Starting phenix.real_space_refine on Mon Dec 30 03:21:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8c4v_16430/12_2024/8c4v_16430.cif Found real_map, /net/cci-nas-00/data/ceres_data/8c4v_16430/12_2024/8c4v_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8c4v_16430/12_2024/8c4v_16430.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8c4v_16430/12_2024/8c4v_16430.map" model { file = "/net/cci-nas-00/data/ceres_data/8c4v_16430/12_2024/8c4v_16430.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8c4v_16430/12_2024/8c4v_16430.cif" } resolution = 3.14 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/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: {'RNA': 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: {'RNA': 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: {'RNA': 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: {'RNA': 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: {'RNA': 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: 7.65, per 1000 atoms: 0.65 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: 3.24 Conformation dependent library (CDL) restraints added in 1.5 seconds 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: 4.93 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: 6.06 Time building geometry restraints manager: 3.70 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: 15847 2.36 - 4.72: 646 4.72 - 7.07: 98 7.07 - 9.43: 21 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 - 35.46: 6899 35.46 - 70.93: 362 70.93 - 106.39: 27 106.39 - 141.85: 1 141.85 - 177.32: 4 Dihedral angle restraints: 7293 sinusoidal: 3447 harmonic: 3846 Sorted by residual: dihedral pdb=" O4' U H 7 " pdb=" C1' U H 7 " pdb=" N1 U H 7 " pdb=" C2 U H 7 " ideal model delta sinusoidal sigma weight residual 200.00 39.39 160.61 1 1.50e+01 4.44e-03 8.29e+01 dihedral pdb=" O4' C S 23 " pdb=" C1' C S 23 " pdb=" N1 C S 23 " pdb=" C2 C S 23 " ideal model delta sinusoidal sigma weight residual 232.00 54.68 177.32 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' C H 13 " pdb=" C1' C H 13 " pdb=" N1 C H 13 " pdb=" C2 C H 13 " ideal model delta sinusoidal sigma weight residual 232.00 55.62 176.38 1 1.70e+01 3.46e-03 6.64e+01 ... (remaining 7290 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.133: 1782 0.133 - 0.266: 99 0.266 - 0.399: 14 0.399 - 0.533: 1 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=" CA PHE A1132 " pdb=" N PHE A1132 " pdb=" C PHE A1132 " pdb=" CB PHE A1132 " both_signs ideal model delta sigma weight residual False 2.51 2.95 -0.44 2.00e-01 2.50e+01 4.84e+00 chirality pdb=" CA VAL A1574 " pdb=" N VAL A1574 " pdb=" C VAL A1574 " pdb=" CB VAL A1574 " both_signs ideal model delta sigma weight residual False 2.44 2.84 -0.40 2.00e-01 2.50e+01 3.93e+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: 0.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.410 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 36.230 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 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= 0.453 Angle : 1.008 11.791 16615 Z= 0.677 Chirality : 0.067 0.666 1897 Planarity : 0.005 0.062 1890 Dihedral : 19.433 177.318 4803 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 13.76 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.028 0.002 TRP A1131 HIS 0.008 0.001 HIS A1130 PHE 0.042 0.002 PHE A 291 TYR 0.027 0.002 TYR A1104 ARG 0.008 0.001 ARG A 880 *********************** 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 : 1.487 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: 0.2865 time to fit residues: 79.0284 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 : 1.327 ------------------------------------------------------------------------------- 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 111 optimal weight: 0.8980 chunk 100 optimal weight: 0.7980 chunk 55 optimal weight: 0.7980 chunk 34 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 103 optimal weight: 2.9990 chunk 40 optimal weight: 0.0770 chunk 62 optimal weight: 0.9990 chunk 77 optimal weight: 0.3980 chunk 119 optimal weight: 3.9990 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.1022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 12103 Z= 0.221 Angle : 0.559 6.799 16615 Z= 0.291 Chirality : 0.039 0.197 1897 Planarity : 0.004 0.035 1890 Dihedral : 16.971 177.409 2276 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 3.89 % Allowed : 23.16 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.23), residues: 1294 helix: 1.06 (0.19), residues: 701 sheet: -1.45 (0.49), residues: 100 loop : -1.26 (0.26), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 748 HIS 0.005 0.001 HIS A 501 PHE 0.016 0.001 PHE A1143 TYR 0.013 0.001 TYR A1106 ARG 0.005 0.001 ARG A1300 *********************** 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 234 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 189 time to evaluate : 1.360 Fit side-chains REVERT: A 816 ASN cc_start: 0.7965 (OUTLIER) cc_final: 0.7693 (m-40) REVERT: A 931 LYS cc_start: 0.8612 (OUTLIER) cc_final: 0.8055 (mttp) REVERT: A 1000 LYS cc_start: 0.8088 (mttt) cc_final: 0.7819 (mttt) REVERT: A 1119 PHE cc_start: 0.8099 (t80) cc_final: 0.7865 (t80) REVERT: A 1275 GLU cc_start: 0.7605 (tm-30) cc_final: 0.7084 (tm-30) REVERT: A 1276 LEU cc_start: 0.8521 (OUTLIER) cc_final: 0.8113 (mt) REVERT: A 1283 MET cc_start: 0.6799 (OUTLIER) cc_final: 0.6059 (mpt) REVERT: A 1414 MET cc_start: 0.8152 (OUTLIER) cc_final: 0.7069 (mtm) outliers start: 45 outliers final: 23 residues processed: 219 average time/residue: 0.2656 time to fit residues: 82.7652 Evaluate side-chains 198 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 170 time to evaluate : 1.364 ------------------------------------------------------------------------------- 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 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 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 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 1397 THR Chi-restraints excluded: chain A residue 1414 MET Chi-restraints excluded: chain A residue 1443 THR Chi-restraints excluded: chain A residue 1550 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 66 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 99 optimal weight: 0.5980 chunk 81 optimal weight: 0.5980 chunk 33 optimal weight: 0.5980 chunk 120 optimal weight: 3.9990 chunk 129 optimal weight: 3.9990 chunk 106 optimal weight: 0.7980 chunk 119 optimal weight: 6.9990 chunk 40 optimal weight: 0.0060 chunk 96 optimal weight: 0.0970 overall best weight: 0.3794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.1400 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= 0.171 Angle : 0.514 6.632 16615 Z= 0.266 Chirality : 0.038 0.182 1897 Planarity : 0.003 0.034 1890 Dihedral : 16.686 179.208 2265 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 3.63 % Allowed : 22.90 % Favored : 73.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.23), residues: 1294 helix: 1.24 (0.19), residues: 704 sheet: -1.19 (0.50), residues: 98 loop : -1.16 (0.27), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 473 HIS 0.002 0.001 HIS A 489 PHE 0.020 0.001 PHE A1357 TYR 0.015 0.001 TYR A 912 ARG 0.006 0.000 ARG A 873 *********************** 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 231 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 189 time to evaluate : 1.284 Fit side-chains REVERT: A 744 GLU cc_start: 0.8304 (OUTLIER) cc_final: 0.7984 (tm-30) REVERT: A 755 LYS cc_start: 0.8305 (OUTLIER) cc_final: 0.7057 (mtmt) REVERT: A 782 GLN cc_start: 0.8855 (mt0) cc_final: 0.8539 (mt0) REVERT: A 931 LYS cc_start: 0.8509 (OUTLIER) cc_final: 0.7884 (mttp) REVERT: A 1276 LEU cc_start: 0.8523 (mt) cc_final: 0.8177 (mt) REVERT: A 1283 MET cc_start: 0.6665 (OUTLIER) cc_final: 0.5930 (mpt) REVERT: A 1403 GLN cc_start: 0.7123 (mt0) cc_final: 0.6767 (mt0) REVERT: A 1414 MET cc_start: 0.7883 (OUTLIER) cc_final: 0.6785 (mtm) REVERT: A 1562 MET cc_start: 0.7063 (ptp) cc_final: 0.6693 (mtm) outliers start: 42 outliers final: 22 residues processed: 217 average time/residue: 0.2602 time to fit residues: 80.7154 Evaluate side-chains 198 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 171 time to evaluate : 1.394 ------------------------------------------------------------------------------- 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 402 ILE 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 816 ASN 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 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 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 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 7.9990 chunk 90 optimal weight: 1.9990 chunk 62 optimal weight: 0.5980 chunk 13 optimal weight: 0.0570 chunk 57 optimal weight: 1.9990 chunk 80 optimal weight: 0.7980 chunk 120 optimal weight: 5.9990 chunk 127 optimal weight: 1.9990 chunk 114 optimal weight: 0.2980 chunk 34 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 overall best weight: 0.7500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 712 HIS ** A 827 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.1513 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= 0.235 Angle : 0.538 7.185 16615 Z= 0.276 Chirality : 0.039 0.181 1897 Planarity : 0.003 0.035 1890 Dihedral : 16.652 178.841 2259 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 4.67 % Allowed : 22.64 % Favored : 72.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.23), residues: 1294 helix: 1.25 (0.19), residues: 704 sheet: -1.06 (0.50), residues: 99 loop : -1.16 (0.27), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 473 HIS 0.004 0.001 HIS A 501 PHE 0.020 0.002 PHE A1090 TYR 0.015 0.001 TYR A 912 ARG 0.007 0.000 ARG A 873 *********************** 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 239 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 185 time to evaluate : 1.351 Fit side-chains REVERT: A 744 GLU cc_start: 0.8327 (OUTLIER) cc_final: 0.8051 (tm-30) REVERT: A 755 LYS cc_start: 0.8356 (OUTLIER) cc_final: 0.7032 (mtmt) REVERT: A 782 GLN cc_start: 0.8888 (mt0) cc_final: 0.8552 (mt0) REVERT: A 931 LYS cc_start: 0.8549 (OUTLIER) cc_final: 0.7973 (mttp) REVERT: A 986 ARG cc_start: 0.9143 (OUTLIER) cc_final: 0.8008 (mtp180) REVERT: A 1119 PHE cc_start: 0.8060 (t80) cc_final: 0.7715 (t80) REVERT: A 1276 LEU cc_start: 0.8490 (mt) cc_final: 0.8255 (mt) REVERT: A 1283 MET cc_start: 0.6711 (OUTLIER) cc_final: 0.6014 (mpt) REVERT: A 1403 GLN cc_start: 0.7188 (mt0) cc_final: 0.6818 (mt0) REVERT: A 1414 MET cc_start: 0.7966 (OUTLIER) cc_final: 0.6943 (mtm) REVERT: A 1562 MET cc_start: 0.7165 (ptp) cc_final: 0.6844 (mtm) outliers start: 54 outliers final: 34 residues processed: 222 average time/residue: 0.2727 time to fit residues: 85.5208 Evaluate side-chains 213 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 173 time to evaluate : 1.306 ------------------------------------------------------------------------------- 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 377 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 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 814 SER 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 982 SER Chi-restraints excluded: chain A residue 986 ARG Chi-restraints excluded: chain A residue 1041 LEU Chi-restraints excluded: chain A residue 1083 LEU Chi-restraints excluded: chain A residue 1089 CYS Chi-restraints excluded: chain A residue 1134 VAL Chi-restraints excluded: chain A residue 1135 ASN 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 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 72 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 95 optimal weight: 0.7980 chunk 52 optimal weight: 0.0470 chunk 108 optimal weight: 2.9990 chunk 88 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 chunk 65 optimal weight: 0.5980 chunk 114 optimal weight: 5.9990 chunk 32 optimal weight: 0.5980 chunk 42 optimal weight: 3.9990 overall best weight: 0.6080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 816 ASN ** A 827 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1287 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.1613 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= 0.205 Angle : 0.522 7.147 16615 Z= 0.268 Chirality : 0.038 0.184 1897 Planarity : 0.003 0.034 1890 Dihedral : 16.639 177.663 2259 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 4.84 % Allowed : 23.08 % Favored : 72.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.23), residues: 1294 helix: 1.31 (0.19), residues: 707 sheet: -1.10 (0.51), residues: 99 loop : -1.14 (0.27), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 473 HIS 0.003 0.001 HIS A1148 PHE 0.020 0.002 PHE A1357 TYR 0.023 0.001 TYR A 353 ARG 0.007 0.000 ARG A 714 *********************** 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 236 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 180 time to evaluate : 1.275 Fit side-chains REVERT: A 479 ILE cc_start: 0.9167 (OUTLIER) cc_final: 0.8965 (mm) REVERT: A 704 PHE cc_start: 0.7803 (t80) cc_final: 0.7593 (t80) REVERT: A 744 GLU cc_start: 0.8292 (OUTLIER) cc_final: 0.7979 (tm-30) REVERT: A 755 LYS cc_start: 0.8336 (OUTLIER) cc_final: 0.7006 (mtmt) REVERT: A 782 GLN cc_start: 0.8869 (mt0) cc_final: 0.8515 (mt0) REVERT: A 874 GLU cc_start: 0.7222 (OUTLIER) cc_final: 0.6903 (mp0) REVERT: A 931 LYS cc_start: 0.8520 (OUTLIER) cc_final: 0.7969 (mttp) REVERT: A 986 ARG cc_start: 0.9103 (OUTLIER) cc_final: 0.7981 (mtp180) REVERT: A 1119 PHE cc_start: 0.8078 (t80) cc_final: 0.7714 (t80) REVERT: A 1276 LEU cc_start: 0.8463 (mt) cc_final: 0.8093 (mt) REVERT: A 1283 MET cc_start: 0.6669 (OUTLIER) cc_final: 0.5936 (mpt) REVERT: A 1322 PHE cc_start: 0.5438 (OUTLIER) cc_final: 0.4504 (t80) REVERT: A 1414 MET cc_start: 0.7893 (OUTLIER) cc_final: 0.6961 (mtm) REVERT: A 1562 MET cc_start: 0.7173 (ptp) cc_final: 0.6822 (mtm) outliers start: 56 outliers final: 31 residues processed: 220 average time/residue: 0.2621 time to fit residues: 82.3516 Evaluate side-chains 215 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 175 time to evaluate : 1.564 ------------------------------------------------------------------------------- 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 471 THR Chi-restraints excluded: chain A residue 479 ILE 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 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 982 SER Chi-restraints excluded: chain A residue 986 ARG Chi-restraints excluded: chain A residue 1022 LYS Chi-restraints excluded: chain A residue 1048 HIS Chi-restraints excluded: chain A residue 1083 LEU Chi-restraints excluded: chain A residue 1089 CYS Chi-restraints excluded: chain A residue 1134 VAL Chi-restraints excluded: chain A residue 1135 ASN 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 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 114 optimal weight: 5.9990 chunk 25 optimal weight: 0.1980 chunk 74 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 127 optimal weight: 0.7980 chunk 106 optimal weight: 3.9990 chunk 59 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 123 optimal weight: 2.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.1642 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= 0.279 Angle : 0.558 7.757 16615 Z= 0.286 Chirality : 0.040 0.204 1897 Planarity : 0.003 0.036 1890 Dihedral : 16.634 178.178 2259 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 5.01 % Allowed : 23.08 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.23), residues: 1294 helix: 1.24 (0.19), residues: 700 sheet: -1.25 (0.49), residues: 100 loop : -1.12 (0.27), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 473 HIS 0.004 0.001 HIS A1148 PHE 0.020 0.002 PHE A1357 TYR 0.027 0.002 TYR A 353 ARG 0.007 0.000 ARG A 873 *********************** 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 232 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 174 time to evaluate : 1.338 Fit side-chains REVERT: A 755 LYS cc_start: 0.8330 (OUTLIER) cc_final: 0.7009 (mtmt) REVERT: A 782 GLN cc_start: 0.8902 (mt0) cc_final: 0.8506 (tt0) REVERT: A 874 GLU cc_start: 0.7267 (OUTLIER) cc_final: 0.6903 (mp0) REVERT: A 931 LYS cc_start: 0.8558 (OUTLIER) cc_final: 0.7948 (mttp) REVERT: A 986 ARG cc_start: 0.9188 (OUTLIER) cc_final: 0.7944 (mtp180) REVERT: A 1275 GLU cc_start: 0.7412 (tm-30) cc_final: 0.6939 (tm-30) REVERT: A 1276 LEU cc_start: 0.8477 (mt) cc_final: 0.8146 (mt) REVERT: A 1283 MET cc_start: 0.6726 (OUTLIER) cc_final: 0.6028 (mpt) REVERT: A 1322 PHE cc_start: 0.5417 (OUTLIER) cc_final: 0.4604 (t80) REVERT: A 1414 MET cc_start: 0.8026 (OUTLIER) cc_final: 0.7019 (mtm) REVERT: A 1562 MET cc_start: 0.7210 (ptp) cc_final: 0.6779 (mtm) outliers start: 58 outliers final: 41 residues processed: 217 average time/residue: 0.2536 time to fit residues: 79.0494 Evaluate side-chains 218 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 170 time to evaluate : 1.288 ------------------------------------------------------------------------------- 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 377 MET Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 454 PHE 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 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 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 977 SER Chi-restraints excluded: chain A residue 982 SER Chi-restraints excluded: chain A residue 986 ARG Chi-restraints excluded: chain A residue 1022 LYS Chi-restraints excluded: chain A residue 1032 SER Chi-restraints excluded: chain A residue 1048 HIS Chi-restraints excluded: chain A residue 1053 LYS Chi-restraints excluded: chain A residue 1083 LEU Chi-restraints excluded: chain A residue 1089 CYS Chi-restraints excluded: chain A residue 1134 VAL Chi-restraints excluded: chain A residue 1135 ASN 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 14 optimal weight: 0.9990 chunk 72 optimal weight: 0.9980 chunk 93 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 71 optimal weight: 0.9990 chunk 127 optimal weight: 0.8980 chunk 79 optimal weight: 0.5980 chunk 77 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 chunk 78 optimal weight: 0.0970 chunk 50 optimal weight: 0.6980 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1287 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.1723 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= 0.216 Angle : 0.532 8.456 16615 Z= 0.272 Chirality : 0.039 0.193 1897 Planarity : 0.003 0.035 1890 Dihedral : 16.550 176.403 2259 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 4.84 % Allowed : 23.60 % Favored : 71.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.23), residues: 1294 helix: 1.28 (0.19), residues: 708 sheet: -1.12 (0.50), residues: 98 loop : -1.27 (0.27), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 473 HIS 0.004 0.001 HIS A1148 PHE 0.021 0.002 PHE A1357 TYR 0.022 0.001 TYR A 353 ARG 0.007 0.000 ARG A 873 *********************** 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 237 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 181 time to evaluate : 1.213 Fit side-chains REVERT: A 462 TYR cc_start: 0.8014 (m-80) cc_final: 0.7665 (m-80) REVERT: A 744 GLU cc_start: 0.8283 (OUTLIER) cc_final: 0.7996 (tm-30) REVERT: A 755 LYS cc_start: 0.8356 (OUTLIER) cc_final: 0.7054 (mtmt) REVERT: A 782 GLN cc_start: 0.8886 (mt0) cc_final: 0.8472 (tt0) REVERT: A 874 GLU cc_start: 0.7138 (OUTLIER) cc_final: 0.6779 (mp0) REVERT: A 906 GLU cc_start: 0.8338 (mt-10) cc_final: 0.8134 (mt-10) REVERT: A 931 LYS cc_start: 0.8524 (OUTLIER) cc_final: 0.7994 (mttp) REVERT: A 986 ARG cc_start: 0.9149 (OUTLIER) cc_final: 0.7964 (mtp180) REVERT: A 1119 PHE cc_start: 0.8070 (t80) cc_final: 0.7748 (t80) REVERT: A 1276 LEU cc_start: 0.8454 (mt) cc_final: 0.8095 (mt) REVERT: A 1283 MET cc_start: 0.6686 (OUTLIER) cc_final: 0.5958 (mpt) REVERT: A 1322 PHE cc_start: 0.5463 (OUTLIER) cc_final: 0.4755 (t80) REVERT: A 1414 MET cc_start: 0.7990 (OUTLIER) cc_final: 0.7096 (mtm) REVERT: A 1562 MET cc_start: 0.7201 (ptp) cc_final: 0.6793 (mtm) outliers start: 56 outliers final: 38 residues processed: 221 average time/residue: 0.2619 time to fit residues: 83.1611 Evaluate side-chains 219 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 173 time to evaluate : 1.312 ------------------------------------------------------------------------------- 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 377 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 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 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 931 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 1048 HIS Chi-restraints excluded: chain A residue 1083 LEU Chi-restraints excluded: chain A residue 1089 CYS Chi-restraints excluded: chain A residue 1134 VAL Chi-restraints excluded: chain A residue 1135 ASN 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 75 optimal weight: 0.9990 chunk 38 optimal weight: 0.3980 chunk 24 optimal weight: 0.0770 chunk 80 optimal weight: 1.9990 chunk 86 optimal weight: 0.4980 chunk 62 optimal weight: 0.5980 chunk 11 optimal weight: 1.9990 chunk 100 optimal weight: 0.9980 chunk 115 optimal weight: 0.3980 chunk 121 optimal weight: 8.9990 chunk 111 optimal weight: 0.6980 overall best weight: 0.3938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1287 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.1891 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= 0.170 Angle : 0.515 10.674 16615 Z= 0.263 Chirality : 0.038 0.185 1897 Planarity : 0.003 0.039 1890 Dihedral : 16.454 174.235 2259 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 4.49 % Allowed : 24.46 % Favored : 71.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.23), residues: 1294 helix: 1.34 (0.19), residues: 711 sheet: -0.84 (0.52), residues: 100 loop : -1.26 (0.27), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 473 HIS 0.003 0.001 HIS A1148 PHE 0.021 0.001 PHE A1357 TYR 0.019 0.001 TYR A 353 ARG 0.007 0.000 ARG A 873 *********************** 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 236 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 184 time to evaluate : 1.309 Fit side-chains REVERT: A 462 TYR cc_start: 0.7971 (m-80) cc_final: 0.7745 (m-80) REVERT: A 744 GLU cc_start: 0.8271 (OUTLIER) cc_final: 0.7944 (tm-30) REVERT: A 755 LYS cc_start: 0.8308 (OUTLIER) cc_final: 0.6990 (mtmt) REVERT: A 782 GLN cc_start: 0.8846 (mt0) cc_final: 0.8434 (tt0) REVERT: A 874 GLU cc_start: 0.7410 (OUTLIER) cc_final: 0.6895 (pm20) REVERT: A 931 LYS cc_start: 0.8489 (OUTLIER) cc_final: 0.7979 (mttp) REVERT: A 986 ARG cc_start: 0.9107 (OUTLIER) cc_final: 0.7947 (mtp180) REVERT: A 1119 PHE cc_start: 0.8039 (t80) cc_final: 0.7728 (t80) REVERT: A 1276 LEU cc_start: 0.8406 (mt) cc_final: 0.8023 (mt) REVERT: A 1283 MET cc_start: 0.6661 (OUTLIER) cc_final: 0.5945 (mpt) REVERT: A 1322 PHE cc_start: 0.5216 (OUTLIER) cc_final: 0.4065 (t80) REVERT: A 1414 MET cc_start: 0.7865 (OUTLIER) cc_final: 0.7122 (mtm) REVERT: A 1562 MET cc_start: 0.7207 (ptp) cc_final: 0.6861 (ptp) outliers start: 52 outliers final: 37 residues processed: 220 average time/residue: 0.2658 time to fit residues: 84.1451 Evaluate side-chains 223 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 178 time to evaluate : 1.397 ------------------------------------------------------------------------------- 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 661 TYR 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 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 977 SER Chi-restraints excluded: chain A residue 982 SER Chi-restraints excluded: chain A residue 986 ARG Chi-restraints excluded: chain A residue 1022 LYS Chi-restraints excluded: chain A residue 1032 SER Chi-restraints excluded: chain A residue 1048 HIS Chi-restraints excluded: chain A residue 1083 LEU Chi-restraints excluded: chain A residue 1089 CYS Chi-restraints excluded: chain A residue 1134 VAL Chi-restraints excluded: chain A residue 1135 ASN 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 1466 ASP Chi-restraints excluded: chain A residue 1514 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 3.9990 chunk 121 optimal weight: 7.9990 chunk 71 optimal weight: 0.0570 chunk 51 optimal weight: 0.6980 chunk 93 optimal weight: 2.9990 chunk 36 optimal weight: 0.8980 chunk 107 optimal weight: 2.9990 chunk 112 optimal weight: 2.9990 chunk 77 optimal weight: 0.6980 chunk 125 optimal weight: 7.9990 chunk 76 optimal weight: 0.9980 overall best weight: 0.6698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1223 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.1862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12103 Z= 0.224 Angle : 0.548 11.263 16615 Z= 0.277 Chirality : 0.039 0.186 1897 Planarity : 0.003 0.034 1890 Dihedral : 16.448 175.298 2259 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 4.49 % Allowed : 24.55 % Favored : 70.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.23), residues: 1294 helix: 1.33 (0.19), residues: 707 sheet: -0.91 (0.52), residues: 99 loop : -1.22 (0.27), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A1131 HIS 0.003 0.001 HIS A1148 PHE 0.022 0.002 PHE A1347 TYR 0.018 0.001 TYR A 353 ARG 0.008 0.000 ARG A 873 *********************** 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 233 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 181 time to evaluate : 1.228 Fit side-chains REVERT: A 462 TYR cc_start: 0.7895 (m-80) cc_final: 0.7653 (m-80) REVERT: A 744 GLU cc_start: 0.8182 (OUTLIER) cc_final: 0.7869 (tm-30) REVERT: A 755 LYS cc_start: 0.8348 (OUTLIER) cc_final: 0.7033 (mtmt) REVERT: A 782 GLN cc_start: 0.8881 (mt0) cc_final: 0.8465 (tt0) REVERT: A 874 GLU cc_start: 0.7404 (OUTLIER) cc_final: 0.6872 (pm20) REVERT: A 931 LYS cc_start: 0.8481 (OUTLIER) cc_final: 0.7829 (mttp) REVERT: A 986 ARG cc_start: 0.9132 (OUTLIER) cc_final: 0.7935 (mtp180) REVERT: A 1119 PHE cc_start: 0.8079 (t80) cc_final: 0.7732 (t80) REVERT: A 1276 LEU cc_start: 0.8400 (mt) cc_final: 0.8051 (mt) REVERT: A 1283 MET cc_start: 0.6702 (OUTLIER) cc_final: 0.5980 (mpt) REVERT: A 1322 PHE cc_start: 0.5190 (OUTLIER) cc_final: 0.4099 (t80) REVERT: A 1562 MET cc_start: 0.7233 (ptp) cc_final: 0.6891 (ptp) outliers start: 52 outliers final: 41 residues processed: 217 average time/residue: 0.2519 time to fit residues: 78.8311 Evaluate side-chains 224 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 176 time to evaluate : 1.365 ------------------------------------------------------------------------------- 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 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 470 THR Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 630 ILE 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 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 977 SER Chi-restraints excluded: chain A residue 982 SER Chi-restraints excluded: chain A residue 986 ARG Chi-restraints excluded: chain A residue 1022 LYS Chi-restraints excluded: chain A residue 1032 SER Chi-restraints excluded: chain A residue 1048 HIS Chi-restraints excluded: chain A residue 1083 LEU Chi-restraints excluded: chain A residue 1089 CYS Chi-restraints excluded: chain A residue 1134 VAL Chi-restraints excluded: chain A residue 1135 ASN 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 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 59 optimal weight: 0.7980 chunk 87 optimal weight: 0.0970 chunk 131 optimal weight: 3.9990 chunk 121 optimal weight: 10.0000 chunk 104 optimal weight: 5.9990 chunk 10 optimal weight: 0.6980 chunk 80 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 chunk 83 optimal weight: 0.6980 chunk 111 optimal weight: 0.9980 chunk 32 optimal weight: 0.5980 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.1935 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= 0.205 Angle : 0.549 13.902 16615 Z= 0.275 Chirality : 0.039 0.183 1897 Planarity : 0.004 0.039 1890 Dihedral : 16.387 174.540 2256 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 4.06 % Allowed : 25.15 % Favored : 70.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.23), residues: 1294 helix: 1.32 (0.19), residues: 707 sheet: -0.91 (0.52), residues: 100 loop : -1.20 (0.27), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A1131 HIS 0.004 0.001 HIS A1148 PHE 0.023 0.002 PHE A1357 TYR 0.018 0.001 TYR A 353 ARG 0.009 0.000 ARG A 880 ********************** 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 224 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 177 time to evaluate : 1.221 Fit side-chains REVERT: A 744 GLU cc_start: 0.8154 (OUTLIER) cc_final: 0.7806 (tm-30) REVERT: A 755 LYS cc_start: 0.8339 (OUTLIER) cc_final: 0.7019 (mtmt) REVERT: A 782 GLN cc_start: 0.8896 (mt0) cc_final: 0.8538 (mt0) REVERT: A 874 GLU cc_start: 0.7423 (OUTLIER) cc_final: 0.6922 (pm20) REVERT: A 931 LYS cc_start: 0.8464 (OUTLIER) cc_final: 0.7860 (mttp) REVERT: A 986 ARG cc_start: 0.9119 (OUTLIER) cc_final: 0.7965 (mtp180) REVERT: A 1119 PHE cc_start: 0.8086 (t80) cc_final: 0.7734 (t80) REVERT: A 1276 LEU cc_start: 0.8406 (mt) cc_final: 0.8041 (mt) REVERT: A 1283 MET cc_start: 0.6693 (OUTLIER) cc_final: 0.5956 (mpt) REVERT: A 1322 PHE cc_start: 0.5043 (OUTLIER) cc_final: 0.3811 (t80) REVERT: A 1562 MET cc_start: 0.7175 (ptp) cc_final: 0.6813 (ptp) outliers start: 47 outliers final: 39 residues processed: 211 average time/residue: 0.2787 time to fit residues: 83.7994 Evaluate side-chains 221 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 175 time to evaluate : 1.345 ------------------------------------------------------------------------------- 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 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 470 THR Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 630 ILE 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 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 977 SER Chi-restraints excluded: chain A residue 982 SER Chi-restraints excluded: chain A residue 986 ARG Chi-restraints excluded: chain A residue 1022 LYS Chi-restraints excluded: chain A residue 1032 SER Chi-restraints excluded: chain A residue 1048 HIS Chi-restraints excluded: chain A residue 1083 LEU Chi-restraints excluded: chain A residue 1134 VAL Chi-restraints excluded: chain A residue 1135 ASN 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 1394 THR 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 96 optimal weight: 1.9990 chunk 15 optimal weight: 6.9990 chunk 29 optimal weight: 2.9990 chunk 104 optimal weight: 5.9990 chunk 43 optimal weight: 0.7980 chunk 107 optimal weight: 3.9990 chunk 13 optimal weight: 0.0870 chunk 19 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 5 optimal weight: 5.9990 chunk 75 optimal weight: 0.7980 overall best weight: 1.1362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3961 r_free = 0.3961 target = 0.178748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.146663 restraints weight = 12573.018| |-----------------------------------------------------------------------------| r_work (start): 0.3646 rms_B_bonded: 1.31 r_work: 0.3503 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3370 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.1874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 12103 Z= 0.319 Angle : 0.603 13.146 16615 Z= 0.305 Chirality : 0.041 0.198 1897 Planarity : 0.004 0.036 1890 Dihedral : 16.472 177.508 2256 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 3.98 % Allowed : 25.32 % Favored : 70.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.23), residues: 1294 helix: 1.18 (0.19), residues: 701 sheet: -1.00 (0.51), residues: 96 loop : -1.19 (0.27), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A1131 HIS 0.004 0.001 HIS A1148 PHE 0.023 0.002 PHE A1357 TYR 0.020 0.002 TYR A 353 ARG 0.008 0.000 ARG A 873 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2744.60 seconds wall clock time: 51 minutes 5.75 seconds (3065.75 seconds total)