Starting phenix.real_space_refine on Tue Feb 20 20:14:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6klh_0710/02_2024/6klh_0710.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6klh_0710/02_2024/6klh_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6klh_0710/02_2024/6klh_0710.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6klh_0710/02_2024/6klh_0710.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6klh_0710/02_2024/6klh_0710.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6klh_0710/02_2024/6klh_0710.pdb" } 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 Symmetric amino acids flipped None Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 28834 Number of models: 1 Model: "" Number of chains: 6 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: "C" 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: "D" 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} Chain: "C" 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 ATOM 16586 SG CYS C 284 16.877 58.575 53.437 1.00110.60 S ATOM 16610 SG CYS C 287 17.614 54.629 53.693 1.00 96.37 S ATOM 17889 SG CYS C 470 14.516 55.521 51.944 1.00135.76 S Time building chain proxies: 14.43, per 1000 atoms: 0.50 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 - 3.50 Amino acid : False - 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: 10.97 Conformation dependent library (CDL) restraints added in 5.6 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: 4.20 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: 13.11 Time building geometry restraints manager: 11.90 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: 97.47 - 104.79: 397 104.79 - 112.12: 14608 112.12 - 119.44: 9993 119.44 - 126.76: 14409 126.76 - 134.09: 309 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 2.440 nonbonded pdb=" OG1 THR C 345 " pdb=" OD1 ASN C 348 " model vdw 2.233 2.440 nonbonded pdb=" O ALA A 619 " pdb=" OG SER A 623 " model vdw 2.247 2.440 nonbonded pdb=" O ALA C 619 " pdb=" OG SER C 623 " model vdw 2.247 2.440 nonbonded pdb=" O THR A 345 " pdb=" OG1 THR A 349 " model vdw 2.253 2.440 ... (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 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: 0.350 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: 0.010 Extract box with map and model: 3.250 Check model and map are aligned: 0.400 Set scattering table: 0.230 Process input model: 84.520 Find NCS groups from input model: 1.590 Set up NCS constraints: 0.190 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:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 93.590 ------------------------------------------------------------------------------- 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 0.039 29318 Z= 0.192 Angle : 0.724 11.676 39716 Z= 0.381 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 *********************** 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 fitting. rotamer outliers: 16 poor density : 496 time to evaluate : 3.245 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: 0.3708 time to fit residues: 305.0723 Evaluate side-chains 368 residues out of total 3448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 363 time to evaluate : 3.222 ------------------------------------------------------------------------------- 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: 2.9990 chunk 284 optimal weight: 5.9990 chunk 158 optimal weight: 5.9990 chunk 97 optimal weight: 0.7980 chunk 192 optimal weight: 3.9990 chunk 152 optimal weight: 0.7980 chunk 294 optimal weight: 0.7980 chunk 114 optimal weight: 0.9980 chunk 179 optimal weight: 4.9990 chunk 219 optimal weight: 10.0000 chunk 341 optimal weight: 6.9990 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 629 GLN A 633 GLN A 704 HIS ** A 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 788 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 633 GLN ** C 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 788 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.1596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 29318 Z= 0.175 Angle : 0.621 9.710 39716 Z= 0.313 Chirality : 0.042 0.166 4666 Planarity : 0.003 0.048 5024 Dihedral : 8.229 93.693 4206 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.29 % Favored : 91.60 % Rotamer: Outliers : 1.57 % Allowed : 11.03 % Favored : 87.40 % 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: -1.37 (0.14), residues: 3692 helix: 0.66 (0.13), residues: 1750 sheet: -0.83 (0.31), residues: 272 loop : -2.76 (0.14), residues: 1670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP C1717 HIS 0.004 0.001 HIS C1231 PHE 0.033 0.001 PHE A 352 TYR 0.018 0.001 TYR C 701 ARG 0.006 0.000 ARG C1769 *********************** 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 445 residues out of total 3448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 398 time to evaluate : 3.385 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.8177 (tpt) cc_final: 0.7191 (tpt) REVERT: A 333 LEU cc_start: 0.9319 (mt) cc_final: 0.9036 (mt) REVERT: A 351 LEU cc_start: 0.9508 (mt) cc_final: 0.9178 (mt) REVERT: A 435 LEU cc_start: 0.8211 (tt) cc_final: 0.7804 (tt) REVERT: A 550 GLU cc_start: 0.8442 (tp30) cc_final: 0.8177 (tp30) REVERT: A 594 GLU cc_start: 0.8453 (pp20) cc_final: 0.8070 (pp20) REVERT: A 900 GLU cc_start: 0.9346 (mt-10) cc_final: 0.9063 (mm-30) REVERT: A 919 MET cc_start: 0.8152 (ptm) cc_final: 0.7903 (ptp) REVERT: A 1097 TYR cc_start: 0.5625 (t80) cc_final: 0.5197 (t80) REVERT: A 1210 LEU cc_start: 0.7954 (mm) cc_final: 0.7717 (mm) REVERT: A 1285 MET cc_start: 0.7325 (tpt) cc_final: 0.7056 (tpt) REVERT: A 1289 ASP cc_start: 0.7443 (t70) cc_final: 0.6938 (t70) REVERT: A 1417 GLU cc_start: 0.8210 (mm-30) cc_final: 0.7858 (mm-30) REVERT: A 1440 SER cc_start: 0.8978 (m) cc_final: 0.8367 (p) REVERT: A 1540 GLU cc_start: 0.7044 (mm-30) cc_final: 0.6467 (mm-30) REVERT: A 1733 MET cc_start: 0.2347 (tpt) cc_final: 0.2094 (mmm) REVERT: A 1861 ASN cc_start: 0.8261 (m-40) cc_final: 0.7997 (m-40) REVERT: C 120 MET cc_start: 0.8124 (tpt) cc_final: 0.7073 (tpt) REVERT: C 207 LEU cc_start: 0.7911 (mm) cc_final: 0.7456 (mt) REVERT: C 401 LYS cc_start: 0.9024 (mmtm) cc_final: 0.8779 (mmtm) REVERT: C 900 GLU cc_start: 0.8586 (mt-10) cc_final: 0.8361 (mm-30) REVERT: C 1097 TYR cc_start: 0.4825 (t80) cc_final: 0.4479 (t80) REVERT: C 1143 ARG cc_start: 0.8779 (OUTLIER) cc_final: 0.8487 (ptm160) REVERT: C 1269 PHE cc_start: 0.8937 (t80) cc_final: 0.8675 (t80) REVERT: C 1274 MET cc_start: 0.5757 (pmm) cc_final: 0.5527 (pmm) REVERT: C 1466 LYS cc_start: 0.7915 (ttpt) cc_final: 0.7447 (mtmt) REVERT: C 1678 ILE cc_start: 0.8942 (tp) cc_final: 0.8648 (tp) REVERT: C 1728 GLU cc_start: 0.7307 (tm-30) cc_final: 0.6936 (tm-30) REVERT: C 1731 LEU cc_start: 0.7570 (mt) cc_final: 0.6837 (mt) REVERT: C 1765 MET cc_start: 0.4607 (mmm) cc_final: 0.4034 (mmm) REVERT: C 1793 LEU cc_start: 0.8437 (OUTLIER) cc_final: 0.8167 (pp) outliers start: 47 outliers final: 22 residues processed: 425 average time/residue: 0.3575 time to fit residues: 252.7162 Evaluate side-chains 362 residues out of total 3448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 338 time to evaluate : 3.266 ------------------------------------------------------------------------------- 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 666 VAL Chi-restraints excluded: chain A residue 1532 GLN 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 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 1301 LEU Chi-restraints excluded: chain C residue 1462 ASP Chi-restraints excluded: chain C residue 1691 CYS Chi-restraints excluded: chain C residue 1770 LEU Chi-restraints excluded: chain C residue 1791 HIS Chi-restraints excluded: chain C residue 1792 LEU Chi-restraints excluded: chain C residue 1793 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 189 optimal weight: 6.9990 chunk 105 optimal weight: 2.9990 chunk 284 optimal weight: 2.9990 chunk 232 optimal weight: 0.8980 chunk 94 optimal weight: 0.0010 chunk 342 optimal weight: 10.0000 chunk 369 optimal weight: 40.0000 chunk 304 optimal weight: 8.9990 chunk 339 optimal weight: 3.9990 chunk 116 optimal weight: 9.9990 chunk 274 optimal weight: 4.9990 overall best weight: 2.1792 ------------------------------------------------------------------------------- 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 788 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 872 ASN ** A1034 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 788 ASN ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.2730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 29318 Z= 0.223 Angle : 0.628 12.242 39716 Z= 0.319 Chirality : 0.042 0.196 4666 Planarity : 0.004 0.038 5024 Dihedral : 8.090 94.633 4192 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.91 % Favored : 90.95 % Rotamer: Outliers : 2.10 % Allowed : 15.83 % Favored : 82.07 % 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: -1.16 (0.14), residues: 3692 helix: 0.88 (0.13), residues: 1758 sheet: -0.89 (0.30), residues: 268 loop : -2.70 (0.14), residues: 1666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP C1717 HIS 0.007 0.001 HIS C1296 PHE 0.029 0.001 PHE A 352 TYR 0.020 0.001 TYR C 701 ARG 0.011 0.001 ARG C 231 *********************** 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 422 residues out of total 3448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 359 time to evaluate : 3.551 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: 0.9047 (OUTLIER) cc_final: 0.8809 (pm20) REVERT: A 44 LYS cc_start: 0.9035 (ptpt) cc_final: 0.8665 (ptpp) REVERT: A 120 MET cc_start: 0.8169 (tpt) cc_final: 0.7236 (tpt) REVERT: A 333 LEU cc_start: 0.9373 (OUTLIER) cc_final: 0.9024 (mt) REVERT: A 351 LEU cc_start: 0.9445 (mt) cc_final: 0.9189 (mt) REVERT: A 387 MET cc_start: 0.7675 (pmm) cc_final: 0.7386 (pmm) REVERT: A 398 GLU cc_start: 0.8738 (mp0) cc_final: 0.8413 (mp0) REVERT: A 550 GLU cc_start: 0.8589 (tp30) cc_final: 0.8247 (tp30) REVERT: A 594 GLU cc_start: 0.8503 (pp20) cc_final: 0.8166 (pp20) REVERT: A 786 LEU cc_start: 0.8709 (tt) cc_final: 0.8495 (tt) REVERT: A 900 GLU cc_start: 0.9378 (mt-10) cc_final: 0.9095 (mm-30) REVERT: A 1097 TYR cc_start: 0.5947 (t80) cc_final: 0.5369 (t80) REVERT: A 1417 GLU cc_start: 0.8051 (mm-30) cc_final: 0.7769 (mm-30) REVERT: A 1540 GLU cc_start: 0.7361 (mm-30) cc_final: 0.6735 (mm-30) REVERT: A 1861 ASN cc_start: 0.8872 (m-40) cc_final: 0.8633 (m-40) REVERT: C 120 MET cc_start: 0.8558 (tpt) cc_final: 0.7903 (tpp) REVERT: C 401 LYS cc_start: 0.9069 (mmtm) cc_final: 0.8825 (mmtm) REVERT: C 591 MET cc_start: 0.8096 (mtp) cc_final: 0.7868 (mtp) REVERT: C 598 TRP cc_start: 0.8833 (OUTLIER) cc_final: 0.8064 (m-10) REVERT: C 709 GLU cc_start: 0.8339 (mm-30) cc_final: 0.8129 (mt-10) REVERT: C 1097 TYR cc_start: 0.4998 (t80) cc_final: 0.4645 (t80) REVERT: C 1143 ARG cc_start: 0.8790 (OUTLIER) cc_final: 0.8529 (ptm160) REVERT: C 1146 GLU cc_start: 0.8572 (mm-30) cc_final: 0.8337 (mm-30) REVERT: C 1244 GLU cc_start: 0.7825 (OUTLIER) cc_final: 0.7564 (mp0) REVERT: C 1269 PHE cc_start: 0.8827 (t80) cc_final: 0.8589 (t80) REVERT: C 1678 ILE cc_start: 0.9003 (tp) cc_final: 0.8734 (tp) REVERT: C 1728 GLU cc_start: 0.7347 (tm-30) cc_final: 0.6970 (tm-30) REVERT: C 1731 LEU cc_start: 0.7850 (mt) cc_final: 0.7108 (mt) REVERT: C 1765 MET cc_start: 0.5368 (mmm) cc_final: 0.5091 (mmm) REVERT: C 1829 GLN cc_start: 0.9067 (tm-30) cc_final: 0.8766 (tm-30) REVERT: C 1882 LEU cc_start: 0.9351 (mm) cc_final: 0.9118 (mm) outliers start: 63 outliers final: 39 residues processed: 397 average time/residue: 0.3688 time to fit residues: 243.3854 Evaluate side-chains 369 residues out of total 3448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 325 time to evaluate : 3.381 ------------------------------------------------------------------------------- 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 333 LEU Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 481 PHE Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 591 MET Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 707 THR Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 1185 CYS 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 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 388 LEU Chi-restraints excluded: chain C residue 444 LEU Chi-restraints excluded: chain C residue 481 PHE Chi-restraints excluded: chain C residue 503 THR Chi-restraints excluded: chain C residue 535 LEU Chi-restraints excluded: chain C residue 587 VAL Chi-restraints excluded: chain C residue 598 TRP Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 798 LEU Chi-restraints excluded: chain C residue 1143 ARG Chi-restraints excluded: chain C residue 1244 GLU 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 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 1792 LEU 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 337 optimal weight: 6.9990 chunk 257 optimal weight: 0.5980 chunk 177 optimal weight: 30.0000 chunk 37 optimal weight: 3.9990 chunk 163 optimal weight: 6.9990 chunk 229 optimal weight: 0.0030 chunk 343 optimal weight: 0.6980 chunk 363 optimal weight: 0.8980 chunk 179 optimal weight: 10.0000 chunk 325 optimal weight: 3.9990 chunk 97 optimal weight: 3.9990 overall best weight: 1.2392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 788 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1034 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1414 GLN ** A1689 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1730 GLN A1798 ASN A1837 GLN A1871 GLN ** C 416 ASN ** 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 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 788 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1034 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1405 HIS C1886 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.3007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 29318 Z= 0.163 Angle : 0.592 10.412 39716 Z= 0.297 Chirality : 0.040 0.161 4666 Planarity : 0.003 0.039 5024 Dihedral : 7.935 92.149 4192 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.07 % Favored : 91.82 % Rotamer: Outliers : 2.63 % Allowed : 17.93 % Favored : 79.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.14), residues: 3692 helix: 1.01 (0.13), residues: 1776 sheet: -0.35 (0.32), residues: 252 loop : -2.59 (0.14), residues: 1664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C1717 HIS 0.005 0.001 HIS A1296 PHE 0.021 0.001 PHE C 352 TYR 0.013 0.001 TYR C 701 ARG 0.003 0.000 ARG C 532 *********************** 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 430 residues out of total 3448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 351 time to evaluate : 3.530 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: 0.9032 (OUTLIER) cc_final: 0.8695 (pm20) REVERT: A 44 LYS cc_start: 0.9062 (ptpt) cc_final: 0.8697 (ptpp) REVERT: A 120 MET cc_start: 0.8206 (tpt) cc_final: 0.7342 (tpt) REVERT: A 268 GLU cc_start: 0.8514 (OUTLIER) cc_final: 0.8215 (mt-10) REVERT: A 333 LEU cc_start: 0.9400 (OUTLIER) cc_final: 0.9058 (mt) REVERT: A 398 GLU cc_start: 0.8719 (mp0) cc_final: 0.8239 (mp0) REVERT: A 550 GLU cc_start: 0.8579 (tp30) cc_final: 0.8264 (tp30) REVERT: A 594 GLU cc_start: 0.8491 (pp20) cc_final: 0.8058 (pp20) REVERT: A 606 MET cc_start: 0.9075 (mpp) cc_final: 0.8717 (mpp) REVERT: A 900 GLU cc_start: 0.9382 (mt-10) cc_final: 0.9101 (mm-30) REVERT: A 919 MET cc_start: 0.8132 (ptm) cc_final: 0.7918 (ptp) REVERT: A 1097 TYR cc_start: 0.5870 (t80) cc_final: 0.5218 (t80) REVERT: A 1156 MET cc_start: 0.8024 (mmm) cc_final: 0.7474 (mmm) REVERT: A 1196 MET cc_start: 0.8255 (mmt) cc_final: 0.8024 (mmm) REVERT: A 1289 ASP cc_start: 0.7491 (t70) cc_final: 0.6952 (t70) REVERT: A 1417 GLU cc_start: 0.8082 (mm-30) cc_final: 0.7781 (mm-30) REVERT: A 1540 GLU cc_start: 0.7439 (mm-30) cc_final: 0.6820 (mm-30) REVERT: A 1861 ASN cc_start: 0.8834 (m-40) cc_final: 0.8627 (m-40) REVERT: C 120 MET cc_start: 0.8538 (tpt) cc_final: 0.7829 (tpp) REVERT: C 224 ILE cc_start: 0.8950 (pt) cc_final: 0.8718 (mm) REVERT: C 357 MET cc_start: 0.8460 (OUTLIER) cc_final: 0.7815 (tpp) REVERT: C 401 LYS cc_start: 0.9147 (mmtm) cc_final: 0.8904 (mmtm) REVERT: C 1097 TYR cc_start: 0.5262 (t80) cc_final: 0.4777 (t80) REVERT: C 1146 GLU cc_start: 0.8457 (mm-30) cc_final: 0.8218 (mm-30) REVERT: C 1269 PHE cc_start: 0.8915 (t80) cc_final: 0.8655 (t80) REVERT: C 1307 GLU cc_start: 0.7990 (tp30) cc_final: 0.7727 (tp30) REVERT: C 1728 GLU cc_start: 0.7263 (tm-30) cc_final: 0.6854 (tm-30) REVERT: C 1731 LEU cc_start: 0.7936 (mt) cc_final: 0.7549 (mt) REVERT: C 1781 MET cc_start: 0.8222 (mmm) cc_final: 0.7946 (tpt) REVERT: C 1782 MET cc_start: 0.7822 (mmm) cc_final: 0.7573 (mmt) REVERT: C 1829 GLN cc_start: 0.9180 (tm-30) cc_final: 0.8833 (tm-30) REVERT: C 1882 LEU cc_start: 0.9419 (mm) cc_final: 0.9177 (mm) outliers start: 79 outliers final: 45 residues processed: 399 average time/residue: 0.3557 time to fit residues: 238.4057 Evaluate side-chains 369 residues out of total 3448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 320 time to evaluate : 3.447 ------------------------------------------------------------------------------- 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 268 GLU Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 666 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 1285 MET Chi-restraints excluded: chain A residue 1532 GLN Chi-restraints excluded: chain A residue 1560 LEU Chi-restraints excluded: chain A residue 1588 LYS Chi-restraints excluded: chain A residue 1648 SER Chi-restraints excluded: chain A residue 1687 LEU Chi-restraints excluded: chain A residue 1770 LEU Chi-restraints excluded: chain A residue 1789 ILE Chi-restraints excluded: chain A residue 1791 HIS Chi-restraints excluded: chain A residue 1882 LEU Chi-restraints excluded: chain A residue 1884 VAL Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 357 MET Chi-restraints excluded: chain C residue 360 LEU Chi-restraints excluded: chain C residue 431 HIS Chi-restraints excluded: chain C residue 444 LEU Chi-restraints excluded: chain C residue 481 PHE Chi-restraints excluded: chain C residue 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 866 ASP Chi-restraints excluded: chain C residue 1144 LEU Chi-restraints excluded: chain C residue 1202 LEU Chi-restraints excluded: chain C residue 1274 MET Chi-restraints excluded: chain C residue 1296 HIS Chi-restraints excluded: chain C residue 1301 LEU Chi-restraints excluded: chain C residue 1320 VAL Chi-restraints excluded: chain C residue 1462 ASP Chi-restraints excluded: chain C residue 1532 GLN Chi-restraints excluded: chain C residue 1691 CYS Chi-restraints excluded: chain C residue 1770 LEU Chi-restraints excluded: chain C residue 1791 HIS Chi-restraints excluded: chain C residue 1792 LEU Chi-restraints excluded: chain C residue 1884 VAL Chi-restraints excluded: chain C residue 1886 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 302 optimal weight: 4.9990 chunk 206 optimal weight: 6.9990 chunk 5 optimal weight: 0.8980 chunk 270 optimal weight: 6.9990 chunk 149 optimal weight: 3.9990 chunk 310 optimal weight: 0.9980 chunk 251 optimal weight: 0.6980 chunk 0 optimal weight: 20.0000 chunk 185 optimal weight: 5.9990 chunk 326 optimal weight: 7.9990 chunk 91 optimal weight: 40.0000 overall best weight: 2.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 788 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1296 HIS ** A1414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1738 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 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 788 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1730 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.3629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 29318 Z= 0.229 Angle : 0.627 9.689 39716 Z= 0.316 Chirality : 0.041 0.176 4666 Planarity : 0.003 0.040 5024 Dihedral : 7.958 93.331 4192 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.97 % Favored : 90.98 % Rotamer: Outliers : 3.10 % Allowed : 19.77 % Favored : 77.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.14), residues: 3692 helix: 1.08 (0.13), residues: 1772 sheet: -0.24 (0.33), residues: 240 loop : -2.51 (0.15), residues: 1680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A1717 HIS 0.007 0.001 HIS A1296 PHE 0.021 0.001 PHE C1858 TYR 0.013 0.001 TYR C 701 ARG 0.005 0.000 ARG C1814 *********************** 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 411 residues out of total 3448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 318 time to evaluate : 3.222 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: 0.9071 (OUTLIER) cc_final: 0.8710 (pm20) REVERT: A 44 LYS cc_start: 0.9125 (ptpt) cc_final: 0.8790 (ptpp) REVERT: A 120 MET cc_start: 0.8215 (tpt) cc_final: 0.7401 (tpt) REVERT: A 333 LEU cc_start: 0.9462 (OUTLIER) cc_final: 0.9134 (mt) REVERT: A 351 LEU cc_start: 0.9416 (mt) cc_final: 0.9149 (mt) REVERT: A 387 MET cc_start: 0.7801 (pmm) cc_final: 0.7534 (pmm) REVERT: A 398 GLU cc_start: 0.8724 (mp0) cc_final: 0.8349 (mp0) REVERT: A 550 GLU cc_start: 0.8568 (tp30) cc_final: 0.8164 (tp30) REVERT: A 594 GLU cc_start: 0.8483 (pp20) cc_final: 0.7937 (pp20) REVERT: A 598 TRP cc_start: 0.8674 (OUTLIER) cc_final: 0.8407 (m-10) REVERT: A 696 LEU cc_start: 0.9422 (OUTLIER) cc_final: 0.9100 (mm) REVERT: A 900 GLU cc_start: 0.9390 (mt-10) cc_final: 0.9108 (mm-30) REVERT: A 919 MET cc_start: 0.8197 (ptm) cc_final: 0.7918 (ptp) REVERT: A 1097 TYR cc_start: 0.6116 (t80) cc_final: 0.5450 (t80) REVERT: A 1141 MET cc_start: 0.9508 (mmp) cc_final: 0.9225 (mmp) REVERT: A 1156 MET cc_start: 0.8149 (mmm) cc_final: 0.7850 (mmm) REVERT: A 1417 GLU cc_start: 0.8165 (mm-30) cc_final: 0.7950 (mm-30) REVERT: A 1446 LEU cc_start: 0.9545 (tp) cc_final: 0.9317 (tp) REVERT: A 1782 MET cc_start: 0.8017 (mmm) cc_final: 0.7754 (mmt) REVERT: C 120 MET cc_start: 0.8576 (tpt) cc_final: 0.7882 (tpp) REVERT: C 380 LEU cc_start: 0.8734 (pt) cc_final: 0.8475 (pp) REVERT: C 387 MET cc_start: 0.7427 (pmm) cc_final: 0.7145 (pmm) REVERT: C 598 TRP cc_start: 0.8848 (OUTLIER) cc_final: 0.7997 (m-10) REVERT: C 1097 TYR cc_start: 0.5441 (t80) cc_final: 0.4846 (t80) REVERT: C 1123 GLU cc_start: 0.8089 (mp0) cc_final: 0.7783 (mp0) REVERT: C 1146 GLU cc_start: 0.8160 (mm-30) cc_final: 0.7791 (mm-30) REVERT: C 1150 GLU cc_start: 0.7670 (mt-10) cc_final: 0.7162 (mt-10) REVERT: C 1269 PHE cc_start: 0.8922 (t80) cc_final: 0.8693 (t80) REVERT: C 1307 GLU cc_start: 0.8114 (tp30) cc_final: 0.7642 (tp30) REVERT: C 1532 GLN cc_start: 0.8538 (OUTLIER) cc_final: 0.8120 (mp10) REVERT: C 1678 ILE cc_start: 0.9002 (tp) cc_final: 0.8708 (tp) REVERT: C 1728 GLU cc_start: 0.7526 (tm-30) cc_final: 0.6705 (tm-30) REVERT: C 1829 GLN cc_start: 0.9192 (tm-30) cc_final: 0.8843 (tm-30) outliers start: 93 outliers final: 54 residues processed: 382 average time/residue: 0.3597 time to fit residues: 231.5947 Evaluate side-chains 364 residues out of total 3448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 304 time to evaluate : 3.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 GLU Chi-restraints excluded: chain A residue 89 ASP 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 396 ILE Chi-restraints excluded: chain A residue 440 ASP 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 696 LEU Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 906 ASN Chi-restraints excluded: chain A residue 1011 LEU Chi-restraints excluded: chain A residue 1185 CYS Chi-restraints excluded: chain A residue 1285 MET Chi-restraints excluded: chain A residue 1541 VAL Chi-restraints excluded: chain A residue 1560 LEU Chi-restraints excluded: chain A residue 1588 LYS Chi-restraints excluded: chain A residue 1648 SER Chi-restraints excluded: chain A residue 1687 LEU Chi-restraints excluded: chain A residue 1724 VAL Chi-restraints excluded: chain A residue 1770 LEU Chi-restraints excluded: chain A residue 1789 ILE Chi-restraints excluded: chain A residue 1791 HIS Chi-restraints excluded: chain A residue 1882 LEU Chi-restraints excluded: chain A residue 1884 VAL Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 267 LEU Chi-restraints excluded: chain C residue 331 LEU Chi-restraints excluded: chain C residue 431 HIS Chi-restraints excluded: chain C residue 481 PHE 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 1274 MET Chi-restraints excluded: chain C residue 1296 HIS Chi-restraints excluded: chain C residue 1301 LEU Chi-restraints excluded: chain C residue 1462 ASP 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 1771 LYS 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 1836 THR 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 122 optimal weight: 0.8980 chunk 327 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 213 optimal weight: 3.9990 chunk 89 optimal weight: 5.9990 chunk 363 optimal weight: 40.0000 chunk 301 optimal weight: 0.4980 chunk 168 optimal weight: 8.9990 chunk 30 optimal weight: 6.9990 chunk 120 optimal weight: 7.9990 chunk 190 optimal weight: 3.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 788 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 800 ASN A1296 HIS ** A1414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1689 ASN A1730 GLN ** A1738 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1837 GLN ** C 629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 717 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 788 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 800 ASN C1405 HIS C1837 GLN ** C1886 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.3984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 29318 Z= 0.208 Angle : 0.620 11.958 39716 Z= 0.309 Chirality : 0.041 0.158 4666 Planarity : 0.003 0.038 5024 Dihedral : 7.922 92.111 4192 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.13 % Favored : 91.82 % Rotamer: Outliers : 3.50 % Allowed : 20.80 % Favored : 75.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.14), residues: 3692 helix: 1.09 (0.13), residues: 1788 sheet: -0.14 (0.34), residues: 240 loop : -2.49 (0.15), residues: 1664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C1717 HIS 0.003 0.001 HIS A1283 PHE 0.019 0.001 PHE A1860 TYR 0.013 0.001 TYR C 701 ARG 0.004 0.000 ARG A 376 *********************** 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 446 residues out of total 3448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 341 time to evaluate : 3.665 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 41 GLU cc_start: 0.9065 (OUTLIER) cc_final: 0.8768 (pm20) REVERT: A 44 LYS cc_start: 0.9140 (ptpt) cc_final: 0.8791 (ptpt) REVERT: A 120 MET cc_start: 0.8215 (tpt) cc_final: 0.7410 (tpt) REVERT: A 333 LEU cc_start: 0.9467 (OUTLIER) cc_final: 0.9116 (mt) REVERT: A 351 LEU cc_start: 0.9436 (mt) cc_final: 0.9165 (mt) REVERT: A 387 MET cc_start: 0.7695 (pmm) cc_final: 0.7443 (pmm) REVERT: A 398 GLU cc_start: 0.8756 (mp0) cc_final: 0.8430 (mp0) REVERT: A 501 MET cc_start: 0.8042 (tpt) cc_final: 0.7446 (tpp) REVERT: A 550 GLU cc_start: 0.8590 (tp30) cc_final: 0.8301 (tp30) REVERT: A 594 GLU cc_start: 0.8482 (pp20) cc_final: 0.8070 (pp20) REVERT: A 598 TRP cc_start: 0.8681 (OUTLIER) cc_final: 0.8394 (m-10) REVERT: A 900 GLU cc_start: 0.9398 (mt-10) cc_final: 0.9115 (mm-30) REVERT: A 1097 TYR cc_start: 0.6131 (t80) cc_final: 0.5564 (t80) REVERT: A 1156 MET cc_start: 0.8196 (mmm) cc_final: 0.7980 (mmm) REVERT: A 1196 MET cc_start: 0.8369 (mmt) cc_final: 0.8093 (mmm) REVERT: A 1531 LEU cc_start: 0.8950 (OUTLIER) cc_final: 0.8741 (mm) REVERT: A 1532 GLN cc_start: 0.8978 (OUTLIER) cc_final: 0.8616 (mp10) REVERT: A 1887 GLN cc_start: 0.7350 (mt0) cc_final: 0.7132 (mp10) REVERT: C 120 MET cc_start: 0.8591 (tpt) cc_final: 0.7857 (tpp) REVERT: C 222 LEU cc_start: 0.9056 (mt) cc_final: 0.8817 (tp) REVERT: C 598 TRP cc_start: 0.8801 (OUTLIER) cc_final: 0.7908 (m-10) REVERT: C 606 MET cc_start: 0.8818 (mpp) cc_final: 0.8594 (mpp) REVERT: C 1097 TYR cc_start: 0.5517 (t80) cc_final: 0.4957 (t80) REVERT: C 1146 GLU cc_start: 0.8071 (mm-30) cc_final: 0.7422 (mm-30) REVERT: C 1150 GLU cc_start: 0.7741 (mt-10) cc_final: 0.7016 (mt-10) REVERT: C 1244 GLU cc_start: 0.8196 (OUTLIER) cc_final: 0.7814 (mp0) REVERT: C 1296 HIS cc_start: 0.6587 (OUTLIER) cc_final: 0.6350 (m170) REVERT: C 1307 GLU cc_start: 0.8086 (tp30) cc_final: 0.7628 (tp30) REVERT: C 1532 GLN cc_start: 0.8608 (OUTLIER) cc_final: 0.8205 (mp10) REVERT: C 1678 ILE cc_start: 0.8989 (tp) cc_final: 0.8726 (tp) REVERT: C 1829 GLN cc_start: 0.9123 (tm-30) cc_final: 0.8780 (pp30) outliers start: 105 outliers final: 59 residues processed: 417 average time/residue: 0.3507 time to fit residues: 246.7831 Evaluate side-chains 385 residues out of total 3448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 317 time to evaluate : 3.346 ------------------------------------------------------------------------------- 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 333 LEU Chi-restraints excluded: chain A residue 440 ASP Chi-restraints excluded: chain A residue 481 PHE Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 598 TRP Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 707 THR Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 906 ASN Chi-restraints excluded: chain A residue 1011 LEU Chi-restraints excluded: chain A residue 1185 CYS Chi-restraints excluded: chain A residue 1285 MET Chi-restraints excluded: chain A residue 1409 CYS Chi-restraints excluded: chain A residue 1531 LEU Chi-restraints excluded: chain A residue 1532 GLN Chi-restraints excluded: chain A residue 1560 LEU Chi-restraints excluded: chain A residue 1588 LYS Chi-restraints excluded: chain A residue 1641 LYS Chi-restraints excluded: chain A residue 1648 SER Chi-restraints excluded: chain A residue 1687 LEU Chi-restraints excluded: chain A residue 1724 VAL Chi-restraints excluded: chain A residue 1789 ILE Chi-restraints excluded: chain A residue 1791 HIS Chi-restraints excluded: chain A residue 1822 GLU Chi-restraints excluded: chain A residue 1882 LEU Chi-restraints excluded: chain A residue 1884 VAL Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 220 GLU Chi-restraints excluded: chain C residue 267 LEU Chi-restraints excluded: chain C residue 322 ASN Chi-restraints excluded: chain C residue 360 LEU Chi-restraints excluded: chain C residue 394 LEU Chi-restraints excluded: chain C residue 431 HIS Chi-restraints excluded: chain C residue 440 ASP 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 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 1244 GLU Chi-restraints excluded: chain C residue 1296 HIS Chi-restraints excluded: chain C residue 1301 LEU Chi-restraints excluded: chain C residue 1409 CYS Chi-restraints excluded: chain C residue 1436 VAL Chi-restraints excluded: chain C residue 1462 ASP 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 1771 LYS Chi-restraints excluded: chain C residue 1786 LEU Chi-restraints excluded: chain C residue 1792 LEU Chi-restraints excluded: chain C residue 1836 THR Chi-restraints excluded: chain C residue 1882 LEU Chi-restraints excluded: chain C residue 1884 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 350 optimal weight: 20.0000 chunk 41 optimal weight: 4.9990 chunk 207 optimal weight: 7.9990 chunk 265 optimal weight: 30.0000 chunk 205 optimal weight: 9.9990 chunk 306 optimal weight: 5.9990 chunk 203 optimal weight: 7.9990 chunk 362 optimal weight: 5.9990 chunk 226 optimal weight: 1.9990 chunk 220 optimal weight: 0.0000 chunk 167 optimal weight: 30.0000 overall best weight: 3.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 788 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 859 ASN A1275 GLN ** A1414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1689 ASN ** A1730 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 335 ASN ** C 629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 717 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 788 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1275 GLN C1296 HIS C1689 ASN C1886 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.4712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.088 29318 Z= 0.337 Angle : 0.709 12.189 39716 Z= 0.359 Chirality : 0.043 0.229 4666 Planarity : 0.004 0.051 5024 Dihedral : 8.187 95.374 4192 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 15.58 Ramachandran Plot: Outliers : 0.05 % Allowed : 10.24 % Favored : 89.71 % Rotamer: Outliers : 3.57 % Allowed : 22.07 % Favored : 74.37 % 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: -1.01 (0.14), residues: 3692 helix: 0.94 (0.13), residues: 1780 sheet: -0.55 (0.34), residues: 260 loop : -2.64 (0.15), residues: 1652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 598 HIS 0.008 0.001 HIS A1296 PHE 0.036 0.002 PHE A 352 TYR 0.020 0.002 TYR C1682 ARG 0.007 0.001 ARG C1814 *********************** 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 439 residues out of total 3448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 332 time to evaluate : 3.284 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 44 LYS cc_start: 0.9196 (ptpt) cc_final: 0.8899 (ptpp) REVERT: A 120 MET cc_start: 0.8162 (tpt) cc_final: 0.7498 (tpp) REVERT: A 333 LEU cc_start: 0.9525 (OUTLIER) cc_final: 0.9184 (mt) REVERT: A 351 LEU cc_start: 0.9457 (mt) cc_final: 0.9216 (mt) REVERT: A 398 GLU cc_start: 0.8755 (mp0) cc_final: 0.8401 (mp0) REVERT: A 501 MET cc_start: 0.7951 (tpt) cc_final: 0.7299 (tpp) REVERT: A 594 GLU cc_start: 0.8546 (pp20) cc_final: 0.7964 (pp20) REVERT: A 598 TRP cc_start: 0.8877 (OUTLIER) cc_final: 0.8148 (m-10) REVERT: A 848 MET cc_start: 0.8352 (mmt) cc_final: 0.8100 (mmp) REVERT: A 900 GLU cc_start: 0.9409 (mt-10) cc_final: 0.9141 (mm-30) REVERT: A 1097 TYR cc_start: 0.6429 (t80) cc_final: 0.5750 (t80) REVERT: A 1141 MET cc_start: 0.9521 (mmp) cc_final: 0.9191 (mmp) REVERT: A 1196 MET cc_start: 0.8444 (mmt) cc_final: 0.8047 (mmm) REVERT: A 1446 LEU cc_start: 0.9555 (tp) cc_final: 0.9353 (tp) REVERT: A 1887 GLN cc_start: 0.8060 (mt0) cc_final: 0.7646 (mm110) REVERT: C 120 MET cc_start: 0.8521 (tpt) cc_final: 0.7843 (tpp) REVERT: C 598 TRP cc_start: 0.9031 (OUTLIER) cc_final: 0.8250 (m-10) REVERT: C 1097 TYR cc_start: 0.5569 (t80) cc_final: 0.5145 (t80) REVERT: C 1121 TYR cc_start: 0.8466 (p90) cc_final: 0.8209 (p90) REVERT: C 1146 GLU cc_start: 0.8126 (mm-30) cc_final: 0.7883 (mm-30) REVERT: C 1244 GLU cc_start: 0.8095 (OUTLIER) cc_final: 0.7771 (mp0) REVERT: C 1307 GLU cc_start: 0.8081 (tp30) cc_final: 0.7803 (tp30) REVERT: C 1511 PHE cc_start: 0.7517 (m-10) cc_final: 0.6235 (m-80) REVERT: C 1532 GLN cc_start: 0.8735 (OUTLIER) cc_final: 0.8322 (mp10) REVERT: C 1822 GLU cc_start: 0.8101 (tm-30) cc_final: 0.7784 (tm-30) REVERT: C 1829 GLN cc_start: 0.9120 (tm-30) cc_final: 0.8738 (tm-30) outliers start: 107 outliers final: 74 residues processed: 410 average time/residue: 0.3483 time to fit residues: 239.8091 Evaluate side-chains 388 residues out of total 3448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 309 time to evaluate : 3.223 ------------------------------------------------------------------------------- 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 89 ASP Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 322 ASN Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 440 ASP Chi-restraints excluded: chain A residue 481 PHE Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 591 MET Chi-restraints excluded: chain A residue 598 TRP Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 707 THR Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 906 ASN Chi-restraints excluded: chain A residue 1011 LEU Chi-restraints excluded: chain A residue 1185 CYS Chi-restraints excluded: chain A residue 1409 CYS Chi-restraints excluded: chain A residue 1436 VAL Chi-restraints excluded: chain A residue 1524 ASP Chi-restraints excluded: chain A residue 1532 GLN 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 1770 LEU Chi-restraints excluded: chain A residue 1789 ILE Chi-restraints excluded: chain A residue 1822 GLU Chi-restraints excluded: chain A residue 1842 SER Chi-restraints excluded: chain A residue 1854 LEU Chi-restraints excluded: chain A residue 1882 LEU Chi-restraints excluded: chain A residue 1884 VAL Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 212 LEU 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 331 LEU Chi-restraints excluded: chain C residue 335 ASN Chi-restraints excluded: chain C residue 360 LEU Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 440 ASP 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 707 THR Chi-restraints excluded: chain C residue 735 VAL Chi-restraints excluded: chain C residue 780 LEU Chi-restraints excluded: chain C residue 798 LEU Chi-restraints excluded: chain C residue 836 ASP Chi-restraints excluded: chain C residue 1202 LEU Chi-restraints excluded: chain C residue 1244 GLU 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 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 1688 THR Chi-restraints excluded: chain C residue 1770 LEU Chi-restraints excluded: chain C residue 1771 LYS Chi-restraints excluded: chain C residue 1786 LEU Chi-restraints excluded: chain C residue 1792 LEU Chi-restraints excluded: chain C residue 1813 ILE Chi-restraints excluded: chain C residue 1836 THR Chi-restraints excluded: chain C residue 1842 SER Chi-restraints excluded: chain C residue 1866 LEU 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 224 optimal weight: 2.9990 chunk 144 optimal weight: 0.9990 chunk 216 optimal weight: 3.9990 chunk 109 optimal weight: 10.0000 chunk 71 optimal weight: 1.9990 chunk 70 optimal weight: 8.9990 chunk 230 optimal weight: 3.9990 chunk 246 optimal weight: 0.0270 chunk 179 optimal weight: 7.9990 chunk 33 optimal weight: 0.9980 chunk 284 optimal weight: 8.9990 overall best weight: 1.4044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 788 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1689 ASN ** A1730 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 629 GLN ** C 717 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 788 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1275 GLN C1689 ASN C1886 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.4729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 29318 Z= 0.177 Angle : 0.650 13.280 39716 Z= 0.320 Chirality : 0.041 0.188 4666 Planarity : 0.003 0.042 5024 Dihedral : 8.010 91.362 4192 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.83 % Favored : 92.12 % Rotamer: Outliers : 2.67 % Allowed : 23.33 % Favored : 74.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.14), residues: 3692 helix: 1.09 (0.13), residues: 1786 sheet: -0.02 (0.35), residues: 240 loop : -2.53 (0.15), residues: 1666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A1351 HIS 0.005 0.001 HIS A1296 PHE 0.029 0.001 PHE A1860 TYR 0.012 0.001 TYR C1030 ARG 0.006 0.000 ARG C1507 *********************** 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 427 residues out of total 3448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 347 time to evaluate : 3.554 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: 0.9052 (OUTLIER) cc_final: 0.8846 (pm20) REVERT: A 44 LYS cc_start: 0.9179 (ptpt) cc_final: 0.8886 (ptpp) REVERT: A 120 MET cc_start: 0.8203 (tpt) cc_final: 0.7425 (tpt) REVERT: A 293 GLU cc_start: 0.8527 (OUTLIER) cc_final: 0.8127 (tp30) REVERT: A 333 LEU cc_start: 0.9523 (OUTLIER) cc_final: 0.9184 (mp) REVERT: A 351 LEU cc_start: 0.9456 (mt) cc_final: 0.9211 (mt) REVERT: A 398 GLU cc_start: 0.8629 (mp0) cc_final: 0.8251 (mp0) REVERT: A 478 MET cc_start: 0.8364 (mmm) cc_final: 0.8068 (tpp) REVERT: A 594 GLU cc_start: 0.8498 (pp20) cc_final: 0.8041 (pp20) REVERT: A 598 TRP cc_start: 0.8717 (OUTLIER) cc_final: 0.8464 (m-10) REVERT: A 602 ASP cc_start: 0.8125 (m-30) cc_final: 0.7795 (m-30) REVERT: A 848 MET cc_start: 0.8227 (mmt) cc_final: 0.7980 (mmp) REVERT: A 900 GLU cc_start: 0.9411 (mt-10) cc_final: 0.9139 (mm-30) REVERT: A 1097 TYR cc_start: 0.6218 (t80) cc_final: 0.5721 (t80) REVERT: A 1887 GLN cc_start: 0.7501 (mt0) cc_final: 0.7282 (mm110) REVERT: C 120 MET cc_start: 0.8450 (tpt) cc_final: 0.7751 (tpp) REVERT: C 351 LEU cc_start: 0.9451 (mt) cc_final: 0.9214 (mt) REVERT: C 598 TRP cc_start: 0.8832 (OUTLIER) cc_final: 0.8096 (m-10) REVERT: C 606 MET cc_start: 0.8818 (mpp) cc_final: 0.8548 (mpp) REVERT: C 736 VAL cc_start: 0.8511 (t) cc_final: 0.8308 (p) REVERT: C 919 MET cc_start: 0.7972 (ptp) cc_final: 0.7474 (ppp) REVERT: C 1097 TYR cc_start: 0.5497 (t80) cc_final: 0.4917 (t80) REVERT: C 1146 GLU cc_start: 0.8120 (mm-30) cc_final: 0.7743 (mm-30) REVERT: C 1150 GLU cc_start: 0.7721 (mt-10) cc_final: 0.6974 (mt-10) REVERT: C 1244 GLU cc_start: 0.8193 (OUTLIER) cc_final: 0.7899 (mp0) REVERT: C 1307 GLU cc_start: 0.8087 (tp30) cc_final: 0.7666 (tp30) REVERT: C 1678 ILE cc_start: 0.8972 (tp) cc_final: 0.8724 (tp) REVERT: C 1793 LEU cc_start: 0.8719 (OUTLIER) cc_final: 0.8508 (pp) REVERT: C 1822 GLU cc_start: 0.8139 (tm-30) cc_final: 0.7845 (tm-30) REVERT: C 1829 GLN cc_start: 0.9073 (tm-30) cc_final: 0.8678 (tm-30) REVERT: C 1886 ASN cc_start: 0.8535 (OUTLIER) cc_final: 0.7999 (p0) outliers start: 80 outliers final: 52 residues processed: 402 average time/residue: 0.3691 time to fit residues: 247.1236 Evaluate side-chains 382 residues out of total 3448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 322 time to evaluate : 3.153 ------------------------------------------------------------------------------- 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 322 ASN Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 440 ASP 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 735 VAL Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 906 ASN Chi-restraints excluded: chain A residue 1011 LEU Chi-restraints excluded: chain A residue 1395 LEU Chi-restraints excluded: chain A residue 1409 CYS Chi-restraints excluded: chain A residue 1524 ASP 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 1789 ILE Chi-restraints excluded: chain A residue 1882 LEU Chi-restraints excluded: chain A residue 1884 VAL Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 267 LEU Chi-restraints excluded: chain C residue 322 ASN Chi-restraints excluded: chain C residue 360 LEU Chi-restraints excluded: chain C residue 394 LEU Chi-restraints excluded: chain C residue 440 ASP 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 655 LEU Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 735 VAL Chi-restraints excluded: chain C residue 780 LEU Chi-restraints excluded: chain C residue 798 LEU Chi-restraints excluded: chain C residue 836 ASP Chi-restraints excluded: chain C residue 1244 GLU Chi-restraints excluded: chain C residue 1301 LEU Chi-restraints excluded: chain C residue 1436 VAL Chi-restraints excluded: chain C residue 1460 ILE Chi-restraints excluded: chain C residue 1462 ASP Chi-restraints excluded: chain C residue 1532 GLN Chi-restraints excluded: chain C residue 1560 LEU Chi-restraints excluded: chain C residue 1619 ILE Chi-restraints excluded: chain C residue 1731 LEU Chi-restraints excluded: chain C residue 1770 LEU Chi-restraints excluded: chain C residue 1771 LYS Chi-restraints excluded: chain C residue 1786 LEU Chi-restraints excluded: chain C residue 1792 LEU Chi-restraints excluded: chain C residue 1793 LEU Chi-restraints excluded: chain C residue 1813 ILE Chi-restraints excluded: chain C residue 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 329 optimal weight: 0.7980 chunk 347 optimal weight: 4.9990 chunk 316 optimal weight: 1.9990 chunk 337 optimal weight: 7.9990 chunk 203 optimal weight: 0.9980 chunk 147 optimal weight: 4.9990 chunk 265 optimal weight: 8.9990 chunk 103 optimal weight: 5.9990 chunk 305 optimal weight: 0.6980 chunk 319 optimal weight: 0.0670 chunk 336 optimal weight: 0.0010 overall best weight: 0.5124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 788 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1275 GLN ** A1414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1730 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1738 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 717 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 788 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1887 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.4749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.065 29318 Z= 0.156 Angle : 0.662 16.315 39716 Z= 0.322 Chirality : 0.041 0.213 4666 Planarity : 0.003 0.039 5024 Dihedral : 7.835 88.724 4192 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.59 % Favored : 91.36 % Rotamer: Outliers : 2.20 % Allowed : 24.30 % Favored : 73.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.14), residues: 3692 helix: 1.13 (0.13), residues: 1790 sheet: 0.33 (0.35), residues: 236 loop : -2.50 (0.15), residues: 1666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A1351 HIS 0.008 0.001 HIS C1296 PHE 0.043 0.001 PHE A 43 TYR 0.011 0.001 TYR C1030 ARG 0.010 0.000 ARG A1507 *********************** 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 421 residues out of total 3448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 355 time to evaluate : 3.423 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 44 LYS cc_start: 0.9234 (ptpt) cc_final: 0.9008 (ptpp) REVERT: A 120 MET cc_start: 0.8184 (tpt) cc_final: 0.7410 (tpt) REVERT: A 333 LEU cc_start: 0.9574 (OUTLIER) cc_final: 0.9329 (mt) REVERT: A 351 LEU cc_start: 0.9466 (mt) cc_final: 0.9206 (mt) REVERT: A 398 GLU cc_start: 0.8670 (mp0) cc_final: 0.8230 (mp0) REVERT: A 478 MET cc_start: 0.8403 (mmm) cc_final: 0.8143 (tpp) REVERT: A 594 GLU cc_start: 0.8388 (pp20) cc_final: 0.8122 (pp20) REVERT: A 900 GLU cc_start: 0.9403 (mt-10) cc_final: 0.9140 (mm-30) REVERT: A 1097 TYR cc_start: 0.6238 (t80) cc_final: 0.5471 (t80) REVERT: A 1196 MET cc_start: 0.8291 (mmt) cc_final: 0.8014 (mmm) REVERT: A 1289 ASP cc_start: 0.7565 (t70) cc_final: 0.7304 (t70) REVERT: A 1417 GLU cc_start: 0.8230 (mm-30) cc_final: 0.7944 (mm-30) REVERT: C 13 ARG cc_start: 0.6836 (mmm160) cc_final: 0.6595 (mmm160) REVERT: C 120 MET cc_start: 0.8468 (tpt) cc_final: 0.7795 (tpp) REVERT: C 261 THR cc_start: 0.8134 (OUTLIER) cc_final: 0.7776 (p) REVERT: C 351 LEU cc_start: 0.9428 (mt) cc_final: 0.9192 (mt) REVERT: C 598 TRP cc_start: 0.8740 (OUTLIER) cc_final: 0.8343 (m-10) REVERT: C 606 MET cc_start: 0.8824 (mpp) cc_final: 0.8588 (mpp) REVERT: C 1097 TYR cc_start: 0.5345 (t80) cc_final: 0.4728 (t80) REVERT: C 1146 GLU cc_start: 0.7986 (mm-30) cc_final: 0.7449 (mm-30) REVERT: C 1150 GLU cc_start: 0.7723 (mt-10) cc_final: 0.6903 (mt-10) REVERT: C 1307 GLU cc_start: 0.7978 (tp30) cc_final: 0.7515 (tp30) REVERT: C 1507 ARG cc_start: 0.8149 (ttp80) cc_final: 0.7938 (ttp80) REVERT: C 1731 LEU cc_start: 0.8057 (OUTLIER) cc_final: 0.7660 (mt) REVERT: C 1793 LEU cc_start: 0.8493 (OUTLIER) cc_final: 0.8249 (pp) REVERT: C 1829 GLN cc_start: 0.9067 (tm-30) cc_final: 0.8673 (tm-30) outliers start: 66 outliers final: 36 residues processed: 399 average time/residue: 0.3683 time to fit residues: 244.1472 Evaluate side-chains 375 residues out of total 3448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 334 time to evaluate : 3.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 322 ASN Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 481 PHE Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 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 786 LEU Chi-restraints excluded: chain A residue 1185 CYS Chi-restraints excluded: chain A residue 1409 CYS Chi-restraints excluded: chain A residue 1648 SER Chi-restraints excluded: chain A residue 1687 LEU 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 360 LEU Chi-restraints excluded: chain C residue 440 ASP 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 780 LEU Chi-restraints excluded: chain C residue 798 LEU Chi-restraints excluded: chain C residue 1202 LEU Chi-restraints excluded: chain C residue 1301 LEU Chi-restraints excluded: chain C residue 1379 VAL Chi-restraints excluded: chain C residue 1462 ASP Chi-restraints excluded: chain C residue 1532 GLN Chi-restraints excluded: chain C residue 1619 ILE Chi-restraints excluded: chain C residue 1731 LEU Chi-restraints excluded: chain C residue 1770 LEU Chi-restraints excluded: chain C residue 1771 LYS Chi-restraints excluded: chain C residue 1793 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 221 optimal weight: 1.9990 chunk 357 optimal weight: 10.0000 chunk 217 optimal weight: 7.9990 chunk 169 optimal weight: 4.9990 chunk 248 optimal weight: 5.9990 chunk 374 optimal weight: 6.9990 chunk 344 optimal weight: 0.7980 chunk 298 optimal weight: 9.9990 chunk 30 optimal weight: 0.9990 chunk 230 optimal weight: 4.9990 chunk 182 optimal weight: 0.7980 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 788 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1689 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1730 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1738 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 704 HIS ** C 717 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 788 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1887 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.4957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 29318 Z= 0.209 Angle : 0.685 16.595 39716 Z= 0.337 Chirality : 0.042 0.218 4666 Planarity : 0.003 0.037 5024 Dihedral : 7.873 90.388 4192 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 13.38 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.97 % Favored : 90.98 % Rotamer: Outliers : 2.00 % Allowed : 24.73 % Favored : 73.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.14), residues: 3692 helix: 1.10 (0.13), residues: 1794 sheet: 0.29 (0.35), residues: 236 loop : -2.51 (0.15), residues: 1662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A1351 HIS 0.009 0.001 HIS C1296 PHE 0.047 0.001 PHE A 43 TYR 0.012 0.001 TYR C 327 ARG 0.008 0.000 ARG A1507 ********************** 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 390 residues out of total 3448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 330 time to evaluate : 3.535 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: 0.9163 (ptpt) cc_final: 0.8871 (ptpp) REVERT: A 120 MET cc_start: 0.8179 (tpt) cc_final: 0.7423 (tpt) REVERT: A 261 THR cc_start: 0.8187 (OUTLIER) cc_final: 0.7804 (p) REVERT: A 333 LEU cc_start: 0.9587 (OUTLIER) cc_final: 0.9350 (mt) REVERT: A 351 LEU cc_start: 0.9463 (mt) cc_final: 0.9193 (mt) REVERT: A 398 GLU cc_start: 0.8668 (mp0) cc_final: 0.8236 (mp0) REVERT: A 594 GLU cc_start: 0.8414 (pp20) cc_final: 0.8193 (pp20) REVERT: A 602 ASP cc_start: 0.7999 (m-30) cc_final: 0.7727 (m-30) REVERT: A 606 MET cc_start: 0.8949 (mpt) cc_final: 0.8466 (mpt) REVERT: A 900 GLU cc_start: 0.9406 (mt-10) cc_final: 0.9135 (mm-30) REVERT: A 1097 TYR cc_start: 0.6201 (t80) cc_final: 0.5584 (t80) REVERT: C 120 MET cc_start: 0.8475 (tpt) cc_final: 0.7805 (tpp) REVERT: C 261 THR cc_start: 0.8165 (OUTLIER) cc_final: 0.7829 (p) REVERT: C 351 LEU cc_start: 0.9379 (mt) cc_final: 0.9138 (mt) REVERT: C 598 TRP cc_start: 0.8751 (OUTLIER) cc_final: 0.8052 (m-10) REVERT: C 606 MET cc_start: 0.8864 (mpp) cc_final: 0.8628 (mpp) REVERT: C 1097 TYR cc_start: 0.5491 (t80) cc_final: 0.4836 (t80) REVERT: C 1307 GLU cc_start: 0.8019 (tp30) cc_final: 0.7551 (tp30) REVERT: C 1507 ARG cc_start: 0.8243 (ttp80) cc_final: 0.8024 (ttp80) REVERT: C 1793 LEU cc_start: 0.8546 (OUTLIER) cc_final: 0.8328 (pp) REVERT: C 1829 GLN cc_start: 0.9087 (tm-30) cc_final: 0.8684 (tm-30) outliers start: 60 outliers final: 45 residues processed: 369 average time/residue: 0.3738 time to fit residues: 229.5543 Evaluate side-chains 368 residues out of total 3448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 318 time to evaluate : 3.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 322 ASN Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 481 PHE Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 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 786 LEU Chi-restraints excluded: chain A residue 1185 CYS Chi-restraints excluded: chain A residue 1265 LEU Chi-restraints excluded: chain A residue 1352 LEU Chi-restraints excluded: chain A residue 1395 LEU Chi-restraints excluded: chain A residue 1409 CYS Chi-restraints excluded: chain A residue 1436 VAL 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 1822 GLU Chi-restraints excluded: chain A residue 1882 LEU Chi-restraints excluded: chain A residue 1884 VAL Chi-restraints excluded: chain C residue 212 LEU 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 394 LEU Chi-restraints excluded: chain C residue 440 ASP 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 798 LEU Chi-restraints excluded: chain C residue 836 ASP Chi-restraints excluded: chain C residue 1301 LEU Chi-restraints excluded: chain C residue 1379 VAL Chi-restraints excluded: chain C residue 1436 VAL Chi-restraints excluded: chain C residue 1462 ASP Chi-restraints excluded: chain C residue 1619 ILE Chi-restraints excluded: chain C residue 1731 LEU Chi-restraints excluded: chain C residue 1770 LEU Chi-restraints excluded: chain C residue 1771 LYS Chi-restraints excluded: chain C residue 1793 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 236 optimal weight: 7.9990 chunk 317 optimal weight: 1.9990 chunk 91 optimal weight: 20.0000 chunk 275 optimal weight: 1.9990 chunk 44 optimal weight: 0.0980 chunk 82 optimal weight: 10.0000 chunk 298 optimal weight: 0.8980 chunk 125 optimal weight: 6.9990 chunk 306 optimal weight: 0.7980 chunk 37 optimal weight: 0.9990 chunk 55 optimal weight: 0.9980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 788 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1730 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1738 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 717 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 788 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.126563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.093940 restraints weight = 81992.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.093240 restraints weight = 47828.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.093850 restraints weight = 40010.195| |-----------------------------------------------------------------------------| r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.5000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 29318 Z= 0.159 Angle : 0.678 15.941 39716 Z= 0.330 Chirality : 0.041 0.210 4666 Planarity : 0.003 0.033 5024 Dihedral : 7.809 88.618 4192 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.21 % Favored : 91.77 % Rotamer: Outliers : 1.60 % Allowed : 25.17 % Favored : 73.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.14), residues: 3692 helix: 1.02 (0.13), residues: 1816 sheet: 0.48 (0.35), residues: 236 loop : -2.50 (0.15), residues: 1640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A1351 HIS 0.008 0.001 HIS C1296 PHE 0.042 0.001 PHE A 43 TYR 0.011 0.001 TYR C1533 ARG 0.006 0.000 ARG A1507 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5439.79 seconds wall clock time: 100 minutes 34.77 seconds (6034.77 seconds total)