Starting phenix.real_space_refine on Fri Mar 15 01:38:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c4s_16427/03_2024/8c4s_16427.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c4s_16427/03_2024/8c4s_16427.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.27 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c4s_16427/03_2024/8c4s_16427.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c4s_16427/03_2024/8c4s_16427.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c4s_16427/03_2024/8c4s_16427.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c4s_16427/03_2024/8c4s_16427.pdb" } resolution = 3.27 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= 0.004 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: 4 Type Number sf(0) Gaussians S 56 5.16 5 C 6632 2.51 5 N 1723 2.21 5 O 1881 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 320": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 341": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 503": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 599": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 640": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 649": "OE1" <-> "OE2" Residue "A TYR 661": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 713": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 727": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 906": "OE1" <-> "OE2" Residue "A GLU 940": "OE1" <-> "OE2" Residue "A PHE 959": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1040": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1042": "OD1" <-> "OD2" Residue "A PHE 1117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1217": "OD1" <-> "OD2" Residue "A ASP 1285": "OD1" <-> "OD2" Residue "A PHE 1436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1462": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1467": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1579": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 10292 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 10292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1277, 10292 Classifications: {'peptide': 1277} Link IDs: {'PTRANS': 41, 'TRANS': 1235} Chain breaks: 12 Time building chain proxies: 6.18, per 1000 atoms: 0.60 Number of scatterers: 10292 At special positions: 0 Unit cell: (89.31, 101.905, 123.66, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 56 16.00 O 1881 8.00 N 1723 7.00 C 6632 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 - 3.50 Amino acid : False - 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: 4.35 Conformation dependent library (CDL) restraints added in 1.8 seconds 2502 Ramachandran restraints generated. 1251 Oldfield, 0 Emsley, 1251 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2440 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 10 sheets defined 60.5% alpha, 10.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.19 Creating SS restraints... Processing helix chain 'A' and resid 239 through 252 removed outlier: 3.681A pdb=" N LEU A 243 " --> pdb=" O ASN A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 282 Processing helix chain 'A' and resid 306 through 323 Processing helix chain 'A' and resid 328 through 343 Processing helix chain 'A' and resid 345 through 354 Processing helix chain 'A' and resid 379 through 391 Processing helix chain 'A' and resid 409 through 428 removed outlier: 3.502A pdb=" N GLN A 413 " --> pdb=" O SER A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 458 Processing helix chain 'A' and resid 458 through 463 Processing helix chain 'A' and resid 463 through 469 removed outlier: 4.320A pdb=" N LYS A 469 " --> pdb=" O ASP A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 470 through 490 removed outlier: 3.872A pdb=" N HIS A 474 " --> pdb=" O THR A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 563 through 572 removed outlier: 3.564A pdb=" N ILE A 572 " --> pdb=" O LEU A 568 " (cutoff:3.500A) 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 635 removed outlier: 4.017A 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 647 Processing helix chain 'A' and resid 654 through 674 removed outlier: 3.611A pdb=" N VAL A 658 " --> pdb=" O SER A 654 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ASN A 674 " --> pdb=" O ALA A 670 " (cutoff:3.500A) Processing helix chain 'A' and resid 712 through 726 removed outlier: 4.139A pdb=" N LEU A 716 " --> pdb=" O HIS A 712 " (cutoff:3.500A) Processing helix chain 'A' and resid 735 through 760 Processing helix chain 'A' and resid 760 through 767 Processing helix chain 'A' and resid 769 through 777 Processing helix chain 'A' and resid 786 through 802 removed outlier: 3.851A 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 825 through 829 removed outlier: 3.990A pdb=" N SER A 829 " --> pdb=" O ARG A 826 " (cutoff:3.500A) Processing helix chain 'A' and resid 847 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 918 through 920 No H-bonds generated for 'chain 'A' and resid 918 through 920' Processing helix chain 'A' and resid 932 through 948 Processing helix chain 'A' and resid 982 through 992 removed outlier: 4.159A pdb=" N ARG A 986 " --> pdb=" O SER A 982 " (cutoff:3.500A) removed outlier: 3.893A 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 1034 through 1043 Processing helix chain 'A' and resid 1061 through 1084 Processing helix chain 'A' and resid 1114 through 1126 Processing helix chain 'A' and resid 1128 through 1133 removed outlier: 3.776A pdb=" N SER A1133 " --> pdb=" O HIS A1130 " (cutoff:3.500A) Processing helix chain 'A' and resid 1137 through 1152 removed outlier: 3.536A pdb=" N SER A1141 " --> pdb=" O GLU A1137 " (cutoff:3.500A) Processing helix chain 'A' and resid 1168 through 1181 Processing helix chain 'A' and resid 1184 through 1195 removed outlier: 4.018A pdb=" N ILE A1188 " --> pdb=" O PRO A1184 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N LEU A1193 " --> pdb=" O LEU A1189 " (cutoff:3.500A) Processing helix chain 'A' and resid 1200 through 1219 Processing helix chain 'A' and resid 1221 through 1241 Processing helix chain 'A' and resid 1249 through 1253 Processing helix chain 'A' and resid 1272 through 1279 Processing helix chain 'A' and resid 1282 through 1298 removed outlier: 3.817A 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 1371 removed outlier: 4.196A pdb=" N TYR A1370 " --> pdb=" O VAL A1366 " (cutoff:3.500A) Processing helix chain 'A' and resid 1375 through 1388 removed outlier: 4.210A pdb=" N ILE A1381 " --> pdb=" O ASP A1377 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ASN A1388 " --> pdb=" O VAL A1384 " (cutoff:3.500A) Processing helix chain 'A' and resid 1389 through 1397 removed outlier: 3.539A pdb=" N THR A1394 " --> pdb=" O PRO A1390 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ALA A1395 " --> pdb=" O SER A1391 " (cutoff:3.500A) Processing helix chain 'A' and resid 1407 through 1412 removed outlier: 4.217A pdb=" N LYS A1411 " --> pdb=" O ARG A1407 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLN A1412 " --> pdb=" O MET A1408 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1407 through 1412' Processing helix chain 'A' and resid 1426 through 1439 Processing helix chain 'A' and resid 1443 through 1457 Processing helix chain 'A' and resid 1463 through 1471 Processing helix chain 'A' and resid 1502 through 1511 removed outlier: 3.581A pdb=" N VAL A1506 " --> pdb=" O SER A1502 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N PHE A1511 " --> pdb=" O ILE A1507 " (cutoff:3.500A) Processing helix chain 'A' and resid 1514 through 1525 Processing helix chain 'A' and resid 1530 through 1545 removed outlier: 4.304A pdb=" N ASP A1540 " --> pdb=" O LYS A1536 " (cutoff:3.500A) Processing helix chain 'A' and resid 1552 through 1560 removed outlier: 3.548A pdb=" N MET A1556 " --> pdb=" O LEU A1552 " (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 removed outlier: 3.741A pdb=" N THR A1163 " --> pdb=" O SER A 970 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 260 through 261 removed outlier: 3.741A pdb=" N THR A1163 " --> pdb=" O SER A 970 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER A 950 " --> pdb=" O MET A 962 " (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 833 through 837 removed outlier: 4.599A pdb=" N SER A 844 " --> pdb=" O GLY A 835 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 877 through 879 removed outlier: 7.228A pdb=" N ALA A 877 " --> pdb=" O ASP A1016 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1415 through 1419 Processing sheet with id=AA9, first strand: chain 'A' and resid 1474 through 1479 removed outlier: 4.246A pdb=" N THR A1598 " --> pdb=" O ILE A1476 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1485 through 1489 600 hydrogen bonds defined for protein. 1725 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: 3.14 Time building geometry restraints manager: 4.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.28: 1655 1.28 - 1.41: 2693 1.41 - 1.55: 6076 1.55 - 1.68: 0 1.68 - 1.82: 93 Bond restraints: 10517 Sorted by residual: bond pdb=" C PRO A1373 " pdb=" O PRO A1373 " ideal model delta sigma weight residual 1.233 1.157 0.076 1.13e-02 7.83e+03 4.49e+01 bond pdb=" C LEU A1265 " pdb=" O LEU A1265 " ideal model delta sigma weight residual 1.234 1.147 0.088 1.33e-02 5.65e+03 4.34e+01 bond pdb=" C TYR A 637 " pdb=" O TYR A 637 " ideal model delta sigma weight residual 1.234 1.171 0.063 1.26e-02 6.30e+03 2.52e+01 bond pdb=" CA SER A1284 " pdb=" CB SER A1284 " ideal model delta sigma weight residual 1.529 1.458 0.071 1.55e-02 4.16e+03 2.10e+01 bond pdb=" C THR A1162 " pdb=" O THR A1162 " ideal model delta sigma weight residual 1.235 1.179 0.056 1.28e-02 6.10e+03 1.92e+01 ... (remaining 10512 not shown) Histogram of bond angle deviations from ideal: 97.88 - 105.17: 184 105.17 - 112.47: 5358 112.47 - 119.76: 3643 119.76 - 127.06: 4918 127.06 - 134.36: 104 Bond angle restraints: 14207 Sorted by residual: angle pdb=" C PRO A1373 " pdb=" CA PRO A1373 " pdb=" CB PRO A1373 " ideal model delta sigma weight residual 111.46 99.72 11.74 1.21e+00 6.83e-01 9.42e+01 angle pdb=" N LEU A1265 " pdb=" CA LEU A1265 " pdb=" C LEU A1265 " ideal model delta sigma weight residual 110.55 98.10 12.45 1.35e+00 5.49e-01 8.50e+01 angle pdb=" N MET A 735 " pdb=" CA MET A 735 " pdb=" C MET A 735 " ideal model delta sigma weight residual 114.64 102.04 12.60 1.52e+00 4.33e-01 6.87e+01 angle pdb=" N GLN A1409 " pdb=" CA GLN A1409 " pdb=" C GLN A1409 " ideal model delta sigma weight residual 113.15 104.84 8.31 1.19e+00 7.06e-01 4.87e+01 angle pdb=" N GLN A1403 " pdb=" CA GLN A1403 " pdb=" C GLN A1403 " ideal model delta sigma weight residual 112.38 104.21 8.17 1.22e+00 6.72e-01 4.48e+01 ... (remaining 14202 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.76: 5482 17.76 - 35.52: 632 35.52 - 53.28: 154 53.28 - 71.04: 24 71.04 - 88.80: 11 Dihedral angle restraints: 6303 sinusoidal: 2544 harmonic: 3759 Sorted by residual: dihedral pdb=" C LYS A1411 " pdb=" N LYS A1411 " pdb=" CA LYS A1411 " pdb=" CB LYS A1411 " ideal model delta harmonic sigma weight residual -122.60 -137.57 14.97 0 2.50e+00 1.60e-01 3.59e+01 dihedral pdb=" C PRO A1373 " pdb=" N PRO A1373 " pdb=" CA PRO A1373 " pdb=" CB PRO A1373 " ideal model delta harmonic sigma weight residual -120.70 -106.58 -14.12 0 2.50e+00 1.60e-01 3.19e+01 dihedral pdb=" C LYS A1161 " pdb=" N LYS A1161 " pdb=" CA LYS A1161 " pdb=" CB LYS A1161 " ideal model delta harmonic sigma weight residual -122.60 -136.08 13.48 0 2.50e+00 1.60e-01 2.91e+01 ... (remaining 6300 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.103: 1508 0.103 - 0.205: 65 0.205 - 0.308: 9 0.308 - 0.411: 3 0.411 - 0.513: 2 Chirality restraints: 1587 Sorted by residual: chirality pdb=" CA LYS A1411 " pdb=" N LYS A1411 " pdb=" C LYS A1411 " pdb=" CB LYS A1411 " both_signs ideal model delta sigma weight residual False 2.51 2.00 0.51 2.00e-01 2.50e+01 6.59e+00 chirality pdb=" CA LYS A1161 " pdb=" N LYS A1161 " pdb=" C LYS A1161 " pdb=" CB LYS A1161 " both_signs ideal model delta sigma weight residual False 2.51 2.05 0.46 2.00e-01 2.50e+01 5.34e+00 chirality pdb=" CA LEU A1265 " pdb=" N LEU A1265 " pdb=" C LEU A1265 " pdb=" CB LEU A1265 " both_signs ideal model delta sigma weight residual False 2.51 2.91 -0.40 2.00e-01 2.50e+01 3.95e+00 ... (remaining 1584 not shown) Planarity restraints: 1783 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY A1280 " -0.024 2.00e-02 2.50e+03 4.61e-02 2.12e+01 pdb=" C GLY A1280 " 0.080 2.00e-02 2.50e+03 pdb=" O GLY A1280 " -0.030 2.00e-02 2.50e+03 pdb=" N ILE A1281 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 973 " 0.021 2.00e-02 2.50e+03 4.05e-02 1.64e+01 pdb=" C ALA A 973 " -0.070 2.00e-02 2.50e+03 pdb=" O ALA A 973 " 0.026 2.00e-02 2.50e+03 pdb=" N THR A 974 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO A1401 " -0.016 2.00e-02 2.50e+03 3.57e-02 1.27e+01 pdb=" C PRO A1401 " 0.062 2.00e-02 2.50e+03 pdb=" O PRO A1401 " -0.024 2.00e-02 2.50e+03 pdb=" N LEU A1402 " -0.021 2.00e-02 2.50e+03 ... (remaining 1780 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 2424 2.79 - 3.31: 9865 3.31 - 3.84: 17293 3.84 - 4.37: 20242 4.37 - 4.90: 34986 Nonbonded interactions: 84810 Sorted by model distance: nonbonded pdb=" O VAL A 520 " pdb=" OG SER A 523 " model vdw 2.258 2.440 nonbonded pdb=" OH TYR A 855 " pdb=" OE1 GLU A 871 " model vdw 2.265 2.440 nonbonded pdb=" OG1 THR A 459 " pdb=" OE1 GLN A1223 " model vdw 2.265 2.440 nonbonded pdb=" O TYR A 821 " pdb=" ND2 ASN A 827 " model vdw 2.285 2.520 nonbonded pdb=" OH TYR A 701 " pdb=" OE1 GLU A1170 " model vdw 2.291 2.440 ... (remaining 84805 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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: 0.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 4.050 Check model and map are aligned: 0.160 Set scattering table: 0.100 Process input model: 31.410 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 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 : 0.005 0.088 10517 Z= 0.337 Angle : 0.849 12.599 14207 Z= 0.566 Chirality : 0.054 0.513 1587 Planarity : 0.004 0.046 1783 Dihedral : 15.993 88.798 3863 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.24 % Allowed : 2.88 % Favored : 96.88 % Rotamer: Outliers : 1.24 % Allowed : 20.14 % Favored : 78.62 % Cbeta Deviations : 0.49 % 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: 1.15 (0.24), residues: 1251 helix: 1.75 (0.19), residues: 716 sheet: 0.19 (0.59), residues: 90 loop : -0.74 (0.29), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 976 HIS 0.005 0.001 HIS A1036 PHE 0.040 0.001 PHE A1467 TYR 0.020 0.001 TYR A 637 ARG 0.005 0.000 ARG A1407 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2502 Ramachandran restraints generated. 1251 Oldfield, 0 Emsley, 1251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2502 Ramachandran restraints generated. 1251 Oldfield, 0 Emsley, 1251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 106 time to evaluate : 1.147 Fit side-chains revert: symmetry clash REVERT: A 1405 ARG cc_start: 0.5768 (OUTLIER) cc_final: 0.4351 (mmm160) outliers start: 14 outliers final: 6 residues processed: 117 average time/residue: 0.2187 time to fit residues: 36.8307 Evaluate side-chains 97 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 90 time to evaluate : 1.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 533 ILE Chi-restraints excluded: chain A residue 1160 LYS Chi-restraints excluded: chain A residue 1281 ILE Chi-restraints excluded: chain A residue 1400 SER Chi-restraints excluded: chain A residue 1404 LEU Chi-restraints excluded: chain A residue 1405 ARG Chi-restraints excluded: chain A residue 1408 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 107 optimal weight: 1.9990 chunk 96 optimal weight: 0.9980 chunk 53 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 chunk 51 optimal weight: 0.7980 chunk 99 optimal weight: 4.9990 chunk 38 optimal weight: 0.5980 chunk 60 optimal weight: 1.9990 chunk 74 optimal weight: 10.0000 chunk 115 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 505 ASN A 776 ASN A1048 HIS A1078 GLN A1096 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.0851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10517 Z= 0.209 Angle : 0.494 7.142 14207 Z= 0.257 Chirality : 0.038 0.276 1587 Planarity : 0.004 0.039 1783 Dihedral : 4.777 57.803 1394 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.16 % Favored : 97.68 % Rotamer: Outliers : 2.56 % Allowed : 19.52 % Favored : 77.92 % 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: 1.47 (0.24), residues: 1251 helix: 2.02 (0.19), residues: 728 sheet: 0.35 (0.60), residues: 91 loop : -0.70 (0.31), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 473 HIS 0.005 0.001 HIS A1095 PHE 0.022 0.001 PHE A1467 TYR 0.011 0.001 TYR A 637 ARG 0.003 0.000 ARG A1405 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2502 Ramachandran restraints generated. 1251 Oldfield, 0 Emsley, 1251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2502 Ramachandran restraints generated. 1251 Oldfield, 0 Emsley, 1251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 95 time to evaluate : 1.520 Fit side-chains revert: symmetry clash REVERT: A 633 VAL cc_start: 0.9513 (OUTLIER) cc_final: 0.9297 (t) REVERT: A 1117 PHE cc_start: 0.7815 (m-80) cc_final: 0.7495 (m-80) REVERT: A 1408 MET cc_start: 0.6284 (OUTLIER) cc_final: 0.6015 (tmm) REVERT: A 1518 MET cc_start: 0.8279 (tmm) cc_final: 0.8030 (tmm) outliers start: 29 outliers final: 15 residues processed: 119 average time/residue: 0.1953 time to fit residues: 35.8819 Evaluate side-chains 105 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 88 time to evaluate : 1.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 533 ILE Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 633 VAL Chi-restraints excluded: chain A residue 974 THR Chi-restraints excluded: chain A residue 1096 HIS Chi-restraints excluded: chain A residue 1160 LYS Chi-restraints excluded: chain A residue 1164 VAL Chi-restraints excluded: chain A residue 1193 LEU Chi-restraints excluded: chain A residue 1247 VAL Chi-restraints excluded: chain A residue 1400 SER Chi-restraints excluded: chain A residue 1404 LEU Chi-restraints excluded: chain A residue 1408 MET Chi-restraints excluded: chain A residue 1449 LEU Chi-restraints excluded: chain A residue 1529 ASP Chi-restraints excluded: chain A residue 1571 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 64 optimal weight: 0.7980 chunk 35 optimal weight: 0.6980 chunk 95 optimal weight: 3.9990 chunk 78 optimal weight: 0.5980 chunk 31 optimal weight: 1.9990 chunk 115 optimal weight: 6.9990 chunk 124 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 114 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 92 optimal weight: 0.6980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 842 HIS A1078 GLN A1096 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.1056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 10517 Z= 0.225 Angle : 0.482 7.135 14207 Z= 0.247 Chirality : 0.038 0.150 1587 Planarity : 0.003 0.039 1783 Dihedral : 4.426 58.768 1388 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.32 % Favored : 97.52 % Rotamer: Outliers : 2.39 % Allowed : 19.70 % Favored : 77.92 % 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: 1.52 (0.24), residues: 1251 helix: 2.10 (0.19), residues: 728 sheet: 0.38 (0.59), residues: 91 loop : -0.76 (0.30), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 473 HIS 0.006 0.001 HIS A1096 PHE 0.018 0.001 PHE A1040 TYR 0.012 0.001 TYR A 637 ARG 0.002 0.000 ARG A1376 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2502 Ramachandran restraints generated. 1251 Oldfield, 0 Emsley, 1251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2502 Ramachandran restraints generated. 1251 Oldfield, 0 Emsley, 1251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 92 time to evaluate : 1.287 Fit side-chains revert: symmetry clash REVERT: A 633 VAL cc_start: 0.9523 (OUTLIER) cc_final: 0.9313 (t) REVERT: A 1407 ARG cc_start: 0.6941 (mmm160) cc_final: 0.6444 (tpp-160) REVERT: A 1408 MET cc_start: 0.6260 (OUTLIER) cc_final: 0.6019 (tmm) REVERT: A 1518 MET cc_start: 0.8323 (tmm) cc_final: 0.8061 (tmm) outliers start: 27 outliers final: 20 residues processed: 115 average time/residue: 0.1896 time to fit residues: 33.2919 Evaluate side-chains 109 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 87 time to evaluate : 1.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 519 GLU Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 633 VAL Chi-restraints excluded: chain A residue 897 THR Chi-restraints excluded: chain A residue 974 THR Chi-restraints excluded: chain A residue 1041 LEU Chi-restraints excluded: chain A residue 1160 LYS Chi-restraints excluded: chain A residue 1164 VAL Chi-restraints excluded: chain A residue 1193 LEU Chi-restraints excluded: chain A residue 1247 VAL Chi-restraints excluded: chain A residue 1354 THR Chi-restraints excluded: chain A residue 1371 ILE Chi-restraints excluded: chain A residue 1404 LEU Chi-restraints excluded: chain A residue 1408 MET Chi-restraints excluded: chain A residue 1449 LEU Chi-restraints excluded: chain A residue 1503 ILE Chi-restraints excluded: chain A residue 1529 ASP Chi-restraints excluded: chain A residue 1571 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 114 optimal weight: 8.9990 chunk 86 optimal weight: 0.8980 chunk 59 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 chunk 55 optimal weight: 5.9990 chunk 77 optimal weight: 2.9990 chunk 115 optimal weight: 0.9990 chunk 122 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 109 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.1328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 10517 Z= 0.303 Angle : 0.519 7.467 14207 Z= 0.264 Chirality : 0.039 0.193 1587 Planarity : 0.004 0.041 1783 Dihedral : 4.364 58.720 1385 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.56 % Favored : 97.28 % Rotamer: Outliers : 2.92 % Allowed : 19.43 % Favored : 77.65 % 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: 1.42 (0.24), residues: 1251 helix: 2.03 (0.19), residues: 730 sheet: 0.28 (0.58), residues: 91 loop : -0.82 (0.31), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 473 HIS 0.004 0.001 HIS A1095 PHE 0.019 0.002 PHE A1040 TYR 0.012 0.001 TYR A 637 ARG 0.002 0.000 ARG A1376 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2502 Ramachandran restraints generated. 1251 Oldfield, 0 Emsley, 1251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2502 Ramachandran restraints generated. 1251 Oldfield, 0 Emsley, 1251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 95 time to evaluate : 1.418 Fit side-chains revert: symmetry clash REVERT: A 1407 ARG cc_start: 0.6986 (mmm160) cc_final: 0.6467 (tpp-160) REVERT: A 1511 PHE cc_start: 0.9045 (m-80) cc_final: 0.8614 (m-80) REVERT: A 1518 MET cc_start: 0.8248 (OUTLIER) cc_final: 0.7955 (tmm) outliers start: 33 outliers final: 20 residues processed: 124 average time/residue: 0.1878 time to fit residues: 35.8894 Evaluate side-chains 108 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 87 time to evaluate : 1.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 533 ILE Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 897 THR Chi-restraints excluded: chain A residue 974 THR Chi-restraints excluded: chain A residue 1160 LYS Chi-restraints excluded: chain A residue 1164 VAL Chi-restraints excluded: chain A residue 1193 LEU Chi-restraints excluded: chain A residue 1247 VAL Chi-restraints excluded: chain A residue 1354 THR Chi-restraints excluded: chain A residue 1371 ILE Chi-restraints excluded: chain A residue 1404 LEU Chi-restraints excluded: chain A residue 1449 LEU Chi-restraints excluded: chain A residue 1481 VAL Chi-restraints excluded: chain A residue 1503 ILE Chi-restraints excluded: chain A residue 1518 MET Chi-restraints excluded: chain A residue 1529 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 102 optimal weight: 3.9990 chunk 69 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 50 optimal weight: 0.0980 chunk 104 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 62 optimal weight: 0.9980 chunk 110 optimal weight: 8.9990 chunk 30 optimal weight: 1.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.1488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 10517 Z= 0.309 Angle : 0.520 7.801 14207 Z= 0.264 Chirality : 0.039 0.175 1587 Planarity : 0.004 0.044 1783 Dihedral : 4.164 58.388 1382 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.72 % Favored : 97.12 % Rotamer: Outliers : 3.45 % Allowed : 19.43 % Favored : 77.12 % 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: 1.35 (0.24), residues: 1251 helix: 2.00 (0.19), residues: 727 sheet: 0.09 (0.57), residues: 91 loop : -0.87 (0.30), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 473 HIS 0.003 0.001 HIS A1095 PHE 0.021 0.002 PHE A1040 TYR 0.012 0.001 TYR A 637 ARG 0.002 0.000 ARG A1376 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2502 Ramachandran restraints generated. 1251 Oldfield, 0 Emsley, 1251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2502 Ramachandran restraints generated. 1251 Oldfield, 0 Emsley, 1251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 90 time to evaluate : 1.300 Fit side-chains revert: symmetry clash REVERT: A 732 HIS cc_start: 0.5266 (m90) cc_final: 0.5004 (m170) REVERT: A 870 GLU cc_start: 0.7769 (mm-30) cc_final: 0.7532 (mm-30) REVERT: A 1408 MET cc_start: 0.6681 (OUTLIER) cc_final: 0.6440 (tmm) REVERT: A 1464 TRP cc_start: 0.8539 (m100) cc_final: 0.7994 (m100) REVERT: A 1511 PHE cc_start: 0.9032 (m-80) cc_final: 0.8639 (m-80) REVERT: A 1518 MET cc_start: 0.8263 (OUTLIER) cc_final: 0.7972 (tmm) outliers start: 39 outliers final: 24 residues processed: 125 average time/residue: 0.1788 time to fit residues: 35.1179 Evaluate side-chains 113 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 87 time to evaluate : 1.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 529 THR Chi-restraints excluded: chain A residue 533 ILE Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 834 SER Chi-restraints excluded: chain A residue 897 THR Chi-restraints excluded: chain A residue 974 THR Chi-restraints excluded: chain A residue 1041 LEU Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1160 LYS Chi-restraints excluded: chain A residue 1164 VAL Chi-restraints excluded: chain A residue 1247 VAL Chi-restraints excluded: chain A residue 1354 THR Chi-restraints excluded: chain A residue 1366 VAL Chi-restraints excluded: chain A residue 1371 ILE Chi-restraints excluded: chain A residue 1404 LEU Chi-restraints excluded: chain A residue 1408 MET Chi-restraints excluded: chain A residue 1449 LEU Chi-restraints excluded: chain A residue 1481 VAL Chi-restraints excluded: chain A residue 1503 ILE Chi-restraints excluded: chain A residue 1518 MET Chi-restraints excluded: chain A residue 1529 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 41 optimal weight: 0.5980 chunk 110 optimal weight: 6.9990 chunk 24 optimal weight: 3.9990 chunk 72 optimal weight: 0.8980 chunk 30 optimal weight: 0.7980 chunk 122 optimal weight: 6.9990 chunk 102 optimal weight: 0.5980 chunk 56 optimal weight: 5.9990 chunk 10 optimal weight: 0.9990 chunk 40 optimal weight: 0.5980 chunk 64 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.1544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 10517 Z= 0.182 Angle : 0.470 8.453 14207 Z= 0.237 Chirality : 0.037 0.186 1587 Planarity : 0.003 0.042 1783 Dihedral : 3.934 55.229 1382 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.80 % Favored : 97.04 % Rotamer: Outliers : 3.27 % Allowed : 19.70 % Favored : 77.03 % 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: 1.60 (0.24), residues: 1251 helix: 2.22 (0.19), residues: 726 sheet: 0.38 (0.56), residues: 97 loop : -0.84 (0.30), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 473 HIS 0.003 0.001 HIS A1036 PHE 0.022 0.001 PHE A1040 TYR 0.012 0.001 TYR A 353 ARG 0.002 0.000 ARG A 892 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2502 Ramachandran restraints generated. 1251 Oldfield, 0 Emsley, 1251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2502 Ramachandran restraints generated. 1251 Oldfield, 0 Emsley, 1251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 96 time to evaluate : 1.194 Fit side-chains revert: symmetry clash REVERT: A 732 HIS cc_start: 0.5233 (m90) cc_final: 0.4985 (m170) REVERT: A 920 SER cc_start: 0.8632 (p) cc_final: 0.8183 (t) REVERT: A 1291 ARG cc_start: 0.8772 (OUTLIER) cc_final: 0.8013 (ptp90) REVERT: A 1407 ARG cc_start: 0.7048 (mmm160) cc_final: 0.6398 (tpp-160) REVERT: A 1408 MET cc_start: 0.6772 (OUTLIER) cc_final: 0.6537 (tmm) REVERT: A 1464 TRP cc_start: 0.8567 (m100) cc_final: 0.8042 (m100) REVERT: A 1511 PHE cc_start: 0.8998 (m-80) cc_final: 0.8657 (m-80) REVERT: A 1518 MET cc_start: 0.8249 (OUTLIER) cc_final: 0.7994 (tmm) outliers start: 37 outliers final: 24 residues processed: 128 average time/residue: 0.2211 time to fit residues: 42.0964 Evaluate side-chains 118 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 91 time to evaluate : 1.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 529 THR Chi-restraints excluded: chain A residue 561 SER Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 974 THR Chi-restraints excluded: chain A residue 1041 LEU Chi-restraints excluded: chain A residue 1101 LEU Chi-restraints excluded: chain A residue 1160 LYS Chi-restraints excluded: chain A residue 1164 VAL Chi-restraints excluded: chain A residue 1182 SER Chi-restraints excluded: chain A residue 1193 LEU Chi-restraints excluded: chain A residue 1247 VAL Chi-restraints excluded: chain A residue 1291 ARG Chi-restraints excluded: chain A residue 1354 THR Chi-restraints excluded: chain A residue 1366 VAL Chi-restraints excluded: chain A residue 1371 ILE Chi-restraints excluded: chain A residue 1404 LEU Chi-restraints excluded: chain A residue 1408 MET Chi-restraints excluded: chain A residue 1425 THR Chi-restraints excluded: chain A residue 1449 LEU Chi-restraints excluded: chain A residue 1481 VAL Chi-restraints excluded: chain A residue 1518 MET Chi-restraints excluded: chain A residue 1529 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 118 optimal weight: 6.9990 chunk 13 optimal weight: 3.9990 chunk 70 optimal weight: 0.9980 chunk 89 optimal weight: 0.6980 chunk 69 optimal weight: 4.9990 chunk 103 optimal weight: 4.9990 chunk 68 optimal weight: 0.5980 chunk 122 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 74 optimal weight: 0.1980 chunk 56 optimal weight: 5.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.1651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 10517 Z= 0.251 Angle : 0.502 9.092 14207 Z= 0.251 Chirality : 0.038 0.170 1587 Planarity : 0.003 0.043 1783 Dihedral : 4.004 56.536 1382 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.64 % Favored : 97.20 % Rotamer: Outliers : 3.45 % Allowed : 19.88 % Favored : 76.68 % 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: 1.53 (0.24), residues: 1251 helix: 2.18 (0.19), residues: 727 sheet: 0.33 (0.57), residues: 95 loop : -0.90 (0.30), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 473 HIS 0.002 0.001 HIS A 278 PHE 0.024 0.001 PHE A1040 TYR 0.010 0.001 TYR A 637 ARG 0.001 0.000 ARG A 346 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2502 Ramachandran restraints generated. 1251 Oldfield, 0 Emsley, 1251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2502 Ramachandran restraints generated. 1251 Oldfield, 0 Emsley, 1251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 93 time to evaluate : 1.230 Fit side-chains revert: symmetry clash REVERT: A 732 HIS cc_start: 0.5379 (m90) cc_final: 0.5090 (m170) REVERT: A 920 SER cc_start: 0.8632 (p) cc_final: 0.8199 (t) REVERT: A 1291 ARG cc_start: 0.8789 (OUTLIER) cc_final: 0.8006 (ptp90) REVERT: A 1407 ARG cc_start: 0.6987 (mmm160) cc_final: 0.6299 (tpp-160) REVERT: A 1408 MET cc_start: 0.6790 (OUTLIER) cc_final: 0.6570 (tmm) REVERT: A 1464 TRP cc_start: 0.8622 (m100) cc_final: 0.8109 (m100) REVERT: A 1511 PHE cc_start: 0.8991 (m-80) cc_final: 0.8661 (m-80) REVERT: A 1518 MET cc_start: 0.8153 (OUTLIER) cc_final: 0.7881 (tmm) outliers start: 39 outliers final: 30 residues processed: 127 average time/residue: 0.2030 time to fit residues: 38.0126 Evaluate side-chains 124 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 91 time to evaluate : 1.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain A residue 273 SER Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 529 THR Chi-restraints excluded: chain A residue 533 ILE Chi-restraints excluded: chain A residue 561 SER Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 834 SER Chi-restraints excluded: chain A residue 897 THR Chi-restraints excluded: chain A residue 974 THR Chi-restraints excluded: chain A residue 1041 LEU Chi-restraints excluded: chain A residue 1101 LEU Chi-restraints excluded: chain A residue 1160 LYS Chi-restraints excluded: chain A residue 1164 VAL Chi-restraints excluded: chain A residue 1182 SER Chi-restraints excluded: chain A residue 1193 LEU Chi-restraints excluded: chain A residue 1247 VAL Chi-restraints excluded: chain A residue 1291 ARG Chi-restraints excluded: chain A residue 1354 THR Chi-restraints excluded: chain A residue 1371 ILE Chi-restraints excluded: chain A residue 1404 LEU Chi-restraints excluded: chain A residue 1408 MET Chi-restraints excluded: chain A residue 1425 THR Chi-restraints excluded: chain A residue 1449 LEU Chi-restraints excluded: chain A residue 1481 VAL Chi-restraints excluded: chain A residue 1503 ILE Chi-restraints excluded: chain A residue 1518 MET Chi-restraints excluded: chain A residue 1529 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 75 optimal weight: 2.9990 chunk 48 optimal weight: 0.0670 chunk 73 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 24 optimal weight: 0.4980 chunk 23 optimal weight: 0.8980 chunk 77 optimal weight: 0.5980 chunk 83 optimal weight: 9.9990 chunk 60 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 chunk 96 optimal weight: 0.6980 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1439 ASN ** A1501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.1730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 10517 Z= 0.154 Angle : 0.467 8.000 14207 Z= 0.232 Chirality : 0.037 0.163 1587 Planarity : 0.003 0.039 1783 Dihedral : 3.768 49.649 1382 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.04 % Favored : 96.80 % Rotamer: Outliers : 2.65 % Allowed : 20.05 % Favored : 77.30 % 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: 1.66 (0.24), residues: 1251 helix: 2.24 (0.19), residues: 737 sheet: 0.41 (0.56), residues: 97 loop : -0.86 (0.31), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 473 HIS 0.003 0.001 HIS A1036 PHE 0.024 0.001 PHE A1040 TYR 0.011 0.001 TYR A 912 ARG 0.004 0.000 ARG A 526 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2502 Ramachandran restraints generated. 1251 Oldfield, 0 Emsley, 1251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2502 Ramachandran restraints generated. 1251 Oldfield, 0 Emsley, 1251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 102 time to evaluate : 1.139 Fit side-chains revert: symmetry clash REVERT: A 732 HIS cc_start: 0.5393 (m90) cc_final: 0.5116 (m170) REVERT: A 736 ASN cc_start: 0.7570 (m-40) cc_final: 0.7032 (t0) REVERT: A 920 SER cc_start: 0.8648 (p) cc_final: 0.8184 (t) REVERT: A 1291 ARG cc_start: 0.8784 (OUTLIER) cc_final: 0.8027 (ptp90) REVERT: A 1407 ARG cc_start: 0.6821 (mmm160) cc_final: 0.6140 (tpp-160) REVERT: A 1408 MET cc_start: 0.6744 (OUTLIER) cc_final: 0.6539 (tmm) REVERT: A 1511 PHE cc_start: 0.8947 (m-80) cc_final: 0.8593 (m-80) REVERT: A 1518 MET cc_start: 0.8173 (OUTLIER) cc_final: 0.7894 (tmm) outliers start: 30 outliers final: 22 residues processed: 128 average time/residue: 0.2180 time to fit residues: 40.4491 Evaluate side-chains 122 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 97 time to evaluate : 1.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain A residue 273 SER Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 529 THR Chi-restraints excluded: chain A residue 561 SER Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 897 THR Chi-restraints excluded: chain A residue 974 THR Chi-restraints excluded: chain A residue 1101 LEU Chi-restraints excluded: chain A residue 1160 LYS Chi-restraints excluded: chain A residue 1164 VAL Chi-restraints excluded: chain A residue 1193 LEU Chi-restraints excluded: chain A residue 1247 VAL Chi-restraints excluded: chain A residue 1291 ARG Chi-restraints excluded: chain A residue 1371 ILE Chi-restraints excluded: chain A residue 1404 LEU Chi-restraints excluded: chain A residue 1408 MET Chi-restraints excluded: chain A residue 1425 THR Chi-restraints excluded: chain A residue 1449 LEU Chi-restraints excluded: chain A residue 1481 VAL Chi-restraints excluded: chain A residue 1518 MET Chi-restraints excluded: chain A residue 1529 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 111 optimal weight: 3.9990 chunk 117 optimal weight: 7.9990 chunk 106 optimal weight: 1.9990 chunk 114 optimal weight: 7.9990 chunk 68 optimal weight: 0.7980 chunk 49 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 35 optimal weight: 0.5980 chunk 103 optimal weight: 5.9990 chunk 107 optimal weight: 4.9990 chunk 113 optimal weight: 0.9980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 742 HIS A1439 ASN ** A1501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 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 0.069 10517 Z= 0.286 Angle : 0.523 7.674 14207 Z= 0.262 Chirality : 0.039 0.156 1587 Planarity : 0.003 0.042 1783 Dihedral : 3.961 53.849 1382 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.96 % Favored : 96.88 % Rotamer: Outliers : 2.74 % Allowed : 20.32 % Favored : 76.94 % 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: 1.49 (0.24), residues: 1251 helix: 2.09 (0.19), residues: 739 sheet: 0.31 (0.57), residues: 95 loop : -0.91 (0.31), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 473 HIS 0.003 0.001 HIS A1095 PHE 0.023 0.002 PHE A1040 TYR 0.025 0.001 TYR A 332 ARG 0.002 0.000 ARG A 379 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2502 Ramachandran restraints generated. 1251 Oldfield, 0 Emsley, 1251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2502 Ramachandran restraints generated. 1251 Oldfield, 0 Emsley, 1251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 95 time to evaluate : 1.221 Fit side-chains revert: symmetry clash REVERT: A 732 HIS cc_start: 0.5437 (m90) cc_final: 0.5145 (m170) REVERT: A 736 ASN cc_start: 0.7590 (m-40) cc_final: 0.7049 (t0) REVERT: A 742 HIS cc_start: 0.8082 (OUTLIER) cc_final: 0.7521 (m90) REVERT: A 920 SER cc_start: 0.8617 (p) cc_final: 0.8183 (t) REVERT: A 1291 ARG cc_start: 0.8782 (OUTLIER) cc_final: 0.8006 (ptp90) REVERT: A 1511 PHE cc_start: 0.8979 (m-80) cc_final: 0.8620 (m-80) REVERT: A 1518 MET cc_start: 0.8204 (OUTLIER) cc_final: 0.7892 (tmm) outliers start: 31 outliers final: 27 residues processed: 123 average time/residue: 0.2082 time to fit residues: 37.9746 Evaluate side-chains 120 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 90 time to evaluate : 1.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain A residue 273 SER Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 529 THR Chi-restraints excluded: chain A residue 533 ILE Chi-restraints excluded: chain A residue 561 SER Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 742 HIS Chi-restraints excluded: chain A residue 834 SER Chi-restraints excluded: chain A residue 897 THR Chi-restraints excluded: chain A residue 974 THR Chi-restraints excluded: chain A residue 1041 LEU Chi-restraints excluded: chain A residue 1101 LEU Chi-restraints excluded: chain A residue 1160 LYS Chi-restraints excluded: chain A residue 1164 VAL Chi-restraints excluded: chain A residue 1193 LEU Chi-restraints excluded: chain A residue 1247 VAL Chi-restraints excluded: chain A residue 1291 ARG Chi-restraints excluded: chain A residue 1371 ILE Chi-restraints excluded: chain A residue 1404 LEU Chi-restraints excluded: chain A residue 1425 THR Chi-restraints excluded: chain A residue 1449 LEU Chi-restraints excluded: chain A residue 1481 VAL Chi-restraints excluded: chain A residue 1518 MET Chi-restraints excluded: chain A residue 1529 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 74 optimal weight: 3.9990 chunk 120 optimal weight: 5.9990 chunk 73 optimal weight: 0.9990 chunk 57 optimal weight: 0.9980 chunk 83 optimal weight: 0.7980 chunk 126 optimal weight: 0.5980 chunk 116 optimal weight: 4.9990 chunk 100 optimal weight: 5.9990 chunk 10 optimal weight: 0.6980 chunk 77 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1078 GLN ** A1501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 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 0.057 10517 Z= 0.200 Angle : 0.505 8.046 14207 Z= 0.250 Chirality : 0.038 0.153 1587 Planarity : 0.003 0.039 1783 Dihedral : 3.869 50.660 1382 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.96 % Favored : 96.88 % Rotamer: Outliers : 2.65 % Allowed : 20.41 % Favored : 76.94 % 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: 1.53 (0.24), residues: 1251 helix: 2.12 (0.19), residues: 739 sheet: 0.33 (0.57), residues: 95 loop : -0.89 (0.31), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 473 HIS 0.006 0.001 HIS A 742 PHE 0.027 0.001 PHE A1040 TYR 0.014 0.001 TYR A 332 ARG 0.001 0.000 ARG A 961 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2502 Ramachandran restraints generated. 1251 Oldfield, 0 Emsley, 1251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2502 Ramachandran restraints generated. 1251 Oldfield, 0 Emsley, 1251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 93 time to evaluate : 1.295 Fit side-chains revert: symmetry clash REVERT: A 732 HIS cc_start: 0.5434 (m90) cc_final: 0.5139 (m170) REVERT: A 736 ASN cc_start: 0.7566 (m-40) cc_final: 0.6962 (t0) REVERT: A 920 SER cc_start: 0.8602 (p) cc_final: 0.8158 (t) REVERT: A 1291 ARG cc_start: 0.8773 (OUTLIER) cc_final: 0.8004 (ptp90) REVERT: A 1511 PHE cc_start: 0.8967 (m-80) cc_final: 0.8600 (m-80) REVERT: A 1518 MET cc_start: 0.8189 (OUTLIER) cc_final: 0.7836 (tmm) outliers start: 30 outliers final: 28 residues processed: 121 average time/residue: 0.2192 time to fit residues: 39.8154 Evaluate side-chains 123 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 93 time to evaluate : 1.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain A residue 273 SER Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 529 THR Chi-restraints excluded: chain A residue 533 ILE Chi-restraints excluded: chain A residue 561 SER Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 834 SER Chi-restraints excluded: chain A residue 897 THR Chi-restraints excluded: chain A residue 974 THR Chi-restraints excluded: chain A residue 1041 LEU Chi-restraints excluded: chain A residue 1101 LEU Chi-restraints excluded: chain A residue 1160 LYS Chi-restraints excluded: chain A residue 1164 VAL Chi-restraints excluded: chain A residue 1193 LEU Chi-restraints excluded: chain A residue 1247 VAL Chi-restraints excluded: chain A residue 1291 ARG Chi-restraints excluded: chain A residue 1371 ILE Chi-restraints excluded: chain A residue 1404 LEU Chi-restraints excluded: chain A residue 1425 THR Chi-restraints excluded: chain A residue 1449 LEU Chi-restraints excluded: chain A residue 1481 VAL Chi-restraints excluded: chain A residue 1503 ILE Chi-restraints excluded: chain A residue 1515 VAL Chi-restraints excluded: chain A residue 1518 MET Chi-restraints excluded: chain A residue 1529 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 80 optimal weight: 0.5980 chunk 107 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 chunk 92 optimal weight: 2.9990 chunk 14 optimal weight: 0.3980 chunk 27 optimal weight: 1.9990 chunk 100 optimal weight: 5.9990 chunk 42 optimal weight: 1.9990 chunk 103 optimal weight: 0.0050 chunk 12 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1078 GLN A1439 ASN ** A1501 ASN ** 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 = 0.3623 r_free = 0.3623 target = 0.125041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.094115 restraints weight = 16635.240| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 2.20 r_work: 0.2943 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.1852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 10517 Z= 0.165 Angle : 0.482 8.263 14207 Z= 0.238 Chirality : 0.037 0.138 1587 Planarity : 0.003 0.039 1783 Dihedral : 3.707 45.847 1382 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.72 % Favored : 97.12 % Rotamer: Outliers : 2.65 % Allowed : 20.49 % Favored : 76.86 % 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: 1.66 (0.25), residues: 1251 helix: 2.25 (0.19), residues: 736 sheet: 0.27 (0.55), residues: 102 loop : -0.82 (0.31), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 473 HIS 0.003 0.001 HIS A1036 PHE 0.023 0.001 PHE A1040 TYR 0.010 0.001 TYR A 637 ARG 0.001 0.000 ARG A 961 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2053.76 seconds wall clock time: 38 minutes 5.26 seconds (2285.26 seconds total)