Starting phenix.real_space_refine on Tue May 13 19:11:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qh3_18397/05_2025/8qh3_18397.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qh3_18397/05_2025/8qh3_18397.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.81 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8qh3_18397/05_2025/8qh3_18397.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qh3_18397/05_2025/8qh3_18397.map" model { file = "/net/cci-nas-00/data/ceres_data/8qh3_18397/05_2025/8qh3_18397.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qh3_18397/05_2025/8qh3_18397.cif" } resolution = 2.81 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= 0.001 sd= 0.065 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 11 5.49 5 Mg 1 5.21 5 S 58 5.16 5 C 6907 2.51 5 N 1815 2.21 5 O 2004 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 10796 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 10556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1310, 10556 Classifications: {'peptide': 1310} Link IDs: {'PTRANS': 43, 'TRANS': 1266} Chain breaks: 5 Chain: "C" Number of atoms: 239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 239 Classifications: {'RNA': 11} Modifications used: {'rna2p_pur': 3, 'rna3p_pur': 5, 'rna3p_pyr': 3} Link IDs: {'rna2p': 2, 'rna3p': 8} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.88, per 1000 atoms: 0.64 Number of scatterers: 10796 At special positions: 0 Unit cell: (94.807, 99.841, 121.655, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 58 16.00 P 11 15.00 Mg 1 11.99 O 2004 8.00 N 1815 7.00 C 6907 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.58 Conformation dependent library (CDL) restraints added in 1.3 seconds 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2498 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 11 sheets defined 58.2% alpha, 11.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.62 Creating SS restraints... Processing helix chain 'A' and resid 239 through 251 removed outlier: 3.740A pdb=" N LEU A 243 " --> pdb=" O ASN A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 278 Processing helix chain 'A' and resid 279 through 281 No H-bonds generated for 'chain 'A' and resid 279 through 281' Processing helix chain 'A' and resid 306 through 322 Processing helix chain 'A' and resid 328 through 343 Processing helix chain 'A' and resid 345 through 352 Processing helix chain 'A' and resid 374 through 378 Processing helix chain 'A' and resid 379 through 390 Processing helix chain 'A' and resid 409 through 428 removed outlier: 3.564A pdb=" N GLN A 413 " --> pdb=" O SER A 409 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N SER A 414 " --> pdb=" O HIS A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 458 Processing helix chain 'A' and resid 463 through 468 Processing helix chain 'A' and resid 470 through 490 removed outlier: 3.616A pdb=" N HIS A 474 " --> pdb=" O THR A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 563 through 572 Processing helix chain 'A' and resid 572 through 593 Processing helix chain 'A' and resid 597 through 614 Processing helix chain 'A' and resid 616 through 634 removed outlier: 3.835A pdb=" N TYR A 628 " --> pdb=" O ASP A 624 " (cutoff:3.500A) Proline residue: A 631 - end of helix Processing helix chain 'A' and resid 639 through 648 Processing helix chain 'A' and resid 654 through 674 Processing helix chain 'A' and resid 712 through 726 removed outlier: 3.657A pdb=" N LEU A 716 " --> pdb=" O HIS A 712 " (cutoff:3.500A) Processing helix chain 'A' and resid 733 through 760 removed outlier: 3.725A pdb=" N ALA A 739 " --> pdb=" O MET A 735 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N HIS A 742 " --> pdb=" O GLU A 738 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N GLU A 744 " --> pdb=" O LYS A 740 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N THR A 745 " --> pdb=" O ILE A 741 " (cutoff:3.500A) Processing helix chain 'A' and resid 760 through 767 Processing helix chain 'A' and resid 769 through 776 Processing helix chain 'A' and resid 777 through 780 removed outlier: 3.644A pdb=" N ALA A 780 " --> pdb=" O ALA A 777 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 777 through 780' Processing helix chain 'A' and resid 786 through 802 removed outlier: 4.015A pdb=" N VAL A 800 " --> pdb=" O GLU A 796 " (cutoff:3.500A) Processing helix chain 'A' and resid 804 through 814 Processing helix chain 'A' and resid 824 through 828 Processing helix chain 'A' and resid 848 through 859 Processing helix chain 'A' and resid 864 through 872 Processing helix chain 'A' and resid 898 through 917 Processing helix chain 'A' and resid 929 through 946 removed outlier: 3.870A pdb=" N LEU A 933 " --> pdb=" O GLU A 929 " (cutoff:3.500A) Processing helix chain 'A' and resid 983 through 992 removed outlier: 4.044A pdb=" N ARG A 987 " --> pdb=" O ALA A 983 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N PHE A 988 " --> pdb=" O LYS A 984 " (cutoff:3.500A) Processing helix chain 'A' and resid 999 through 1012 Processing helix chain 'A' and resid 1020 through 1029 Processing helix chain 'A' and resid 1034 through 1042 Processing helix chain 'A' and resid 1061 through 1084 Processing helix chain 'A' and resid 1116 through 1126 Processing helix chain 'A' and resid 1128 through 1135 removed outlier: 3.553A pdb=" N ASN A1135 " --> pdb=" O PHE A1132 " (cutoff:3.500A) Processing helix chain 'A' and resid 1137 through 1153 removed outlier: 3.923A pdb=" N SER A1141 " --> pdb=" O GLU A1137 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLY A1153 " --> pdb=" O ILE A1149 " (cutoff:3.500A) Processing helix chain 'A' and resid 1185 through 1193 removed outlier: 3.943A pdb=" N LEU A1193 " --> pdb=" O LEU A1189 " (cutoff:3.500A) Processing helix chain 'A' and resid 1200 through 1218 Processing helix chain 'A' and resid 1221 through 1240 Processing helix chain 'A' and resid 1249 through 1253 Processing helix chain 'A' and resid 1262 through 1266 Processing helix chain 'A' and resid 1272 through 1279 Processing helix chain 'A' and resid 1282 through 1299 removed outlier: 3.543A pdb=" N LYS A1286 " --> pdb=" O GLY A1282 " (cutoff:3.500A) Processing helix chain 'A' and resid 1301 through 1321 Processing helix chain 'A' and resid 1354 through 1365 Processing helix chain 'A' and resid 1366 through 1370 Processing helix chain 'A' and resid 1375 through 1385 removed outlier: 3.717A pdb=" N ILE A1381 " --> pdb=" O ASP A1377 " (cutoff:3.500A) Processing helix chain 'A' and resid 1386 through 1388 No H-bonds generated for 'chain 'A' and resid 1386 through 1388' Processing helix chain 'A' and resid 1389 through 1396 Processing helix chain 'A' and resid 1400 through 1408 removed outlier: 4.196A pdb=" N GLN A1403 " --> pdb=" O SER A1400 " (cutoff:3.500A) Processing helix chain 'A' and resid 1425 through 1439 Processing helix chain 'A' and resid 1443 through 1457 Processing helix chain 'A' and resid 1460 through 1471 removed outlier: 3.561A pdb=" N TRP A1464 " --> pdb=" O LYS A1460 " (cutoff:3.500A) Processing helix chain 'A' and resid 1503 through 1512 Processing helix chain 'A' and resid 1514 through 1525 Processing helix chain 'A' and resid 1530 through 1546 removed outlier: 3.587A pdb=" N ASP A1540 " --> pdb=" O LYS A1536 " (cutoff:3.500A) Processing helix chain 'A' and resid 1552 through 1564 Proline residue: A1561 - end of helix removed outlier: 3.804A pdb=" N TYR A1564 " --> pdb=" O ALA A1560 " (cutoff:3.500A) Processing helix chain 'A' and resid 1581 through 1592 removed outlier: 3.926A pdb=" N CYS A1586 " --> pdb=" O ALA A1582 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ARG A1587 " --> pdb=" O GLU A1583 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 260 through 261 Processing sheet with id=AA2, first strand: chain 'A' and resid 260 through 261 removed outlier: 3.674A pdb=" N ASP A1099 " --> pdb=" O HIS A1096 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 499 through 503 Processing sheet with id=AA4, first strand: chain 'A' and resid 499 through 503 Processing sheet with id=AA5, first strand: chain 'A' and resid 701 through 702 Processing sheet with id=AA6, first strand: chain 'A' and resid 832 through 837 removed outlier: 5.365A pdb=" N SER A 844 " --> pdb=" O GLY A 835 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 893 through 897 removed outlier: 7.040A pdb=" N ALA A 877 " --> pdb=" O ASP A1016 " (cutoff:3.500A) removed outlier: 8.088A pdb=" N PHE A1018 " --> pdb=" O ALA A 877 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N ALA A 879 " --> pdb=" O PHE A1018 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1168 through 1171 Processing sheet with id=AA9, first strand: chain 'A' and resid 1417 through 1419 Processing sheet with id=AB1, first strand: chain 'A' and resid 1474 through 1479 removed outlier: 4.263A pdb=" N THR A1598 " --> pdb=" O ILE A1476 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 1485 through 1489 596 hydrogen bonds defined for protein. 1668 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.27 Time building geometry restraints manager: 3.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3325 1.34 - 1.46: 2022 1.46 - 1.58: 5597 1.58 - 1.70: 21 1.70 - 1.82: 97 Bond restraints: 11062 Sorted by residual: bond pdb=" CE1 HIS A 957 " pdb=" NE2 HIS A 957 " ideal model delta sigma weight residual 1.321 1.361 -0.040 1.00e-02 1.00e+04 1.59e+01 bond pdb=" CA SER A 715 " pdb=" CB SER A 715 " ideal model delta sigma weight residual 1.529 1.482 0.047 1.55e-02 4.16e+03 9.05e+00 bond pdb=" N LYS A 876 " pdb=" CA LYS A 876 " ideal model delta sigma weight residual 1.454 1.488 -0.034 1.17e-02 7.31e+03 8.28e+00 bond pdb=" N ILE A 960 " pdb=" CA ILE A 960 " ideal model delta sigma weight residual 1.459 1.492 -0.033 1.19e-02 7.06e+03 7.60e+00 bond pdb=" N ILE A 952 " pdb=" CA ILE A 952 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.24e-02 6.50e+03 7.43e+00 ... (remaining 11057 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.69: 14691 1.69 - 3.38: 259 3.38 - 5.07: 37 5.07 - 6.76: 11 6.76 - 8.45: 3 Bond angle restraints: 15001 Sorted by residual: angle pdb=" CA GLN A 875 " pdb=" C GLN A 875 " pdb=" O GLN A 875 " ideal model delta sigma weight residual 121.87 117.70 4.17 1.10e+00 8.26e-01 1.44e+01 angle pdb=" CA ASN A 956 " pdb=" C ASN A 956 " pdb=" O ASN A 956 " ideal model delta sigma weight residual 122.64 117.96 4.68 1.25e+00 6.40e-01 1.40e+01 angle pdb=" C3' A C 2 " pdb=" O3' A C 2 " pdb=" P G C 3 " ideal model delta sigma weight residual 120.20 114.73 5.47 1.50e+00 4.44e-01 1.33e+01 angle pdb=" C GLN A1412 " pdb=" N HIS A1413 " pdb=" CA HIS A1413 " ideal model delta sigma weight residual 121.54 127.47 -5.93 1.91e+00 2.74e-01 9.63e+00 angle pdb=" CA ARG A 961 " pdb=" C ARG A 961 " pdb=" O ARG A 961 " ideal model delta sigma weight residual 121.87 118.42 3.45 1.16e+00 7.43e-01 8.83e+00 ... (remaining 14996 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.79: 6258 29.79 - 59.59: 348 59.59 - 89.38: 30 89.38 - 119.18: 1 119.18 - 148.97: 1 Dihedral angle restraints: 6638 sinusoidal: 2780 harmonic: 3858 Sorted by residual: dihedral pdb=" O4' U C 7 " pdb=" C1' U C 7 " pdb=" N1 U C 7 " pdb=" C2 U C 7 " ideal model delta sinusoidal sigma weight residual 200.00 51.03 148.97 1 1.50e+01 4.44e-03 7.92e+01 dihedral pdb=" CA MET A1246 " pdb=" C MET A1246 " pdb=" N VAL A1247 " pdb=" CA VAL A1247 " ideal model delta harmonic sigma weight residual -180.00 -163.15 -16.85 0 5.00e+00 4.00e-02 1.14e+01 dihedral pdb=" CB GLU A1092 " pdb=" CG GLU A1092 " pdb=" CD GLU A1092 " pdb=" OE1 GLU A1092 " ideal model delta sinusoidal sigma weight residual 0.00 -89.86 89.86 1 3.00e+01 1.11e-03 1.06e+01 ... (remaining 6635 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.110: 1643 0.110 - 0.220: 31 0.220 - 0.331: 0 0.331 - 0.441: 0 0.441 - 0.551: 1 Chirality restraints: 1675 Sorted by residual: chirality pdb=" P A C 2 " pdb=" OP1 A C 2 " pdb=" OP2 A C 2 " pdb=" O5' A C 2 " both_signs ideal model delta sigma weight residual True 2.41 -2.96 -0.55 2.00e-01 2.50e+01 7.59e+00 chirality pdb=" CA ILE A 952 " pdb=" N ILE A 952 " pdb=" C ILE A 952 " pdb=" CB ILE A 952 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.22 2.00e-01 2.50e+01 1.18e+00 chirality pdb=" CA ILE A 960 " pdb=" N ILE A 960 " pdb=" C ILE A 960 " pdb=" CB ILE A 960 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.20 2.00e-01 2.50e+01 9.60e-01 ... (remaining 1672 not shown) Planarity restraints: 1848 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A1503 " 0.052 5.00e-02 4.00e+02 7.77e-02 9.66e+00 pdb=" N PRO A1504 " -0.134 5.00e-02 4.00e+02 pdb=" CA PRO A1504 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO A1504 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 961 " -0.272 9.50e-02 1.11e+02 1.22e-01 9.12e+00 pdb=" NE ARG A 961 " 0.017 2.00e-02 2.50e+03 pdb=" CZ ARG A 961 " 0.000 2.00e-02 2.50e+03 pdb=" NH1 ARG A 961 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A 961 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 904 " 0.266 9.50e-02 1.11e+02 1.19e-01 8.74e+00 pdb=" NE ARG A 904 " -0.016 2.00e-02 2.50e+03 pdb=" CZ ARG A 904 " -0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG A 904 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 904 " 0.009 2.00e-02 2.50e+03 ... (remaining 1845 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 100 2.61 - 3.18: 9243 3.18 - 3.76: 17605 3.76 - 4.33: 25326 4.33 - 4.90: 40832 Nonbonded interactions: 93106 Sorted by model distance: nonbonded pdb=" OD1 ASP A1099 " pdb="MG MG A2201 " model vdw 2.038 2.170 nonbonded pdb=" N GLU A1275 " pdb=" OE1 GLU A1275 " model vdw 2.188 3.120 nonbonded pdb=" OD2 ASP A 544 " pdb=" OG1 THR A 545 " model vdw 2.202 3.040 nonbonded pdb=" OH TYR A 855 " pdb=" OE1 GLU A 871 " model vdw 2.242 3.040 nonbonded pdb=" OH TYR A 302 " pdb=" OD2 ASP A 481 " model vdw 2.252 3.040 ... (remaining 93101 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.410 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: 0.010 Extract box with map and model: 0.430 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 28.150 Find NCS groups from input model: 0.300 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:12.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 11062 Z= 0.177 Angle : 0.553 8.452 15001 Z= 0.312 Chirality : 0.042 0.551 1675 Planarity : 0.006 0.122 1848 Dihedral : 17.219 148.971 4140 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.16 % Allowed : 23.02 % Favored : 74.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.67 (0.24), residues: 1298 helix: 1.11 (0.20), residues: 714 sheet: 0.26 (0.53), residues: 93 loop : -0.40 (0.29), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 473 HIS 0.005 0.001 HIS A1413 PHE 0.016 0.001 PHE A 894 TYR 0.014 0.001 TYR A 912 ARG 0.004 0.000 ARG A1405 Details of bonding type rmsd hydrogen bonds : bond 0.14059 ( 578) hydrogen bonds : angle 5.57755 ( 1668) covalent geometry : bond 0.00315 (11062) covalent geometry : angle 0.55270 (15001) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 201 time to evaluate : 1.213 Fit side-chains REVERT: A 280 GLN cc_start: 0.7655 (OUTLIER) cc_final: 0.7088 (mm110) outliers start: 25 outliers final: 8 residues processed: 220 average time/residue: 1.2660 time to fit residues: 300.2328 Evaluate side-chains 170 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 161 time to evaluate : 1.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 280 GLN Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 845 SER Chi-restraints excluded: chain A residue 847 VAL Chi-restraints excluded: chain A residue 1098 ASP Chi-restraints excluded: chain A residue 1229 VAL Chi-restraints excluded: chain A residue 1239 LEU Chi-restraints excluded: chain A residue 1247 VAL Chi-restraints excluded: chain A residue 1592 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 111 optimal weight: 0.0970 chunk 100 optimal weight: 0.9990 chunk 55 optimal weight: 3.9990 chunk 34 optimal weight: 0.7980 chunk 67 optimal weight: 6.9990 chunk 53 optimal weight: 2.9990 chunk 103 optimal weight: 0.8980 chunk 40 optimal weight: 0.9990 chunk 62 optimal weight: 0.5980 chunk 77 optimal weight: 3.9990 chunk 119 optimal weight: 9.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 592 GLN A 875 GLN A 936 GLN A1058 GLN A1078 GLN A1122 GLN A1268 ASN A1364 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.171713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.141948 restraints weight = 11635.422| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 1.07 r_work: 0.3285 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3179 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.2108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11062 Z= 0.147 Angle : 0.535 7.152 15001 Z= 0.283 Chirality : 0.040 0.142 1675 Planarity : 0.004 0.054 1848 Dihedral : 9.394 150.251 1591 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 4.05 % Allowed : 21.12 % Favored : 74.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.92 (0.24), residues: 1298 helix: 1.38 (0.20), residues: 721 sheet: 0.52 (0.52), residues: 93 loop : -0.48 (0.29), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 473 HIS 0.006 0.001 HIS A1413 PHE 0.041 0.002 PHE A 959 TYR 0.017 0.002 TYR A 912 ARG 0.004 0.000 ARG A 892 Details of bonding type rmsd hydrogen bonds : bond 0.04527 ( 578) hydrogen bonds : angle 4.52076 ( 1668) covalent geometry : bond 0.00324 (11062) covalent geometry : angle 0.53460 (15001) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 168 time to evaluate : 1.152 Fit side-chains revert: symmetry clash REVERT: A 269 GLU cc_start: 0.7626 (tm-30) cc_final: 0.7362 (tp30) REVERT: A 549 ASP cc_start: 0.6465 (OUTLIER) cc_final: 0.6258 (m-30) REVERT: A 770 MET cc_start: 0.8394 (OUTLIER) cc_final: 0.8194 (tpt) REVERT: A 902 ARG cc_start: 0.7834 (OUTLIER) cc_final: 0.7405 (mmp-170) REVERT: A 1316 LYS cc_start: 0.7816 (ttmm) cc_final: 0.7495 (mtmm) REVERT: A 1364 GLN cc_start: 0.7229 (OUTLIER) cc_final: 0.7004 (tt0) REVERT: A 1585 ILE cc_start: 0.7057 (OUTLIER) cc_final: 0.6791 (mm) outliers start: 47 outliers final: 14 residues processed: 197 average time/residue: 1.1744 time to fit residues: 250.5650 Evaluate side-chains 169 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 150 time to evaluate : 1.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 358 GLN Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 549 ASP Chi-restraints excluded: chain A residue 666 SER Chi-restraints excluded: chain A residue 706 SER Chi-restraints excluded: chain A residue 719 GLU Chi-restraints excluded: chain A residue 743 LEU Chi-restraints excluded: chain A residue 770 MET Chi-restraints excluded: chain A residue 902 ARG Chi-restraints excluded: chain A residue 949 GLU Chi-restraints excluded: chain A residue 1098 ASP Chi-restraints excluded: chain A residue 1114 THR Chi-restraints excluded: chain A residue 1239 LEU Chi-restraints excluded: chain A residue 1247 VAL Chi-restraints excluded: chain A residue 1364 GLN Chi-restraints excluded: chain A residue 1404 LEU Chi-restraints excluded: chain A residue 1408 MET Chi-restraints excluded: chain A residue 1457 THR Chi-restraints excluded: chain A residue 1585 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 71 optimal weight: 0.9980 chunk 2 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 131 optimal weight: 2.9990 chunk 7 optimal weight: 0.5980 chunk 84 optimal weight: 0.0170 chunk 4 optimal weight: 3.9990 chunk 130 optimal weight: 2.9990 chunk 107 optimal weight: 5.9990 chunk 54 optimal weight: 2.9990 chunk 35 optimal weight: 0.8980 overall best weight: 1.1020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 413 GLN A 936 GLN A1122 GLN A1268 ASN ** A1413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.170032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.143072 restraints weight = 11677.802| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 1.00 r_work: 0.3262 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3163 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.2801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 11062 Z= 0.182 Angle : 0.550 7.816 15001 Z= 0.290 Chirality : 0.041 0.180 1675 Planarity : 0.004 0.050 1848 Dihedral : 9.300 149.301 1584 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 4.83 % Allowed : 20.52 % Favored : 74.66 % 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: 0.82 (0.24), residues: 1298 helix: 1.34 (0.20), residues: 715 sheet: 0.49 (0.51), residues: 93 loop : -0.58 (0.28), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 473 HIS 0.007 0.001 HIS A1413 PHE 0.018 0.002 PHE A1132 TYR 0.018 0.002 TYR A 912 ARG 0.005 0.000 ARG A 650 Details of bonding type rmsd hydrogen bonds : bond 0.05049 ( 578) hydrogen bonds : angle 4.62221 ( 1668) covalent geometry : bond 0.00418 (11062) covalent geometry : angle 0.54974 (15001) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 159 time to evaluate : 1.367 Fit side-chains revert: symmetry clash REVERT: A 236 ILE cc_start: 0.8771 (OUTLIER) cc_final: 0.8464 (pt) REVERT: A 377 MET cc_start: 0.7943 (mtt) cc_final: 0.7722 (mtt) REVERT: A 770 MET cc_start: 0.8507 (OUTLIER) cc_final: 0.8290 (tpp) REVERT: A 902 ARG cc_start: 0.7918 (OUTLIER) cc_final: 0.7503 (mmp-170) REVERT: A 1316 LYS cc_start: 0.8057 (OUTLIER) cc_final: 0.7844 (ttpp) REVERT: A 1355 SER cc_start: 0.8333 (t) cc_final: 0.8043 (m) REVERT: A 1585 ILE cc_start: 0.7166 (OUTLIER) cc_final: 0.6834 (mm) outliers start: 56 outliers final: 23 residues processed: 196 average time/residue: 1.1948 time to fit residues: 253.4692 Evaluate side-chains 182 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 154 time to evaluate : 1.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain A residue 358 GLN Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 549 ASP Chi-restraints excluded: chain A residue 666 SER Chi-restraints excluded: chain A residue 706 SER Chi-restraints excluded: chain A residue 719 GLU Chi-restraints excluded: chain A residue 743 LEU Chi-restraints excluded: chain A residue 770 MET Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 845 SER Chi-restraints excluded: chain A residue 847 VAL Chi-restraints excluded: chain A residue 902 ARG Chi-restraints excluded: chain A residue 943 LEU Chi-restraints excluded: chain A residue 949 GLU Chi-restraints excluded: chain A residue 1098 ASP Chi-restraints excluded: chain A residue 1229 VAL Chi-restraints excluded: chain A residue 1239 LEU Chi-restraints excluded: chain A residue 1247 VAL Chi-restraints excluded: chain A residue 1259 THR Chi-restraints excluded: chain A residue 1281 ILE Chi-restraints excluded: chain A residue 1316 LYS Chi-restraints excluded: chain A residue 1408 MET Chi-restraints excluded: chain A residue 1457 THR Chi-restraints excluded: chain A residue 1481 VAL Chi-restraints excluded: chain A residue 1554 ASP Chi-restraints excluded: chain A residue 1585 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 56 optimal weight: 4.9990 chunk 25 optimal weight: 2.9990 chunk 91 optimal weight: 4.9990 chunk 15 optimal weight: 3.9990 chunk 122 optimal weight: 1.9990 chunk 113 optimal weight: 1.9990 chunk 42 optimal weight: 0.0770 chunk 130 optimal weight: 6.9990 chunk 78 optimal weight: 1.9990 chunk 114 optimal weight: 1.9990 chunk 129 optimal weight: 0.9990 overall best weight: 1.4146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 936 GLN A1058 GLN A1122 GLN A1268 ASN A1364 GLN A1434 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.168566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.140659 restraints weight = 11637.904| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 1.04 r_work: 0.3231 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3121 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.3134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 11062 Z= 0.215 Angle : 0.587 9.925 15001 Z= 0.308 Chirality : 0.042 0.180 1675 Planarity : 0.004 0.055 1848 Dihedral : 9.316 147.622 1584 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 4.57 % Allowed : 20.60 % Favored : 74.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.62 (0.23), residues: 1298 helix: 1.19 (0.20), residues: 722 sheet: 0.48 (0.50), residues: 93 loop : -0.71 (0.28), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A1338 HIS 0.013 0.001 HIS A1413 PHE 0.020 0.002 PHE A 894 TYR 0.021 0.002 TYR A 912 ARG 0.013 0.001 ARG A1427 Details of bonding type rmsd hydrogen bonds : bond 0.05234 ( 578) hydrogen bonds : angle 4.68843 ( 1668) covalent geometry : bond 0.00499 (11062) covalent geometry : angle 0.58690 (15001) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 157 time to evaluate : 1.238 Fit side-chains revert: symmetry clash REVERT: A 236 ILE cc_start: 0.8806 (OUTLIER) cc_final: 0.8544 (pt) REVERT: A 770 MET cc_start: 0.8519 (OUTLIER) cc_final: 0.8319 (tpp) REVERT: A 902 ARG cc_start: 0.8016 (OUTLIER) cc_final: 0.7576 (mmp-170) REVERT: A 1033 LEU cc_start: 0.8751 (OUTLIER) cc_final: 0.8404 (mt) REVERT: A 1107 LEU cc_start: 0.8958 (OUTLIER) cc_final: 0.8722 (mm) REVERT: A 1211 ARG cc_start: 0.8284 (mtt180) cc_final: 0.8072 (mtm-85) REVERT: A 1355 SER cc_start: 0.8358 (t) cc_final: 0.8032 (m) REVERT: A 1408 MET cc_start: 0.7232 (OUTLIER) cc_final: 0.7020 (ttt) REVERT: A 1585 ILE cc_start: 0.7164 (OUTLIER) cc_final: 0.6864 (mm) outliers start: 53 outliers final: 22 residues processed: 191 average time/residue: 1.0948 time to fit residues: 227.5680 Evaluate side-chains 184 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 155 time to evaluate : 1.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 549 ASP Chi-restraints excluded: chain A residue 666 SER Chi-restraints excluded: chain A residue 706 SER Chi-restraints excluded: chain A residue 719 GLU Chi-restraints excluded: chain A residue 743 LEU Chi-restraints excluded: chain A residue 770 MET Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 845 SER Chi-restraints excluded: chain A residue 847 VAL Chi-restraints excluded: chain A residue 902 ARG Chi-restraints excluded: chain A residue 949 GLU Chi-restraints excluded: chain A residue 1033 LEU Chi-restraints excluded: chain A residue 1098 ASP Chi-restraints excluded: chain A residue 1107 LEU Chi-restraints excluded: chain A residue 1229 VAL Chi-restraints excluded: chain A residue 1239 LEU Chi-restraints excluded: chain A residue 1247 VAL Chi-restraints excluded: chain A residue 1259 THR Chi-restraints excluded: chain A residue 1281 ILE Chi-restraints excluded: chain A residue 1290 LYS Chi-restraints excluded: chain A residue 1408 MET Chi-restraints excluded: chain A residue 1457 THR Chi-restraints excluded: chain A residue 1481 VAL Chi-restraints excluded: chain A residue 1554 ASP Chi-restraints excluded: chain A residue 1556 MET Chi-restraints excluded: chain A residue 1585 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 77 optimal weight: 0.9990 chunk 112 optimal weight: 3.9990 chunk 127 optimal weight: 7.9990 chunk 63 optimal weight: 1.9990 chunk 103 optimal weight: 0.6980 chunk 14 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 101 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 80 optimal weight: 0.0270 chunk 97 optimal weight: 2.9990 overall best weight: 1.1444 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 936 GLN A1058 GLN A1268 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.169154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.142259 restraints weight = 11560.266| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 0.96 r_work: 0.3263 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3159 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.3225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 11062 Z= 0.182 Angle : 0.554 7.801 15001 Z= 0.292 Chirality : 0.041 0.145 1675 Planarity : 0.004 0.050 1848 Dihedral : 9.218 147.343 1584 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 3.79 % Allowed : 21.81 % Favored : 74.40 % 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: 0.74 (0.23), residues: 1298 helix: 1.32 (0.20), residues: 716 sheet: 0.55 (0.50), residues: 93 loop : -0.72 (0.28), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A1338 HIS 0.004 0.001 HIS A 501 PHE 0.022 0.002 PHE A1132 TYR 0.018 0.002 TYR A 912 ARG 0.006 0.000 ARG A 650 Details of bonding type rmsd hydrogen bonds : bond 0.04856 ( 578) hydrogen bonds : angle 4.57540 ( 1668) covalent geometry : bond 0.00420 (11062) covalent geometry : angle 0.55383 (15001) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 156 time to evaluate : 1.189 Fit side-chains revert: symmetry clash REVERT: A 236 ILE cc_start: 0.8793 (OUTLIER) cc_final: 0.8520 (pt) REVERT: A 770 MET cc_start: 0.8474 (OUTLIER) cc_final: 0.8248 (tpp) REVERT: A 902 ARG cc_start: 0.7974 (OUTLIER) cc_final: 0.7526 (mmp-170) REVERT: A 1033 LEU cc_start: 0.8765 (OUTLIER) cc_final: 0.8403 (mt) REVERT: A 1107 LEU cc_start: 0.8909 (OUTLIER) cc_final: 0.8665 (mm) REVERT: A 1211 ARG cc_start: 0.8226 (mtt180) cc_final: 0.7991 (mtm-85) REVERT: A 1585 ILE cc_start: 0.7208 (OUTLIER) cc_final: 0.6926 (mm) outliers start: 44 outliers final: 25 residues processed: 185 average time/residue: 1.1136 time to fit residues: 224.1768 Evaluate side-chains 185 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 154 time to evaluate : 1.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 358 GLN Chi-restraints excluded: chain A residue 523 SER Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 549 ASP Chi-restraints excluded: chain A residue 666 SER Chi-restraints excluded: chain A residue 706 SER Chi-restraints excluded: chain A residue 719 GLU Chi-restraints excluded: chain A residue 734 ASN Chi-restraints excluded: chain A residue 743 LEU Chi-restraints excluded: chain A residue 770 MET Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 847 VAL Chi-restraints excluded: chain A residue 902 ARG Chi-restraints excluded: chain A residue 949 GLU Chi-restraints excluded: chain A residue 955 SER Chi-restraints excluded: chain A residue 1033 LEU Chi-restraints excluded: chain A residue 1098 ASP Chi-restraints excluded: chain A residue 1107 LEU Chi-restraints excluded: chain A residue 1114 THR Chi-restraints excluded: chain A residue 1229 VAL Chi-restraints excluded: chain A residue 1239 LEU Chi-restraints excluded: chain A residue 1259 THR Chi-restraints excluded: chain A residue 1281 ILE Chi-restraints excluded: chain A residue 1398 MET Chi-restraints excluded: chain A residue 1457 THR Chi-restraints excluded: chain A residue 1481 VAL Chi-restraints excluded: chain A residue 1516 GLU Chi-restraints excluded: chain A residue 1554 ASP Chi-restraints excluded: chain A residue 1556 MET Chi-restraints excluded: chain A residue 1585 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 69 optimal weight: 2.9990 chunk 131 optimal weight: 2.9990 chunk 118 optimal weight: 0.1980 chunk 44 optimal weight: 0.7980 chunk 6 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 chunk 107 optimal weight: 0.0030 chunk 66 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 111 optimal weight: 0.7980 overall best weight: 0.5390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 363 GLN A 736 ASN A 936 GLN A1268 ASN A1482 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.170315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.143142 restraints weight = 11746.267| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 0.93 r_work: 0.3304 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3203 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.3280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11062 Z= 0.120 Angle : 0.490 6.932 15001 Z= 0.259 Chirality : 0.038 0.139 1675 Planarity : 0.004 0.043 1848 Dihedral : 9.074 148.399 1583 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.08 % Favored : 97.84 % Rotamer: Outliers : 3.10 % Allowed : 23.28 % Favored : 73.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.01 (0.24), residues: 1298 helix: 1.56 (0.20), residues: 715 sheet: 0.62 (0.50), residues: 93 loop : -0.62 (0.28), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 748 HIS 0.003 0.001 HIS A 742 PHE 0.017 0.001 PHE A 894 TYR 0.015 0.001 TYR A 912 ARG 0.004 0.000 ARG A 650 Details of bonding type rmsd hydrogen bonds : bond 0.04065 ( 578) hydrogen bonds : angle 4.38688 ( 1668) covalent geometry : bond 0.00263 (11062) covalent geometry : angle 0.49005 (15001) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 163 time to evaluate : 1.143 Fit side-chains revert: symmetry clash REVERT: A 236 ILE cc_start: 0.8787 (OUTLIER) cc_final: 0.8536 (pt) REVERT: A 770 MET cc_start: 0.8391 (OUTLIER) cc_final: 0.8185 (tpt) REVERT: A 902 ARG cc_start: 0.7858 (OUTLIER) cc_final: 0.7409 (mmp-170) outliers start: 36 outliers final: 17 residues processed: 186 average time/residue: 1.1812 time to fit residues: 238.2282 Evaluate side-chains 171 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 151 time to evaluate : 1.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 523 SER Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 549 ASP Chi-restraints excluded: chain A residue 706 SER Chi-restraints excluded: chain A residue 743 LEU Chi-restraints excluded: chain A residue 770 MET Chi-restraints excluded: chain A residue 902 ARG Chi-restraints excluded: chain A residue 949 GLU Chi-restraints excluded: chain A residue 1033 LEU Chi-restraints excluded: chain A residue 1098 ASP Chi-restraints excluded: chain A residue 1114 THR Chi-restraints excluded: chain A residue 1239 LEU Chi-restraints excluded: chain A residue 1281 ILE Chi-restraints excluded: chain A residue 1404 LEU Chi-restraints excluded: chain A residue 1457 THR Chi-restraints excluded: chain A residue 1481 VAL Chi-restraints excluded: chain A residue 1554 ASP Chi-restraints excluded: chain A residue 1556 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 97 optimal weight: 2.9990 chunk 102 optimal weight: 0.6980 chunk 9 optimal weight: 1.9990 chunk 115 optimal weight: 1.9990 chunk 12 optimal weight: 0.4980 chunk 96 optimal weight: 0.8980 chunk 93 optimal weight: 1.9990 chunk 124 optimal weight: 10.0000 chunk 37 optimal weight: 1.9990 chunk 121 optimal weight: 0.9990 chunk 79 optimal weight: 0.6980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 GLN A 936 GLN ** A1413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.170339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.143723 restraints weight = 11724.699| |-----------------------------------------------------------------------------| r_work (start): 0.3467 rms_B_bonded: 1.05 r_work: 0.3253 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3146 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.3298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11062 Z= 0.143 Angle : 0.517 7.261 15001 Z= 0.273 Chirality : 0.039 0.136 1675 Planarity : 0.004 0.043 1848 Dihedral : 9.094 148.479 1583 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.62 % Favored : 97.30 % Rotamer: Outliers : 3.79 % Allowed : 23.45 % Favored : 72.76 % 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: 1.02 (0.24), residues: 1298 helix: 1.57 (0.20), residues: 716 sheet: 0.61 (0.50), residues: 93 loop : -0.60 (0.28), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 473 HIS 0.005 0.001 HIS A1413 PHE 0.028 0.002 PHE A1132 TYR 0.016 0.001 TYR A 912 ARG 0.004 0.000 ARG A 650 Details of bonding type rmsd hydrogen bonds : bond 0.04340 ( 578) hydrogen bonds : angle 4.40240 ( 1668) covalent geometry : bond 0.00323 (11062) covalent geometry : angle 0.51685 (15001) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 150 time to evaluate : 1.138 Fit side-chains revert: symmetry clash REVERT: A 236 ILE cc_start: 0.8784 (OUTLIER) cc_final: 0.8497 (pt) REVERT: A 902 ARG cc_start: 0.7935 (OUTLIER) cc_final: 0.7503 (mmp-170) outliers start: 44 outliers final: 26 residues processed: 183 average time/residue: 1.1619 time to fit residues: 230.7283 Evaluate side-chains 173 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 145 time to evaluate : 1.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 358 GLN Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 523 SER Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 549 ASP Chi-restraints excluded: chain A residue 666 SER Chi-restraints excluded: chain A residue 706 SER Chi-restraints excluded: chain A residue 743 LEU Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 847 VAL Chi-restraints excluded: chain A residue 902 ARG Chi-restraints excluded: chain A residue 949 GLU Chi-restraints excluded: chain A residue 955 SER Chi-restraints excluded: chain A residue 960 ILE Chi-restraints excluded: chain A residue 1033 LEU Chi-restraints excluded: chain A residue 1098 ASP Chi-restraints excluded: chain A residue 1114 THR Chi-restraints excluded: chain A residue 1239 LEU Chi-restraints excluded: chain A residue 1247 VAL Chi-restraints excluded: chain A residue 1259 THR Chi-restraints excluded: chain A residue 1281 ILE Chi-restraints excluded: chain A residue 1404 LEU Chi-restraints excluded: chain A residue 1457 THR Chi-restraints excluded: chain A residue 1481 VAL Chi-restraints excluded: chain A residue 1516 GLU Chi-restraints excluded: chain A residue 1554 ASP Chi-restraints excluded: chain A residue 1556 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 2 optimal weight: 3.9990 chunk 91 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 121 optimal weight: 5.9990 chunk 42 optimal weight: 0.0070 chunk 105 optimal weight: 2.9990 chunk 35 optimal weight: 0.7980 chunk 54 optimal weight: 0.9980 chunk 70 optimal weight: 2.9990 chunk 67 optimal weight: 4.9990 chunk 52 optimal weight: 1.9990 overall best weight: 1.3602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 GLN ** A 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 936 GLN A1413 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.166845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.139637 restraints weight = 11655.294| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 1.08 r_work: 0.3233 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3126 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.3368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 11062 Z= 0.210 Angle : 0.593 11.099 15001 Z= 0.310 Chirality : 0.043 0.237 1675 Planarity : 0.004 0.048 1848 Dihedral : 9.202 147.694 1583 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.93 % Favored : 97.00 % Rotamer: Outliers : 3.62 % Allowed : 23.62 % Favored : 72.76 % 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: 0.74 (0.23), residues: 1298 helix: 1.29 (0.20), residues: 722 sheet: 0.52 (0.50), residues: 93 loop : -0.69 (0.28), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 473 HIS 0.005 0.001 HIS A1413 PHE 0.013 0.002 PHE A1091 TYR 0.021 0.002 TYR A 912 ARG 0.005 0.000 ARG A 650 Details of bonding type rmsd hydrogen bonds : bond 0.05106 ( 578) hydrogen bonds : angle 4.59578 ( 1668) covalent geometry : bond 0.00489 (11062) covalent geometry : angle 0.59342 (15001) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 149 time to evaluate : 1.143 Fit side-chains revert: symmetry clash REVERT: A 236 ILE cc_start: 0.8796 (OUTLIER) cc_final: 0.8521 (pt) REVERT: A 303 LYS cc_start: 0.8609 (OUTLIER) cc_final: 0.8351 (mmtt) REVERT: A 1107 LEU cc_start: 0.8935 (OUTLIER) cc_final: 0.8682 (mm) REVERT: A 1316 LYS cc_start: 0.8182 (ttpp) cc_final: 0.7818 (ptmm) REVERT: A 1402 LEU cc_start: 0.5031 (mt) cc_final: 0.4727 (mt) outliers start: 42 outliers final: 24 residues processed: 179 average time/residue: 1.1398 time to fit residues: 221.3755 Evaluate side-chains 177 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 150 time to evaluate : 1.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 303 LYS Chi-restraints excluded: chain A residue 523 SER Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 549 ASP Chi-restraints excluded: chain A residue 666 SER Chi-restraints excluded: chain A residue 706 SER Chi-restraints excluded: chain A residue 743 LEU Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 847 VAL Chi-restraints excluded: chain A residue 949 GLU Chi-restraints excluded: chain A residue 955 SER Chi-restraints excluded: chain A residue 960 ILE Chi-restraints excluded: chain A residue 1033 LEU Chi-restraints excluded: chain A residue 1098 ASP Chi-restraints excluded: chain A residue 1107 LEU Chi-restraints excluded: chain A residue 1114 THR Chi-restraints excluded: chain A residue 1229 VAL Chi-restraints excluded: chain A residue 1239 LEU Chi-restraints excluded: chain A residue 1247 VAL Chi-restraints excluded: chain A residue 1259 THR Chi-restraints excluded: chain A residue 1281 ILE Chi-restraints excluded: chain A residue 1457 THR Chi-restraints excluded: chain A residue 1481 VAL Chi-restraints excluded: chain A residue 1516 GLU Chi-restraints excluded: chain A residue 1554 ASP Chi-restraints excluded: chain A residue 1556 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 16 optimal weight: 3.9990 chunk 37 optimal weight: 0.2980 chunk 112 optimal weight: 0.7980 chunk 10 optimal weight: 0.5980 chunk 42 optimal weight: 0.7980 chunk 69 optimal weight: 1.9990 chunk 109 optimal weight: 0.9980 chunk 12 optimal weight: 0.5980 chunk 115 optimal weight: 0.8980 chunk 56 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 GLN A 456 GLN A 936 GLN ** A1413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.169296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.142132 restraints weight = 11745.718| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 0.92 r_work: 0.3299 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3194 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.3387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11062 Z= 0.132 Angle : 0.527 10.194 15001 Z= 0.275 Chirality : 0.039 0.201 1675 Planarity : 0.004 0.044 1848 Dihedral : 9.111 148.206 1583 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.08 % Favored : 97.84 % Rotamer: Outliers : 3.19 % Allowed : 24.22 % Favored : 72.59 % 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: 0.99 (0.24), residues: 1298 helix: 1.54 (0.20), residues: 716 sheet: 0.56 (0.50), residues: 93 loop : -0.61 (0.28), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 473 HIS 0.008 0.001 HIS A1413 PHE 0.012 0.001 PHE A 585 TYR 0.016 0.001 TYR A 912 ARG 0.005 0.000 ARG A 650 Details of bonding type rmsd hydrogen bonds : bond 0.04234 ( 578) hydrogen bonds : angle 4.41763 ( 1668) covalent geometry : bond 0.00296 (11062) covalent geometry : angle 0.52714 (15001) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 146 time to evaluate : 1.287 Fit side-chains revert: symmetry clash REVERT: A 236 ILE cc_start: 0.8772 (OUTLIER) cc_final: 0.8494 (pt) REVERT: A 902 ARG cc_start: 0.7885 (OUTLIER) cc_final: 0.7438 (mmp-170) REVERT: A 1107 LEU cc_start: 0.8884 (OUTLIER) cc_final: 0.8643 (mm) REVERT: A 1316 LYS cc_start: 0.8107 (ttpp) cc_final: 0.7764 (ptmm) REVERT: A 1427 ARG cc_start: 0.7786 (OUTLIER) cc_final: 0.7241 (mpp80) outliers start: 37 outliers final: 22 residues processed: 174 average time/residue: 1.1787 time to fit residues: 223.0640 Evaluate side-chains 171 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 145 time to evaluate : 1.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 523 SER Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 549 ASP Chi-restraints excluded: chain A residue 666 SER Chi-restraints excluded: chain A residue 706 SER Chi-restraints excluded: chain A residue 743 LEU Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 847 VAL Chi-restraints excluded: chain A residue 902 ARG Chi-restraints excluded: chain A residue 949 GLU Chi-restraints excluded: chain A residue 955 SER Chi-restraints excluded: chain A residue 960 ILE Chi-restraints excluded: chain A residue 1033 LEU Chi-restraints excluded: chain A residue 1098 ASP Chi-restraints excluded: chain A residue 1107 LEU Chi-restraints excluded: chain A residue 1114 THR Chi-restraints excluded: chain A residue 1229 VAL Chi-restraints excluded: chain A residue 1247 VAL Chi-restraints excluded: chain A residue 1259 THR Chi-restraints excluded: chain A residue 1281 ILE Chi-restraints excluded: chain A residue 1427 ARG Chi-restraints excluded: chain A residue 1457 THR Chi-restraints excluded: chain A residue 1481 VAL Chi-restraints excluded: chain A residue 1554 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 57 optimal weight: 0.9980 chunk 30 optimal weight: 4.9990 chunk 77 optimal weight: 3.9990 chunk 74 optimal weight: 0.9980 chunk 7 optimal weight: 0.9990 chunk 109 optimal weight: 0.8980 chunk 85 optimal weight: 0.4980 chunk 61 optimal weight: 1.9990 chunk 95 optimal weight: 3.9990 chunk 105 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 GLN A 936 GLN ** A1413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.170723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.143190 restraints weight = 11569.759| |-----------------------------------------------------------------------------| r_work (start): 0.3462 rms_B_bonded: 0.95 r_work: 0.3280 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3174 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.3412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 11062 Z= 0.155 Angle : 0.549 10.387 15001 Z= 0.287 Chirality : 0.040 0.212 1675 Planarity : 0.004 0.044 1848 Dihedral : 9.107 148.324 1581 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.70 % Favored : 97.23 % Rotamer: Outliers : 2.59 % Allowed : 24.83 % Favored : 72.59 % 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: 0.93 (0.23), residues: 1298 helix: 1.47 (0.20), residues: 716 sheet: 0.53 (0.50), residues: 93 loop : -0.61 (0.28), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 473 HIS 0.009 0.001 HIS A1413 PHE 0.026 0.002 PHE A1132 TYR 0.017 0.002 TYR A 912 ARG 0.005 0.000 ARG A1427 Details of bonding type rmsd hydrogen bonds : bond 0.04526 ( 578) hydrogen bonds : angle 4.45855 ( 1668) covalent geometry : bond 0.00355 (11062) covalent geometry : angle 0.54899 (15001) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 146 time to evaluate : 1.142 Fit side-chains revert: symmetry clash REVERT: A 236 ILE cc_start: 0.8772 (OUTLIER) cc_final: 0.8494 (pt) REVERT: A 902 ARG cc_start: 0.7896 (OUTLIER) cc_final: 0.7462 (mmp-170) REVERT: A 1107 LEU cc_start: 0.8903 (OUTLIER) cc_final: 0.8656 (mm) REVERT: A 1316 LYS cc_start: 0.8132 (ttpp) cc_final: 0.7788 (ptmm) REVERT: A 1427 ARG cc_start: 0.7851 (OUTLIER) cc_final: 0.7336 (mpp80) outliers start: 30 outliers final: 23 residues processed: 170 average time/residue: 1.2370 time to fit residues: 227.7498 Evaluate side-chains 173 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 146 time to evaluate : 1.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 523 SER Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 549 ASP Chi-restraints excluded: chain A residue 666 SER Chi-restraints excluded: chain A residue 706 SER Chi-restraints excluded: chain A residue 743 LEU Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 839 GLU Chi-restraints excluded: chain A residue 847 VAL Chi-restraints excluded: chain A residue 902 ARG Chi-restraints excluded: chain A residue 949 GLU Chi-restraints excluded: chain A residue 955 SER Chi-restraints excluded: chain A residue 960 ILE Chi-restraints excluded: chain A residue 1033 LEU Chi-restraints excluded: chain A residue 1098 ASP Chi-restraints excluded: chain A residue 1107 LEU Chi-restraints excluded: chain A residue 1114 THR Chi-restraints excluded: chain A residue 1229 VAL Chi-restraints excluded: chain A residue 1247 VAL Chi-restraints excluded: chain A residue 1259 THR Chi-restraints excluded: chain A residue 1281 ILE Chi-restraints excluded: chain A residue 1427 ARG Chi-restraints excluded: chain A residue 1457 THR Chi-restraints excluded: chain A residue 1481 VAL Chi-restraints excluded: chain A residue 1554 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 18 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 chunk 74 optimal weight: 0.7980 chunk 130 optimal weight: 4.9990 chunk 118 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 117 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 chunk 97 optimal weight: 0.9990 chunk 96 optimal weight: 0.9980 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 GLN ** A1413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.167487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.140999 restraints weight = 11668.174| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 0.94 r_work: 0.3266 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3162 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.3419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 11062 Z= 0.185 Angle : 0.579 10.383 15001 Z= 0.303 Chirality : 0.042 0.197 1675 Planarity : 0.004 0.046 1848 Dihedral : 9.160 147.889 1581 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.70 % Favored : 97.23 % Rotamer: Outliers : 2.67 % Allowed : 24.57 % Favored : 72.76 % 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: 0.79 (0.23), residues: 1298 helix: 1.35 (0.20), residues: 715 sheet: 0.51 (0.50), residues: 93 loop : -0.66 (0.28), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 473 HIS 0.009 0.001 HIS A1413 PHE 0.013 0.002 PHE A 585 TYR 0.020 0.002 TYR A 912 ARG 0.006 0.000 ARG A1427 Details of bonding type rmsd hydrogen bonds : bond 0.04847 ( 578) hydrogen bonds : angle 4.54233 ( 1668) covalent geometry : bond 0.00429 (11062) covalent geometry : angle 0.57935 (15001) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7879.36 seconds wall clock time: 136 minutes 54.43 seconds (8214.43 seconds total)