Starting phenix.real_space_refine on Wed Mar 4 03:16:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8c4s_16427/03_2026/8c4s_16427.cif Found real_map, /net/cci-nas-00/data/ceres_data/8c4s_16427/03_2026/8c4s_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 { model { file = "/net/cci-nas-00/data/ceres_data/8c4s_16427/03_2026/8c4s_16427.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8c4s_16427/03_2026/8c4s_16427.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8c4s_16427/03_2026/8c4s_16427.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8c4s_16427/03_2026/8c4s_16427.map" } resolution = 3.27 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: 2.35, per 1000 atoms: 0.23 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: 0.83 Conformation dependent library (CDL) restraints added in 545.2 milliseconds 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: 0.47 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: 2.28 Time building geometry restraints manager: 1.14 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: 1.200 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: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 11.590 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.250 ------------------------------------------------------------------------------- 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= 0.373 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.005 0.000 ARG A1407 TYR 0.020 0.001 TYR A 637 PHE 0.040 0.001 PHE A1467 TRP 0.017 0.001 TRP A 976 HIS 0.005 0.001 HIS A1036 Details of bonding type rmsd covalent geometry : bond 0.00530 (10517) covalent geometry : angle 0.84895 (14207) hydrogen bonds : bond 0.13488 ( 583) hydrogen bonds : angle 5.51280 ( 1725) *********************** 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 : 0.396 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: 0.0997 time to fit residues: 17.0363 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 : 0.371 ------------------------------------------------------------------------------- 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 108 optimal weight: 0.8980 chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 0.0470 chunk 113 optimal weight: 0.9990 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 0.5980 chunk 123 optimal weight: 10.0000 chunk 65 optimal weight: 7.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.6980 overall best weight: 0.6478 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.130693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.098740 restraints weight = 16752.584| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 2.48 r_work: 0.3039 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.0927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10517 Z= 0.127 Angle : 0.501 7.343 14207 Z= 0.261 Chirality : 0.039 0.278 1587 Planarity : 0.004 0.041 1783 Dihedral : 4.779 59.859 1394 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.00 % Favored : 97.84 % Rotamer: Outliers : 2.39 % Allowed : 18.73 % Favored : 78.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.48 (0.24), residues: 1251 helix: 2.02 (0.19), residues: 727 sheet: 0.34 (0.61), residues: 91 loop : -0.68 (0.30), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1405 TYR 0.011 0.001 TYR A1509 PHE 0.021 0.001 PHE A1467 TRP 0.014 0.001 TRP A 473 HIS 0.004 0.001 HIS A1095 Details of bonding type rmsd covalent geometry : bond 0.00288 (10517) covalent geometry : angle 0.50077 (14207) hydrogen bonds : bond 0.03944 ( 583) hydrogen bonds : angle 4.24900 ( 1725) *********************** 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 127 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 100 time to evaluate : 0.359 Fit side-chains revert: symmetry clash REVERT: A 460 GLN cc_start: 0.9147 (OUTLIER) cc_final: 0.7876 (tm-30) REVERT: A 1408 MET cc_start: 0.6277 (OUTLIER) cc_final: 0.5971 (tmm) REVERT: A 1518 MET cc_start: 0.8439 (tmm) cc_final: 0.8180 (tmm) outliers start: 27 outliers final: 12 residues processed: 121 average time/residue: 0.0807 time to fit residues: 15.1230 Evaluate side-chains 102 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 88 time to evaluate : 0.359 ------------------------------------------------------------------------------- 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 120 optimal weight: 8.9990 chunk 49 optimal weight: 0.6980 chunk 91 optimal weight: 1.9990 chunk 73 optimal weight: 0.9990 chunk 36 optimal weight: 0.6980 chunk 31 optimal weight: 0.7980 chunk 16 optimal weight: 7.9990 chunk 108 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 chunk 12 optimal weight: 0.0370 chunk 44 optimal weight: 0.9980 overall best weight: 0.6458 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.130611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.098414 restraints weight = 16662.770| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 2.41 r_work: 0.3038 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.1123 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= 0.121 Angle : 0.473 6.880 14207 Z= 0.243 Chirality : 0.037 0.153 1587 Planarity : 0.003 0.040 1783 Dihedral : 4.308 53.322 1388 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.24 % Favored : 97.60 % Rotamer: Outliers : 1.94 % Allowed : 18.64 % Favored : 79.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.55 (0.24), residues: 1251 helix: 2.12 (0.19), residues: 728 sheet: 0.39 (0.60), residues: 91 loop : -0.74 (0.30), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 880 TYR 0.012 0.001 TYR A 661 PHE 0.019 0.001 PHE A1040 TRP 0.014 0.001 TRP A 473 HIS 0.006 0.001 HIS A1096 Details of bonding type rmsd covalent geometry : bond 0.00279 (10517) covalent geometry : angle 0.47312 (14207) hydrogen bonds : bond 0.03680 ( 583) hydrogen bonds : angle 4.05558 ( 1725) *********************** 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 120 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 98 time to evaluate : 0.329 Fit side-chains revert: symmetry clash REVERT: A 460 GLN cc_start: 0.9142 (OUTLIER) cc_final: 0.7886 (tm-30) REVERT: A 1407 ARG cc_start: 0.6938 (mmm160) cc_final: 0.6301 (tpp-160) REVERT: A 1408 MET cc_start: 0.6294 (OUTLIER) cc_final: 0.6010 (tmm) REVERT: A 1518 MET cc_start: 0.8459 (OUTLIER) cc_final: 0.8188 (tmm) outliers start: 22 outliers final: 14 residues processed: 115 average time/residue: 0.0838 time to fit residues: 14.6921 Evaluate side-chains 104 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 87 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 460 GLN 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 1371 ILE Chi-restraints excluded: chain A residue 1404 LEU Chi-restraints excluded: chain A residue 1408 MET Chi-restraints excluded: chain A residue 1449 LEU Chi-restraints excluded: chain A residue 1503 ILE Chi-restraints excluded: chain A residue 1518 MET 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 92 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 119 optimal weight: 1.9990 chunk 33 optimal weight: 0.3980 chunk 83 optimal weight: 9.9990 chunk 9 optimal weight: 0.9990 chunk 96 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 chunk 90 optimal weight: 0.7980 overall best weight: 1.0384 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.128724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.096883 restraints weight = 16841.114| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 2.57 r_work: 0.2995 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.1344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10517 Z= 0.161 Angle : 0.498 7.317 14207 Z= 0.254 Chirality : 0.039 0.207 1587 Planarity : 0.003 0.039 1783 Dihedral : 4.224 52.193 1385 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.40 % Favored : 97.44 % Rotamer: Outliers : 3.00 % Allowed : 18.37 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.50 (0.24), residues: 1251 helix: 2.11 (0.19), residues: 729 sheet: 0.34 (0.59), residues: 91 loop : -0.82 (0.30), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1376 TYR 0.013 0.001 TYR A 713 PHE 0.019 0.001 PHE A1040 TRP 0.014 0.001 TRP A 473 HIS 0.003 0.001 HIS A1413 Details of bonding type rmsd covalent geometry : bond 0.00382 (10517) covalent geometry : angle 0.49830 (14207) hydrogen bonds : bond 0.03840 ( 583) hydrogen bonds : angle 4.04542 ( 1725) *********************** 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 131 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 97 time to evaluate : 0.339 Fit side-chains revert: symmetry clash REVERT: A 1407 ARG cc_start: 0.7008 (mmm160) cc_final: 0.6317 (tpp-160) REVERT: A 1408 MET cc_start: 0.6688 (OUTLIER) cc_final: 0.6334 (tmm) REVERT: A 1511 PHE cc_start: 0.9053 (m-80) cc_final: 0.8540 (m-80) REVERT: A 1518 MET cc_start: 0.8436 (OUTLIER) cc_final: 0.8166 (tmm) outliers start: 34 outliers final: 17 residues processed: 123 average time/residue: 0.0794 time to fit residues: 15.1842 Evaluate side-chains 110 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 91 time to evaluate : 0.389 ------------------------------------------------------------------------------- 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 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 13 optimal weight: 3.9990 chunk 43 optimal weight: 0.6980 chunk 36 optimal weight: 1.9990 chunk 15 optimal weight: 10.0000 chunk 24 optimal weight: 3.9990 chunk 97 optimal weight: 0.9990 chunk 55 optimal weight: 4.9990 chunk 3 optimal weight: 0.8980 chunk 79 optimal weight: 0.2980 chunk 27 optimal weight: 0.4980 chunk 118 optimal weight: 3.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.130017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.097717 restraints weight = 16693.194| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 2.28 r_work: 0.3032 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.1472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10517 Z= 0.121 Angle : 0.472 7.838 14207 Z= 0.239 Chirality : 0.038 0.177 1587 Planarity : 0.003 0.040 1783 Dihedral : 4.084 47.251 1385 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.32 % Favored : 97.52 % Rotamer: Outliers : 2.47 % Allowed : 18.90 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.59 (0.24), residues: 1251 helix: 2.21 (0.19), residues: 725 sheet: 0.41 (0.59), residues: 91 loop : -0.83 (0.29), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 880 TYR 0.013 0.001 TYR A 353 PHE 0.021 0.001 PHE A1040 TRP 0.015 0.001 TRP A 473 HIS 0.003 0.001 HIS A1413 Details of bonding type rmsd covalent geometry : bond 0.00284 (10517) covalent geometry : angle 0.47196 (14207) hydrogen bonds : bond 0.03493 ( 583) hydrogen bonds : angle 3.91540 ( 1725) *********************** 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 127 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 99 time to evaluate : 0.391 Fit side-chains revert: symmetry clash REVERT: A 920 SER cc_start: 0.8584 (p) cc_final: 0.8116 (t) REVERT: A 1407 ARG cc_start: 0.6955 (mmm160) cc_final: 0.6294 (tpp-160) REVERT: A 1408 MET cc_start: 0.6721 (OUTLIER) cc_final: 0.6454 (tmm) REVERT: A 1511 PHE cc_start: 0.9032 (m-80) cc_final: 0.8626 (m-80) REVERT: A 1518 MET cc_start: 0.8327 (OUTLIER) cc_final: 0.8033 (tmm) outliers start: 28 outliers final: 16 residues processed: 121 average time/residue: 0.0841 time to fit residues: 15.4797 Evaluate side-chains 113 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 95 time to evaluate : 0.387 ------------------------------------------------------------------------------- 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 622 ILE Chi-restraints excluded: chain A residue 1134 VAL 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 1518 MET Chi-restraints excluded: chain A residue 1571 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 61 optimal weight: 0.9980 chunk 96 optimal weight: 3.9990 chunk 92 optimal weight: 3.9990 chunk 97 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 chunk 35 optimal weight: 0.5980 chunk 5 optimal weight: 5.9990 chunk 70 optimal weight: 0.7980 chunk 39 optimal weight: 0.9980 chunk 9 optimal weight: 0.7980 chunk 98 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.129586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.097369 restraints weight = 16963.642| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 2.29 r_work: 0.3021 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.1579 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= 0.132 Angle : 0.482 8.460 14207 Z= 0.243 Chirality : 0.038 0.168 1587 Planarity : 0.003 0.040 1783 Dihedral : 4.089 47.170 1385 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.40 % Favored : 97.44 % Rotamer: Outliers : 2.74 % Allowed : 19.08 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.62 (0.24), residues: 1251 helix: 2.23 (0.19), residues: 726 sheet: 0.60 (0.58), residues: 97 loop : -0.87 (0.30), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A1376 TYR 0.013 0.001 TYR A 661 PHE 0.022 0.001 PHE A1040 TRP 0.014 0.001 TRP A 473 HIS 0.003 0.001 HIS A1413 Details of bonding type rmsd covalent geometry : bond 0.00313 (10517) covalent geometry : angle 0.48238 (14207) hydrogen bonds : bond 0.03522 ( 583) hydrogen bonds : angle 3.90049 ( 1725) *********************** 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 128 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 97 time to evaluate : 0.380 Fit side-chains revert: symmetry clash REVERT: A 732 HIS cc_start: 0.5286 (m90) cc_final: 0.5066 (m170) REVERT: A 920 SER cc_start: 0.8636 (p) cc_final: 0.8200 (t) REVERT: A 1407 ARG cc_start: 0.6941 (mmm160) cc_final: 0.6265 (tpp-160) REVERT: A 1408 MET cc_start: 0.6702 (OUTLIER) cc_final: 0.6486 (tmm) REVERT: A 1464 TRP cc_start: 0.8557 (m100) cc_final: 0.8114 (m100) REVERT: A 1511 PHE cc_start: 0.9019 (m-80) cc_final: 0.8612 (m-80) REVERT: A 1518 MET cc_start: 0.8302 (OUTLIER) cc_final: 0.7985 (tmm) outliers start: 31 outliers final: 21 residues processed: 123 average time/residue: 0.0810 time to fit residues: 15.4918 Evaluate side-chains 117 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 94 time to evaluate : 0.411 ------------------------------------------------------------------------------- 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 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 1134 VAL 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 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 81 optimal weight: 0.5980 chunk 76 optimal weight: 4.9990 chunk 97 optimal weight: 1.9990 chunk 2 optimal weight: 0.6980 chunk 102 optimal weight: 2.9990 chunk 11 optimal weight: 0.7980 chunk 73 optimal weight: 0.6980 chunk 66 optimal weight: 5.9990 chunk 1 optimal weight: 1.9990 chunk 88 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3704 r_free = 0.3704 target = 0.129748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.097390 restraints weight = 16652.093| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 2.28 r_work: 0.3022 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.1670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10517 Z= 0.126 Angle : 0.476 8.551 14207 Z= 0.239 Chirality : 0.037 0.145 1587 Planarity : 0.003 0.040 1783 Dihedral : 4.028 46.469 1385 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.48 % Favored : 97.36 % Rotamer: Outliers : 2.74 % Allowed : 18.99 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.66 (0.24), residues: 1251 helix: 2.26 (0.19), residues: 726 sheet: 0.59 (0.58), residues: 97 loop : -0.85 (0.30), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A1376 TYR 0.020 0.001 TYR A 713 PHE 0.024 0.001 PHE A1040 TRP 0.014 0.001 TRP A 473 HIS 0.003 0.001 HIS A1413 Details of bonding type rmsd covalent geometry : bond 0.00298 (10517) covalent geometry : angle 0.47564 (14207) hydrogen bonds : bond 0.03437 ( 583) hydrogen bonds : angle 3.85260 ( 1725) *********************** 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 131 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 100 time to evaluate : 0.400 Fit side-chains revert: symmetry clash REVERT: A 230 TYR cc_start: 0.7340 (m-80) cc_final: 0.6964 (m-80) REVERT: A 732 HIS cc_start: 0.5261 (m90) cc_final: 0.5046 (m170) REVERT: A 736 ASN cc_start: 0.7642 (m-40) cc_final: 0.6986 (t0) REVERT: A 920 SER cc_start: 0.8636 (p) cc_final: 0.8196 (t) REVERT: A 1291 ARG cc_start: 0.8731 (OUTLIER) cc_final: 0.7972 (ptp90) REVERT: A 1407 ARG cc_start: 0.7054 (mmm160) cc_final: 0.6320 (tpp-160) REVERT: A 1464 TRP cc_start: 0.8577 (m100) cc_final: 0.8147 (m100) REVERT: A 1511 PHE cc_start: 0.9011 (m-80) cc_final: 0.8574 (m-80) REVERT: A 1518 MET cc_start: 0.8306 (OUTLIER) cc_final: 0.7989 (tmm) outliers start: 31 outliers final: 23 residues processed: 127 average time/residue: 0.0880 time to fit residues: 16.8705 Evaluate side-chains 120 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 95 time to evaluate : 0.375 ------------------------------------------------------------------------------- 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 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 629 LEU Chi-restraints excluded: chain A residue 834 SER Chi-restraints excluded: chain A residue 897 THR Chi-restraints excluded: chain A residue 1134 VAL 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 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 Chi-restraints excluded: chain A residue 1571 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 123 optimal weight: 0.3980 chunk 58 optimal weight: 0.0670 chunk 12 optimal weight: 2.9990 chunk 9 optimal weight: 0.8980 chunk 117 optimal weight: 9.9990 chunk 52 optimal weight: 2.9990 chunk 110 optimal weight: 9.9990 chunk 71 optimal weight: 0.6980 chunk 29 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 44 optimal weight: 0.5980 overall best weight: 0.5318 ------------------------------------------------------------------------------- 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 = 0.3714 r_free = 0.3714 target = 0.130530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.097934 restraints weight = 16673.041| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 2.47 r_work: 0.3047 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.1737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 10517 Z= 0.109 Angle : 0.479 7.799 14207 Z= 0.238 Chirality : 0.037 0.149 1587 Planarity : 0.003 0.039 1783 Dihedral : 3.711 43.848 1382 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.48 % Favored : 97.36 % Rotamer: Outliers : 2.39 % Allowed : 19.52 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.76 (0.24), residues: 1251 helix: 2.34 (0.19), residues: 725 sheet: 0.65 (0.58), residues: 96 loop : -0.79 (0.30), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 880 TYR 0.019 0.001 TYR A 713 PHE 0.024 0.001 PHE A1040 TRP 0.014 0.001 TRP A 473 HIS 0.003 0.001 HIS A1413 Details of bonding type rmsd covalent geometry : bond 0.00255 (10517) covalent geometry : angle 0.47883 (14207) hydrogen bonds : bond 0.03271 ( 583) hydrogen bonds : angle 3.78925 ( 1725) *********************** 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 125 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 98 time to evaluate : 0.392 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 230 TYR cc_start: 0.7298 (m-80) cc_final: 0.6962 (m-80) REVERT: A 732 HIS cc_start: 0.5315 (m90) cc_final: 0.5098 (m170) REVERT: A 736 ASN cc_start: 0.7633 (m-40) cc_final: 0.6973 (t0) REVERT: A 920 SER cc_start: 0.8607 (p) cc_final: 0.8173 (t) REVERT: A 1291 ARG cc_start: 0.8727 (OUTLIER) cc_final: 0.7969 (ptp90) REVERT: A 1464 TRP cc_start: 0.8616 (m100) cc_final: 0.8214 (m100) REVERT: A 1511 PHE cc_start: 0.8984 (m-80) cc_final: 0.8564 (m-80) REVERT: A 1518 MET cc_start: 0.8298 (OUTLIER) cc_final: 0.7977 (tmm) REVERT: A 1556 MET cc_start: 0.9129 (tpp) cc_final: 0.8925 (tpt) outliers start: 27 outliers final: 19 residues processed: 121 average time/residue: 0.0871 time to fit residues: 15.8424 Evaluate side-chains 119 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 98 time to evaluate : 0.261 ------------------------------------------------------------------------------- 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 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 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 1518 MET Chi-restraints excluded: chain A residue 1571 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 18 optimal weight: 0.8980 chunk 42 optimal weight: 0.4980 chunk 120 optimal weight: 5.9990 chunk 26 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 113 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 72 optimal weight: 0.8980 chunk 22 optimal weight: 0.9980 chunk 32 optimal weight: 0.0970 overall best weight: 0.6778 ------------------------------------------------------------------------------- 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 = 0.3711 r_free = 0.3711 target = 0.130359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.095365 restraints weight = 16570.109| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 2.37 r_work: 0.3047 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.1806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 10517 Z= 0.121 Angle : 0.481 10.741 14207 Z= 0.239 Chirality : 0.037 0.145 1587 Planarity : 0.003 0.039 1783 Dihedral : 3.510 25.085 1378 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.64 % Favored : 97.20 % Rotamer: Outliers : 2.21 % Allowed : 19.96 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.73 (0.24), residues: 1251 helix: 2.32 (0.19), residues: 726 sheet: 0.65 (0.58), residues: 96 loop : -0.82 (0.30), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A1376 TYR 0.019 0.001 TYR A 713 PHE 0.024 0.001 PHE A1040 TRP 0.013 0.001 TRP A 473 HIS 0.003 0.001 HIS A1413 Details of bonding type rmsd covalent geometry : bond 0.00287 (10517) covalent geometry : angle 0.48147 (14207) hydrogen bonds : bond 0.03339 ( 583) hydrogen bonds : angle 3.79911 ( 1725) *********************** 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 120 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 95 time to evaluate : 0.326 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 230 TYR cc_start: 0.7266 (m-80) cc_final: 0.6970 (m-80) REVERT: A 732 HIS cc_start: 0.5325 (m90) cc_final: 0.5062 (m170) REVERT: A 736 ASN cc_start: 0.7584 (m-40) cc_final: 0.6957 (t0) REVERT: A 920 SER cc_start: 0.8611 (p) cc_final: 0.8179 (t) REVERT: A 1291 ARG cc_start: 0.8738 (OUTLIER) cc_final: 0.7986 (ptp90) REVERT: A 1511 PHE cc_start: 0.8983 (m-80) cc_final: 0.8556 (m-80) REVERT: A 1518 MET cc_start: 0.8293 (OUTLIER) cc_final: 0.7969 (tmm) outliers start: 25 outliers final: 21 residues processed: 117 average time/residue: 0.0869 time to fit residues: 15.3019 Evaluate side-chains 116 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 93 time to evaluate : 0.362 ------------------------------------------------------------------------------- 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 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 622 ILE Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 708 ILE Chi-restraints excluded: chain A residue 834 SER 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 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 104 optimal weight: 0.3980 chunk 108 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 59 optimal weight: 0.9980 chunk 41 optimal weight: 0.7980 chunk 5 optimal weight: 4.9990 chunk 10 optimal weight: 0.7980 chunk 45 optimal weight: 0.5980 chunk 51 optimal weight: 0.8980 chunk 3 optimal weight: 0.9990 chunk 99 optimal weight: 3.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3631 r_free = 0.3631 target = 0.125543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.094487 restraints weight = 16544.976| |-----------------------------------------------------------------------------| r_work (start): 0.3160 rms_B_bonded: 2.20 r_work: 0.2940 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 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 0.047 10517 Z= 0.124 Angle : 0.487 10.317 14207 Z= 0.242 Chirality : 0.037 0.143 1587 Planarity : 0.003 0.039 1783 Dihedral : 3.502 25.457 1378 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.40 % Favored : 97.44 % Rotamer: Outliers : 2.12 % Allowed : 20.14 % Favored : 77.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.73 (0.24), residues: 1251 helix: 2.28 (0.19), residues: 732 sheet: 0.72 (0.58), residues: 95 loop : -0.83 (0.30), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 526 TYR 0.019 0.001 TYR A 713 PHE 0.024 0.001 PHE A1040 TRP 0.014 0.001 TRP A 473 HIS 0.003 0.001 HIS A1413 Details of bonding type rmsd covalent geometry : bond 0.00293 (10517) covalent geometry : angle 0.48737 (14207) hydrogen bonds : bond 0.03326 ( 583) hydrogen bonds : angle 3.78833 ( 1725) ********************** 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 120 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 96 time to evaluate : 0.402 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 230 TYR cc_start: 0.7250 (m-80) cc_final: 0.6992 (m-80) REVERT: A 732 HIS cc_start: 0.5393 (m90) cc_final: 0.5132 (m170) REVERT: A 736 ASN cc_start: 0.7477 (m-40) cc_final: 0.6969 (t0) REVERT: A 920 SER cc_start: 0.8723 (p) cc_final: 0.8308 (t) REVERT: A 1291 ARG cc_start: 0.8762 (OUTLIER) cc_final: 0.7978 (ptp90) REVERT: A 1511 PHE cc_start: 0.8970 (m-80) cc_final: 0.8597 (m-80) REVERT: A 1518 MET cc_start: 0.8271 (OUTLIER) cc_final: 0.7944 (tmm) outliers start: 24 outliers final: 21 residues processed: 117 average time/residue: 0.0806 time to fit residues: 14.2552 Evaluate side-chains 117 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 94 time to evaluate : 0.402 ------------------------------------------------------------------------------- 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 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 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 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 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 Chi-restraints excluded: chain A residue 1571 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 47 optimal weight: 3.9990 chunk 109 optimal weight: 1.9990 chunk 4 optimal weight: 0.6980 chunk 85 optimal weight: 0.9990 chunk 122 optimal weight: 2.9990 chunk 93 optimal weight: 0.5980 chunk 57 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 chunk 31 optimal weight: 0.9980 chunk 77 optimal weight: 0.5980 chunk 116 optimal weight: 4.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3631 r_free = 0.3631 target = 0.125443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.094366 restraints weight = 16776.541| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 2.23 r_work: 0.2945 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.1899 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= 0.123 Angle : 0.489 10.041 14207 Z= 0.242 Chirality : 0.037 0.145 1587 Planarity : 0.003 0.038 1783 Dihedral : 3.492 25.729 1378 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.80 % Favored : 97.04 % Rotamer: Outliers : 1.94 % Allowed : 20.23 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.74 (0.24), residues: 1251 helix: 2.30 (0.19), residues: 731 sheet: 0.53 (0.55), residues: 102 loop : -0.81 (0.30), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 526 TYR 0.019 0.001 TYR A 713 PHE 0.025 0.001 PHE A1040 TRP 0.014 0.001 TRP A 473 HIS 0.003 0.001 HIS A1413 Details of bonding type rmsd covalent geometry : bond 0.00293 (10517) covalent geometry : angle 0.48929 (14207) hydrogen bonds : bond 0.03330 ( 583) hydrogen bonds : angle 3.79325 ( 1725) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2115.57 seconds wall clock time: 37 minutes 8.08 seconds (2228.08 seconds total)