIER) cc_final: 0.7110 (mt0) outliers start: 18 outliers final: 8 residues processed: 157 average time/residue: 1.1417 time to fit residues: 193.9092 Evaluate side-chains 152 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 142 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 457 ASN Chi-restraints excluded: chain A residue 485 SER Chi-restraints excluded: chain A residue 594 GLN Chi-restraints excluded: chain A residue 818 GLU Chi-restraints excluded: chain A residue 845 SER Chi-restraints excluded: chain A residue 954 LEU Chi-restraints excluded: chain A residue 1108 GLU Chi-restraints excluded: chain A residue 1451 GLN Chi-restraints excluded: chain A residue 1486 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 47 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 116 optimal weight: 6.9990 chunk 71 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 97 optimal weight: 5.9990 chunk 48 optimal weight: 0.6980 chunk 41 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 117 optimal weight: 5.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1039 GLN A1125 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.147514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.120031 restraints weight = 35721.225| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 1.93 r_work: 0.3351 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3257 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7433 moved from start: 0.1183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 10712 Z= 0.166 Angle : 0.508 5.799 14495 Z= 0.271 Chirality : 0.038 0.317 1618 Planarity : 0.004 0.046 1806 Dihedral : 6.210 63.874 1468 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.94 % Favored : 94.98 % Rotamer: Outliers : 1.32 % Allowed : 8.60 % Favored : 90.09 % 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: 1275 helix: 0.57 (0.19), residues: 698 sheet: -0.34 (0.49), residues: 92 loop : -1.51 (0.27), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 904 TYR 0.012 0.001 TYR A 912 PHE 0.018 0.001 PHE A 585 TRP 0.011 0.001 TRP A 771 HIS 0.006 0.001 HIS A1413 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.17 (10712) covalent geometry : angle 0.50802 / 0.27 (14495) hydrogen bonds : bond 0.04652 / 3.07 ( 546) hydrogen bonds : angle 4.90324 / 3.50 ( 1584) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 153 time to evaluate : 0.556 Fit side-chains revert: symmetry clash REVERT: A 594 GLN cc_start: 0.7866 (OUTLIER) cc_final: 0.7414 (pt0) REVERT: A 1030 MET cc_start: 0.7140 (ttp) cc_final: 0.6432 (mtm) REVERT: A 1036 HIS cc_start: 0.7228 (m-70) cc_final: 0.6810 (t-170) REVERT: A 1257 LYS cc_start: 0.7142 (mtmt) cc_final: 0.5968 (mptt) REVERT: A 1348 GLU cc_start: 0.7410 (mt-10) cc_final: 0.6211 (mp0) REVERT: A 1448 ASP cc_start: 0.6245 (m-30) cc_final: 0.6016 (m-30) REVERT: A 1451 GLN cc_start: 0.7343 (OUTLIER) cc_final: 0.6961 (mt0) REVERT: A 1483 ARG cc_start: 0.5730 (mtt180) cc_final: 0.5412 (mmp80) outliers start: 15 outliers final: 7 residues processed: 159 average time/residue: 1.2534 time to fit residues: 216.4974 Evaluate side-chains 150 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 141 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 453 LYS Chi-restraints excluded: chain A residue 594 GLN Chi-restraints excluded: chain A residue 818 GLU Chi-restraints excluded: chain A residue 845 SER Chi-restraints excluded: chain A residue 846 SER Chi-restraints excluded: chain A residue 954 LEU Chi-restraints excluded: chain A residue 1108 GLU Chi-restraints excluded: chain A residue 1451 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 123 optimal weight: 6.9990 chunk 100 optimal weight: 4.9990 chunk 61 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 99 optimal weight: 3.9990 chunk 109 optimal weight: 3.9990 chunk 103 optimal weight: 3.9990 chunk 67 optimal weight: 6.9990 chunk 56 optimal weight: 3.9990 chunk 84 optimal weight: 0.7980 chunk 20 optimal weight: 3.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1039 GLN A1125 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.144919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.117387 restraints weight = 36075.856| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 1.92 r_work: 0.3316 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3220 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7484 moved from start: 0.1415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.056 10712 Z= 0.285 Angle : 0.580 6.073 14495 Z= 0.310 Chirality : 0.042 0.318 1618 Planarity : 0.004 0.046 1806 Dihedral : 6.435 63.980 1468 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.18 % Favored : 94.75 % Rotamer: Outliers : 1.93 % Allowed : 9.47 % Favored : 88.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.82 (0.23), residues: 1275 helix: 0.24 (0.19), residues: 700 sheet: -0.35 (0.49), residues: 92 loop : -1.69 (0.27), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 904 TYR 0.016 0.002 TYR A 912 PHE 0.022 0.002 PHE A 585 TRP 0.011 0.002 TRP A 771 HIS 0.007 0.001 HIS A 732 Details of bonding type rmsd/Z covalent geometry : bond 0.00688 / 0.29 (10712) covalent geometry : angle 0.57974 / 0.31 (14495) hydrogen bonds : bond 0.05151 / 3.39 ( 546) hydrogen bonds : angle 4.98038 / 3.56 ( 1584) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 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: 22 poor density : 144 time to evaluate : 0.638 Fit side-chains revert: symmetry clash REVERT: A 594 GLN cc_start: 0.7906 (OUTLIER) cc_final: 0.7433 (pt0) REVERT: A 836 GLN cc_start: 0.8122 (mp10) cc_final: 0.7668 (mp10) REVERT: A 1030 MET cc_start: 0.7206 (ttp) cc_final: 0.6529 (mtm) REVERT: A 1036 HIS cc_start: 0.7375 (m-70) cc_final: 0.6847 (t-170) REVERT: A 1329 GLN cc_start: 0.6537 (OUTLIER) cc_final: 0.5907 (tm-30) REVERT: A 1348 GLU cc_start: 0.7375 (mt-10) cc_final: 0.6184 (mp0) REVERT: A 1409 GLN cc_start: 0.6186 (pp30) cc_final: 0.5169 (tt0) REVERT: A 1448 ASP cc_start: 0.6216 (m-30) cc_final: 0.5939 (m-30) REVERT: A 1483 ARG cc_start: 0.5754 (mtt180) cc_final: 0.5436 (mmp80) outliers start: 22 outliers final: 12 residues processed: 159 average time/residue: 1.2454 time to fit residues: 215.5511 Evaluate side-chains 156 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 142 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 453 LYS Chi-restraints excluded: chain A residue 485 SER Chi-restraints excluded: chain A residue 594 GLN Chi-restraints excluded: chain A residue 705 MET Chi-restraints excluded: chain A residue 778 GLU Chi-restraints excluded: chain A residue 818 GLU Chi-restraints excluded: chain A residue 845 SER Chi-restraints excluded: chain A residue 846 SER Chi-restraints excluded: chain A residue 944 ARG Chi-restraints excluded: chain A residue 954 LEU Chi-restraints excluded: chain A residue 1108 GLU Chi-restraints excluded: chain A residue 1329 GLN Chi-restraints excluded: chain A residue 1451 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 120 optimal weight: 5.9990 chunk 32 optimal weight: 0.7980 chunk 106 optimal weight: 8.9990 chunk 30 optimal weight: 0.3980 chunk 56 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 71 optimal weight: 0.6980 chunk 25 optimal weight: 2.9990 chunk 101 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1039 GLN A1125 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.147334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.119825 restraints weight = 35458.830| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 1.92 r_work: 0.3348 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3252 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7420 moved from start: 0.1428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10712 Z= 0.134 Angle : 0.499 5.731 14495 Z= 0.265 Chirality : 0.038 0.315 1618 Planarity : 0.004 0.042 1806 Dihedral : 6.239 63.837 1468 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.31 % Favored : 95.61 % Rotamer: Outliers : 1.23 % Allowed : 10.18 % Favored : 88.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.44 (0.23), residues: 1275 helix: 0.60 (0.20), residues: 700 sheet: -0.21 (0.49), residues: 90 loop : -1.59 (0.27), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 904 TYR 0.013 0.001 TYR A1026 PHE 0.018 0.001 PHE A 585 TRP 0.011 0.001 TRP A 771 HIS 0.004 0.001 HIS A 732 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.13 (10712) covalent geometry : angle 0.49886 / 0.26 (14495) hydrogen bonds : bond 0.04332 / 2.85 ( 546) hydrogen bonds : angle 4.70281 / 3.36 ( 1584) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 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: 14 poor density : 152 time to evaluate : 0.520 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 594 GLN cc_start: 0.7893 (OUTLIER) cc_final: 0.7433 (pt0) REVERT: A 906 GLU cc_start: 0.8147 (mt-10) cc_final: 0.7881 (mp0) REVERT: A 1036 HIS cc_start: 0.7346 (m-70) cc_final: 0.6850 (t-90) REVERT: A 1316 LYS cc_start: 0.7323 (ptpt) cc_final: 0.7100 (ptpt) REVERT: A 1348 GLU cc_start: 0.7337 (mt-10) cc_final: 0.6148 (mp0) REVERT: A 1409 GLN cc_start: 0.6135 (pp30) cc_final: 0.5114 (tt0) REVERT: A 1448 ASP cc_start: 0.6111 (m-30) cc_final: 0.5844 (m-30) REVERT: A 1483 ARG cc_start: 0.5742 (mtt180) cc_final: 0.5415 (mmp80) outliers start: 14 outliers final: 8 residues processed: 158 average time/residue: 1.2701 time to fit residues: 217.7576 Evaluate side-chains 155 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 146 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 594 GLN Chi-restraints excluded: chain A residue 778 GLU Chi-restraints excluded: chain A residue 845 SER Chi-restraints excluded: chain A residue 944 ARG Chi-restraints excluded: chain A residue 954 LEU Chi-restraints excluded: chain A residue 1108 GLU Chi-restraints excluded: chain A residue 1398 MET Chi-restraints excluded: chain A residue 1451 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 29 optimal weight: 0.0970 chunk 55 optimal weight: 2.9990 chunk 107 optimal weight: 4.9990 chunk 1 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 chunk 67 optimal weight: 0.0370 chunk 117 optimal weight: 6.9990 chunk 35 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 overall best weight: 1.0262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1039 GLN A1125 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.148130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.120649 restraints weight = 35742.422| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 1.93 r_work: 0.3356 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3259 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7415 moved from start: 0.1501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10712 Z= 0.128 Angle : 0.480 5.748 14495 Z= 0.253 Chirality : 0.037 0.318 1618 Planarity : 0.004 0.041 1806 Dihedral : 6.129 63.842 1468 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.47 % Favored : 95.45 % Rotamer: Outliers : 1.32 % Allowed : 10.18 % Favored : 88.51 % 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: -0.18 (0.23), residues: 1275 helix: 0.83 (0.20), residues: 700 sheet: -0.15 (0.50), residues: 90 loop : -1.51 (0.27), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 904 TYR 0.012 0.001 TYR A 912 PHE 0.016 0.001 PHE A1132 TRP 0.010 0.001 TRP A 771 HIS 0.006 0.001 HIS A 732 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 (10712) covalent geometry : angle 0.48018 / 0.25 (14495) hydrogen bonds : bond 0.04037 / 2.65 ( 546) hydrogen bonds : angle 4.53993 / 3.24 ( 1584) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 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: 15 poor density : 155 time to evaluate : 0.526 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 277 ASN cc_start: 0.6920 (m-40) cc_final: 0.6654 (m-40) REVERT: A 594 GLN cc_start: 0.7896 (OUTLIER) cc_final: 0.7441 (pt0) REVERT: A 1036 HIS cc_start: 0.7368 (m-70) cc_final: 0.6868 (t-170) REVERT: A 1163 THR cc_start: 0.8355 (m) cc_final: 0.8119 (p) REVERT: A 1348 GLU cc_start: 0.7338 (mt-10) cc_final: 0.6145 (mp0) REVERT: A 1483 ARG cc_start: 0.5698 (mtt180) cc_final: 0.5377 (mmp80) outliers start: 15 outliers final: 9 residues processed: 162 average time/residue: 1.2279 time to fit residues: 216.2942 Evaluate side-chains 158 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 148 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 453 LYS Chi-restraints excluded: chain A residue 484 GLU Chi-restraints excluded: chain A residue 594 GLN Chi-restraints excluded: chain A residue 705 MET Chi-restraints excluded: chain A residue 778 GLU Chi-restraints excluded: chain A residue 845 SER Chi-restraints excluded: chain A residue 1108 GLU Chi-restraints excluded: chain A residue 1398 MET Chi-restraints excluded: chain A residue 1451 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 80 optimal weight: 0.3980 chunk 97 optimal weight: 6.9990 chunk 32 optimal weight: 0.6980 chunk 76 optimal weight: 0.8980 chunk 94 optimal weight: 2.9990 chunk 44 optimal weight: 0.6980 chunk 9 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 chunk 90 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1039 GLN A1125 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.150869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.124041 restraints weight = 35649.440| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 1.85 r_work: 0.3421 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3327 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7458 moved from start: 0.1532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 10712 Z= 0.104 Angle : 0.470 5.664 14495 Z= 0.246 Chirality : 0.037 0.319 1618 Planarity : 0.003 0.039 1806 Dihedral : 6.049 63.835 1468 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.00 % Favored : 95.92 % Rotamer: Outliers : 0.96 % Allowed : 10.88 % Favored : 88.16 % 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: -0.00 (0.23), residues: 1275 helix: 1.01 (0.20), residues: 702 sheet: -0.21 (0.49), residues: 92 loop : -1.47 (0.27), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 944 TYR 0.011 0.001 TYR A1026 PHE 0.016 0.001 PHE A1132 TRP 0.010 0.001 TRP A 748 HIS 0.004 0.001 HIS A 732 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.10 (10712) covalent geometry : angle 0.47029 / 0.25 (14495) hydrogen bonds : bond 0.03820 / 2.50 ( 546) hydrogen bonds : angle 4.42962 / 3.16 ( 1584) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 152 time to evaluate : 0.539 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 277 ASN cc_start: 0.6926 (m-40) cc_final: 0.6663 (m-40) REVERT: A 594 GLN cc_start: 0.7962 (OUTLIER) cc_final: 0.7483 (pt0) REVERT: A 778 GLU cc_start: 0.8385 (OUTLIER) cc_final: 0.7966 (mt-10) REVERT: A 836 GLN cc_start: 0.8098 (mp10) cc_final: 0.7581 (mp10) REVERT: A 1036 HIS cc_start: 0.7279 (m-70) cc_final: 0.6910 (t-170) REVERT: A 1163 THR cc_start: 0.8359 (m) cc_final: 0.8158 (p) REVERT: A 1348 GLU cc_start: 0.7329 (mt-10) cc_final: 0.6179 (mp0) REVERT: A 1447 MET cc_start: 0.7551 (OUTLIER) cc_final: 0.7272 (mpp) REVERT: A 1483 ARG cc_start: 0.5782 (mtt180) cc_final: 0.5414 (mmp80) outliers start: 11 outliers final: 6 residues processed: 157 average time/residue: 1.1810 time to fit residues: 201.9855 Evaluate side-chains 156 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 147 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 485 SER Chi-restraints excluded: chain A residue 594 GLN Chi-restraints excluded: chain A residue 778 GLU Chi-restraints excluded: chain A residue 845 SER Chi-restraints excluded: chain A residue 954 LEU Chi-restraints excluded: chain A residue 1108 GLU Chi-restraints excluded: chain A residue 1398 MET Chi-restraints excluded: chain A residue 1447 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 19 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 84 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 110 optimal weight: 2.9990 chunk 7 optimal weight: 0.3980 chunk 23 optimal weight: 2.9990 chunk 29 optimal weight: 0.0170 chunk 11 optimal weight: 3.9990 overall best weight: 1.2824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1039 GLN A1125 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.149839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.122927 restraints weight = 35667.032| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 1.85 r_work: 0.3408 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3314 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7469 moved from start: 0.1558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10712 Z= 0.140 Angle : 0.481 5.778 14495 Z= 0.252 Chirality : 0.037 0.320 1618 Planarity : 0.004 0.038 1806 Dihedral : 6.071 63.863 1468 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.16 % Favored : 95.76 % Rotamer: Outliers : 0.96 % Allowed : 11.14 % Favored : 87.89 % 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: -0.03 (0.23), residues: 1275 helix: 0.99 (0.20), residues: 702 sheet: -0.18 (0.50), residues: 92 loop : -1.50 (0.27), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 904 TYR 0.013 0.001 TYR A 912 PHE 0.019 0.001 PHE A1132 TRP 0.009 0.001 TRP A 748 HIS 0.005 0.001 HIS A 732 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.14 (10712) covalent geometry : angle 0.48063 / 0.25 (14495) hydrogen bonds : bond 0.03971 / 2.60 ( 546) hydrogen bonds : angle 4.42945 / 3.16 ( 1584) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 146 time to evaluate : 0.558 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 594 GLN cc_start: 0.7978 (OUTLIER) cc_final: 0.7496 (pt0) REVERT: A 778 GLU cc_start: 0.8394 (OUTLIER) cc_final: 0.7963 (mt-10) REVERT: A 1036 HIS cc_start: 0.7287 (m-70) cc_final: 0.6901 (t-170) REVERT: A 1348 GLU cc_start: 0.7346 (mt-10) cc_final: 0.6192 (mp0) REVERT: A 1447 MET cc_start: 0.7581 (OUTLIER) cc_final: 0.7376 (mmm) REVERT: A 1483 ARG cc_start: 0.5724 (mtt180) cc_final: 0.5411 (mmp80) outliers start: 11 outliers final: 7 residues processed: 152 average time/residue: 1.1799 time to fit residues: 195.1816 Evaluate side-chains 152 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 142 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 485 SER Chi-restraints excluded: chain A residue 594 GLN Chi-restraints excluded: chain A residue 778 GLU Chi-restraints excluded: chain A residue 845 SER Chi-restraints excluded: chain A residue 954 LEU Chi-restraints excluded: chain A residue 1108 GLU Chi-restraints excluded: chain A residue 1398 MET Chi-restraints excluded: chain A residue 1447 MET Chi-restraints excluded: chain A residue 1451 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 20 optimal weight: 3.9990 chunk 92 optimal weight: 0.9990 chunk 78 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 89 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 123 optimal weight: 5.9990 chunk 68 optimal weight: 0.9990 chunk 122 optimal weight: 5.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1039 GLN A1125 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.149187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.122356 restraints weight = 35633.838| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 1.84 r_work: 0.3401 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3307 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7476 moved from start: 0.1593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 10712 Z= 0.157 Angle : 0.492 5.777 14495 Z= 0.259 Chirality : 0.038 0.321 1618 Planarity : 0.004 0.037 1806 Dihedral : 6.121 63.875 1468 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.47 % Favored : 95.45 % Rotamer: Outliers : 1.23 % Allowed : 11.32 % Favored : 87.46 % 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: -0.08 (0.23), residues: 1275 helix: 0.94 (0.20), residues: 702 sheet: -0.27 (0.49), residues: 94 loop : -1.49 (0.27), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 904 TYR 0.012 0.001 TYR A 912 PHE 0.019 0.001 PHE A1132 TRP 0.009 0.001 TRP A 771 HIS 0.006 0.001 HIS A 732 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.16 (10712) covalent geometry : angle 0.49202 / 0.26 (14495) hydrogen bonds : bond 0.04095 / 2.68 ( 546) hydrogen bonds : angle 4.45008 / 3.18 ( 1584) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 143 time to evaluate : 0.619 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 594 GLN cc_start: 0.7993 (OUTLIER) cc_final: 0.7504 (pt0) REVERT: A 778 GLU cc_start: 0.8405 (OUTLIER) cc_final: 0.7952 (mt-10) REVERT: A 1036 HIS cc_start: 0.7285 (m-70) cc_final: 0.6912 (t-170) REVERT: A 1329 GLN cc_start: 0.6479 (OUTLIER) cc_final: 0.5833 (tm-30) REVERT: A 1348 GLU cc_start: 0.7344 (mt-10) cc_final: 0.6196 (mp0) REVERT: A 1447 MET cc_start: 0.7559 (OUTLIER) cc_final: 0.7312 (mmm) REVERT: A 1483 ARG cc_start: 0.5725 (mtt180) cc_final: 0.5418 (mmp80) outliers start: 14 outliers final: 7 residues processed: 149 average time/residue: 1.1776 time to fit residues: 191.5194 Evaluate side-chains 153 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 142 time to evaluate : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 485 SER Chi-restraints excluded: chain A residue 594 GLN Chi-restraints excluded: chain A residue 778 GLU Chi-restraints excluded: chain A residue 845 SER Chi-restraints excluded: chain A residue 1108 GLU Chi-restraints excluded: chain A residue 1329 GLN Chi-restraints excluded: chain A residue 1351 ASP Chi-restraints excluded: chain A residue 1398 MET Chi-restraints excluded: chain A residue 1447 MET Chi-restraints excluded: chain A residue 1451 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 66 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 chunk 53 optimal weight: 0.9990 chunk 94 optimal weight: 1.9990 chunk 98 optimal weight: 0.9990 chunk 91 optimal weight: 0.8980 chunk 89 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 86 optimal weight: 0.9990 chunk 97 optimal weight: 5.9990 overall best weight: 1.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1039 GLN A1125 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.149868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.123036 restraints weight = 35645.218| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 1.85 r_work: 0.3409 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3315 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7466 moved from start: 0.1626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 10712 Z= 0.128 Angle : 0.478 5.790 14495 Z= 0.251 Chirality : 0.037 0.321 1618 Planarity : 0.004 0.037 1806 Dihedral : 6.071 63.850 1468 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.16 % Favored : 95.76 % Rotamer: Outliers : 1.05 % Allowed : 11.67 % Favored : 87.28 % 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: 0.04 (0.23), residues: 1275 helix: 1.05 (0.20), residues: 702 sheet: -0.16 (0.50), residues: 92 loop : -1.45 (0.27), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 315 TYR 0.013 0.001 TYR A 912 PHE 0.020 0.001 PHE A1132 TRP 0.009 0.001 TRP A 771 HIS 0.005 0.001 HIS A 732 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 (10712) covalent geometry : angle 0.47780 / 0.25 (14495) hydrogen bonds : bond 0.03907 / 2.56 ( 546) hydrogen bonds : angle 4.38269 / 3.13 ( 1584) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 145 time to evaluate : 0.592 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 594 GLN cc_start: 0.7991 (OUTLIER) cc_final: 0.7494 (pt0) REVERT: A 778 GLU cc_start: 0.8419 (OUTLIER) cc_final: 0.7970 (mt-10) REVERT: A 836 GLN cc_start: 0.8113 (mp10) cc_final: 0.7593 (mp10) REVERT: A 1348 GLU cc_start: 0.7341 (mt-10) cc_final: 0.6185 (mp0) REVERT: A 1483 ARG cc_start: 0.5712 (mtt180) cc_final: 0.5414 (mmp80) outliers start: 12 outliers final: 7 residues processed: 150 average time/residue: 1.1835 time to fit residues: 193.5937 Evaluate side-chains 152 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 143 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 485 SER Chi-restraints excluded: chain A residue 594 GLN Chi-restraints excluded: chain A residue 778 GLU Chi-restraints excluded: chain A residue 845 SER Chi-restraints excluded: chain A residue 1108 GLU Chi-restraints excluded: chain A residue 1351 ASP Chi-restraints excluded: chain A residue 1398 MET Chi-restraints excluded: chain A residue 1451 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 62 optimal weight: 0.8980 chunk 29 optimal weight: 0.0010 chunk 40 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 122 optimal weight: 7.9990 chunk 119 optimal weight: 3.9990 chunk 91 optimal weight: 0.0040 chunk 74 optimal weight: 3.9990 overall best weight: 1.1802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1039 GLN A1125 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.149846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.123045 restraints weight = 35635.282| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 1.84 r_work: 0.3410 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3315 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7469 moved from start: 0.1656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10712 Z= 0.132 Angle : 0.479 5.774 14495 Z= 0.251 Chirality : 0.037 0.322 1618 Planarity : 0.003 0.038 1806 Dihedral : 6.064 63.850 1468 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.31 % Favored : 95.61 % Rotamer: Outliers : 0.88 % Allowed : 11.75 % Favored : 87.37 % 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: 0.06 (0.23), residues: 1275 helix: 1.07 (0.20), residues: 702 sheet: -0.26 (0.50), residues: 94 loop : -1.43 (0.28), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 826 TYR 0.014 0.001 TYR A 912 PHE 0.019 0.001 PHE A1132 TRP 0.009 0.001 TRP A 771 HIS 0.005 0.001 HIS A 732 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.13 (10712) covalent geometry : angle 0.47853 / 0.25 (14495) hydrogen bonds : bond 0.03906 / 2.56 ( 546) hydrogen bonds : angle 4.36812 / 3.12 ( 1584) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6852.31 seconds wall clock time: 116 minutes 45.68 seconds (7005.68 seconds total)