Starting phenix.real_space_refine on Wed Aug 5 22:26:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8c4v_16430/08_2026/8c4v_16430.cif Found real_map, /net/cci-nas-00/data/ceres_data/8c4v_16430/08_2026/8c4v_16430.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8c4v_16430/08_2026/8c4v_16430.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8c4v_16430/08_2026/8c4v_16430.cif" model { file = "/net/cci-nas-00/data/ceres_data/8c4v_16430/08_2026/8c4v_16430.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8c4v_16430/08_2026/8c4v_16430.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8c4v_16430/08_2026/8c4v_16430.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8c4v_16430/08_2026/8c4v_16430.map" } resolution = 3.14 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= 0.005 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: 6 Type Number sf(0) Gaussians P 56 5.49 5 Mg 1 5.21 5 S 57 5.16 5 C 7318 2.51 5 N 1984 2.21 5 O 2315 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11731 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 10536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1308, 10536 Classifications: {'peptide': 1308} Link IDs: {'PTRANS': 43, 'TRANS': 1264} Unresolved chain links: 1 Chain breaks: 5 Unresolved chain link angles: 3 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "H" Number of atoms: 409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 409 Classifications: {'RNAv2': 19} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 2, 'rna3p_pur': 10, 'rna3p_pyr': 5} Link IDs: {'rna2p': 3, 'rna3p': 15} Chain: "V" Number of atoms: 191 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 191 Classifications: {'RNAv2': 9} Modifications used: {'rna3p_pur': 4, 'rna3p_pyr': 5} Link IDs: {'rna3p': 8} Chain: "T" Number of atoms: 251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 251 Classifications: {'RNAv2': 12} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 4, 'rna3p_pyr': 7} Link IDs: {'rna3p': 11} Chain: "P" Number of atoms: 197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 197 Classifications: {'RNAv2': 9} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 6, 'rna3p_pyr': 2} Link IDs: {'rna3p': 8} Chain: "S" Number of atoms: 146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 146 Classifications: {'RNAv2': 7} Modifications used: {'rna2p_pyr': 2, 'rna3p_pur': 3, 'rna3p_pyr': 2} Link IDs: {'rna2p': 2, 'rna3p': 4} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.76, per 1000 atoms: 0.15 Number of scatterers: 11731 At special positions: 0 Unit cell: (97.9, 103.4, 114.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 57 16.00 P 56 15.00 Mg 1 11.99 O 2315 8.00 N 1984 7.00 C 7318 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: 0.79 Conformation dependent library (CDL) restraints added in 349.4 milliseconds 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2490 Finding SS restraints... Secondary structure from input PDB file: 61 helices and 13 sheets defined 58.1% alpha, 12.2% beta 17 base pairs and 25 stacking pairs defined. Time for finding SS restraints: 1.12 Creating SS restraints... Processing helix chain 'A' and resid 239 through 253 removed outlier: 3.643A pdb=" N LEU A 243 " --> pdb=" O ASN A 239 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ARG A 253 " --> pdb=" O ASP A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 279 removed outlier: 3.803A pdb=" N CYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 322 Processing helix chain 'A' and resid 328 through 343 removed outlier: 4.092A pdb=" N ILE A 334 " --> pdb=" O ALA A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 352 Processing helix chain 'A' and resid 355 through 359 removed outlier: 3.528A pdb=" N PHE A 359 " --> pdb=" O ARG A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 378 Processing helix chain 'A' and resid 379 through 391 Processing helix chain 'A' and resid 409 through 429 removed outlier: 3.784A pdb=" N VAL A 417 " --> pdb=" O GLN A 413 " (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 470 through 490 removed outlier: 3.510A pdb=" N HIS A 474 " --> pdb=" O THR A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 541 No H-bonds generated for 'chain 'A' and resid 539 through 541' Processing helix chain 'A' and resid 564 through 572 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: 3.954A 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 648 Processing helix chain 'A' and resid 654 through 674 removed outlier: 4.062A pdb=" N ASN A 674 " --> pdb=" O ALA A 670 " (cutoff:3.500A) Processing helix chain 'A' and resid 712 through 726 removed outlier: 3.652A pdb=" N LEU A 716 " --> pdb=" O HIS A 712 " (cutoff:3.500A) Processing helix chain 'A' and resid 735 through 760 removed outlier: 3.592A pdb=" N LYS A 740 " --> pdb=" O ASN A 736 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ILE A 741 " --> pdb=" O GLU A 737 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N HIS A 742 " --> pdb=" O GLU A 738 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU A 743 " --> pdb=" O ALA A 739 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLU A 744 " --> pdb=" O LYS A 740 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N THR A 745 " --> pdb=" O ILE A 741 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N TRP A 748 " --> pdb=" O GLU A 744 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ARG A 753 " --> pdb=" O ALA A 749 " (cutoff:3.500A) Processing helix chain 'A' and resid 769 through 777 Processing helix chain 'A' and resid 786 through 802 removed outlier: 3.813A pdb=" N VAL A 800 " --> pdb=" O GLU A 796 " (cutoff:3.500A) Processing helix chain 'A' and resid 804 through 815 removed outlier: 3.619A pdb=" N LYS A 815 " --> pdb=" O SER A 811 " (cutoff:3.500A) Processing helix chain 'A' and resid 824 through 829 removed outlier: 3.600A pdb=" N ILE A 828 " --> pdb=" O GLN A 824 " (cutoff:3.500A) Processing helix chain 'A' and resid 848 through 858 Processing helix chain 'A' and resid 864 through 872 Processing helix chain 'A' and resid 898 through 917 Processing helix chain 'A' and resid 929 through 947 Processing helix chain 'A' and resid 982 through 990 removed outlier: 3.772A pdb=" N ARG A 986 " --> pdb=" O SER A 982 " (cutoff:3.500A) removed outlier: 3.541A 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 1028 Processing helix chain 'A' and resid 1034 through 1044 removed outlier: 3.559A pdb=" N PHE A1043 " --> pdb=" O GLN A1039 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N PHE A1044 " --> pdb=" O PHE A1040 " (cutoff:3.500A) Processing helix chain 'A' and resid 1061 through 1084 Processing helix chain 'A' and resid 1113 through 1127 Processing helix chain 'A' and resid 1128 through 1132 Processing helix chain 'A' and resid 1137 through 1153 removed outlier: 3.925A pdb=" N SER A1141 " --> pdb=" O GLU A1137 " (cutoff:3.500A) Processing helix chain 'A' and resid 1185 through 1192 Processing helix chain 'A' and resid 1200 through 1211 Processing helix chain 'A' and resid 1212 through 1219 Processing helix chain 'A' and resid 1221 through 1241 Processing helix chain 'A' and resid 1249 through 1254 removed outlier: 3.953A pdb=" N TYR A1253 " --> pdb=" O HIS A1249 " (cutoff:3.500A) Processing helix chain 'A' and resid 1262 through 1266 Processing helix chain 'A' and resid 1272 through 1279 Processing helix chain 'A' and resid 1282 through 1298 removed outlier: 3.829A pdb=" N LYS A1286 " --> pdb=" O GLY A1282 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLY A1295 " --> pdb=" O ARG A1291 " (cutoff:3.500A) Processing helix chain 'A' and resid 1301 through 1319 Processing helix chain 'A' and resid 1347 through 1351 removed outlier: 4.286A pdb=" N ASP A1351 " --> pdb=" O GLU A1348 " (cutoff:3.500A) Processing helix chain 'A' and resid 1354 through 1365 Processing helix chain 'A' and resid 1366 through 1370 removed outlier: 3.557A pdb=" N ASP A1369 " --> pdb=" O VAL A1366 " (cutoff:3.500A) Processing helix chain 'A' and resid 1375 through 1388 removed outlier: 3.859A pdb=" N ILE A1381 " --> pdb=" O ASP A1377 " (cutoff:3.500A) Processing helix chain 'A' and resid 1389 through 1396 Processing helix chain 'A' and resid 1400 through 1411 removed outlier: 3.818A pdb=" N LYS A1411 " --> pdb=" O ARG A1407 " (cutoff:3.500A) Processing helix chain 'A' and resid 1425 through 1440 Processing helix chain 'A' and resid 1445 through 1453 Processing helix chain 'A' and resid 1465 through 1470 Processing helix chain 'A' and resid 1505 through 1511 Processing helix chain 'A' and resid 1514 through 1525 Processing helix chain 'A' and resid 1527 through 1529 No H-bonds generated for 'chain 'A' and resid 1527 through 1529' Processing helix chain 'A' and resid 1530 through 1546 removed outlier: 3.548A pdb=" N THR A1537 " --> pdb=" O VAL A1533 " (cutoff:3.500A) Processing helix chain 'A' and resid 1552 through 1565 removed outlier: 3.524A pdb=" N ARG A1558 " --> pdb=" O ASP A1554 " (cutoff:3.500A) Proline residue: A1561 - end of helix removed outlier: 3.704A pdb=" N LYS A1565 " --> pdb=" O PRO A1561 " (cutoff:3.500A) Processing helix chain 'A' and resid 1581 through 1592 removed outlier: 3.571A pdb=" N CYS A1586 " --> pdb=" O ALA A1582 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 260 through 261 removed outlier: 3.692A 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: 3.692A pdb=" N THR A1163 " --> pdb=" O SER A 970 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 284 through 285 Processing sheet with id=AA4, first strand: chain 'A' and resid 296 through 297 Processing sheet with id=AA5, first strand: chain 'A' and resid 499 through 503 removed outlier: 4.721A pdb=" N THR A 529 " --> pdb=" O SER A 557 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 499 through 503 removed outlier: 3.561A pdb=" N ILE A 562 " --> pdb=" O ILE A 525 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 701 through 702 Processing sheet with id=AA8, first strand: chain 'A' and resid 832 through 837 removed outlier: 5.664A pdb=" N SER A 844 " --> pdb=" O GLY A 835 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 893 through 897 removed outlier: 4.065A pdb=" N ALA A 877 " --> pdb=" O LYS A1014 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ILE A 881 " --> pdb=" O PHE A1018 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1168 through 1171 Processing sheet with id=AB2, first strand: chain 'A' and resid 1337 through 1338 removed outlier: 4.748A pdb=" N GLN A1337 " --> pdb=" O ARG A1418 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1474 through 1479 removed outlier: 4.090A pdb=" N ASP A1474 " --> pdb=" O ARG A1600 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ARG A1600 " --> pdb=" O ASP A1474 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N THR A1598 " --> pdb=" O ILE A1476 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1485 through 1490 584 hydrogen bonds defined for protein. 1671 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 42 hydrogen bonds 84 hydrogen bond angles 0 basepair planarities 17 basepair parallelities 25 stacking parallelities Total time for adding SS restraints: 2.14 Time building geometry restraints manager: 1.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 1752 1.29 - 1.43: 3543 1.43 - 1.56: 6605 1.56 - 1.69: 107 1.69 - 1.82: 96 Bond restraints: 12103 Sorted by residual: bond pdb=" C SER A 309 " pdb=" O SER A 309 " ideal model delta sigma weight residual 1.237 1.165 0.072 1.17e-02 7.31e+03 3.79e+01 bond pdb=" C ARG A 904 " pdb=" O ARG A 904 " ideal model delta sigma weight residual 1.236 1.170 0.066 1.16e-02 7.43e+03 3.19e+01 bond pdb=" C GLN A 460 " pdb=" O GLN A 460 " ideal model delta sigma weight residual 1.236 1.172 0.065 1.15e-02 7.56e+03 3.17e+01 bond pdb=" C PRO A1222 " pdb=" O PRO A1222 " ideal model delta sigma weight residual 1.237 1.169 0.069 1.26e-02 6.30e+03 2.98e+01 bond pdb=" C LEU A 463 " pdb=" O LEU A 463 " ideal model delta sigma weight residual 1.235 1.170 0.065 1.26e-02 6.30e+03 2.66e+01 ... (remaining 12098 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.36: 15731 2.36 - 4.72: 748 4.72 - 7.07: 113 7.07 - 9.43: 20 9.43 - 11.79: 3 Bond angle restraints: 16615 Sorted by residual: angle pdb=" N ARG A 627 " pdb=" CA ARG A 627 " pdb=" C ARG A 627 " ideal model delta sigma weight residual 113.28 102.14 11.14 1.22e+00 6.72e-01 8.34e+01 angle pdb=" C LYS A 287 " pdb=" CA LYS A 287 " pdb=" CB LYS A 287 " ideal model delta sigma weight residual 110.17 102.54 7.63 9.90e-01 1.02e+00 5.93e+01 angle pdb=" N TYR A 628 " pdb=" CA TYR A 628 " pdb=" C TYR A 628 " ideal model delta sigma weight residual 113.41 105.25 8.16 1.22e+00 6.72e-01 4.47e+01 angle pdb=" CA PHE A 291 " pdb=" CB PHE A 291 " pdb=" CG PHE A 291 " ideal model delta sigma weight residual 113.80 120.48 -6.68 1.00e+00 1.00e+00 4.46e+01 angle pdb=" N LEU A 731 " pdb=" CA LEU A 731 " pdb=" C LEU A 731 " ideal model delta sigma weight residual 113.02 105.11 7.91 1.20e+00 6.94e-01 4.35e+01 ... (remaining 16610 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.86: 6619 29.86 - 59.72: 458 59.72 - 89.58: 41 89.58 - 119.44: 2 119.44 - 149.30: 1 Dihedral angle restraints: 7121 sinusoidal: 3275 harmonic: 3846 Sorted by residual: dihedral pdb=" C4' U S 24 " pdb=" C3' U S 24 " pdb=" C2' U S 24 " pdb=" C1' U S 24 " ideal model delta sinusoidal sigma weight residual 36.34 -36.57 72.91 1 3.10e+00 1.04e-01 7.05e+02 dihedral pdb=" C4' U H 9 " pdb=" C3' U H 9 " pdb=" C2' U H 9 " pdb=" C1' U H 9 " ideal model delta sinusoidal sigma weight residual 36.34 -36.38 72.73 1 3.10e+00 1.04e-01 7.02e+02 dihedral pdb=" C4' A T 25 " pdb=" C3' A T 25 " pdb=" C2' A T 25 " pdb=" C1' A T 25 " ideal model delta sinusoidal sigma weight residual 36.34 -35.77 72.11 1 3.10e+00 1.04e-01 6.92e+02 ... (remaining 7118 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.133: 1720 0.133 - 0.266: 148 0.266 - 0.399: 24 0.399 - 0.533: 4 0.533 - 0.666: 1 Chirality restraints: 1897 Sorted by residual: chirality pdb=" CA THR A1242 " pdb=" N THR A1242 " pdb=" C THR A1242 " pdb=" CB THR A1242 " both_signs ideal model delta sigma weight residual False 2.53 1.86 0.67 2.00e-01 2.50e+01 1.11e+01 chirality pdb=" P G H 19 " pdb=" OP1 G H 19 " pdb=" OP2 G H 19 " pdb=" O5' G H 19 " both_signs ideal model delta sigma weight residual True 2.17 -2.70 -0.52 2.00e-01 2.50e+01 6.89e+00 chirality pdb=" P G H 3 " pdb=" OP1 G H 3 " pdb=" OP2 G H 3 " pdb=" O5' G H 3 " both_signs ideal model delta sigma weight residual True 2.17 -2.64 -0.47 2.00e-01 2.50e+01 5.48e+00 ... (remaining 1894 not shown) Planarity restraints: 1890 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA CYS A1212 " 0.021 2.00e-02 2.50e+03 4.23e-02 1.79e+01 pdb=" C CYS A1212 " -0.073 2.00e-02 2.50e+03 pdb=" O CYS A1212 " 0.027 2.00e-02 2.50e+03 pdb=" N VAL A1213 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 873 " 0.019 2.00e-02 2.50e+03 3.76e-02 1.42e+01 pdb=" C ARG A 873 " -0.065 2.00e-02 2.50e+03 pdb=" O ARG A 873 " 0.024 2.00e-02 2.50e+03 pdb=" N GLU A 874 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 459 " 0.014 2.00e-02 2.50e+03 2.75e-02 7.54e+00 pdb=" C THR A 459 " -0.048 2.00e-02 2.50e+03 pdb=" O THR A 459 " 0.017 2.00e-02 2.50e+03 pdb=" N GLN A 460 " 0.016 2.00e-02 2.50e+03 ... (remaining 1887 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 64 2.53 - 3.12: 8964 3.12 - 3.71: 20140 3.71 - 4.31: 29583 4.31 - 4.90: 47571 Nonbonded interactions: 106322 Sorted by model distance: nonbonded pdb=" OD1 ASP A1099 " pdb="MG MG A2201 " model vdw 1.935 2.170 nonbonded pdb=" OG1 THR A 328 " pdb=" OG1 THR A 545 " model vdw 2.216 3.040 nonbonded pdb=" O ASP A 549 " pdb=" OG SER A 552 " model vdw 2.251 3.040 nonbonded pdb=" O ARG A 714 " pdb=" OG SER A 718 " model vdw 2.255 3.040 nonbonded pdb=" O THR A 421 " pdb=" OG SER A 425 " model vdw 2.266 3.040 ... (remaining 106317 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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=1.00 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: 1.060 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: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 10.130 Find NCS groups from input model: 0.030 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:0.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 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 : 0.007 0.076 12103 Z= 0.480 Angle : 1.052 11.791 16615 Z= 0.675 Chirality : 0.082 0.666 1897 Planarity : 0.005 0.062 1890 Dihedral : 18.531 149.297 4631 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 13.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 2.51 % Allowed : 24.72 % Favored : 72.77 % Cbeta Deviations : 0.56 % 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: -0.71 (0.23), residues: 1294 helix: 0.43 (0.19), residues: 682 sheet: -1.67 (0.47), residues: 104 loop : -1.37 (0.26), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 880 TYR 0.027 0.002 TYR A1104 PHE 0.042 0.002 PHE A 291 TRP 0.028 0.002 TRP A1131 HIS 0.008 0.001 HIS A1130 Details of bonding type rmsd/Z covalent geometry : bond 0.00707 / 0.48 (12103) covalent geometry : angle 1.05170 / 0.68 (16615) hydrogen bonds : bond 0.16604 / 11.41 ( 609) hydrogen bonds : angle 7.04952 / 5.06 ( 1755) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 173 time to evaluate : 0.261 Fit side-chains REVERT: A 452 ASP cc_start: 0.6388 (t0) cc_final: 0.6152 (t0) REVERT: A 461 LYS cc_start: 0.8448 (mtpp) cc_final: 0.8206 (ttmm) REVERT: A 1000 LYS cc_start: 0.8210 (mttt) cc_final: 0.7836 (mttt) REVERT: A 1414 MET cc_start: 0.8623 (OUTLIER) cc_final: 0.8031 (mtm) outliers start: 29 outliers final: 14 residues processed: 194 average time/residue: 0.0881 time to fit residues: 24.5156 Evaluate side-chains 175 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 160 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 377 MET Chi-restraints excluded: chain A residue 459 THR Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 874 GLU Chi-restraints excluded: chain A residue 1048 HIS Chi-restraints excluded: chain A residue 1134 VAL Chi-restraints excluded: chain A residue 1135 ASN Chi-restraints excluded: chain A residue 1276 LEU Chi-restraints excluded: chain A residue 1283 MET Chi-restraints excluded: chain A residue 1322 PHE Chi-restraints excluded: chain A residue 1403 GLN Chi-restraints excluded: chain A residue 1414 MET Chi-restraints excluded: chain A residue 1417 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 0.3980 chunk 122 optimal weight: 7.9990 chunk 91 optimal weight: 0.9990 chunk 55 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 295 GLN A 999 ASN ** A1130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1323 GLN A1324 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.169720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.137861 restraints weight = 12805.518| |-----------------------------------------------------------------------------| r_work (start): 0.3478 rms_B_bonded: 1.26 r_work: 0.3363 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3235 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.1070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 12103 Z= 0.184 Angle : 0.755 14.686 16615 Z= 0.343 Chirality : 0.057 1.015 1897 Planarity : 0.004 0.036 1890 Dihedral : 12.496 154.614 2104 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 12.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 3.98 % Allowed : 23.16 % Favored : 72.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.10 (0.23), residues: 1294 helix: 1.01 (0.19), residues: 701 sheet: -1.51 (0.48), residues: 100 loop : -1.28 (0.26), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1300 TYR 0.013 0.001 TYR A1106 PHE 0.017 0.002 PHE A1143 TRP 0.013 0.001 TRP A 976 HIS 0.005 0.001 HIS A 501 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.18 (12103) covalent geometry : angle 0.75458 / 0.34 (16615) hydrogen bonds : bond 0.04345 / 2.91 ( 609) hydrogen bonds : angle 4.98208 / 3.55 ( 1755) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 181 time to evaluate : 0.275 Fit side-chains REVERT: A 344 LEU cc_start: 0.7433 (OUTLIER) cc_final: 0.7200 (mp) REVERT: A 816 ASN cc_start: 0.8150 (OUTLIER) cc_final: 0.7887 (m-40) REVERT: A 931 LYS cc_start: 0.8421 (OUTLIER) cc_final: 0.7785 (mttp) REVERT: A 941 LYS cc_start: 0.8203 (OUTLIER) cc_final: 0.7941 (ptpt) REVERT: A 1000 LYS cc_start: 0.8244 (mttt) cc_final: 0.7921 (mttt) REVERT: A 1119 PHE cc_start: 0.7935 (t80) cc_final: 0.7670 (t80) REVERT: A 1275 GLU cc_start: 0.7664 (tm-30) cc_final: 0.7050 (tm-30) REVERT: A 1276 LEU cc_start: 0.8456 (OUTLIER) cc_final: 0.8003 (mt) REVERT: A 1283 MET cc_start: 0.6680 (OUTLIER) cc_final: 0.6001 (mpt) REVERT: A 1346 GLU cc_start: 0.7484 (tp30) cc_final: 0.7273 (tp30) REVERT: A 1414 MET cc_start: 0.8252 (OUTLIER) cc_final: 0.7030 (mtm) outliers start: 46 outliers final: 24 residues processed: 213 average time/residue: 0.0925 time to fit residues: 28.3243 Evaluate side-chains 200 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 169 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 377 MET Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 515 SER Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 654 SER Chi-restraints excluded: chain A residue 816 ASN Chi-restraints excluded: chain A residue 833 MET Chi-restraints excluded: chain A residue 874 GLU Chi-restraints excluded: chain A residue 878 MET Chi-restraints excluded: chain A residue 931 LYS Chi-restraints excluded: chain A residue 941 LYS Chi-restraints excluded: chain A residue 986 ARG Chi-restraints excluded: chain A residue 1089 CYS Chi-restraints excluded: chain A residue 1134 VAL Chi-restraints excluded: chain A residue 1164 VAL Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1246 MET Chi-restraints excluded: chain A residue 1276 LEU Chi-restraints excluded: chain A residue 1283 MET Chi-restraints excluded: chain A residue 1322 PHE Chi-restraints excluded: chain A residue 1358 LEU Chi-restraints excluded: chain A residue 1394 THR Chi-restraints excluded: chain A residue 1414 MET Chi-restraints excluded: chain A residue 1416 VAL Chi-restraints excluded: chain A residue 1443 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 23 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 71 optimal weight: 0.7980 chunk 104 optimal weight: 3.9990 chunk 32 optimal weight: 0.5980 chunk 72 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 7 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 110 optimal weight: 0.9980 chunk 56 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 460 GLN ** A 827 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1287 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.169747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.138047 restraints weight = 12793.402| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 1.26 r_work: 0.3366 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3236 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.1430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 12103 Z= 0.179 Angle : 0.656 9.884 16615 Z= 0.311 Chirality : 0.048 0.347 1897 Planarity : 0.004 0.037 1890 Dihedral : 11.819 146.889 2093 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 4.32 % Allowed : 22.64 % Favored : 73.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.01 (0.23), residues: 1294 helix: 1.09 (0.19), residues: 701 sheet: -1.43 (0.49), residues: 100 loop : -1.23 (0.27), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 873 TYR 0.016 0.002 TYR A 353 PHE 0.021 0.002 PHE A1347 TRP 0.012 0.001 TRP A 976 HIS 0.003 0.001 HIS A1148 Details of bonding type rmsd/Z covalent geometry : bond 0.00405 / 0.18 (12103) covalent geometry : angle 0.65593 / 0.31 (16615) hydrogen bonds : bond 0.03910 / 2.62 ( 609) hydrogen bonds : angle 4.76035 / 3.39 ( 1755) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 183 time to evaluate : 0.265 Fit side-chains REVERT: A 755 LYS cc_start: 0.8239 (OUTLIER) cc_final: 0.6819 (mtmt) REVERT: A 782 GLN cc_start: 0.8885 (mt0) cc_final: 0.8543 (mt0) REVERT: A 931 LYS cc_start: 0.8361 (OUTLIER) cc_final: 0.7746 (mttp) REVERT: A 941 LYS cc_start: 0.8212 (OUTLIER) cc_final: 0.7993 (ptpt) REVERT: A 1000 LYS cc_start: 0.8274 (mttt) cc_final: 0.7964 (mttt) REVERT: A 1275 GLU cc_start: 0.7364 (tm-30) cc_final: 0.6668 (tm-30) REVERT: A 1276 LEU cc_start: 0.8416 (mt) cc_final: 0.8088 (mt) REVERT: A 1283 MET cc_start: 0.6634 (OUTLIER) cc_final: 0.5903 (mpt) REVERT: A 1403 GLN cc_start: 0.7207 (mt0) cc_final: 0.6825 (mt0) REVERT: A 1414 MET cc_start: 0.8265 (OUTLIER) cc_final: 0.6869 (mtm) REVERT: A 1562 MET cc_start: 0.7114 (ptp) cc_final: 0.6793 (mtm) outliers start: 50 outliers final: 31 residues processed: 216 average time/residue: 0.0981 time to fit residues: 29.8319 Evaluate side-chains 210 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 174 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain A residue 280 GLN Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 377 MET Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain A residue 515 SER Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 654 SER Chi-restraints excluded: chain A residue 714 ARG Chi-restraints excluded: chain A residue 744 GLU Chi-restraints excluded: chain A residue 755 LYS Chi-restraints excluded: chain A residue 814 SER Chi-restraints excluded: chain A residue 874 GLU Chi-restraints excluded: chain A residue 878 MET Chi-restraints excluded: chain A residue 931 LYS Chi-restraints excluded: chain A residue 941 LYS Chi-restraints excluded: chain A residue 982 SER Chi-restraints excluded: chain A residue 986 ARG Chi-restraints excluded: chain A residue 1089 CYS Chi-restraints excluded: chain A residue 1134 VAL Chi-restraints excluded: chain A residue 1164 VAL Chi-restraints excluded: chain A residue 1179 CYS Chi-restraints excluded: chain A residue 1182 SER Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1246 MET Chi-restraints excluded: chain A residue 1283 MET Chi-restraints excluded: chain A residue 1322 PHE Chi-restraints excluded: chain A residue 1358 LEU Chi-restraints excluded: chain A residue 1359 GLU Chi-restraints excluded: chain A residue 1367 THR Chi-restraints excluded: chain A residue 1394 THR Chi-restraints excluded: chain A residue 1414 MET Chi-restraints excluded: chain A residue 1443 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 18 optimal weight: 0.4980 chunk 94 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 68 optimal weight: 0.0050 chunk 108 optimal weight: 2.9990 chunk 27 optimal weight: 0.5980 chunk 100 optimal weight: 0.6980 chunk 25 optimal weight: 0.9980 chunk 92 optimal weight: 1.9990 chunk 28 optimal weight: 0.7980 overall best weight: 0.5194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 816 ASN ** A1130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1287 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.171646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.140300 restraints weight = 12755.104| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 1.26 r_work: 0.3399 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3270 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.1635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12103 Z= 0.141 Angle : 0.606 8.230 16615 Z= 0.288 Chirality : 0.046 0.326 1897 Planarity : 0.003 0.035 1890 Dihedral : 11.842 159.054 2090 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 4.32 % Allowed : 22.73 % Favored : 72.95 % 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: 0.18 (0.23), residues: 1294 helix: 1.24 (0.19), residues: 709 sheet: -1.17 (0.50), residues: 99 loop : -1.25 (0.27), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 873 TYR 0.023 0.001 TYR A 353 PHE 0.020 0.002 PHE A1357 TRP 0.013 0.001 TRP A 976 HIS 0.003 0.001 HIS A1148 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.14 (12103) covalent geometry : angle 0.60596 / 0.29 (16615) hydrogen bonds : bond 0.03613 / 2.40 ( 609) hydrogen bonds : angle 4.56000 / 3.24 ( 1755) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 195 time to evaluate : 0.379 Fit side-chains REVERT: A 704 PHE cc_start: 0.7862 (t80) cc_final: 0.7610 (t80) REVERT: A 744 GLU cc_start: 0.8329 (OUTLIER) cc_final: 0.7933 (tm-30) REVERT: A 755 LYS cc_start: 0.8198 (OUTLIER) cc_final: 0.6792 (mtmt) REVERT: A 782 GLN cc_start: 0.8872 (mt0) cc_final: 0.8537 (mt0) REVERT: A 931 LYS cc_start: 0.8304 (OUTLIER) cc_final: 0.7729 (mttp) REVERT: A 941 LYS cc_start: 0.8181 (OUTLIER) cc_final: 0.7968 (ptpt) REVERT: A 986 ARG cc_start: 0.9029 (OUTLIER) cc_final: 0.7907 (mtp180) REVERT: A 1119 PHE cc_start: 0.7982 (t80) cc_final: 0.7600 (t80) REVERT: A 1275 GLU cc_start: 0.7377 (tm-30) cc_final: 0.6769 (tm-30) REVERT: A 1283 MET cc_start: 0.6538 (OUTLIER) cc_final: 0.5821 (mpt) REVERT: A 1403 GLN cc_start: 0.7125 (mt0) cc_final: 0.6759 (mt0) REVERT: A 1414 MET cc_start: 0.8186 (OUTLIER) cc_final: 0.6843 (mtm) REVERT: A 1562 MET cc_start: 0.7115 (ptp) cc_final: 0.6842 (ptp) outliers start: 50 outliers final: 30 residues processed: 228 average time/residue: 0.0989 time to fit residues: 32.2433 Evaluate side-chains 214 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 177 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 280 GLN Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 349 MET Chi-restraints excluded: chain A residue 377 MET Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 654 SER Chi-restraints excluded: chain A residue 744 GLU Chi-restraints excluded: chain A residue 755 LYS Chi-restraints excluded: chain A residue 833 MET Chi-restraints excluded: chain A residue 874 GLU Chi-restraints excluded: chain A residue 903 CYS Chi-restraints excluded: chain A residue 931 LYS Chi-restraints excluded: chain A residue 941 LYS Chi-restraints excluded: chain A residue 982 SER Chi-restraints excluded: chain A residue 986 ARG Chi-restraints excluded: chain A residue 1041 LEU Chi-restraints excluded: chain A residue 1048 HIS Chi-restraints excluded: chain A residue 1089 CYS Chi-restraints excluded: chain A residue 1134 VAL Chi-restraints excluded: chain A residue 1164 VAL Chi-restraints excluded: chain A residue 1179 CYS Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1246 MET Chi-restraints excluded: chain A residue 1283 MET Chi-restraints excluded: chain A residue 1322 PHE Chi-restraints excluded: chain A residue 1358 LEU Chi-restraints excluded: chain A residue 1359 GLU Chi-restraints excluded: chain A residue 1367 THR Chi-restraints excluded: chain A residue 1394 THR Chi-restraints excluded: chain A residue 1414 MET Chi-restraints excluded: chain A residue 1429 VAL Chi-restraints excluded: chain A residue 1443 THR Chi-restraints excluded: chain A residue 1466 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 102 optimal weight: 0.8980 chunk 46 optimal weight: 0.3980 chunk 54 optimal weight: 0.9980 chunk 27 optimal weight: 0.6980 chunk 100 optimal weight: 2.9990 chunk 69 optimal weight: 0.0370 chunk 4 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 79 optimal weight: 0.5980 chunk 129 optimal weight: 0.4980 overall best weight: 0.4458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 460 GLN A 712 HIS ** A1130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1287 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 = 0.3870 r_free = 0.3870 target = 0.172631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.141401 restraints weight = 12777.745| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 1.26 r_work: 0.3422 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3293 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.1802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12103 Z= 0.132 Angle : 0.598 7.603 16615 Z= 0.284 Chirality : 0.046 0.309 1897 Planarity : 0.003 0.033 1890 Dihedral : 11.803 167.616 2090 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 4.58 % Allowed : 23.25 % Favored : 72.17 % 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: 0.33 (0.23), residues: 1294 helix: 1.37 (0.19), residues: 706 sheet: -1.08 (0.51), residues: 100 loop : -1.19 (0.27), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 873 TYR 0.019 0.001 TYR A 353 PHE 0.020 0.001 PHE A1357 TRP 0.013 0.001 TRP A 473 HIS 0.003 0.001 HIS A1148 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 (12103) covalent geometry : angle 0.59769 / 0.28 (16615) hydrogen bonds : bond 0.03514 / 2.33 ( 609) hydrogen bonds : angle 4.46727 / 3.17 ( 1755) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 186 time to evaluate : 0.244 Fit side-chains REVERT: A 744 GLU cc_start: 0.8310 (OUTLIER) cc_final: 0.7872 (tm-30) REVERT: A 755 LYS cc_start: 0.8199 (OUTLIER) cc_final: 0.6818 (mtmt) REVERT: A 782 GLN cc_start: 0.8856 (mt0) cc_final: 0.8518 (mt0) REVERT: A 864 SER cc_start: 0.8307 (p) cc_final: 0.7978 (t) REVERT: A 874 GLU cc_start: 0.7347 (OUTLIER) cc_final: 0.7059 (mp0) REVERT: A 931 LYS cc_start: 0.8300 (OUTLIER) cc_final: 0.7746 (mttp) REVERT: A 941 LYS cc_start: 0.8144 (OUTLIER) cc_final: 0.7924 (ptpt) REVERT: A 986 ARG cc_start: 0.9018 (OUTLIER) cc_final: 0.7858 (mtp180) REVERT: A 1119 PHE cc_start: 0.7966 (t80) cc_final: 0.7597 (t80) REVERT: A 1275 GLU cc_start: 0.7411 (tm-30) cc_final: 0.6896 (tm-30) REVERT: A 1276 LEU cc_start: 0.8204 (mt) cc_final: 0.7905 (mt) REVERT: A 1283 MET cc_start: 0.6539 (OUTLIER) cc_final: 0.5815 (mpt) REVERT: A 1322 PHE cc_start: 0.5400 (OUTLIER) cc_final: 0.4438 (t80) REVERT: A 1414 MET cc_start: 0.8128 (OUTLIER) cc_final: 0.6758 (mtm) REVERT: A 1562 MET cc_start: 0.7124 (ptp) cc_final: 0.6824 (ptp) outliers start: 53 outliers final: 33 residues processed: 224 average time/residue: 0.0917 time to fit residues: 29.7671 Evaluate side-chains 215 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 173 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 280 GLN Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 349 MET Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain A residue 515 SER Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 654 SER Chi-restraints excluded: chain A residue 707 ARG Chi-restraints excluded: chain A residue 744 GLU Chi-restraints excluded: chain A residue 755 LYS Chi-restraints excluded: chain A residue 814 SER Chi-restraints excluded: chain A residue 816 ASN Chi-restraints excluded: chain A residue 833 MET Chi-restraints excluded: chain A residue 874 GLU Chi-restraints excluded: chain A residue 878 MET Chi-restraints excluded: chain A residue 931 LYS Chi-restraints excluded: chain A residue 941 LYS Chi-restraints excluded: chain A residue 982 SER Chi-restraints excluded: chain A residue 986 ARG Chi-restraints excluded: chain A residue 1041 LEU Chi-restraints excluded: chain A residue 1048 HIS Chi-restraints excluded: chain A residue 1089 CYS Chi-restraints excluded: chain A residue 1134 VAL Chi-restraints excluded: chain A residue 1164 VAL Chi-restraints excluded: chain A residue 1179 CYS Chi-restraints excluded: chain A residue 1182 SER Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1246 MET Chi-restraints excluded: chain A residue 1283 MET Chi-restraints excluded: chain A residue 1322 PHE Chi-restraints excluded: chain A residue 1332 PHE Chi-restraints excluded: chain A residue 1358 LEU Chi-restraints excluded: chain A residue 1359 GLU Chi-restraints excluded: chain A residue 1394 THR Chi-restraints excluded: chain A residue 1414 MET Chi-restraints excluded: chain A residue 1429 VAL Chi-restraints excluded: chain A residue 1443 THR Chi-restraints excluded: chain A residue 1514 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 65 optimal weight: 0.7980 chunk 47 optimal weight: 0.7980 chunk 35 optimal weight: 0.5980 chunk 12 optimal weight: 0.9990 chunk 74 optimal weight: 0.3980 chunk 33 optimal weight: 0.6980 chunk 21 optimal weight: 0.7980 chunk 70 optimal weight: 0.1980 chunk 90 optimal weight: 2.9990 chunk 75 optimal weight: 0.8980 chunk 122 optimal weight: 3.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 460 GLN ** A1130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1287 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 = 0.3924 r_free = 0.3924 target = 0.176767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.144137 restraints weight = 12824.110| |-----------------------------------------------------------------------------| r_work (start): 0.3713 rms_B_bonded: 1.35 r_work: 0.3580 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3441 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.1906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12103 Z= 0.140 Angle : 0.597 7.556 16615 Z= 0.283 Chirality : 0.046 0.313 1897 Planarity : 0.003 0.034 1890 Dihedral : 11.763 168.882 2087 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 5.19 % Allowed : 22.90 % Favored : 71.91 % 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: 0.36 (0.23), residues: 1294 helix: 1.41 (0.19), residues: 707 sheet: -1.04 (0.50), residues: 101 loop : -1.21 (0.27), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 873 TYR 0.017 0.001 TYR A 912 PHE 0.020 0.001 PHE A1357 TRP 0.014 0.001 TRP A 976 HIS 0.003 0.001 HIS A1148 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 (12103) covalent geometry : angle 0.59671 / 0.28 (16615) hydrogen bonds : bond 0.03513 / 2.32 ( 609) hydrogen bonds : angle 4.45583 / 3.16 ( 1755) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 184 time to evaluate : 0.355 Fit side-chains REVERT: A 462 TYR cc_start: 0.8194 (m-80) cc_final: 0.7586 (m-80) REVERT: A 744 GLU cc_start: 0.8295 (OUTLIER) cc_final: 0.7958 (tm-30) REVERT: A 755 LYS cc_start: 0.8288 (OUTLIER) cc_final: 0.6912 (mtmt) REVERT: A 782 GLN cc_start: 0.8873 (mt0) cc_final: 0.8527 (mt0) REVERT: A 864 SER cc_start: 0.8266 (p) cc_final: 0.7994 (t) REVERT: A 874 GLU cc_start: 0.7330 (OUTLIER) cc_final: 0.7019 (mp0) REVERT: A 931 LYS cc_start: 0.8416 (OUTLIER) cc_final: 0.7852 (mttp) REVERT: A 941 LYS cc_start: 0.8173 (OUTLIER) cc_final: 0.7912 (ptpt) REVERT: A 986 ARG cc_start: 0.9035 (OUTLIER) cc_final: 0.7910 (mtp180) REVERT: A 1091 PHE cc_start: 0.8136 (m-80) cc_final: 0.7895 (m-10) REVERT: A 1119 PHE cc_start: 0.8053 (t80) cc_final: 0.7663 (t80) REVERT: A 1275 GLU cc_start: 0.7485 (tm-30) cc_final: 0.7020 (tm-30) REVERT: A 1276 LEU cc_start: 0.8283 (mt) cc_final: 0.7995 (mt) REVERT: A 1283 MET cc_start: 0.6644 (OUTLIER) cc_final: 0.5922 (mpt) REVERT: A 1322 PHE cc_start: 0.5600 (OUTLIER) cc_final: 0.4871 (t80) REVERT: A 1414 MET cc_start: 0.8168 (OUTLIER) cc_final: 0.6892 (mtm) REVERT: A 1559 ILE cc_start: 0.8337 (mt) cc_final: 0.8063 (tp) REVERT: A 1562 MET cc_start: 0.7202 (ptp) cc_final: 0.6841 (ptp) REVERT: A 1570 ARG cc_start: 0.7011 (ptp-170) cc_final: 0.6690 (ptp90) outliers start: 60 outliers final: 41 residues processed: 227 average time/residue: 0.0999 time to fit residues: 32.4818 Evaluate side-chains 231 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 181 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain A residue 280 GLN Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 349 MET Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 407 ILE Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain A residue 515 SER Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 654 SER Chi-restraints excluded: chain A residue 661 TYR Chi-restraints excluded: chain A residue 707 ARG Chi-restraints excluded: chain A residue 714 ARG Chi-restraints excluded: chain A residue 744 GLU Chi-restraints excluded: chain A residue 755 LYS Chi-restraints excluded: chain A residue 814 SER Chi-restraints excluded: chain A residue 816 ASN Chi-restraints excluded: chain A residue 833 MET Chi-restraints excluded: chain A residue 874 GLU Chi-restraints excluded: chain A residue 878 MET Chi-restraints excluded: chain A residue 903 CYS Chi-restraints excluded: chain A residue 931 LYS Chi-restraints excluded: chain A residue 941 LYS Chi-restraints excluded: chain A residue 977 SER Chi-restraints excluded: chain A residue 982 SER Chi-restraints excluded: chain A residue 986 ARG Chi-restraints excluded: chain A residue 1041 LEU Chi-restraints excluded: chain A residue 1048 HIS Chi-restraints excluded: chain A residue 1089 CYS Chi-restraints excluded: chain A residue 1134 VAL Chi-restraints excluded: chain A residue 1164 VAL Chi-restraints excluded: chain A residue 1179 CYS Chi-restraints excluded: chain A residue 1182 SER Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1246 MET Chi-restraints excluded: chain A residue 1283 MET Chi-restraints excluded: chain A residue 1322 PHE Chi-restraints excluded: chain A residue 1332 PHE Chi-restraints excluded: chain A residue 1358 LEU Chi-restraints excluded: chain A residue 1359 GLU Chi-restraints excluded: chain A residue 1394 THR Chi-restraints excluded: chain A residue 1414 MET Chi-restraints excluded: chain A residue 1429 VAL Chi-restraints excluded: chain A residue 1441 SER Chi-restraints excluded: chain A residue 1443 THR Chi-restraints excluded: chain A residue 1466 ASP Chi-restraints excluded: chain A residue 1514 THR Chi-restraints excluded: chain A residue 1593 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 50 optimal weight: 0.5980 chunk 103 optimal weight: 0.7980 chunk 117 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 chunk 47 optimal weight: 0.6980 chunk 115 optimal weight: 0.8980 chunk 18 optimal weight: 0.7980 chunk 125 optimal weight: 8.9990 chunk 78 optimal weight: 0.8980 chunk 77 optimal weight: 0.1980 chunk 46 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 460 GLN ** A1130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1287 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 = 0.3958 r_free = 0.3958 target = 0.179323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.147247 restraints weight = 12700.131| |-----------------------------------------------------------------------------| r_work (start): 0.3708 rms_B_bonded: 1.33 r_work: 0.3571 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3437 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.1954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12103 Z= 0.146 Angle : 0.601 7.672 16615 Z= 0.285 Chirality : 0.046 0.316 1897 Planarity : 0.003 0.034 1890 Dihedral : 11.770 169.892 2087 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 4.67 % Allowed : 23.85 % Favored : 71.48 % 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: 0.33 (0.23), residues: 1294 helix: 1.40 (0.19), residues: 709 sheet: -1.05 (0.50), residues: 100 loop : -1.27 (0.26), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 880 TYR 0.016 0.001 TYR A 912 PHE 0.021 0.002 PHE A1357 TRP 0.013 0.001 TRP A 976 HIS 0.003 0.001 HIS A1148 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.15 (12103) covalent geometry : angle 0.60114 / 0.29 (16615) hydrogen bonds : bond 0.03530 / 2.33 ( 609) hydrogen bonds : angle 4.45271 / 3.15 ( 1755) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 185 time to evaluate : 0.383 Fit side-chains REVERT: A 462 TYR cc_start: 0.8211 (m-80) cc_final: 0.7640 (m-80) REVERT: A 744 GLU cc_start: 0.8295 (OUTLIER) cc_final: 0.7926 (tm-30) REVERT: A 755 LYS cc_start: 0.8307 (OUTLIER) cc_final: 0.6930 (mtmt) REVERT: A 782 GLN cc_start: 0.8899 (mt0) cc_final: 0.8555 (mt0) REVERT: A 864 SER cc_start: 0.8257 (p) cc_final: 0.7982 (t) REVERT: A 874 GLU cc_start: 0.7349 (OUTLIER) cc_final: 0.7059 (mp0) REVERT: A 931 LYS cc_start: 0.8412 (OUTLIER) cc_final: 0.7839 (mttp) REVERT: A 941 LYS cc_start: 0.8185 (OUTLIER) cc_final: 0.7920 (ptpt) REVERT: A 986 ARG cc_start: 0.9076 (OUTLIER) cc_final: 0.7849 (mtp180) REVERT: A 1119 PHE cc_start: 0.8057 (t80) cc_final: 0.7777 (t80) REVERT: A 1275 GLU cc_start: 0.7469 (tm-30) cc_final: 0.7005 (tm-30) REVERT: A 1276 LEU cc_start: 0.8278 (mt) cc_final: 0.8000 (mt) REVERT: A 1283 MET cc_start: 0.6632 (OUTLIER) cc_final: 0.5902 (mpt) REVERT: A 1322 PHE cc_start: 0.5411 (OUTLIER) cc_final: 0.4374 (t80) REVERT: A 1414 MET cc_start: 0.8166 (OUTLIER) cc_final: 0.6956 (mtm) REVERT: A 1559 ILE cc_start: 0.8298 (mt) cc_final: 0.8033 (tp) REVERT: A 1562 MET cc_start: 0.7203 (ptp) cc_final: 0.6842 (ptp) REVERT: A 1570 ARG cc_start: 0.6902 (ptp-170) cc_final: 0.6655 (ptp90) outliers start: 54 outliers final: 42 residues processed: 223 average time/residue: 0.0984 time to fit residues: 32.0180 Evaluate side-chains 233 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 182 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 280 GLN Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 349 MET Chi-restraints excluded: chain A residue 377 MET Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 407 ILE Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain A residue 515 SER Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 654 SER Chi-restraints excluded: chain A residue 661 TYR Chi-restraints excluded: chain A residue 707 ARG Chi-restraints excluded: chain A residue 714 ARG Chi-restraints excluded: chain A residue 744 GLU Chi-restraints excluded: chain A residue 755 LYS Chi-restraints excluded: chain A residue 814 SER Chi-restraints excluded: chain A residue 816 ASN Chi-restraints excluded: chain A residue 833 MET Chi-restraints excluded: chain A residue 874 GLU Chi-restraints excluded: chain A residue 878 MET Chi-restraints excluded: chain A residue 903 CYS Chi-restraints excluded: chain A residue 931 LYS Chi-restraints excluded: chain A residue 941 LYS Chi-restraints excluded: chain A residue 977 SER Chi-restraints excluded: chain A residue 982 SER Chi-restraints excluded: chain A residue 986 ARG Chi-restraints excluded: chain A residue 1032 SER Chi-restraints excluded: chain A residue 1041 LEU Chi-restraints excluded: chain A residue 1048 HIS Chi-restraints excluded: chain A residue 1134 VAL Chi-restraints excluded: chain A residue 1164 VAL Chi-restraints excluded: chain A residue 1179 CYS Chi-restraints excluded: chain A residue 1182 SER Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1246 MET Chi-restraints excluded: chain A residue 1247 VAL Chi-restraints excluded: chain A residue 1283 MET Chi-restraints excluded: chain A residue 1322 PHE Chi-restraints excluded: chain A residue 1332 PHE Chi-restraints excluded: chain A residue 1358 LEU Chi-restraints excluded: chain A residue 1359 GLU Chi-restraints excluded: chain A residue 1394 THR Chi-restraints excluded: chain A residue 1414 MET Chi-restraints excluded: chain A residue 1429 VAL Chi-restraints excluded: chain A residue 1441 SER Chi-restraints excluded: chain A residue 1443 THR Chi-restraints excluded: chain A residue 1466 ASP Chi-restraints excluded: chain A residue 1514 THR Chi-restraints excluded: chain A residue 1593 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 8 optimal weight: 3.9990 chunk 40 optimal weight: 0.9990 chunk 109 optimal weight: 3.9990 chunk 63 optimal weight: 0.5980 chunk 91 optimal weight: 0.9990 chunk 117 optimal weight: 0.7980 chunk 45 optimal weight: 0.9980 chunk 61 optimal weight: 0.6980 chunk 103 optimal weight: 0.6980 chunk 79 optimal weight: 0.5980 chunk 107 optimal weight: 3.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 460 GLN ** A1130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1287 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 = 0.3952 r_free = 0.3952 target = 0.178678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.146437 restraints weight = 12727.456| |-----------------------------------------------------------------------------| r_work (start): 0.3699 rms_B_bonded: 1.33 r_work: 0.3560 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3428 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.1959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 12103 Z= 0.156 Angle : 0.612 8.484 16615 Z= 0.291 Chirality : 0.047 0.324 1897 Planarity : 0.003 0.037 1890 Dihedral : 11.788 170.721 2087 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 4.93 % Allowed : 23.34 % Favored : 71.74 % 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: 0.33 (0.23), residues: 1294 helix: 1.39 (0.19), residues: 706 sheet: -1.04 (0.50), residues: 101 loop : -1.24 (0.27), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 880 TYR 0.015 0.001 TYR A 912 PHE 0.021 0.002 PHE A1357 TRP 0.014 0.001 TRP A 976 HIS 0.003 0.001 HIS A1148 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.16 (12103) covalent geometry : angle 0.61231 / 0.29 (16615) hydrogen bonds : bond 0.03567 / 2.36 ( 609) hydrogen bonds : angle 4.49956 / 3.18 ( 1755) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 178 time to evaluate : 0.412 Fit side-chains REVERT: A 462 TYR cc_start: 0.8193 (m-80) cc_final: 0.7632 (m-80) REVERT: A 744 GLU cc_start: 0.8313 (OUTLIER) cc_final: 0.7971 (tm-30) REVERT: A 782 GLN cc_start: 0.8904 (mt0) cc_final: 0.8663 (mt0) REVERT: A 864 SER cc_start: 0.8234 (p) cc_final: 0.7952 (t) REVERT: A 874 GLU cc_start: 0.7526 (OUTLIER) cc_final: 0.7001 (pm20) REVERT: A 931 LYS cc_start: 0.8418 (OUTLIER) cc_final: 0.7843 (mttp) REVERT: A 941 LYS cc_start: 0.8194 (OUTLIER) cc_final: 0.7912 (ptpt) REVERT: A 986 ARG cc_start: 0.9067 (OUTLIER) cc_final: 0.7879 (mtp180) REVERT: A 1119 PHE cc_start: 0.8078 (t80) cc_final: 0.7776 (t80) REVERT: A 1276 LEU cc_start: 0.8255 (mt) cc_final: 0.7911 (mt) REVERT: A 1283 MET cc_start: 0.6651 (OUTLIER) cc_final: 0.5899 (mpt) REVERT: A 1322 PHE cc_start: 0.5442 (OUTLIER) cc_final: 0.4428 (t80) REVERT: A 1414 MET cc_start: 0.8164 (OUTLIER) cc_final: 0.6992 (mtm) REVERT: A 1562 MET cc_start: 0.7236 (ptp) cc_final: 0.6948 (ptp) outliers start: 57 outliers final: 42 residues processed: 218 average time/residue: 0.1082 time to fit residues: 34.5026 Evaluate side-chains 225 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 175 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 280 GLN Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 349 MET Chi-restraints excluded: chain A residue 377 MET Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 407 ILE Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain A residue 515 SER Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 654 SER Chi-restraints excluded: chain A residue 661 TYR Chi-restraints excluded: chain A residue 707 ARG Chi-restraints excluded: chain A residue 714 ARG Chi-restraints excluded: chain A residue 744 GLU Chi-restraints excluded: chain A residue 814 SER Chi-restraints excluded: chain A residue 816 ASN Chi-restraints excluded: chain A residue 833 MET Chi-restraints excluded: chain A residue 874 GLU Chi-restraints excluded: chain A residue 903 CYS Chi-restraints excluded: chain A residue 931 LYS Chi-restraints excluded: chain A residue 941 LYS Chi-restraints excluded: chain A residue 977 SER Chi-restraints excluded: chain A residue 982 SER Chi-restraints excluded: chain A residue 986 ARG Chi-restraints excluded: chain A residue 1032 SER Chi-restraints excluded: chain A residue 1048 HIS Chi-restraints excluded: chain A residue 1089 CYS Chi-restraints excluded: chain A residue 1134 VAL Chi-restraints excluded: chain A residue 1164 VAL Chi-restraints excluded: chain A residue 1179 CYS Chi-restraints excluded: chain A residue 1182 SER Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1246 MET Chi-restraints excluded: chain A residue 1247 VAL Chi-restraints excluded: chain A residue 1283 MET Chi-restraints excluded: chain A residue 1322 PHE Chi-restraints excluded: chain A residue 1332 PHE Chi-restraints excluded: chain A residue 1358 LEU Chi-restraints excluded: chain A residue 1359 GLU Chi-restraints excluded: chain A residue 1394 THR Chi-restraints excluded: chain A residue 1414 MET Chi-restraints excluded: chain A residue 1429 VAL Chi-restraints excluded: chain A residue 1441 SER Chi-restraints excluded: chain A residue 1443 THR Chi-restraints excluded: chain A residue 1466 ASP Chi-restraints excluded: chain A residue 1514 THR Chi-restraints excluded: chain A residue 1593 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 108 optimal weight: 1.9990 chunk 59 optimal weight: 0.8980 chunk 60 optimal weight: 2.9990 chunk 119 optimal weight: 5.9990 chunk 123 optimal weight: 0.0040 chunk 105 optimal weight: 0.5980 chunk 9 optimal weight: 1.9990 chunk 76 optimal weight: 0.2980 chunk 79 optimal weight: 0.9980 chunk 55 optimal weight: 0.9980 chunk 91 optimal weight: 0.5980 overall best weight: 0.4792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 460 GLN ** A1130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1287 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 = 0.3973 r_free = 0.3973 target = 0.180754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.148768 restraints weight = 12656.514| |-----------------------------------------------------------------------------| r_work (start): 0.3722 rms_B_bonded: 1.33 r_work: 0.3585 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3453 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.2051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12103 Z= 0.135 Angle : 0.608 10.302 16615 Z= 0.287 Chirality : 0.046 0.318 1897 Planarity : 0.003 0.041 1890 Dihedral : 11.761 171.345 2087 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 4.49 % Allowed : 24.29 % Favored : 71.22 % 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: 0.35 (0.23), residues: 1294 helix: 1.38 (0.19), residues: 709 sheet: -0.95 (0.51), residues: 100 loop : -1.22 (0.27), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 880 TYR 0.014 0.001 TYR A 912 PHE 0.021 0.001 PHE A1357 TRP 0.015 0.001 TRP A 976 HIS 0.003 0.001 HIS A1148 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.13 (12103) covalent geometry : angle 0.60843 / 0.29 (16615) hydrogen bonds : bond 0.03502 / 2.31 ( 609) hydrogen bonds : angle 4.45195 / 3.15 ( 1755) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 184 time to evaluate : 0.393 Fit side-chains REVERT: A 462 TYR cc_start: 0.8117 (m-80) cc_final: 0.7624 (m-80) REVERT: A 744 GLU cc_start: 0.8302 (OUTLIER) cc_final: 0.7988 (tm-30) REVERT: A 755 LYS cc_start: 0.8295 (OUTLIER) cc_final: 0.6894 (mtmt) REVERT: A 782 GLN cc_start: 0.8892 (mt0) cc_final: 0.8564 (mt0) REVERT: A 864 SER cc_start: 0.8224 (p) cc_final: 0.7953 (t) REVERT: A 874 GLU cc_start: 0.7543 (OUTLIER) cc_final: 0.7051 (pm20) REVERT: A 931 LYS cc_start: 0.8390 (OUTLIER) cc_final: 0.7825 (mttp) REVERT: A 941 LYS cc_start: 0.8163 (OUTLIER) cc_final: 0.7907 (ptpt) REVERT: A 986 ARG cc_start: 0.9047 (OUTLIER) cc_final: 0.7880 (mtp180) REVERT: A 1119 PHE cc_start: 0.8058 (t80) cc_final: 0.7788 (t80) REVERT: A 1276 LEU cc_start: 0.8220 (mt) cc_final: 0.7896 (mt) REVERT: A 1283 MET cc_start: 0.6610 (OUTLIER) cc_final: 0.5865 (mpt) REVERT: A 1322 PHE cc_start: 0.5196 (OUTLIER) cc_final: 0.4016 (t80) REVERT: A 1414 MET cc_start: 0.8103 (OUTLIER) cc_final: 0.6912 (mtm) REVERT: A 1562 MET cc_start: 0.7236 (ptp) cc_final: 0.6923 (ptp) outliers start: 52 outliers final: 41 residues processed: 222 average time/residue: 0.1091 time to fit residues: 34.9189 Evaluate side-chains 234 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 184 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 280 GLN Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 349 MET Chi-restraints excluded: chain A residue 377 MET Chi-restraints excluded: chain A residue 401 GLN Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain A residue 515 SER Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 654 SER Chi-restraints excluded: chain A residue 661 TYR Chi-restraints excluded: chain A residue 700 VAL Chi-restraints excluded: chain A residue 707 ARG Chi-restraints excluded: chain A residue 714 ARG Chi-restraints excluded: chain A residue 744 GLU Chi-restraints excluded: chain A residue 755 LYS Chi-restraints excluded: chain A residue 814 SER Chi-restraints excluded: chain A residue 816 ASN Chi-restraints excluded: chain A residue 833 MET Chi-restraints excluded: chain A residue 874 GLU Chi-restraints excluded: chain A residue 903 CYS Chi-restraints excluded: chain A residue 931 LYS Chi-restraints excluded: chain A residue 941 LYS Chi-restraints excluded: chain A residue 977 SER Chi-restraints excluded: chain A residue 982 SER Chi-restraints excluded: chain A residue 986 ARG Chi-restraints excluded: chain A residue 1032 SER Chi-restraints excluded: chain A residue 1048 HIS Chi-restraints excluded: chain A residue 1134 VAL Chi-restraints excluded: chain A residue 1164 VAL Chi-restraints excluded: chain A residue 1179 CYS Chi-restraints excluded: chain A residue 1182 SER Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1246 MET Chi-restraints excluded: chain A residue 1247 VAL Chi-restraints excluded: chain A residue 1283 MET Chi-restraints excluded: chain A residue 1322 PHE Chi-restraints excluded: chain A residue 1358 LEU Chi-restraints excluded: chain A residue 1359 GLU Chi-restraints excluded: chain A residue 1367 THR Chi-restraints excluded: chain A residue 1394 THR Chi-restraints excluded: chain A residue 1414 MET Chi-restraints excluded: chain A residue 1429 VAL Chi-restraints excluded: chain A residue 1441 SER Chi-restraints excluded: chain A residue 1443 THR Chi-restraints excluded: chain A residue 1466 ASP Chi-restraints excluded: chain A residue 1514 THR Chi-restraints excluded: chain A residue 1593 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 52 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 62 optimal weight: 0.5980 chunk 96 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 34 optimal weight: 0.8980 chunk 106 optimal weight: 0.4980 chunk 61 optimal weight: 0.0060 chunk 98 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 460 GLN ** A1248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1287 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 = 0.4031 r_free = 0.4031 target = 0.185441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.154465 restraints weight = 12576.404| |-----------------------------------------------------------------------------| r_work (start): 0.3716 rms_B_bonded: 1.28 r_work: 0.3577 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3445 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.2060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12103 Z= 0.149 Angle : 0.628 13.211 16615 Z= 0.295 Chirality : 0.047 0.315 1897 Planarity : 0.003 0.034 1890 Dihedral : 11.762 171.823 2087 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 4.84 % Allowed : 24.29 % Favored : 70.87 % 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: 0.35 (0.23), residues: 1294 helix: 1.37 (0.19), residues: 706 sheet: -0.99 (0.51), residues: 100 loop : -1.18 (0.27), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1300 TYR 0.016 0.001 TYR A1106 PHE 0.022 0.002 PHE A1357 TRP 0.027 0.001 TRP A1131 HIS 0.003 0.001 HIS A1148 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.15 (12103) covalent geometry : angle 0.62847 / 0.29 (16615) hydrogen bonds : bond 0.03578 / 2.35 ( 609) hydrogen bonds : angle 4.49230 / 3.18 ( 1755) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 179 time to evaluate : 0.494 Fit side-chains REVERT: A 462 TYR cc_start: 0.8147 (m-80) cc_final: 0.7661 (m-80) REVERT: A 744 GLU cc_start: 0.8345 (OUTLIER) cc_final: 0.8010 (tm-30) REVERT: A 755 LYS cc_start: 0.8340 (OUTLIER) cc_final: 0.6941 (mtmt) REVERT: A 782 GLN cc_start: 0.8880 (mt0) cc_final: 0.8556 (mt0) REVERT: A 864 SER cc_start: 0.8203 (p) cc_final: 0.7944 (t) REVERT: A 874 GLU cc_start: 0.7476 (OUTLIER) cc_final: 0.7004 (pm20) REVERT: A 931 LYS cc_start: 0.8390 (OUTLIER) cc_final: 0.7807 (mttp) REVERT: A 941 LYS cc_start: 0.8169 (OUTLIER) cc_final: 0.7844 (ttpt) REVERT: A 986 ARG cc_start: 0.9056 (OUTLIER) cc_final: 0.7885 (mtp180) REVERT: A 1119 PHE cc_start: 0.8045 (t80) cc_final: 0.7633 (t80) REVERT: A 1276 LEU cc_start: 0.8230 (mt) cc_final: 0.7907 (mt) REVERT: A 1283 MET cc_start: 0.6646 (OUTLIER) cc_final: 0.5904 (mpt) REVERT: A 1322 PHE cc_start: 0.5144 (OUTLIER) cc_final: 0.3827 (t80) REVERT: A 1414 MET cc_start: 0.8115 (OUTLIER) cc_final: 0.6936 (mtm) REVERT: A 1562 MET cc_start: 0.7255 (ptp) cc_final: 0.6930 (ptp) outliers start: 56 outliers final: 42 residues processed: 220 average time/residue: 0.1151 time to fit residues: 36.4715 Evaluate side-chains 229 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 178 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 280 GLN Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 349 MET Chi-restraints excluded: chain A residue 377 MET Chi-restraints excluded: chain A residue 401 GLN Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 407 ILE Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain A residue 515 SER Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 654 SER Chi-restraints excluded: chain A residue 661 TYR Chi-restraints excluded: chain A residue 700 VAL Chi-restraints excluded: chain A residue 714 ARG Chi-restraints excluded: chain A residue 744 GLU Chi-restraints excluded: chain A residue 755 LYS Chi-restraints excluded: chain A residue 814 SER Chi-restraints excluded: chain A residue 816 ASN Chi-restraints excluded: chain A residue 833 MET Chi-restraints excluded: chain A residue 874 GLU Chi-restraints excluded: chain A residue 903 CYS Chi-restraints excluded: chain A residue 931 LYS Chi-restraints excluded: chain A residue 941 LYS Chi-restraints excluded: chain A residue 977 SER Chi-restraints excluded: chain A residue 982 SER Chi-restraints excluded: chain A residue 986 ARG Chi-restraints excluded: chain A residue 1032 SER Chi-restraints excluded: chain A residue 1048 HIS Chi-restraints excluded: chain A residue 1134 VAL Chi-restraints excluded: chain A residue 1164 VAL Chi-restraints excluded: chain A residue 1179 CYS Chi-restraints excluded: chain A residue 1182 SER Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1246 MET Chi-restraints excluded: chain A residue 1247 VAL Chi-restraints excluded: chain A residue 1283 MET Chi-restraints excluded: chain A residue 1322 PHE Chi-restraints excluded: chain A residue 1358 LEU Chi-restraints excluded: chain A residue 1359 GLU Chi-restraints excluded: chain A residue 1367 THR Chi-restraints excluded: chain A residue 1394 THR Chi-restraints excluded: chain A residue 1414 MET Chi-restraints excluded: chain A residue 1429 VAL Chi-restraints excluded: chain A residue 1441 SER Chi-restraints excluded: chain A residue 1443 THR Chi-restraints excluded: chain A residue 1466 ASP Chi-restraints excluded: chain A residue 1514 THR Chi-restraints excluded: chain A residue 1593 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 5 optimal weight: 5.9990 chunk 15 optimal weight: 0.8980 chunk 0 optimal weight: 7.9990 chunk 47 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 118 optimal weight: 0.1980 chunk 111 optimal weight: 0.8980 chunk 80 optimal weight: 0.5980 chunk 110 optimal weight: 0.9990 chunk 73 optimal weight: 0.7980 chunk 62 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1287 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 = 0.4033 r_free = 0.4033 target = 0.185623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.154917 restraints weight = 12561.808| |-----------------------------------------------------------------------------| r_work (start): 0.3718 rms_B_bonded: 1.26 r_work: 0.3582 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3449 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.2081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12103 Z= 0.150 Angle : 0.629 12.821 16615 Z= 0.295 Chirality : 0.047 0.318 1897 Planarity : 0.003 0.034 1890 Dihedral : 11.765 172.003 2087 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 4.67 % Allowed : 24.46 % Favored : 70.87 % 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: 0.35 (0.23), residues: 1294 helix: 1.39 (0.19), residues: 702 sheet: -0.98 (0.51), residues: 99 loop : -1.20 (0.26), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 873 TYR 0.017 0.001 TYR A1106 PHE 0.023 0.002 PHE A1357 TRP 0.024 0.001 TRP A1131 HIS 0.003 0.001 HIS A1148 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.15 (12103) covalent geometry : angle 0.62867 / 0.29 (16615) hydrogen bonds : bond 0.03593 / 2.36 ( 609) hydrogen bonds : angle 4.50701 / 3.19 ( 1755) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2622.88 seconds wall clock time: 45 minutes 52.43 seconds (2752.43 seconds total)