Starting phenix.real_space_refine on Sat Dec 9 06:30:33 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c4s_16427/12_2023/8c4s_16427.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c4s_16427/12_2023/8c4s_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_16427/12_2023/8c4s_16427.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c4s_16427/12_2023/8c4s_16427.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c4s_16427/12_2023/8c4s_16427.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c4s_16427/12_2023/8c4s_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-1.21rc1-5172/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: 5.94, per 1000 atoms: 0.58 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: 4.14 Conformation dependent library (CDL) restraints added in 3.3 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: 1.33 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: 4.72 Time building geometry restraints manager: 4.50 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: 1.420 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: 4.280 Check model and map are aligned: 0.160 Set scattering table: 0.100 Process input model: 34.930 Find NCS groups from input model: 0.310 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:2.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.780 ------------------------------------------------------------------------------- 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 : 1.355 Fit side-chains revert: symmetry clash outliers start: 14 outliers final: 6 residues processed: 117 average time/residue: 0.2397 time to fit residues: 40.4806 Evaluate side-chains 96 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 90 time to evaluate : 1.282 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1574 time to fit residues: 3.1920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 2.9990 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: 0.0873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10517 Z= 0.208 Angle : 0.497 7.120 14207 Z= 0.258 Chirality : 0.038 0.274 1587 Planarity : 0.004 0.038 1783 Dihedral : 3.687 15.997 1376 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.00 % Favored : 97.84 % Rotamer: Outliers : 2.12 % Allowed : 19.70 % Favored : 78.18 % 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: 2.03 (0.19), residues: 728 sheet: 0.37 (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 0.023 0.001 PHE A1467 TYR 0.011 0.001 TYR A 637 ARG 0.005 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 120 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 96 time to evaluate : 1.272 Fit side-chains revert: symmetry clash outliers start: 24 outliers final: 11 residues processed: 117 average time/residue: 0.2045 time to fit residues: 36.8083 Evaluate side-chains 98 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 87 time to evaluate : 1.505 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1034 time to fit residues: 3.8497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 64 optimal weight: 0.0270 chunk 35 optimal weight: 0.4980 chunk 95 optimal weight: 2.9990 chunk 78 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 chunk 115 optimal weight: 6.9990 chunk 124 optimal weight: 2.9990 chunk 102 optimal weight: 1.9990 chunk 114 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 chunk 92 optimal weight: 0.8980 overall best weight: 0.6038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 842 HIS A1078 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.1100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10517 Z= 0.168 Angle : 0.468 8.067 14207 Z= 0.238 Chirality : 0.037 0.161 1587 Planarity : 0.003 0.040 1783 Dihedral : 3.532 14.996 1376 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.24 % Favored : 97.60 % Rotamer: Outliers : 1.06 % Allowed : 20.23 % Favored : 78.71 % 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: 2.17 (0.19), residues: 731 sheet: 0.40 (0.59), residues: 91 loop : -0.76 (0.30), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 473 HIS 0.003 0.001 HIS A1095 PHE 0.018 0.001 PHE A1040 TYR 0.012 0.001 TYR A 637 ARG 0.003 0.000 ARG A1405 *********************** 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 109 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 97 time to evaluate : 1.175 Fit side-chains revert: symmetry clash outliers start: 12 outliers final: 5 residues processed: 106 average time/residue: 0.1982 time to fit residues: 32.4097 Evaluate side-chains 92 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 87 time to evaluate : 1.286 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0985 time to fit residues: 2.6417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 1.9990 chunk 59 optimal weight: 2.9990 chunk 12 optimal weight: 0.6980 chunk 55 optimal weight: 5.9990 chunk 77 optimal weight: 4.9990 chunk 115 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 chunk 60 optimal weight: 4.9990 chunk 109 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 overall best weight: 1.5384 ------------------------------------------------------------------------------- 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: 0.1404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 10517 Z= 0.332 Angle : 0.540 7.515 14207 Z= 0.274 Chirality : 0.040 0.170 1587 Planarity : 0.004 0.041 1783 Dihedral : 3.754 18.843 1376 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.64 % Favored : 97.20 % Rotamer: Outliers : 1.59 % Allowed : 20.58 % Favored : 77.83 % 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: 1.42 (0.24), residues: 1251 helix: 2.02 (0.19), residues: 730 sheet: 0.23 (0.58), residues: 91 loop : -0.79 (0.30), 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 0.018 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 113 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 95 time to evaluate : 1.333 Fit side-chains revert: symmetry clash outliers start: 18 outliers final: 9 residues processed: 111 average time/residue: 0.1898 time to fit residues: 32.9263 Evaluate side-chains 95 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 86 time to evaluate : 1.229 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0989 time to fit residues: 3.3771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 102 optimal weight: 0.5980 chunk 69 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 91 optimal weight: 0.7980 chunk 50 optimal weight: 0.7980 chunk 104 optimal weight: 5.9990 chunk 84 optimal weight: 0.7980 chunk 0 optimal weight: 4.9990 chunk 62 optimal weight: 0.9980 chunk 110 optimal weight: 8.9990 chunk 30 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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: 0.1442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10517 Z= 0.193 Angle : 0.477 8.172 14207 Z= 0.242 Chirality : 0.038 0.154 1587 Planarity : 0.003 0.041 1783 Dihedral : 3.587 17.035 1376 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.40 % Favored : 97.44 % Rotamer: Outliers : 1.33 % Allowed : 20.49 % Favored : 78.18 % 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: 1.57 (0.24), residues: 1251 helix: 2.16 (0.19), residues: 727 sheet: 0.43 (0.57), residues: 97 loop : -0.80 (0.31), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 473 HIS 0.003 0.001 HIS A1036 PHE 0.021 0.001 PHE A1040 TYR 0.014 0.001 TYR A 353 ARG 0.001 0.000 ARG A1405 *********************** 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 110 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 95 time to evaluate : 1.356 Fit side-chains revert: symmetry clash outliers start: 15 outliers final: 4 residues processed: 109 average time/residue: 0.1990 time to fit residues: 33.2617 Evaluate side-chains 93 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 89 time to evaluate : 1.182 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1913 time to fit residues: 2.9261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 41 optimal weight: 0.9990 chunk 110 optimal weight: 4.9990 chunk 24 optimal weight: 0.8980 chunk 72 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 122 optimal weight: 4.9990 chunk 102 optimal weight: 0.8980 chunk 56 optimal weight: 5.9990 chunk 10 optimal weight: 0.9990 chunk 40 optimal weight: 0.5980 chunk 64 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 858 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: 0.8366 moved from start: 0.1593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 10517 Z= 0.198 Angle : 0.486 8.367 14207 Z= 0.243 Chirality : 0.038 0.172 1587 Planarity : 0.003 0.041 1783 Dihedral : 3.535 16.427 1376 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.56 % Favored : 97.28 % Rotamer: Outliers : 0.97 % Allowed : 21.20 % Favored : 77.83 % 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: 1.56 (0.24), residues: 1251 helix: 2.12 (0.19), residues: 739 sheet: 0.40 (0.56), residues: 97 loop : -0.81 (0.31), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 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 637 ARG 0.001 0.000 ARG A 961 *********************** 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 107 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 96 time to evaluate : 1.283 Fit side-chains revert: symmetry clash outliers start: 11 outliers final: 6 residues processed: 106 average time/residue: 0.2297 time to fit residues: 36.5606 Evaluate side-chains 97 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 91 time to evaluate : 1.262 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0974 time to fit residues: 2.7093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 118 optimal weight: 3.9990 chunk 13 optimal weight: 0.8980 chunk 70 optimal weight: 0.9990 chunk 89 optimal weight: 0.7980 chunk 69 optimal weight: 0.7980 chunk 103 optimal weight: 4.9990 chunk 68 optimal weight: 0.6980 chunk 122 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 74 optimal weight: 0.9980 chunk 56 optimal weight: 5.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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: 0.8369 moved from start: 0.1678 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= 0.205 Angle : 0.477 8.016 14207 Z= 0.241 Chirality : 0.038 0.161 1587 Planarity : 0.003 0.040 1783 Dihedral : 3.494 15.867 1376 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.72 % Favored : 97.12 % Rotamer: Outliers : 1.06 % Allowed : 20.58 % Favored : 78.36 % 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: 2.15 (0.19), residues: 739 sheet: 0.42 (0.56), residues: 97 loop : -0.80 (0.31), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 473 HIS 0.003 0.001 HIS A1036 PHE 0.023 0.001 PHE A1040 TYR 0.011 0.001 TYR A 637 ARG 0.002 0.000 ARG A 526 *********************** 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 108 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 96 time to evaluate : 1.347 Fit side-chains revert: symmetry clash outliers start: 12 outliers final: 2 residues processed: 106 average time/residue: 0.2245 time to fit residues: 35.7189 Evaluate side-chains 94 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 92 time to evaluate : 1.326 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1027 time to fit residues: 2.3744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.2980 chunk 73 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 23 optimal weight: 0.8980 chunk 77 optimal weight: 1.9990 chunk 83 optimal weight: 7.9990 chunk 60 optimal weight: 0.8980 chunk 11 optimal weight: 0.8980 chunk 96 optimal weight: 0.0370 overall best weight: 0.6058 ------------------------------------------------------------------------------- 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: 0.8353 moved from start: 0.1758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10517 Z= 0.166 Angle : 0.481 8.075 14207 Z= 0.240 Chirality : 0.037 0.151 1587 Planarity : 0.003 0.039 1783 Dihedral : 3.425 15.059 1376 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.72 % Favored : 97.12 % Rotamer: Outliers : 0.44 % Allowed : 21.02 % Favored : 78.53 % 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: 1.69 (0.25), residues: 1251 helix: 2.23 (0.19), residues: 738 sheet: 0.50 (0.57), residues: 95 loop : -0.77 (0.31), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 473 HIS 0.003 0.001 HIS A1036 PHE 0.024 0.001 PHE A1040 TYR 0.011 0.001 TYR A 637 ARG 0.001 0.000 ARG A1407 *********************** 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 105 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 100 time to evaluate : 1.193 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 102 average time/residue: 0.2075 time to fit residues: 32.1833 Evaluate side-chains 98 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 96 time to evaluate : 1.334 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1219 time to fit residues: 2.0627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 111 optimal weight: 5.9990 chunk 117 optimal weight: 10.0000 chunk 106 optimal weight: 0.8980 chunk 114 optimal weight: 7.9990 chunk 68 optimal weight: 0.7980 chunk 49 optimal weight: 2.9990 chunk 89 optimal weight: 0.6980 chunk 35 optimal weight: 0.5980 chunk 103 optimal weight: 4.9990 chunk 107 optimal weight: 4.9990 chunk 113 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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: 0.8360 moved from start: 0.1836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 10517 Z= 0.194 Angle : 0.495 10.322 14207 Z= 0.245 Chirality : 0.037 0.150 1587 Planarity : 0.003 0.038 1783 Dihedral : 3.435 14.504 1376 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.88 % Favored : 96.96 % Rotamer: Outliers : 0.44 % Allowed : 21.64 % 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: 1.67 (0.25), residues: 1251 helix: 2.20 (0.19), residues: 738 sheet: 0.48 (0.57), residues: 95 loop : -0.77 (0.31), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 498 HIS 0.003 0.001 HIS A1036 PHE 0.025 0.001 PHE A1040 TYR 0.023 0.001 TYR A 332 ARG 0.003 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 102 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 97 time to evaluate : 1.412 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 102 average time/residue: 0.2159 time to fit residues: 33.0574 Evaluate side-chains 94 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 92 time to evaluate : 1.295 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0970 time to fit residues: 2.1566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 74 optimal weight: 6.9990 chunk 120 optimal weight: 0.0870 chunk 73 optimal weight: 0.6980 chunk 57 optimal weight: 0.9990 chunk 83 optimal weight: 0.0770 chunk 126 optimal weight: 2.9990 chunk 116 optimal weight: 5.9990 chunk 100 optimal weight: 3.9990 chunk 10 optimal weight: 0.3980 chunk 77 optimal weight: 0.8980 chunk 61 optimal weight: 0.0970 overall best weight: 0.2714 ------------------------------------------------------------------------------- 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: 0.8319 moved from start: 0.1951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 10517 Z= 0.126 Angle : 0.476 11.143 14207 Z= 0.233 Chirality : 0.037 0.144 1587 Planarity : 0.003 0.037 1783 Dihedral : 3.291 13.612 1376 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.56 % Favored : 97.28 % Rotamer: Outliers : 0.35 % Allowed : 21.38 % Favored : 78.27 % 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: 1.88 (0.25), residues: 1251 helix: 2.40 (0.19), residues: 731 sheet: 0.44 (0.55), residues: 101 loop : -0.66 (0.31), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 473 HIS 0.003 0.001 HIS A1036 PHE 0.025 0.001 PHE A1040 TYR 0.016 0.001 TYR A 332 ARG 0.002 0.000 ARG A 379 ********************** 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 104 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 100 time to evaluate : 1.251 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 102 average time/residue: 0.1944 time to fit residues: 30.8943 Evaluate side-chains 96 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 95 time to evaluate : 1.243 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0968 time to fit residues: 1.8754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 80 optimal weight: 1.9990 chunk 107 optimal weight: 3.9990 chunk 30 optimal weight: 4.9990 chunk 92 optimal weight: 3.9990 chunk 14 optimal weight: 0.6980 chunk 27 optimal weight: 0.9980 chunk 100 optimal weight: 5.9990 chunk 42 optimal weight: 1.9990 chunk 103 optimal weight: 5.9990 chunk 12 optimal weight: 0.9980 chunk 18 optimal weight: 0.6980 overall best weight: 1.0782 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.123668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.092451 restraints weight = 16569.487| |-----------------------------------------------------------------------------| r_work (start): 0.3142 rms_B_bonded: 2.23 r_work: 0.2918 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.1937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 10517 Z= 0.252 Angle : 0.514 11.191 14207 Z= 0.254 Chirality : 0.038 0.155 1587 Planarity : 0.003 0.039 1783 Dihedral : 3.428 14.427 1376 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.72 % Favored : 97.12 % Rotamer: Outliers : 0.00 % Allowed : 21.91 % Favored : 78.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.69 (0.25), residues: 1251 helix: 2.24 (0.19), residues: 736 sheet: 0.33 (0.54), residues: 102 loop : -0.76 (0.31), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 473 HIS 0.003 0.001 HIS A 474 PHE 0.024 0.001 PHE A1040 TYR 0.022 0.001 TYR A 661 ARG 0.002 0.000 ARG A1488 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2079.29 seconds wall clock time: 38 minutes 59.27 seconds (2339.27 seconds total)