Starting phenix.real_space_refine on Mon Jul 28 14:32:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8c4s_16427/07_2025/8c4s_16427.cif Found real_map, /net/cci-nas-00/data/ceres_data/8c4s_16427/07_2025/8c4s_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/cci-nas-00/data/ceres_data/8c4s_16427/07_2025/8c4s_16427.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8c4s_16427/07_2025/8c4s_16427.map" model { file = "/net/cci-nas-00/data/ceres_data/8c4s_16427/07_2025/8c4s_16427.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8c4s_16427/07_2025/8c4s_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-5711/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: 6.46, per 1000 atoms: 0.63 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: 2.80 Conformation dependent library (CDL) restraints added in 1.5 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: 1.38 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: 3.36 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: 1.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.420 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 28.480 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.510 ------------------------------------------------------------------------------- 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 (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 Details of bonding type rmsd hydrogen bonds : bond 0.13488 ( 583) hydrogen bonds : angle 5.51280 ( 1725) covalent geometry : bond 0.00530 (10517) covalent geometry : angle 0.84895 (14207) *********************** 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 : 1.165 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: 0.2426 time to fit residues: 40.7963 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 : 2.123 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.129697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.097538 restraints weight = 16474.933| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 2.39 r_work: 0.3029 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 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= 0.150 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 Details of bonding type rmsd hydrogen bonds : bond 0.04135 ( 583) hydrogen bonds : angle 4.30917 ( 1725) covalent geometry : bond 0.00348 (10517) covalent geometry : angle 0.51347 (14207) *********************** 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 : 1.359 Fit side-chains revert: symmetry clash REVERT: A 460 GLN cc_start: 0.9149 (OUTLIER) cc_final: 0.7875 (tm-30) REVERT: A 1408 MET cc_start: 0.6281 (OUTLIER) cc_final: 0.5989 (tmm) REVERT: A 1518 MET cc_start: 0.8327 (tmm) cc_final: 0.8078 (tmm) outliers start: 28 outliers final: 12 residues processed: 122 average time/residue: 0.2116 time to fit residues: 40.0060 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 : 1.169 ------------------------------------------------------------------------------- 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 91 optimal weight: 1.9990 chunk 35 optimal weight: 0.6980 chunk 13 optimal weight: 0.8980 chunk 20 optimal weight: 0.9990 chunk 39 optimal weight: 0.8980 chunk 73 optimal weight: 0.8980 chunk 87 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 102 optimal weight: 0.7980 chunk 67 optimal weight: 9.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3699 r_free = 0.3699 target = 0.129575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.097745 restraints weight = 16863.108| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 2.51 r_work: 0.3001 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 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 0.048 10517 Z= 0.140 Angle : 0.485 6.683 14207 Z= 0.250 Chirality : 0.038 0.147 1587 Planarity : 0.003 0.040 1783 Dihedral : 4.422 55.760 1388 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 6.26 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: 1.47 (0.24), residues: 1251 helix: 2.05 (0.19), residues: 729 sheet: 0.33 (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 0.004 0.001 HIS A1413 PHE 0.015 0.001 PHE A 585 TYR 0.012 0.001 TYR A 661 ARG 0.002 0.000 ARG A1405 Details of bonding type rmsd hydrogen bonds : bond 0.03865 ( 583) hydrogen bonds : angle 4.12104 ( 1725) covalent geometry : bond 0.00329 (10517) covalent geometry : angle 0.48542 (14207) *********************** 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 117 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 94 time to evaluate : 1.187 Fit side-chains revert: symmetry clash REVERT: A 1407 ARG cc_start: 0.7110 (mmm160) cc_final: 0.6324 (tpp-160) REVERT: A 1408 MET cc_start: 0.6535 (OUTLIER) cc_final: 0.6242 (tmm) REVERT: A 1518 MET cc_start: 0.8458 (tmm) cc_final: 0.8187 (tmm) outliers start: 23 outliers final: 16 residues processed: 113 average time/residue: 0.2010 time to fit residues: 34.8134 Evaluate side-chains 103 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 86 time to evaluate : 1.130 ------------------------------------------------------------------------------- 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 33 optimal weight: 0.7980 chunk 96 optimal weight: 0.5980 chunk 80 optimal weight: 0.4980 chunk 73 optimal weight: 0.6980 chunk 99 optimal weight: 3.9990 chunk 74 optimal weight: 5.9990 chunk 40 optimal weight: 1.9990 chunk 43 optimal weight: 0.1980 chunk 15 optimal weight: 7.9990 chunk 97 optimal weight: 0.0670 chunk 3 optimal weight: 0.9980 overall best weight: 0.4118 ------------------------------------------------------------------------------- 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 = 0.3725 r_free = 0.3725 target = 0.131507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.099537 restraints weight = 16598.873| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 2.53 r_work: 0.3036 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.1347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 10517 Z= 0.100 Angle : 0.461 7.268 14207 Z= 0.234 Chirality : 0.037 0.195 1587 Planarity : 0.003 0.041 1783 Dihedral : 4.062 47.301 1385 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.08 % Favored : 97.76 % Rotamer: Outliers : 2.39 % Allowed : 18.82 % 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: 1.63 (0.24), residues: 1251 helix: 2.23 (0.19), residues: 728 sheet: 0.37 (0.59), residues: 91 loop : -0.78 (0.30), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 473 HIS 0.003 0.001 HIS A1413 PHE 0.020 0.001 PHE A1040 TYR 0.014 0.001 TYR A 230 ARG 0.002 0.000 ARG A 880 Details of bonding type rmsd hydrogen bonds : bond 0.03342 ( 583) hydrogen bonds : angle 3.89808 ( 1725) covalent geometry : bond 0.00222 (10517) covalent geometry : angle 0.46098 (14207) *********************** 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 127 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 100 time to evaluate : 1.237 Fit side-chains revert: symmetry clash REVERT: A 1117 PHE cc_start: 0.7706 (m-80) cc_final: 0.7417 (m-80) REVERT: A 1408 MET cc_start: 0.6708 (OUTLIER) cc_final: 0.6443 (tmm) REVERT: A 1518 MET cc_start: 0.8405 (OUTLIER) cc_final: 0.8116 (tmm) outliers start: 27 outliers final: 14 residues processed: 119 average time/residue: 0.1869 time to fit residues: 34.3443 Evaluate side-chains 104 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 88 time to evaluate : 1.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 386 LEU 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 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 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 29 optimal weight: 0.9980 chunk 73 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 121 optimal weight: 5.9990 chunk 44 optimal weight: 0.9990 chunk 101 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 chunk 82 optimal weight: 3.9990 chunk 126 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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 = 0.3701 r_free = 0.3701 target = 0.129664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.098003 restraints weight = 16656.687| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 2.41 r_work: 0.3020 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.1463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 10517 Z= 0.149 Angle : 0.491 8.011 14207 Z= 0.248 Chirality : 0.038 0.180 1587 Planarity : 0.003 0.040 1783 Dihedral : 4.114 48.801 1385 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.40 % Favored : 97.44 % Rotamer: Outliers : 2.47 % Allowed : 19.08 % Favored : 78.45 % 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: 1.59 (0.24), residues: 1251 helix: 2.20 (0.19), residues: 729 sheet: 0.32 (0.58), residues: 91 loop : -0.82 (0.30), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 473 HIS 0.003 0.001 HIS A1413 PHE 0.021 0.001 PHE A1040 TYR 0.014 0.001 TYR A 353 ARG 0.001 0.000 ARG A 346 Details of bonding type rmsd hydrogen bonds : bond 0.03631 ( 583) hydrogen bonds : angle 3.94258 ( 1725) covalent geometry : bond 0.00357 (10517) covalent geometry : angle 0.49118 (14207) *********************** 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 124 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 96 time to evaluate : 1.254 Fit side-chains revert: symmetry clash REVERT: A 1408 MET cc_start: 0.6708 (OUTLIER) cc_final: 0.6484 (tmm) REVERT: A 1511 PHE cc_start: 0.9040 (m-80) cc_final: 0.8563 (m-80) REVERT: A 1518 MET cc_start: 0.8433 (OUTLIER) cc_final: 0.8132 (tmm) outliers start: 28 outliers final: 20 residues processed: 117 average time/residue: 0.1890 time to fit residues: 34.2358 Evaluate side-chains 114 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 92 time to evaluate : 1.222 ------------------------------------------------------------------------------- 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 70 optimal weight: 0.9980 chunk 103 optimal weight: 6.9990 chunk 39 optimal weight: 0.8980 chunk 112 optimal weight: 0.7980 chunk 53 optimal weight: 0.9990 chunk 110 optimal weight: 3.9990 chunk 120 optimal weight: 7.9990 chunk 21 optimal weight: 0.9980 chunk 69 optimal weight: 0.8980 chunk 101 optimal weight: 10.0000 chunk 51 optimal weight: 0.5980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3703 r_free = 0.3703 target = 0.129708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.094800 restraints weight = 16743.274| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 2.37 r_work: 0.3035 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.1578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 10517 Z= 0.138 Angle : 0.481 7.721 14207 Z= 0.244 Chirality : 0.038 0.169 1587 Planarity : 0.003 0.041 1783 Dihedral : 4.098 47.803 1385 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.40 % Favored : 97.44 % Rotamer: Outliers : 2.65 % Allowed : 19.17 % 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: 1.62 (0.24), residues: 1251 helix: 2.22 (0.19), residues: 726 sheet: 0.55 (0.57), residues: 97 loop : -0.85 (0.30), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 473 HIS 0.003 0.001 HIS A1413 PHE 0.022 0.001 PHE A1040 TYR 0.011 0.001 TYR A 713 ARG 0.001 0.000 ARG A1376 Details of bonding type rmsd hydrogen bonds : bond 0.03549 ( 583) hydrogen bonds : angle 3.91705 ( 1725) covalent geometry : bond 0.00328 (10517) covalent geometry : angle 0.48093 (14207) *********************** 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 126 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 96 time to evaluate : 1.134 Fit side-chains revert: symmetry clash REVERT: A 230 TYR cc_start: 0.7189 (m-80) cc_final: 0.6734 (m-80) REVERT: A 732 HIS cc_start: 0.5332 (m90) cc_final: 0.5120 (m170) REVERT: A 920 SER cc_start: 0.8629 (p) cc_final: 0.8193 (t) REVERT: A 1464 TRP cc_start: 0.8517 (m100) cc_final: 0.8084 (m100) REVERT: A 1511 PHE cc_start: 0.9024 (m-80) cc_final: 0.8583 (m-80) REVERT: A 1518 MET cc_start: 0.8321 (OUTLIER) cc_final: 0.8019 (tmm) outliers start: 30 outliers final: 20 residues processed: 120 average time/residue: 0.1822 time to fit residues: 33.7362 Evaluate side-chains 114 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 93 time to evaluate : 1.222 ------------------------------------------------------------------------------- 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 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 22 optimal weight: 0.9990 chunk 29 optimal weight: 0.6980 chunk 50 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 9 optimal weight: 0.7980 chunk 55 optimal weight: 4.9990 chunk 65 optimal weight: 5.9990 chunk 2 optimal weight: 0.4980 chunk 37 optimal weight: 0.7980 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 = 0.3706 r_free = 0.3706 target = 0.130048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.097538 restraints weight = 16797.363| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 2.30 r_work: 0.3024 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.1650 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= 0.129 Angle : 0.475 8.218 14207 Z= 0.240 Chirality : 0.038 0.168 1587 Planarity : 0.003 0.041 1783 Dihedral : 3.827 46.768 1382 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.56 % Favored : 97.28 % Rotamer: Outliers : 2.65 % Allowed : 19.17 % 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: 1.61 (0.24), residues: 1251 helix: 2.21 (0.19), residues: 732 sheet: 0.64 (0.58), residues: 96 loop : -0.90 (0.30), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 473 HIS 0.003 0.001 HIS A1413 PHE 0.024 0.001 PHE A1040 TYR 0.012 0.001 TYR A 912 ARG 0.002 0.000 ARG A1407 Details of bonding type rmsd hydrogen bonds : bond 0.03468 ( 583) hydrogen bonds : angle 3.87176 ( 1725) covalent geometry : bond 0.00305 (10517) covalent geometry : angle 0.47504 (14207) *********************** 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 127 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 97 time to evaluate : 1.250 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 230 TYR cc_start: 0.7211 (m-80) cc_final: 0.6815 (m-80) REVERT: A 732 HIS cc_start: 0.5347 (m90) cc_final: 0.5088 (m170) REVERT: A 736 ASN cc_start: 0.7656 (m-40) cc_final: 0.6990 (t0) REVERT: A 920 SER cc_start: 0.8629 (p) cc_final: 0.8196 (t) REVERT: A 1291 ARG cc_start: 0.8728 (OUTLIER) cc_final: 0.7981 (ptp90) REVERT: A 1296 TYR cc_start: 0.8514 (t80) cc_final: 0.8210 (t80) REVERT: A 1464 TRP cc_start: 0.8576 (m100) cc_final: 0.8130 (m100) REVERT: A 1511 PHE cc_start: 0.9014 (m-80) cc_final: 0.8591 (m-80) REVERT: A 1518 MET cc_start: 0.8330 (OUTLIER) cc_final: 0.8075 (tmm) outliers start: 30 outliers final: 21 residues processed: 124 average time/residue: 0.2031 time to fit residues: 37.8040 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 : 1.210 ------------------------------------------------------------------------------- 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 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 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 17 optimal weight: 5.9990 chunk 25 optimal weight: 0.9990 chunk 115 optimal weight: 3.9990 chunk 66 optimal weight: 5.9990 chunk 15 optimal weight: 7.9990 chunk 93 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 102 optimal weight: 0.7980 chunk 6 optimal weight: 0.9990 chunk 98 optimal weight: 0.0040 chunk 46 optimal weight: 4.9990 overall best weight: 0.9598 ------------------------------------------------------------------------------- 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 = 0.3695 r_free = 0.3695 target = 0.129101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.096476 restraints weight = 16774.377| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 2.29 r_work: 0.3009 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.1713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 10517 Z= 0.152 Angle : 0.499 8.514 14207 Z= 0.250 Chirality : 0.038 0.172 1587 Planarity : 0.003 0.042 1783 Dihedral : 3.860 48.073 1382 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.64 % Favored : 97.20 % Rotamer: Outliers : 2.65 % Allowed : 19.08 % Favored : 78.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.24), residues: 1251 helix: 2.20 (0.19), residues: 732 sheet: 0.56 (0.58), residues: 97 loop : -0.94 (0.30), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 473 HIS 0.003 0.001 HIS A1413 PHE 0.024 0.001 PHE A1040 TYR 0.014 0.001 TYR A 353 ARG 0.001 0.000 ARG A1376 Details of bonding type rmsd hydrogen bonds : bond 0.03618 ( 583) hydrogen bonds : angle 3.89641 ( 1725) covalent geometry : bond 0.00364 (10517) covalent geometry : angle 0.49943 (14207) *********************** 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: 30 poor density : 95 time to evaluate : 1.219 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 230 TYR cc_start: 0.7270 (m-80) cc_final: 0.6621 (m-80) REVERT: A 732 HIS cc_start: 0.5359 (m90) cc_final: 0.5120 (m170) REVERT: A 736 ASN cc_start: 0.7638 (m-40) cc_final: 0.6975 (t0) REVERT: A 870 GLU cc_start: 0.8277 (mm-30) cc_final: 0.8020 (mm-30) REVERT: A 920 SER cc_start: 0.8627 (p) cc_final: 0.8200 (t) REVERT: A 1291 ARG cc_start: 0.8756 (OUTLIER) cc_final: 0.7993 (ptp90) REVERT: A 1464 TRP cc_start: 0.8627 (m100) cc_final: 0.8179 (m100) REVERT: A 1511 PHE cc_start: 0.9011 (m-80) cc_final: 0.8592 (m-80) REVERT: A 1518 MET cc_start: 0.8347 (OUTLIER) cc_final: 0.8098 (tmm) outliers start: 30 outliers final: 26 residues processed: 122 average time/residue: 0.2065 time to fit residues: 37.7937 Evaluate side-chains 122 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 94 time to evaluate : 1.295 ------------------------------------------------------------------------------- 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 87 optimal weight: 0.7980 chunk 106 optimal weight: 4.9990 chunk 96 optimal weight: 0.7980 chunk 25 optimal weight: 0.6980 chunk 34 optimal weight: 0.2980 chunk 63 optimal weight: 0.2980 chunk 41 optimal weight: 0.8980 chunk 124 optimal weight: 4.9990 chunk 47 optimal weight: 3.9990 chunk 119 optimal weight: 2.9990 chunk 83 optimal weight: 0.0970 overall best weight: 0.4378 ------------------------------------------------------------------------------- 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 = 0.3723 r_free = 0.3723 target = 0.131262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.099309 restraints weight = 16756.393| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 2.62 r_work: 0.3034 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 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 : 0.002 0.047 10517 Z= 0.099 Angle : 0.474 10.839 14207 Z= 0.234 Chirality : 0.037 0.162 1587 Planarity : 0.003 0.039 1783 Dihedral : 3.680 42.282 1382 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.40 % Favored : 97.44 % Rotamer: Outliers : 1.94 % Allowed : 19.79 % Favored : 78.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.77 (0.24), residues: 1251 helix: 2.35 (0.19), residues: 731 sheet: 0.69 (0.58), residues: 96 loop : -0.86 (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 A1036 PHE 0.024 0.001 PHE A1040 TYR 0.012 0.001 TYR A 912 ARG 0.001 0.000 ARG A 526 Details of bonding type rmsd hydrogen bonds : bond 0.03187 ( 583) hydrogen bonds : angle 3.75408 ( 1725) covalent geometry : bond 0.00226 (10517) covalent geometry : angle 0.47396 (14207) *********************** 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 124 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 102 time to evaluate : 1.141 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 230 TYR cc_start: 0.7260 (m-80) cc_final: 0.6675 (m-80) REVERT: A 732 HIS cc_start: 0.5319 (m90) cc_final: 0.5075 (m170) REVERT: A 736 ASN cc_start: 0.7627 (m-40) cc_final: 0.7042 (t0) REVERT: A 870 GLU cc_start: 0.8348 (mm-30) cc_final: 0.8106 (mm-30) REVERT: A 920 SER cc_start: 0.8748 (p) cc_final: 0.8334 (t) REVERT: A 1291 ARG cc_start: 0.8746 (OUTLIER) cc_final: 0.7990 (ptp90) REVERT: A 1464 TRP cc_start: 0.8599 (m100) cc_final: 0.8198 (m100) REVERT: A 1511 PHE cc_start: 0.8983 (m-80) cc_final: 0.8556 (m-80) REVERT: A 1518 MET cc_start: 0.8342 (OUTLIER) cc_final: 0.8077 (tmm) outliers start: 22 outliers final: 17 residues processed: 122 average time/residue: 0.1978 time to fit residues: 36.9230 Evaluate side-chains 116 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 97 time to evaluate : 1.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 1101 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 34 optimal weight: 2.9990 chunk 113 optimal weight: 0.9990 chunk 67 optimal weight: 9.9990 chunk 80 optimal weight: 0.3980 chunk 123 optimal weight: 8.9990 chunk 122 optimal weight: 4.9990 chunk 9 optimal weight: 0.6980 chunk 53 optimal weight: 0.5980 chunk 36 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 51 optimal weight: 0.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- 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 = 0.3707 r_free = 0.3707 target = 0.130004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.097642 restraints weight = 16745.182| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 2.41 r_work: 0.3033 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.1857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 10517 Z= 0.128 Angle : 0.499 11.202 14207 Z= 0.245 Chirality : 0.038 0.151 1587 Planarity : 0.003 0.039 1783 Dihedral : 3.514 26.738 1378 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.40 % Favored : 97.44 % Rotamer: Outliers : 1.77 % Allowed : 20.41 % Favored : 77.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.76 (0.24), residues: 1251 helix: 2.31 (0.19), residues: 731 sheet: 0.78 (0.58), residues: 95 loop : -0.83 (0.30), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 473 HIS 0.003 0.001 HIS A1413 PHE 0.026 0.001 PHE A1040 TYR 0.021 0.001 TYR A 713 ARG 0.002 0.000 ARG A 526 Details of bonding type rmsd hydrogen bonds : bond 0.03392 ( 583) hydrogen bonds : angle 3.80861 ( 1725) covalent geometry : bond 0.00306 (10517) covalent geometry : angle 0.49916 (14207) ********************** 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: 20 poor density : 100 time to evaluate : 1.158 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 230 TYR cc_start: 0.7282 (m-80) cc_final: 0.6678 (m-80) REVERT: A 732 HIS cc_start: 0.5422 (m90) cc_final: 0.5165 (m170) REVERT: A 736 ASN cc_start: 0.7568 (m-40) cc_final: 0.6970 (t0) REVERT: A 870 GLU cc_start: 0.8296 (mm-30) cc_final: 0.8053 (mm-30) REVERT: A 920 SER cc_start: 0.8724 (p) cc_final: 0.8319 (t) REVERT: A 1291 ARG cc_start: 0.8751 (OUTLIER) cc_final: 0.7989 (ptp90) REVERT: A 1407 ARG cc_start: 0.7020 (mmm160) cc_final: 0.6101 (tpp-160) REVERT: A 1464 TRP cc_start: 0.8631 (m100) cc_final: 0.8237 (m100) REVERT: A 1511 PHE cc_start: 0.8998 (m-80) cc_final: 0.8557 (m-80) REVERT: A 1518 MET cc_start: 0.8325 (OUTLIER) cc_final: 0.8061 (tmm) outliers start: 20 outliers final: 18 residues processed: 118 average time/residue: 0.2082 time to fit residues: 36.4358 Evaluate side-chains 117 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 97 time to evaluate : 1.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 529 THR Chi-restraints excluded: chain A residue 533 ILE Chi-restraints excluded: chain A residue 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 1101 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 46 optimal weight: 0.8980 chunk 104 optimal weight: 0.8980 chunk 38 optimal weight: 0.0170 chunk 30 optimal weight: 3.9990 chunk 95 optimal weight: 0.0870 chunk 114 optimal weight: 4.9990 chunk 12 optimal weight: 0.7980 chunk 94 optimal weight: 0.9990 chunk 122 optimal weight: 3.9990 chunk 123 optimal weight: 9.9990 chunk 33 optimal weight: 0.5980 overall best weight: 0.4796 ------------------------------------------------------------------------------- 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 = 0.3643 r_free = 0.3643 target = 0.126465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.095317 restraints weight = 16495.203| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 2.18 r_work: 0.2959 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.1941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 10517 Z= 0.105 Angle : 0.488 11.454 14207 Z= 0.239 Chirality : 0.037 0.145 1587 Planarity : 0.003 0.039 1783 Dihedral : 3.460 27.196 1378 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.64 % Favored : 97.20 % 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 (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: 1.79 (0.24), residues: 1251 helix: 2.31 (0.19), residues: 738 sheet: 0.82 (0.58), residues: 95 loop : -0.82 (0.30), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 473 HIS 0.003 0.001 HIS A1413 PHE 0.025 0.001 PHE A1040 TYR 0.020 0.001 TYR A 713 ARG 0.001 0.000 ARG A 902 Details of bonding type rmsd hydrogen bonds : bond 0.03194 ( 583) hydrogen bonds : angle 3.74382 ( 1725) covalent geometry : bond 0.00242 (10517) covalent geometry : angle 0.48797 (14207) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4824.33 seconds wall clock time: 83 minutes 56.95 seconds (5036.95 seconds total)