Starting phenix.real_space_refine on Fri Aug 7 10:31:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8p1n_17355/08_2026/8p1n_17355.cif Found real_map, /net/cci-nas-00/data/ceres_data/8p1n_17355/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8p1n_17355/08_2026/8p1n_17355.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8p1n_17355/08_2026/8p1n_17355.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8p1n_17355/08_2026/8p1n_17355.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8p1n_17355/08_2026/8p1n_17355.map" } 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-2.2rc3-6140/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: 3.56, per 1000 atoms: 0.17 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: 2.15 Conformation dependent library (CDL) restraints added in 591.1 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: 0.66 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: 6.20 Time building geometry restraints manager: 2.84 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: 1480 0.064 - 0.128: 126 0.128 - 0.192: 11 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: 2.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.070 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 22.970 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 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:9.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.720 ------------------------------------------------------------------------------- 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= 0.127 Angle : 0.528 5.571 14495 Z= 0.313 Chirality : 0.038 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 0.00263 / 0.13 (10712) covalent geometry : angle 0.52786 / 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 : 0.560 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: 1.2199 time to fit residues: 242.4635 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 : 0.565 ------------------------------------------------------------------------------- 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 = 0.146937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.119405 restraints weight = 36024.428| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 1.93 r_work: 0.3346 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3250 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7441 moved from start: 0.1013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 10712 Z= 0.232 Angle : 0.561 5.937 14495 Z= 0.300 Chirality : 0.040 0.321 1618 Planarity : 0.004 0.047 1806 Dihedral : 6.265 63.919 1468 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.02 % Favored : 94.90 % Rotamer: Outliers : 1.58 % Allowed : 7.02 % Favored : 91.40 % 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: 698 sheet: -0.50 (0.49), residues: 94 loop : -1.57 (0.27), residues: 483 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 0.012 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 0.56067 / 0.30 (14495) hydrogen bonds : bond 0.05218 / 3.44 ( 546) hydrogen bonds : angle 5.14492 / 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 163 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 145 time to evaluate : 0.397 Fit side-chains revert: symmetry clash REVERT: A 594 GLN cc_start: 0.7846 (OUTLIER) cc_final: 0.7398 (pt0) REVERT: A 735 MET cc_start: 0.7759 (tpp) cc_final: 0.7557 (mmm) REVERT: A 1030 MET cc_start: 0.7222 (ttp) cc_final: 0.6497 (mtm) REVERT: A 1036 HIS cc_start: 0.7303 (m-70) cc_final: 0.6795 (t-170) REVERT: A 1246 MET cc_start: 0.6809 (mtm) cc_final: 0.6538 (ttm) REVERT: A 1257 LYS cc_start: 0.7083 (mtmt) cc_final: 0.5903 (mptt) REVERT: A 1348 GLU cc_start: 0.7426 (mt-10) cc_final: 0.6218 (mp0) REVERT: A 1448 ASP cc_start: 0.6280 (m-30) cc_final: 0.6014 (m-30) REVERT: A 1451 GLN cc_start: 0.7422 (OUTLIER) cc_final: 0.7106 (mt0) outliers start: 18 outliers final: 8 residues processed: 158 average time/residue: 1.2418 time to fit residues: 213.0344 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 : 0.555 ------------------------------------------------------------------------------- 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: 6.9990 chunk 48 optimal weight: 1.9990 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: 1.9990 ------------------------------------------------------------------------------- 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 = 0.3712 r_free = 0.3712 target = 0.147002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.119476 restraints weight = 35721.762| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 1.93 r_work: 0.3346 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3250 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7429 moved from start: 0.1207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 10712 Z= 0.186 Angle : 0.519 5.858 14495 Z= 0.277 Chirality : 0.039 0.318 1618 Planarity : 0.004 0.047 1806 Dihedral : 6.251 63.894 1468 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.94 % Favored : 94.98 % Rotamer: Outliers : 1.32 % Allowed : 8.77 % Favored : 89.91 % 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: -0.54 (0.23), residues: 1275 helix: 0.47 (0.19), residues: 702 sheet: -0.43 (0.48), residues: 94 loop : -1.53 (0.27), residues: 479 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 0.019 0.001 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 0.00441 / 0.19 (10712) covalent geometry : angle 0.51894 / 0.28 (14495) hydrogen bonds : bond 0.04787 / 3.16 ( 546) hydrogen bonds : angle 4.92467 / 3.51 ( 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 167 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 152 time to evaluate : 0.575 Fit side-chains REVERT: A 594 GLN cc_start: 0.7854 (OUTLIER) cc_final: 0.7394 (pt0) REVERT: A 735 MET cc_start: 0.7682 (tpp) cc_final: 0.7473 (mmm) REVERT: A 1030 MET cc_start: 0.7160 (ttp) cc_final: 0.6453 (mtm) REVERT: A 1036 HIS cc_start: 0.7253 (m-70) cc_final: 0.6802 (t-170) REVERT: A 1257 LYS cc_start: 0.7128 (mtmt) cc_final: 0.5954 (mptt) REVERT: A 1348 GLU cc_start: 0.7403 (mt-10) cc_final: 0.6200 (mp0) REVERT: A 1396 MET cc_start: 0.7272 (mtm) cc_final: 0.7035 (mtm) REVERT: A 1448 ASP cc_start: 0.6235 (m-30) cc_final: 0.6005 (m-30) REVERT: A 1451 GLN cc_start: 0.7312 (OUTLIER) cc_final: 0.6920 (mt0) REVERT: A 1483 ARG cc_start: 0.5732 (mtt180) cc_final: 0.5405 (mmp80) outliers start: 15 outliers final: 7 residues processed: 159 average time/residue: 1.2360 time to fit residues: 213.7022 Evaluate side-chains 151 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 142 time to evaluate : 0.537 ------------------------------------------------------------------------------- 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: 5.9990 chunk 61 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 99 optimal weight: 0.7980 chunk 109 optimal weight: 2.9990 chunk 103 optimal weight: 4.9990 chunk 67 optimal weight: 5.9990 chunk 56 optimal weight: 4.9990 chunk 84 optimal weight: 0.6980 chunk 20 optimal weight: 3.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- 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 = 0.3702 r_free = 0.3702 target = 0.146289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.118928 restraints weight = 35828.588| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 1.92 r_work: 0.3338 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3242 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7433 moved from start: 0.1357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 10712 Z= 0.201 Angle : 0.527 5.873 14495 Z= 0.280 Chirality : 0.039 0.317 1618 Planarity : 0.004 0.045 1806 Dihedral : 6.272 63.908 1468 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.02 % Favored : 94.90 % Rotamer: Outliers : 1.67 % Allowed : 9.47 % Favored : 88.86 % 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: -0.57 (0.23), residues: 1275 helix: 0.46 (0.19), residues: 701 sheet: -0.26 (0.49), residues: 90 loop : -1.61 (0.27), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 904 TYR 0.014 0.002 TYR A 912 PHE 0.019 0.001 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 0.00479 / 0.20 (10712) covalent geometry : angle 0.52743 / 0.28 (14495) hydrogen bonds : bond 0.04624 / 3.04 ( 546) hydrogen bonds : angle 4.81355 / 3.44 ( 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 164 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 145 time to evaluate : 0.499 Fit side-chains revert: symmetry clash REVERT: A 594 GLN cc_start: 0.7896 (OUTLIER) cc_final: 0.7438 (pt0) REVERT: A 735 MET cc_start: 0.7692 (tpp) cc_final: 0.7476 (mmm) REVERT: A 1030 MET cc_start: 0.7185 (ttp) cc_final: 0.6514 (mtm) REVERT: A 1036 HIS cc_start: 0.7352 (m-70) cc_final: 0.6823 (t-170) REVERT: A 1329 GLN cc_start: 0.6551 (OUTLIER) cc_final: 0.5776 (tm-30) REVERT: A 1348 GLU cc_start: 0.7353 (mt-10) cc_final: 0.6158 (mp0) REVERT: A 1409 GLN cc_start: 0.6200 (pp30) cc_final: 0.5160 (tt0) REVERT: A 1448 ASP cc_start: 0.6190 (m-30) cc_final: 0.5922 (m-30) REVERT: A 1483 ARG cc_start: 0.5719 (mtt180) cc_final: 0.5425 (mmp80) outliers start: 19 outliers final: 8 residues processed: 156 average time/residue: 1.1432 time to fit residues: 194.1238 Evaluate side-chains 154 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 144 time to evaluate : 0.546 ------------------------------------------------------------------------------- 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 846 SER 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: 0.9980 chunk 106 optimal weight: 8.9990 chunk 30 optimal weight: 4.9990 chunk 56 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 71 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 101 optimal weight: 3.9990 chunk 24 optimal weight: 0.6980 overall best weight: 1.7386 ------------------------------------------------------------------------------- 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 = 0.3710 r_free = 0.3710 target = 0.146871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.119356 restraints weight = 35508.232| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 1.92 r_work: 0.3344 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3247 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7434 moved from start: 0.1461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 10712 Z= 0.167 Angle : 0.504 5.791 14495 Z= 0.268 Chirality : 0.038 0.318 1618 Planarity : 0.004 0.040 1806 Dihedral : 6.227 63.888 1468 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.78 % Favored : 95.14 % Rotamer: Outliers : 1.23 % Allowed : 10.00 % Favored : 88.77 % 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: 0.59 (0.19), residues: 702 sheet: -0.20 (0.49), residues: 90 loop : -1.59 (0.27), residues: 483 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 0.018 0.001 PHE A 585 TRP 0.010 0.001 TRP A 771 HIS 0.005 0.001 HIS A 732 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.17 (10712) covalent geometry : angle 0.50431 / 0.27 (14495) hydrogen bonds : bond 0.04405 / 2.89 ( 546) hydrogen bonds : angle 4.68530 / 3.35 ( 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 163 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 149 time to evaluate : 0.570 Fit side-chains revert: symmetry clash REVERT: A 594 GLN cc_start: 0.7916 (OUTLIER) cc_final: 0.7455 (pt0) REVERT: A 735 MET cc_start: 0.7670 (tpp) cc_final: 0.7444 (mmm) REVERT: A 836 GLN cc_start: 0.8066 (mp10) cc_final: 0.7621 (mp10) REVERT: A 1030 MET cc_start: 0.7194 (ttp) cc_final: 0.6555 (mtm) REVERT: A 1036 HIS cc_start: 0.7357 (m-70) cc_final: 0.6840 (t-170) REVERT: A 1316 LYS cc_start: 0.7319 (ptpt) cc_final: 0.7106 (ptpt) REVERT: A 1348 GLU cc_start: 0.7349 (mt-10) cc_final: 0.6152 (mp0) REVERT: A 1409 GLN cc_start: 0.6088 (pp30) cc_final: 0.5092 (tt0) REVERT: A 1483 ARG cc_start: 0.5710 (mtt180) cc_final: 0.5422 (mmp80) outliers start: 14 outliers final: 8 residues processed: 155 average time/residue: 1.1269 time to fit residues: 189.8256 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 : 0.559 ------------------------------------------------------------------------------- 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 845 SER Chi-restraints excluded: chain A residue 1108 GLU 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: 0.2980 chunk 55 optimal weight: 2.9990 chunk 107 optimal weight: 3.9990 chunk 1 optimal weight: 0.0270 chunk 54 optimal weight: 1.9990 chunk 67 optimal weight: 0.0970 chunk 117 optimal weight: 6.9990 chunk 35 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 overall best weight: 0.8840 ------------------------------------------------------------------------------- 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 = 0.3761 r_free = 0.3761 target = 0.149958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.122945 restraints weight = 35779.479| |-----------------------------------------------------------------------------| r_work (start): 0.3480 rms_B_bonded: 1.87 r_work: 0.3407 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3314 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.1468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 10712 Z= 0.113 Angle : 0.477 5.672 14495 Z= 0.252 Chirality : 0.037 0.316 1618 Planarity : 0.004 0.040 1806 Dihedral : 6.113 63.837 1468 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.31 % Favored : 95.61 % Rotamer: Outliers : 1.23 % Allowed : 10.44 % Favored : 88.33 % 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: -0.20 (0.23), residues: 1275 helix: 0.84 (0.20), residues: 700 sheet: -0.28 (0.49), residues: 92 loop : -1.53 (0.27), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 826 TYR 0.011 0.001 TYR A 912 PHE 0.016 0.001 PHE A1132 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 0.00254 / 0.11 (10712) covalent geometry : angle 0.47718 / 0.25 (14495) hydrogen bonds : bond 0.03988 / 2.61 ( 546) hydrogen bonds : angle 4.53126 / 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 166 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 152 time to evaluate : 0.569 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 594 GLN cc_start: 0.7972 (OUTLIER) cc_final: 0.7490 (pt0) REVERT: A 735 MET cc_start: 0.7714 (tpp) cc_final: 0.7481 (mmm) REVERT: A 836 GLN cc_start: 0.8134 (mp10) cc_final: 0.7605 (mp10) REVERT: A 1036 HIS cc_start: 0.7282 (m-70) cc_final: 0.6917 (t-170) REVERT: A 1163 THR cc_start: 0.8411 (m) cc_final: 0.8162 (p) REVERT: A 1348 GLU cc_start: 0.7333 (mt-10) cc_final: 0.6195 (mp0) REVERT: A 1483 ARG cc_start: 0.5770 (mtt180) cc_final: 0.5437 (mmp80) outliers start: 14 outliers final: 9 residues processed: 159 average time/residue: 1.1589 time to fit residues: 200.7551 Evaluate side-chains 159 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 149 time to evaluate : 0.615 ------------------------------------------------------------------------------- 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 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 1451 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 80 optimal weight: 0.4980 chunk 97 optimal weight: 6.9990 chunk 32 optimal weight: 0.9990 chunk 76 optimal weight: 0.8980 chunk 94 optimal weight: 3.9990 chunk 44 optimal weight: 0.6980 chunk 9 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- 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 = 0.3764 r_free = 0.3764 target = 0.150279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.123325 restraints weight = 35665.299| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 1.85 r_work: 0.3414 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3320 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7465 moved from start: 0.1556 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= 0.124 Angle : 0.474 5.727 14495 Z= 0.249 Chirality : 0.037 0.318 1618 Planarity : 0.003 0.039 1806 Dihedral : 6.068 63.840 1468 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.31 % Favored : 95.61 % Rotamer: Outliers : 1.23 % Allowed : 10.96 % Favored : 87.81 % 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: -0.05 (0.23), residues: 1275 helix: 0.97 (0.20), residues: 702 sheet: -0.24 (0.49), 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 0.018 0.001 PHE A1132 TRP 0.010 0.001 TRP A 748 HIS 0.004 0.001 HIS A 489 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.12 (10712) covalent geometry : angle 0.47410 / 0.25 (14495) hydrogen bonds : bond 0.03908 / 2.56 ( 546) hydrogen bonds : angle 4.43198 / 3.17 ( 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 166 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 152 time to evaluate : 0.363 Fit side-chains REVERT: A 594 GLN cc_start: 0.7980 (OUTLIER) cc_final: 0.7498 (pt0) REVERT: A 735 MET cc_start: 0.7683 (tpp) cc_final: 0.7407 (mmm) REVERT: A 778 GLU cc_start: 0.8400 (OUTLIER) cc_final: 0.7974 (mt-10) REVERT: A 836 GLN cc_start: 0.8116 (mp10) cc_final: 0.7593 (mp10) REVERT: A 1030 MET cc_start: 0.7176 (ttp) cc_final: 0.6592 (mtm) REVERT: A 1036 HIS cc_start: 0.7281 (m-70) cc_final: 0.6901 (t-170) REVERT: A 1163 THR cc_start: 0.8383 (m) cc_final: 0.8173 (p) REVERT: A 1329 GLN cc_start: 0.6468 (OUTLIER) cc_final: 0.5830 (tm-30) REVERT: A 1348 GLU cc_start: 0.7339 (mt-10) cc_final: 0.6189 (mp0) REVERT: A 1447 MET cc_start: 0.7564 (OUTLIER) cc_final: 0.7347 (mmm) REVERT: A 1483 ARG cc_start: 0.5723 (mtt180) cc_final: 0.5413 (mmp80) outliers start: 14 outliers final: 8 residues processed: 158 average time/residue: 1.1127 time to fit residues: 191.5278 Evaluate side-chains 160 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 148 time to evaluate : 0.589 ------------------------------------------------------------------------------- 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 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 1329 GLN 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: 4.9990 chunk 7 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 29 optimal weight: 0.2980 chunk 11 optimal weight: 3.9990 overall best weight: 1.4588 ------------------------------------------------------------------------------- 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 = 0.3754 r_free = 0.3754 target = 0.149379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.122507 restraints weight = 35729.802| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 1.85 r_work: 0.3396 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3302 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.1575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 10712 Z= 0.150 Angle : 0.486 5.776 14495 Z= 0.256 Chirality : 0.038 0.320 1618 Planarity : 0.004 0.047 1806 Dihedral : 6.099 63.871 1468 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.39 % Favored : 95.53 % Rotamer: Outliers : 1.23 % Allowed : 11.40 % 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: -0.10 (0.23), residues: 1275 helix: 0.94 (0.20), residues: 702 sheet: -0.22 (0.50), residues: 92 loop : -1.52 (0.27), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 904 TYR 0.015 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 0.00354 / 0.15 (10712) covalent geometry : angle 0.48593 / 0.26 (14495) hydrogen bonds : bond 0.04056 / 2.66 ( 546) hydrogen bonds : angle 4.45287 / 3.18 ( 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 162 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 148 time to evaluate : 0.561 Fit side-chains revert: symmetry clash REVERT: A 594 GLN cc_start: 0.8027 (OUTLIER) cc_final: 0.7530 (pt0) REVERT: A 735 MET cc_start: 0.7769 (tpp) cc_final: 0.7530 (mmm) REVERT: A 778 GLU cc_start: 0.8413 (OUTLIER) cc_final: 0.7976 (mt-10) REVERT: A 1030 MET cc_start: 0.7197 (ttp) cc_final: 0.6623 (mtm) REVERT: A 1036 HIS cc_start: 0.7291 (m-70) cc_final: 0.6930 (t-170) REVERT: A 1329 GLN cc_start: 0.6495 (OUTLIER) cc_final: 0.5691 (tm-30) REVERT: A 1348 GLU cc_start: 0.7350 (mt-10) cc_final: 0.6219 (mp0) REVERT: A 1447 MET cc_start: 0.7612 (OUTLIER) cc_final: 0.7397 (mmm) REVERT: A 1483 ARG cc_start: 0.5767 (mtt180) cc_final: 0.5455 (mmp80) outliers start: 14 outliers final: 8 residues processed: 154 average time/residue: 1.1741 time to fit residues: 196.9697 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 : 0.347 ------------------------------------------------------------------------------- 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 20 optimal weight: 2.9990 chunk 92 optimal weight: 0.8980 chunk 78 optimal weight: 2.9990 chunk 44 optimal weight: 0.9990 chunk 89 optimal weight: 0.9980 chunk 48 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 88 optimal weight: 0.9990 chunk 123 optimal weight: 5.9990 chunk 68 optimal weight: 2.9990 chunk 122 optimal weight: 4.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- 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 = 0.3763 r_free = 0.3763 target = 0.150238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.123402 restraints weight = 35528.005| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 1.85 r_work: 0.3413 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3318 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7462 moved from start: 0.1612 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= 0.115 Angle : 0.470 5.685 14495 Z= 0.247 Chirality : 0.037 0.320 1618 Planarity : 0.004 0.040 1806 Dihedral : 6.050 63.838 1468 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.08 % Favored : 95.84 % 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: 0.06 (0.23), residues: 1275 helix: 1.07 (0.20), residues: 702 sheet: -0.20 (0.50), residues: 92 loop : -1.46 (0.28), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 650 TYR 0.011 0.001 TYR A 912 PHE 0.018 0.001 PHE A1132 TRP 0.010 0.001 TRP A 748 HIS 0.006 0.001 HIS A 732 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.11 (10712) covalent geometry : angle 0.47036 / 0.25 (14495) hydrogen bonds : bond 0.03833 / 2.51 ( 546) hydrogen bonds : angle 4.36941 / 3.12 ( 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 161 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 147 time to evaluate : 0.538 Fit side-chains revert: symmetry clash REVERT: A 594 GLN cc_start: 0.7994 (OUTLIER) cc_final: 0.7499 (pt0) REVERT: A 735 MET cc_start: 0.7674 (tpp) cc_final: 0.7392 (mmm) REVERT: A 778 GLU cc_start: 0.8406 (OUTLIER) cc_final: 0.7953 (mt-10) REVERT: A 836 GLN cc_start: 0.8107 (mp10) cc_final: 0.7595 (mp10) REVERT: A 1030 MET cc_start: 0.7163 (ttp) cc_final: 0.6608 (mtm) REVERT: A 1036 HIS cc_start: 0.7272 (m-70) cc_final: 0.6929 (t-170) REVERT: A 1348 GLU cc_start: 0.7332 (mt-10) cc_final: 0.6179 (mp0) REVERT: A 1483 ARG cc_start: 0.5744 (mtt180) cc_final: 0.5413 (mmp80) outliers start: 14 outliers final: 7 residues processed: 153 average time/residue: 1.0875 time to fit residues: 181.3255 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 : 0.581 ------------------------------------------------------------------------------- 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 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 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: 4.9990 chunk 53 optimal weight: 0.9980 chunk 94 optimal weight: 1.9990 chunk 98 optimal weight: 0.7980 chunk 91 optimal weight: 0.0870 chunk 89 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 86 optimal weight: 1.9990 chunk 97 optimal weight: 5.9990 overall best weight: 1.1762 ------------------------------------------------------------------------------- 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 = 0.3760 r_free = 0.3760 target = 0.149987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.123048 restraints weight = 35639.667| |-----------------------------------------------------------------------------| r_work (start): 0.3478 rms_B_bonded: 1.85 r_work: 0.3405 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3312 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7496 moved from start: 0.1641 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= 0.131 Angle : 0.477 5.846 14495 Z= 0.250 Chirality : 0.037 0.321 1618 Planarity : 0.004 0.039 1806 Dihedral : 6.051 63.846 1468 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.16 % Favored : 95.76 % Rotamer: Outliers : 0.96 % Allowed : 11.67 % 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: 0.07 (0.23), residues: 1275 helix: 1.08 (0.20), residues: 702 sheet: -0.18 (0.50), residues: 92 loop : -1.45 (0.28), residues: 481 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 0.020 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 0.00307 / 0.13 (10712) covalent geometry : angle 0.47659 / 0.25 (14495) hydrogen bonds : bond 0.03885 / 2.54 ( 546) hydrogen bonds : angle 4.36248 / 3.12 ( 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 154 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 143 time to evaluate : 0.510 Fit side-chains revert: symmetry clash REVERT: A 594 GLN cc_start: 0.8015 (OUTLIER) cc_final: 0.7514 (pt0) REVERT: A 735 MET cc_start: 0.7705 (tpp) cc_final: 0.7421 (mmm) REVERT: A 778 GLU cc_start: 0.8431 (OUTLIER) cc_final: 0.7976 (mt-10) REVERT: A 836 GLN cc_start: 0.8128 (mp10) cc_final: 0.7621 (mp10) REVERT: A 1030 MET cc_start: 0.7160 (ttp) cc_final: 0.6605 (mtm) REVERT: A 1348 GLU cc_start: 0.7340 (mt-10) cc_final: 0.6196 (mp0) REVERT: A 1483 ARG cc_start: 0.5712 (mtt180) cc_final: 0.5430 (mmp80) outliers start: 11 outliers final: 6 residues processed: 149 average time/residue: 1.1814 time to fit residues: 191.4241 Evaluate side-chains 150 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 142 time to evaluate : 0.554 ------------------------------------------------------------------------------- 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 778 GLU Chi-restraints excluded: chain A residue 845 SER Chi-restraints excluded: chain A residue 1108 GLU 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: 0.8980 chunk 40 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 122 optimal weight: 7.9990 chunk 119 optimal weight: 2.9990 chunk 91 optimal weight: 0.8980 chunk 74 optimal weight: 3.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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 = 0.3757 r_free = 0.3757 target = 0.149685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.122799 restraints weight = 35676.681| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 1.85 r_work: 0.3404 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3310 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 moved from start: 0.1661 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= 0.138 Angle : 0.479 5.804 14495 Z= 0.252 Chirality : 0.037 0.321 1618 Planarity : 0.004 0.037 1806 Dihedral : 6.061 63.859 1468 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.39 % Favored : 95.53 % 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: 0.05 (0.23), residues: 1275 helix: 1.07 (0.20), residues: 702 sheet: -0.28 (0.50), residues: 94 loop : -1.45 (0.28), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 650 TYR 0.013 0.001 TYR A 912 PHE 0.020 0.001 PHE A1132 TRP 0.009 0.001 TRP A 748 HIS 0.006 0.001 HIS A 732 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 (10712) covalent geometry : angle 0.47880 / 0.25 (14495) hydrogen bonds : bond 0.03942 / 2.58 ( 546) hydrogen bonds : angle 4.37031 / 3.13 ( 1584) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6344.81 seconds wall clock time: 108 minutes 12.08 seconds (6492.08 seconds total)