Starting phenix.real_space_refine on Sat Nov 16 05:19:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c4s_16427/11_2024/8c4s_16427.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c4s_16427/11_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_16427/11_2024/8c4s_16427.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c4s_16427/11_2024/8c4s_16427.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c4s_16427/11_2024/8c4s_16427.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c4s_16427/11_2024/8c4s_16427.cif" } 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. Time to flip 24 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/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: 6.29, per 1000 atoms: 0.61 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.95 Conformation dependent library (CDL) restraints added in 1.4 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: 1.36 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: 4.01 Time building geometry restraints manager: 3.37 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: 0.00 - 2.52: 13834 2.52 - 5.04: 321 5.04 - 7.56: 37 7.56 - 10.08: 12 10.08 - 12.60: 3 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 3.040 nonbonded pdb=" OH TYR A 855 " pdb=" OE1 GLU A 871 " model vdw 2.265 3.040 nonbonded pdb=" OG1 THR A 459 " pdb=" OE1 GLN A1223 " model vdw 2.265 3.040 nonbonded pdb=" O TYR A 821 " pdb=" ND2 ASN A 827 " model vdw 2.285 3.120 nonbonded pdb=" OH TYR A 701 " pdb=" OE1 GLU A1170 " model vdw 2.291 3.040 ... (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: 5.620 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: 2.350 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 25.440 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:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.790 ------------------------------------------------------------------------------- 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 to be fit. rotamer outliers: 14 poor density : 106 time to evaluate : 1.135 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: 0.2452 time to fit residues: 41.1344 Evaluate side-chains 97 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 90 time to evaluate : 1.150 ------------------------------------------------------------------------------- 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: 0.7980 chunk 96 optimal weight: 0.9990 chunk 53 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 64 optimal weight: 4.9990 chunk 51 optimal weight: 0.6980 chunk 99 optimal weight: 3.9990 chunk 38 optimal weight: 0.9980 chunk 60 optimal weight: 1.9990 chunk 74 optimal weight: 8.9990 chunk 115 optimal weight: 0.7980 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 A1096 HIS ** A1501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.0901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10517 Z= 0.221 Angle : 0.513 7.293 14207 Z= 0.267 Chirality : 0.039 0.250 1587 Planarity : 0.004 0.039 1783 Dihedral : 4.833 59.551 1394 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.92 % Favored : 97.92 % Rotamer: Outliers : 2.47 % Allowed : 18.82 % 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: 1.43 (0.24), residues: 1251 helix: 1.98 (0.19), residues: 728 sheet: 0.32 (0.61), residues: 91 loop : -0.69 (0.30), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 473 HIS 0.004 0.001 HIS A1095 PHE 0.021 0.001 PHE A1467 TYR 0.012 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 128 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 100 time to evaluate : 1.269 Fit side-chains revert: symmetry clash REVERT: A 460 GLN cc_start: 0.9146 (OUTLIER) cc_final: 0.7835 (tm-30) REVERT: A 1408 MET cc_start: 0.6304 (OUTLIER) cc_final: 0.6040 (tmm) REVERT: A 1464 TRP cc_start: 0.8353 (m100) cc_final: 0.8153 (m100) REVERT: A 1518 MET cc_start: 0.8181 (tmm) cc_final: 0.7938 (tmm) outliers start: 28 outliers final: 12 residues processed: 122 average time/residue: 0.2018 time to fit residues: 37.2204 Evaluate side-chains 104 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 90 time to evaluate : 1.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 460 GLN 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 1096 HIS 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 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 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: 2.9990 chunk 78 optimal weight: 0.9980 chunk 31 optimal weight: 0.7980 chunk 115 optimal weight: 0.7980 chunk 124 optimal weight: 2.9990 chunk 102 optimal weight: 0.9990 chunk 114 optimal weight: 3.9990 chunk 39 optimal weight: 0.8980 chunk 92 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 842 HIS A1096 HIS ** A1501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.1115 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= 0.202 Angle : 0.483 6.743 14207 Z= 0.248 Chirality : 0.038 0.146 1587 Planarity : 0.003 0.040 1783 Dihedral : 4.413 55.494 1388 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.16 % Favored : 97.68 % Rotamer: Outliers : 2.03 % Allowed : 19.17 % Favored : 78.80 % 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: 1.48 (0.24), residues: 1251 helix: 2.06 (0.19), residues: 729 sheet: 0.34 (0.59), residues: 91 loop : -0.77 (0.30), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 473 HIS 0.007 0.001 HIS A1096 PHE 0.015 0.001 PHE A 585 TYR 0.012 0.001 TYR A 661 ARG 0.002 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 118 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 95 time to evaluate : 1.269 Fit side-chains revert: symmetry clash REVERT: A 1407 ARG cc_start: 0.7117 (mmm160) cc_final: 0.6347 (tpp-160) REVERT: A 1408 MET cc_start: 0.6498 (OUTLIER) cc_final: 0.6249 (tmm) REVERT: A 1518 MET cc_start: 0.8279 (tmm) cc_final: 0.8015 (tmm) outliers start: 23 outliers final: 16 residues processed: 114 average time/residue: 0.2085 time to fit residues: 36.2046 Evaluate side-chains 102 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 85 time to evaluate : 1.347 ------------------------------------------------------------------------------- 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 897 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 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 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: 0.5980 chunk 59 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 chunk 55 optimal weight: 4.9990 chunk 77 optimal weight: 4.9990 chunk 115 optimal weight: 1.9990 chunk 122 optimal weight: 3.9990 chunk 60 optimal weight: 5.9990 chunk 109 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 overall best weight: 1.4384 ------------------------------------------------------------------------------- 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: 0.8401 moved from start: 0.1393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 10517 Z= 0.315 Angle : 0.532 7.409 14207 Z= 0.271 Chirality : 0.040 0.221 1587 Planarity : 0.004 0.041 1783 Dihedral : 4.418 57.582 1385 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.40 % Favored : 97.44 % Rotamer: Outliers : 2.74 % Allowed : 18.64 % Favored : 78.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.24), residues: 1251 helix: 1.98 (0.19), residues: 729 sheet: 0.22 (0.58), residues: 91 loop : -0.91 (0.30), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 473 HIS 0.004 0.001 HIS A1413 PHE 0.019 0.002 PHE A1040 TYR 0.011 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 126 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 95 time to evaluate : 1.447 Fit side-chains revert: symmetry clash REVERT: A 1407 ARG cc_start: 0.7245 (mmm160) cc_final: 0.6348 (tpp-160) REVERT: A 1408 MET cc_start: 0.6658 (OUTLIER) cc_final: 0.6378 (tmm) REVERT: A 1511 PHE cc_start: 0.9049 (m-80) cc_final: 0.8618 (m-80) REVERT: A 1518 MET cc_start: 0.8264 (OUTLIER) cc_final: 0.7979 (tmm) outliers start: 31 outliers final: 16 residues processed: 120 average time/residue: 0.1987 time to fit residues: 37.0720 Evaluate side-chains 107 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 89 time to evaluate : 1.331 ------------------------------------------------------------------------------- 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 520 VAL Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 897 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 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 1571 VAL 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: 0.6980 chunk 1 optimal weight: 2.9990 chunk 91 optimal weight: 0.9980 chunk 50 optimal weight: 0.9980 chunk 104 optimal weight: 5.9990 chunk 84 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 chunk 62 optimal weight: 0.8980 chunk 110 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 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: 0.8372 moved from start: 0.1481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10517 Z= 0.198 Angle : 0.483 8.102 14207 Z= 0.246 Chirality : 0.038 0.194 1587 Planarity : 0.003 0.041 1783 Dihedral : 4.220 50.921 1385 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.40 % Favored : 97.44 % Rotamer: Outliers : 2.74 % Allowed : 19.35 % 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: 1.45 (0.24), residues: 1251 helix: 2.11 (0.19), residues: 726 sheet: 0.22 (0.58), residues: 91 loop : -0.87 (0.30), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 473 HIS 0.003 0.001 HIS A1413 PHE 0.021 0.001 PHE A1040 TYR 0.012 0.001 TYR A 353 ARG 0.002 0.000 ARG A 880 *********************** 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 126 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 95 time to evaluate : 1.216 Fit side-chains revert: symmetry clash REVERT: A 732 HIS cc_start: 0.5246 (m90) cc_final: 0.5011 (m170) REVERT: A 1408 MET cc_start: 0.6729 (OUTLIER) cc_final: 0.6527 (tmm) REVERT: A 1464 TRP cc_start: 0.8517 (m100) cc_final: 0.8002 (m100) REVERT: A 1511 PHE cc_start: 0.9014 (m-80) cc_final: 0.8569 (m-80) REVERT: A 1518 MET cc_start: 0.8243 (OUTLIER) cc_final: 0.7992 (tmm) outliers start: 31 outliers final: 20 residues processed: 120 average time/residue: 0.1876 time to fit residues: 34.6141 Evaluate side-chains 112 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 90 time to evaluate : 1.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 386 LEU 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 622 ILE Chi-restraints excluded: chain A residue 834 SER Chi-restraints excluded: chain A residue 897 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 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 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: 0.9990 chunk 24 optimal weight: 0.7980 chunk 72 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 122 optimal weight: 9.9990 chunk 102 optimal weight: 0.5980 chunk 56 optimal weight: 5.9990 chunk 10 optimal weight: 0.6980 chunk 40 optimal weight: 0.6980 chunk 64 optimal weight: 0.0030 overall best weight: 0.5190 ------------------------------------------------------------------------------- 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: 0.8350 moved from start: 0.1605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 10517 Z= 0.157 Angle : 0.472 8.673 14207 Z= 0.236 Chirality : 0.038 0.203 1587 Planarity : 0.003 0.040 1783 Dihedral : 4.024 47.571 1385 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.40 % Favored : 97.44 % Rotamer: Outliers : 3.27 % Allowed : 18.64 % 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: 1.61 (0.24), residues: 1251 helix: 2.20 (0.19), residues: 731 sheet: 0.59 (0.58), residues: 96 loop : -0.88 (0.30), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 473 HIS 0.003 0.001 HIS A1413 PHE 0.022 0.001 PHE A1040 TYR 0.016 0.001 TYR A 661 ARG 0.002 0.000 ARG A 880 *********************** 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 135 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 98 time to evaluate : 1.210 Fit side-chains revert: symmetry clash REVERT: A 732 HIS cc_start: 0.5179 (m90) cc_final: 0.4952 (m170) REVERT: A 920 SER cc_start: 0.8651 (p) cc_final: 0.8184 (t) REVERT: A 1291 ARG cc_start: 0.8772 (OUTLIER) cc_final: 0.7999 (ptp90) REVERT: A 1464 TRP cc_start: 0.8552 (m100) cc_final: 0.8067 (m100) REVERT: A 1511 PHE cc_start: 0.8976 (m-80) cc_final: 0.8648 (m-80) REVERT: A 1518 MET cc_start: 0.8146 (OUTLIER) cc_final: 0.7887 (tmm) outliers start: 37 outliers final: 24 residues processed: 129 average time/residue: 0.2025 time to fit residues: 39.5609 Evaluate side-chains 118 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 92 time to evaluate : 1.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 374 THR Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 402 ILE 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 1101 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 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 1518 MET Chi-restraints excluded: chain A residue 1571 VAL 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: 2.9990 chunk 70 optimal weight: 0.8980 chunk 89 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 103 optimal weight: 6.9990 chunk 68 optimal weight: 0.8980 chunk 122 optimal weight: 3.9990 chunk 76 optimal weight: 1.9990 chunk 74 optimal weight: 5.9990 chunk 56 optimal weight: 4.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- 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: 0.8426 moved from start: 0.1757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.070 10517 Z= 0.417 Angle : 0.581 8.438 14207 Z= 0.294 Chirality : 0.042 0.196 1587 Planarity : 0.004 0.045 1783 Dihedral : 4.231 56.299 1382 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.64 % Favored : 97.20 % Rotamer: Outliers : 3.45 % Allowed : 18.37 % 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: 1.22 (0.24), residues: 1251 helix: 1.90 (0.19), residues: 730 sheet: 0.35 (0.57), residues: 97 loop : -1.04 (0.30), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1056 HIS 0.004 0.001 HIS A1413 PHE 0.023 0.002 PHE A1040 TYR 0.016 0.002 TYR A 661 ARG 0.003 0.000 ARG A1488 *********************** 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 to be fit. rotamer outliers: 39 poor density : 93 time to evaluate : 1.296 Fit side-chains revert: symmetry clash REVERT: A 293 LEU cc_start: 0.9062 (OUTLIER) cc_final: 0.8845 (tt) REVERT: A 732 HIS cc_start: 0.5286 (m90) cc_final: 0.5020 (m170) REVERT: A 912 TYR cc_start: 0.9119 (m-80) cc_final: 0.8894 (m-80) REVERT: A 1291 ARG cc_start: 0.8803 (OUTLIER) cc_final: 0.8009 (ptp90) REVERT: A 1511 PHE cc_start: 0.9030 (m-80) cc_final: 0.8705 (m-80) REVERT: A 1518 MET cc_start: 0.8208 (OUTLIER) cc_final: 0.7864 (tmm) outliers start: 39 outliers final: 29 residues processed: 129 average time/residue: 0.2020 time to fit residues: 38.9236 Evaluate side-chains 123 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 91 time to evaluate : 1.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 374 THR Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 402 ILE 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 1041 LEU Chi-restraints excluded: chain A residue 1101 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 1182 SER 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 1425 THR Chi-restraints excluded: chain A residue 1434 ASN 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 75 optimal weight: 3.9990 chunk 48 optimal weight: 0.7980 chunk 73 optimal weight: 0.7980 chunk 36 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 77 optimal weight: 2.9990 chunk 83 optimal weight: 6.9990 chunk 60 optimal weight: 0.7980 chunk 11 optimal weight: 0.7980 chunk 96 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 742 HIS ** A1501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.1783 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= 0.197 Angle : 0.498 7.466 14207 Z= 0.250 Chirality : 0.038 0.172 1587 Planarity : 0.003 0.039 1783 Dihedral : 3.965 48.457 1382 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.72 % Favored : 97.12 % Rotamer: Outliers : 2.83 % Allowed : 19.08 % 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: 1.44 (0.24), residues: 1251 helix: 2.08 (0.19), residues: 732 sheet: 0.47 (0.57), residues: 96 loop : -0.99 (0.30), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 473 HIS 0.003 0.001 HIS A 335 PHE 0.024 0.001 PHE A1040 TYR 0.015 0.001 TYR A 661 ARG 0.001 0.000 ARG A 880 *********************** 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 129 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 97 time to evaluate : 1.167 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 732 HIS cc_start: 0.5368 (m90) cc_final: 0.5069 (m170) REVERT: A 736 ASN cc_start: 0.7597 (m-40) cc_final: 0.7053 (t0) REVERT: A 742 HIS cc_start: 0.8054 (OUTLIER) cc_final: 0.7582 (m90) REVERT: A 920 SER cc_start: 0.8659 (p) cc_final: 0.8202 (t) REVERT: A 1291 ARG cc_start: 0.8782 (OUTLIER) cc_final: 0.8014 (ptp90) REVERT: A 1305 LEU cc_start: 0.8685 (OUTLIER) cc_final: 0.8454 (tp) REVERT: A 1511 PHE cc_start: 0.8981 (m-80) cc_final: 0.8632 (m-80) REVERT: A 1518 MET cc_start: 0.8188 (OUTLIER) cc_final: 0.7855 (tmm) REVERT: A 1556 MET cc_start: 0.8909 (tpp) cc_final: 0.8705 (tpt) outliers start: 32 outliers final: 25 residues processed: 125 average time/residue: 0.2230 time to fit residues: 41.3302 Evaluate side-chains 123 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 94 time to evaluate : 1.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 265 THR 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 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 897 THR Chi-restraints excluded: chain A residue 1041 LEU Chi-restraints excluded: chain A residue 1101 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 1291 ARG Chi-restraints excluded: chain A residue 1305 LEU 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 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 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: 9.9990 chunk 106 optimal weight: 0.7980 chunk 114 optimal weight: 7.9990 chunk 68 optimal weight: 0.8980 chunk 49 optimal weight: 2.9990 chunk 89 optimal weight: 0.9980 chunk 35 optimal weight: 0.5980 chunk 103 optimal weight: 5.9990 chunk 107 optimal weight: 4.9990 chunk 113 optimal weight: 2.9990 overall best weight: 1.2582 ------------------------------------------------------------------------------- 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: 0.8399 moved from start: 0.1825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 10517 Z= 0.283 Angle : 0.532 10.009 14207 Z= 0.265 Chirality : 0.039 0.158 1587 Planarity : 0.003 0.041 1783 Dihedral : 4.025 51.415 1382 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.96 % Favored : 96.88 % Rotamer: Outliers : 2.83 % Allowed : 19.26 % 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: 1.36 (0.24), residues: 1251 helix: 2.02 (0.19), residues: 733 sheet: 0.37 (0.57), residues: 97 loop : -1.00 (0.30), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 473 HIS 0.003 0.001 HIS A1413 PHE 0.023 0.002 PHE A1040 TYR 0.013 0.001 TYR A 661 ARG 0.001 0.000 ARG A 526 *********************** 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 128 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 96 time to evaluate : 1.223 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 732 HIS cc_start: 0.5412 (m90) cc_final: 0.5121 (m170) REVERT: A 736 ASN cc_start: 0.7636 (m-40) cc_final: 0.7072 (t0) REVERT: A 883 ARG cc_start: 0.6540 (mtp180) cc_final: 0.6005 (mtp180) REVERT: A 920 SER cc_start: 0.8632 (p) cc_final: 0.8202 (t) REVERT: A 1291 ARG cc_start: 0.8799 (OUTLIER) cc_final: 0.8017 (ptp90) REVERT: A 1511 PHE cc_start: 0.8994 (m-80) cc_final: 0.8655 (m-80) REVERT: A 1518 MET cc_start: 0.8222 (OUTLIER) cc_final: 0.7867 (tmm) REVERT: A 1556 MET cc_start: 0.8911 (tpp) cc_final: 0.8707 (tpt) outliers start: 32 outliers final: 27 residues processed: 124 average time/residue: 0.2138 time to fit residues: 39.6665 Evaluate side-chains 124 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 95 time to evaluate : 1.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 265 THR 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 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 1041 LEU Chi-restraints excluded: chain A residue 1101 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 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 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 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: 4.9990 chunk 73 optimal weight: 0.6980 chunk 57 optimal weight: 1.9990 chunk 83 optimal weight: 7.9990 chunk 126 optimal weight: 0.3980 chunk 116 optimal weight: 1.9990 chunk 100 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 61 optimal weight: 0.4980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 742 HIS ** A1501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.1883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 10517 Z= 0.258 Angle : 0.523 9.569 14207 Z= 0.261 Chirality : 0.039 0.151 1587 Planarity : 0.003 0.041 1783 Dihedral : 4.007 50.864 1382 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.04 % Favored : 96.80 % Rotamer: Outliers : 2.74 % Allowed : 19.26 % Favored : 78.00 % 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: 1.38 (0.24), residues: 1251 helix: 2.05 (0.19), residues: 733 sheet: 0.20 (0.57), residues: 97 loop : -0.98 (0.30), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 473 HIS 0.003 0.001 HIS A1413 PHE 0.024 0.002 PHE A1040 TYR 0.013 0.001 TYR A 661 ARG 0.001 0.000 ARG A 986 ********************** 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 132 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 101 time to evaluate : 1.296 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 230 TYR cc_start: 0.7415 (m-10) cc_final: 0.7120 (m-80) REVERT: A 732 HIS cc_start: 0.5440 (m90) cc_final: 0.5141 (m170) REVERT: A 736 ASN cc_start: 0.7578 (m-40) cc_final: 0.7051 (t0) REVERT: A 742 HIS cc_start: 0.8092 (OUTLIER) cc_final: 0.7545 (m90) REVERT: A 883 ARG cc_start: 0.6536 (mtp180) cc_final: 0.5989 (mtp180) REVERT: A 920 SER cc_start: 0.8633 (p) cc_final: 0.8188 (t) REVERT: A 1291 ARG cc_start: 0.8789 (OUTLIER) cc_final: 0.7995 (ptp90) REVERT: A 1296 TYR cc_start: 0.8340 (t80) cc_final: 0.8020 (t80) REVERT: A 1407 ARG cc_start: 0.7120 (mmm160) cc_final: 0.6192 (tpp-160) REVERT: A 1511 PHE cc_start: 0.8988 (m-80) cc_final: 0.8639 (m-80) REVERT: A 1518 MET cc_start: 0.8258 (OUTLIER) cc_final: 0.7904 (tmm) REVERT: A 1556 MET cc_start: 0.8898 (tpp) cc_final: 0.8692 (tpt) outliers start: 31 outliers final: 26 residues processed: 130 average time/residue: 0.2187 time to fit residues: 41.7616 Evaluate side-chains 124 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 95 time to evaluate : 1.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 265 THR 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 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 1041 LEU Chi-restraints excluded: chain A residue 1101 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 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 1425 THR Chi-restraints excluded: chain A residue 1481 VAL Chi-restraints excluded: chain A residue 1503 ILE Chi-restraints excluded: chain A residue 1518 MET 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: 2.9990 chunk 92 optimal weight: 3.9990 chunk 14 optimal weight: 5.9990 chunk 27 optimal weight: 0.9990 chunk 100 optimal weight: 5.9990 chunk 42 optimal weight: 0.7980 chunk 103 optimal weight: 6.9990 chunk 12 optimal weight: 0.7980 chunk 18 optimal weight: 0.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1096 HIS ** 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 = 0.3678 r_free = 0.3678 target = 0.127929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.092782 restraints weight = 16633.242| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 2.37 r_work: 0.3003 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.1909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 10517 Z= 0.259 Angle : 0.539 11.394 14207 Z= 0.267 Chirality : 0.039 0.151 1587 Planarity : 0.003 0.041 1783 Dihedral : 4.014 51.006 1382 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.04 % Favored : 96.80 % Rotamer: Outliers : 2.74 % Allowed : 19.61 % 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: 1.37 (0.24), residues: 1251 helix: 2.03 (0.19), residues: 733 sheet: 0.34 (0.57), residues: 95 loop : -0.99 (0.30), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 473 HIS 0.003 0.001 HIS A1413 PHE 0.027 0.002 PHE A1040 TYR 0.013 0.001 TYR A 661 ARG 0.001 0.000 ARG A 526 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2114.59 seconds wall clock time: 39 minutes 44.40 seconds (2384.40 seconds total)