Starting phenix.real_space_refine on Fri Mar 6 07:24:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6klh_0710/03_2026/6klh_0710.cif Found real_map, /net/cci-nas-00/data/ceres_data/6klh_0710/03_2026/6klh_0710.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6klh_0710/03_2026/6klh_0710.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6klh_0710/03_2026/6klh_0710.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6klh_0710/03_2026/6klh_0710.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6klh_0710/03_2026/6klh_0710.map" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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: 7 Type Number sf(0) Gaussians Mn 2 7.51 5 Zn 2 6.06 5 P 14 5.49 5 S 176 5.16 5 C 18240 2.51 5 N 4908 2.21 5 O 5492 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 28834 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 14266 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1884, 14266 Classifications: {'peptide': 1884} Incomplete info: {'truncation_to_alanine': 224} Link IDs: {'PTRANS': 54, 'TRANS': 1829} Chain breaks: 18 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 808 Unresolved non-hydrogen angles: 1024 Unresolved non-hydrogen dihedrals: 675 Unresolved non-hydrogen chiralities: 67 Planarities with less than four sites: {'GLN:plan1': 10, 'ARG:plan': 12, 'TRP:plan': 2, 'ASP:plan': 17, 'GLU:plan': 24, 'HIS:plan': 6, 'PHE:plan': 14, 'ASN:plan1': 7, 'TYR:plan': 8} Unresolved non-hydrogen planarities: 456 Chain: "B" Number of atoms: 149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 149 Classifications: {'RNA': 7} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 3, 'rna3p_pur': 2, 'rna3p_pyr': 1} Link IDs: {'rna2p': 4, 'rna3p': 2} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2171 SG CYS A 284 148.409 107.169 114.304 1.00129.21 S ATOM 2195 SG CYS A 287 150.333 103.636 114.286 1.00117.64 S ATOM 3474 SG CYS A 470 152.151 106.387 115.891 1.00161.90 S Restraints were copied for chains: C, D Time building chain proxies: 21.92, per 1000 atoms: 0.76 Number of scatterers: 28834 At special positions: 0 Unit cell: (175.44, 152.32, 170, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 Mn 2 24.99 S 176 16.00 P 14 15.00 O 5492 8.00 N 4908 7.00 C 18240 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 55 " - pdb=" SG CYS A 60 " distance=2.03 Simple disulfide: pdb=" SG CYS A1691 " - pdb=" SG CYS A1776 " distance=2.03 Simple disulfide: pdb=" SG CYS C 55 " - pdb=" SG CYS C 60 " distance=2.03 Simple disulfide: pdb=" SG CYS C1691 " - pdb=" SG CYS C1776 " 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: 2.28 Conformation dependent library (CDL) restraints added in 1.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2302 " pdb="ZN ZN A2302 " - pdb=" ND1 HIS A 472 " pdb="ZN ZN A2302 " - pdb=" SG CYS A 284 " pdb="ZN ZN A2302 " - pdb=" SG CYS A 287 " pdb="ZN ZN A2302 " - pdb=" SG CYS A 470 " pdb=" ZN C2302 " pdb="ZN ZN C2302 " - pdb=" ND1 HIS C 472 " pdb="ZN ZN C2302 " - pdb=" SG CYS C 284 " pdb="ZN ZN C2302 " - pdb=" SG CYS C 287 " pdb="ZN ZN C2302 " - pdb=" SG CYS C 470 " Number of angles added : 6 7384 Ramachandran restraints generated. 3692 Oldfield, 0 Emsley, 3692 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7172 Finding SS restraints... Secondary structure from input PDB file: 160 helices and 24 sheets defined 50.4% alpha, 6.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.04 Creating SS restraints... Processing helix chain 'A' and resid 4 through 12 Processing helix chain 'A' and resid 19 through 31 removed outlier: 3.600A pdb=" N GLY A 23 " --> pdb=" O ARG A 19 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR A 28 " --> pdb=" O HIS A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 57 Processing helix chain 'A' and resid 68 through 76 removed outlier: 3.620A pdb=" N ILE A 72 " --> pdb=" O PHE A 68 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N ASN A 76 " --> pdb=" O ILE A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 125 removed outlier: 3.508A pdb=" N ASN A 125 " --> pdb=" O SER A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 131 Processing helix chain 'A' and resid 156 through 171 Processing helix chain 'A' and resid 181 through 190 removed outlier: 3.668A pdb=" N GLN A 185 " --> pdb=" O ASP A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 220 removed outlier: 3.556A pdb=" N LEU A 218 " --> pdb=" O TYR A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 248 removed outlier: 3.934A pdb=" N VAL A 235 " --> pdb=" O ARG A 231 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ASP A 248 " --> pdb=" O LEU A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 275 Processing helix chain 'A' and resid 284 through 288 Processing helix chain 'A' and resid 289 through 303 Processing helix chain 'A' and resid 322 through 338 Processing helix chain 'A' and resid 339 through 341 No H-bonds generated for 'chain 'A' and resid 339 through 341' Processing helix chain 'A' and resid 346 through 365 Processing helix chain 'A' and resid 389 through 391 No H-bonds generated for 'chain 'A' and resid 389 through 391' Processing helix chain 'A' and resid 396 through 405 removed outlier: 3.668A pdb=" N LYS A 405 " --> pdb=" O LYS A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 420 removed outlier: 3.684A pdb=" N ILE A 420 " --> pdb=" O ASN A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 451 removed outlier: 3.579A pdb=" N LEU A 444 " --> pdb=" O ASP A 440 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU A 451 " --> pdb=" O ILE A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 478 Processing helix chain 'A' and resid 481 through 502 removed outlier: 3.650A pdb=" N ARG A 485 " --> pdb=" O PHE A 481 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 583 removed outlier: 3.998A pdb=" N PHE A 579 " --> pdb=" O LYS A 576 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N LEU A 580 " --> pdb=" O ARG A 577 " (cutoff:3.500A) Proline residue: A 581 - end of helix Processing helix chain 'A' and resid 586 through 598 Processing helix chain 'A' and resid 609 through 623 Processing helix chain 'A' and resid 625 through 644 removed outlier: 3.776A pdb=" N GLN A 629 " --> pdb=" O SER A 625 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASN A 644 " --> pdb=" O MET A 640 " (cutoff:3.500A) Processing helix chain 'A' and resid 651 through 655 Processing helix chain 'A' and resid 663 through 680 removed outlier: 3.975A pdb=" N VAL A 667 " --> pdb=" O SER A 663 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 702 removed outlier: 4.066A pdb=" N ARG A 692 " --> pdb=" O PHE A 688 " (cutoff:3.500A) Processing helix chain 'A' and resid 703 through 706 Processing helix chain 'A' and resid 713 through 732 Proline residue: A 727 - end of helix Processing helix chain 'A' and resid 745 through 760 Processing helix chain 'A' and resid 776 through 789 removed outlier: 3.620A pdb=" N ARG A 789 " --> pdb=" O SER A 785 " (cutoff:3.500A) Processing helix chain 'A' and resid 833 through 852 Processing helix chain 'A' and resid 863 through 874 removed outlier: 3.894A pdb=" N TYR A 867 " --> pdb=" O ASP A 863 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N THR A 874 " --> pdb=" O LEU A 870 " (cutoff:3.500A) Processing helix chain 'A' and resid 898 through 921 Processing helix chain 'A' and resid 963 through 968 removed outlier: 4.142A pdb=" N VAL A 967 " --> pdb=" O SER A 963 " (cutoff:3.500A) Processing helix chain 'A' and resid 971 through 975 removed outlier: 3.721A pdb=" N VAL A 974 " --> pdb=" O ASP A 971 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU A 975 " --> pdb=" O PRO A 972 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 971 through 975' Processing helix chain 'A' and resid 981 through 989 Processing helix chain 'A' and resid 1009 through 1021 Processing helix chain 'A' and resid 1024 through 1035 Processing helix chain 'A' and resid 1135 through 1156 Processing helix chain 'A' and resid 1163 through 1181 Processing helix chain 'A' and resid 1191 through 1196 removed outlier: 3.782A pdb=" N MET A1196 " --> pdb=" O TRP A1192 " (cutoff:3.500A) Processing helix chain 'A' and resid 1197 through 1208 removed outlier: 3.948A pdb=" N PHE A1201 " --> pdb=" O SER A1197 " (cutoff:3.500A) Processing helix chain 'A' and resid 1221 through 1233 Processing helix chain 'A' and resid 1239 through 1249 removed outlier: 3.779A pdb=" N ALA A1243 " --> pdb=" O PRO A1239 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLY A1249 " --> pdb=" O ALA A1245 " (cutoff:3.500A) Processing helix chain 'A' and resid 1264 through 1273 Processing helix chain 'A' and resid 1295 through 1319 Processing helix chain 'A' and resid 1351 through 1365 removed outlier: 3.528A pdb=" N ILE A1355 " --> pdb=" O TRP A1351 " (cutoff:3.500A) Processing helix chain 'A' and resid 1395 through 1405 removed outlier: 3.661A pdb=" N PHE A1399 " --> pdb=" O LEU A1395 " (cutoff:3.500A) Processing helix chain 'A' and resid 1411 through 1429 removed outlier: 3.765A pdb=" N ASN A1429 " --> pdb=" O GLN A1425 " (cutoff:3.500A) Processing helix chain 'A' and resid 1435 through 1450 removed outlier: 3.740A pdb=" N SER A1450 " --> pdb=" O LEU A1446 " (cutoff:3.500A) Processing helix chain 'A' and resid 1472 through 1485 removed outlier: 3.647A pdb=" N PHE A1485 " --> pdb=" O ILE A1481 " (cutoff:3.500A) Processing helix chain 'A' and resid 1489 through 1507 removed outlier: 4.039A pdb=" N ARG A1507 " --> pdb=" O ASN A1503 " (cutoff:3.500A) Processing helix chain 'A' and resid 1514 through 1520 removed outlier: 3.910A pdb=" N GLY A1520 " --> pdb=" O ILE A1516 " (cutoff:3.500A) Processing helix chain 'A' and resid 1523 through 1535 Processing helix chain 'A' and resid 1537 through 1545 removed outlier: 3.783A pdb=" N LEU A1545 " --> pdb=" O VAL A1541 " (cutoff:3.500A) Processing helix chain 'A' and resid 1579 through 1590 removed outlier: 3.700A pdb=" N LYS A1583 " --> pdb=" O PRO A1579 " (cutoff:3.500A) Processing helix chain 'A' and resid 1613 through 1625 Processing helix chain 'A' and resid 1640 through 1646 Processing helix chain 'A' and resid 1665 through 1669 removed outlier: 3.677A pdb=" N ASN A1669 " --> pdb=" O ASN A1666 " (cutoff:3.500A) Processing helix chain 'A' and resid 1678 through 1694 removed outlier: 3.784A pdb=" N GLY A1694 " --> pdb=" O ALA A1690 " (cutoff:3.500A) Processing helix chain 'A' and resid 1695 through 1699 removed outlier: 4.065A pdb=" N SER A1699 " --> pdb=" O TRP A1696 " (cutoff:3.500A) Processing helix chain 'A' and resid 1735 through 1744 Processing helix chain 'A' and resid 1744 through 1750 Processing helix chain 'A' and resid 1758 through 1764 removed outlier: 4.268A pdb=" N SER A1762 " --> pdb=" O ASP A1758 " (cutoff:3.500A) Processing helix chain 'A' and resid 1777 through 1783 Processing helix chain 'A' and resid 1788 through 1793 removed outlier: 3.654A pdb=" N LEU A1793 " --> pdb=" O ILE A1789 " (cutoff:3.500A) Processing helix chain 'A' and resid 1805 through 1810 removed outlier: 4.172A pdb=" N LEU A1810 " --> pdb=" O SER A1806 " (cutoff:3.500A) Processing helix chain 'A' and resid 1826 through 1843 Processing helix chain 'A' and resid 1850 through 1855 Processing helix chain 'A' and resid 1873 through 1877 removed outlier: 3.682A pdb=" N LEU A1877 " --> pdb=" O LEU A1874 " (cutoff:3.500A) Processing helix chain 'A' and resid 1878 through 1883 Processing helix chain 'A' and resid 2005 through 2015 removed outlier: 4.014A pdb=" N ALA A2015 " --> pdb=" O VAL A2011 " (cutoff:3.500A) Processing helix chain 'A' and resid 2031 through 2037 Processing helix chain 'A' and resid 2102 through 2108 Processing helix chain 'A' and resid 2113 through 2129 removed outlier: 4.043A pdb=" N VAL A2117 " --> pdb=" O ASP A2113 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N TRP A2125 " --> pdb=" O LEU A2121 " (cutoff:3.500A) Proline residue: A2126 - end of helix Processing helix chain 'A' and resid 2139 through 2147 removed outlier: 3.749A pdb=" N THR A2143 " --> pdb=" O GLN A2139 " (cutoff:3.500A) Processing helix chain 'A' and resid 2150 through 2157 removed outlier: 3.887A pdb=" N ILE A2157 " --> pdb=" O LEU A2153 " (cutoff:3.500A) Processing helix chain 'C' and resid 4 through 12 Processing helix chain 'C' and resid 19 through 31 removed outlier: 3.600A pdb=" N GLY C 23 " --> pdb=" O ARG C 19 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR C 28 " --> pdb=" O HIS C 24 " (cutoff:3.500A) Processing helix chain 'C' and resid 37 through 57 Processing helix chain 'C' and resid 68 through 76 removed outlier: 3.619A pdb=" N ILE C 72 " --> pdb=" O PHE C 68 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N ASN C 76 " --> pdb=" O ILE C 72 " (cutoff:3.500A) Processing helix chain 'C' and resid 108 through 125 removed outlier: 3.508A pdb=" N ASN C 125 " --> pdb=" O SER C 121 " (cutoff:3.500A) Processing helix chain 'C' and resid 126 through 131 Processing helix chain 'C' and resid 156 through 171 Processing helix chain 'C' and resid 181 through 190 removed outlier: 3.668A pdb=" N GLN C 185 " --> pdb=" O ASP C 181 " (cutoff:3.500A) Processing helix chain 'C' and resid 214 through 220 removed outlier: 3.555A pdb=" N LEU C 218 " --> pdb=" O TYR C 214 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 248 removed outlier: 3.935A pdb=" N VAL C 235 " --> pdb=" O ARG C 231 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ASP C 248 " --> pdb=" O LEU C 244 " (cutoff:3.500A) Processing helix chain 'C' and resid 262 through 275 Processing helix chain 'C' and resid 284 through 288 Processing helix chain 'C' and resid 289 through 303 Processing helix chain 'C' and resid 322 through 338 Processing helix chain 'C' and resid 339 through 341 No H-bonds generated for 'chain 'C' and resid 339 through 341' Processing helix chain 'C' and resid 346 through 365 Processing helix chain 'C' and resid 389 through 391 No H-bonds generated for 'chain 'C' and resid 389 through 391' Processing helix chain 'C' and resid 396 through 405 removed outlier: 3.669A pdb=" N LYS C 405 " --> pdb=" O LYS C 401 " (cutoff:3.500A) Processing helix chain 'C' and resid 412 through 420 removed outlier: 3.685A pdb=" N ILE C 420 " --> pdb=" O ASN C 416 " (cutoff:3.500A) Processing helix chain 'C' and resid 440 through 451 removed outlier: 3.579A pdb=" N LEU C 444 " --> pdb=" O ASP C 440 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU C 451 " --> pdb=" O ILE C 447 " (cutoff:3.500A) Processing helix chain 'C' and resid 474 through 478 Processing helix chain 'C' and resid 481 through 502 removed outlier: 3.650A pdb=" N ARG C 485 " --> pdb=" O PHE C 481 " (cutoff:3.500A) Processing helix chain 'C' and resid 574 through 583 removed outlier: 3.998A pdb=" N PHE C 579 " --> pdb=" O LYS C 576 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N LEU C 580 " --> pdb=" O ARG C 577 " (cutoff:3.500A) Proline residue: C 581 - end of helix Processing helix chain 'C' and resid 586 through 598 Processing helix chain 'C' and resid 609 through 623 Processing helix chain 'C' and resid 625 through 644 removed outlier: 3.776A pdb=" N GLN C 629 " --> pdb=" O SER C 625 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASN C 644 " --> pdb=" O MET C 640 " (cutoff:3.500A) Processing helix chain 'C' and resid 651 through 655 Processing helix chain 'C' and resid 663 through 680 removed outlier: 3.975A pdb=" N VAL C 667 " --> pdb=" O SER C 663 " (cutoff:3.500A) Processing helix chain 'C' and resid 688 through 702 removed outlier: 4.067A pdb=" N ARG C 692 " --> pdb=" O PHE C 688 " (cutoff:3.500A) Processing helix chain 'C' and resid 703 through 706 Processing helix chain 'C' and resid 713 through 732 Proline residue: C 727 - end of helix Processing helix chain 'C' and resid 745 through 760 Processing helix chain 'C' and resid 776 through 789 removed outlier: 3.620A pdb=" N ARG C 789 " --> pdb=" O SER C 785 " (cutoff:3.500A) Processing helix chain 'C' and resid 833 through 852 Processing helix chain 'C' and resid 863 through 874 removed outlier: 3.894A pdb=" N TYR C 867 " --> pdb=" O ASP C 863 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N THR C 874 " --> pdb=" O LEU C 870 " (cutoff:3.500A) Processing helix chain 'C' and resid 898 through 921 Processing helix chain 'C' and resid 963 through 968 removed outlier: 4.142A pdb=" N VAL C 967 " --> pdb=" O SER C 963 " (cutoff:3.500A) Processing helix chain 'C' and resid 971 through 975 removed outlier: 3.722A pdb=" N VAL C 974 " --> pdb=" O ASP C 971 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU C 975 " --> pdb=" O PRO C 972 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 971 through 975' Processing helix chain 'C' and resid 981 through 989 Processing helix chain 'C' and resid 1009 through 1021 Processing helix chain 'C' and resid 1024 through 1035 Processing helix chain 'C' and resid 1135 through 1156 Processing helix chain 'C' and resid 1163 through 1181 Processing helix chain 'C' and resid 1191 through 1196 removed outlier: 3.782A pdb=" N MET C1196 " --> pdb=" O TRP C1192 " (cutoff:3.500A) Processing helix chain 'C' and resid 1197 through 1208 removed outlier: 3.949A pdb=" N PHE C1201 " --> pdb=" O SER C1197 " (cutoff:3.500A) Processing helix chain 'C' and resid 1221 through 1233 Processing helix chain 'C' and resid 1239 through 1249 removed outlier: 3.779A pdb=" N ALA C1243 " --> pdb=" O PRO C1239 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLY C1249 " --> pdb=" O ALA C1245 " (cutoff:3.500A) Processing helix chain 'C' and resid 1264 through 1273 Processing helix chain 'C' and resid 1295 through 1319 Processing helix chain 'C' and resid 1351 through 1365 removed outlier: 3.528A pdb=" N ILE C1355 " --> pdb=" O TRP C1351 " (cutoff:3.500A) Processing helix chain 'C' and resid 1395 through 1405 removed outlier: 3.661A pdb=" N PHE C1399 " --> pdb=" O LEU C1395 " (cutoff:3.500A) Processing helix chain 'C' and resid 1411 through 1429 removed outlier: 3.766A pdb=" N ASN C1429 " --> pdb=" O GLN C1425 " (cutoff:3.500A) Processing helix chain 'C' and resid 1435 through 1450 removed outlier: 3.740A pdb=" N SER C1450 " --> pdb=" O LEU C1446 " (cutoff:3.500A) Processing helix chain 'C' and resid 1472 through 1485 removed outlier: 3.646A pdb=" N PHE C1485 " --> pdb=" O ILE C1481 " (cutoff:3.500A) Processing helix chain 'C' and resid 1489 through 1507 removed outlier: 4.039A pdb=" N ARG C1507 " --> pdb=" O ASN C1503 " (cutoff:3.500A) Processing helix chain 'C' and resid 1514 through 1520 removed outlier: 3.910A pdb=" N GLY C1520 " --> pdb=" O ILE C1516 " (cutoff:3.500A) Processing helix chain 'C' and resid 1523 through 1535 Processing helix chain 'C' and resid 1537 through 1545 removed outlier: 3.783A pdb=" N LEU C1545 " --> pdb=" O VAL C1541 " (cutoff:3.500A) Processing helix chain 'C' and resid 1579 through 1590 removed outlier: 3.700A pdb=" N LYS C1583 " --> pdb=" O PRO C1579 " (cutoff:3.500A) Processing helix chain 'C' and resid 1613 through 1625 Processing helix chain 'C' and resid 1640 through 1646 Processing helix chain 'C' and resid 1665 through 1669 removed outlier: 3.677A pdb=" N ASN C1669 " --> pdb=" O ASN C1666 " (cutoff:3.500A) Processing helix chain 'C' and resid 1678 through 1694 removed outlier: 3.784A pdb=" N GLY C1694 " --> pdb=" O ALA C1690 " (cutoff:3.500A) Processing helix chain 'C' and resid 1695 through 1699 removed outlier: 4.065A pdb=" N SER C1699 " --> pdb=" O TRP C1696 " (cutoff:3.500A) Processing helix chain 'C' and resid 1735 through 1744 Processing helix chain 'C' and resid 1744 through 1750 Processing helix chain 'C' and resid 1758 through 1764 removed outlier: 4.268A pdb=" N SER C1762 " --> pdb=" O ASP C1758 " (cutoff:3.500A) Processing helix chain 'C' and resid 1777 through 1783 Processing helix chain 'C' and resid 1788 through 1793 removed outlier: 3.654A pdb=" N LEU C1793 " --> pdb=" O ILE C1789 " (cutoff:3.500A) Processing helix chain 'C' and resid 1805 through 1810 removed outlier: 4.172A pdb=" N LEU C1810 " --> pdb=" O SER C1806 " (cutoff:3.500A) Processing helix chain 'C' and resid 1826 through 1843 Processing helix chain 'C' and resid 1850 through 1855 Processing helix chain 'C' and resid 1873 through 1877 removed outlier: 3.682A pdb=" N LEU C1877 " --> pdb=" O LEU C1874 " (cutoff:3.500A) Processing helix chain 'C' and resid 1878 through 1883 Processing helix chain 'C' and resid 2005 through 2015 removed outlier: 4.014A pdb=" N ALA C2015 " --> pdb=" O VAL C2011 " (cutoff:3.500A) Processing helix chain 'C' and resid 2031 through 2037 Processing helix chain 'C' and resid 2102 through 2108 Processing helix chain 'C' and resid 2113 through 2129 removed outlier: 4.043A pdb=" N VAL C2117 " --> pdb=" O ASP C2113 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N TRP C2125 " --> pdb=" O LEU C2121 " (cutoff:3.500A) Proline residue: C2126 - end of helix Processing helix chain 'C' and resid 2139 through 2147 removed outlier: 3.749A pdb=" N THR C2143 " --> pdb=" O GLN C2139 " (cutoff:3.500A) Processing helix chain 'C' and resid 2150 through 2157 removed outlier: 3.887A pdb=" N ILE C2157 " --> pdb=" O LEU C2153 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 90 through 94 removed outlier: 7.008A pdb=" N LEU A 98 " --> pdb=" O VAL A 138 " (cutoff:3.500A) removed outlier: 7.702A pdb=" N ILE A 140 " --> pdb=" O LEU A 98 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N LEU A 100 " --> pdb=" O ILE A 140 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N ASP A 142 " --> pdb=" O LEU A 100 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N GLU A 102 " --> pdb=" O ASP A 142 " (cutoff:3.500A) removed outlier: 8.077A pdb=" N ARG A 144 " --> pdb=" O GLU A 102 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N PHE A 104 " --> pdb=" O ARG A 144 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 258 through 260 Processing sheet with id=AA3, first strand: chain 'A' and resid 385 through 387 Processing sheet with id=AA4, first strand: chain 'A' and resid 529 through 534 removed outlier: 6.372A pdb=" N LEU A 559 " --> pdb=" O GLU A 567 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N GLU A 567 " --> pdb=" O LEU A 559 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1129 through 1134 removed outlier: 6.784A pdb=" N PHE A1117 " --> pdb=" O GLU A1237 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1183 through 1188 Processing sheet with id=AA7, first strand: chain 'A' and resid 1379 through 1380 Processing sheet with id=AA8, first strand: chain 'A' and resid 1548 through 1549 Processing sheet with id=AA9, first strand: chain 'A' and resid 1630 through 1631 Processing sheet with id=AB1, first strand: chain 'A' and resid 1716 through 1719 Processing sheet with id=AB2, first strand: chain 'A' and resid 1954 through 1961 removed outlier: 6.850A pdb=" N GLU A1974 " --> pdb=" O VAL A1998 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N VAL A1998 " --> pdb=" O GLU A1974 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N ILE A1976 " --> pdb=" O GLN A1996 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N GLN A1996 " --> pdb=" O ILE A1976 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N ASP A1978 " --> pdb=" O VAL A1994 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N VAL A1994 " --> pdb=" O ASP A1978 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N GLY A1980 " --> pdb=" O VAL A1992 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 2079 through 2080 removed outlier: 6.288A pdb=" N PHE A2085 " --> pdb=" O LEU A2092 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 90 through 94 removed outlier: 7.008A pdb=" N LEU C 98 " --> pdb=" O VAL C 138 " (cutoff:3.500A) removed outlier: 7.703A pdb=" N ILE C 140 " --> pdb=" O LEU C 98 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N LEU C 100 " --> pdb=" O ILE C 140 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N ASP C 142 " --> pdb=" O LEU C 100 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N GLU C 102 " --> pdb=" O ASP C 142 " (cutoff:3.500A) removed outlier: 8.077A pdb=" N ARG C 144 " --> pdb=" O GLU C 102 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N PHE C 104 " --> pdb=" O ARG C 144 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 258 through 260 Processing sheet with id=AB6, first strand: chain 'C' and resid 385 through 387 Processing sheet with id=AB7, first strand: chain 'C' and resid 529 through 534 removed outlier: 6.373A pdb=" N LEU C 559 " --> pdb=" O GLU C 567 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N GLU C 567 " --> pdb=" O LEU C 559 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 1129 through 1134 removed outlier: 6.784A pdb=" N PHE C1117 " --> pdb=" O GLU C1237 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 1183 through 1188 Processing sheet with id=AC1, first strand: chain 'C' and resid 1379 through 1380 Processing sheet with id=AC2, first strand: chain 'C' and resid 1548 through 1549 Processing sheet with id=AC3, first strand: chain 'C' and resid 1630 through 1631 Processing sheet with id=AC4, first strand: chain 'C' and resid 1716 through 1719 Processing sheet with id=AC5, first strand: chain 'C' and resid 1954 through 1961 removed outlier: 6.849A pdb=" N GLU C1974 " --> pdb=" O VAL C1998 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N VAL C1998 " --> pdb=" O GLU C1974 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N ILE C1976 " --> pdb=" O GLN C1996 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N GLN C1996 " --> pdb=" O ILE C1976 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N ASP C1978 " --> pdb=" O VAL C1994 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N VAL C1994 " --> pdb=" O ASP C1978 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N GLY C1980 " --> pdb=" O VAL C1992 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 2079 through 2080 removed outlier: 6.288A pdb=" N PHE C2085 " --> pdb=" O LEU C2092 " (cutoff:3.500A) 1306 hydrogen bonds defined for protein. 3756 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: 6.16 Time building geometry restraints manager: 3.05 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: 9384 1.34 - 1.46: 5850 1.46 - 1.58: 13806 1.58 - 1.70: 26 1.70 - 1.82: 252 Bond restraints: 29318 Sorted by residual: bond pdb=" N VAL A1374 " pdb=" CA VAL A1374 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.17e-02 7.31e+03 8.45e+00 bond pdb=" N VAL C1374 " pdb=" CA VAL C1374 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.17e-02 7.31e+03 8.03e+00 bond pdb=" N ILE A1375 " pdb=" CA ILE A1375 " ideal model delta sigma weight residual 1.459 1.490 -0.031 1.25e-02 6.40e+03 6.14e+00 bond pdb=" N ILE C1375 " pdb=" CA ILE C1375 " ideal model delta sigma weight residual 1.459 1.490 -0.031 1.25e-02 6.40e+03 6.06e+00 bond pdb=" N GLN A1532 " pdb=" CA GLN A1532 " ideal model delta sigma weight residual 1.457 1.478 -0.021 1.33e-02 5.65e+03 2.53e+00 ... (remaining 29313 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.34: 38938 2.34 - 4.67: 658 4.67 - 7.01: 103 7.01 - 9.34: 15 9.34 - 11.68: 2 Bond angle restraints: 39716 Sorted by residual: angle pdb=" CA GLU A1822 " pdb=" CB GLU A1822 " pdb=" CG GLU A1822 " ideal model delta sigma weight residual 114.10 122.24 -8.14 2.00e+00 2.50e-01 1.66e+01 angle pdb=" CA GLU C1822 " pdb=" CB GLU C1822 " pdb=" CG GLU C1822 " ideal model delta sigma weight residual 114.10 122.23 -8.13 2.00e+00 2.50e-01 1.65e+01 angle pdb=" N GLU C 593 " pdb=" CA GLU C 593 " pdb=" CB GLU C 593 " ideal model delta sigma weight residual 110.28 116.39 -6.11 1.55e+00 4.16e-01 1.55e+01 angle pdb=" N GLU A 593 " pdb=" CA GLU A 593 " pdb=" CB GLU A 593 " ideal model delta sigma weight residual 110.28 116.38 -6.10 1.55e+00 4.16e-01 1.55e+01 angle pdb=" CB MET C 385 " pdb=" CG MET C 385 " pdb=" SD MET C 385 " ideal model delta sigma weight residual 112.70 124.38 -11.68 3.00e+00 1.11e-01 1.51e+01 ... (remaining 39711 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.87: 16276 18.87 - 37.74: 1228 37.74 - 56.61: 224 56.61 - 75.49: 52 75.49 - 94.36: 18 Dihedral angle restraints: 17798 sinusoidal: 6804 harmonic: 10994 Sorted by residual: dihedral pdb=" CA TRP C1859 " pdb=" C TRP C1859 " pdb=" N PHE C1860 " pdb=" CA PHE C1860 " ideal model delta harmonic sigma weight residual 180.00 156.24 23.76 0 5.00e+00 4.00e-02 2.26e+01 dihedral pdb=" CA TRP A1859 " pdb=" C TRP A1859 " pdb=" N PHE A1860 " pdb=" CA PHE A1860 " ideal model delta harmonic sigma weight residual 180.00 156.30 23.70 0 5.00e+00 4.00e-02 2.25e+01 dihedral pdb=" CA PHE C1858 " pdb=" C PHE C1858 " pdb=" N TRP C1859 " pdb=" CA TRP C1859 " ideal model delta harmonic sigma weight residual -180.00 -156.40 -23.60 0 5.00e+00 4.00e-02 2.23e+01 ... (remaining 17795 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 3696 0.052 - 0.103: 825 0.103 - 0.155: 123 0.155 - 0.207: 20 0.207 - 0.258: 2 Chirality restraints: 4666 Sorted by residual: chirality pdb=" CA VAL A1374 " pdb=" N VAL A1374 " pdb=" C VAL A1374 " pdb=" CB VAL A1374 " both_signs ideal model delta sigma weight residual False 2.44 2.70 -0.26 2.00e-01 2.50e+01 1.67e+00 chirality pdb=" CA VAL C1374 " pdb=" N VAL C1374 " pdb=" C VAL C1374 " pdb=" CB VAL C1374 " both_signs ideal model delta sigma weight residual False 2.44 2.70 -0.26 2.00e-01 2.50e+01 1.65e+00 chirality pdb=" CA GLU C 41 " pdb=" N GLU C 41 " pdb=" C GLU C 41 " pdb=" CB GLU C 41 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.02e+00 ... (remaining 4663 not shown) Planarity restraints: 5024 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A1717 " 0.015 2.00e-02 2.50e+03 1.44e-02 5.19e+00 pdb=" CG TRP A1717 " -0.039 2.00e-02 2.50e+03 pdb=" CD1 TRP A1717 " 0.019 2.00e-02 2.50e+03 pdb=" CD2 TRP A1717 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A1717 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A1717 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A1717 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP A1717 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A1717 " 0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP A1717 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C1717 " 0.014 2.00e-02 2.50e+03 1.43e-02 5.10e+00 pdb=" CG TRP C1717 " -0.038 2.00e-02 2.50e+03 pdb=" CD1 TRP C1717 " 0.019 2.00e-02 2.50e+03 pdb=" CD2 TRP C1717 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP C1717 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP C1717 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP C1717 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP C1717 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP C1717 " 0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP C1717 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A1821 " -0.011 2.00e-02 2.50e+03 1.29e-02 4.16e+00 pdb=" CG TRP A1821 " 0.035 2.00e-02 2.50e+03 pdb=" CD1 TRP A1821 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 TRP A1821 " -0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP A1821 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A1821 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A1821 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP A1821 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A1821 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP A1821 " 0.001 2.00e-02 2.50e+03 ... (remaining 5021 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 5196 2.77 - 3.30: 29606 3.30 - 3.83: 45577 3.83 - 4.37: 51738 4.37 - 4.90: 85975 Nonbonded interactions: 218092 Sorted by model distance: nonbonded pdb=" OG1 THR A 345 " pdb=" OD1 ASN A 348 " model vdw 2.233 3.040 nonbonded pdb=" OG1 THR C 345 " pdb=" OD1 ASN C 348 " model vdw 2.233 3.040 nonbonded pdb=" O ALA A 619 " pdb=" OG SER A 623 " model vdw 2.247 3.040 nonbonded pdb=" O ALA C 619 " pdb=" OG SER C 623 " model vdw 2.247 3.040 nonbonded pdb=" O THR A 345 " pdb=" OG1 THR A 349 " model vdw 2.253 3.040 ... (remaining 218087 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } 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 group one per residue 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: 0.540 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: 0.020 Extract box with map and model: 0.400 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 44.620 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 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 : 0.003 0.088 29330 Z= 0.151 Angle : 0.732 12.726 39730 Z= 0.382 Chirality : 0.045 0.258 4666 Planarity : 0.004 0.053 5024 Dihedral : 14.134 94.357 10614 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.11 % Allowed : 9.05 % Favored : 90.85 % Rotamer: Outliers : 0.53 % Allowed : 1.70 % Favored : 97.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.80 (0.13), residues: 3692 helix: 0.17 (0.13), residues: 1712 sheet: -0.22 (0.33), residues: 222 loop : -2.86 (0.13), residues: 1758 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C1509 TYR 0.017 0.001 TYR C1818 PHE 0.024 0.001 PHE A1858 TRP 0.039 0.002 TRP A1717 HIS 0.005 0.001 HIS C1791 Details of bonding type rmsd covalent geometry : bond 0.00294 (29318) covalent geometry : angle 0.72419 (39716) SS BOND : bond 0.00121 ( 4) SS BOND : angle 1.63508 ( 8) hydrogen bonds : bond 0.13743 ( 1306) hydrogen bonds : angle 5.93347 ( 3756) metal coordination : bond 0.07316 ( 8) metal coordination : angle 8.39398 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7384 Ramachandran restraints generated. 3692 Oldfield, 0 Emsley, 3692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7384 Ramachandran restraints generated. 3692 Oldfield, 0 Emsley, 3692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 512 residues out of total 3448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 496 time to evaluate : 1.031 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 LEU cc_start: 0.9172 (OUTLIER) cc_final: 0.8924 (mp) REVERT: A 120 MET cc_start: 0.8188 (tpt) cc_final: 0.7130 (tpt) REVERT: A 333 LEU cc_start: 0.9193 (OUTLIER) cc_final: 0.8930 (mm) REVERT: A 351 LEU cc_start: 0.9511 (mt) cc_final: 0.9163 (mt) REVERT: A 356 ILE cc_start: 0.8834 (mt) cc_final: 0.8629 (mt) REVERT: A 382 VAL cc_start: 0.7593 (m) cc_final: 0.7316 (m) REVERT: A 488 LYS cc_start: 0.9024 (ttmt) cc_final: 0.8815 (ttmm) REVERT: A 550 GLU cc_start: 0.8158 (tp30) cc_final: 0.7868 (tp30) REVERT: A 591 MET cc_start: 0.7428 (ttp) cc_final: 0.7223 (ttm) REVERT: A 606 MET cc_start: 0.9019 (mpp) cc_final: 0.8652 (mpp) REVERT: A 848 MET cc_start: 0.8227 (mmt) cc_final: 0.7996 (mmt) REVERT: A 900 GLU cc_start: 0.9386 (mt-10) cc_final: 0.9146 (mm-30) REVERT: A 1097 TYR cc_start: 0.5522 (t80) cc_final: 0.5129 (t80) REVERT: A 1142 THR cc_start: 0.9550 (p) cc_final: 0.9340 (p) REVERT: A 1210 LEU cc_start: 0.7888 (mm) cc_final: 0.7671 (mm) REVERT: A 1289 ASP cc_start: 0.7543 (t70) cc_final: 0.7116 (t70) REVERT: A 1440 SER cc_start: 0.8729 (m) cc_final: 0.8238 (p) REVERT: A 1509 ARG cc_start: 0.6773 (OUTLIER) cc_final: 0.6330 (mmp80) REVERT: A 1733 MET cc_start: 0.1463 (tpt) cc_final: 0.0258 (tpt) REVERT: A 1765 MET cc_start: 0.3652 (mmm) cc_final: 0.3158 (mmp) REVERT: C 120 MET cc_start: 0.8034 (tpt) cc_final: 0.6920 (tpt) REVERT: C 207 LEU cc_start: 0.7915 (mm) cc_final: 0.7279 (mt) REVERT: C 231 ARG cc_start: 0.8221 (ptm-80) cc_final: 0.7638 (ptm-80) REVERT: C 356 ILE cc_start: 0.8234 (mt) cc_final: 0.8033 (mt) REVERT: C 395 ASP cc_start: 0.7787 (t0) cc_final: 0.7252 (t70) REVERT: C 900 GLU cc_start: 0.8442 (mt-10) cc_final: 0.8238 (mm-30) REVERT: C 1097 TYR cc_start: 0.4781 (t80) cc_final: 0.4573 (t80) REVERT: C 1142 THR cc_start: 0.9403 (p) cc_final: 0.9117 (p) REVERT: C 1336 LYS cc_start: 0.8394 (mppt) cc_final: 0.8137 (tppt) REVERT: C 1509 ARG cc_start: 0.5875 (OUTLIER) cc_final: 0.5649 (mmp80) REVERT: C 1678 ILE cc_start: 0.9051 (tp) cc_final: 0.8714 (tp) REVERT: C 1731 LEU cc_start: 0.7212 (mt) cc_final: 0.6865 (mt) REVERT: C 1733 MET cc_start: 0.2583 (tpt) cc_final: 0.1351 (tpt) REVERT: C 1765 MET cc_start: 0.4598 (mmm) cc_final: 0.4068 (mmp) REVERT: C 1780 ASP cc_start: 0.7616 (t0) cc_final: 0.7330 (m-30) outliers start: 16 outliers final: 1 residues processed: 500 average time/residue: 0.1656 time to fit residues: 138.0589 Evaluate side-chains 368 residues out of total 3448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 363 time to evaluate : 1.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 1509 ARG Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 1509 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 197 optimal weight: 6.9990 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 8.9990 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 9.9990 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 0.0010 chunk 183 optimal weight: 0.9990 chunk 298 optimal weight: 9.9990 overall best weight: 1.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 629 GLN A 633 GLN A 704 HIS A 788 ASN A 801 ASN A 910 HIS ** A1034 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1738 GLN ** A1812 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 416 ASN ** C 629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 633 GLN C 788 ASN C 801 ASN C 910 HIS ** C1034 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1358 HIS ** C1405 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.134341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.103212 restraints weight = 81927.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.101034 restraints weight = 49243.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.102288 restraints weight = 41800.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.102481 restraints weight = 36775.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.102786 restraints weight = 31724.374| |-----------------------------------------------------------------------------| r_work (final): 0.3630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.1810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 29330 Z= 0.139 Angle : 0.651 9.353 39730 Z= 0.330 Chirality : 0.043 0.186 4666 Planarity : 0.004 0.037 5024 Dihedral : 8.323 94.216 4206 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.32 % Favored : 91.58 % Rotamer: Outliers : 1.67 % Allowed : 10.73 % Favored : 87.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.41 (0.14), residues: 3692 helix: 0.60 (0.13), residues: 1740 sheet: -0.90 (0.31), residues: 260 loop : -2.72 (0.14), residues: 1692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C1769 TYR 0.021 0.001 TYR C 701 PHE 0.033 0.001 PHE A 352 TRP 0.039 0.002 TRP C1717 HIS 0.003 0.001 HIS C1231 Details of bonding type rmsd covalent geometry : bond 0.00310 (29318) covalent geometry : angle 0.64770 (39716) SS BOND : bond 0.00863 ( 4) SS BOND : angle 1.75219 ( 8) hydrogen bonds : bond 0.03546 ( 1306) hydrogen bonds : angle 4.46100 ( 3756) metal coordination : bond 0.03645 ( 8) metal coordination : angle 4.67537 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7384 Ramachandran restraints generated. 3692 Oldfield, 0 Emsley, 3692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7384 Ramachandran restraints generated. 3692 Oldfield, 0 Emsley, 3692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 3448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 401 time to evaluate : 1.051 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.8231 (tpt) cc_final: 0.7206 (tpt) REVERT: A 333 LEU cc_start: 0.9358 (mt) cc_final: 0.9073 (mt) REVERT: A 351 LEU cc_start: 0.9532 (mt) cc_final: 0.9159 (mt) REVERT: A 435 LEU cc_start: 0.8333 (tt) cc_final: 0.7783 (tt) REVERT: A 550 GLU cc_start: 0.8331 (tp30) cc_final: 0.7886 (tp30) REVERT: A 594 GLU cc_start: 0.8338 (pp20) cc_final: 0.7972 (pp20) REVERT: A 900 GLU cc_start: 0.9290 (mt-10) cc_final: 0.9029 (mm-30) REVERT: A 919 MET cc_start: 0.8132 (ptm) cc_final: 0.7869 (ptp) REVERT: A 1097 TYR cc_start: 0.5543 (t80) cc_final: 0.5139 (t80) REVERT: A 1141 MET cc_start: 0.9492 (mmm) cc_final: 0.9150 (mmp) REVERT: A 1210 LEU cc_start: 0.7986 (mm) cc_final: 0.7750 (mm) REVERT: A 1289 ASP cc_start: 0.7475 (t70) cc_final: 0.6996 (t70) REVERT: A 1294 ILE cc_start: 0.9021 (mm) cc_final: 0.8737 (mt) REVERT: A 1440 SER cc_start: 0.8954 (m) cc_final: 0.8371 (p) REVERT: A 1540 GLU cc_start: 0.7144 (mm-30) cc_final: 0.6580 (mm-30) REVERT: A 1731 LEU cc_start: 0.8191 (mt) cc_final: 0.7912 (mt) REVERT: A 1733 MET cc_start: 0.2653 (tpt) cc_final: 0.1302 (tpt) REVERT: A 1861 ASN cc_start: 0.8243 (m-40) cc_final: 0.7995 (m-40) REVERT: C 120 MET cc_start: 0.8210 (tpt) cc_final: 0.7318 (tpp) REVERT: C 207 LEU cc_start: 0.7953 (mm) cc_final: 0.7458 (mt) REVERT: C 293 GLU cc_start: 0.8026 (tp30) cc_final: 0.7678 (tp30) REVERT: C 401 LYS cc_start: 0.8997 (mmtm) cc_final: 0.8770 (mmtm) REVERT: C 585 ASP cc_start: 0.7713 (p0) cc_final: 0.7399 (p0) REVERT: C 709 GLU cc_start: 0.8277 (mm-30) cc_final: 0.8031 (mt-10) REVERT: C 1097 TYR cc_start: 0.4948 (t80) cc_final: 0.4656 (t80) REVERT: C 1143 ARG cc_start: 0.8785 (OUTLIER) cc_final: 0.8503 (ptm160) REVERT: C 1269 PHE cc_start: 0.8908 (t80) cc_final: 0.8639 (t80) REVERT: C 1274 MET cc_start: 0.5799 (pmm) cc_final: 0.5554 (pmm) REVERT: C 1466 LYS cc_start: 0.7986 (ttpt) cc_final: 0.7628 (ttmt) REVERT: C 1511 PHE cc_start: 0.6593 (m-80) cc_final: 0.6223 (m-10) REVERT: C 1678 ILE cc_start: 0.8908 (tp) cc_final: 0.8618 (tp) REVERT: C 1728 GLU cc_start: 0.7447 (tm-30) cc_final: 0.7015 (tm-30) REVERT: C 1731 LEU cc_start: 0.7627 (mt) cc_final: 0.6904 (mt) REVERT: C 1765 MET cc_start: 0.4763 (mmm) cc_final: 0.4184 (mmm) REVERT: C 1780 ASP cc_start: 0.8156 (t0) cc_final: 0.7950 (t0) REVERT: C 1793 LEU cc_start: 0.8446 (OUTLIER) cc_final: 0.8199 (pp) outliers start: 50 outliers final: 24 residues processed: 428 average time/residue: 0.1627 time to fit residues: 116.9104 Evaluate side-chains 363 residues out of total 3448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 337 time to evaluate : 1.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 565 MET Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 1356 CYS Chi-restraints excluded: chain A residue 1687 LEU Chi-restraints excluded: chain A residue 1770 LEU Chi-restraints excluded: chain A residue 1791 HIS Chi-restraints excluded: chain A residue 1882 LEU Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 481 PHE Chi-restraints excluded: chain C residue 503 THR Chi-restraints excluded: chain C residue 587 VAL Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 798 LEU Chi-restraints excluded: chain C residue 1143 ARG Chi-restraints excluded: chain C residue 1144 LEU Chi-restraints excluded: chain C residue 1212 THR Chi-restraints excluded: chain C residue 1301 LEU Chi-restraints excluded: chain C residue 1691 CYS Chi-restraints excluded: chain C residue 1770 LEU Chi-restraints excluded: chain C residue 1791 HIS Chi-restraints excluded: chain C residue 1792 LEU Chi-restraints excluded: chain C residue 1793 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 87 optimal weight: 0.9990 chunk 240 optimal weight: 5.9990 chunk 299 optimal weight: 7.9990 chunk 303 optimal weight: 0.9990 chunk 2 optimal weight: 8.9990 chunk 321 optimal weight: 1.9990 chunk 78 optimal weight: 9.9990 chunk 69 optimal weight: 3.9990 chunk 203 optimal weight: 0.0060 chunk 84 optimal weight: 50.0000 chunk 52 optimal weight: 8.9990 overall best weight: 1.6004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 704 HIS A 872 ASN ** A1034 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1414 GLN A1689 ASN ** C 629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 872 ASN ** C1034 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1296 HIS ** C1405 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1738 GLN C1886 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.132518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.100526 restraints weight = 81033.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.098900 restraints weight = 47913.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.099934 restraints weight = 40939.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.100236 restraints weight = 36426.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.100542 restraints weight = 30886.598| |-----------------------------------------------------------------------------| r_work (final): 0.3590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.2514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 29330 Z= 0.131 Angle : 0.619 12.398 39730 Z= 0.312 Chirality : 0.042 0.198 4666 Planarity : 0.003 0.038 5024 Dihedral : 8.054 93.555 4192 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.99 % Favored : 91.96 % Rotamer: Outliers : 2.10 % Allowed : 14.40 % Favored : 83.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.15 (0.14), residues: 3692 helix: 0.76 (0.13), residues: 1776 sheet: -0.46 (0.32), residues: 240 loop : -2.62 (0.14), residues: 1676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 231 TYR 0.016 0.001 TYR C 701 PHE 0.027 0.001 PHE A 352 TRP 0.030 0.001 TRP C1717 HIS 0.006 0.001 HIS C1296 Details of bonding type rmsd covalent geometry : bond 0.00287 (29318) covalent geometry : angle 0.61722 (39716) SS BOND : bond 0.00435 ( 4) SS BOND : angle 1.02398 ( 8) hydrogen bonds : bond 0.03246 ( 1306) hydrogen bonds : angle 4.15880 ( 3756) metal coordination : bond 0.02945 ( 8) metal coordination : angle 3.91996 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7384 Ramachandran restraints generated. 3692 Oldfield, 0 Emsley, 3692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7384 Ramachandran restraints generated. 3692 Oldfield, 0 Emsley, 3692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 3448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 365 time to evaluate : 0.831 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.8137 (tpt) cc_final: 0.7123 (tpt) REVERT: A 292 MET cc_start: 0.8315 (mtp) cc_final: 0.8091 (mtp) REVERT: A 398 GLU cc_start: 0.8825 (mp0) cc_final: 0.8233 (mp0) REVERT: A 550 GLU cc_start: 0.8353 (tp30) cc_final: 0.8121 (tp30) REVERT: A 594 GLU cc_start: 0.8313 (pp20) cc_final: 0.7982 (pp20) REVERT: A 900 GLU cc_start: 0.9295 (mt-10) cc_final: 0.9042 (mm-30) REVERT: A 1097 TYR cc_start: 0.5652 (t80) cc_final: 0.5246 (t80) REVERT: A 1141 MET cc_start: 0.9530 (mmm) cc_final: 0.9180 (mmp) REVERT: A 1289 ASP cc_start: 0.7600 (t70) cc_final: 0.7098 (t70) REVERT: A 1540 GLU cc_start: 0.7366 (mm-30) cc_final: 0.6762 (mm-30) REVERT: A 1733 MET cc_start: 0.3660 (tpt) cc_final: 0.2561 (tpt) REVERT: C 120 MET cc_start: 0.8522 (tpt) cc_final: 0.7739 (tpp) REVERT: C 401 LYS cc_start: 0.9056 (mmtm) cc_final: 0.8837 (mmtm) REVERT: C 598 TRP cc_start: 0.8794 (OUTLIER) cc_final: 0.8223 (m-10) REVERT: C 708 LYS cc_start: 0.8483 (OUTLIER) cc_final: 0.8054 (pttp) REVERT: C 1097 TYR cc_start: 0.5404 (t80) cc_final: 0.5041 (t80) REVERT: C 1143 ARG cc_start: 0.8785 (OUTLIER) cc_final: 0.8503 (ptm160) REVERT: C 1150 GLU cc_start: 0.7642 (mt-10) cc_final: 0.7067 (mp0) REVERT: C 1678 ILE cc_start: 0.8897 (tp) cc_final: 0.8614 (tp) REVERT: C 1728 GLU cc_start: 0.7199 (tm-30) cc_final: 0.6806 (tm-30) REVERT: C 1731 LEU cc_start: 0.7815 (mt) cc_final: 0.7140 (mt) REVERT: C 1829 GLN cc_start: 0.9049 (tm-30) cc_final: 0.8770 (tm-30) REVERT: C 1882 LEU cc_start: 0.9245 (mm) cc_final: 0.9034 (mm) outliers start: 63 outliers final: 37 residues processed: 404 average time/residue: 0.1507 time to fit residues: 103.3531 Evaluate side-chains 365 residues out of total 3448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 325 time to evaluate : 1.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 GLU Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 481 PHE Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 598 TRP Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 1011 LEU Chi-restraints excluded: chain A residue 1185 CYS Chi-restraints excluded: chain A residue 1532 GLN Chi-restraints excluded: chain A residue 1687 LEU Chi-restraints excluded: chain A residue 1770 LEU Chi-restraints excluded: chain A residue 1789 ILE Chi-restraints excluded: chain A residue 1791 HIS Chi-restraints excluded: chain A residue 1882 LEU Chi-restraints excluded: chain A residue 1884 VAL Chi-restraints excluded: chain C residue 41 GLU Chi-restraints excluded: chain C residue 388 LEU Chi-restraints excluded: chain C residue 444 LEU Chi-restraints excluded: chain C residue 481 PHE Chi-restraints excluded: chain C residue 503 THR Chi-restraints excluded: chain C residue 587 VAL Chi-restraints excluded: chain C residue 598 TRP Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 708 LYS Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 798 LEU Chi-restraints excluded: chain C residue 1143 ARG Chi-restraints excluded: chain C residue 1212 THR Chi-restraints excluded: chain C residue 1301 LEU Chi-restraints excluded: chain C residue 1431 VAL Chi-restraints excluded: chain C residue 1532 GLN Chi-restraints excluded: chain C residue 1541 VAL Chi-restraints excluded: chain C residue 1691 CYS Chi-restraints excluded: chain C residue 1770 LEU Chi-restraints excluded: chain C residue 1791 HIS Chi-restraints excluded: chain C residue 1792 LEU Chi-restraints excluded: chain C residue 1813 ILE Chi-restraints excluded: chain C residue 1886 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 71 optimal weight: 5.9990 chunk 67 optimal weight: 5.9990 chunk 153 optimal weight: 0.7980 chunk 251 optimal weight: 7.9990 chunk 34 optimal weight: 5.9990 chunk 60 optimal weight: 6.9990 chunk 252 optimal weight: 5.9990 chunk 24 optimal weight: 9.9990 chunk 142 optimal weight: 0.9990 chunk 161 optimal weight: 8.9990 chunk 309 optimal weight: 4.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 430 HIS ** A 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 607 ASN ** A 704 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1296 HIS A1414 GLN A1689 ASN A1798 ASN A1837 GLN C 430 HIS ** C 629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 717 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1405 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1689 ASN C1886 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.124180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.091216 restraints weight = 81900.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.089156 restraints weight = 54550.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.090013 restraints weight = 43799.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.091413 restraints weight = 35946.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.091385 restraints weight = 30475.772| |-----------------------------------------------------------------------------| r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.3788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.090 29330 Z= 0.227 Angle : 0.710 10.881 39730 Z= 0.362 Chirality : 0.044 0.189 4666 Planarity : 0.004 0.054 5024 Dihedral : 8.351 97.882 4192 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.99 % Favored : 89.95 % Rotamer: Outliers : 3.40 % Allowed : 16.73 % Favored : 79.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.20 (0.14), residues: 3692 helix: 0.73 (0.12), residues: 1764 sheet: -1.06 (0.30), residues: 286 loop : -2.56 (0.15), residues: 1642 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C1814 TYR 0.022 0.002 TYR C 701 PHE 0.026 0.002 PHE A 352 TRP 0.025 0.002 TRP A1717 HIS 0.006 0.001 HIS A1296 Details of bonding type rmsd covalent geometry : bond 0.00514 (29318) covalent geometry : angle 0.70587 (39716) SS BOND : bond 0.00843 ( 4) SS BOND : angle 0.79729 ( 8) hydrogen bonds : bond 0.04116 ( 1306) hydrogen bonds : angle 4.38829 ( 3756) metal coordination : bond 0.02940 ( 8) metal coordination : angle 6.13834 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7384 Ramachandran restraints generated. 3692 Oldfield, 0 Emsley, 3692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7384 Ramachandran restraints generated. 3692 Oldfield, 0 Emsley, 3692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 3448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 332 time to evaluate : 1.099 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 PHE cc_start: 0.6693 (p90) cc_final: 0.6230 (p90) REVERT: A 120 MET cc_start: 0.8190 (tpt) cc_final: 0.7355 (tpt) REVERT: A 268 GLU cc_start: 0.8491 (OUTLIER) cc_final: 0.8162 (mt-10) REVERT: A 333 LEU cc_start: 0.9506 (OUTLIER) cc_final: 0.9149 (mt) REVERT: A 351 LEU cc_start: 0.9498 (mt) cc_final: 0.9279 (mt) REVERT: A 398 GLU cc_start: 0.8894 (mp0) cc_final: 0.7916 (mp0) REVERT: A 401 LYS cc_start: 0.9425 (mmtm) cc_final: 0.9140 (mttt) REVERT: A 550 GLU cc_start: 0.8514 (tp30) cc_final: 0.8159 (tp30) REVERT: A 594 GLU cc_start: 0.8471 (pp20) cc_final: 0.7798 (pp20) REVERT: A 598 TRP cc_start: 0.8992 (OUTLIER) cc_final: 0.8374 (m-10) REVERT: A 900 GLU cc_start: 0.9341 (mt-10) cc_final: 0.9092 (mm-30) REVERT: A 919 MET cc_start: 0.8249 (ptm) cc_final: 0.7983 (ptp) REVERT: A 1097 TYR cc_start: 0.5982 (t80) cc_final: 0.5427 (t80) REVERT: A 1141 MET cc_start: 0.9620 (mmm) cc_final: 0.9207 (mmp) REVERT: A 1156 MET cc_start: 0.7911 (mmm) cc_final: 0.7191 (mmm) REVERT: A 1285 MET cc_start: 0.7624 (tpt) cc_final: 0.6928 (tpt) REVERT: A 1829 GLN cc_start: 0.9222 (tp40) cc_final: 0.9002 (tp40) REVERT: C 120 MET cc_start: 0.8578 (tpt) cc_final: 0.7914 (tpp) REVERT: C 182 GLN cc_start: 0.8134 (OUTLIER) cc_final: 0.7801 (pp30) REVERT: C 585 ASP cc_start: 0.7940 (p0) cc_final: 0.7618 (p0) REVERT: C 598 TRP cc_start: 0.9038 (OUTLIER) cc_final: 0.8207 (m-10) REVERT: C 1121 TYR cc_start: 0.8847 (p90) cc_final: 0.8351 (p90) REVERT: C 1146 GLU cc_start: 0.8206 (mm-30) cc_final: 0.7829 (mm-30) REVERT: C 1244 GLU cc_start: 0.7959 (OUTLIER) cc_final: 0.7580 (mp0) REVERT: C 1307 GLU cc_start: 0.8202 (tp30) cc_final: 0.7963 (tp30) REVERT: C 1531 LEU cc_start: 0.8717 (OUTLIER) cc_final: 0.8441 (mm) REVERT: C 1781 MET cc_start: 0.8514 (mmm) cc_final: 0.8311 (mmm) REVERT: C 1829 GLN cc_start: 0.9150 (tm-30) cc_final: 0.8846 (tm-30) REVERT: C 1886 ASN cc_start: 0.8246 (m110) cc_final: 0.7502 (t0) outliers start: 102 outliers final: 61 residues processed: 405 average time/residue: 0.1527 time to fit residues: 104.6937 Evaluate side-chains 373 residues out of total 3448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 305 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 268 GLU Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 416 ASN Chi-restraints excluded: chain A residue 481 PHE Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 591 MET Chi-restraints excluded: chain A residue 598 TRP Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 707 THR Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 906 ASN Chi-restraints excluded: chain A residue 1011 LEU Chi-restraints excluded: chain A residue 1185 CYS Chi-restraints excluded: chain A residue 1560 LEU Chi-restraints excluded: chain A residue 1588 LYS Chi-restraints excluded: chain A residue 1619 ILE Chi-restraints excluded: chain A residue 1648 SER Chi-restraints excluded: chain A residue 1687 LEU Chi-restraints excluded: chain A residue 1770 LEU Chi-restraints excluded: chain A residue 1789 ILE Chi-restraints excluded: chain A residue 1791 HIS Chi-restraints excluded: chain A residue 1877 LEU Chi-restraints excluded: chain A residue 1882 LEU Chi-restraints excluded: chain A residue 1884 VAL Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 182 GLN Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 331 LEU Chi-restraints excluded: chain C residue 360 LEU Chi-restraints excluded: chain C residue 416 ASN Chi-restraints excluded: chain C residue 431 HIS Chi-restraints excluded: chain C residue 444 LEU Chi-restraints excluded: chain C residue 481 PHE Chi-restraints excluded: chain C residue 503 THR Chi-restraints excluded: chain C residue 587 VAL Chi-restraints excluded: chain C residue 598 TRP Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 735 VAL Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 780 LEU Chi-restraints excluded: chain C residue 1144 LEU Chi-restraints excluded: chain C residue 1202 LEU Chi-restraints excluded: chain C residue 1212 THR Chi-restraints excluded: chain C residue 1244 GLU Chi-restraints excluded: chain C residue 1265 LEU Chi-restraints excluded: chain C residue 1274 MET Chi-restraints excluded: chain C residue 1296 HIS Chi-restraints excluded: chain C residue 1301 LEU Chi-restraints excluded: chain C residue 1320 VAL Chi-restraints excluded: chain C residue 1431 VAL Chi-restraints excluded: chain C residue 1436 VAL Chi-restraints excluded: chain C residue 1531 LEU Chi-restraints excluded: chain C residue 1532 GLN Chi-restraints excluded: chain C residue 1541 VAL Chi-restraints excluded: chain C residue 1560 LEU Chi-restraints excluded: chain C residue 1619 ILE Chi-restraints excluded: chain C residue 1691 CYS Chi-restraints excluded: chain C residue 1751 HIS Chi-restraints excluded: chain C residue 1770 LEU Chi-restraints excluded: chain C residue 1786 LEU Chi-restraints excluded: chain C residue 1792 LEU Chi-restraints excluded: chain C residue 1842 SER Chi-restraints excluded: chain C residue 1882 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 43 optimal weight: 5.9990 chunk 23 optimal weight: 8.9990 chunk 316 optimal weight: 0.9980 chunk 59 optimal weight: 2.9990 chunk 364 optimal weight: 0.1980 chunk 219 optimal weight: 4.9990 chunk 198 optimal weight: 5.9990 chunk 26 optimal weight: 20.0000 chunk 142 optimal weight: 2.9990 chunk 205 optimal weight: 9.9990 chunk 180 optimal weight: 40.0000 overall best weight: 2.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 704 HIS A 800 ASN A1414 GLN A1730 GLN ** C 629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 800 ASN C 910 HIS ** C1405 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1730 GLN C1887 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.124876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.087066 restraints weight = 81042.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.089672 restraints weight = 45602.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.091277 restraints weight = 32039.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.092336 restraints weight = 25743.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.092919 restraints weight = 22412.941| |-----------------------------------------------------------------------------| r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.4121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 29330 Z= 0.157 Angle : 0.644 11.139 39730 Z= 0.325 Chirality : 0.042 0.177 4666 Planarity : 0.003 0.040 5024 Dihedral : 8.155 94.410 4192 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.15 % Favored : 91.79 % Rotamer: Outliers : 3.23 % Allowed : 19.80 % Favored : 76.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.99 (0.14), residues: 3692 helix: 0.92 (0.13), residues: 1770 sheet: -0.74 (0.32), residues: 262 loop : -2.52 (0.15), residues: 1660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 231 TYR 0.016 0.001 TYR C1682 PHE 0.022 0.001 PHE A 352 TRP 0.020 0.002 TRP C1717 HIS 0.003 0.001 HIS C 648 Details of bonding type rmsd covalent geometry : bond 0.00354 (29318) covalent geometry : angle 0.64184 (39716) SS BOND : bond 0.00546 ( 4) SS BOND : angle 0.62149 ( 8) hydrogen bonds : bond 0.03327 ( 1306) hydrogen bonds : angle 4.14832 ( 3756) metal coordination : bond 0.02787 ( 8) metal coordination : angle 4.58820 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7384 Ramachandran restraints generated. 3692 Oldfield, 0 Emsley, 3692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7384 Ramachandran restraints generated. 3692 Oldfield, 0 Emsley, 3692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 436 residues out of total 3448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 339 time to evaluate : 0.997 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 PHE cc_start: 0.7059 (p90) cc_final: 0.6468 (p90) REVERT: A 120 MET cc_start: 0.8365 (tpt) cc_final: 0.7569 (tpt) REVERT: A 333 LEU cc_start: 0.9510 (OUTLIER) cc_final: 0.9168 (mt) REVERT: A 351 LEU cc_start: 0.9520 (mt) cc_final: 0.9304 (mt) REVERT: A 398 GLU cc_start: 0.8907 (mp0) cc_final: 0.8510 (mp0) REVERT: A 550 GLU cc_start: 0.8567 (tp30) cc_final: 0.8181 (tp30) REVERT: A 594 GLU cc_start: 0.8501 (pp20) cc_final: 0.7925 (pp20) REVERT: A 598 TRP cc_start: 0.8889 (OUTLIER) cc_final: 0.8570 (m-10) REVERT: A 848 MET cc_start: 0.8371 (mmt) cc_final: 0.8104 (mmm) REVERT: A 900 GLU cc_start: 0.9326 (mt-10) cc_final: 0.9088 (mm-30) REVERT: A 919 MET cc_start: 0.7909 (ptm) cc_final: 0.7648 (ptp) REVERT: A 1141 MET cc_start: 0.9596 (mmm) cc_final: 0.9241 (mmp) REVERT: A 1156 MET cc_start: 0.8186 (mmm) cc_final: 0.7959 (mmm) REVERT: A 1417 GLU cc_start: 0.8301 (mm-30) cc_final: 0.7826 (mm-30) REVERT: A 1511 PHE cc_start: 0.7507 (m-80) cc_final: 0.6583 (m-80) REVERT: A 1782 MET cc_start: 0.8207 (mmm) cc_final: 0.7929 (mmt) REVERT: A 1829 GLN cc_start: 0.9225 (tp40) cc_final: 0.8926 (tp40) REVERT: C 120 MET cc_start: 0.8594 (tpt) cc_final: 0.7959 (tpp) REVERT: C 182 GLN cc_start: 0.8026 (OUTLIER) cc_final: 0.7722 (pp30) REVERT: C 508 ARG cc_start: 0.7723 (mmt180) cc_final: 0.7518 (mmt180) REVERT: C 598 TRP cc_start: 0.8928 (OUTLIER) cc_final: 0.8198 (m-10) REVERT: C 1121 TYR cc_start: 0.8779 (p90) cc_final: 0.8293 (p90) REVERT: C 1146 GLU cc_start: 0.8365 (mm-30) cc_final: 0.7896 (mm-30) REVERT: C 1150 GLU cc_start: 0.7795 (mt-10) cc_final: 0.7316 (mt-10) REVERT: C 1285 MET cc_start: 0.7437 (tpt) cc_final: 0.7220 (tpt) REVERT: C 1296 HIS cc_start: 0.6864 (OUTLIER) cc_final: 0.6657 (m170) REVERT: C 1307 GLU cc_start: 0.8232 (tp30) cc_final: 0.7916 (tp30) REVERT: C 1417 GLU cc_start: 0.7831 (mm-30) cc_final: 0.7566 (mm-30) REVERT: C 1781 MET cc_start: 0.8460 (mmm) cc_final: 0.8252 (tpt) REVERT: C 1821 TRP cc_start: 0.7976 (OUTLIER) cc_final: 0.6293 (t60) REVERT: C 1829 GLN cc_start: 0.9087 (tm-30) cc_final: 0.8708 (tm-30) outliers start: 97 outliers final: 54 residues processed: 409 average time/residue: 0.1650 time to fit residues: 113.9603 Evaluate side-chains 371 residues out of total 3448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 311 time to evaluate : 1.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 481 PHE Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 598 TRP Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 707 THR Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 1011 LEU Chi-restraints excluded: chain A residue 1185 CYS Chi-restraints excluded: chain A residue 1352 LEU Chi-restraints excluded: chain A residue 1395 LEU Chi-restraints excluded: chain A residue 1436 VAL Chi-restraints excluded: chain A residue 1532 GLN Chi-restraints excluded: chain A residue 1540 GLU Chi-restraints excluded: chain A residue 1541 VAL Chi-restraints excluded: chain A residue 1560 LEU Chi-restraints excluded: chain A residue 1588 LYS Chi-restraints excluded: chain A residue 1648 SER Chi-restraints excluded: chain A residue 1687 LEU Chi-restraints excluded: chain A residue 1724 VAL Chi-restraints excluded: chain A residue 1770 LEU Chi-restraints excluded: chain A residue 1789 ILE Chi-restraints excluded: chain A residue 1842 SER Chi-restraints excluded: chain A residue 1882 LEU Chi-restraints excluded: chain A residue 1884 VAL Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 182 GLN Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 220 GLU Chi-restraints excluded: chain C residue 322 ASN Chi-restraints excluded: chain C residue 431 HIS Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain C residue 481 PHE Chi-restraints excluded: chain C residue 503 THR Chi-restraints excluded: chain C residue 587 VAL Chi-restraints excluded: chain C residue 598 TRP Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 735 VAL Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 780 LEU Chi-restraints excluded: chain C residue 1212 THR Chi-restraints excluded: chain C residue 1274 MET Chi-restraints excluded: chain C residue 1296 HIS Chi-restraints excluded: chain C residue 1301 LEU Chi-restraints excluded: chain C residue 1431 VAL Chi-restraints excluded: chain C residue 1436 VAL Chi-restraints excluded: chain C residue 1532 GLN Chi-restraints excluded: chain C residue 1541 VAL Chi-restraints excluded: chain C residue 1619 ILE Chi-restraints excluded: chain C residue 1691 CYS Chi-restraints excluded: chain C residue 1770 LEU Chi-restraints excluded: chain C residue 1786 LEU Chi-restraints excluded: chain C residue 1792 LEU Chi-restraints excluded: chain C residue 1813 ILE Chi-restraints excluded: chain C residue 1821 TRP Chi-restraints excluded: chain C residue 1842 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 105 optimal weight: 4.9990 chunk 321 optimal weight: 4.9990 chunk 224 optimal weight: 6.9990 chunk 74 optimal weight: 10.0000 chunk 45 optimal weight: 0.9990 chunk 266 optimal weight: 6.9990 chunk 38 optimal weight: 0.5980 chunk 338 optimal weight: 3.9990 chunk 131 optimal weight: 4.9990 chunk 79 optimal weight: 3.9990 chunk 98 optimal weight: 9.9990 overall best weight: 2.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1366 ASN A1414 GLN A1425 GLN A1730 GLN ** C 629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 704 HIS ** C1405 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1886 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.123504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.089768 restraints weight = 81285.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.088853 restraints weight = 51705.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.089315 restraints weight = 41245.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.089816 restraints weight = 34946.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.090474 restraints weight = 31371.774| |-----------------------------------------------------------------------------| r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.4583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 29330 Z= 0.182 Angle : 0.677 13.672 39730 Z= 0.342 Chirality : 0.043 0.217 4666 Planarity : 0.004 0.041 5024 Dihedral : 8.199 95.179 4192 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.59 % Favored : 90.36 % Rotamer: Outliers : 3.63 % Allowed : 21.47 % Favored : 74.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.98 (0.14), residues: 3692 helix: 0.86 (0.12), residues: 1778 sheet: -0.35 (0.34), residues: 240 loop : -2.49 (0.15), residues: 1674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C1814 TYR 0.027 0.001 TYR A1097 PHE 0.041 0.002 PHE C 43 TRP 0.020 0.002 TRP C1351 HIS 0.007 0.001 HIS C 910 Details of bonding type rmsd covalent geometry : bond 0.00414 (29318) covalent geometry : angle 0.67446 (39716) SS BOND : bond 0.00659 ( 4) SS BOND : angle 0.59686 ( 8) hydrogen bonds : bond 0.03637 ( 1306) hydrogen bonds : angle 4.20508 ( 3756) metal coordination : bond 0.02639 ( 8) metal coordination : angle 5.13455 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7384 Ramachandran restraints generated. 3692 Oldfield, 0 Emsley, 3692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7384 Ramachandran restraints generated. 3692 Oldfield, 0 Emsley, 3692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 3448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 328 time to evaluate : 1.088 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 PHE cc_start: 0.7000 (p90) cc_final: 0.6475 (p90) REVERT: A 120 MET cc_start: 0.8303 (tpt) cc_final: 0.7570 (tpt) REVERT: A 187 LEU cc_start: 0.9626 (OUTLIER) cc_final: 0.9419 (tt) REVERT: A 333 LEU cc_start: 0.9576 (OUTLIER) cc_final: 0.9300 (mp) REVERT: A 351 LEU cc_start: 0.9525 (mt) cc_final: 0.9321 (mt) REVERT: A 550 GLU cc_start: 0.8667 (tp30) cc_final: 0.8312 (tp30) REVERT: A 594 GLU cc_start: 0.8442 (pp20) cc_final: 0.7939 (pp20) REVERT: A 598 TRP cc_start: 0.8884 (OUTLIER) cc_final: 0.8518 (m-10) REVERT: A 848 MET cc_start: 0.8511 (mmt) cc_final: 0.8302 (mmm) REVERT: A 900 GLU cc_start: 0.9433 (mt-10) cc_final: 0.9159 (mm-30) REVERT: A 916 LEU cc_start: 0.8586 (mm) cc_final: 0.8284 (mm) REVERT: A 1141 MET cc_start: 0.9614 (mmm) cc_final: 0.9213 (mmp) REVERT: A 1196 MET cc_start: 0.8415 (mmt) cc_final: 0.8093 (mmp) REVERT: A 1366 ASN cc_start: 0.8377 (OUTLIER) cc_final: 0.7111 (t0) REVERT: A 1414 GLN cc_start: 0.7941 (OUTLIER) cc_final: 0.7731 (pp30) REVERT: A 1417 GLU cc_start: 0.8337 (mm-30) cc_final: 0.7907 (mm-30) REVERT: A 1782 MET cc_start: 0.8145 (mmm) cc_final: 0.7851 (mmt) REVERT: A 1829 GLN cc_start: 0.9197 (tp40) cc_final: 0.8835 (tp40) REVERT: C 44 LYS cc_start: 0.9031 (ptpt) cc_final: 0.8813 (pttt) REVERT: C 120 MET cc_start: 0.8330 (tpt) cc_final: 0.7648 (tpp) REVERT: C 182 GLN cc_start: 0.8273 (OUTLIER) cc_final: 0.8041 (pp30) REVERT: C 361 MET cc_start: 0.8717 (ttp) cc_final: 0.8482 (ptm) REVERT: C 598 TRP cc_start: 0.8977 (OUTLIER) cc_final: 0.8111 (m-10) REVERT: C 1121 TYR cc_start: 0.8810 (p90) cc_final: 0.8309 (p90) REVERT: C 1146 GLU cc_start: 0.8195 (mm-30) cc_final: 0.7978 (mm-30) REVERT: C 1244 GLU cc_start: 0.8068 (OUTLIER) cc_final: 0.7668 (mp0) REVERT: C 1285 MET cc_start: 0.7486 (tpt) cc_final: 0.7272 (tpt) REVERT: C 1296 HIS cc_start: 0.6860 (OUTLIER) cc_final: 0.6610 (m170) REVERT: C 1307 GLU cc_start: 0.8179 (tp30) cc_final: 0.7868 (tp30) REVERT: C 1531 LEU cc_start: 0.8722 (OUTLIER) cc_final: 0.8198 (mt) REVERT: C 1765 MET cc_start: 0.5343 (tpp) cc_final: 0.5138 (tpp) REVERT: C 1793 LEU cc_start: 0.8758 (OUTLIER) cc_final: 0.8549 (pp) REVERT: C 1821 TRP cc_start: 0.8286 (OUTLIER) cc_final: 0.6647 (t60) REVERT: C 1829 GLN cc_start: 0.9127 (tm-30) cc_final: 0.8860 (tm-30) outliers start: 109 outliers final: 66 residues processed: 406 average time/residue: 0.1617 time to fit residues: 111.4406 Evaluate side-chains 388 residues out of total 3448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 310 time to evaluate : 1.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 GLU Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 481 PHE Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 598 TRP Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 707 THR Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 906 ASN Chi-restraints excluded: chain A residue 1011 LEU Chi-restraints excluded: chain A residue 1185 CYS Chi-restraints excluded: chain A residue 1352 LEU Chi-restraints excluded: chain A residue 1366 ASN Chi-restraints excluded: chain A residue 1395 LEU Chi-restraints excluded: chain A residue 1414 GLN Chi-restraints excluded: chain A residue 1541 VAL Chi-restraints excluded: chain A residue 1560 LEU Chi-restraints excluded: chain A residue 1588 LYS Chi-restraints excluded: chain A residue 1619 ILE Chi-restraints excluded: chain A residue 1648 SER Chi-restraints excluded: chain A residue 1687 LEU Chi-restraints excluded: chain A residue 1730 GLN Chi-restraints excluded: chain A residue 1789 ILE Chi-restraints excluded: chain A residue 1842 SER Chi-restraints excluded: chain A residue 1853 CYS Chi-restraints excluded: chain A residue 1882 LEU Chi-restraints excluded: chain A residue 1884 VAL Chi-restraints excluded: chain C residue 41 GLU Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 182 GLN Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 322 ASN Chi-restraints excluded: chain C residue 416 ASN Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 431 HIS Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain C residue 481 PHE Chi-restraints excluded: chain C residue 503 THR Chi-restraints excluded: chain C residue 587 VAL Chi-restraints excluded: chain C residue 598 TRP Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 735 VAL Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 780 LEU Chi-restraints excluded: chain C residue 1212 THR Chi-restraints excluded: chain C residue 1244 GLU Chi-restraints excluded: chain C residue 1296 HIS Chi-restraints excluded: chain C residue 1301 LEU Chi-restraints excluded: chain C residue 1379 VAL Chi-restraints excluded: chain C residue 1431 VAL Chi-restraints excluded: chain C residue 1436 VAL Chi-restraints excluded: chain C residue 1531 LEU Chi-restraints excluded: chain C residue 1532 GLN Chi-restraints excluded: chain C residue 1540 GLU Chi-restraints excluded: chain C residue 1541 VAL Chi-restraints excluded: chain C residue 1560 LEU Chi-restraints excluded: chain C residue 1619 ILE Chi-restraints excluded: chain C residue 1691 CYS Chi-restraints excluded: chain C residue 1770 LEU Chi-restraints excluded: chain C residue 1771 LYS Chi-restraints excluded: chain C residue 1786 LEU Chi-restraints excluded: chain C residue 1792 LEU Chi-restraints excluded: chain C residue 1793 LEU Chi-restraints excluded: chain C residue 1813 ILE Chi-restraints excluded: chain C residue 1821 TRP Chi-restraints excluded: chain C residue 1842 SER Chi-restraints excluded: chain C residue 1864 LEU Chi-restraints excluded: chain C residue 1882 LEU Chi-restraints excluded: chain C residue 1886 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 198 optimal weight: 10.0000 chunk 244 optimal weight: 5.9990 chunk 336 optimal weight: 8.9990 chunk 201 optimal weight: 0.0670 chunk 47 optimal weight: 8.9990 chunk 99 optimal weight: 9.9990 chunk 338 optimal weight: 0.6980 chunk 180 optimal weight: 40.0000 chunk 104 optimal weight: 5.9990 chunk 27 optimal weight: 0.9990 chunk 247 optimal weight: 4.9990 overall best weight: 2.5524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1414 GLN A1425 GLN ** A1730 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1405 HIS C1414 GLN C1886 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.123483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.089451 restraints weight = 80957.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.089264 restraints weight = 49014.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.090027 restraints weight = 37560.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.090414 restraints weight = 32214.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.090674 restraints weight = 28884.554| |-----------------------------------------------------------------------------| r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.4793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 29330 Z= 0.164 Angle : 0.675 14.254 39730 Z= 0.337 Chirality : 0.042 0.221 4666 Planarity : 0.004 0.040 5024 Dihedral : 8.159 94.086 4192 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.94 % Favored : 91.01 % Rotamer: Outliers : 3.60 % Allowed : 22.13 % Favored : 74.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.93 (0.14), residues: 3692 helix: 0.93 (0.13), residues: 1774 sheet: -0.16 (0.34), residues: 236 loop : -2.52 (0.15), residues: 1682 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 532 TYR 0.014 0.001 TYR C1682 PHE 0.021 0.001 PHE C1858 TRP 0.026 0.002 TRP C1351 HIS 0.004 0.001 HIS A1296 Details of bonding type rmsd covalent geometry : bond 0.00373 (29318) covalent geometry : angle 0.67224 (39716) SS BOND : bond 0.00582 ( 4) SS BOND : angle 0.51958 ( 8) hydrogen bonds : bond 0.03442 ( 1306) hydrogen bonds : angle 4.16902 ( 3756) metal coordination : bond 0.02633 ( 8) metal coordination : angle 4.73395 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7384 Ramachandran restraints generated. 3692 Oldfield, 0 Emsley, 3692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7384 Ramachandran restraints generated. 3692 Oldfield, 0 Emsley, 3692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 443 residues out of total 3448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 335 time to evaluate : 1.147 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 PHE cc_start: 0.6980 (p90) cc_final: 0.6463 (p90) REVERT: A 120 MET cc_start: 0.8159 (tpt) cc_final: 0.7501 (tpp) REVERT: A 333 LEU cc_start: 0.9581 (OUTLIER) cc_final: 0.9277 (mp) REVERT: A 351 LEU cc_start: 0.9485 (mt) cc_final: 0.9247 (mt) REVERT: A 398 GLU cc_start: 0.8974 (mp0) cc_final: 0.8587 (mp0) REVERT: A 550 GLU cc_start: 0.8449 (tp30) cc_final: 0.8169 (tp30) REVERT: A 594 GLU cc_start: 0.8432 (pp20) cc_final: 0.7925 (pp20) REVERT: A 598 TRP cc_start: 0.8878 (OUTLIER) cc_final: 0.8550 (m-10) REVERT: A 848 MET cc_start: 0.8578 (mmt) cc_final: 0.8286 (mmm) REVERT: A 900 GLU cc_start: 0.9417 (mt-10) cc_final: 0.9156 (mm-30) REVERT: A 1141 MET cc_start: 0.9612 (mmm) cc_final: 0.9244 (mmp) REVERT: A 1196 MET cc_start: 0.8427 (mmt) cc_final: 0.8200 (mmp) REVERT: A 1244 GLU cc_start: 0.8455 (mp0) cc_final: 0.7968 (mm-30) REVERT: A 1285 MET cc_start: 0.7668 (tpt) cc_final: 0.7346 (tpt) REVERT: A 1417 GLU cc_start: 0.8373 (mm-30) cc_final: 0.7973 (mm-30) REVERT: A 1728 GLU cc_start: 0.8424 (tm-30) cc_final: 0.7976 (tm-30) REVERT: A 1829 GLN cc_start: 0.9233 (tp40) cc_final: 0.8879 (tp40) REVERT: C 120 MET cc_start: 0.7953 (tpt) cc_final: 0.7194 (tpp) REVERT: C 182 GLN cc_start: 0.8295 (OUTLIER) cc_final: 0.8075 (pp30) REVERT: C 361 MET cc_start: 0.8753 (ttp) cc_final: 0.8519 (ptm) REVERT: C 598 TRP cc_start: 0.8924 (OUTLIER) cc_final: 0.8038 (m-10) REVERT: C 1121 TYR cc_start: 0.8763 (p90) cc_final: 0.8291 (p90) REVERT: C 1146 GLU cc_start: 0.8221 (mm-30) cc_final: 0.7814 (mm-30) REVERT: C 1150 GLU cc_start: 0.7787 (mt-10) cc_final: 0.7099 (mt-10) REVERT: C 1244 GLU cc_start: 0.8200 (OUTLIER) cc_final: 0.7766 (mp0) REVERT: C 1296 HIS cc_start: 0.6786 (OUTLIER) cc_final: 0.6582 (m170) REVERT: C 1307 GLU cc_start: 0.8232 (tp30) cc_final: 0.7780 (tp30) REVERT: C 1781 MET cc_start: 0.8422 (mmm) cc_final: 0.8146 (tpt) REVERT: C 1793 LEU cc_start: 0.8802 (OUTLIER) cc_final: 0.8574 (pp) REVERT: C 1821 TRP cc_start: 0.8387 (OUTLIER) cc_final: 0.6752 (t60) REVERT: C 1829 GLN cc_start: 0.9098 (tm-30) cc_final: 0.8684 (tm-30) outliers start: 108 outliers final: 63 residues processed: 418 average time/residue: 0.1647 time to fit residues: 116.3697 Evaluate side-chains 384 residues out of total 3448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 313 time to evaluate : 1.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 GLU Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 481 PHE Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 598 TRP Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 707 THR Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 906 ASN Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain A residue 1185 CYS Chi-restraints excluded: chain A residue 1352 LEU Chi-restraints excluded: chain A residue 1395 LEU Chi-restraints excluded: chain A residue 1436 VAL Chi-restraints excluded: chain A residue 1541 VAL Chi-restraints excluded: chain A residue 1560 LEU Chi-restraints excluded: chain A residue 1588 LYS Chi-restraints excluded: chain A residue 1619 ILE Chi-restraints excluded: chain A residue 1648 SER Chi-restraints excluded: chain A residue 1678 ILE Chi-restraints excluded: chain A residue 1687 LEU Chi-restraints excluded: chain A residue 1724 VAL Chi-restraints excluded: chain A residue 1789 ILE Chi-restraints excluded: chain A residue 1842 SER Chi-restraints excluded: chain A residue 1882 LEU Chi-restraints excluded: chain A residue 1884 VAL Chi-restraints excluded: chain C residue 41 GLU Chi-restraints excluded: chain C residue 182 GLN Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 322 ASN Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 431 HIS Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain C residue 481 PHE Chi-restraints excluded: chain C residue 503 THR Chi-restraints excluded: chain C residue 587 VAL Chi-restraints excluded: chain C residue 598 TRP Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 735 VAL Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 780 LEU Chi-restraints excluded: chain C residue 836 ASP Chi-restraints excluded: chain C residue 848 MET Chi-restraints excluded: chain C residue 1212 THR Chi-restraints excluded: chain C residue 1244 GLU Chi-restraints excluded: chain C residue 1296 HIS Chi-restraints excluded: chain C residue 1301 LEU Chi-restraints excluded: chain C residue 1351 TRP Chi-restraints excluded: chain C residue 1431 VAL Chi-restraints excluded: chain C residue 1436 VAL Chi-restraints excluded: chain C residue 1532 GLN Chi-restraints excluded: chain C residue 1540 GLU Chi-restraints excluded: chain C residue 1541 VAL Chi-restraints excluded: chain C residue 1560 LEU Chi-restraints excluded: chain C residue 1619 ILE Chi-restraints excluded: chain C residue 1770 LEU Chi-restraints excluded: chain C residue 1786 LEU Chi-restraints excluded: chain C residue 1793 LEU Chi-restraints excluded: chain C residue 1813 ILE Chi-restraints excluded: chain C residue 1821 TRP Chi-restraints excluded: chain C residue 1842 SER Chi-restraints excluded: chain C residue 1864 LEU Chi-restraints excluded: chain C residue 1882 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 32 optimal weight: 3.9990 chunk 358 optimal weight: 10.0000 chunk 164 optimal weight: 0.7980 chunk 286 optimal weight: 6.9990 chunk 310 optimal weight: 0.8980 chunk 214 optimal weight: 0.0470 chunk 315 optimal weight: 0.9980 chunk 170 optimal weight: 0.8980 chunk 146 optimal weight: 0.6980 chunk 240 optimal weight: 0.0030 chunk 12 optimal weight: 6.9990 overall best weight: 0.4888 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1414 GLN A1689 ASN A1730 GLN A1887 GLN C 629 GLN ** C 717 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1296 HIS C1405 HIS ** C1414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1689 ASN C1837 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.126042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.093451 restraints weight = 80314.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.092850 restraints weight = 45435.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.093376 restraints weight = 38398.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.094811 restraints weight = 31958.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.094732 restraints weight = 26619.437| |-----------------------------------------------------------------------------| r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.4802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 29330 Z= 0.116 Angle : 0.676 15.872 39730 Z= 0.331 Chirality : 0.042 0.203 4666 Planarity : 0.003 0.038 5024 Dihedral : 7.968 90.535 4192 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.83 % Favored : 92.12 % Rotamer: Outliers : 2.33 % Allowed : 23.50 % Favored : 74.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.80 (0.14), residues: 3692 helix: 0.99 (0.13), residues: 1786 sheet: 0.10 (0.35), residues: 236 loop : -2.45 (0.15), residues: 1670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1507 TYR 0.025 0.001 TYR A1097 PHE 0.025 0.001 PHE C1858 TRP 0.020 0.001 TRP A1351 HIS 0.003 0.001 HIS A1296 Details of bonding type rmsd covalent geometry : bond 0.00247 (29318) covalent geometry : angle 0.67386 (39716) SS BOND : bond 0.00667 ( 4) SS BOND : angle 2.86325 ( 8) hydrogen bonds : bond 0.03005 ( 1306) hydrogen bonds : angle 3.99504 ( 3756) metal coordination : bond 0.02921 ( 8) metal coordination : angle 3.48404 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7384 Ramachandran restraints generated. 3692 Oldfield, 0 Emsley, 3692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7384 Ramachandran restraints generated. 3692 Oldfield, 0 Emsley, 3692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 3448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 368 time to evaluate : 1.119 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.8298 (tpt) cc_final: 0.7516 (tpt) REVERT: A 333 LEU cc_start: 0.9554 (OUTLIER) cc_final: 0.9304 (mt) REVERT: A 351 LEU cc_start: 0.9467 (mt) cc_final: 0.9224 (mt) REVERT: A 398 GLU cc_start: 0.8928 (mp0) cc_final: 0.8527 (mp0) REVERT: A 550 GLU cc_start: 0.8280 (tp30) cc_final: 0.8055 (tp30) REVERT: A 594 GLU cc_start: 0.8335 (pp20) cc_final: 0.8054 (pp20) REVERT: A 606 MET cc_start: 0.8877 (mpp) cc_final: 0.8571 (mpp) REVERT: A 848 MET cc_start: 0.8310 (mmt) cc_final: 0.8071 (mmm) REVERT: A 900 GLU cc_start: 0.9374 (mt-10) cc_final: 0.9117 (mm-30) REVERT: A 1141 MET cc_start: 0.9587 (mmm) cc_final: 0.9261 (mmp) REVERT: A 1156 MET cc_start: 0.7942 (mmm) cc_final: 0.7331 (mmm) REVERT: A 1414 GLN cc_start: 0.7855 (OUTLIER) cc_final: 0.7627 (pp30) REVERT: A 1417 GLU cc_start: 0.8289 (mm-30) cc_final: 0.7793 (mm-30) REVERT: A 1531 LEU cc_start: 0.8836 (OUTLIER) cc_final: 0.8335 (mt) REVERT: A 1728 GLU cc_start: 0.8371 (tm-30) cc_final: 0.7904 (tm-30) REVERT: A 1829 GLN cc_start: 0.9183 (tp40) cc_final: 0.8775 (tp40) REVERT: C 120 MET cc_start: 0.7799 (tpt) cc_final: 0.6980 (tpp) REVERT: C 387 MET cc_start: 0.7712 (pmm) cc_final: 0.7382 (pmm) REVERT: C 598 TRP cc_start: 0.8718 (OUTLIER) cc_final: 0.8439 (m-10) REVERT: C 1146 GLU cc_start: 0.8206 (mm-30) cc_final: 0.7637 (mm-30) REVERT: C 1150 GLU cc_start: 0.7793 (mt-10) cc_final: 0.6993 (mt-10) REVERT: C 1182 ASP cc_start: 0.7502 (m-30) cc_final: 0.7207 (m-30) REVERT: C 1244 GLU cc_start: 0.8262 (OUTLIER) cc_final: 0.7823 (mp0) REVERT: C 1285 MET cc_start: 0.7402 (tpt) cc_final: 0.7143 (tpt) REVERT: C 1307 GLU cc_start: 0.8155 (tp30) cc_final: 0.7711 (tp30) REVERT: C 1511 PHE cc_start: 0.7291 (m-10) cc_final: 0.5202 (m-10) REVERT: C 1532 GLN cc_start: 0.8519 (OUTLIER) cc_final: 0.8170 (mp10) REVERT: C 1678 ILE cc_start: 0.8844 (tp) cc_final: 0.8566 (tp) REVERT: C 1731 LEU cc_start: 0.8124 (mt) cc_final: 0.7863 (mt) REVERT: C 1760 GLN cc_start: 0.7775 (pm20) cc_final: 0.7374 (pm20) REVERT: C 1793 LEU cc_start: 0.8652 (OUTLIER) cc_final: 0.8426 (pp) REVERT: C 1821 TRP cc_start: 0.8297 (OUTLIER) cc_final: 0.6579 (t60) REVERT: C 1829 GLN cc_start: 0.9133 (tm-30) cc_final: 0.8730 (tm-30) REVERT: C 1871 GLN cc_start: 0.8489 (mm-40) cc_final: 0.8277 (mm110) REVERT: C 1876 GLU cc_start: 0.8200 (mt-10) cc_final: 0.7968 (mm-30) outliers start: 70 outliers final: 37 residues processed: 416 average time/residue: 0.1659 time to fit residues: 116.3336 Evaluate side-chains 385 residues out of total 3448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 340 time to evaluate : 1.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 598 TRP Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain A residue 1185 CYS Chi-restraints excluded: chain A residue 1395 LEU Chi-restraints excluded: chain A residue 1414 GLN Chi-restraints excluded: chain A residue 1531 LEU Chi-restraints excluded: chain A residue 1687 LEU Chi-restraints excluded: chain A residue 1724 VAL Chi-restraints excluded: chain A residue 1882 LEU Chi-restraints excluded: chain A residue 1884 VAL Chi-restraints excluded: chain A residue 1887 GLN Chi-restraints excluded: chain C residue 41 GLU Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 322 ASN Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain C residue 587 VAL Chi-restraints excluded: chain C residue 598 TRP Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 780 LEU Chi-restraints excluded: chain C residue 848 MET Chi-restraints excluded: chain C residue 1212 THR Chi-restraints excluded: chain C residue 1244 GLU Chi-restraints excluded: chain C residue 1301 LEU Chi-restraints excluded: chain C residue 1354 MET Chi-restraints excluded: chain C residue 1379 VAL Chi-restraints excluded: chain C residue 1431 VAL Chi-restraints excluded: chain C residue 1436 VAL Chi-restraints excluded: chain C residue 1532 GLN Chi-restraints excluded: chain C residue 1619 ILE Chi-restraints excluded: chain C residue 1770 LEU Chi-restraints excluded: chain C residue 1786 LEU Chi-restraints excluded: chain C residue 1793 LEU Chi-restraints excluded: chain C residue 1813 ILE Chi-restraints excluded: chain C residue 1821 TRP Chi-restraints excluded: chain C residue 1882 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 37 optimal weight: 0.7980 chunk 204 optimal weight: 10.0000 chunk 307 optimal weight: 0.4980 chunk 253 optimal weight: 3.9990 chunk 114 optimal weight: 0.9990 chunk 292 optimal weight: 5.9990 chunk 143 optimal weight: 0.8980 chunk 252 optimal weight: 6.9990 chunk 233 optimal weight: 0.8980 chunk 72 optimal weight: 9.9990 chunk 7 optimal weight: 50.0000 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1414 GLN A1887 GLN ** C 717 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1405 HIS C1887 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.126144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.092630 restraints weight = 81098.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.092519 restraints weight = 50622.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.093034 restraints weight = 39042.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.093224 restraints weight = 37935.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.093485 restraints weight = 31610.154| |-----------------------------------------------------------------------------| r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.4884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 29330 Z= 0.117 Angle : 0.680 17.252 39730 Z= 0.333 Chirality : 0.042 0.198 4666 Planarity : 0.003 0.036 5024 Dihedral : 7.893 90.041 4192 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.91 % Favored : 92.04 % Rotamer: Outliers : 2.10 % Allowed : 23.73 % Favored : 74.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.77 (0.14), residues: 3692 helix: 1.01 (0.13), residues: 1788 sheet: 0.12 (0.34), residues: 236 loop : -2.43 (0.15), residues: 1668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A1507 TYR 0.012 0.001 TYR C1121 PHE 0.049 0.001 PHE A 43 TRP 0.020 0.001 TRP A1351 HIS 0.006 0.001 HIS C1296 Details of bonding type rmsd covalent geometry : bond 0.00253 (29318) covalent geometry : angle 0.67835 (39716) SS BOND : bond 0.00612 ( 4) SS BOND : angle 2.55340 ( 8) hydrogen bonds : bond 0.03031 ( 1306) hydrogen bonds : angle 3.99278 ( 3756) metal coordination : bond 0.02809 ( 8) metal coordination : angle 3.40400 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7384 Ramachandran restraints generated. 3692 Oldfield, 0 Emsley, 3692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7384 Ramachandran restraints generated. 3692 Oldfield, 0 Emsley, 3692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 3448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 352 time to evaluate : 1.041 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.8269 (tpt) cc_final: 0.7532 (tpt) REVERT: A 131 GLN cc_start: 0.8412 (tp40) cc_final: 0.8202 (tp40) REVERT: A 333 LEU cc_start: 0.9576 (OUTLIER) cc_final: 0.9344 (mt) REVERT: A 351 LEU cc_start: 0.9473 (mt) cc_final: 0.9214 (mt) REVERT: A 398 GLU cc_start: 0.8996 (mp0) cc_final: 0.8560 (mp0) REVERT: A 594 GLU cc_start: 0.8307 (pp20) cc_final: 0.8059 (pp20) REVERT: A 696 LEU cc_start: 0.9435 (OUTLIER) cc_final: 0.9153 (mm) REVERT: A 848 MET cc_start: 0.8281 (mmt) cc_final: 0.8045 (mmm) REVERT: A 900 GLU cc_start: 0.9398 (mt-10) cc_final: 0.9136 (mm-30) REVERT: A 1141 MET cc_start: 0.9594 (mmm) cc_final: 0.9261 (mmp) REVERT: A 1156 MET cc_start: 0.8056 (mmm) cc_final: 0.7415 (mmm) REVERT: A 1414 GLN cc_start: 0.7595 (OUTLIER) cc_final: 0.6956 (pp30) REVERT: A 1417 GLU cc_start: 0.8315 (mm-30) cc_final: 0.7828 (mm-30) REVERT: A 1728 GLU cc_start: 0.8417 (tm-30) cc_final: 0.7919 (tm-30) REVERT: A 1829 GLN cc_start: 0.9209 (tp40) cc_final: 0.8799 (tp40) REVERT: C 120 MET cc_start: 0.7762 (tpt) cc_final: 0.6964 (tpp) REVERT: C 598 TRP cc_start: 0.8657 (OUTLIER) cc_final: 0.8406 (m-10) REVERT: C 1121 TYR cc_start: 0.8473 (p90) cc_final: 0.8219 (p90) REVERT: C 1146 GLU cc_start: 0.8180 (mm-30) cc_final: 0.7610 (mm-30) REVERT: C 1150 GLU cc_start: 0.7826 (mt-10) cc_final: 0.6998 (mt-10) REVERT: C 1182 ASP cc_start: 0.7412 (m-30) cc_final: 0.7005 (m-30) REVERT: C 1244 GLU cc_start: 0.8348 (OUTLIER) cc_final: 0.7958 (mp0) REVERT: C 1307 GLU cc_start: 0.8138 (tp30) cc_final: 0.7686 (tp30) REVERT: C 1678 ILE cc_start: 0.8879 (tp) cc_final: 0.8652 (tp) REVERT: C 1731 LEU cc_start: 0.8186 (mt) cc_final: 0.7898 (mt) REVERT: C 1793 LEU cc_start: 0.8653 (OUTLIER) cc_final: 0.8432 (pp) REVERT: C 1821 TRP cc_start: 0.8304 (OUTLIER) cc_final: 0.6582 (t60) REVERT: C 1829 GLN cc_start: 0.9120 (tm-30) cc_final: 0.8681 (tm-30) REVERT: C 1871 GLN cc_start: 0.8334 (mm-40) cc_final: 0.8119 (mm110) REVERT: C 1876 GLU cc_start: 0.8259 (mt-10) cc_final: 0.7973 (mm-30) outliers start: 63 outliers final: 45 residues processed: 395 average time/residue: 0.1629 time to fit residues: 108.8166 Evaluate side-chains 383 residues out of total 3448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 331 time to evaluate : 1.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 293 GLU Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 598 TRP Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 696 LEU Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain A residue 1185 CYS Chi-restraints excluded: chain A residue 1352 LEU Chi-restraints excluded: chain A residue 1395 LEU Chi-restraints excluded: chain A residue 1397 THR Chi-restraints excluded: chain A residue 1414 GLN Chi-restraints excluded: chain A residue 1687 LEU Chi-restraints excluded: chain A residue 1724 VAL Chi-restraints excluded: chain A residue 1854 LEU Chi-restraints excluded: chain A residue 1882 LEU Chi-restraints excluded: chain A residue 1884 VAL Chi-restraints excluded: chain A residue 1887 GLN Chi-restraints excluded: chain C residue 41 GLU Chi-restraints excluded: chain C residue 322 ASN Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain C residue 587 VAL Chi-restraints excluded: chain C residue 598 TRP Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 714 LEU Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 780 LEU Chi-restraints excluded: chain C residue 848 MET Chi-restraints excluded: chain C residue 1143 ARG Chi-restraints excluded: chain C residue 1212 THR Chi-restraints excluded: chain C residue 1244 GLU Chi-restraints excluded: chain C residue 1301 LEU Chi-restraints excluded: chain C residue 1354 MET Chi-restraints excluded: chain C residue 1379 VAL Chi-restraints excluded: chain C residue 1431 VAL Chi-restraints excluded: chain C residue 1436 VAL Chi-restraints excluded: chain C residue 1532 GLN Chi-restraints excluded: chain C residue 1647 VAL Chi-restraints excluded: chain C residue 1770 LEU Chi-restraints excluded: chain C residue 1793 LEU Chi-restraints excluded: chain C residue 1821 TRP Chi-restraints excluded: chain C residue 1825 LEU Chi-restraints excluded: chain C residue 1882 LEU Chi-restraints excluded: chain C residue 1887 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 43 optimal weight: 5.9990 chunk 365 optimal weight: 7.9990 chunk 112 optimal weight: 6.9990 chunk 289 optimal weight: 7.9990 chunk 215 optimal weight: 4.9990 chunk 267 optimal weight: 9.9990 chunk 136 optimal weight: 3.9990 chunk 189 optimal weight: 6.9990 chunk 305 optimal weight: 3.9990 chunk 91 optimal weight: 0.5980 chunk 236 optimal weight: 20.0000 overall best weight: 3.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1689 ASN ** A1738 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1887 GLN C 335 ASN ** C 717 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1405 HIS ** C1414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1689 ASN C1760 GLN C1845 ASN C1887 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.120923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.083698 restraints weight = 81088.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.086131 restraints weight = 47132.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.087656 restraints weight = 33479.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 60)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.088629 restraints weight = 27129.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.089208 restraints weight = 23771.738| |-----------------------------------------------------------------------------| r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.5352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.093 29330 Z= 0.231 Angle : 0.773 15.070 39730 Z= 0.387 Chirality : 0.044 0.220 4666 Planarity : 0.004 0.079 5024 Dihedral : 8.216 94.651 4192 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 13.24 Ramachandran Plot: Outliers : 0.05 % Allowed : 10.40 % Favored : 89.54 % Rotamer: Outliers : 2.40 % Allowed : 24.00 % Favored : 73.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.93 (0.14), residues: 3692 helix: 0.90 (0.12), residues: 1778 sheet: -0.38 (0.34), residues: 256 loop : -2.48 (0.15), residues: 1658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A1507 TYR 0.023 0.002 TYR A1097 PHE 0.043 0.002 PHE A 43 TRP 0.026 0.002 TRP A1351 HIS 0.010 0.001 HIS C1296 Details of bonding type rmsd covalent geometry : bond 0.00525 (29318) covalent geometry : angle 0.76895 (39716) SS BOND : bond 0.01062 ( 4) SS BOND : angle 3.24120 ( 8) hydrogen bonds : bond 0.04028 ( 1306) hydrogen bonds : angle 4.32623 ( 3756) metal coordination : bond 0.02259 ( 8) metal coordination : angle 5.66782 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7384 Ramachandran restraints generated. 3692 Oldfield, 0 Emsley, 3692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7384 Ramachandran restraints generated. 3692 Oldfield, 0 Emsley, 3692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 3448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 324 time to evaluate : 1.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.8263 (tpt) cc_final: 0.7586 (tpp) REVERT: A 333 LEU cc_start: 0.9584 (OUTLIER) cc_final: 0.9320 (mp) REVERT: A 361 MET cc_start: 0.8906 (ppp) cc_final: 0.8550 (ppp) REVERT: A 398 GLU cc_start: 0.8909 (mp0) cc_final: 0.8615 (mp0) REVERT: A 594 GLU cc_start: 0.8454 (pp20) cc_final: 0.7775 (pp20) REVERT: A 598 TRP cc_start: 0.8984 (OUTLIER) cc_final: 0.8350 (m-10) REVERT: A 696 LEU cc_start: 0.9448 (OUTLIER) cc_final: 0.9190 (mm) REVERT: A 848 MET cc_start: 0.8250 (mmt) cc_final: 0.7987 (mmm) REVERT: A 900 GLU cc_start: 0.9319 (mt-10) cc_final: 0.9057 (mm-30) REVERT: A 1141 MET cc_start: 0.9629 (mmm) cc_final: 0.9363 (mmm) REVERT: A 1156 MET cc_start: 0.8193 (mmm) cc_final: 0.7918 (mmm) REVERT: A 1417 GLU cc_start: 0.8275 (mm-30) cc_final: 0.7866 (mm-30) REVERT: A 1829 GLN cc_start: 0.9165 (tp40) cc_final: 0.8743 (tp40) REVERT: C 120 MET cc_start: 0.7682 (tpt) cc_final: 0.6878 (tpp) REVERT: C 598 TRP cc_start: 0.9024 (OUTLIER) cc_final: 0.7982 (m-10) REVERT: C 1121 TYR cc_start: 0.8585 (p90) cc_final: 0.8333 (p90) REVERT: C 1146 GLU cc_start: 0.8172 (mm-30) cc_final: 0.7969 (mm-30) REVERT: C 1244 GLU cc_start: 0.8273 (OUTLIER) cc_final: 0.7848 (mp0) REVERT: C 1307 GLU cc_start: 0.8189 (tp30) cc_final: 0.7875 (tp30) REVERT: C 1507 ARG cc_start: 0.7745 (ttp80) cc_final: 0.7417 (ttp80) REVERT: C 1521 ARG cc_start: 0.8237 (mmt-90) cc_final: 0.7783 (mmt-90) REVERT: C 1760 GLN cc_start: 0.8919 (mm110) cc_final: 0.8254 (pm20) REVERT: C 1793 LEU cc_start: 0.8805 (OUTLIER) cc_final: 0.8581 (pp) REVERT: C 1821 TRP cc_start: 0.8609 (OUTLIER) cc_final: 0.6733 (t60) REVERT: C 1829 GLN cc_start: 0.9047 (tm-30) cc_final: 0.8602 (tm-30) outliers start: 72 outliers final: 50 residues processed: 380 average time/residue: 0.1704 time to fit residues: 109.5578 Evaluate side-chains 353 residues out of total 3448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 296 time to evaluate : 1.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 481 PHE Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 598 TRP Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 696 LEU Chi-restraints excluded: chain A residue 707 THR Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 906 ASN Chi-restraints excluded: chain A residue 1185 CYS Chi-restraints excluded: chain A residue 1265 LEU Chi-restraints excluded: chain A residue 1352 LEU Chi-restraints excluded: chain A residue 1395 LEU Chi-restraints excluded: chain A residue 1397 THR Chi-restraints excluded: chain A residue 1436 VAL Chi-restraints excluded: chain A residue 1648 SER Chi-restraints excluded: chain A residue 1687 LEU Chi-restraints excluded: chain A residue 1724 VAL Chi-restraints excluded: chain A residue 1770 LEU Chi-restraints excluded: chain A residue 1882 LEU Chi-restraints excluded: chain A residue 1884 VAL Chi-restraints excluded: chain C residue 41 GLU Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 322 ASN Chi-restraints excluded: chain C residue 335 ASN Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain C residue 587 VAL Chi-restraints excluded: chain C residue 598 TRP Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 714 LEU Chi-restraints excluded: chain C residue 735 VAL Chi-restraints excluded: chain C residue 780 LEU Chi-restraints excluded: chain C residue 798 LEU Chi-restraints excluded: chain C residue 836 ASP Chi-restraints excluded: chain C residue 1143 ARG Chi-restraints excluded: chain C residue 1212 THR Chi-restraints excluded: chain C residue 1244 GLU Chi-restraints excluded: chain C residue 1301 LEU Chi-restraints excluded: chain C residue 1379 VAL Chi-restraints excluded: chain C residue 1431 VAL Chi-restraints excluded: chain C residue 1436 VAL Chi-restraints excluded: chain C residue 1560 LEU Chi-restraints excluded: chain C residue 1619 ILE Chi-restraints excluded: chain C residue 1647 VAL Chi-restraints excluded: chain C residue 1770 LEU Chi-restraints excluded: chain C residue 1793 LEU Chi-restraints excluded: chain C residue 1821 TRP Chi-restraints excluded: chain C residue 1851 THR Chi-restraints excluded: chain C residue 1882 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 6 optimal weight: 5.9990 chunk 354 optimal weight: 8.9990 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 2.9990 chunk 195 optimal weight: 5.9990 chunk 45 optimal weight: 1.9990 chunk 265 optimal weight: 0.3980 chunk 93 optimal weight: 0.9990 chunk 133 optimal weight: 0.9980 chunk 373 optimal weight: 8.9990 chunk 62 optimal weight: 7.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1414 GLN A1738 GLN A1886 ASN ** C 717 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1405 HIS ** C1414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1532 GLN ** C1887 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.124087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.090828 restraints weight = 81314.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.090674 restraints weight = 50301.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.091240 restraints weight = 37337.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.091912 restraints weight = 31575.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.092077 restraints weight = 28146.356| |-----------------------------------------------------------------------------| r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.5325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 29330 Z= 0.129 Angle : 0.735 14.817 39730 Z= 0.361 Chirality : 0.043 0.245 4666 Planarity : 0.004 0.062 5024 Dihedral : 8.051 91.377 4192 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.10 % Favored : 91.85 % Rotamer: Outliers : 2.00 % Allowed : 24.70 % Favored : 73.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.83 (0.14), residues: 3692 helix: 0.97 (0.13), residues: 1776 sheet: 0.01 (0.35), residues: 236 loop : -2.44 (0.15), residues: 1680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A1507 TYR 0.024 0.001 TYR A1097 PHE 0.044 0.001 PHE A 43 TRP 0.035 0.002 TRP A1351 HIS 0.006 0.001 HIS C1296 Details of bonding type rmsd covalent geometry : bond 0.00288 (29318) covalent geometry : angle 0.73283 (39716) SS BOND : bond 0.00635 ( 4) SS BOND : angle 2.25894 ( 8) hydrogen bonds : bond 0.03335 ( 1306) hydrogen bonds : angle 4.10705 ( 3756) metal coordination : bond 0.03184 ( 8) metal coordination : angle 3.98825 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5079.33 seconds wall clock time: 88 minutes 51.02 seconds (5331.02 seconds total)