Starting phenix.real_space_refine on Tue May 27 07:04:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6klh_0710/05_2025/6klh_0710.cif Found real_map, /net/cci-nas-00/data/ceres_data/6klh_0710/05_2025/6klh_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_0710/05_2025/6klh_0710.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6klh_0710/05_2025/6klh_0710.map" model { file = "/net/cci-nas-00/data/ceres_data/6klh_0710/05_2025/6klh_0710.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6klh_0710/05_2025/6klh_0710.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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, 'ASP:plan': 17, 'TYR:plan': 8, 'ASN:plan1': 7, 'TRP:plan': 2, 'HIS:plan': 6, 'PHE:plan': 14, 'GLU:plan': 24, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 456 Chain: "B" Number of atoms: 149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 149 Classifications: {'RNA': 7} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 3, 'rna3p_pur': 2, 'rna3p_pyr': 1} Link IDs: {'rna2p': 4, 'rna3p': 2} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2171 SG CYS A 284 148.409 107.169 114.304 1.00129.21 S ATOM 2195 SG CYS A 287 150.333 103.636 114.286 1.00117.64 S ATOM 3474 SG CYS A 470 152.151 106.387 115.891 1.00161.90 S Restraints were copied for chains: C, D Time building chain proxies: 48.31, per 1000 atoms: 1.68 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: 7.76 Conformation dependent library (CDL) restraints added in 3.7 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: 3.70 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: 11.15 Time building geometry restraints manager: 8.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9384 1.34 - 1.46: 5850 1.46 - 1.58: 13806 1.58 - 1.70: 26 1.70 - 1.82: 252 Bond restraints: 29318 Sorted by residual: bond pdb=" N VAL A1374 " pdb=" CA VAL A1374 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.17e-02 7.31e+03 8.45e+00 bond pdb=" N VAL C1374 " pdb=" CA VAL C1374 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.17e-02 7.31e+03 8.03e+00 bond pdb=" N ILE A1375 " pdb=" CA ILE A1375 " ideal model delta sigma weight residual 1.459 1.490 -0.031 1.25e-02 6.40e+03 6.14e+00 bond pdb=" N ILE C1375 " pdb=" CA ILE C1375 " ideal model delta sigma weight residual 1.459 1.490 -0.031 1.25e-02 6.40e+03 6.06e+00 bond pdb=" N GLN A1532 " pdb=" CA GLN A1532 " ideal model delta sigma weight residual 1.457 1.478 -0.021 1.33e-02 5.65e+03 2.53e+00 ... (remaining 29313 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.34: 38938 2.34 - 4.67: 658 4.67 - 7.01: 103 7.01 - 9.34: 15 9.34 - 11.68: 2 Bond angle restraints: 39716 Sorted by residual: angle pdb=" CA GLU A1822 " pdb=" CB GLU A1822 " pdb=" CG GLU A1822 " ideal model delta sigma weight residual 114.10 122.24 -8.14 2.00e+00 2.50e-01 1.66e+01 angle pdb=" CA GLU C1822 " pdb=" CB GLU C1822 " pdb=" CG GLU C1822 " ideal model delta sigma weight residual 114.10 122.23 -8.13 2.00e+00 2.50e-01 1.65e+01 angle pdb=" N GLU C 593 " pdb=" CA GLU C 593 " pdb=" CB GLU C 593 " ideal model delta sigma weight residual 110.28 116.39 -6.11 1.55e+00 4.16e-01 1.55e+01 angle pdb=" N GLU A 593 " pdb=" CA GLU A 593 " pdb=" CB GLU A 593 " ideal model delta sigma weight residual 110.28 116.38 -6.10 1.55e+00 4.16e-01 1.55e+01 angle pdb=" CB MET C 385 " pdb=" CG MET C 385 " pdb=" SD MET C 385 " ideal model delta sigma weight residual 112.70 124.38 -11.68 3.00e+00 1.11e-01 1.51e+01 ... (remaining 39711 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.87: 16276 18.87 - 37.74: 1228 37.74 - 56.61: 224 56.61 - 75.49: 52 75.49 - 94.36: 18 Dihedral angle restraints: 17798 sinusoidal: 6804 harmonic: 10994 Sorted by residual: dihedral pdb=" CA TRP C1859 " pdb=" C TRP C1859 " pdb=" N PHE C1860 " pdb=" CA PHE C1860 " ideal model delta harmonic sigma weight residual 180.00 156.24 23.76 0 5.00e+00 4.00e-02 2.26e+01 dihedral pdb=" CA TRP A1859 " pdb=" C TRP A1859 " pdb=" N PHE A1860 " pdb=" CA PHE A1860 " ideal model delta harmonic sigma weight residual 180.00 156.30 23.70 0 5.00e+00 4.00e-02 2.25e+01 dihedral pdb=" CA PHE C1858 " pdb=" C PHE C1858 " pdb=" N TRP C1859 " pdb=" CA TRP C1859 " ideal model delta harmonic sigma weight residual -180.00 -156.40 -23.60 0 5.00e+00 4.00e-02 2.23e+01 ... (remaining 17795 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 3696 0.052 - 0.103: 825 0.103 - 0.155: 123 0.155 - 0.207: 20 0.207 - 0.258: 2 Chirality restraints: 4666 Sorted by residual: chirality pdb=" CA VAL A1374 " pdb=" N VAL A1374 " pdb=" C VAL A1374 " pdb=" CB VAL A1374 " both_signs ideal model delta sigma weight residual False 2.44 2.70 -0.26 2.00e-01 2.50e+01 1.67e+00 chirality pdb=" CA VAL C1374 " pdb=" N VAL C1374 " pdb=" C VAL C1374 " pdb=" CB VAL C1374 " both_signs ideal model delta sigma weight residual False 2.44 2.70 -0.26 2.00e-01 2.50e+01 1.65e+00 chirality pdb=" CA GLU C 41 " pdb=" N GLU C 41 " pdb=" C GLU C 41 " pdb=" CB GLU C 41 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.02e+00 ... (remaining 4663 not shown) Planarity restraints: 5024 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A1717 " 0.015 2.00e-02 2.50e+03 1.44e-02 5.19e+00 pdb=" CG TRP A1717 " -0.039 2.00e-02 2.50e+03 pdb=" CD1 TRP A1717 " 0.019 2.00e-02 2.50e+03 pdb=" CD2 TRP A1717 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A1717 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A1717 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A1717 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP A1717 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A1717 " 0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP A1717 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C1717 " 0.014 2.00e-02 2.50e+03 1.43e-02 5.10e+00 pdb=" CG TRP C1717 " -0.038 2.00e-02 2.50e+03 pdb=" CD1 TRP C1717 " 0.019 2.00e-02 2.50e+03 pdb=" CD2 TRP C1717 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP C1717 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP C1717 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP C1717 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP C1717 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP C1717 " 0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP C1717 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A1821 " -0.011 2.00e-02 2.50e+03 1.29e-02 4.16e+00 pdb=" CG TRP A1821 " 0.035 2.00e-02 2.50e+03 pdb=" CD1 TRP A1821 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 TRP A1821 " -0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP A1821 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A1821 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A1821 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP A1821 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A1821 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP A1821 " 0.001 2.00e-02 2.50e+03 ... (remaining 5021 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 5196 2.77 - 3.30: 29606 3.30 - 3.83: 45577 3.83 - 4.37: 51738 4.37 - 4.90: 85975 Nonbonded interactions: 218092 Sorted by model distance: nonbonded pdb=" OG1 THR A 345 " pdb=" OD1 ASN A 348 " model vdw 2.233 3.040 nonbonded pdb=" OG1 THR C 345 " pdb=" OD1 ASN C 348 " model vdw 2.233 3.040 nonbonded pdb=" O ALA A 619 " pdb=" OG SER A 623 " model vdw 2.247 3.040 nonbonded pdb=" O ALA C 619 " pdb=" OG SER C 623 " model vdw 2.247 3.040 nonbonded pdb=" O THR A 345 " pdb=" OG1 THR A 349 " model vdw 2.253 3.040 ... (remaining 218087 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.14 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: 0.390 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: 0.020 Extract box with map and model: 0.960 Check model and map are aligned: 0.180 Set scattering table: 0.230 Process input model: 99.830 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 104.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.088 29330 Z= 0.151 Angle : 0.732 12.726 39730 Z= 0.382 Chirality : 0.045 0.258 4666 Planarity : 0.004 0.053 5024 Dihedral : 14.134 94.357 10614 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.11 % Allowed : 9.05 % Favored : 90.85 % Rotamer: Outliers : 0.53 % Allowed : 1.70 % Favored : 97.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.039 0.002 TRP A1717 HIS 0.005 0.001 HIS C1791 PHE 0.024 0.001 PHE A1858 TYR 0.017 0.001 TYR C1818 ARG 0.012 0.001 ARG C1509 Details of bonding type rmsd hydrogen bonds : bond 0.13743 ( 1306) hydrogen bonds : angle 5.93347 ( 3756) metal coordination : bond 0.07316 ( 8) metal coordination : angle 8.39398 ( 6) SS BOND : bond 0.00121 ( 4) SS BOND : angle 1.63508 ( 8) covalent geometry : bond 0.00294 (29318) covalent geometry : angle 0.72419 (39716) *********************** 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 : 2.971 Fit side-chains 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: 0.8905 (mp) REVERT: A 120 MET cc_start: 0.8188 (tpt) cc_final: 0.7131 (tpt) REVERT: A 333 LEU cc_start: 0.9193 (OUTLIER) cc_final: 0.8931 (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: 0.8630 (mt) REVERT: A 382 VAL cc_start: 0.7593 (m) cc_final: 0.7317 (m) REVERT: A 488 LYS cc_start: 0.9024 (ttmt) cc_final: 0.8813 (ttmm) REVERT: A 550 GLU cc_start: 0.8158 (tp30) cc_final: 0.7867 (tp30) REVERT: A 591 MET cc_start: 0.7428 (ttp) cc_final: 0.7224 (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: 0.7997 (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: 0.5127 (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: 0.7672 (mm) REVERT: A 1289 ASP cc_start: 0.7543 (t70) cc_final: 0.7114 (t70) REVERT: A 1440 SER cc_start: 0.8729 (m) cc_final: 0.8237 (p) REVERT: A 1509 ARG cc_start: 0.6773 (OUTLIER) cc_final: 0.6329 (mmp80) REVERT: A 1733 MET cc_start: 0.1463 (tpt) cc_final: 0.0256 (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: 0.6919 (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: 0.7643 (ptm-80) REVERT: C 356 ILE cc_start: 0.8234 (mt) cc_final: 0.8034 (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: 0.8237 (mm-30) REVERT: C 1097 TYR cc_start: 0.4781 (t80) cc_final: 0.4574 (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: 0.8713 (tp) REVERT: C 1731 LEU cc_start: 0.7212 (mt) cc_final: 0.6864 (mt) REVERT: C 1733 MET cc_start: 0.2583 (tpt) cc_final: 0.1352 (tpt) REVERT: C 1765 MET cc_start: 0.4598 (mmm) cc_final: 0.4067 (mmp) REVERT: C 1780 ASP cc_start: 0.7616 (t0) cc_final: 0.7329 (m-30) outliers start: 16 outliers final: 1 residues processed: 500 average time/residue: 0.3565 time to fit residues: 294.5342 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 : 3.384 ------------------------------------------------------------------------------- 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 317 optimal weight: 1.9990 chunk 284 optimal weight: 4.9990 chunk 158 optimal weight: 6.9990 chunk 97 optimal weight: 0.6980 chunk 192 optimal weight: 2.9990 chunk 152 optimal weight: 5.9990 chunk 294 optimal weight: 0.9990 chunk 114 optimal weight: 9.9990 chunk 179 optimal weight: 0.0010 chunk 219 optimal weight: 9.9990 chunk 341 optimal weight: 8.9990 overall best weight: 1.3392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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** A1738 GLN 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** ** C1405 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.135740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.104024 restraints weight = 80999.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.101770 restraints weight = 49698.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.103267 restraints weight = 41242.933| |-----------------------------------------------------------------------------| r_work (final): 0.3634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.1614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 29330 Z= 0.134 Angle : 0.646 9.655 39730 Z= 0.328 Chirality : 0.043 0.205 4666 Planarity : 0.004 0.037 5024 Dihedral : 8.314 93.896 4206 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.32 % Favored : 91.58 % Rotamer: Outliers : 1.53 % Allowed : 10.53 % Favored : 87.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.45 (0.14), residues: 3692 helix: 0.55 (0.13), residues: 1748 sheet: -0.89 (0.30), residues: 272 loop : -2.75 (0.14), residues: 1672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP C1717 HIS 0.004 0.001 HIS A 431 PHE 0.033 0.001 PHE A 352 TYR 0.019 0.001 TYR C 701 ARG 0.007 0.001 ARG C 508 Details of bonding type rmsd hydrogen bonds : bond 0.03480 ( 1306) hydrogen bonds : angle 4.47962 ( 3756) metal coordination : bond 0.03473 ( 8) metal coordination : angle 4.36500 ( 6) SS BOND : bond 0.01309 ( 4) SS BOND : angle 1.75155 ( 8) covalent geometry : bond 0.00290 (29318) covalent geometry : angle 0.64296 (39716) *********************** 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 442 residues out of total 3448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 396 time to evaluate : 3.376 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.8210 (tpt) cc_final: 0.7191 (tpt) REVERT: A 333 LEU cc_start: 0.9313 (OUTLIER) cc_final: 0.9033 (mt) REVERT: A 351 LEU cc_start: 0.9530 (mt) cc_final: 0.9184 (mt) REVERT: A 416 ASN cc_start: 0.9391 (m110) cc_final: 0.9191 (p0) REVERT: A 435 LEU cc_start: 0.8380 (tt) cc_final: 0.7842 (tt) REVERT: A 550 GLU cc_start: 0.8312 (tp30) cc_final: 0.8000 (tp30) REVERT: A 594 GLU cc_start: 0.8375 (pp20) cc_final: 0.7962 (pp20) REVERT: A 900 GLU cc_start: 0.9311 (mt-10) cc_final: 0.9047 (mm-30) REVERT: A 919 MET cc_start: 0.8156 (ptm) cc_final: 0.7880 (ptp) REVERT: A 1097 TYR cc_start: 0.5612 (t80) cc_final: 0.5158 (t80) REVERT: A 1210 LEU cc_start: 0.7909 (mm) cc_final: 0.7674 (mm) REVERT: A 1289 ASP cc_start: 0.7424 (t70) cc_final: 0.6938 (t70) REVERT: A 1440 SER cc_start: 0.8927 (m) cc_final: 0.8349 (p) REVERT: A 1540 GLU cc_start: 0.7075 (mm-30) cc_final: 0.6502 (mm-30) REVERT: A 1731 LEU cc_start: 0.8208 (mt) cc_final: 0.7963 (mt) REVERT: A 1733 MET cc_start: 0.2266 (tpt) cc_final: 0.2037 (mmm) REVERT: A 1861 ASN cc_start: 0.8197 (m-40) cc_final: 0.7974 (m-40) REVERT: C 120 MET cc_start: 0.8143 (tpt) cc_final: 0.7070 (tpt) REVERT: C 207 LEU cc_start: 0.8022 (mm) cc_final: 0.7501 (mt) REVERT: C 293 GLU cc_start: 0.8097 (tp30) cc_final: 0.7777 (tp30) REVERT: C 401 LYS cc_start: 0.8999 (mmtm) cc_final: 0.8766 (mmtm) REVERT: C 585 ASP cc_start: 0.7647 (p0) cc_final: 0.7315 (p0) REVERT: C 1097 TYR cc_start: 0.5030 (t80) cc_final: 0.4682 (t80) REVERT: C 1143 ARG cc_start: 0.8776 (OUTLIER) cc_final: 0.8495 (ptm160) REVERT: C 1269 PHE cc_start: 0.8905 (t80) cc_final: 0.8633 (t80) REVERT: C 1274 MET cc_start: 0.5773 (pmm) cc_final: 0.5498 (pmm) REVERT: C 1417 GLU cc_start: 0.7621 (mm-30) cc_final: 0.7417 (mm-30) REVERT: C 1466 LYS cc_start: 0.7884 (ttpt) cc_final: 0.7431 (mtmt) REVERT: C 1511 PHE cc_start: 0.6587 (m-80) cc_final: 0.6174 (m-10) REVERT: C 1678 ILE cc_start: 0.8911 (tp) cc_final: 0.8636 (tp) REVERT: C 1728 GLU cc_start: 0.7465 (tm-30) cc_final: 0.7074 (tm-30) REVERT: C 1731 LEU cc_start: 0.7561 (mt) cc_final: 0.6860 (mt) REVERT: C 1765 MET cc_start: 0.4750 (mmm) cc_final: 0.4145 (mmm) outliers start: 46 outliers final: 23 residues processed: 422 average time/residue: 0.3591 time to fit residues: 252.7194 Evaluate side-chains 358 residues out of total 3448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 333 time to evaluate : 3.145 ------------------------------------------------------------------------------- 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 1719 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 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 105 optimal weight: 0.9990 chunk 7 optimal weight: 4.9990 chunk 209 optimal weight: 8.9990 chunk 89 optimal weight: 20.0000 chunk 373 optimal weight: 30.0000 chunk 193 optimal weight: 20.0000 chunk 174 optimal weight: 7.9990 chunk 291 optimal weight: 2.9990 chunk 77 optimal weight: 9.9990 chunk 228 optimal weight: 0.9980 chunk 127 optimal weight: 7.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 430 HIS A 607 ASN ** A 629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 872 ASN ** A1414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4055 r_free = 0.4055 target = 0.127590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.093792 restraints weight = 79785.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.093130 restraints weight = 49486.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.093699 restraints weight = 38862.721| |-----------------------------------------------------------------------------| r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.3267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.092 29330 Z= 0.218 Angle : 0.701 9.795 39730 Z= 0.360 Chirality : 0.044 0.177 4666 Planarity : 0.004 0.051 5024 Dihedral : 8.384 98.008 4194 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.72 % Favored : 90.22 % Rotamer: Outliers : 2.67 % Allowed : 14.80 % Favored : 82.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.14), residues: 3692 helix: 0.59 (0.12), residues: 1766 sheet: -0.70 (0.33), residues: 240 loop : -2.63 (0.14), residues: 1686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP C1717 HIS 0.009 0.001 HIS C1296 PHE 0.028 0.002 PHE A 352 TYR 0.026 0.002 TYR C 701 ARG 0.013 0.001 ARG C 231 Details of bonding type rmsd hydrogen bonds : bond 0.04136 ( 1306) hydrogen bonds : angle 4.45463 ( 3756) metal coordination : bond 0.03388 ( 8) metal coordination : angle 5.77299 ( 6) SS BOND : bond 0.00790 ( 4) SS BOND : angle 1.37537 ( 8) covalent geometry : bond 0.00494 (29318) covalent geometry : angle 0.69688 (39716) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7384 Ramachandran restraints generated. 3692 Oldfield, 0 Emsley, 3692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7384 Ramachandran restraints generated. 3692 Oldfield, 0 Emsley, 3692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 3448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 348 time to evaluate : 2.993 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.8145 (tpt) cc_final: 0.7289 (tpt) REVERT: A 351 LEU cc_start: 0.9485 (mt) cc_final: 0.9230 (mt) REVERT: A 398 GLU cc_start: 0.8919 (mp0) cc_final: 0.8543 (mp0) REVERT: A 550 GLU cc_start: 0.8405 (tp30) cc_final: 0.8017 (tp30) REVERT: A 594 GLU cc_start: 0.8426 (pp20) cc_final: 0.7905 (pp20) REVERT: A 598 TRP cc_start: 0.8824 (OUTLIER) cc_final: 0.8458 (m-10) REVERT: A 708 LYS cc_start: 0.9216 (OUTLIER) cc_final: 0.8978 (pttp) REVERT: A 848 MET cc_start: 0.8543 (mmt) cc_final: 0.8135 (mmm) REVERT: A 900 GLU cc_start: 0.9369 (mt-10) cc_final: 0.9109 (mm-30) REVERT: A 1097 TYR cc_start: 0.6290 (t80) cc_final: 0.5467 (t80) REVERT: A 1285 MET cc_start: 0.7971 (tpt) cc_final: 0.7662 (tpt) REVERT: A 1557 ASP cc_start: 0.8151 (t0) cc_final: 0.7899 (t0) REVERT: A 1765 MET cc_start: 0.4010 (mmm) cc_final: 0.3773 (mmm) REVERT: C 120 MET cc_start: 0.8543 (tpt) cc_final: 0.7907 (tpp) REVERT: C 182 GLN cc_start: 0.8140 (OUTLIER) cc_final: 0.7275 (pp30) REVERT: C 237 GLU cc_start: 0.8560 (OUTLIER) cc_final: 0.8327 (pm20) REVERT: C 398 GLU cc_start: 0.8452 (mp0) cc_final: 0.8155 (mp0) REVERT: C 598 TRP cc_start: 0.9060 (OUTLIER) cc_final: 0.8324 (m-10) REVERT: C 708 LYS cc_start: 0.9094 (OUTLIER) cc_final: 0.8865 (pttt) REVERT: C 1123 GLU cc_start: 0.8250 (mp0) cc_final: 0.8045 (mp0) REVERT: C 1146 GLU cc_start: 0.8696 (mm-30) cc_final: 0.8385 (mm-30) REVERT: C 1269 PHE cc_start: 0.8821 (t80) cc_final: 0.8595 (t80) REVERT: C 1285 MET cc_start: 0.7565 (tpt) cc_final: 0.7319 (tpt) REVERT: C 1531 LEU cc_start: 0.8814 (OUTLIER) cc_final: 0.8237 (mt) REVERT: C 1728 GLU cc_start: 0.7415 (tm-30) cc_final: 0.6826 (tm-30) REVERT: C 1731 LEU cc_start: 0.7964 (mt) cc_final: 0.7272 (mt) REVERT: C 1829 GLN cc_start: 0.9121 (tm-30) cc_final: 0.8882 (tm-30) REVERT: C 1882 LEU cc_start: 0.9346 (mm) cc_final: 0.9075 (mm) outliers start: 80 outliers final: 46 residues processed: 403 average time/residue: 0.3511 time to fit residues: 236.6631 Evaluate side-chains 358 residues out of total 3448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 305 time to evaluate : 2.993 ------------------------------------------------------------------------------- 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 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 598 TRP Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 707 THR Chi-restraints excluded: chain A residue 708 LYS Chi-restraints excluded: chain A residue 906 ASN Chi-restraints excluded: chain A residue 1185 CYS Chi-restraints excluded: chain A residue 1560 LEU Chi-restraints excluded: chain A residue 1648 SER Chi-restraints excluded: chain A residue 1678 ILE Chi-restraints excluded: chain A residue 1687 LEU Chi-restraints excluded: chain A residue 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 182 GLN Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 237 GLU 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 735 VAL Chi-restraints excluded: chain C residue 736 VAL 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 1436 VAL Chi-restraints excluded: chain C residue 1462 ASP Chi-restraints excluded: chain C residue 1531 LEU Chi-restraints excluded: chain C residue 1532 GLN Chi-restraints excluded: chain C residue 1541 VAL Chi-restraints excluded: chain C residue 1560 LEU Chi-restraints excluded: chain C residue 1619 ILE Chi-restraints excluded: chain C residue 1691 CYS Chi-restraints excluded: chain C residue 1770 LEU Chi-restraints excluded: chain C residue 1792 LEU Chi-restraints excluded: chain C residue 1886 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 72.4063 > 50: distance: 41 - 55: 31.384 distance: 50 - 55: 34.941 distance: 55 - 56: 69.114 distance: 56 - 59: 11.122 distance: 57 - 66: 40.835 distance: 59 - 60: 11.358 distance: 60 - 61: 39.767 distance: 60 - 62: 57.813 distance: 61 - 63: 39.633 distance: 62 - 64: 40.808 distance: 63 - 65: 40.544 distance: 64 - 65: 55.422 distance: 66 - 67: 40.940 distance: 67 - 68: 40.755 distance: 67 - 70: 40.006 distance: 68 - 72: 40.253 distance: 70 - 71: 39.400 distance: 72 - 73: 55.946 distance: 74 - 75: 38.920 distance: 74 - 79: 57.876 distance: 76 - 77: 55.998 distance: 76 - 78: 38.896 distance: 79 - 80: 56.518 distance: 81 - 82: 40.055 distance: 83 - 84: 39.352 distance: 83 - 85: 38.539 distance: 86 - 87: 39.403 distance: 87 - 88: 57.769 distance: 87 - 90: 57.253 distance: 88 - 95: 56.018 distance: 90 - 91: 39.078 distance: 91 - 92: 55.741 distance: 92 - 93: 57.342 distance: 93 - 94: 68.227 distance: 95 - 96: 69.041 distance: 96 - 99: 57.067 distance: 97 - 98: 57.575 distance: 97 - 104: 38.746 distance: 99 - 100: 58.011 distance: 100 - 101: 49.366 distance: 101 - 102: 49.388 distance: 101 - 103: 58.035 distance: 104 - 110: 56.673 distance: 105 - 106: 57.829 distance: 105 - 108: 55.827 distance: 106 - 111: 55.758 distance: 108 - 109: 39.578 distance: 109 - 110: 40.002 distance: 111 - 112: 40.409 distance: 112 - 115: 66.517 distance: 113 - 114: 39.979 distance: 117 - 118: 52.782 distance: 117 - 119: 54.316 distance: 120 - 121: 55.590 distance: 121 - 122: 55.475 distance: 121 - 124: 41.436 distance: 122 - 128: 40.379 distance: 125 - 126: 40.820 distance: 125 - 127: 38.712 distance: 129 - 130: 40.091 distance: 129 - 132: 23.035 distance: 130 - 131: 39.424 distance: 130 - 136: 35.368 distance: 132 - 133: 43.726 distance: 133 - 134: 56.927 distance: 133 - 135: 56.425