Starting phenix.real_space_refine on Fri Oct 23 05:22:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/23py_69161/10_2026/23py_69161.cif Found real_map, /net/cci-nas-00/data/ceres_data/23py_69161/10_2026/23py_69161.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/23py_69161/10_2026/23py_69161.cif" } default_model = "/net/cci-nas-00/data/ceres_data/23py_69161/10_2026/23py_69161.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/23py_69161/10_2026/23py_69161.map" default_real_map = "/net/cci-nas-00/data/ceres_data/23py_69161/10_2026/23py_69161.map" } resolution = 3.0 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= 0.003 sd= 0.037 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: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 37 5.16 5 C 5342 2.51 5 N 1435 2.21 5 O 1659 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8474 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 8473 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1079, 8473 Classifications: {'peptide': 1079} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 5, 'PTRANS': 50, 'TRANS': 1023} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.64, per 1000 atoms: 0.19 Number of scatterers: 8474 At special positions: 0 Unit cell: (91.797, 91.797, 116.607, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 1 29.99 S 37 16.00 O 1659 8.00 N 1435 7.00 C 5342 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 983 " - pdb=" SG CYS A 995 " distance=2.03 Simple disulfide: pdb=" SG CYS A1435 " - pdb=" SG CYS A1449 " distance=2.03 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: 0.71 Conformation dependent library (CDL) restraints added in 289.8 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1601 " pdb="ZN ZN A1601 " - pdb=" NE2 HIS A1307 " pdb="ZN ZN A1601 " - pdb=" NE2 HIS A1303 " 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1990 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 13 sheets defined 29.5% alpha, 14.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'A' and resid 443 through 446 Processing helix chain 'A' and resid 447 through 457 Processing helix chain 'A' and resid 540 through 544 Processing helix chain 'A' and resid 568 through 575 removed outlier: 3.666A pdb=" N ILE A 572 " --> pdb=" O HIS A 568 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LEU A 573 " --> pdb=" O TYR A 569 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ARG A 574 " --> pdb=" O ASN A 570 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 612 removed outlier: 3.657A pdb=" N GLU A 605 " --> pdb=" O LYS A 601 " (cutoff:3.500A) Processing helix chain 'A' and resid 706 through 719 Processing helix chain 'A' and resid 738 through 749 removed outlier: 3.561A pdb=" N ALA A 748 " --> pdb=" O LEU A 744 " (cutoff:3.500A) Processing helix chain 'A' and resid 805 through 809 Processing helix chain 'A' and resid 811 through 815 removed outlier: 3.955A pdb=" N LYS A 815 " --> pdb=" O PRO A 812 " (cutoff:3.500A) Processing helix chain 'A' and resid 841 through 843 No H-bonds generated for 'chain 'A' and resid 841 through 843' Processing helix chain 'A' and resid 845 through 860 removed outlier: 3.568A pdb=" N LEU A 849 " --> pdb=" O THR A 845 " (cutoff:3.500A) Processing helix chain 'A' and resid 905 through 909 Processing helix chain 'A' and resid 917 through 932 Processing helix chain 'A' and resid 941 through 957 removed outlier: 3.523A pdb=" N ARG A 947 " --> pdb=" O VAL A 943 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL A 954 " --> pdb=" O GLN A 950 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N TRP A 955 " --> pdb=" O ASN A 951 " (cutoff:3.500A) Processing helix chain 'A' and resid 973 through 985 Processing helix chain 'A' and resid 996 through 1006 Processing helix chain 'A' and resid 1031 through 1041 Processing helix chain 'A' and resid 1119 through 1124 removed outlier: 3.947A pdb=" N VAL A1124 " --> pdb=" O GLU A1120 " (cutoff:3.500A) Processing helix chain 'A' and resid 1208 through 1213 removed outlier: 3.678A pdb=" N ALA A1213 " --> pdb=" O ASN A1210 " (cutoff:3.500A) Processing helix chain 'A' and resid 1218 through 1238 removed outlier: 3.636A pdb=" N GLN A1222 " --> pdb=" O GLY A1218 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N TYR A1238 " --> pdb=" O MET A1234 " (cutoff:3.500A) Processing helix chain 'A' and resid 1298 through 1310 removed outlier: 3.764A pdb=" N TRP A1302 " --> pdb=" O ASP A1298 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N HIS A1307 " --> pdb=" O HIS A1303 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ASN A1308 " --> pdb=" O GLU A1304 " (cutoff:3.500A) Processing helix chain 'A' and resid 1324 through 1336 removed outlier: 3.869A pdb=" N GLN A1332 " --> pdb=" O ALA A1328 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ASP A1333 " --> pdb=" O LEU A1329 " (cutoff:3.500A) Processing helix chain 'A' and resid 1341 through 1347 removed outlier: 4.415A pdb=" N ASP A1345 " --> pdb=" O ARG A1341 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N THR A1347 " --> pdb=" O ALA A1343 " (cutoff:3.500A) Processing helix chain 'A' and resid 1348 through 1356 removed outlier: 3.734A pdb=" N GLU A1354 " --> pdb=" O PRO A1350 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLU A1355 " --> pdb=" O GLU A1351 " (cutoff:3.500A) Processing helix chain 'A' and resid 1365 through 1384 removed outlier: 3.508A pdb=" N LEU A1370 " --> pdb=" O ALA A1366 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N LEU A1371 " --> pdb=" O GLY A1367 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N MET A1372 " --> pdb=" O ASP A1368 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N TYR A1373 " --> pdb=" O ARG A1369 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LYS A1377 " --> pdb=" O TYR A1373 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N LYS A1382 " --> pdb=" O GLU A1378 " (cutoff:3.500A) Processing helix chain 'A' and resid 1408 through 1421 removed outlier: 4.090A pdb=" N PHE A1412 " --> pdb=" O GLY A1408 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLY A1421 " --> pdb=" O ARG A1417 " (cutoff:3.500A) Processing helix chain 'A' and resid 1442 through 1455 removed outlier: 3.676A pdb=" N LEU A1446 " --> pdb=" O ALA A1442 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N MET A1447 " --> pdb=" O ALA A1443 " (cutoff:3.500A) Processing helix chain 'A' and resid 1458 through 1466 removed outlier: 3.652A pdb=" N LYS A1464 " --> pdb=" O GLU A1460 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N TRP A1465 " --> pdb=" O PHE A1461 " (cutoff:3.500A) Processing helix chain 'A' and resid 1487 through 1496 removed outlier: 3.614A pdb=" N TYR A1491 " --> pdb=" O SER A1487 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASN A1492 " --> pdb=" O GLN A1488 " (cutoff:3.500A) Processing helix chain 'A' and resid 1505 through 1509 removed outlier: 3.538A pdb=" N ILE A1509 " --> pdb=" O PRO A1506 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 468 through 471 Processing sheet with id=AA2, first strand: chain 'A' and resid 491 through 492 Processing sheet with id=AA3, first strand: chain 'A' and resid 498 through 504 removed outlier: 7.574A pdb=" N ILE A 551 " --> pdb=" O PRO A 499 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N LEU A 501 " --> pdb=" O PRO A 549 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N ALA A 503 " --> pdb=" O ASN A 547 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N LYS A 560 " --> pdb=" O VAL A 723 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N ILE A 725 " --> pdb=" O LYS A 560 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N MET A 562 " --> pdb=" O ILE A 725 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N LEU A 676 " --> pdb=" O LEU A 724 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N MET A 726 " --> pdb=" O LEU A 676 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N LEU A 678 " --> pdb=" O MET A 726 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N THR A 625 " --> pdb=" O LEU A 675 " (cutoff:3.500A) removed outlier: 8.286A pdb=" N ILE A 677 " --> pdb=" O THR A 625 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N GLY A 627 " --> pdb=" O ILE A 677 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N SER A 658 " --> pdb=" O MET A 624 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 632 through 635 Processing sheet with id=AA5, first strand: chain 'A' and resid 681 through 683 removed outlier: 4.257A pdb=" N GLU A 682 " --> pdb=" O ASP A 699 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 838 through 839 removed outlier: 3.510A pdb=" N ILE A 778 " --> pdb=" O ARG A 881 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ARG A 881 " --> pdb=" O ILE A 778 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 782 through 783 Processing sheet with id=AA8, first strand: chain 'A' and resid 793 through 796 removed outlier: 3.651A pdb=" N GLU A 801 " --> pdb=" O ASP A 796 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 822 through 827 Processing sheet with id=AB1, first strand: chain 'A' and resid 1063 through 1070 removed outlier: 4.716A pdb=" N GLN A1063 " --> pdb=" O GLY A1172 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N GLN A1084 " --> pdb=" O GLY A1158 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N GLY A1158 " --> pdb=" O GLN A1084 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N THR A1086 " --> pdb=" O ILE A1156 " (cutoff:3.500A) removed outlier: 8.676A pdb=" N ILE A1156 " --> pdb=" O THR A1086 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N LEU A1088 " --> pdb=" O ILE A1154 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLY A1152 " --> pdb=" O ALA A1090 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 1063 through 1070 removed outlier: 4.716A pdb=" N GLN A1063 " --> pdb=" O GLY A1172 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1183 through 1186 removed outlier: 6.631A pdb=" N PHE A1178 " --> pdb=" O LYS A1185 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N TYR A1179 " --> pdb=" O GLU A1198 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N VAL A1203 " --> pdb=" O PHE A1262 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N ASN A1264 " --> pdb=" O VAL A1203 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N THR A1205 " --> pdb=" O ASN A1264 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N ARG A1261 " --> pdb=" O VAL A1279 " (cutoff:3.500A) removed outlier: 8.067A pdb=" N ASN A1281 " --> pdb=" O ARG A1261 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N THR A1263 " --> pdb=" O ASN A1281 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1471 through 1472 246 hydrogen bonds defined for protein. 675 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.51 Time building geometry restraints manager: 0.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2788 1.34 - 1.46: 1449 1.46 - 1.57: 4381 1.57 - 1.69: 0 1.69 - 1.81: 66 Bond restraints: 8684 Sorted by residual: bond pdb=" CA SER A 751 " pdb=" CB SER A 751 " ideal model delta sigma weight residual 1.531 1.475 0.056 1.83e-02 2.99e+03 9.35e+00 bond pdb=" N LEU A 754 " pdb=" CA LEU A 754 " ideal model delta sigma weight residual 1.457 1.485 -0.028 1.29e-02 6.01e+03 4.58e+00 bond pdb=" CA LEU A 733 " pdb=" C LEU A 733 " ideal model delta sigma weight residual 1.531 1.507 0.024 1.12e-02 7.97e+03 4.46e+00 bond pdb=" CA ALA A 753 " pdb=" CB ALA A 753 " ideal model delta sigma weight residual 1.530 1.501 0.029 1.63e-02 3.76e+03 3.17e+00 bond pdb=" C TYR A1390 " pdb=" O TYR A1390 " ideal model delta sigma weight residual 1.242 1.221 0.021 1.16e-02 7.43e+03 3.17e+00 ... (remaining 8679 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.95: 11533 1.95 - 3.90: 232 3.90 - 5.85: 24 5.85 - 7.80: 4 7.80 - 9.75: 5 Bond angle restraints: 11798 Sorted by residual: angle pdb=" N ASN A 732 " pdb=" CA ASN A 732 " pdb=" C ASN A 732 " ideal model delta sigma weight residual 108.73 100.85 7.88 1.63e+00 3.76e-01 2.34e+01 angle pdb=" N ASN A 728 " pdb=" CA ASN A 728 " pdb=" C ASN A 728 " ideal model delta sigma weight residual 108.53 98.80 9.73 2.07e+00 2.33e-01 2.21e+01 angle pdb=" CA ASN A 755 " pdb=" C ASN A 755 " pdb=" O ASN A 755 " ideal model delta sigma weight residual 122.36 117.16 5.20 1.21e+00 6.83e-01 1.84e+01 angle pdb=" N SER A 739 " pdb=" CA SER A 739 " pdb=" C SER A 739 " ideal model delta sigma weight residual 111.28 115.79 -4.51 1.09e+00 8.42e-01 1.71e+01 angle pdb=" N MET A 752 " pdb=" CA MET A 752 " pdb=" C MET A 752 " ideal model delta sigma weight residual 111.81 105.55 6.26 1.54e+00 4.22e-01 1.65e+01 ... (remaining 11793 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.73: 4717 17.73 - 35.46: 381 35.46 - 53.19: 54 53.19 - 70.92: 7 70.92 - 88.65: 4 Dihedral angle restraints: 5163 sinusoidal: 2042 harmonic: 3121 Sorted by residual: dihedral pdb=" CA PRO A1467 " pdb=" C PRO A1467 " pdb=" N GLY A1468 " pdb=" CA GLY A1468 " ideal model delta harmonic sigma weight residual 180.00 -149.79 -30.21 0 5.00e+00 4.00e-02 3.65e+01 dihedral pdb=" CA TRP A 779 " pdb=" C TRP A 779 " pdb=" N VAL A 780 " pdb=" CA VAL A 780 " ideal model delta harmonic sigma weight residual -180.00 -157.43 -22.57 0 5.00e+00 4.00e-02 2.04e+01 dihedral pdb=" CA ARG A 769 " pdb=" C ARG A 769 " pdb=" N VAL A 770 " pdb=" CA VAL A 770 " ideal model delta harmonic sigma weight residual -180.00 -157.73 -22.27 0 5.00e+00 4.00e-02 1.98e+01 ... (remaining 5160 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 1141 0.078 - 0.156: 98 0.156 - 0.235: 6 0.235 - 0.313: 1 0.313 - 0.391: 1 Chirality restraints: 1247 Sorted by residual: chirality pdb=" CA MET A 730 " pdb=" N MET A 730 " pdb=" C MET A 730 " pdb=" CB MET A 730 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.82e+00 chirality pdb=" CA TRP A1389 " pdb=" N TRP A1389 " pdb=" C TRP A1389 " pdb=" CB TRP A1389 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.38e+00 chirality pdb=" CA ASN A 728 " pdb=" N ASN A 728 " pdb=" C ASN A 728 " pdb=" CB ASN A 728 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 9.89e-01 ... (remaining 1244 not shown) Planarity restraints: 1557 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET A 673 " -0.053 5.00e-02 4.00e+02 8.05e-02 1.04e+01 pdb=" N PRO A 674 " 0.139 5.00e-02 4.00e+02 pdb=" CA PRO A 674 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO A 674 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP A1385 " -0.014 2.00e-02 2.50e+03 2.96e-02 8.74e+00 pdb=" C ASP A1385 " 0.051 2.00e-02 2.50e+03 pdb=" O ASP A1385 " -0.020 2.00e-02 2.50e+03 pdb=" N ILE A1386 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A1255 " -0.033 5.00e-02 4.00e+02 4.94e-02 3.90e+00 pdb=" N PRO A1256 " 0.085 5.00e-02 4.00e+02 pdb=" CA PRO A1256 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A1256 " -0.027 5.00e-02 4.00e+02 ... (remaining 1554 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 163 2.67 - 3.22: 8271 3.22 - 3.78: 13140 3.78 - 4.34: 18619 4.34 - 4.90: 30577 Nonbonded interactions: 70770 Sorted by model distance: nonbonded pdb=" O GLU A 529 " pdb=" OG SER A 532 " model vdw 2.108 3.040 nonbonded pdb=" OG1 THR A 845 " pdb=" OD1 ASP A 847 " model vdw 2.183 3.040 nonbonded pdb=" O LEU A 928 " pdb=" OG1 THR A 932 " model vdw 2.205 3.040 nonbonded pdb=" OG SER A1041 " pdb=" OH TYR A1150 " model vdw 2.225 3.040 nonbonded pdb=" OE2 GLU A 927 " pdb=" NH1 ARG A 931 " model vdw 2.252 3.120 ... (remaining 70765 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 0.490 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: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.950 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 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 : 0.004 0.058 8688 Z= 0.196 Angle : 0.670 9.752 11802 Z= 0.377 Chirality : 0.046 0.391 1247 Planarity : 0.005 0.081 1557 Dihedral : 12.879 88.654 3167 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 14.11 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.74 % Favored : 95.08 % Rotamer: Outliers : 0.88 % Allowed : 0.66 % Favored : 98.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.69 (0.25), residues: 1077 helix: 0.25 (0.33), residues: 264 sheet: -0.08 (0.42), residues: 147 loop : -0.83 (0.23), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 769 TYR 0.017 0.001 TYR A1216 PHE 0.014 0.002 PHE A1230 TRP 0.013 0.001 TRP A 510 HIS 0.007 0.001 HIS A1307 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.20 ( 8684) covalent geometry : angle 0.67040 / 0.38 (11798) SS BOND : bond 0.00155 / 0.08 ( 2) SS BOND : angle 0.50147 / 0.26 ( 4) hydrogen bonds : bond 0.23204 / 14.82 ( 239) hydrogen bonds : angle 7.72420 / 5.62 ( 675) metal coordination : bond 0.00199 / 0.10 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 282 time to evaluate : 0.288 Fit side-chains revert: symmetry clash REVERT: A 474 ASP cc_start: 0.7159 (m-30) cc_final: 0.6925 (m-30) REVERT: A 571 SER cc_start: 0.8195 (t) cc_final: 0.7862 (m) REVERT: A 613 ASP cc_start: 0.7303 (m-30) cc_final: 0.7054 (m-30) REVERT: A 625 THR cc_start: 0.8679 (t) cc_final: 0.7946 (t) REVERT: A 709 ASP cc_start: 0.6674 (m-30) cc_final: 0.6434 (m-30) REVERT: A 712 ASP cc_start: 0.6666 (m-30) cc_final: 0.6363 (m-30) REVERT: A 718 ASN cc_start: 0.7925 (m110) cc_final: 0.7657 (m110) REVERT: A 728 ASN cc_start: 0.7430 (t0) cc_final: 0.7210 (t0) REVERT: A 741 PHE cc_start: 0.7988 (t80) cc_final: 0.7766 (t80) REVERT: A 814 ASP cc_start: 0.7016 (p0) cc_final: 0.6702 (p0) REVERT: A 819 GLU cc_start: 0.7320 (pt0) cc_final: 0.6989 (pp20) REVERT: A 871 TYR cc_start: 0.7532 (t80) cc_final: 0.7252 (t80) REVERT: A 1001 LYS cc_start: 0.7999 (tppp) cc_final: 0.7769 (tppp) REVERT: A 1074 ASN cc_start: 0.7166 (t0) cc_final: 0.6911 (t0) REVERT: A 1181 ASP cc_start: 0.7027 (m-30) cc_final: 0.6789 (m-30) REVERT: A 1338 LYS cc_start: 0.7703 (ttmm) cc_final: 0.7452 (tttp) REVERT: A 1351 GLU cc_start: 0.6969 (mp0) cc_final: 0.6671 (mp0) REVERT: A 1403 ARG cc_start: 0.8043 (ttp80) cc_final: 0.7194 (ttt180) REVERT: A 1410 ASN cc_start: 0.7467 (m110) cc_final: 0.7096 (m110) outliers start: 8 outliers final: 3 residues processed: 290 average time/residue: 0.4603 time to fit residues: 143.5041 Evaluate side-chains 263 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 260 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 733 LEU Chi-restraints excluded: chain A residue 754 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: [49, 97, 53, 5, 33, 65, 62, 51, 100, 106, 38] chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.0270 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 0.0570 chunk 100 optimal weight: 0.0980 chunk 106 optimal weight: 3.9990 chunk 38 optimal weight: 0.7980 overall best weight: 0.3958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 477 ASN A 555 GLN A 638 HIS A 732 ASN A 868 ASN A 925 GLN A1006 ASN ** A1046 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1084 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1303 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1357 ASN A1358 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.124298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.113154 restraints weight = 12550.570| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 2.14 r_work: 0.3362 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3209 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.1638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8688 Z= 0.129 Angle : 0.594 7.817 11802 Z= 0.309 Chirality : 0.043 0.168 1247 Planarity : 0.005 0.046 1557 Dihedral : 4.834 35.543 1173 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.09 % Favored : 95.73 % Rotamer: Outliers : 1.87 % Allowed : 13.42 % Favored : 84.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.59 (0.24), residues: 1077 helix: 0.33 (0.32), residues: 265 sheet: 0.01 (0.42), residues: 155 loop : -0.78 (0.23), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 834 TYR 0.015 0.001 TYR A 897 PHE 0.021 0.002 PHE A 498 TRP 0.010 0.001 TRP A 510 HIS 0.010 0.001 HIS A1307 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 ( 8684) covalent geometry : angle 0.59383 / 0.31 (11798) SS BOND : bond 0.00049 / 0.03 ( 2) SS BOND : angle 0.36158 / 0.20 ( 4) hydrogen bonds : bond 0.04515 / 2.88 ( 239) hydrogen bonds : angle 5.17655 / 3.64 ( 675) metal coordination : bond 0.00090 / 0.05 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 270 time to evaluate : 0.323 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 474 ASP cc_start: 0.7844 (m-30) cc_final: 0.7605 (m-30) REVERT: A 533 LEU cc_start: 0.8422 (mt) cc_final: 0.8144 (mp) REVERT: A 571 SER cc_start: 0.8253 (t) cc_final: 0.8052 (m) REVERT: A 613 ASP cc_start: 0.8022 (m-30) cc_final: 0.7714 (m-30) REVERT: A 709 ASP cc_start: 0.7514 (m-30) cc_final: 0.7204 (m-30) REVERT: A 712 ASP cc_start: 0.7495 (m-30) cc_final: 0.7197 (m-30) REVERT: A 718 ASN cc_start: 0.8298 (m110) cc_final: 0.7661 (m110) REVERT: A 728 ASN cc_start: 0.7360 (t0) cc_final: 0.6955 (t0) REVERT: A 732 ASN cc_start: 0.7904 (OUTLIER) cc_final: 0.7678 (p0) REVERT: A 735 GLU cc_start: 0.7731 (pm20) cc_final: 0.6992 (tp30) REVERT: A 814 ASP cc_start: 0.7391 (p0) cc_final: 0.7177 (p0) REVERT: A 819 GLU cc_start: 0.8030 (pt0) cc_final: 0.7502 (pp20) REVERT: A 880 TYR cc_start: 0.7787 (t80) cc_final: 0.7387 (t80) REVERT: A 1001 LYS cc_start: 0.8157 (tppp) cc_final: 0.7868 (tppp) REVERT: A 1074 ASN cc_start: 0.7735 (t0) cc_final: 0.7431 (t0) REVERT: A 1209 LYS cc_start: 0.8272 (mmmm) cc_final: 0.7914 (mmtm) REVERT: A 1228 ASP cc_start: 0.7287 (t0) cc_final: 0.6886 (m-30) REVERT: A 1261 ARG cc_start: 0.8224 (ttm-80) cc_final: 0.7876 (mtt-85) REVERT: A 1301 ILE cc_start: 0.8472 (OUTLIER) cc_final: 0.8230 (mp) REVERT: A 1338 LYS cc_start: 0.7968 (ttmm) cc_final: 0.7632 (ttmt) REVERT: A 1351 GLU cc_start: 0.7636 (mp0) cc_final: 0.7321 (mp0) REVERT: A 1355 GLU cc_start: 0.8048 (OUTLIER) cc_final: 0.7192 (tp30) REVERT: A 1381 GLU cc_start: 0.7504 (pt0) cc_final: 0.7288 (pt0) REVERT: A 1403 ARG cc_start: 0.8272 (ttp80) cc_final: 0.7680 (ttt180) REVERT: A 1422 ASP cc_start: 0.7119 (t0) cc_final: 0.6510 (m-30) REVERT: A 1434 TYR cc_start: 0.7020 (m-10) cc_final: 0.6350 (m-10) REVERT: A 1464 LYS cc_start: 0.8772 (mttt) cc_final: 0.8486 (mttm) outliers start: 17 outliers final: 2 residues processed: 276 average time/residue: 0.4684 time to fit residues: 138.9033 Evaluate side-chains 260 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 255 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 732 ASN Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 1301 ILE Chi-restraints excluded: chain A residue 1355 GLU Chi-restraints excluded: chain A residue 1486 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: [80, 2, 101, 97, 102, 82, 54, 18, 40, 9, 16] chunk 80 optimal weight: 4.9990 chunk 2 optimal weight: 0.2980 chunk 101 optimal weight: 0.6980 chunk 97 optimal weight: 2.9990 chunk 102 optimal weight: 0.5980 chunk 82 optimal weight: 3.9990 chunk 54 optimal weight: 0.6980 chunk 18 optimal weight: 3.9990 chunk 40 optimal weight: 3.9990 chunk 9 optimal weight: 5.9990 chunk 16 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 477 ASN ** A 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 638 HIS A 732 ASN A 772 GLN ** A1046 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1084 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1210 ASN ** A1303 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1357 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.124226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.113278 restraints weight = 12625.640| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 2.08 r_work: 0.3382 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3233 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.1962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8688 Z= 0.132 Angle : 0.578 7.733 11802 Z= 0.297 Chirality : 0.042 0.171 1247 Planarity : 0.004 0.040 1557 Dihedral : 4.667 30.347 1170 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.36 % Favored : 95.45 % Rotamer: Outliers : 2.64 % Allowed : 16.94 % Favored : 80.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.51 (0.24), residues: 1077 helix: 0.47 (0.32), residues: 265 sheet: 0.07 (0.42), residues: 155 loop : -0.77 (0.23), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 834 TYR 0.016 0.001 TYR A 716 PHE 0.024 0.002 PHE A 741 TRP 0.011 0.001 TRP A1089 HIS 0.009 0.001 HIS A1307 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.13 ( 8684) covalent geometry : angle 0.57801 / 0.30 (11798) SS BOND : bond 0.00142 / 0.07 ( 2) SS BOND : angle 0.34736 / 0.17 ( 4) hydrogen bonds : bond 0.03937 / 2.53 ( 239) hydrogen bonds : angle 4.74846 / 3.32 ( 675) metal coordination : bond 0.00115 / 0.06 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 272 time to evaluate : 0.378 Fit side-chains revert: symmetry clash REVERT: A 533 LEU cc_start: 0.8399 (mt) cc_final: 0.8114 (mp) REVERT: A 613 ASP cc_start: 0.8005 (m-30) cc_final: 0.7681 (m-30) REVERT: A 637 ARG cc_start: 0.8404 (mmm-85) cc_final: 0.8149 (mmm-85) REVERT: A 704 LYS cc_start: 0.8723 (OUTLIER) cc_final: 0.8459 (ptmt) REVERT: A 709 ASP cc_start: 0.7513 (m-30) cc_final: 0.7195 (m-30) REVERT: A 712 ASP cc_start: 0.7560 (m-30) cc_final: 0.7240 (m-30) REVERT: A 718 ASN cc_start: 0.8244 (m110) cc_final: 0.7801 (m110) REVERT: A 728 ASN cc_start: 0.7426 (t0) cc_final: 0.7065 (t0) REVERT: A 735 GLU cc_start: 0.7657 (pm20) cc_final: 0.7375 (tt0) REVERT: A 759 VAL cc_start: 0.8094 (m) cc_final: 0.7827 (p) REVERT: A 766 TYR cc_start: 0.7892 (OUTLIER) cc_final: 0.7246 (m-10) REVERT: A 814 ASP cc_start: 0.7437 (p0) cc_final: 0.7216 (p0) REVERT: A 880 TYR cc_start: 0.7755 (t80) cc_final: 0.7499 (t80) REVERT: A 964 TYR cc_start: 0.8048 (t80) cc_final: 0.7330 (t80) REVERT: A 1001 LYS cc_start: 0.8150 (tppp) cc_final: 0.7862 (tppp) REVERT: A 1010 TYR cc_start: 0.7668 (m-80) cc_final: 0.7025 (m-80) REVERT: A 1067 GLU cc_start: 0.7256 (pm20) cc_final: 0.7012 (pm20) REVERT: A 1074 ASN cc_start: 0.7779 (t0) cc_final: 0.7461 (t0) REVERT: A 1209 LYS cc_start: 0.8260 (mmmm) cc_final: 0.7920 (mmtm) REVERT: A 1228 ASP cc_start: 0.7236 (t0) cc_final: 0.6826 (m-30) REVERT: A 1333 ASP cc_start: 0.7705 (m-30) cc_final: 0.7126 (m-30) REVERT: A 1338 LYS cc_start: 0.8019 (ttmm) cc_final: 0.7712 (ttmm) REVERT: A 1355 GLU cc_start: 0.8034 (OUTLIER) cc_final: 0.7192 (tp30) REVERT: A 1381 GLU cc_start: 0.7513 (pt0) cc_final: 0.7291 (pt0) REVERT: A 1403 ARG cc_start: 0.8272 (ttp80) cc_final: 0.7263 (ttt180) REVERT: A 1406 MET cc_start: 0.7515 (mmm) cc_final: 0.7215 (tpp) REVERT: A 1422 ASP cc_start: 0.7181 (t0) cc_final: 0.6497 (m-30) REVERT: A 1434 TYR cc_start: 0.7082 (m-10) cc_final: 0.6460 (m-10) REVERT: A 1464 LYS cc_start: 0.8767 (mttt) cc_final: 0.8497 (mttm) outliers start: 24 outliers final: 7 residues processed: 278 average time/residue: 0.5024 time to fit residues: 149.7049 Evaluate side-chains 265 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 255 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 617 LYS Chi-restraints excluded: chain A residue 704 LYS Chi-restraints excluded: chain A residue 766 TYR Chi-restraints excluded: chain A residue 794 THR Chi-restraints excluded: chain A residue 845 THR Chi-restraints excluded: chain A residue 1112 LEU Chi-restraints excluded: chain A residue 1188 LEU Chi-restraints excluded: chain A residue 1355 GLU Chi-restraints excluded: chain A residue 1371 LEU Chi-restraints excluded: chain A residue 1486 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: [88, 14, 104, 45, 36, 25, 30, 21, 12, 97, 52] chunk 88 optimal weight: 0.9990 chunk 14 optimal weight: 5.9990 chunk 104 optimal weight: 0.0870 chunk 45 optimal weight: 0.5980 chunk 36 optimal weight: 0.8980 chunk 25 optimal weight: 0.0570 chunk 30 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 12 optimal weight: 0.9980 chunk 97 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 overall best weight: 0.5276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 477 ASN ** A 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 555 GLN A 638 HIS A 640 GLN A1046 ASN ** A1093 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1215 ASN A1235 ASN ** A1303 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1308 ASN A1357 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.124015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.113066 restraints weight = 12955.833| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 2.10 r_work: 0.3379 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3226 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.2277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8688 Z= 0.125 Angle : 0.567 8.490 11802 Z= 0.291 Chirality : 0.042 0.164 1247 Planarity : 0.004 0.039 1557 Dihedral : 4.456 30.603 1168 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.18 % Favored : 95.64 % Rotamer: Outliers : 2.97 % Allowed : 18.48 % Favored : 78.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.47 (0.24), residues: 1077 helix: 0.55 (0.32), residues: 265 sheet: 0.01 (0.41), residues: 155 loop : -0.75 (0.23), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 834 TYR 0.015 0.001 TYR A 716 PHE 0.027 0.002 PHE A 498 TRP 0.014 0.001 TRP A1089 HIS 0.008 0.001 HIS A1307 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.12 ( 8684) covalent geometry : angle 0.56732 / 0.29 (11798) SS BOND : bond 0.00023 / 0.01 ( 2) SS BOND : angle 0.38776 / 0.23 ( 4) hydrogen bonds : bond 0.03561 / 2.30 ( 239) hydrogen bonds : angle 4.49515 / 3.15 ( 675) metal coordination : bond 0.00114 / 0.06 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 264 time to evaluate : 0.285 Fit side-chains REVERT: A 533 LEU cc_start: 0.8403 (mt) cc_final: 0.8114 (mp) REVERT: A 613 ASP cc_start: 0.8015 (m-30) cc_final: 0.7668 (m-30) REVERT: A 649 ASP cc_start: 0.7676 (t0) cc_final: 0.7412 (m-30) REVERT: A 686 GLN cc_start: 0.7535 (tm-30) cc_final: 0.7317 (tm-30) REVERT: A 704 LYS cc_start: 0.8743 (OUTLIER) cc_final: 0.8486 (ptmt) REVERT: A 709 ASP cc_start: 0.7536 (m-30) cc_final: 0.7216 (m-30) REVERT: A 712 ASP cc_start: 0.7578 (m-30) cc_final: 0.7249 (m-30) REVERT: A 718 ASN cc_start: 0.8298 (m110) cc_final: 0.7758 (m110) REVERT: A 726 MET cc_start: 0.7854 (mtt) cc_final: 0.7305 (mtt) REVERT: A 728 ASN cc_start: 0.7476 (t0) cc_final: 0.7004 (t0) REVERT: A 735 GLU cc_start: 0.7665 (pm20) cc_final: 0.7356 (tt0) REVERT: A 741 PHE cc_start: 0.8206 (t80) cc_final: 0.7967 (t80) REVERT: A 745 LEU cc_start: 0.8417 (mm) cc_final: 0.8101 (mp) REVERT: A 814 ASP cc_start: 0.7515 (p0) cc_final: 0.7297 (p0) REVERT: A 959 ASP cc_start: 0.7891 (t0) cc_final: 0.7432 (t0) REVERT: A 1001 LYS cc_start: 0.8163 (tppp) cc_final: 0.7875 (tppp) REVERT: A 1008 MET cc_start: 0.8211 (mtp) cc_final: 0.8011 (mtt) REVERT: A 1010 TYR cc_start: 0.7687 (m-80) cc_final: 0.7003 (m-80) REVERT: A 1074 ASN cc_start: 0.7813 (t0) cc_final: 0.7526 (t0) REVERT: A 1209 LYS cc_start: 0.8255 (mmmm) cc_final: 0.7878 (mmtp) REVERT: A 1228 ASP cc_start: 0.7315 (t0) cc_final: 0.6900 (m-30) REVERT: A 1333 ASP cc_start: 0.7723 (m-30) cc_final: 0.7163 (m-30) REVERT: A 1355 GLU cc_start: 0.8083 (OUTLIER) cc_final: 0.7247 (tp30) REVERT: A 1403 ARG cc_start: 0.8268 (ttp80) cc_final: 0.7207 (ttt180) REVERT: A 1406 MET cc_start: 0.7574 (mmm) cc_final: 0.7246 (tpp) REVERT: A 1434 TYR cc_start: 0.7109 (m-10) cc_final: 0.6577 (m-10) outliers start: 27 outliers final: 13 residues processed: 274 average time/residue: 0.4791 time to fit residues: 140.9246 Evaluate side-chains 270 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 255 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 617 LYS Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 704 LYS Chi-restraints excluded: chain A residue 794 THR Chi-restraints excluded: chain A residue 845 THR Chi-restraints excluded: chain A residue 886 VAL Chi-restraints excluded: chain A residue 1065 VAL Chi-restraints excluded: chain A residue 1112 LEU Chi-restraints excluded: chain A residue 1188 LEU Chi-restraints excluded: chain A residue 1312 THR Chi-restraints excluded: chain A residue 1355 GLU Chi-restraints excluded: chain A residue 1470 ASN Chi-restraints excluded: chain A residue 1480 MET Chi-restraints excluded: chain A residue 1486 VAL Chi-restraints excluded: chain A residue 1499 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: [28, 46, 69, 53, 100, 66, 70, 95, 43, 22, 34] chunk 28 optimal weight: 3.9990 chunk 46 optimal weight: 0.7980 chunk 69 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 100 optimal weight: 0.8980 chunk 66 optimal weight: 0.9980 chunk 70 optimal weight: 0.6980 chunk 95 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 chunk 22 optimal weight: 0.0670 chunk 34 optimal weight: 3.9990 overall best weight: 0.6918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 477 ASN ** A 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 594 ASN A 638 HIS A 640 GLN A 868 ASN A 876 ASN A1046 ASN ** A1093 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1303 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1357 ASN A1359 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.122750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.111860 restraints weight = 12811.004| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 2.08 r_work: 0.3371 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3220 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.2463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 8688 Z= 0.141 Angle : 0.586 8.871 11802 Z= 0.301 Chirality : 0.043 0.168 1247 Planarity : 0.004 0.042 1557 Dihedral : 4.485 30.800 1168 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.74 % Favored : 95.08 % Rotamer: Outliers : 3.85 % Allowed : 19.80 % Favored : 76.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.50 (0.24), residues: 1077 helix: 0.48 (0.31), residues: 274 sheet: 0.09 (0.42), residues: 150 loop : -0.78 (0.23), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 834 TYR 0.024 0.001 TYR A 716 PHE 0.040 0.002 PHE A 498 TRP 0.011 0.001 TRP A1089 HIS 0.008 0.001 HIS A1307 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.14 ( 8684) covalent geometry : angle 0.58570 / 0.30 (11798) SS BOND : bond 0.00087 / 0.04 ( 2) SS BOND : angle 0.42008 / 0.24 ( 4) hydrogen bonds : bond 0.03602 / 2.30 ( 239) hydrogen bonds : angle 4.46029 / 3.14 ( 675) metal coordination : bond 0.00102 / 0.05 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 268 time to evaluate : 0.311 Fit side-chains REVERT: A 450 GLN cc_start: 0.8359 (tp-100) cc_final: 0.8157 (mm-40) REVERT: A 613 ASP cc_start: 0.7991 (m-30) cc_final: 0.7663 (m-30) REVERT: A 637 ARG cc_start: 0.8395 (mmm-85) cc_final: 0.8128 (mmm-85) REVERT: A 649 ASP cc_start: 0.7708 (t0) cc_final: 0.7445 (m-30) REVERT: A 686 GLN cc_start: 0.7595 (tm-30) cc_final: 0.7330 (tm-30) REVERT: A 702 LYS cc_start: 0.8621 (mtpt) cc_final: 0.8195 (mtpp) REVERT: A 704 LYS cc_start: 0.8760 (OUTLIER) cc_final: 0.8433 (ptmt) REVERT: A 709 ASP cc_start: 0.7550 (m-30) cc_final: 0.7223 (m-30) REVERT: A 712 ASP cc_start: 0.7563 (m-30) cc_final: 0.7244 (m-30) REVERT: A 718 ASN cc_start: 0.8299 (m110) cc_final: 0.7661 (m110) REVERT: A 726 MET cc_start: 0.7877 (mtt) cc_final: 0.7332 (mtt) REVERT: A 735 GLU cc_start: 0.7757 (pm20) cc_final: 0.7513 (tt0) REVERT: A 814 ASP cc_start: 0.7579 (p0) cc_final: 0.7349 (p0) REVERT: A 892 MET cc_start: 0.8339 (OUTLIER) cc_final: 0.7920 (mpp) REVERT: A 959 ASP cc_start: 0.7910 (t0) cc_final: 0.7474 (t0) REVERT: A 1001 LYS cc_start: 0.8195 (tppp) cc_final: 0.7661 (tppp) REVERT: A 1010 TYR cc_start: 0.7682 (m-80) cc_final: 0.7002 (m-80) REVERT: A 1065 VAL cc_start: 0.8400 (OUTLIER) cc_final: 0.8153 (t) REVERT: A 1074 ASN cc_start: 0.7780 (t0) cc_final: 0.7473 (t0) REVERT: A 1173 VAL cc_start: 0.7221 (m) cc_final: 0.6903 (m) REVERT: A 1209 LYS cc_start: 0.8281 (mmmm) cc_final: 0.7931 (mmtm) REVERT: A 1228 ASP cc_start: 0.7349 (t0) cc_final: 0.6953 (m-30) REVERT: A 1338 LYS cc_start: 0.8299 (OUTLIER) cc_final: 0.7588 (tttp) REVERT: A 1355 GLU cc_start: 0.8118 (OUTLIER) cc_final: 0.7306 (tp30) REVERT: A 1403 ARG cc_start: 0.8289 (ttp80) cc_final: 0.7731 (ttt180) REVERT: A 1404 GLU cc_start: 0.7661 (tm-30) cc_final: 0.7388 (tm-30) REVERT: A 1422 ASP cc_start: 0.7198 (t0) cc_final: 0.6518 (m-30) REVERT: A 1434 TYR cc_start: 0.7141 (m-10) cc_final: 0.6626 (m-10) REVERT: A 1453 VAL cc_start: 0.8311 (t) cc_final: 0.8047 (m) REVERT: A 1464 LYS cc_start: 0.8774 (mttt) cc_final: 0.8509 (mttm) outliers start: 35 outliers final: 17 residues processed: 280 average time/residue: 0.4803 time to fit residues: 144.5426 Evaluate side-chains 280 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 258 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 542 ASP Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 704 LYS Chi-restraints excluded: chain A residue 778 ILE Chi-restraints excluded: chain A residue 794 THR Chi-restraints excluded: chain A residue 845 THR Chi-restraints excluded: chain A residue 886 VAL Chi-restraints excluded: chain A residue 892 MET Chi-restraints excluded: chain A residue 1029 MET Chi-restraints excluded: chain A residue 1065 VAL Chi-restraints excluded: chain A residue 1112 LEU Chi-restraints excluded: chain A residue 1167 SER Chi-restraints excluded: chain A residue 1188 LEU Chi-restraints excluded: chain A residue 1301 ILE Chi-restraints excluded: chain A residue 1312 THR Chi-restraints excluded: chain A residue 1338 LYS Chi-restraints excluded: chain A residue 1354 GLU Chi-restraints excluded: chain A residue 1355 GLU Chi-restraints excluded: chain A residue 1470 ASN Chi-restraints excluded: chain A residue 1480 MET Chi-restraints excluded: chain A residue 1486 VAL Chi-restraints excluded: chain A residue 1499 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: [86, 6, 92, 79, 57, 30, 43, 55, 96, 21, 45] chunk 86 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 57 optimal weight: 0.7980 chunk 30 optimal weight: 0.9980 chunk 43 optimal weight: 0.7980 chunk 55 optimal weight: 0.9990 chunk 96 optimal weight: 3.9990 chunk 21 optimal weight: 4.9990 chunk 45 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 477 ASN ** A 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 594 ASN A 638 HIS A 640 GLN A 679 ASN A 868 ASN A 876 ASN A1046 ASN ** A1093 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1215 ASN ** A1303 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1357 ASN A1488 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.122239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.111192 restraints weight = 12717.981| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 2.08 r_work: 0.3359 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3206 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.2611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8688 Z= 0.159 Angle : 0.599 7.714 11802 Z= 0.309 Chirality : 0.043 0.169 1247 Planarity : 0.004 0.049 1557 Dihedral : 4.551 31.520 1168 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.64 % Favored : 95.17 % Rotamer: Outliers : 4.73 % Allowed : 19.80 % Favored : 75.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.57 (0.25), residues: 1077 helix: 0.33 (0.31), residues: 286 sheet: -0.14 (0.40), residues: 166 loop : -0.76 (0.24), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 834 TYR 0.025 0.001 TYR A 716 PHE 0.019 0.002 PHE A 681 TRP 0.013 0.001 TRP A1089 HIS 0.008 0.001 HIS A1307 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.16 ( 8684) covalent geometry : angle 0.59905 / 0.31 (11798) SS BOND : bond 0.00150 / 0.07 ( 2) SS BOND : angle 0.44097 / 0.24 ( 4) hydrogen bonds : bond 0.03665 / 2.36 ( 239) hydrogen bonds : angle 4.41788 / 3.11 ( 675) metal coordination : bond 0.00131 / 0.07 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 269 time to evaluate : 0.254 Fit side-chains REVERT: A 450 GLN cc_start: 0.8328 (tp-100) cc_final: 0.8126 (mm-40) REVERT: A 498 PHE cc_start: 0.8542 (p90) cc_final: 0.8318 (p90) REVERT: A 533 LEU cc_start: 0.8472 (mt) cc_final: 0.8192 (mp) REVERT: A 613 ASP cc_start: 0.7940 (m-30) cc_final: 0.7627 (m-30) REVERT: A 637 ARG cc_start: 0.8422 (mmm-85) cc_final: 0.8153 (mmm-85) REVERT: A 649 ASP cc_start: 0.7719 (t0) cc_final: 0.7452 (m-30) REVERT: A 686 GLN cc_start: 0.7700 (tm-30) cc_final: 0.7399 (tm-30) REVERT: A 702 LYS cc_start: 0.8654 (mtpt) cc_final: 0.8225 (mtpp) REVERT: A 704 LYS cc_start: 0.8820 (ptmt) cc_final: 0.8497 (ptmt) REVERT: A 709 ASP cc_start: 0.7547 (m-30) cc_final: 0.7203 (m-30) REVERT: A 712 ASP cc_start: 0.7629 (m-30) cc_final: 0.7288 (m-30) REVERT: A 718 ASN cc_start: 0.8276 (m110) cc_final: 0.7679 (m110) REVERT: A 735 GLU cc_start: 0.7774 (pm20) cc_final: 0.7535 (tt0) REVERT: A 774 ARG cc_start: 0.8424 (OUTLIER) cc_final: 0.8204 (mtt180) REVERT: A 892 MET cc_start: 0.8344 (OUTLIER) cc_final: 0.7929 (mpp) REVERT: A 959 ASP cc_start: 0.7954 (t0) cc_final: 0.7506 (t0) REVERT: A 1001 LYS cc_start: 0.8161 (tppp) cc_final: 0.7820 (ttmm) REVERT: A 1010 TYR cc_start: 0.7660 (m-80) cc_final: 0.7033 (m-80) REVERT: A 1065 VAL cc_start: 0.8363 (OUTLIER) cc_final: 0.8148 (t) REVERT: A 1074 ASN cc_start: 0.7808 (t0) cc_final: 0.7487 (t0) REVERT: A 1145 LYS cc_start: 0.8134 (ttmm) cc_final: 0.7849 (ttmm) REVERT: A 1209 LYS cc_start: 0.8301 (mmmm) cc_final: 0.7960 (mmtm) REVERT: A 1228 ASP cc_start: 0.7367 (t0) cc_final: 0.6950 (m-30) REVERT: A 1333 ASP cc_start: 0.7630 (p0) cc_final: 0.7418 (p0) REVERT: A 1338 LYS cc_start: 0.8166 (OUTLIER) cc_final: 0.7641 (tttp) REVERT: A 1355 GLU cc_start: 0.8092 (OUTLIER) cc_final: 0.7326 (tp30) REVERT: A 1377 LYS cc_start: 0.8190 (OUTLIER) cc_final: 0.7634 (tptt) REVERT: A 1403 ARG cc_start: 0.8359 (ttp80) cc_final: 0.7626 (ttt180) REVERT: A 1404 GLU cc_start: 0.7625 (tm-30) cc_final: 0.7387 (tm-30) REVERT: A 1406 MET cc_start: 0.7485 (mmm) cc_final: 0.7164 (mmm) REVERT: A 1407 LYS cc_start: 0.7893 (mtpt) cc_final: 0.7661 (mtpp) REVERT: A 1434 TYR cc_start: 0.7089 (m-10) cc_final: 0.6614 (m-10) REVERT: A 1453 VAL cc_start: 0.8296 (t) cc_final: 0.8038 (m) REVERT: A 1464 LYS cc_start: 0.8775 (mttt) cc_final: 0.8523 (mttm) outliers start: 43 outliers final: 23 residues processed: 288 average time/residue: 0.4780 time to fit residues: 147.6586 Evaluate side-chains 291 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 262 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 542 ASP Chi-restraints excluded: chain A residue 617 LYS Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 774 ARG Chi-restraints excluded: chain A residue 778 ILE Chi-restraints excluded: chain A residue 794 THR Chi-restraints excluded: chain A residue 845 THR Chi-restraints excluded: chain A residue 886 VAL Chi-restraints excluded: chain A residue 892 MET Chi-restraints excluded: chain A residue 900 LEU Chi-restraints excluded: chain A residue 961 SER Chi-restraints excluded: chain A residue 1065 VAL Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1112 LEU Chi-restraints excluded: chain A residue 1167 SER Chi-restraints excluded: chain A residue 1188 LEU Chi-restraints excluded: chain A residue 1242 SER Chi-restraints excluded: chain A residue 1301 ILE Chi-restraints excluded: chain A residue 1312 THR Chi-restraints excluded: chain A residue 1338 LYS Chi-restraints excluded: chain A residue 1354 GLU Chi-restraints excluded: chain A residue 1355 GLU Chi-restraints excluded: chain A residue 1377 LYS Chi-restraints excluded: chain A residue 1470 ASN Chi-restraints excluded: chain A residue 1480 MET Chi-restraints excluded: chain A residue 1486 VAL Chi-restraints excluded: chain A residue 1497 LEU Chi-restraints excluded: chain A residue 1499 LEU Chi-restraints excluded: chain A residue 1514 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: [22, 67, 35, 98, 75, 93, 99, 44, 3, 46, 59] chunk 22 optimal weight: 0.7980 chunk 67 optimal weight: 0.5980 chunk 35 optimal weight: 0.8980 chunk 98 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 chunk 93 optimal weight: 0.9980 chunk 99 optimal weight: 2.9990 chunk 44 optimal weight: 0.0970 chunk 3 optimal weight: 1.9990 chunk 46 optimal weight: 0.8980 chunk 59 optimal weight: 2.9990 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 477 ASN ** A 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 594 ASN A 638 HIS A 640 GLN A 868 ASN A 876 ASN A1046 ASN ** A1093 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1303 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1357 ASN A1488 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.122936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.111707 restraints weight = 12897.542| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 2.12 r_work: 0.3361 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3208 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.2769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8688 Z= 0.142 Angle : 0.614 7.557 11802 Z= 0.315 Chirality : 0.043 0.165 1247 Planarity : 0.004 0.049 1557 Dihedral : 4.561 31.057 1168 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.83 % Favored : 94.99 % Rotamer: Outliers : 4.18 % Allowed : 21.23 % Favored : 74.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.51 (0.25), residues: 1077 helix: 0.46 (0.31), residues: 279 sheet: -0.07 (0.41), residues: 161 loop : -0.75 (0.24), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 834 TYR 0.029 0.001 TYR A 716 PHE 0.018 0.002 PHE A 681 TRP 0.012 0.001 TRP A1089 HIS 0.008 0.001 HIS A1307 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.14 ( 8684) covalent geometry : angle 0.61362 / 0.31 (11798) SS BOND : bond 0.00113 / 0.05 ( 2) SS BOND : angle 0.39760 / 0.22 ( 4) hydrogen bonds : bond 0.03555 / 2.28 ( 239) hydrogen bonds : angle 4.40121 / 3.11 ( 675) metal coordination : bond 0.00089 / 0.05 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 272 time to evaluate : 0.274 Fit side-chains REVERT: A 533 LEU cc_start: 0.8457 (mt) cc_final: 0.8183 (mp) REVERT: A 613 ASP cc_start: 0.7943 (m-30) cc_final: 0.7648 (m-30) REVERT: A 637 ARG cc_start: 0.8434 (mmm-85) cc_final: 0.8127 (mmm-85) REVERT: A 649 ASP cc_start: 0.7719 (t0) cc_final: 0.7460 (m-30) REVERT: A 702 LYS cc_start: 0.8655 (mtpt) cc_final: 0.8237 (mtpp) REVERT: A 704 LYS cc_start: 0.8796 (ptmt) cc_final: 0.8484 (ptmt) REVERT: A 709 ASP cc_start: 0.7508 (m-30) cc_final: 0.7165 (m-30) REVERT: A 712 ASP cc_start: 0.7567 (m-30) cc_final: 0.7239 (m-30) REVERT: A 718 ASN cc_start: 0.8249 (m110) cc_final: 0.7756 (m110) REVERT: A 719 LYS cc_start: 0.8486 (mtpp) cc_final: 0.8221 (mtpp) REVERT: A 735 GLU cc_start: 0.7785 (pm20) cc_final: 0.7233 (tp30) REVERT: A 774 ARG cc_start: 0.8394 (OUTLIER) cc_final: 0.8155 (mtt180) REVERT: A 892 MET cc_start: 0.8382 (OUTLIER) cc_final: 0.7964 (mpp) REVERT: A 959 ASP cc_start: 0.7901 (t0) cc_final: 0.7441 (t0) REVERT: A 1001 LYS cc_start: 0.8182 (tppp) cc_final: 0.7831 (tppp) REVERT: A 1010 TYR cc_start: 0.7663 (m-80) cc_final: 0.6976 (m-80) REVERT: A 1065 VAL cc_start: 0.8376 (OUTLIER) cc_final: 0.8158 (t) REVERT: A 1074 ASN cc_start: 0.7791 (t0) cc_final: 0.7492 (t0) REVERT: A 1209 LYS cc_start: 0.8290 (mmmm) cc_final: 0.7937 (mmtm) REVERT: A 1228 ASP cc_start: 0.7363 (t0) cc_final: 0.6949 (m-30) REVERT: A 1338 LYS cc_start: 0.8168 (OUTLIER) cc_final: 0.7640 (ttmm) REVERT: A 1355 GLU cc_start: 0.8087 (OUTLIER) cc_final: 0.7334 (tp30) REVERT: A 1377 LYS cc_start: 0.8214 (OUTLIER) cc_final: 0.7974 (tmmt) REVERT: A 1403 ARG cc_start: 0.8343 (ttp80) cc_final: 0.7609 (ttt180) REVERT: A 1404 GLU cc_start: 0.7622 (tm-30) cc_final: 0.7394 (tm-30) REVERT: A 1422 ASP cc_start: 0.7172 (t0) cc_final: 0.6539 (m-30) REVERT: A 1434 TYR cc_start: 0.7161 (m-10) cc_final: 0.6677 (m-10) REVERT: A 1453 VAL cc_start: 0.8295 (t) cc_final: 0.8027 (m) REVERT: A 1464 LYS cc_start: 0.8758 (mttt) cc_final: 0.8503 (mttm) outliers start: 38 outliers final: 21 residues processed: 287 average time/residue: 0.4618 time to fit residues: 142.6656 Evaluate side-chains 284 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 257 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 542 ASP Chi-restraints excluded: chain A residue 617 LYS Chi-restraints excluded: chain A residue 766 TYR Chi-restraints excluded: chain A residue 774 ARG Chi-restraints excluded: chain A residue 778 ILE Chi-restraints excluded: chain A residue 791 LEU Chi-restraints excluded: chain A residue 794 THR Chi-restraints excluded: chain A residue 845 THR Chi-restraints excluded: chain A residue 886 VAL Chi-restraints excluded: chain A residue 892 MET Chi-restraints excluded: chain A residue 900 LEU Chi-restraints excluded: chain A residue 1065 VAL Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1112 LEU Chi-restraints excluded: chain A residue 1167 SER Chi-restraints excluded: chain A residue 1242 SER Chi-restraints excluded: chain A residue 1301 ILE Chi-restraints excluded: chain A residue 1312 THR Chi-restraints excluded: chain A residue 1338 LYS Chi-restraints excluded: chain A residue 1354 GLU Chi-restraints excluded: chain A residue 1355 GLU Chi-restraints excluded: chain A residue 1377 LYS Chi-restraints excluded: chain A residue 1470 ASN Chi-restraints excluded: chain A residue 1480 MET Chi-restraints excluded: chain A residue 1486 VAL Chi-restraints excluded: chain A residue 1497 LEU Chi-restraints excluded: chain A residue 1499 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: [53, 72, 65, 38, 12, 37, 79, 39, 11, 29, 74] chunk 53 optimal weight: 0.9980 chunk 72 optimal weight: 0.9980 chunk 65 optimal weight: 0.5980 chunk 38 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 37 optimal weight: 0.0980 chunk 79 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 chunk 11 optimal weight: 0.7980 chunk 29 optimal weight: 0.6980 chunk 74 optimal weight: 3.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 477 ASN ** A 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 594 ASN A 638 HIS A 640 GLN A 868 ASN A 876 ASN A 926 HIS A1046 ASN ** A1093 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1215 ASN A1235 ASN ** A1303 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1357 ASN A1488 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.123330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.112074 restraints weight = 12740.796| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 2.12 r_work: 0.3369 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3218 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.2869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8688 Z= 0.139 Angle : 0.627 9.377 11802 Z= 0.322 Chirality : 0.043 0.154 1247 Planarity : 0.004 0.048 1557 Dihedral : 4.540 31.014 1168 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.64 % Favored : 95.17 % Rotamer: Outliers : 3.96 % Allowed : 21.78 % Favored : 74.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.51 (0.25), residues: 1077 helix: 0.34 (0.30), residues: 279 sheet: -0.02 (0.41), residues: 161 loop : -0.70 (0.24), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 834 TYR 0.033 0.001 TYR A 716 PHE 0.031 0.002 PHE A 681 TRP 0.020 0.001 TRP A 510 HIS 0.007 0.001 HIS A1307 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.14 ( 8684) covalent geometry : angle 0.62699 / 0.32 (11798) SS BOND : bond 0.00086 / 0.04 ( 2) SS BOND : angle 0.38813 / 0.22 ( 4) hydrogen bonds : bond 0.03439 / 2.17 ( 239) hydrogen bonds : angle 4.37505 / 3.11 ( 675) metal coordination : bond 0.00084 / 0.04 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 261 time to evaluate : 0.324 Fit side-chains REVERT: A 533 LEU cc_start: 0.8414 (mt) cc_final: 0.8126 (mp) REVERT: A 613 ASP cc_start: 0.7923 (m-30) cc_final: 0.7650 (m-30) REVERT: A 637 ARG cc_start: 0.8437 (mmm-85) cc_final: 0.8108 (mmm-85) REVERT: A 649 ASP cc_start: 0.7717 (t0) cc_final: 0.7454 (m-30) REVERT: A 702 LYS cc_start: 0.8634 (mtpt) cc_final: 0.8258 (mtpp) REVERT: A 704 LYS cc_start: 0.8799 (ptmt) cc_final: 0.8483 (ptmt) REVERT: A 709 ASP cc_start: 0.7499 (m-30) cc_final: 0.7161 (m-30) REVERT: A 712 ASP cc_start: 0.7583 (m-30) cc_final: 0.7250 (m-30) REVERT: A 718 ASN cc_start: 0.8258 (m110) cc_final: 0.7583 (m110) REVERT: A 719 LYS cc_start: 0.8504 (mtpp) cc_final: 0.8286 (mtpp) REVERT: A 735 GLU cc_start: 0.7791 (pm20) cc_final: 0.7525 (tt0) REVERT: A 774 ARG cc_start: 0.8382 (OUTLIER) cc_final: 0.8136 (mtt180) REVERT: A 880 TYR cc_start: 0.7756 (t80) cc_final: 0.7355 (t80) REVERT: A 959 ASP cc_start: 0.7890 (t0) cc_final: 0.7438 (t0) REVERT: A 1001 LYS cc_start: 0.8163 (tppp) cc_final: 0.7826 (tppp) REVERT: A 1010 TYR cc_start: 0.7652 (m-80) cc_final: 0.7032 (m-80) REVERT: A 1037 MET cc_start: 0.8694 (mmm) cc_final: 0.8166 (mmm) REVERT: A 1065 VAL cc_start: 0.8343 (OUTLIER) cc_final: 0.8127 (t) REVERT: A 1074 ASN cc_start: 0.7785 (t0) cc_final: 0.7465 (t0) REVERT: A 1209 LYS cc_start: 0.8257 (mmmm) cc_final: 0.7905 (mmtm) REVERT: A 1228 ASP cc_start: 0.7321 (t0) cc_final: 0.7086 (t0) REVERT: A 1236 ASP cc_start: 0.8104 (m-30) cc_final: 0.7859 (t0) REVERT: A 1338 LYS cc_start: 0.8168 (OUTLIER) cc_final: 0.7511 (ttmm) REVERT: A 1355 GLU cc_start: 0.8102 (OUTLIER) cc_final: 0.7354 (tp30) REVERT: A 1377 LYS cc_start: 0.8185 (OUTLIER) cc_final: 0.7702 (tptt) REVERT: A 1403 ARG cc_start: 0.8317 (ttp80) cc_final: 0.7370 (ttt180) REVERT: A 1404 GLU cc_start: 0.7613 (tm-30) cc_final: 0.7385 (tm-30) REVERT: A 1406 MET cc_start: 0.7738 (mmm) cc_final: 0.7215 (mmt) REVERT: A 1434 TYR cc_start: 0.7141 (m-10) cc_final: 0.6648 (m-10) REVERT: A 1453 VAL cc_start: 0.8259 (t) cc_final: 0.7980 (m) REVERT: A 1464 LYS cc_start: 0.8780 (mttt) cc_final: 0.8515 (mttm) outliers start: 36 outliers final: 24 residues processed: 277 average time/residue: 0.4592 time to fit residues: 136.9094 Evaluate side-chains 282 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 253 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 542 ASP Chi-restraints excluded: chain A residue 617 LYS Chi-restraints excluded: chain A residue 624 MET Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 726 MET Chi-restraints excluded: chain A residue 766 TYR Chi-restraints excluded: chain A residue 774 ARG Chi-restraints excluded: chain A residue 778 ILE Chi-restraints excluded: chain A residue 791 LEU Chi-restraints excluded: chain A residue 794 THR Chi-restraints excluded: chain A residue 845 THR Chi-restraints excluded: chain A residue 886 VAL Chi-restraints excluded: chain A residue 961 SER Chi-restraints excluded: chain A residue 1065 VAL Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1112 LEU Chi-restraints excluded: chain A residue 1167 SER Chi-restraints excluded: chain A residue 1188 LEU Chi-restraints excluded: chain A residue 1242 SER Chi-restraints excluded: chain A residue 1301 ILE Chi-restraints excluded: chain A residue 1312 THR Chi-restraints excluded: chain A residue 1338 LYS Chi-restraints excluded: chain A residue 1355 GLU Chi-restraints excluded: chain A residue 1377 LYS Chi-restraints excluded: chain A residue 1470 ASN Chi-restraints excluded: chain A residue 1480 MET Chi-restraints excluded: chain A residue 1486 VAL Chi-restraints excluded: chain A residue 1497 LEU Chi-restraints excluded: chain A residue 1499 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: [73, 3, 19, 26, 7, 49, 35, 68, 39, 61, 88] chunk 73 optimal weight: 0.6980 chunk 3 optimal weight: 0.7980 chunk 19 optimal weight: 0.8980 chunk 26 optimal weight: 0.0770 chunk 7 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 35 optimal weight: 0.0060 chunk 68 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 chunk 88 optimal weight: 0.5980 overall best weight: 0.4354 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 477 ASN ** A 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 594 ASN A 638 HIS A 640 GLN A 868 ASN A 876 ASN A1046 ASN ** A1093 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1303 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1308 ASN A1357 ASN A1488 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.124384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.113186 restraints weight = 12718.754| |-----------------------------------------------------------------------------| r_work (start): 0.3494 rms_B_bonded: 2.12 r_work: 0.3386 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3235 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.2960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8688 Z= 0.128 Angle : 0.633 11.294 11802 Z= 0.323 Chirality : 0.043 0.199 1247 Planarity : 0.004 0.046 1557 Dihedral : 4.462 30.616 1168 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.83 % Favored : 95.08 % Rotamer: Outliers : 4.51 % Allowed : 22.66 % Favored : 72.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.47 (0.25), residues: 1077 helix: 0.34 (0.30), residues: 279 sheet: 0.04 (0.41), residues: 161 loop : -0.68 (0.24), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 834 TYR 0.034 0.001 TYR A 716 PHE 0.023 0.002 PHE A 498 TRP 0.024 0.001 TRP A 510 HIS 0.006 0.001 HIS A1307 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.13 ( 8684) covalent geometry : angle 0.63280 / 0.32 (11798) SS BOND : bond 0.00077 / 0.04 ( 2) SS BOND : angle 0.44722 / 0.25 ( 4) hydrogen bonds : bond 0.03362 / 2.13 ( 239) hydrogen bonds : angle 4.40881 / 3.15 ( 675) metal coordination : bond 0.00090 / 0.04 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 262 time to evaluate : 0.300 Fit side-chains REVERT: A 533 LEU cc_start: 0.8378 (mt) cc_final: 0.8094 (mp) REVERT: A 542 ASP cc_start: 0.8142 (OUTLIER) cc_final: 0.7703 (p0) REVERT: A 613 ASP cc_start: 0.7936 (m-30) cc_final: 0.7651 (m-30) REVERT: A 637 ARG cc_start: 0.8415 (mmm-85) cc_final: 0.8064 (mmm-85) REVERT: A 649 ASP cc_start: 0.7706 (t0) cc_final: 0.7442 (m-30) REVERT: A 686 GLN cc_start: 0.7724 (tm-30) cc_final: 0.7495 (tm-30) REVERT: A 702 LYS cc_start: 0.8644 (mtpt) cc_final: 0.8279 (mtpp) REVERT: A 704 LYS cc_start: 0.8769 (ptmt) cc_final: 0.8459 (ptmt) REVERT: A 709 ASP cc_start: 0.7518 (m-30) cc_final: 0.7177 (m-30) REVERT: A 712 ASP cc_start: 0.7592 (m-30) cc_final: 0.7295 (m-30) REVERT: A 718 ASN cc_start: 0.8117 (m110) cc_final: 0.7626 (m110) REVERT: A 719 LYS cc_start: 0.8473 (mtpp) cc_final: 0.8157 (mtpp) REVERT: A 726 MET cc_start: 0.7780 (mtt) cc_final: 0.7194 (mtt) REVERT: A 735 GLU cc_start: 0.7774 (pm20) cc_final: 0.7074 (tp30) REVERT: A 774 ARG cc_start: 0.8415 (OUTLIER) cc_final: 0.8173 (mtt180) REVERT: A 817 LYS cc_start: 0.8335 (tttt) cc_final: 0.8093 (ttpp) REVERT: A 840 GLU cc_start: 0.7457 (OUTLIER) cc_final: 0.7229 (mp0) REVERT: A 872 HIS cc_start: 0.6945 (m-70) cc_final: 0.6718 (m170) REVERT: A 892 MET cc_start: 0.8374 (OUTLIER) cc_final: 0.7960 (mpp) REVERT: A 959 ASP cc_start: 0.7856 (t0) cc_final: 0.7368 (t0) REVERT: A 1001 LYS cc_start: 0.8130 (tppp) cc_final: 0.7793 (tppp) REVERT: A 1010 TYR cc_start: 0.7658 (m-80) cc_final: 0.6948 (m-80) REVERT: A 1065 VAL cc_start: 0.8343 (OUTLIER) cc_final: 0.8116 (t) REVERT: A 1074 ASN cc_start: 0.7781 (t0) cc_final: 0.7458 (t0) REVERT: A 1167 SER cc_start: 0.8323 (OUTLIER) cc_final: 0.8045 (p) REVERT: A 1209 LYS cc_start: 0.8194 (mmmm) cc_final: 0.7808 (mmtp) REVERT: A 1228 ASP cc_start: 0.7331 (t0) cc_final: 0.7083 (t0) REVERT: A 1236 ASP cc_start: 0.8062 (m-30) cc_final: 0.7827 (t0) REVERT: A 1338 LYS cc_start: 0.8121 (OUTLIER) cc_final: 0.7462 (ttmm) REVERT: A 1355 GLU cc_start: 0.8074 (OUTLIER) cc_final: 0.7354 (tp30) REVERT: A 1403 ARG cc_start: 0.8311 (ttp80) cc_final: 0.7361 (ttt180) REVERT: A 1404 GLU cc_start: 0.7645 (tm-30) cc_final: 0.7410 (tm-30) REVERT: A 1406 MET cc_start: 0.7691 (mmm) cc_final: 0.7152 (mmt) REVERT: A 1418 LYS cc_start: 0.7909 (tppt) cc_final: 0.7648 (mmpt) REVERT: A 1422 ASP cc_start: 0.7134 (t0) cc_final: 0.6350 (m-30) REVERT: A 1434 TYR cc_start: 0.7126 (m-10) cc_final: 0.6669 (m-10) REVERT: A 1453 VAL cc_start: 0.8252 (t) cc_final: 0.7973 (m) REVERT: A 1464 LYS cc_start: 0.8789 (mttt) cc_final: 0.8530 (mttm) outliers start: 41 outliers final: 21 residues processed: 285 average time/residue: 0.4645 time to fit residues: 142.1676 Evaluate side-chains 284 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 255 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 542 ASP Chi-restraints excluded: chain A residue 624 MET Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 766 TYR Chi-restraints excluded: chain A residue 774 ARG Chi-restraints excluded: chain A residue 778 ILE Chi-restraints excluded: chain A residue 791 LEU Chi-restraints excluded: chain A residue 794 THR Chi-restraints excluded: chain A residue 840 GLU Chi-restraints excluded: chain A residue 845 THR Chi-restraints excluded: chain A residue 886 VAL Chi-restraints excluded: chain A residue 892 MET Chi-restraints excluded: chain A residue 961 SER Chi-restraints excluded: chain A residue 1065 VAL Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1098 ILE Chi-restraints excluded: chain A residue 1112 LEU Chi-restraints excluded: chain A residue 1133 THR Chi-restraints excluded: chain A residue 1167 SER Chi-restraints excluded: chain A residue 1188 LEU Chi-restraints excluded: chain A residue 1242 SER Chi-restraints excluded: chain A residue 1301 ILE Chi-restraints excluded: chain A residue 1312 THR Chi-restraints excluded: chain A residue 1338 LYS Chi-restraints excluded: chain A residue 1354 GLU Chi-restraints excluded: chain A residue 1355 GLU Chi-restraints excluded: chain A residue 1470 ASN Chi-restraints excluded: chain A residue 1480 MET Chi-restraints excluded: chain A residue 1499 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: [93, 15, 75, 61, 106, 45, 7, 73, 40, 29, 77] chunk 93 optimal weight: 0.8980 chunk 15 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 106 optimal weight: 3.9990 chunk 45 optimal weight: 0.1980 chunk 7 optimal weight: 1.9990 chunk 73 optimal weight: 0.0000 chunk 40 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 overall best weight: 1.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 594 ASN A 638 HIS A 772 GLN A 831 GLN A 868 ASN A 876 ASN A1046 ASN ** A1084 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1093 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1215 ASN A1235 ASN ** A1303 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1357 ASN A1359 GLN A1488 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.121822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.110690 restraints weight = 12756.102| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 2.10 r_work: 0.3346 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3192 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.2965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 8688 Z= 0.205 Angle : 0.697 13.490 11802 Z= 0.354 Chirality : 0.045 0.204 1247 Planarity : 0.005 0.052 1557 Dihedral : 4.770 31.933 1168 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.92 % Favored : 94.99 % Rotamer: Outliers : 3.74 % Allowed : 23.98 % Favored : 72.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.57 (0.25), residues: 1077 helix: 0.21 (0.30), residues: 279 sheet: -0.10 (0.40), residues: 166 loop : -0.69 (0.25), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 834 TYR 0.037 0.002 TYR A 716 PHE 0.038 0.002 PHE A 741 TRP 0.030 0.002 TRP A 510 HIS 0.007 0.002 HIS A1307 Details of bonding type rmsd/Z covalent geometry : bond 0.00474 / 0.20 ( 8684) covalent geometry : angle 0.69660 / 0.35 (11798) SS BOND : bond 0.00198 / 0.09 ( 2) SS BOND : angle 0.44269 / 0.23 ( 4) hydrogen bonds : bond 0.03779 / 2.35 ( 239) hydrogen bonds : angle 4.53865 / 3.22 ( 675) metal coordination : bond 0.00152 / 0.08 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 259 time to evaluate : 0.323 Fit side-chains REVERT: A 613 ASP cc_start: 0.7935 (m-30) cc_final: 0.7662 (m-30) REVERT: A 649 ASP cc_start: 0.7789 (t0) cc_final: 0.7526 (m-30) REVERT: A 668 LEU cc_start: 0.8003 (mt) cc_final: 0.7689 (mt) REVERT: A 686 GLN cc_start: 0.7728 (tm-30) cc_final: 0.7480 (tm-30) REVERT: A 702 LYS cc_start: 0.8667 (mtpt) cc_final: 0.8290 (mtpp) REVERT: A 704 LYS cc_start: 0.8861 (ptmt) cc_final: 0.8603 (ptmt) REVERT: A 709 ASP cc_start: 0.7510 (m-30) cc_final: 0.7163 (m-30) REVERT: A 712 ASP cc_start: 0.7603 (m-30) cc_final: 0.7230 (m-30) REVERT: A 718 ASN cc_start: 0.8164 (m110) cc_final: 0.7679 (m110) REVERT: A 719 LYS cc_start: 0.8546 (mtpp) cc_final: 0.8211 (mtpp) REVERT: A 722 SER cc_start: 0.8637 (m) cc_final: 0.8329 (p) REVERT: A 726 MET cc_start: 0.7900 (mtt) cc_final: 0.7193 (mtt) REVERT: A 735 GLU cc_start: 0.7843 (pm20) cc_final: 0.7235 (tp30) REVERT: A 774 ARG cc_start: 0.8422 (OUTLIER) cc_final: 0.8173 (mtt180) REVERT: A 817 LYS cc_start: 0.8342 (tttt) cc_final: 0.8068 (ttpp) REVERT: A 872 HIS cc_start: 0.7093 (m-70) cc_final: 0.6856 (m170) REVERT: A 892 MET cc_start: 0.8380 (OUTLIER) cc_final: 0.7878 (mpp) REVERT: A 959 ASP cc_start: 0.7934 (t0) cc_final: 0.7478 (t0) REVERT: A 1001 LYS cc_start: 0.8144 (tppp) cc_final: 0.7872 (ttmm) REVERT: A 1010 TYR cc_start: 0.7645 (m-80) cc_final: 0.7028 (m-80) REVERT: A 1037 MET cc_start: 0.8681 (mmm) cc_final: 0.8244 (mtm) REVERT: A 1074 ASN cc_start: 0.7822 (t0) cc_final: 0.7480 (t0) REVERT: A 1228 ASP cc_start: 0.7370 (t0) cc_final: 0.7127 (t0) REVERT: A 1236 ASP cc_start: 0.8056 (m-30) cc_final: 0.7798 (t0) REVERT: A 1338 LYS cc_start: 0.8202 (OUTLIER) cc_final: 0.7993 (ttpp) REVERT: A 1355 GLU cc_start: 0.8060 (OUTLIER) cc_final: 0.7350 (tp30) REVERT: A 1403 ARG cc_start: 0.8335 (ttp80) cc_final: 0.7744 (ttt-90) REVERT: A 1404 GLU cc_start: 0.7661 (tm-30) cc_final: 0.7413 (tm-30) REVERT: A 1406 MET cc_start: 0.7689 (mmm) cc_final: 0.7372 (mmt) REVERT: A 1422 ASP cc_start: 0.7201 (t0) cc_final: 0.6536 (m-30) REVERT: A 1434 TYR cc_start: 0.7182 (m-10) cc_final: 0.6844 (m-10) REVERT: A 1453 VAL cc_start: 0.8260 (t) cc_final: 0.7982 (m) REVERT: A 1464 LYS cc_start: 0.8768 (mttt) cc_final: 0.8520 (mttm) outliers start: 34 outliers final: 22 residues processed: 275 average time/residue: 0.4755 time to fit residues: 140.1074 Evaluate side-chains 282 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 256 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 766 TYR Chi-restraints excluded: chain A residue 774 ARG Chi-restraints excluded: chain A residue 778 ILE Chi-restraints excluded: chain A residue 791 LEU Chi-restraints excluded: chain A residue 794 THR Chi-restraints excluded: chain A residue 845 THR Chi-restraints excluded: chain A residue 886 VAL Chi-restraints excluded: chain A residue 892 MET Chi-restraints excluded: chain A residue 961 SER Chi-restraints excluded: chain A residue 1065 VAL Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1098 ILE Chi-restraints excluded: chain A residue 1112 LEU Chi-restraints excluded: chain A residue 1133 THR Chi-restraints excluded: chain A residue 1167 SER Chi-restraints excluded: chain A residue 1188 LEU Chi-restraints excluded: chain A residue 1242 SER Chi-restraints excluded: chain A residue 1301 ILE Chi-restraints excluded: chain A residue 1312 THR Chi-restraints excluded: chain A residue 1338 LYS Chi-restraints excluded: chain A residue 1354 GLU Chi-restraints excluded: chain A residue 1355 GLU Chi-restraints excluded: chain A residue 1470 ASN Chi-restraints excluded: chain A residue 1480 MET Chi-restraints excluded: chain A residue 1499 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: [27, 6, 63, 73, 0, 53, 74, 39, 41, 19, 22] chunk 27 optimal weight: 1.9990 chunk 6 optimal weight: 0.4980 chunk 63 optimal weight: 3.9990 chunk 73 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 chunk 53 optimal weight: 0.9980 chunk 74 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 41 optimal weight: 0.6980 chunk 19 optimal weight: 0.8980 chunk 22 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 594 ASN A 638 HIS A 640 GLN A 831 GLN A 868 ASN A 876 ASN A1046 ASN ** A1084 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1093 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1303 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1357 ASN A1488 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.122793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.111690 restraints weight = 12627.685| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 2.10 r_work: 0.3368 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3217 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.3029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 8688 Z= 0.162 Angle : 0.688 13.856 11802 Z= 0.350 Chirality : 0.044 0.252 1247 Planarity : 0.005 0.053 1557 Dihedral : 4.729 32.453 1168 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.74 % Favored : 95.17 % Rotamer: Outliers : 3.63 % Allowed : 24.53 % Favored : 71.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.62 (0.25), residues: 1077 helix: 0.11 (0.30), residues: 279 sheet: -0.10 (0.41), residues: 166 loop : -0.70 (0.24), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 834 TYR 0.038 0.002 TYR A 716 PHE 0.039 0.002 PHE A 741 TRP 0.034 0.002 TRP A 510 HIS 0.006 0.001 HIS A1307 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.16 ( 8684) covalent geometry : angle 0.68854 / 0.35 (11798) SS BOND : bond 0.00118 / 0.06 ( 2) SS BOND : angle 0.49344 / 0.28 ( 4) hydrogen bonds : bond 0.03543 / 2.21 ( 239) hydrogen bonds : angle 4.53164 / 3.23 ( 675) metal coordination : bond 0.00108 / 0.06 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3435.67 seconds wall clock time: 59 minutes 9.75 seconds (3549.75 seconds total)