Starting phenix.real_space_refine on Mon Sep 14 08:00:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6klh_0710/09_2026/6klh_0710.cif Found real_map, /net/cci-nas-00/data/ceres_data/6klh_0710/09_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6klh_0710/09_2026/6klh_0710.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6klh_0710/09_2026/6klh_0710.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6klh_0710/09_2026/6klh_0710.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6klh_0710/09_2026/6klh_0710.cif" model { file = "/net/cci-nas-00/data/ceres_data/6klh_0710/09_2026/6klh_0710.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6klh_0710/09_2026/6klh_0710.cif" } 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-2.2.1-6174/lib/python3.11/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: {'RNAv2': 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: 27.31, per 1000 atoms: 0.95 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: 2.77 Conformation dependent library (CDL) restraints added in 1.8 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: 1.11 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: 6.65 Time building geometry restraints manager: 3.74 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: 38880 2.34 - 4.67: 708 4.67 - 7.01: 111 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 - 17.76: 16088 17.76 - 35.51: 1310 35.51 - 53.27: 228 53.27 - 71.02: 74 71.02 - 88.78: 30 Dihedral angle restraints: 17730 sinusoidal: 6736 harmonic: 10994 Sorted by residual: dihedral pdb=" C4' U B 16 " pdb=" C3' U B 16 " pdb=" C2' U B 16 " pdb=" C1' U B 16 " ideal model delta sinusoidal sigma weight residual 36.34 -35.05 71.40 1 3.10e+00 1.04e-01 6.80e+02 dihedral pdb=" C4' U D 16 " pdb=" C3' U D 16 " pdb=" C2' U D 16 " pdb=" C1' U D 16 " ideal model delta sinusoidal sigma weight residual 36.35 -35.02 71.37 1 3.10e+00 1.04e-01 6.80e+02 dihedral pdb=" C4' U D 14 " pdb=" C3' U D 14 " pdb=" C2' U D 14 " pdb=" C1' U D 14 " ideal model delta sinusoidal sigma weight residual 36.34 -34.86 71.21 1 3.10e+00 1.04e-01 6.77e+02 ... (remaining 17727 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 3785 0.055 - 0.110: 740 0.110 - 0.166: 98 0.166 - 0.221: 13 0.221 - 0.276: 30 Chirality restraints: 4666 Sorted by residual: chirality pdb=" C2' U B 16 " pdb=" C3' U B 16 " pdb=" O2' U B 16 " pdb=" C1' U B 16 " both_signs ideal model delta sigma weight residual False -2.79 -2.51 -0.28 2.00e-01 2.50e+01 1.91e+00 chirality pdb=" C2' C B 13 " pdb=" C3' C B 13 " pdb=" O2' C B 13 " pdb=" C1' C B 13 " both_signs ideal model delta sigma weight residual False -2.79 -2.51 -0.28 2.00e-01 2.50e+01 1.90e+00 chirality pdb=" C2' U D 16 " pdb=" C3' U D 16 " pdb=" O2' U D 16 " pdb=" C1' U D 16 " both_signs ideal model delta sigma weight residual False -2.79 -2.51 -0.28 2.00e-01 2.50e+01 1.89e+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: 0.06 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: 0.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 0.440 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 54.160 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.280 ------------------------------------------------------------------------------- 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= 0.152 Angle : 0.745 12.726 39730 Z= 0.385 Chirality : 0.049 0.276 4666 Planarity : 0.004 0.053 5024 Dihedral : 14.208 88.775 10546 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/Z covalent geometry : bond 0.00296 / 0.14 (29318) covalent geometry : angle 0.73801 / 0.38 (39716) SS BOND : bond 0.00121 / 0.06 ( 4) SS BOND : angle 1.63508 / 0.87 ( 8) hydrogen bonds : bond 0.13743 / 9.39 ( 1306) hydrogen bonds : angle 5.93347 / 4.10 ( 3756) metal coordination : bond 0.07316 / 3.88 ( 8) metal coordination : angle 8.39398 / 6.03 ( 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 : 0.997 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: 0.1679 time to fit residues: 140.6563 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 : 1.049 ------------------------------------------------------------------------------- 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... 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 ** C 335 ASN ** 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 = 0.4166 r_free = 0.4166 target = 0.135096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.103768 restraints weight = 80476.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.101428 restraints weight = 49497.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.103039 restraints weight = 41844.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.103101 restraints weight = 35758.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.103273 restraints weight = 30612.630| |-----------------------------------------------------------------------------| r_work (final): 0.3640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.1736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 29330 Z= 0.147 Angle : 0.721 15.517 39730 Z= 0.349 Chirality : 0.049 0.605 4666 Planarity : 0.004 0.038 5024 Dihedral : 7.699 125.214 4138 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.64 % Favored : 91.25 % Rotamer: Outliers : 1.60 % Allowed : 10.57 % Favored : 87.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.45 (0.14), residues: 3692 helix: 0.56 (0.13), residues: 1748 sheet: -0.91 (0.30), residues: 272 loop : -2.75 (0.14), residues: 1672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C1769 TYR 0.020 0.001 TYR C 701 PHE 0.033 0.001 PHE A 352 TRP 0.040 0.002 TRP C1717 HIS 0.004 0.001 HIS C1231 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.15 (29318) covalent geometry : angle 0.71854 / 0.35 (39716) SS BOND : bond 0.00490 / 0.23 ( 4) SS BOND : angle 1.53249 / 0.80 ( 8) hydrogen bonds : bond 0.03550 / 2.42 ( 1306) hydrogen bonds : angle 4.52108 / 3.18 ( 3756) metal coordination : bond 0.03307 / 1.70 ( 8) metal coordination : angle 4.55041 / 3.42 ( 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 440 residues out of total 3448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 392 time to evaluate : 1.139 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 120 MET cc_start: 0.8229 (tpt) cc_final: 0.7205 (tpt) REVERT: A 333 LEU cc_start: 0.9352 (OUTLIER) cc_final: 0.9067 (mt) REVERT: A 351 LEU cc_start: 0.9525 (mt) cc_final: 0.9180 (mt) REVERT: A 435 LEU cc_start: 0.8344 (tt) cc_final: 0.7817 (tt) REVERT: A 550 GLU cc_start: 0.8355 (tp30) cc_final: 0.7948 (tp30) REVERT: A 594 GLU cc_start: 0.8432 (pp20) cc_final: 0.8046 (pp20) REVERT: A 900 GLU cc_start: 0.9298 (mt-10) cc_final: 0.9034 (mm-30) REVERT: A 919 MET cc_start: 0.8157 (ptm) cc_final: 0.7885 (ptp) REVERT: A 1097 TYR cc_start: 0.5626 (t80) cc_final: 0.5172 (t80) REVERT: A 1141 MET cc_start: 0.9524 (mmm) cc_final: 0.9151 (mmp) REVERT: A 1196 MET cc_start: 0.8083 (mmt) cc_final: 0.7872 (mmt) REVERT: A 1210 LEU cc_start: 0.7986 (mm) cc_final: 0.7742 (mm) REVERT: A 1289 ASP cc_start: 0.7559 (t70) cc_final: 0.7008 (t70) REVERT: A 1336 LYS cc_start: 0.8105 (mppt) cc_final: 0.7904 (tppp) REVERT: A 1440 SER cc_start: 0.9026 (m) cc_final: 0.8392 (p) REVERT: A 1540 GLU cc_start: 0.7125 (mm-30) cc_final: 0.6529 (mm-30) REVERT: A 1731 LEU cc_start: 0.8224 (mt) cc_final: 0.7975 (mt) REVERT: A 1733 MET cc_start: 0.2466 (tpt) cc_final: 0.2236 (mmm) REVERT: A 1861 ASN cc_start: 0.8261 (m-40) cc_final: 0.7988 (m-40) REVERT: C 120 MET cc_start: 0.8153 (tpt) cc_final: 0.7084 (tpt) REVERT: C 207 LEU cc_start: 0.7986 (mm) cc_final: 0.7486 (mt) REVERT: C 231 ARG cc_start: 0.8241 (ptm-80) cc_final: 0.8041 (ptm-80) REVERT: C 293 GLU cc_start: 0.8135 (tp30) cc_final: 0.7809 (tp30) REVERT: C 401 LYS cc_start: 0.9022 (mmtm) cc_final: 0.8776 (mmtm) REVERT: C 585 ASP cc_start: 0.7815 (p0) cc_final: 0.7493 (p0) REVERT: C 1097 TYR cc_start: 0.5048 (t80) cc_final: 0.4699 (t80) REVERT: C 1143 ARG cc_start: 0.8848 (OUTLIER) cc_final: 0.8553 (ptm160) REVERT: C 1269 PHE cc_start: 0.8901 (t80) cc_final: 0.8629 (t80) REVERT: C 1274 MET cc_start: 0.5782 (pmm) cc_final: 0.5551 (pmm) REVERT: C 1285 MET cc_start: 0.7244 (tpt) cc_final: 0.7004 (tpt) REVERT: C 1417 GLU cc_start: 0.7721 (mm-30) cc_final: 0.7495 (mm-30) REVERT: C 1511 PHE cc_start: 0.6726 (m-80) cc_final: 0.6137 (m-10) REVERT: C 1678 ILE cc_start: 0.8898 (tp) cc_final: 0.8609 (tp) REVERT: C 1728 GLU cc_start: 0.7434 (tm-30) cc_final: 0.7047 (tm-30) REVERT: C 1731 LEU cc_start: 0.7621 (mt) cc_final: 0.6922 (mt) REVERT: C 1765 MET cc_start: 0.4790 (mmm) cc_final: 0.4202 (mmm) outliers start: 48 outliers final: 22 residues processed: 419 average time/residue: 0.1653 time to fit residues: 116.8850 Evaluate side-chains 358 residues out of total 3448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 334 time to evaluate : 1.142 ------------------------------------------------------------------------------- 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 666 VAL Chi-restraints excluded: chain A residue 779 LEU 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 87 optimal weight: 0.6980 chunk 240 optimal weight: 3.9990 chunk 299 optimal weight: 6.9990 chunk 303 optimal weight: 8.9990 chunk 2 optimal weight: 8.9990 chunk 321 optimal weight: 2.9990 chunk 78 optimal weight: 9.9990 chunk 69 optimal weight: 3.9990 chunk 203 optimal weight: 2.9990 chunk 84 optimal weight: 50.0000 chunk 52 optimal weight: 0.7980 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 430 HIS A 872 ASN ** A1034 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1414 GLN ** C 629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 717 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.130341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.097878 restraints weight = 80592.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.096589 restraints weight = 47233.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.097437 restraints weight = 41056.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.097985 restraints weight = 33520.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.098143 restraints weight = 29831.345| |-----------------------------------------------------------------------------| r_work (final): 0.3548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.2863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 29330 Z= 0.157 Angle : 0.669 11.158 39730 Z= 0.333 Chirality : 0.046 0.501 4666 Planarity : 0.004 0.038 5024 Dihedral : 7.865 141.493 4126 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.61 % Favored : 91.33 % Rotamer: Outliers : 2.30 % Allowed : 14.57 % Favored : 83.13 % 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: -1.21 (0.14), residues: 3692 helix: 0.70 (0.13), residues: 1784 sheet: -0.52 (0.32), residues: 240 loop : -2.64 (0.14), residues: 1668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C1814 TYR 0.025 0.001 TYR C 701 PHE 0.026 0.002 PHE A 352 TRP 0.034 0.002 TRP C1717 HIS 0.008 0.001 HIS C1296 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.16 (29318) covalent geometry : angle 0.66623 / 0.33 (39716) SS BOND : bond 0.00664 / 0.32 ( 4) SS BOND : angle 1.15859 / 0.59 ( 8) hydrogen bonds : bond 0.03551 / 2.40 ( 1306) hydrogen bonds : angle 4.22862 / 3.00 ( 3756) metal coordination : bond 0.03345 / 1.71 ( 8) metal coordination : angle 4.50835 / 3.38 ( 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 434 residues out of total 3448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 365 time to evaluate : 1.080 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 44 LYS cc_start: 0.9093 (ptpt) cc_final: 0.8771 (ptpp) REVERT: A 120 MET cc_start: 0.8201 (tpt) cc_final: 0.7229 (tpt) REVERT: A 292 MET cc_start: 0.8375 (mtp) cc_final: 0.8152 (mtp) REVERT: A 333 LEU cc_start: 0.9425 (mt) cc_final: 0.9127 (mt) REVERT: A 357 MET cc_start: 0.9042 (mmm) cc_final: 0.8822 (tpp) REVERT: A 398 GLU cc_start: 0.8831 (mp0) cc_final: 0.8447 (mp0) REVERT: A 550 GLU cc_start: 0.8376 (tp30) cc_final: 0.8022 (tp30) REVERT: A 594 GLU cc_start: 0.8311 (pp20) cc_final: 0.7970 (pp20) REVERT: A 900 GLU cc_start: 0.9300 (mt-10) cc_final: 0.9048 (mm-30) REVERT: A 1097 TYR cc_start: 0.5829 (t80) cc_final: 0.5247 (t80) REVERT: A 1141 MET cc_start: 0.9543 (mmm) cc_final: 0.9153 (mmp) REVERT: A 1196 MET cc_start: 0.7985 (mmt) cc_final: 0.7771 (mmt) REVERT: A 1414 GLN cc_start: 0.7727 (OUTLIER) cc_final: 0.7513 (pp30) REVERT: A 1540 GLU cc_start: 0.7437 (mm-30) cc_final: 0.6824 (mm-30) REVERT: A 1765 MET cc_start: 0.3652 (mmm) cc_final: 0.3442 (mmm) REVERT: A 1829 GLN cc_start: 0.9141 (tp40) cc_final: 0.8885 (tp40) REVERT: A 1861 ASN cc_start: 0.8786 (m-40) cc_final: 0.8563 (m-40) REVERT: C 120 MET cc_start: 0.8539 (tpt) cc_final: 0.7860 (tpp) REVERT: C 182 GLN cc_start: 0.8066 (OUTLIER) cc_final: 0.7202 (pp30) REVERT: C 231 ARG cc_start: 0.8065 (ptm-80) cc_final: 0.7626 (ptm-80) REVERT: C 401 LYS cc_start: 0.9041 (mmtm) cc_final: 0.8834 (mmtm) REVERT: C 598 TRP cc_start: 0.8840 (OUTLIER) cc_final: 0.8200 (m-10) REVERT: C 708 LYS cc_start: 0.8849 (OUTLIER) cc_final: 0.8535 (pttt) REVERT: C 1143 ARG cc_start: 0.8809 (OUTLIER) cc_final: 0.8605 (ptm160) REVERT: C 1146 GLU cc_start: 0.8491 (mm-30) cc_final: 0.8281 (mm-30) REVERT: C 1269 PHE cc_start: 0.8760 (t80) cc_final: 0.8506 (t80) REVERT: C 1285 MET cc_start: 0.7334 (tpt) cc_final: 0.7087 (tpt) REVERT: C 1417 GLU cc_start: 0.7690 (mm-30) cc_final: 0.7465 (mm-30) REVERT: C 1678 ILE cc_start: 0.8974 (tp) cc_final: 0.8704 (tp) REVERT: C 1728 GLU cc_start: 0.7203 (tm-30) cc_final: 0.6709 (tm-30) REVERT: C 1731 LEU cc_start: 0.7886 (mt) cc_final: 0.7257 (mt) REVERT: C 1782 MET cc_start: 0.7782 (mmm) cc_final: 0.7531 (mmt) REVERT: C 1829 GLN cc_start: 0.9031 (tm-30) cc_final: 0.8754 (tm-30) REVERT: C 1882 LEU cc_start: 0.9296 (mm) cc_final: 0.9084 (mm) outliers start: 69 outliers final: 44 residues processed: 410 average time/residue: 0.1638 time to fit residues: 113.5866 Evaluate side-chains 366 residues out of total 3448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 317 time to evaluate : 1.214 ------------------------------------------------------------------------------- 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 591 MET Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 906 ASN Chi-restraints excluded: chain A residue 1185 CYS Chi-restraints excluded: chain A residue 1414 GLN Chi-restraints excluded: chain A residue 1687 LEU Chi-restraints excluded: chain A residue 1693 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 1853 CYS 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 41 GLU Chi-restraints excluded: chain C residue 182 GLN Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 388 LEU Chi-restraints excluded: chain C residue 416 ASN 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 779 LEU Chi-restraints excluded: chain C residue 798 LEU Chi-restraints excluded: chain C residue 1143 ARG Chi-restraints excluded: chain C residue 1185 CYS 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 1436 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 1786 LEU Chi-restraints excluded: chain C residue 1791 HIS Chi-restraints excluded: chain C residue 1813 ILE Chi-restraints excluded: chain C residue 1884 VAL 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: 6.9990 chunk 153 optimal weight: 0.3980 chunk 251 optimal weight: 6.9990 chunk 34 optimal weight: 0.5980 chunk 60 optimal weight: 6.9990 chunk 252 optimal weight: 3.9990 chunk 24 optimal weight: 5.9990 chunk 142 optimal weight: 0.0770 chunk 161 optimal weight: 8.9990 chunk 309 optimal weight: 2.9990 overall best weight: 1.6142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1034 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1730 GLN A1798 ASN A1837 GLN ** C 629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 717 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1034 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1405 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1886 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.130553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.097183 restraints weight = 80812.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.096327 restraints weight = 49126.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.097373 restraints weight = 41858.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.097422 restraints weight = 36211.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.097737 restraints weight = 31036.072| |-----------------------------------------------------------------------------| r_work (final): 0.3543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.3182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 29330 Z= 0.130 Angle : 0.643 11.830 39730 Z= 0.316 Chirality : 0.044 0.415 4666 Planarity : 0.003 0.037 5024 Dihedral : 7.641 137.290 4124 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.26 % Favored : 91.68 % Rotamer: Outliers : 2.53 % Allowed : 17.30 % Favored : 80.17 % 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: -1.00 (0.14), residues: 3692 helix: 0.87 (0.13), residues: 1774 sheet: -0.44 (0.31), residues: 250 loop : -2.53 (0.15), residues: 1668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1725 TYR 0.013 0.001 TYR C 701 PHE 0.026 0.001 PHE A 352 TRP 0.021 0.001 TRP C1717 HIS 0.006 0.001 HIS A1296 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 (29318) covalent geometry : angle 0.64083 / 0.32 (39716) SS BOND : bond 0.00450 / 0.22 ( 4) SS BOND : angle 1.03299 / 0.75 ( 8) hydrogen bonds : bond 0.03191 / 2.13 ( 1306) hydrogen bonds : angle 4.08042 / 2.90 ( 3756) metal coordination : bond 0.02865 / 1.47 ( 8) metal coordination : angle 4.21325 / 3.25 ( 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 426 residues out of total 3448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 350 time to evaluate : 0.975 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: symmetry clash REVERT: A 41 GLU cc_start: 0.9109 (OUTLIER) cc_final: 0.8873 (pm20) REVERT: A 44 LYS cc_start: 0.9083 (ptpt) cc_final: 0.8704 (ptpp) REVERT: A 120 MET cc_start: 0.8232 (tpt) cc_final: 0.7357 (tpt) REVERT: A 333 LEU cc_start: 0.9425 (mt) cc_final: 0.9129 (mt) REVERT: A 351 LEU cc_start: 0.9470 (mt) cc_final: 0.9218 (mt) REVERT: A 398 GLU cc_start: 0.8884 (mp0) cc_final: 0.8347 (mp0) REVERT: A 550 GLU cc_start: 0.8438 (tp30) cc_final: 0.8104 (tp30) REVERT: A 594 GLU cc_start: 0.8276 (pp20) cc_final: 0.7882 (pp20) REVERT: A 900 GLU cc_start: 0.9351 (mt-10) cc_final: 0.9086 (mm-30) REVERT: A 1097 TYR cc_start: 0.5871 (t80) cc_final: 0.5301 (t80) REVERT: A 1141 MET cc_start: 0.9556 (mmm) cc_final: 0.9163 (mmp) REVERT: A 1156 MET cc_start: 0.8035 (mmm) cc_final: 0.7403 (mmm) REVERT: A 1196 MET cc_start: 0.8040 (mmt) cc_final: 0.7831 (mmt) REVERT: A 1289 ASP cc_start: 0.7657 (t70) cc_final: 0.7054 (t70) REVERT: A 1540 GLU cc_start: 0.7512 (mm-30) cc_final: 0.6861 (mm-30) REVERT: A 1829 GLN cc_start: 0.9156 (tp40) cc_final: 0.8825 (tp40) REVERT: C 120 MET cc_start: 0.8523 (tpt) cc_final: 0.7861 (tpp) REVERT: C 401 LYS cc_start: 0.9086 (mmtm) cc_final: 0.8795 (mmtm) REVERT: C 598 TRP cc_start: 0.8739 (OUTLIER) cc_final: 0.8151 (m-10) REVERT: C 1146 GLU cc_start: 0.8389 (mm-30) cc_final: 0.8162 (mm-30) REVERT: C 1269 PHE cc_start: 0.8844 (t80) cc_final: 0.8585 (t80) REVERT: C 1285 MET cc_start: 0.7414 (tpt) cc_final: 0.7154 (tpt) REVERT: C 1307 GLU cc_start: 0.7914 (tp30) cc_final: 0.7657 (tp30) REVERT: C 1678 ILE cc_start: 0.8931 (tp) cc_final: 0.8643 (tp) REVERT: C 1728 GLU cc_start: 0.7444 (tm-30) cc_final: 0.6876 (tm-30) REVERT: C 1731 LEU cc_start: 0.7954 (mt) cc_final: 0.7690 (mt) REVERT: C 1765 MET cc_start: 0.5683 (mmm) cc_final: 0.5415 (mmm) REVERT: C 1829 GLN cc_start: 0.9141 (tm-30) cc_final: 0.8788 (tm-30) outliers start: 76 outliers final: 49 residues processed: 399 average time/residue: 0.1622 time to fit residues: 109.8015 Evaluate side-chains 376 residues out of total 3448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 325 time to evaluate : 1.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 GLU 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 481 PHE Chi-restraints excluded: chain A residue 587 VAL 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 1011 LEU Chi-restraints excluded: chain A residue 1185 CYS Chi-restraints excluded: chain A residue 1352 LEU Chi-restraints excluded: chain A residue 1409 CYS Chi-restraints excluded: chain A residue 1560 LEU Chi-restraints excluded: chain A residue 1648 SER Chi-restraints excluded: chain A residue 1687 LEU Chi-restraints excluded: chain A residue 1693 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 41 GLU Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 431 HIS 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 798 LEU Chi-restraints excluded: chain C residue 1144 LEU Chi-restraints excluded: chain C residue 1185 CYS Chi-restraints excluded: chain C residue 1202 LEU Chi-restraints excluded: chain C residue 1212 THR Chi-restraints excluded: chain C residue 1274 MET 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 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 1792 LEU Chi-restraints excluded: chain C residue 1884 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 43 optimal weight: 50.0000 chunk 23 optimal weight: 7.9990 chunk 316 optimal weight: 1.9990 chunk 59 optimal weight: 0.8980 chunk 364 optimal weight: 0.0970 chunk 219 optimal weight: 1.9990 chunk 198 optimal weight: 4.9990 chunk 26 optimal weight: 7.9990 chunk 142 optimal weight: 5.9990 chunk 205 optimal weight: 9.9990 chunk 180 optimal weight: 20.0000 overall best weight: 1.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1296 HIS A1414 GLN ** C 629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 717 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1034 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1405 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1861 ASN C1887 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.127092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.094165 restraints weight = 80239.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.093595 restraints weight = 46624.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.094497 restraints weight = 38139.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.094714 restraints weight = 34080.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.094931 restraints weight = 29987.733| |-----------------------------------------------------------------------------| r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.3627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 29330 Z= 0.143 Angle : 0.650 10.511 39730 Z= 0.320 Chirality : 0.044 0.445 4666 Planarity : 0.003 0.038 5024 Dihedral : 7.628 137.905 4124 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.45 % Favored : 91.50 % Rotamer: Outliers : 3.37 % Allowed : 18.30 % Favored : 78.33 % 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: -0.91 (0.14), residues: 3692 helix: 0.96 (0.13), residues: 1774 sheet: -0.61 (0.32), residues: 262 loop : -2.47 (0.15), residues: 1656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 231 TYR 0.031 0.001 TYR C1030 PHE 0.027 0.001 PHE A 352 TRP 0.019 0.001 TRP C1717 HIS 0.006 0.001 HIS C 910 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 (29318) covalent geometry : angle 0.64777 / 0.32 (39716) SS BOND : bond 0.00474 / 0.24 ( 4) SS BOND : angle 1.02839 / 0.88 ( 8) hydrogen bonds : bond 0.03233 / 2.17 ( 1306) hydrogen bonds : angle 4.05895 / 2.88 ( 3756) metal coordination : bond 0.02777 / 1.42 ( 8) metal coordination : angle 4.33611 / 3.35 ( 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 437 residues out of total 3448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 336 time to evaluate : 1.146 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: symmetry clash revert: symmetry clash REVERT: A 41 GLU cc_start: 0.9077 (OUTLIER) cc_final: 0.8860 (pm20) REVERT: A 44 LYS cc_start: 0.9156 (ptpt) cc_final: 0.8789 (ptpp) REVERT: A 120 MET cc_start: 0.8243 (tpt) cc_final: 0.7397 (tpt) REVERT: A 351 LEU cc_start: 0.9480 (mt) cc_final: 0.9247 (mt) REVERT: A 550 GLU cc_start: 0.8431 (tp30) cc_final: 0.8081 (tp30) REVERT: A 594 GLU cc_start: 0.8443 (pp20) cc_final: 0.7973 (pp20) REVERT: A 696 LEU cc_start: 0.9437 (OUTLIER) cc_final: 0.9124 (mm) REVERT: A 900 GLU cc_start: 0.9322 (mt-10) cc_final: 0.9070 (mm-30) REVERT: A 919 MET cc_start: 0.8180 (ptm) cc_final: 0.7865 (ptp) REVERT: A 1097 TYR cc_start: 0.5926 (t80) cc_final: 0.5335 (t80) REVERT: A 1141 MET cc_start: 0.9580 (mmm) cc_final: 0.9214 (mmp) REVERT: A 1156 MET cc_start: 0.8162 (mmm) cc_final: 0.7956 (mmm) REVERT: A 1196 MET cc_start: 0.8253 (mmt) cc_final: 0.7973 (mmt) REVERT: A 1782 MET cc_start: 0.8298 (mmm) cc_final: 0.8073 (mmt) REVERT: A 1829 GLN cc_start: 0.9214 (tp40) cc_final: 0.8826 (tp40) REVERT: C 120 MET cc_start: 0.8504 (tpt) cc_final: 0.7811 (tpp) REVERT: C 182 GLN cc_start: 0.7828 (OUTLIER) cc_final: 0.7101 (pp30) REVERT: C 401 LYS cc_start: 0.9117 (mmtm) cc_final: 0.8836 (mmtm) REVERT: C 598 TRP cc_start: 0.8866 (OUTLIER) cc_final: 0.8348 (m-10) REVERT: C 866 ASP cc_start: 0.7456 (m-30) cc_final: 0.7165 (p0) REVERT: C 1146 GLU cc_start: 0.8283 (mm-30) cc_final: 0.7818 (mm-30) REVERT: C 1150 GLU cc_start: 0.7794 (mt-10) cc_final: 0.7304 (mt-10) REVERT: C 1244 GLU cc_start: 0.7976 (OUTLIER) cc_final: 0.7609 (mp0) REVERT: C 1269 PHE cc_start: 0.8809 (t80) cc_final: 0.8580 (t80) REVERT: C 1285 MET cc_start: 0.7456 (tpt) cc_final: 0.7124 (tpt) REVERT: C 1307 GLU cc_start: 0.8215 (tp30) cc_final: 0.7716 (tp30) REVERT: C 1678 ILE cc_start: 0.8969 (tp) cc_final: 0.8676 (tp) REVERT: C 1728 GLU cc_start: 0.7483 (tm-30) cc_final: 0.6438 (tm-30) REVERT: C 1731 LEU cc_start: 0.8101 (mt) cc_final: 0.7375 (mt) REVERT: C 1829 GLN cc_start: 0.9211 (tm-30) cc_final: 0.8838 (pp30) outliers start: 101 outliers final: 59 residues processed: 413 average time/residue: 0.1617 time to fit residues: 113.5283 Evaluate side-chains 367 residues out of total 3448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 303 time to evaluate : 1.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 GLU 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 360 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 666 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 1011 LEU Chi-restraints excluded: chain A residue 1185 CYS Chi-restraints excluded: chain A residue 1352 LEU Chi-restraints excluded: chain A residue 1409 CYS Chi-restraints excluded: chain A residue 1532 GLN Chi-restraints excluded: chain A residue 1560 LEU Chi-restraints excluded: chain A residue 1648 SER Chi-restraints excluded: chain A residue 1687 LEU Chi-restraints excluded: chain A residue 1693 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 1877 LEU Chi-restraints excluded: chain A residue 1882 LEU Chi-restraints excluded: chain A residue 1884 VAL Chi-restraints excluded: chain C residue 182 GLN Chi-restraints excluded: chain C residue 220 GLU Chi-restraints excluded: chain C residue 322 ASN Chi-restraints excluded: chain C residue 360 LEU Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 431 HIS 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 1202 LEU Chi-restraints excluded: chain C residue 1212 THR Chi-restraints excluded: chain C residue 1244 GLU Chi-restraints excluded: chain C residue 1274 MET Chi-restraints excluded: chain C residue 1301 LEU Chi-restraints excluded: chain C residue 1320 VAL Chi-restraints excluded: chain C residue 1409 CYS 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 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 1786 LEU Chi-restraints excluded: chain C residue 1792 LEU Chi-restraints excluded: chain C residue 1813 ILE Chi-restraints excluded: chain C residue 1842 SER Chi-restraints excluded: chain C residue 1882 LEU Chi-restraints excluded: chain C residue 1884 VAL Chi-restraints excluded: chain C residue 1886 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 105 optimal weight: 5.9990 chunk 321 optimal weight: 4.9990 chunk 224 optimal weight: 6.9990 chunk 74 optimal weight: 7.9990 chunk 45 optimal weight: 0.9990 chunk 266 optimal weight: 6.9990 chunk 38 optimal weight: 0.4980 chunk 338 optimal weight: 3.9990 chunk 131 optimal weight: 4.9990 chunk 79 optimal weight: 8.9990 chunk 98 optimal weight: 0.9990 overall best weight: 2.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 800 ASN A1414 GLN A1425 GLN A1730 GLN A1837 GLN ** C 629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 717 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 800 ASN ** C1034 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1730 GLN C1798 ASN C1887 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.125730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.092846 restraints weight = 79848.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.092215 restraints weight = 46390.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.092894 restraints weight = 38126.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.093669 restraints weight = 32081.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.093752 restraints weight = 28467.413| |-----------------------------------------------------------------------------| r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.4172 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= 0.154 Angle : 0.669 10.449 39730 Z= 0.329 Chirality : 0.045 0.460 4666 Planarity : 0.003 0.039 5024 Dihedral : 7.675 138.187 4124 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.42 % Favored : 91.52 % Rotamer: Outliers : 3.37 % Allowed : 19.80 % Favored : 76.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.92 (0.14), residues: 3692 helix: 0.94 (0.13), residues: 1788 sheet: -0.57 (0.33), residues: 262 loop : -2.50 (0.15), residues: 1642 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C1814 TYR 0.015 0.001 TYR C 701 PHE 0.020 0.001 PHE C 352 TRP 0.018 0.002 TRP C1717 HIS 0.006 0.001 HIS C1296 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.15 (29318) covalent geometry : angle 0.66709 / 0.33 (39716) SS BOND : bond 0.00583 / 0.29 ( 4) SS BOND : angle 1.04249 / 0.91 ( 8) hydrogen bonds : bond 0.03329 / 2.25 ( 1306) hydrogen bonds : angle 4.07006 / 2.91 ( 3756) metal coordination : bond 0.02732 / 1.40 ( 8) metal coordination : angle 4.56816 / 3.60 ( 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 444 residues out of total 3448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 343 time to evaluate : 1.136 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 41 GLU cc_start: 0.9064 (OUTLIER) cc_final: 0.8842 (pm20) REVERT: A 44 LYS cc_start: 0.9167 (ptpt) cc_final: 0.8809 (ptpp) REVERT: A 120 MET cc_start: 0.8337 (tpt) cc_final: 0.7521 (tpt) REVERT: A 333 LEU cc_start: 0.9458 (mt) cc_final: 0.9174 (mt) REVERT: A 351 LEU cc_start: 0.9460 (mt) cc_final: 0.9197 (mt) REVERT: A 398 GLU cc_start: 0.8966 (mp0) cc_final: 0.8529 (mp0) REVERT: A 550 GLU cc_start: 0.8514 (tp30) cc_final: 0.8179 (tp30) REVERT: A 594 GLU cc_start: 0.8395 (pp20) cc_final: 0.7827 (pp20) REVERT: A 598 TRP cc_start: 0.8855 (OUTLIER) cc_final: 0.8534 (m-10) REVERT: A 836 ASP cc_start: 0.7338 (m-30) cc_final: 0.6916 (p0) REVERT: A 848 MET cc_start: 0.8565 (mmt) cc_final: 0.8317 (mmm) REVERT: A 900 GLU cc_start: 0.9332 (mt-10) cc_final: 0.9094 (mm-30) REVERT: A 919 MET cc_start: 0.7987 (ptm) cc_final: 0.7615 (ptp) REVERT: A 1141 MET cc_start: 0.9589 (mmm) cc_final: 0.9235 (mmp) REVERT: A 1196 MET cc_start: 0.8241 (mmt) cc_final: 0.7963 (mmt) REVERT: A 1414 GLN cc_start: 0.8025 (OUTLIER) cc_final: 0.7156 (pp30) REVERT: A 1417 GLU cc_start: 0.8136 (mm-30) cc_final: 0.7672 (mm-30) REVERT: A 1728 GLU cc_start: 0.8344 (tm-30) cc_final: 0.7807 (tm-30) REVERT: A 1757 ASN cc_start: 0.8175 (p0) cc_final: 0.7876 (p0) REVERT: A 1782 MET cc_start: 0.8257 (mmm) cc_final: 0.7942 (mmt) REVERT: A 1829 GLN cc_start: 0.9230 (tp40) cc_final: 0.8848 (tp40) REVERT: C 120 MET cc_start: 0.8558 (tpt) cc_final: 0.7848 (tpp) REVERT: C 182 GLN cc_start: 0.7933 (OUTLIER) cc_final: 0.7146 (pp30) REVERT: C 598 TRP cc_start: 0.8859 (OUTLIER) cc_final: 0.8088 (m-10) REVERT: C 866 ASP cc_start: 0.7339 (m-30) cc_final: 0.7082 (p0) REVERT: C 1146 GLU cc_start: 0.8342 (mm-30) cc_final: 0.7838 (mm-30) REVERT: C 1150 GLU cc_start: 0.7777 (mt-10) cc_final: 0.7062 (mt-10) REVERT: C 1284 ILE cc_start: 0.9307 (tp) cc_final: 0.8916 (tt) REVERT: C 1285 MET cc_start: 0.7809 (tpt) cc_final: 0.7381 (tpt) REVERT: C 1307 GLU cc_start: 0.8234 (tp30) cc_final: 0.7734 (tp30) REVERT: C 1417 GLU cc_start: 0.7834 (mm-30) cc_final: 0.7426 (mm-30) REVERT: C 1731 LEU cc_start: 0.8267 (mt) cc_final: 0.8025 (mt) REVERT: C 1829 GLN cc_start: 0.9151 (tm-30) cc_final: 0.8825 (pp30) outliers start: 101 outliers final: 68 residues processed: 410 average time/residue: 0.1666 time to fit residues: 116.0788 Evaluate side-chains 390 residues out of total 3448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 317 time to evaluate : 1.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 GLU 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 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 1011 LEU Chi-restraints excluded: chain A residue 1185 CYS Chi-restraints excluded: chain A residue 1352 LEU Chi-restraints excluded: chain A residue 1414 GLN Chi-restraints excluded: chain A residue 1532 GLN Chi-restraints excluded: chain A residue 1533 TYR Chi-restraints excluded: chain A residue 1541 VAL Chi-restraints excluded: chain A residue 1560 LEU 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 1693 LEU Chi-restraints excluded: chain A residue 1724 VAL Chi-restraints excluded: chain A residue 1730 GLN 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 56 GLU Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 182 GLN Chi-restraints excluded: chain C residue 220 GLU Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 267 LEU Chi-restraints excluded: chain C residue 322 ASN Chi-restraints excluded: chain C residue 335 ASN Chi-restraints excluded: chain C residue 360 LEU Chi-restraints excluded: chain C residue 394 LEU Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 431 HIS 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 798 LEU Chi-restraints excluded: chain C residue 1202 LEU Chi-restraints excluded: chain C residue 1212 THR Chi-restraints excluded: chain C residue 1301 LEU Chi-restraints excluded: chain C residue 1351 TRP Chi-restraints excluded: chain C residue 1409 CYS 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 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 1786 LEU Chi-restraints excluded: chain C residue 1792 LEU Chi-restraints excluded: chain C residue 1813 ILE Chi-restraints excluded: chain C residue 1842 SER Chi-restraints excluded: chain C residue 1882 LEU Chi-restraints excluded: chain C residue 1884 VAL 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: 0.0770 chunk 244 optimal weight: 7.9990 chunk 336 optimal weight: 0.2980 chunk 201 optimal weight: 6.9990 chunk 47 optimal weight: 0.9980 chunk 99 optimal weight: 4.9990 chunk 338 optimal weight: 1.9990 chunk 180 optimal weight: 30.0000 chunk 104 optimal weight: 5.9990 chunk 27 optimal weight: 0.0170 chunk 247 optimal weight: 0.7980 overall best weight: 0.4376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1414 GLN A1425 GLN ** A1689 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1730 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1812 HIS C 629 GLN ** C 717 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1034 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1414 GLN C1837 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.128363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.096094 restraints weight = 79643.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.095322 restraints weight = 45848.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.096172 restraints weight = 37228.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.096982 restraints weight = 30787.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.097088 restraints weight = 27236.497| |-----------------------------------------------------------------------------| r_work (final): 0.3523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.4210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.061 29330 Z= 0.111 Angle : 0.656 13.486 39730 Z= 0.319 Chirality : 0.043 0.341 4666 Planarity : 0.003 0.069 5024 Dihedral : 7.533 139.147 4124 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.31 % Favored : 92.63 % Rotamer: Outliers : 2.57 % Allowed : 21.63 % Favored : 75.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.02 (0.13), residues: 1792 sheet: -0.34 (0.33), residues: 262 loop : -2.46 (0.15), residues: 1638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 231 TYR 0.027 0.001 TYR A1097 PHE 0.041 0.001 PHE C 43 TRP 0.017 0.001 TRP C1717 HIS 0.005 0.001 HIS C1296 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.11 (29318) covalent geometry : angle 0.65505 / 0.32 (39716) SS BOND : bond 0.00320 / 0.16 ( 4) SS BOND : angle 0.87415 / 0.76 ( 8) hydrogen bonds : bond 0.02854 / 1.93 ( 1306) hydrogen bonds : angle 3.93307 / 2.81 ( 3756) metal coordination : bond 0.03000 / 1.54 ( 8) metal coordination : angle 3.13692 / 2.42 ( 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 447 residues out of total 3448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 370 time to evaluate : 1.102 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: symmetry clash REVERT: A 44 LYS cc_start: 0.9086 (ptpt) cc_final: 0.8753 (ptpt) REVERT: A 120 MET cc_start: 0.8414 (tpt) cc_final: 0.7568 (tpt) REVERT: A 293 GLU cc_start: 0.8594 (OUTLIER) cc_final: 0.7968 (tp30) REVERT: A 351 LEU cc_start: 0.9457 (mt) cc_final: 0.9185 (mt) REVERT: A 397 LEU cc_start: 0.9585 (OUTLIER) cc_final: 0.9193 (mm) REVERT: A 398 GLU cc_start: 0.8916 (mp0) cc_final: 0.8103 (mp0) REVERT: A 550 GLU cc_start: 0.8420 (tp30) cc_final: 0.8102 (tp30) REVERT: A 594 GLU cc_start: 0.8306 (pp20) cc_final: 0.8043 (pp20) REVERT: A 848 MET cc_start: 0.8630 (mmt) cc_final: 0.8148 (mmm) REVERT: A 900 GLU cc_start: 0.9326 (mt-10) cc_final: 0.9073 (mm-30) REVERT: A 919 MET cc_start: 0.7981 (ptm) cc_final: 0.7538 (ppp) REVERT: A 1141 MET cc_start: 0.9564 (mmm) cc_final: 0.9238 (mmp) REVERT: A 1196 MET cc_start: 0.8184 (mmt) cc_final: 0.7901 (mmt) REVERT: A 1221 LEU cc_start: 0.8573 (mt) cc_final: 0.8349 (mp) REVERT: A 1289 ASP cc_start: 0.7545 (t70) cc_final: 0.7013 (t70) REVERT: A 1351 TRP cc_start: 0.8092 (m-10) cc_final: 0.7836 (m-10) REVERT: A 1414 GLN cc_start: 0.7867 (OUTLIER) cc_final: 0.7369 (pp30) REVERT: A 1417 GLU cc_start: 0.8177 (mm-30) cc_final: 0.7722 (mm-30) REVERT: A 1728 GLU cc_start: 0.8319 (tm-30) cc_final: 0.7840 (tm-30) REVERT: A 1757 ASN cc_start: 0.8111 (p0) cc_final: 0.7911 (p0) REVERT: A 1829 GLN cc_start: 0.9177 (tp40) cc_final: 0.8747 (tp40) REVERT: C 120 MET cc_start: 0.8403 (tpt) cc_final: 0.7742 (tpp) REVERT: C 351 LEU cc_start: 0.9267 (mt) cc_final: 0.9020 (mt) REVERT: C 606 MET cc_start: 0.8888 (mpp) cc_final: 0.8656 (mpp) REVERT: C 866 ASP cc_start: 0.7379 (m-30) cc_final: 0.7018 (p0) REVERT: C 1146 GLU cc_start: 0.8179 (mm-30) cc_final: 0.7770 (mm-30) REVERT: C 1150 GLU cc_start: 0.7821 (mt-10) cc_final: 0.7208 (mt-10) REVERT: C 1244 GLU cc_start: 0.7994 (mm-30) cc_final: 0.7789 (mp0) REVERT: C 1284 ILE cc_start: 0.9248 (tp) cc_final: 0.8836 (tt) REVERT: C 1307 GLU cc_start: 0.8168 (tp30) cc_final: 0.7649 (tp30) REVERT: C 1359 GLU cc_start: 0.8442 (tp30) cc_final: 0.8237 (tp30) REVERT: C 1511 PHE cc_start: 0.6673 (m-10) cc_final: 0.6432 (m-10) REVERT: C 1521 ARG cc_start: 0.8237 (mmt-90) cc_final: 0.7990 (mmt-90) REVERT: C 1781 MET cc_start: 0.8460 (mmm) cc_final: 0.8160 (mmm) REVERT: C 1829 GLN cc_start: 0.9109 (tm-30) cc_final: 0.8825 (pp30) REVERT: C 1886 ASN cc_start: 0.8706 (OUTLIER) cc_final: 0.7603 (t0) outliers start: 77 outliers final: 46 residues processed: 421 average time/residue: 0.1684 time to fit residues: 120.0751 Evaluate side-chains 388 residues out of total 3448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 338 time to evaluate : 1.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 GLU Chi-restraints excluded: chain A residue 56 GLU 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 360 LEU Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 1011 LEU Chi-restraints excluded: chain A residue 1185 CYS Chi-restraints excluded: chain A residue 1414 GLN Chi-restraints excluded: chain A residue 1532 GLN Chi-restraints excluded: chain A residue 1533 TYR Chi-restraints excluded: chain A residue 1648 SER Chi-restraints excluded: chain A residue 1687 LEU Chi-restraints excluded: chain A residue 1693 LEU Chi-restraints excluded: chain A residue 1724 VAL Chi-restraints excluded: chain A residue 1770 LEU 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 220 GLU Chi-restraints excluded: chain C residue 322 ASN Chi-restraints excluded: chain C residue 335 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 587 VAL Chi-restraints excluded: chain C residue 655 LEU Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 780 LEU Chi-restraints excluded: chain C residue 798 LEU 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 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 1842 SER Chi-restraints excluded: chain C residue 1882 LEU Chi-restraints excluded: chain C residue 1884 VAL Chi-restraints excluded: chain C residue 1886 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 32 optimal weight: 6.9990 chunk 358 optimal weight: 50.0000 chunk 164 optimal weight: 6.9990 chunk 286 optimal weight: 8.9990 chunk 310 optimal weight: 0.9980 chunk 214 optimal weight: 0.9980 chunk 315 optimal weight: 2.9990 chunk 170 optimal weight: 50.0000 chunk 146 optimal weight: 0.7980 chunk 240 optimal weight: 0.2980 chunk 12 optimal weight: 6.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1296 HIS A1414 GLN A1425 GLN A1730 GLN ** C 717 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1871 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.127419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.095120 restraints weight = 80077.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.094324 restraints weight = 46434.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.095665 restraints weight = 37576.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.096131 restraints weight = 31450.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.096433 restraints weight = 27920.816| |-----------------------------------------------------------------------------| r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.4411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 29330 Z= 0.120 Angle : 0.675 15.855 39730 Z= 0.328 Chirality : 0.044 0.372 4666 Planarity : 0.003 0.057 5024 Dihedral : 7.501 137.990 4124 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.10 % Favored : 91.85 % Rotamer: Outliers : 2.40 % Allowed : 22.50 % Favored : 75.10 % 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: -0.73 (0.14), residues: 3692 helix: 1.07 (0.13), residues: 1778 sheet: -0.25 (0.33), residues: 262 loop : -2.38 (0.15), residues: 1652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1507 TYR 0.025 0.001 TYR C1097 PHE 0.021 0.001 PHE C1858 TRP 0.015 0.001 TRP C1717 HIS 0.008 0.001 HIS C1296 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 (29318) covalent geometry : angle 0.67256 / 0.33 (39716) SS BOND : bond 0.00524 / 0.26 ( 4) SS BOND : angle 3.27004 / 1.49 ( 8) hydrogen bonds : bond 0.02993 / 2.02 ( 1306) hydrogen bonds : angle 3.96310 / 2.83 ( 3756) metal coordination : bond 0.02630 / 1.35 ( 8) metal coordination : angle 3.60571 / 2.78 ( 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 422 residues out of total 3448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 350 time to evaluate : 1.183 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 41 GLU cc_start: 0.8973 (OUTLIER) cc_final: 0.8718 (pm20) REVERT: A 44 LYS cc_start: 0.9103 (ptpt) cc_final: 0.8777 (ptpt) REVERT: A 120 MET cc_start: 0.8792 (tpt) cc_final: 0.8018 (tpt) REVERT: A 351 LEU cc_start: 0.9443 (mt) cc_final: 0.9169 (mt) REVERT: A 398 GLU cc_start: 0.8829 (mp0) cc_final: 0.8472 (mp0) REVERT: A 478 MET cc_start: 0.8432 (mmm) cc_final: 0.8040 (tpp) REVERT: A 550 GLU cc_start: 0.8215 (tp30) cc_final: 0.7965 (tp30) REVERT: A 594 GLU cc_start: 0.8296 (pp20) cc_final: 0.8056 (pp20) REVERT: A 606 MET cc_start: 0.8977 (mpp) cc_final: 0.8718 (mpp) REVERT: A 900 GLU cc_start: 0.9316 (mt-10) cc_final: 0.9075 (mm-30) REVERT: A 919 MET cc_start: 0.7873 (ptm) cc_final: 0.7479 (ppp) REVERT: A 1141 MET cc_start: 0.9576 (mmm) cc_final: 0.9254 (mmp) REVERT: A 1156 MET cc_start: 0.7881 (mmm) cc_final: 0.7370 (mmm) REVERT: A 1196 MET cc_start: 0.8209 (mmt) cc_final: 0.7934 (mmt) REVERT: A 1221 LEU cc_start: 0.8600 (mt) cc_final: 0.8395 (mp) REVERT: A 1289 ASP cc_start: 0.7672 (t70) cc_final: 0.7112 (t70) REVERT: A 1414 GLN cc_start: 0.7803 (OUTLIER) cc_final: 0.6891 (pp30) REVERT: A 1417 GLU cc_start: 0.8193 (mm-30) cc_final: 0.7766 (mm-30) REVERT: A 1765 MET cc_start: 0.5285 (tpp) cc_final: 0.4628 (tpp) REVERT: A 1781 MET cc_start: 0.8686 (mmm) cc_final: 0.8421 (mmm) REVERT: A 1829 GLN cc_start: 0.9182 (tp40) cc_final: 0.8730 (tp40) REVERT: C 120 MET cc_start: 0.8408 (tpt) cc_final: 0.7755 (tpp) REVERT: C 351 LEU cc_start: 0.9255 (mt) cc_final: 0.9023 (mt) REVERT: C 866 ASP cc_start: 0.7299 (m-30) cc_final: 0.6951 (p0) REVERT: C 1146 GLU cc_start: 0.8214 (mm-30) cc_final: 0.7656 (mm-30) REVERT: C 1150 GLU cc_start: 0.7841 (mt-10) cc_final: 0.6966 (mt-10) REVERT: C 1307 GLU cc_start: 0.8181 (tp30) cc_final: 0.7659 (tp30) REVERT: C 1417 GLU cc_start: 0.7839 (mm-30) cc_final: 0.7354 (mm-30) REVERT: C 1507 ARG cc_start: 0.7997 (ttp80) cc_final: 0.7679 (ttp80) REVERT: C 1765 MET cc_start: 0.5052 (tpp) cc_final: 0.4707 (tpp) REVERT: C 1829 GLN cc_start: 0.9103 (tm-30) cc_final: 0.8725 (tm-30) REVERT: C 1886 ASN cc_start: 0.8676 (OUTLIER) cc_final: 0.7624 (t0) outliers start: 72 outliers final: 48 residues processed: 398 average time/residue: 0.1702 time to fit residues: 114.2730 Evaluate side-chains 379 residues out of total 3448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 328 time to evaluate : 1.146 ------------------------------------------------------------------------------- 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 360 LEU Chi-restraints excluded: chain A residue 481 PHE Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 1011 LEU Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain A residue 1150 GLU Chi-restraints excluded: chain A residue 1185 CYS Chi-restraints excluded: chain A residue 1414 GLN Chi-restraints excluded: chain A residue 1532 GLN Chi-restraints excluded: chain A residue 1648 SER Chi-restraints excluded: chain A residue 1687 LEU Chi-restraints excluded: chain A residue 1693 LEU Chi-restraints excluded: chain A residue 1724 VAL 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 A residue 1884 VAL Chi-restraints excluded: chain C residue 322 ASN Chi-restraints excluded: chain C residue 335 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 587 VAL Chi-restraints excluded: chain C residue 655 LEU Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 707 THR 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 798 LEU Chi-restraints excluded: chain C residue 1202 LEU 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 1619 ILE 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 Chi-restraints excluded: chain C residue 1884 VAL Chi-restraints excluded: chain C residue 1886 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 37 optimal weight: 5.9990 chunk 204 optimal weight: 6.9990 chunk 307 optimal weight: 3.9990 chunk 253 optimal weight: 3.9990 chunk 114 optimal weight: 4.9990 chunk 292 optimal weight: 3.9990 chunk 143 optimal weight: 0.3980 chunk 252 optimal weight: 8.9990 chunk 233 optimal weight: 5.9990 chunk 72 optimal weight: 8.9990 chunk 7 optimal weight: 0.0060 overall best weight: 2.4802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 128 HIS ** A 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1296 HIS A1414 GLN ** C 717 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1296 HIS ** C1414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1730 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.124739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.090804 restraints weight = 80677.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.090833 restraints weight = 52548.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.090910 restraints weight = 41099.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.091424 restraints weight = 37424.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.092057 restraints weight = 32190.174| |-----------------------------------------------------------------------------| r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.4777 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= 0.165 Angle : 0.717 13.373 39730 Z= 0.352 Chirality : 0.045 0.458 4666 Planarity : 0.004 0.050 5024 Dihedral : 7.612 136.952 4124 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.80 % Favored : 91.14 % Rotamer: Outliers : 2.37 % Allowed : 22.70 % Favored : 74.93 % 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: -0.73 (0.14), residues: 3692 helix: 1.05 (0.13), residues: 1780 sheet: 0.22 (0.34), residues: 236 loop : -2.43 (0.15), residues: 1676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 231 TYR 0.024 0.001 TYR A1097 PHE 0.023 0.001 PHE C1858 TRP 0.016 0.002 TRP A1351 HIS 0.004 0.001 HIS C 648 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.16 (29318) covalent geometry : angle 0.71366 / 0.35 (39716) SS BOND : bond 0.00873 / 0.43 ( 4) SS BOND : angle 3.39779 / 1.59 ( 8) hydrogen bonds : bond 0.03472 / 2.34 ( 1306) hydrogen bonds : angle 4.08167 / 2.90 ( 3756) metal coordination : bond 0.02513 / 1.29 ( 8) metal coordination : angle 4.55777 / 3.56 ( 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 405 residues out of total 3448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 334 time to evaluate : 1.168 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 41 GLU cc_start: 0.9107 (OUTLIER) cc_final: 0.8883 (pm20) REVERT: A 44 LYS cc_start: 0.9209 (ptpt) cc_final: 0.8918 (ptpp) REVERT: A 120 MET cc_start: 0.8690 (tpt) cc_final: 0.8010 (tpp) REVERT: A 351 LEU cc_start: 0.9485 (mt) cc_final: 0.9242 (mt) REVERT: A 398 GLU cc_start: 0.8809 (mp0) cc_final: 0.8435 (mp0) REVERT: A 478 MET cc_start: 0.8513 (mmm) cc_final: 0.8312 (tpp) REVERT: A 550 GLU cc_start: 0.8341 (tp30) cc_final: 0.8106 (tp30) REVERT: A 594 GLU cc_start: 0.8386 (pp20) cc_final: 0.7839 (pp20) REVERT: A 598 TRP cc_start: 0.8882 (OUTLIER) cc_final: 0.8555 (m-10) REVERT: A 602 ASP cc_start: 0.7914 (m-30) cc_final: 0.7676 (m-30) REVERT: A 836 ASP cc_start: 0.7602 (m-30) cc_final: 0.7106 (p0) REVERT: A 900 GLU cc_start: 0.9386 (mt-10) cc_final: 0.9109 (mm-30) REVERT: A 1141 MET cc_start: 0.9624 (mmm) cc_final: 0.9270 (mmp) REVERT: A 1150 GLU cc_start: 0.8474 (OUTLIER) cc_final: 0.8228 (tp30) REVERT: A 1156 MET cc_start: 0.8075 (mmm) cc_final: 0.7501 (mmm) REVERT: A 1196 MET cc_start: 0.8241 (mmt) cc_final: 0.7956 (mmt) REVERT: A 1414 GLN cc_start: 0.7916 (OUTLIER) cc_final: 0.7694 (pp30) REVERT: A 1511 PHE cc_start: 0.7343 (m-80) cc_final: 0.6709 (m-80) REVERT: A 1664 CYS cc_start: 0.7286 (OUTLIER) cc_final: 0.6800 (p) REVERT: A 1728 GLU cc_start: 0.8561 (tm-30) cc_final: 0.7763 (tm-30) REVERT: A 1730 GLN cc_start: 0.9006 (tm130) cc_final: 0.8702 (tm-30) REVERT: A 1781 MET cc_start: 0.8704 (mmm) cc_final: 0.8398 (mmm) REVERT: A 1829 GLN cc_start: 0.9240 (tp40) cc_final: 0.8794 (tp40) REVERT: C 120 MET cc_start: 0.8463 (tpt) cc_final: 0.7803 (tpp) REVERT: C 182 GLN cc_start: 0.7979 (OUTLIER) cc_final: 0.7342 (pp30) REVERT: C 351 LEU cc_start: 0.9371 (mt) cc_final: 0.9132 (mt) REVERT: C 866 ASP cc_start: 0.7141 (m-30) cc_final: 0.6722 (p0) REVERT: C 1285 MET cc_start: 0.7344 (tpt) cc_final: 0.6851 (tpt) REVERT: C 1307 GLU cc_start: 0.8168 (tp30) cc_final: 0.7687 (tp30) REVERT: C 1417 GLU cc_start: 0.7745 (mm-30) cc_final: 0.7339 (mm-30) REVERT: C 1731 LEU cc_start: 0.8059 (mt) cc_final: 0.7761 (mt) REVERT: C 1765 MET cc_start: 0.5051 (tpp) cc_final: 0.4816 (tpp) REVERT: C 1829 GLN cc_start: 0.9122 (tm-30) cc_final: 0.8706 (tm-30) REVERT: C 1886 ASN cc_start: 0.8897 (OUTLIER) cc_final: 0.7775 (t0) outliers start: 71 outliers final: 51 residues processed: 385 average time/residue: 0.1699 time to fit residues: 111.1087 Evaluate side-chains 367 residues out of total 3448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 309 time to evaluate : 1.132 ------------------------------------------------------------------------------- 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 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 786 LEU Chi-restraints excluded: chain A residue 1011 LEU Chi-restraints excluded: chain A residue 1150 GLU Chi-restraints excluded: chain A residue 1185 CYS Chi-restraints excluded: chain A residue 1352 LEU Chi-restraints excluded: chain A residue 1414 GLN Chi-restraints excluded: chain A residue 1532 GLN Chi-restraints excluded: chain A residue 1648 SER Chi-restraints excluded: chain A residue 1664 CYS Chi-restraints excluded: chain A residue 1687 LEU Chi-restraints excluded: chain A residue 1693 LEU Chi-restraints excluded: chain A residue 1724 VAL 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 A residue 1884 VAL Chi-restraints excluded: chain C residue 182 GLN Chi-restraints excluded: chain C residue 322 ASN Chi-restraints excluded: chain C residue 335 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 587 VAL 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 798 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 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 1560 LEU Chi-restraints excluded: chain C residue 1619 ILE Chi-restraints excluded: chain C residue 1730 GLN 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 1822 GLU Chi-restraints excluded: chain C residue 1842 SER Chi-restraints excluded: chain C residue 1882 LEU Chi-restraints excluded: chain C residue 1884 VAL Chi-restraints excluded: chain C residue 1886 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 43 optimal weight: 50.0000 chunk 365 optimal weight: 9.9990 chunk 112 optimal weight: 0.0470 chunk 289 optimal weight: 1.9990 chunk 215 optimal weight: 0.8980 chunk 267 optimal weight: 6.9990 chunk 136 optimal weight: 2.9990 chunk 189 optimal weight: 5.9990 chunk 305 optimal weight: 4.9990 chunk 91 optimal weight: 6.9990 chunk 236 optimal weight: 2.9990 overall best weight: 1.7884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1296 HIS A1414 GLN ** C 717 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1296 HIS ** C1414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1730 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.125323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.092314 restraints weight = 80049.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.091560 restraints weight = 47201.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.092393 restraints weight = 38565.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.093097 restraints weight = 32275.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.093235 restraints weight = 28813.836| |-----------------------------------------------------------------------------| r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.4879 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= 0.141 Angle : 0.722 13.265 39730 Z= 0.351 Chirality : 0.045 0.418 4666 Planarity : 0.003 0.045 5024 Dihedral : 7.618 137.597 4124 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.42 % Favored : 91.52 % Rotamer: Outliers : 2.10 % Allowed : 23.07 % Favored : 74.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.75 (0.14), residues: 3692 helix: 1.05 (0.13), residues: 1774 sheet: 0.36 (0.35), residues: 226 loop : -2.44 (0.15), residues: 1692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A1507 TYR 0.026 0.001 TYR A1097 PHE 0.029 0.001 PHE A1270 TRP 0.026 0.001 TRP A1351 HIS 0.004 0.001 HIS A1296 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 (29318) covalent geometry : angle 0.71931 / 0.35 (39716) SS BOND : bond 0.00690 / 0.34 ( 4) SS BOND : angle 2.86844 / 1.32 ( 8) hydrogen bonds : bond 0.03282 / 2.22 ( 1306) hydrogen bonds : angle 4.07803 / 2.89 ( 3756) metal coordination : bond 0.02704 / 1.39 ( 8) metal coordination : angle 4.13171 / 3.20 ( 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 402 residues out of total 3448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 339 time to evaluate : 1.156 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 GLU cc_start: 0.9090 (OUTLIER) cc_final: 0.8841 (pm20) REVERT: A 44 LYS cc_start: 0.9198 (ptpt) cc_final: 0.8916 (ptpp) REVERT: A 120 MET cc_start: 0.8675 (tpt) cc_final: 0.7969 (tpp) REVERT: A 164 LEU cc_start: 0.9184 (mt) cc_final: 0.8979 (mt) REVERT: A 333 LEU cc_start: 0.9512 (mt) cc_final: 0.9213 (mt) REVERT: A 351 LEU cc_start: 0.9473 (mt) cc_final: 0.9192 (mt) REVERT: A 398 GLU cc_start: 0.8776 (mp0) cc_final: 0.8411 (mp0) REVERT: A 550 GLU cc_start: 0.8327 (tp30) cc_final: 0.8109 (tp30) REVERT: A 594 GLU cc_start: 0.8355 (pp20) cc_final: 0.7929 (pp20) REVERT: A 900 GLU cc_start: 0.9351 (mt-10) cc_final: 0.9093 (mm-30) REVERT: A 1141 MET cc_start: 0.9617 (mmm) cc_final: 0.9265 (mmp) REVERT: A 1150 GLU cc_start: 0.8441 (OUTLIER) cc_final: 0.8171 (tp30) REVERT: A 1156 MET cc_start: 0.8049 (mmm) cc_final: 0.7403 (mmm) REVERT: A 1196 MET cc_start: 0.8223 (mmt) cc_final: 0.7926 (mmt) REVERT: A 1414 GLN cc_start: 0.7704 (OUTLIER) cc_final: 0.6954 (pp30) REVERT: A 1417 GLU cc_start: 0.8189 (mm-30) cc_final: 0.7801 (mm-30) REVERT: A 1728 GLU cc_start: 0.8534 (tm-30) cc_final: 0.7826 (tm-30) REVERT: A 1730 GLN cc_start: 0.9010 (tm130) cc_final: 0.8731 (tm-30) REVERT: A 1765 MET cc_start: 0.5330 (tpp) cc_final: 0.4706 (tpp) REVERT: A 1781 MET cc_start: 0.8690 (mmm) cc_final: 0.8429 (mmm) REVERT: A 1829 GLN cc_start: 0.9186 (tp40) cc_final: 0.8738 (tp40) REVERT: C 120 MET cc_start: 0.8422 (tpt) cc_final: 0.7722 (tpp) REVERT: C 261 THR cc_start: 0.8231 (OUTLIER) cc_final: 0.7907 (p) REVERT: C 351 LEU cc_start: 0.9362 (mt) cc_final: 0.9124 (mt) REVERT: C 866 ASP cc_start: 0.7263 (m-30) cc_final: 0.6845 (p0) REVERT: C 919 MET cc_start: 0.7823 (ppp) cc_final: 0.7417 (ppp) REVERT: C 1150 GLU cc_start: 0.7796 (mt-10) cc_final: 0.7003 (mt-10) REVERT: C 1182 ASP cc_start: 0.7770 (m-30) cc_final: 0.7394 (m-30) REVERT: C 1285 MET cc_start: 0.7310 (tpt) cc_final: 0.6901 (tpt) REVERT: C 1307 GLU cc_start: 0.8130 (tp30) cc_final: 0.7645 (tp30) REVERT: C 1417 GLU cc_start: 0.7728 (mm-30) cc_final: 0.7326 (mm-30) REVERT: C 1507 ARG cc_start: 0.8182 (ttp80) cc_final: 0.7821 (ttp80) REVERT: C 1511 PHE cc_start: 0.7110 (m-10) cc_final: 0.6637 (m-80) REVERT: C 1678 ILE cc_start: 0.8904 (tp) cc_final: 0.8631 (tp) REVERT: C 1728 GLU cc_start: 0.7794 (tm-30) cc_final: 0.7490 (tm-30) REVERT: C 1731 LEU cc_start: 0.7996 (mt) cc_final: 0.7626 (mt) REVERT: C 1829 GLN cc_start: 0.9098 (tm-30) cc_final: 0.8682 (tm-30) REVERT: C 1886 ASN cc_start: 0.8875 (OUTLIER) cc_final: 0.7755 (t0) outliers start: 63 outliers final: 51 residues processed: 384 average time/residue: 0.1662 time to fit residues: 109.1242 Evaluate side-chains 374 residues out of total 3448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 318 time to evaluate : 1.159 ------------------------------------------------------------------------------- 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 293 GLU 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 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 786 LEU Chi-restraints excluded: chain A residue 1011 LEU Chi-restraints excluded: chain A residue 1150 GLU Chi-restraints excluded: chain A residue 1185 CYS Chi-restraints excluded: chain A residue 1352 LEU Chi-restraints excluded: chain A residue 1414 GLN Chi-restraints excluded: chain A residue 1532 GLN Chi-restraints excluded: chain A residue 1648 SER Chi-restraints excluded: chain A residue 1664 CYS Chi-restraints excluded: chain A residue 1687 LEU Chi-restraints excluded: chain A residue 1693 LEU Chi-restraints excluded: chain A residue 1724 VAL 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 A residue 1884 VAL Chi-restraints excluded: chain C residue 261 THR Chi-restraints excluded: chain C residue 267 LEU Chi-restraints excluded: chain C residue 322 ASN Chi-restraints excluded: chain C residue 335 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 587 VAL 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 798 LEU Chi-restraints excluded: chain C residue 1202 LEU 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 1541 VAL Chi-restraints excluded: chain C residue 1619 ILE Chi-restraints excluded: chain C residue 1688 THR Chi-restraints excluded: chain C residue 1730 GLN 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 Chi-restraints excluded: chain C residue 1884 VAL Chi-restraints excluded: chain C residue 1886 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 6 optimal weight: 8.9990 chunk 354 optimal weight: 0.2980 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 0.9990 chunk 195 optimal weight: 50.0000 chunk 45 optimal weight: 3.9990 chunk 265 optimal weight: 9.9990 chunk 93 optimal weight: 3.9990 chunk 133 optimal weight: 0.9990 chunk 373 optimal weight: 10.0000 chunk 62 optimal weight: 6.9990 overall best weight: 2.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1296 HIS A1414 GLN A1887 GLN ** C 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 717 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1296 HIS ** C1414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1532 GLN ** C1730 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 = 0.4008 r_free = 0.4008 target = 0.124666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.091807 restraints weight = 80763.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.091382 restraints weight = 46856.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.092107 restraints weight = 37517.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.092594 restraints weight = 31654.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.092842 restraints weight = 28700.462| |-----------------------------------------------------------------------------| r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.5036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 29330 Z= 0.150 Angle : 0.732 12.973 39730 Z= 0.356 Chirality : 0.045 0.431 4666 Planarity : 0.003 0.041 5024 Dihedral : 7.633 137.727 4124 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.10 % Favored : 90.85 % Rotamer: Outliers : 2.37 % Allowed : 23.00 % Favored : 74.63 % 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: -0.75 (0.14), residues: 3692 helix: 1.03 (0.13), residues: 1772 sheet: 0.28 (0.34), residues: 236 loop : -2.43 (0.15), residues: 1684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 13 TYR 0.025 0.001 TYR A1097 PHE 0.024 0.001 PHE A1270 TRP 0.031 0.002 TRP A1351 HIS 0.004 0.001 HIS A1296 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.15 (29318) covalent geometry : angle 0.72951 / 0.36 (39716) SS BOND : bond 0.00697 / 0.35 ( 4) SS BOND : angle 2.80301 / 1.28 ( 8) hydrogen bonds : bond 0.03327 / 2.25 ( 1306) hydrogen bonds : angle 4.08474 / 2.89 ( 3756) metal coordination : bond 0.02608 / 1.34 ( 8) metal coordination : angle 4.09574 / 3.21 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4950.21 seconds wall clock time: 86 minutes 36.48 seconds (5196.48 seconds total)