Starting phenix.real_space_refine on Wed Jun 18 10:54:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8p1n_17355/06_2025/8p1n_17355.cif Found real_map, /net/cci-nas-00/data/ceres_data/8p1n_17355/06_2025/8p1n_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_17355/06_2025/8p1n_17355.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8p1n_17355/06_2025/8p1n_17355.map" model { file = "/net/cci-nas-00/data/ceres_data/8p1n_17355/06_2025/8p1n_17355.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8p1n_17355/06_2025/8p1n_17355.cif" } resolution = 2.79 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 9.86, per 1000 atoms: 0.47 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: 5.22 Conformation dependent library (CDL) restraints added in 1.4 seconds 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: 1.75 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: 8.81 Time building geometry restraints manager: 6.38 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.560 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: 0.340 Extract box with map and model: 0.720 Check model and map are aligned: 0.150 Set scattering table: 0.160 Process input model: 44.930 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.050 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:12.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7284 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= 0.125 Angle : 0.523 5.571 14495 Z= 0.308 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.010 0.001 TRP A 748 HIS 0.005 0.001 HIS A 732 PHE 0.014 0.001 PHE A 585 TYR 0.014 0.001 TYR A 912 ARG 0.003 0.000 ARG A 650 Details of bonding type rmsd hydrogen bonds : bond 0.14761 ( 546) hydrogen bonds : angle 6.71997 ( 1584) covalent geometry : bond 0.00262 (10712) covalent geometry : angle 0.52254 (14495) *********************** 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 : 1.434 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: 0.7242 (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: 2.5170 time to fit residues: 499.7305 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 : 1.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 108 optimal weight: 1.9990 chunk 97 optimal weight: 6.9990 chunk 53 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 4.9990 chunk 38 optimal weight: 0.5980 chunk 61 optimal weight: 3.9990 chunk 74 optimal weight: 3.9990 chunk 116 optimal weight: 2.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3772 r_free = 0.3772 target = 0.150420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.123637 restraints weight = 35711.980| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 1.83 r_work: 0.3438 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3344 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7314 moved from start: 0.1081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 10712 Z= 0.174 Angle : 0.514 5.813 14495 Z= 0.275 Chirality : 0.038 0.318 1618 Planarity : 0.004 0.038 1806 Dihedral : 6.193 63.867 1468 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.71 % Favored : 95.22 % Rotamer: Outliers : 1.84 % Allowed : 6.75 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.23), residues: 1275 helix: 0.56 (0.20), residues: 702 sheet: -0.46 (0.49), residues: 94 loop : -1.49 (0.28), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 771 HIS 0.006 0.001 HIS A 732 PHE 0.019 0.001 PHE A 585 TYR 0.012 0.001 TYR A 912 ARG 0.006 0.000 ARG A 904 Details of bonding type rmsd hydrogen bonds : bond 0.04652 ( 546) hydrogen bonds : angle 4.94649 ( 1584) covalent geometry : bond 0.00410 (10712) covalent geometry : angle 0.51399 (14495) *********************** 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 175 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 154 time to evaluate : 1.518 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 594 GLN cc_start: 0.7900 (OUTLIER) cc_final: 0.7430 (pt0) REVERT: A 735 MET cc_start: 0.7678 (tpp) cc_final: 0.7478 (mmm) REVERT: A 1030 MET cc_start: 0.7205 (ttp) cc_final: 0.6477 (mtm) REVERT: A 1036 HIS cc_start: 0.7259 (m-70) cc_final: 0.6829 (t-170) REVERT: A 1257 LYS cc_start: 0.7188 (mtmt) cc_final: 0.6014 (mptt) REVERT: A 1348 GLU cc_start: 0.7421 (mt-10) cc_final: 0.6211 (mp0) REVERT: A 1408 MET cc_start: 0.6829 (tpp) cc_final: 0.6607 (mmm) REVERT: A 1448 ASP cc_start: 0.6293 (m-30) cc_final: 0.6025 (m-30) REVERT: A 1451 GLN cc_start: 0.7368 (OUTLIER) cc_final: 0.6957 (mt0) REVERT: A 1483 ARG cc_start: 0.5752 (mtt180) cc_final: 0.5429 (mmp80) outliers start: 21 outliers final: 6 residues processed: 164 average time/residue: 2.7030 time to fit residues: 478.9241 Evaluate side-chains 156 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 148 time to evaluate : 1.606 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 0 optimal weight: 5.9990 chunk 77 optimal weight: 3.9990 chunk 117 optimal weight: 6.9990 chunk 50 optimal weight: 2.9990 chunk 99 optimal weight: 5.9990 chunk 7 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3744 r_free = 0.3744 target = 0.147846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.121106 restraints weight = 35870.228| |-----------------------------------------------------------------------------| r_work (start): 0.3490 rms_B_bonded: 1.83 r_work: 0.3416 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3323 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7334 moved from start: 0.1411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 10712 Z= 0.221 Angle : 0.541 5.902 14495 Z= 0.290 Chirality : 0.040 0.317 1618 Planarity : 0.004 0.040 1806 Dihedral : 6.359 63.934 1468 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.02 % Favored : 94.90 % Rotamer: Outliers : 1.84 % Allowed : 8.33 % Favored : 89.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.23), residues: 1275 helix: 0.39 (0.19), residues: 700 sheet: -0.49 (0.48), residues: 94 loop : -1.64 (0.27), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 771 HIS 0.006 0.001 HIS A 732 PHE 0.022 0.002 PHE A 585 TYR 0.014 0.002 TYR A 912 ARG 0.005 0.000 ARG A 904 Details of bonding type rmsd hydrogen bonds : bond 0.04899 ( 546) hydrogen bonds : angle 4.83863 ( 1584) covalent geometry : bond 0.00529 (10712) covalent geometry : angle 0.54070 (14495) *********************** 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 172 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 151 time to evaluate : 1.762 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 594 GLN cc_start: 0.7958 (OUTLIER) cc_final: 0.7464 (pt0) REVERT: A 650 ARG cc_start: 0.8032 (OUTLIER) cc_final: 0.7630 (mtt-85) REVERT: A 735 MET cc_start: 0.7722 (tpp) cc_final: 0.7507 (mmm) REVERT: A 836 GLN cc_start: 0.8112 (mp10) cc_final: 0.7693 (mp10) REVERT: A 1030 MET cc_start: 0.7228 (ttp) cc_final: 0.6522 (mtm) REVERT: A 1036 HIS cc_start: 0.7325 (m-70) cc_final: 0.6870 (t-170) REVERT: A 1329 GLN cc_start: 0.6545 (OUTLIER) cc_final: 0.5826 (tm-30) REVERT: A 1348 GLU cc_start: 0.7418 (mt-10) cc_final: 0.6216 (mp0) REVERT: A 1409 GLN cc_start: 0.6121 (pp30) cc_final: 0.5128 (tt0) REVERT: A 1448 ASP cc_start: 0.6322 (m-30) cc_final: 0.6047 (m-30) REVERT: A 1483 ARG cc_start: 0.5839 (mtt180) cc_final: 0.5460 (mmp80) outliers start: 21 outliers final: 9 residues processed: 163 average time/residue: 2.6545 time to fit residues: 468.7257 Evaluate side-chains 156 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 144 time to evaluate : 1.770 ------------------------------------------------------------------------------- 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 650 ARG 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 56 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 9 optimal weight: 4.9990 chunk 105 optimal weight: 5.9990 chunk 119 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 29 optimal weight: 0.6980 chunk 10 optimal weight: 0.9990 chunk 122 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3748 r_free = 0.3748 target = 0.148854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.121710 restraints weight = 35895.262| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 1.86 r_work: 0.3390 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3296 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7380 moved from start: 0.1481 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= 0.154 Angle : 0.495 5.801 14495 Z= 0.263 Chirality : 0.038 0.319 1618 Planarity : 0.004 0.039 1806 Dihedral : 6.206 63.872 1468 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.47 % Favored : 95.45 % Rotamer: Outliers : 1.49 % Allowed : 9.65 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.23), residues: 1275 helix: 0.60 (0.20), residues: 709 sheet: -0.32 (0.49), residues: 92 loop : -1.66 (0.27), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 771 HIS 0.004 0.001 HIS A 732 PHE 0.017 0.001 PHE A 585 TYR 0.013 0.001 TYR A 912 ARG 0.003 0.000 ARG A 904 Details of bonding type rmsd hydrogen bonds : bond 0.04232 ( 546) hydrogen bonds : angle 4.60089 ( 1584) covalent geometry : bond 0.00362 (10712) covalent geometry : angle 0.49513 (14495) *********************** 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 169 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 152 time to evaluate : 1.488 Fit side-chains revert: symmetry clash REVERT: A 594 GLN cc_start: 0.7989 (OUTLIER) cc_final: 0.7502 (pt0) REVERT: A 650 ARG cc_start: 0.7901 (OUTLIER) cc_final: 0.7675 (mtt-85) REVERT: A 735 MET cc_start: 0.7743 (tpp) cc_final: 0.7526 (mmm) REVERT: A 836 GLN cc_start: 0.8107 (mp10) cc_final: 0.7565 (mp10) REVERT: A 1030 MET cc_start: 0.7230 (ttp) cc_final: 0.6614 (mtm) REVERT: A 1036 HIS cc_start: 0.7303 (m-70) cc_final: 0.6925 (t-170) REVERT: A 1163 THR cc_start: 0.8419 (m) cc_final: 0.8154 (p) REVERT: A 1329 GLN cc_start: 0.6510 (OUTLIER) cc_final: 0.5807 (tm-30) REVERT: A 1348 GLU cc_start: 0.7322 (mt-10) cc_final: 0.6166 (mp0) REVERT: A 1483 ARG cc_start: 0.5739 (mtt180) cc_final: 0.5404 (mmp80) outliers start: 17 outliers final: 7 residues processed: 160 average time/residue: 2.8085 time to fit residues: 487.3122 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 : 1.475 ------------------------------------------------------------------------------- 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 650 ARG 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 1329 GLN Chi-restraints excluded: chain A residue 1398 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 123 optimal weight: 6.9990 chunk 90 optimal weight: 2.9990 chunk 98 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 126 optimal weight: 4.9990 chunk 67 optimal weight: 5.9990 chunk 53 optimal weight: 0.6980 chunk 95 optimal weight: 1.9990 chunk 7 optimal weight: 0.4980 chunk 50 optimal weight: 2.9990 chunk 116 optimal weight: 3.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3747 r_free = 0.3747 target = 0.148859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.122555 restraints weight = 35679.127| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 1.79 r_work: 0.3401 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3308 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7357 moved from start: 0.1549 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= 0.149 Angle : 0.487 5.788 14495 Z= 0.258 Chirality : 0.038 0.319 1618 Planarity : 0.004 0.038 1806 Dihedral : 6.152 63.865 1468 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.78 % Favored : 95.14 % Rotamer: Outliers : 1.23 % Allowed : 10.61 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.23), residues: 1275 helix: 0.72 (0.20), residues: 710 sheet: -0.29 (0.49), residues: 92 loop : -1.62 (0.27), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 748 HIS 0.004 0.001 HIS A 732 PHE 0.017 0.001 PHE A 585 TYR 0.014 0.001 TYR A 912 ARG 0.003 0.000 ARG A 904 Details of bonding type rmsd hydrogen bonds : bond 0.04113 ( 546) hydrogen bonds : angle 4.49410 ( 1584) covalent geometry : bond 0.00350 (10712) covalent geometry : angle 0.48722 (14495) *********************** 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 168 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 154 time to evaluate : 1.641 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 594 GLN cc_start: 0.7991 (OUTLIER) cc_final: 0.7499 (pt0) REVERT: A 735 MET cc_start: 0.7723 (tpp) cc_final: 0.7492 (mmm) REVERT: A 778 GLU cc_start: 0.8401 (OUTLIER) cc_final: 0.7942 (mt-10) REVERT: A 836 GLN cc_start: 0.8111 (mp10) cc_final: 0.7714 (mp10) REVERT: A 1030 MET cc_start: 0.7208 (ttp) cc_final: 0.6601 (mtm) REVERT: A 1036 HIS cc_start: 0.7306 (m-70) cc_final: 0.6917 (t-170) REVERT: A 1163 THR cc_start: 0.8462 (m) cc_final: 0.8204 (p) REVERT: A 1316 LYS cc_start: 0.7317 (ptpt) cc_final: 0.7028 (ptpt) REVERT: A 1329 GLN cc_start: 0.6510 (OUTLIER) cc_final: 0.5795 (tm-30) REVERT: A 1348 GLU cc_start: 0.7318 (mt-10) cc_final: 0.6180 (mp0) REVERT: A 1483 ARG cc_start: 0.5768 (mtt180) cc_final: 0.5440 (mmp80) outliers start: 14 outliers final: 7 residues processed: 161 average time/residue: 2.6807 time to fit residues: 472.6423 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 : 1.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 299 ILE 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 1451 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 126 optimal weight: 4.9990 chunk 65 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 101 optimal weight: 3.9990 chunk 100 optimal weight: 0.5980 chunk 13 optimal weight: 4.9990 chunk 83 optimal weight: 3.9990 chunk 42 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 chunk 19 optimal weight: 3.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3737 r_free = 0.3737 target = 0.147933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.121543 restraints weight = 35678.323| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 1.80 r_work: 0.3388 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3295 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7373 moved from start: 0.1675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 10712 Z= 0.182 Angle : 0.506 5.829 14495 Z= 0.269 Chirality : 0.038 0.320 1618 Planarity : 0.004 0.079 1806 Dihedral : 6.237 63.898 1468 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.18 % Favored : 94.75 % Rotamer: Outliers : 1.23 % Allowed : 11.14 % Favored : 87.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.23), residues: 1275 helix: 0.66 (0.20), residues: 708 sheet: -0.31 (0.49), residues: 92 loop : -1.67 (0.27), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1338 HIS 0.005 0.001 HIS A 732 PHE 0.018 0.001 PHE A 585 TYR 0.014 0.001 TYR A 912 ARG 0.004 0.000 ARG A 904 Details of bonding type rmsd hydrogen bonds : bond 0.04333 ( 546) hydrogen bonds : angle 4.53714 ( 1584) covalent geometry : bond 0.00433 (10712) covalent geometry : angle 0.50645 (14495) *********************** 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 159 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 145 time to evaluate : 1.641 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 594 GLN cc_start: 0.8005 (OUTLIER) cc_final: 0.7504 (pt0) REVERT: A 650 ARG cc_start: 0.7989 (OUTLIER) cc_final: 0.7519 (mtt-85) REVERT: A 735 MET cc_start: 0.7753 (tpp) cc_final: 0.7495 (mmm) REVERT: A 778 GLU cc_start: 0.8409 (OUTLIER) cc_final: 0.7926 (mt-10) REVERT: A 836 GLN cc_start: 0.8142 (mp10) cc_final: 0.7745 (mp10) REVERT: A 1030 MET cc_start: 0.7228 (ttp) cc_final: 0.6635 (mtm) REVERT: A 1036 HIS cc_start: 0.7328 (m-70) cc_final: 0.6943 (t-170) REVERT: A 1163 THR cc_start: 0.8380 (m) cc_final: 0.8172 (p) REVERT: A 1329 GLN cc_start: 0.6595 (OUTLIER) cc_final: 0.5857 (tm-30) REVERT: A 1348 GLU cc_start: 0.7323 (mt-10) cc_final: 0.6154 (mp0) REVERT: A 1483 ARG cc_start: 0.5783 (mtt180) cc_final: 0.5459 (mmp80) outliers start: 14 outliers final: 8 residues processed: 154 average time/residue: 2.6826 time to fit residues: 447.1602 Evaluate side-chains 155 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 143 time to evaluate : 1.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 299 ILE 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 650 ARG 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 1451 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 110 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 chunk 113 optimal weight: 0.8980 chunk 127 optimal weight: 2.9990 chunk 42 optimal weight: 4.9990 chunk 63 optimal weight: 1.9990 chunk 72 optimal weight: 0.7980 chunk 126 optimal weight: 3.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1039 GLN A1125 GLN A1413 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.148705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.121552 restraints weight = 35677.242| |-----------------------------------------------------------------------------| r_work (start): 0.3467 rms_B_bonded: 1.87 r_work: 0.3391 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3298 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7351 moved from start: 0.1704 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= 0.153 Angle : 0.489 5.786 14495 Z= 0.259 Chirality : 0.038 0.319 1618 Planarity : 0.004 0.058 1806 Dihedral : 6.175 63.864 1468 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.86 % Favored : 95.06 % Rotamer: Outliers : 1.49 % Allowed : 10.96 % Favored : 87.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.23), residues: 1275 helix: 0.77 (0.20), residues: 709 sheet: -0.25 (0.50), residues: 92 loop : -1.65 (0.27), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 771 HIS 0.006 0.001 HIS A 732 PHE 0.017 0.001 PHE A1132 TYR 0.014 0.001 TYR A 912 ARG 0.003 0.000 ARG A 650 Details of bonding type rmsd hydrogen bonds : bond 0.04125 ( 546) hydrogen bonds : angle 4.45556 ( 1584) covalent geometry : bond 0.00361 (10712) covalent geometry : angle 0.48923 (14495) *********************** 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 164 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 147 time to evaluate : 1.664 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 594 GLN cc_start: 0.7983 (OUTLIER) cc_final: 0.7491 (pt0) REVERT: A 650 ARG cc_start: 0.7872 (OUTLIER) cc_final: 0.7465 (mtt-85) REVERT: A 707 ARG cc_start: 0.7604 (OUTLIER) cc_final: 0.7385 (pmt-80) REVERT: A 735 MET cc_start: 0.7707 (tpp) cc_final: 0.7467 (mmm) REVERT: A 778 GLU cc_start: 0.8394 (OUTLIER) cc_final: 0.7914 (mt-10) REVERT: A 836 GLN cc_start: 0.8102 (mp10) cc_final: 0.7692 (mp10) REVERT: A 1030 MET cc_start: 0.7210 (ttp) cc_final: 0.6683 (mtm) REVERT: A 1163 THR cc_start: 0.8431 (m) cc_final: 0.8212 (p) REVERT: A 1329 GLN cc_start: 0.6559 (OUTLIER) cc_final: 0.5842 (tm-30) REVERT: A 1348 GLU cc_start: 0.7311 (mt-10) cc_final: 0.6118 (mp0) REVERT: A 1483 ARG cc_start: 0.5681 (mtt180) cc_final: 0.5467 (mmp80) outliers start: 17 outliers final: 9 residues processed: 156 average time/residue: 2.6499 time to fit residues: 449.7775 Evaluate side-chains 159 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 145 time to evaluate : 1.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 299 ILE 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 650 ARG Chi-restraints excluded: chain A residue 707 ARG 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 1351 ASP Chi-restraints excluded: chain A residue 1398 MET Chi-restraints excluded: chain A residue 1451 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 46 optimal weight: 2.9990 chunk 115 optimal weight: 7.9990 chunk 40 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 119 optimal weight: 4.9990 chunk 66 optimal weight: 3.9990 chunk 76 optimal weight: 0.5980 chunk 110 optimal weight: 4.9990 chunk 102 optimal weight: 2.9990 chunk 109 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1039 GLN A1125 GLN A1413 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.147440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.120184 restraints weight = 35914.488| |-----------------------------------------------------------------------------| r_work (start): 0.3445 rms_B_bonded: 1.88 r_work: 0.3369 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3274 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7373 moved from start: 0.1792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 10712 Z= 0.197 Angle : 0.517 5.857 14495 Z= 0.276 Chirality : 0.039 0.319 1618 Planarity : 0.004 0.063 1806 Dihedral : 6.281 63.911 1468 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.33 % Favored : 94.59 % Rotamer: Outliers : 1.40 % Allowed : 11.32 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.23), residues: 1275 helix: 0.62 (0.19), residues: 710 sheet: -0.36 (0.47), residues: 99 loop : -1.65 (0.27), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A1338 HIS 0.006 0.001 HIS A 732 PHE 0.020 0.002 PHE A 585 TYR 0.015 0.002 TYR A 912 ARG 0.003 0.000 ARG A 904 Details of bonding type rmsd hydrogen bonds : bond 0.04449 ( 546) hydrogen bonds : angle 4.56123 ( 1584) covalent geometry : bond 0.00469 (10712) covalent geometry : angle 0.51745 (14495) *********************** 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: 16 poor density : 141 time to evaluate : 1.589 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 594 GLN cc_start: 0.7984 (OUTLIER) cc_final: 0.7459 (pt0) REVERT: A 650 ARG cc_start: 0.7944 (OUTLIER) cc_final: 0.7567 (mtt-85) REVERT: A 735 MET cc_start: 0.7751 (tpp) cc_final: 0.7522 (mmm) REVERT: A 778 GLU cc_start: 0.8446 (OUTLIER) cc_final: 0.7958 (mt-10) REVERT: A 836 GLN cc_start: 0.8141 (mp10) cc_final: 0.7724 (mp10) REVERT: A 1030 MET cc_start: 0.7276 (ttp) cc_final: 0.6765 (mtm) REVERT: A 1163 THR cc_start: 0.8408 (m) cc_final: 0.8186 (p) REVERT: A 1281 ILE cc_start: 0.8112 (mm) cc_final: 0.7900 (tp) REVERT: A 1329 GLN cc_start: 0.6587 (OUTLIER) cc_final: 0.5801 (tm-30) REVERT: A 1348 GLU cc_start: 0.7185 (mt-10) cc_final: 0.6049 (mp0) REVERT: A 1483 ARG cc_start: 0.5699 (mtt180) cc_final: 0.5475 (mmp80) outliers start: 16 outliers final: 8 residues processed: 151 average time/residue: 2.5700 time to fit residues: 423.2779 Evaluate side-chains 152 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 140 time to evaluate : 1.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 299 ILE 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 650 ARG 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 1351 ASP 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 48 optimal weight: 1.9990 chunk 113 optimal weight: 0.6980 chunk 67 optimal weight: 0.5980 chunk 110 optimal weight: 0.7980 chunk 60 optimal weight: 2.9990 chunk 107 optimal weight: 3.9990 chunk 21 optimal weight: 0.5980 chunk 6 optimal weight: 0.9980 chunk 65 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1039 GLN A1125 GLN A1413 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.150286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.123464 restraints weight = 35576.286| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 1.85 r_work: 0.3409 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3315 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7353 moved from start: 0.1773 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= 0.105 Angle : 0.464 5.695 14495 Z= 0.244 Chirality : 0.037 0.320 1618 Planarity : 0.004 0.057 1806 Dihedral : 6.046 63.830 1468 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.16 % Favored : 95.76 % Rotamer: Outliers : 0.88 % Allowed : 12.19 % Favored : 86.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.24), residues: 1275 helix: 0.99 (0.20), residues: 712 sheet: -0.19 (0.50), residues: 92 loop : -1.51 (0.27), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 771 HIS 0.006 0.001 HIS A1413 PHE 0.018 0.001 PHE A1132 TYR 0.012 0.001 TYR A 912 ARG 0.004 0.000 ARG A 650 Details of bonding type rmsd hydrogen bonds : bond 0.03715 ( 546) hydrogen bonds : angle 4.30246 ( 1584) covalent geometry : bond 0.00237 (10712) covalent geometry : angle 0.46399 (14495) *********************** 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 160 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 150 time to evaluate : 2.137 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 594 GLN cc_start: 0.7995 (OUTLIER) cc_final: 0.7500 (pt0) REVERT: A 735 MET cc_start: 0.7698 (tpp) cc_final: 0.7369 (mmm) REVERT: A 778 GLU cc_start: 0.8400 (OUTLIER) cc_final: 0.7916 (mt-10) REVERT: A 836 GLN cc_start: 0.8093 (mp10) cc_final: 0.7583 (mp10) REVERT: A 1030 MET cc_start: 0.7191 (ttp) cc_final: 0.6745 (mtm) REVERT: A 1329 GLN cc_start: 0.6551 (OUTLIER) cc_final: 0.5807 (tm-30) REVERT: A 1348 GLU cc_start: 0.7258 (mt-10) cc_final: 0.6125 (mp0) REVERT: A 1483 ARG cc_start: 0.5708 (mtt180) cc_final: 0.5505 (mmp80) outliers start: 10 outliers final: 6 residues processed: 157 average time/residue: 3.0920 time to fit residues: 542.1409 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 : 2.765 ------------------------------------------------------------------------------- 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 1329 GLN 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 110 optimal weight: 0.8980 chunk 3 optimal weight: 2.9990 chunk 111 optimal weight: 4.9990 chunk 74 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 77 optimal weight: 0.6980 chunk 23 optimal weight: 1.9990 chunk 85 optimal weight: 4.9990 chunk 25 optimal weight: 0.5980 chunk 34 optimal weight: 2.9990 chunk 56 optimal weight: 0.8980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1039 GLN A1125 GLN A1413 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.149828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.123025 restraints weight = 35581.576| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 1.84 r_work: 0.3407 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3315 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7350 moved from start: 0.1804 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= 0.120 Angle : 0.467 5.719 14495 Z= 0.246 Chirality : 0.037 0.321 1618 Planarity : 0.004 0.058 1806 Dihedral : 6.034 63.852 1468 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.47 % Favored : 95.45 % Rotamer: Outliers : 0.79 % Allowed : 12.37 % Favored : 86.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.24), residues: 1275 helix: 1.07 (0.20), residues: 710 sheet: -0.07 (0.50), residues: 99 loop : -1.51 (0.28), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 748 HIS 0.007 0.001 HIS A1413 PHE 0.018 0.001 PHE A1132 TYR 0.012 0.001 TYR A 912 ARG 0.003 0.000 ARG A 315 Details of bonding type rmsd hydrogen bonds : bond 0.03752 ( 546) hydrogen bonds : angle 4.28642 ( 1584) covalent geometry : bond 0.00280 (10712) covalent geometry : angle 0.46715 (14495) ********************** 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 153 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 144 time to evaluate : 1.678 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 279 CYS cc_start: 0.7459 (m) cc_final: 0.6573 (t) REVERT: A 594 GLN cc_start: 0.8006 (OUTLIER) cc_final: 0.7506 (pt0) REVERT: A 735 MET cc_start: 0.7683 (tpp) cc_final: 0.7437 (mmm) REVERT: A 778 GLU cc_start: 0.8392 (OUTLIER) cc_final: 0.7901 (mt-10) REVERT: A 836 GLN cc_start: 0.8103 (mp10) cc_final: 0.7607 (mp10) REVERT: A 1030 MET cc_start: 0.7182 (ttp) cc_final: 0.6716 (mtm) REVERT: A 1329 GLN cc_start: 0.6571 (OUTLIER) cc_final: 0.5830 (tm-30) REVERT: A 1348 GLU cc_start: 0.7264 (mt-10) cc_final: 0.6136 (mp0) REVERT: A 1483 ARG cc_start: 0.5755 (mtt180) cc_final: 0.5540 (mmp80) outliers start: 9 outliers final: 6 residues processed: 151 average time/residue: 2.5438 time to fit residues: 417.9684 Evaluate side-chains 149 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 140 time to evaluate : 1.578 ------------------------------------------------------------------------------- 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 1329 GLN 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 127 optimal weight: 2.9990 chunk 93 optimal weight: 4.9990 chunk 80 optimal weight: 0.6980 chunk 81 optimal weight: 2.9990 chunk 121 optimal weight: 0.9980 chunk 90 optimal weight: 0.5980 chunk 32 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 108 optimal weight: 0.7980 chunk 9 optimal weight: 3.9990 chunk 5 optimal weight: 4.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1039 GLN A1125 GLN A1413 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.150651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.123871 restraints weight = 35623.256| |-----------------------------------------------------------------------------| r_work (start): 0.3493 rms_B_bonded: 1.84 r_work: 0.3418 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3325 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7328 moved from start: 0.1821 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= 0.105 Angle : 0.458 5.680 14495 Z= 0.241 Chirality : 0.037 0.322 1618 Planarity : 0.004 0.053 1806 Dihedral : 5.967 63.834 1468 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.24 % Favored : 95.69 % Rotamer: Outliers : 0.96 % Allowed : 12.54 % Favored : 86.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.24), residues: 1275 helix: 1.25 (0.20), residues: 706 sheet: -0.05 (0.50), residues: 99 loop : -1.47 (0.28), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 748 HIS 0.006 0.001 HIS A1413 PHE 0.018 0.001 PHE A1132 TYR 0.009 0.001 TYR A 661 ARG 0.004 0.000 ARG A 650 Details of bonding type rmsd hydrogen bonds : bond 0.03589 ( 546) hydrogen bonds : angle 4.20596 ( 1584) covalent geometry : bond 0.00240 (10712) covalent geometry : angle 0.45829 (14495) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14259.20 seconds wall clock time: 243 minutes 11.70 seconds (14591.70 seconds total)