Starting phenix.real_space_refine on Thu Jul 2 22:25:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7we4_32439/07_2026/7we4_32439.cif Found real_map, /net/cci-nas-00/data/ceres_data/7we4_32439/07_2026/7we4_32439.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7we4_32439/07_2026/7we4_32439.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7we4_32439/07_2026/7we4_32439.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7we4_32439/07_2026/7we4_32439.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7we4_32439/07_2026/7we4_32439.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7we4_32439/07_2026/7we4_32439.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7we4_32439/07_2026/7we4_32439.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.013 sd= 0.105 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: 6 Type Number sf(0) Gaussians P 17 5.49 5 S 63 5.16 5 Cl 1 4.86 5 C 6567 2.51 5 N 1464 2.21 5 O 1694 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 35 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9806 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 9019 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1122, 9009 Classifications: {'peptide': 1122} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 1089} Chain breaks: 3 Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ARG:plan': 2, 'TYR:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 22 Conformer: "B" Number of residues, atoms: 1122, 9009 Classifications: {'peptide': 1122} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 1089} Chain breaks: 3 Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ARG:plan': 2, 'TYR:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 22 bond proxies already assigned to first conformer: 9223 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 731 Unusual residues: {'95T': 1, 'CLR': 4, 'LPE': 9, 'NAG': 3, 'PCW': 5} Classifications: {'peptide': 3, 'undetermined': 22} Link IDs: {'TRANS': 2, None: 22} Not linked: pdbres="NAG A2001 " pdbres="NAG A2002 " Not linked: pdbres="NAG A2002 " pdbres="NAG A2003 " Not linked: pdbres="NAG A2003 " pdbres="95T A2004 " Not linked: pdbres="95T A2004 " pdbres="CLR A2005 " Not linked: pdbres="CLR A2005 " pdbres="PCW A2006 " ... (remaining 17 not shown) Chain breaks: 2 Unresolved non-hydrogen bonds: 189 Unresolved non-hydrogen angles: 198 Unresolved non-hydrogen dihedrals: 178 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PCW:plan-2': 2} Unresolved non-hydrogen planarities: 4 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AHIS A1631 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS A1631 " occ=0.50 Time building chain proxies: 3.31, per 1000 atoms: 0.34 Number of scatterers: 9806 At special positions: 0 Unit cell: (132.065, 119.075, 99.59, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 1 17.00 S 63 16.00 P 17 15.00 O 1694 8.00 N 1464 7.00 C 6567 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 276 " - pdb=" SG CYS A 319 " distance=2.03 Simple disulfide: pdb=" SG CYS A 310 " - pdb=" SG CYS A 325 " distance=2.03 Simple disulfide: pdb=" SG CYS A 857 " - pdb=" SG CYS A 866 " distance=2.03 Simple disulfide: pdb=" SG CYS A1310 " - pdb=" SG CYS A1332 " distance=2.02 Simple disulfide: pdb=" SG CYS A1678 " - pdb=" SG CYS A1692 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG C 1 " - " NAG C 2 " NAG-ASN " NAG A2001 " - " ASN A 819 " " NAG A2002 " - " ASN A 312 " " NAG A2003 " - " ASN A1312 " " NAG B 1 " - " ASN A1328 " " NAG C 1 " - " ASN A1336 " Time building additional restraints: 0.97 Conformation dependent library (CDL) restraints added in 839.7 milliseconds 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2130 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 2 sheets defined 77.5% alpha, 1.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'A' and resid 118 through 128 Processing helix chain 'A' and resid 129 through 149 removed outlier: 4.078A pdb=" N ARG A 149 " --> pdb=" O VAL A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 179 removed outlier: 3.896A pdb=" N THR A 161 " --> pdb=" O GLU A 157 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ALA A 168 " --> pdb=" O TYR A 164 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU A 169 " --> pdb=" O THR A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 187 removed outlier: 3.972A pdb=" N LEU A 185 " --> pdb=" O GLU A 181 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N ASP A 187 " --> pdb=" O THR A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 205 removed outlier: 4.112A pdb=" N TRP A 191 " --> pdb=" O ASP A 187 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N LEU A 192 " --> pdb=" O PRO A 188 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ASP A 193 " --> pdb=" O TRP A 189 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA A 200 " --> pdb=" O VAL A 196 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ALA A 205 " --> pdb=" O TYR A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 219 removed outlier: 3.514A pdb=" N THR A 216 " --> pdb=" O SER A 212 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ARG A 218 " --> pdb=" O LEU A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 224 removed outlier: 4.054A pdb=" N LEU A 223 " --> pdb=" O VAL A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 229 removed outlier: 3.917A pdb=" N VAL A 228 " --> pdb=" O LYS A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 246 removed outlier: 4.000A pdb=" N ILE A 235 " --> pdb=" O GLY A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 269 Processing helix chain 'A' and resid 341 through 355 Processing helix chain 'A' and resid 357 through 370 removed outlier: 3.766A pdb=" N LEU A 361 " --> pdb=" O SER A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 407 removed outlier: 3.591A pdb=" N PHE A 377 " --> pdb=" O TYR A 373 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N SER A 385 " --> pdb=" O ILE A 381 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N LEU A 388 " --> pdb=" O GLY A 384 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N VAL A 389 " --> pdb=" O SER A 385 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N THR A 407 " --> pdb=" O GLN A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 652 through 661 Processing helix chain 'A' and resid 664 through 683 removed outlier: 3.704A pdb=" N GLU A 668 " --> pdb=" O ASP A 664 " (cutoff:3.500A) Processing helix chain 'A' and resid 690 through 717 Processing helix chain 'A' and resid 720 through 726 Processing helix chain 'A' and resid 727 through 746 removed outlier: 3.931A pdb=" N ILE A 731 " --> pdb=" O LYS A 727 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N PHE A 732 " --> pdb=" O LYS A 728 " (cutoff:3.500A) Processing helix chain 'A' and resid 752 through 757 Processing helix chain 'A' and resid 758 through 769 removed outlier: 3.582A pdb=" N LYS A 768 " --> pdb=" O LYS A 765 " (cutoff:3.500A) Processing helix chain 'A' and resid 770 through 783 Processing helix chain 'A' and resid 787 through 816 removed outlier: 3.842A pdb=" N THR A 791 " --> pdb=" O LEU A 787 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N GLU A 811 " --> pdb=" O GLN A 807 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N ASN A 812 " --> pdb=" O LEU A 808 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N TYR A 813 " --> pdb=" O LEU A 809 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ARG A 814 " --> pdb=" O GLY A 810 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 821 removed outlier: 4.165A pdb=" N ILE A 820 " --> pdb=" O ASN A 816 " (cutoff:3.500A) Processing helix chain 'A' and resid 834 through 847 Processing helix chain 'A' and resid 850 through 859 Processing helix chain 'A' and resid 862 through 894 removed outlier: 3.578A pdb=" N VAL A 880 " --> pdb=" O LEU A 876 " (cutoff:3.500A) Processing helix chain 'A' and resid 1137 through 1150 Processing helix chain 'A' and resid 1151 through 1169 removed outlier: 3.677A pdb=" N LEU A1169 " --> pdb=" O SER A1165 " (cutoff:3.500A) Processing helix chain 'A' and resid 1170 through 1172 No H-bonds generated for 'chain 'A' and resid 1170 through 1172' Processing helix chain 'A' and resid 1175 through 1178 Processing helix chain 'A' and resid 1179 through 1208 removed outlier: 3.807A pdb=" N LYS A1183 " --> pdb=" O LYS A1179 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ALA A1184 " --> pdb=" O PRO A1180 " (cutoff:3.500A) Processing helix chain 'A' and resid 1209 through 1215 Processing helix chain 'A' and resid 1219 through 1238 removed outlier: 3.504A pdb=" N PHE A1223 " --> pdb=" O CYS A1219 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ILE A1225 " --> pdb=" O LEU A1221 " (cutoff:3.500A) Processing helix chain 'A' and resid 1243 through 1251 Processing helix chain 'A' and resid 1252 through 1261 Proline residue: A1257 - end of helix removed outlier: 3.539A pdb=" N ALA A1260 " --> pdb=" O PRO A1257 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU A1261 " --> pdb=" O LEU A1258 " (cutoff:3.500A) Processing helix chain 'A' and resid 1264 through 1304 Proline residue: A1279 - end of helix removed outlier: 3.625A pdb=" N ASN A1283 " --> pdb=" O PRO A1279 " (cutoff:3.500A) Processing helix chain 'A' and resid 1328 through 1335 removed outlier: 3.514A pdb=" N ILE A1334 " --> pdb=" O SER A1330 " (cutoff:3.500A) Processing helix chain 'A' and resid 1352 through 1365 removed outlier: 3.725A pdb=" N LEU A1358 " --> pdb=" O ALA A1354 " (cutoff:3.500A) Processing helix chain 'A' and resid 1368 through 1377 Processing helix chain 'A' and resid 1391 through 1393 No H-bonds generated for 'chain 'A' and resid 1391 through 1393' Processing helix chain 'A' and resid 1394 through 1405 removed outlier: 3.796A pdb=" N PHE A1398 " --> pdb=" O MET A1394 " (cutoff:3.500A) Processing helix chain 'A' and resid 1410 through 1428 Processing helix chain 'A' and resid 1436 through 1452 removed outlier: 3.902A pdb=" N SER A1451 " --> pdb=" O LYS A1447 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LYS A1452 " --> pdb=" O LYS A1448 " (cutoff:3.500A) Processing helix chain 'A' and resid 1463 through 1475 removed outlier: 3.793A pdb=" N ARG A1475 " --> pdb=" O ASP A1471 " (cutoff:3.500A) Processing helix chain 'A' and resid 1475 through 1494 removed outlier: 4.142A pdb=" N ASP A1479 " --> pdb=" O ARG A1475 " (cutoff:3.500A) Processing helix chain 'A' and resid 1501 through 1530 Processing helix chain 'A' and resid 1532 through 1537 removed outlier: 3.542A pdb=" N ASN A1537 " --> pdb=" O TYR A1533 " (cutoff:3.500A) Processing helix chain 'A' and resid 1537 through 1561 removed outlier: 3.741A pdb=" N VAL A1541 " --> pdb=" O ASN A1537 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N PHE A1542 " --> pdb=" O GLY A1538 " (cutoff:3.500A) Processing helix chain 'A' and resid 1568 through 1576 removed outlier: 4.234A pdb=" N PHE A1572 " --> pdb=" O SER A1568 " (cutoff:3.500A) Processing helix chain 'A' and resid 1579 through 1585 removed outlier: 3.773A pdb=" N ILE A1583 " --> pdb=" O ARG A1579 " (cutoff:3.500A) Processing helix chain 'A' and resid 1586 through 1589 removed outlier: 3.605A pdb=" N ALA A1589 " --> pdb=" O LEU A1586 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1586 through 1589' Processing helix chain 'A' and resid 1590 through 1629 Proline residue: A1605 - end of helix removed outlier: 3.715A pdb=" N ASN A1609 " --> pdb=" O PRO A1605 " (cutoff:3.500A) Processing helix chain 'A' and resid 1646 through 1659 removed outlier: 4.220A pdb=" N THR A1659 " --> pdb=" O PHE A1655 " (cutoff:3.500A) Processing helix chain 'A' and resid 1662 through 1671 removed outlier: 3.558A pdb=" N LEU A1666 " --> pdb=" O GLY A1662 " (cutoff:3.500A) Proline residue: A1669 - end of helix Processing helix chain 'A' and resid 1694 through 1728 Processing sheet with id=AA1, first strand: chain 'A' and resid 274 through 278 Processing sheet with id=AA2, first strand: chain 'A' and resid 1318 through 1320 597 hydrogen bonds defined for protein. 1758 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.87 Time building geometry restraints manager: 1.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 1401 1.29 - 1.42: 2633 1.42 - 1.55: 5849 1.55 - 1.68: 44 1.68 - 1.81: 104 Bond restraints: 10031 Sorted by residual: bond pdb=" C ALA A 168 " pdb=" N LEU A 169 " ideal model delta sigma weight residual 1.335 1.234 0.101 1.31e-02 5.83e+03 5.90e+01 bond pdb=" C11 PCW A2007 " pdb=" O3 PCW A2007 " ideal model delta sigma weight residual 1.326 1.458 -0.132 2.00e-02 2.50e+03 4.39e+01 bond pdb=" C38 P5S A2024 " pdb=" O37 P5S A2024 " ideal model delta sigma weight residual 1.331 1.463 -0.132 2.00e-02 2.50e+03 4.37e+01 bond pdb=" C38 P5S A2023 " pdb=" O37 P5S A2023 " ideal model delta sigma weight residual 1.331 1.461 -0.130 2.00e-02 2.50e+03 4.25e+01 bond pdb=" C17 P5S A2024 " pdb=" O19 P5S A2024 " ideal model delta sigma weight residual 1.328 1.457 -0.129 2.00e-02 2.50e+03 4.18e+01 ... (remaining 10026 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.08: 13061 4.08 - 8.16: 421 8.16 - 12.25: 60 12.25 - 16.33: 6 16.33 - 20.41: 4 Bond angle restraints: 13552 Sorted by residual: angle pdb=" N GLU A 157 " pdb=" CA GLU A 157 " pdb=" C GLU A 157 " ideal model delta sigma weight residual 111.28 100.51 10.77 1.09e+00 8.42e-01 9.76e+01 angle pdb=" N GLY A1690 " pdb=" CA GLY A1690 " pdb=" C GLY A1690 " ideal model delta sigma weight residual 110.55 122.52 -11.97 1.64e+00 3.72e-01 5.32e+01 angle pdb=" N TRP A1218 " pdb=" CA TRP A1218 " pdb=" C TRP A1218 " ideal model delta sigma weight residual 114.12 104.09 10.03 1.39e+00 5.18e-01 5.20e+01 angle pdb=" N GLU A 811 " pdb=" CA GLU A 811 " pdb=" C GLU A 811 " ideal model delta sigma weight residual 111.71 119.56 -7.85 1.15e+00 7.56e-01 4.66e+01 angle pdb=" C09 95T A2004 " pdb=" C13 95T A2004 " pdb=" N06 95T A2004 " ideal model delta sigma weight residual 119.48 139.89 -20.41 3.00e+00 1.11e-01 4.63e+01 ... (remaining 13547 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.50: 5605 32.50 - 65.01: 226 65.01 - 97.51: 20 97.51 - 130.02: 10 130.02 - 162.52: 3 Dihedral angle restraints: 5864 sinusoidal: 2577 harmonic: 3287 Sorted by residual: dihedral pdb=" CB CYS A 857 " pdb=" SG CYS A 857 " pdb=" SG CYS A 866 " pdb=" CB CYS A 866 " ideal model delta sinusoidal sigma weight residual 93.00 176.58 -83.58 1 1.00e+01 1.00e-02 8.53e+01 dihedral pdb=" CB CYS A 310 " pdb=" SG CYS A 310 " pdb=" SG CYS A 325 " pdb=" CB CYS A 325 " ideal model delta sinusoidal sigma weight residual -86.00 -162.39 76.39 1 1.00e+01 1.00e-02 7.34e+01 dihedral pdb=" CB CYS A1310 " pdb=" SG CYS A1310 " pdb=" SG CYS A1332 " pdb=" CB CYS A1332 " ideal model delta sinusoidal sigma weight residual -86.00 -144.64 58.64 1 1.00e+01 1.00e-02 4.60e+01 ... (remaining 5861 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.312: 1524 0.312 - 0.624: 12 0.624 - 0.936: 1 0.936 - 1.248: 0 1.248 - 1.560: 1 Chirality restraints: 1538 Sorted by residual: chirality pdb=" C1 NAG A2003 " pdb=" ND2 ASN A1312 " pdb=" C2 NAG A2003 " pdb=" O5 NAG A2003 " both_signs ideal model delta sigma weight residual False -2.40 -0.84 -1.56 2.00e-01 2.50e+01 6.09e+01 chirality pdb=" C1 NAG B 2 " pdb=" O4 NAG B 1 " pdb=" C2 NAG B 2 " pdb=" O5 NAG B 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.27 -0.13 2.00e-02 2.50e+03 4.02e+01 chirality pdb=" C1 NAG C 2 " pdb=" O4 NAG C 1 " pdb=" C2 NAG C 2 " pdb=" O5 NAG C 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.32 -0.08 2.00e-02 2.50e+03 1.58e+01 ... (remaining 1535 not shown) Planarity restraints: 1576 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 1 " -0.338 2.00e-02 2.50e+03 2.92e-01 1.06e+03 pdb=" C7 NAG B 1 " 0.077 2.00e-02 2.50e+03 pdb=" C8 NAG B 1 " -0.042 2.00e-02 2.50e+03 pdb=" N2 NAG B 1 " 0.510 2.00e-02 2.50e+03 pdb=" O7 NAG B 1 " -0.207 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A2003 " 0.298 2.00e-02 2.50e+03 2.60e-01 8.44e+02 pdb=" C7 NAG A2003 " -0.070 2.00e-02 2.50e+03 pdb=" C8 NAG A2003 " 0.145 2.00e-02 2.50e+03 pdb=" N2 NAG A2003 " -0.464 2.00e-02 2.50e+03 pdb=" O7 NAG A2003 " 0.090 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A2001 " -0.300 2.00e-02 2.50e+03 2.60e-01 8.44e+02 pdb=" C7 NAG A2001 " 0.072 2.00e-02 2.50e+03 pdb=" C8 NAG A2001 " -0.159 2.00e-02 2.50e+03 pdb=" N2 NAG A2001 " 0.460 2.00e-02 2.50e+03 pdb=" O7 NAG A2001 " -0.073 2.00e-02 2.50e+03 ... (remaining 1573 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1931 2.77 - 3.30: 9605 3.30 - 3.84: 15753 3.84 - 4.37: 19224 4.37 - 4.90: 31833 Nonbonded interactions: 78346 Sorted by model distance: nonbonded pdb=" O ILE A1699 " pdb=" OG1 THR A1703 " model vdw 2.238 3.040 nonbonded pdb=" O LEU A 220 " pdb=" N LEU A 223 " model vdw 2.257 3.120 nonbonded pdb=" O ILE A1700 " pdb=" OG1 THR A1704 " model vdw 2.295 3.040 nonbonded pdb=" O GLY A1405 " pdb=" OG1 THR A1409 " model vdw 2.304 3.040 nonbonded pdb=" OD1 ASN A 390 " pdb=" CD1 TYR A1717 " model vdw 2.309 3.340 ... (remaining 78341 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'C' } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.240 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: 0.180 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 12.220 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 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 : 0.012 0.146 10043 Z= 0.756 Angle : 1.648 20.411 13583 Z= 0.882 Chirality : 0.089 1.560 1538 Planarity : 0.016 0.292 1571 Dihedral : 17.366 162.522 3719 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 17.85 Ramachandran Plot: Outliers : 0.54 % Allowed : 5.30 % Favored : 94.17 % Rotamer: Outliers : 0.31 % Allowed : 2.44 % Favored : 97.25 % Cbeta Deviations : 0.38 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.26), residues: 1117 helix: 0.81 (0.19), residues: 776 sheet: -2.35 (0.95), residues: 22 loop : -2.53 (0.32), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 175 TYR 0.085 0.003 TYR A1374 PHE 0.046 0.002 PHE A 177 TRP 0.086 0.003 TRP A1369 HIS 0.003 0.001 HIS A 129 Details of bonding type rmsd/Z covalent geometry : bond 0.01220 / 0.75 (10031) covalent geometry : angle 1.62267 / 0.88 (13552) SS BOND : bond 0.00756 / 0.57 ( 5) SS BOND : angle 4.38618 / 2.96 ( 10) hydrogen bonds : bond 0.16720 / 11.39 ( 597) hydrogen bonds : angle 6.62495 / 4.80 ( 1758) link_BETA1-4 : bond 0.01235 / 0.65 ( 2) link_BETA1-4 : angle 4.40702 / 2.59 ( 6) link_NAG-ASN : bond 0.07790 / 3.98 ( 5) link_NAG-ASN : angle 7.72081 / 5.37 ( 15) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 169 time to evaluate : 0.380 Fit side-chains REVERT: A 182 PHE cc_start: 0.5153 (t80) cc_final: 0.4855 (m-80) outliers start: 3 outliers final: 0 residues processed: 171 average time/residue: 0.5127 time to fit residues: 94.5964 Evaluate side-chains 126 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 126 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 108 optimal weight: 7.9990 chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 0.6980 chunk 100 optimal weight: 0.5980 chunk 106 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 129 HIS A 271 ASN A 404 ASN ** A 807 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1301 ASN A1411 ASN A1420 ASN ** A1463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.144206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.110939 restraints weight = 25814.708| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 2.71 r_work: 0.3226 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3239 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3239 r_free = 0.3239 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3239 r_free = 0.3239 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3239 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.1701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10043 Z= 0.150 Angle : 0.751 16.818 13583 Z= 0.363 Chirality : 0.043 0.266 1538 Planarity : 0.005 0.058 1571 Dihedral : 17.760 172.347 1656 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 1.63 % Allowed : 9.97 % Favored : 88.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.81 (0.26), residues: 1117 helix: 1.53 (0.19), residues: 765 sheet: -2.29 (0.86), residues: 24 loop : -1.65 (0.34), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 302 TYR 0.038 0.002 TYR A1374 PHE 0.036 0.002 PHE A 693 TRP 0.036 0.002 TRP A 191 HIS 0.003 0.001 HIS A 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.15 (10031) covalent geometry : angle 0.73784 / 0.36 (13552) SS BOND : bond 0.00216 / 0.15 ( 5) SS BOND : angle 1.93520 / 1.27 ( 10) hydrogen bonds : bond 0.04908 / 3.26 ( 597) hydrogen bonds : angle 4.38673 / 3.13 ( 1758) link_BETA1-4 : bond 0.00478 / 0.24 ( 2) link_BETA1-4 : angle 2.02263 / 1.11 ( 6) link_NAG-ASN : bond 0.00355 / 0.18 ( 5) link_NAG-ASN : angle 3.87059 / 2.79 ( 15) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 133 time to evaluate : 0.366 Fit side-chains REVERT: A 398 MET cc_start: 0.8547 (mtp) cc_final: 0.8285 (mtm) REVERT: A 402 GLU cc_start: 0.8121 (tt0) cc_final: 0.7872 (pt0) REVERT: A 668 GLU cc_start: 0.6593 (pt0) cc_final: 0.6333 (tt0) REVERT: A 1147 ARG cc_start: 0.6374 (mtp180) cc_final: 0.5890 (mtm-85) REVERT: A 1250 ARG cc_start: 0.7917 (OUTLIER) cc_final: 0.7713 (ttt90) REVERT: A 1315 ASP cc_start: 0.7397 (p0) cc_final: 0.6941 (p0) REVERT: A 1384 MET cc_start: 0.8934 (mtm) cc_final: 0.8600 (mtm) REVERT: A 1561 LYS cc_start: 0.6774 (ptpt) cc_final: 0.6378 (ptmm) REVERT: A 1722 LEU cc_start: 0.8240 (OUTLIER) cc_final: 0.7949 (mm) outliers start: 16 outliers final: 5 residues processed: 138 average time/residue: 0.5225 time to fit residues: 77.9934 Evaluate side-chains 129 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 122 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 LYS Chi-restraints excluded: chain A residue 761 LEU Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain A residue 1211 LYS Chi-restraints excluded: chain A residue 1250 ARG Chi-restraints excluded: chain A residue 1291 PHE Chi-restraints excluded: chain A residue 1722 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 67 optimal weight: 0.9990 chunk 76 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 105 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 19 optimal weight: 7.9990 chunk 15 optimal weight: 0.7980 chunk 93 optimal weight: 3.9990 chunk 45 optimal weight: 4.9990 chunk 11 optimal weight: 0.6980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 807 GLN ** A1463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1489 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.142033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.108766 restraints weight = 23849.331| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 2.60 r_work: 0.3198 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3213 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3213 r_free = 0.3213 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3213 r_free = 0.3213 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3213 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.2111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10043 Z= 0.146 Angle : 0.651 15.003 13583 Z= 0.324 Chirality : 0.041 0.187 1538 Planarity : 0.005 0.049 1571 Dihedral : 15.876 173.269 1656 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 1.53 % Allowed : 11.80 % Favored : 86.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.34 (0.26), residues: 1117 helix: 1.82 (0.19), residues: 765 sheet: -2.39 (0.81), residues: 24 loop : -1.09 (0.36), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 302 TYR 0.031 0.002 TYR A1374 PHE 0.030 0.002 PHE A 693 TRP 0.028 0.001 TRP A1369 HIS 0.003 0.001 HIS A 687 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.15 (10031) covalent geometry : angle 0.64134 / 0.32 (13552) SS BOND : bond 0.00307 / 0.21 ( 5) SS BOND : angle 1.78007 / 1.15 ( 10) hydrogen bonds : bond 0.04712 / 3.09 ( 597) hydrogen bonds : angle 4.11792 / 2.94 ( 1758) link_BETA1-4 : bond 0.00622 / 0.32 ( 2) link_BETA1-4 : angle 1.42193 / 0.75 ( 6) link_NAG-ASN : bond 0.00162 / 0.08 ( 5) link_NAG-ASN : angle 3.02786 / 2.24 ( 15) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 130 time to evaluate : 0.368 Fit side-chains REVERT: A 165 THR cc_start: 0.6869 (m) cc_final: 0.6440 (p) REVERT: A 302 ARG cc_start: 0.8467 (mtp85) cc_final: 0.8256 (mmm160) REVERT: A 398 MET cc_start: 0.8580 (mtp) cc_final: 0.8258 (mtt) REVERT: A 402 GLU cc_start: 0.8242 (tt0) cc_final: 0.7994 (pt0) REVERT: A 668 GLU cc_start: 0.6642 (pt0) cc_final: 0.6297 (tt0) REVERT: A 726 GLN cc_start: 0.6718 (OUTLIER) cc_final: 0.6435 (mt0) REVERT: A 1145 CYS cc_start: 0.8434 (m) cc_final: 0.8008 (m) REVERT: A 1147 ARG cc_start: 0.6467 (mtp180) cc_final: 0.6063 (mtm-85) REVERT: A 1315 ASP cc_start: 0.7389 (p0) cc_final: 0.6819 (p0) REVERT: A 1384 MET cc_start: 0.8892 (mtm) cc_final: 0.8587 (mtm) REVERT: A 1466 GLN cc_start: 0.6383 (mt0) cc_final: 0.6035 (mp10) outliers start: 15 outliers final: 6 residues processed: 138 average time/residue: 0.5235 time to fit residues: 78.1304 Evaluate side-chains 130 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 123 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 LYS Chi-restraints excluded: chain A residue 726 GLN Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain A residue 1211 LYS Chi-restraints excluded: chain A residue 1233 LEU Chi-restraints excluded: chain A residue 1291 PHE Chi-restraints excluded: chain A residue 1601 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 45 optimal weight: 0.7980 chunk 74 optimal weight: 4.9990 chunk 60 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 97 optimal weight: 0.9990 chunk 75 optimal weight: 0.7980 chunk 86 optimal weight: 0.9990 chunk 73 optimal weight: 2.9990 chunk 70 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 52 optimal weight: 0.7980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 878 ASN A1423 GLN ** A1463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.143432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.110153 restraints weight = 24228.498| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 2.66 r_work: 0.3204 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3210 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3210 r_free = 0.3210 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3210 r_free = 0.3210 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3210 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.2315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10043 Z= 0.129 Angle : 0.611 14.519 13583 Z= 0.303 Chirality : 0.039 0.158 1538 Planarity : 0.004 0.047 1571 Dihedral : 15.058 173.423 1656 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 1.83 % Allowed : 12.31 % Favored : 85.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.59 (0.26), residues: 1117 helix: 1.95 (0.19), residues: 766 sheet: -2.29 (0.84), residues: 24 loop : -0.85 (0.37), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 221 TYR 0.020 0.002 TYR A 184 PHE 0.023 0.001 PHE A 693 TRP 0.020 0.001 TRP A 191 HIS 0.003 0.001 HIS A 687 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 (10031) covalent geometry : angle 0.60305 / 0.30 (13552) SS BOND : bond 0.00462 / 0.35 ( 5) SS BOND : angle 1.39457 / 0.89 ( 10) hydrogen bonds : bond 0.04332 / 2.83 ( 597) hydrogen bonds : angle 4.00454 / 2.86 ( 1758) link_BETA1-4 : bond 0.00465 / 0.24 ( 2) link_BETA1-4 : angle 1.24031 / 0.66 ( 6) link_NAG-ASN : bond 0.00120 / 0.06 ( 5) link_NAG-ASN : angle 2.68663 / 1.95 ( 15) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 124 time to evaluate : 0.350 Fit side-chains REVERT: A 165 THR cc_start: 0.6840 (m) cc_final: 0.6459 (p) REVERT: A 295 PRO cc_start: 0.8478 (Cg_exo) cc_final: 0.8163 (Cg_endo) REVERT: A 302 ARG cc_start: 0.8383 (mtp85) cc_final: 0.8160 (mmm160) REVERT: A 398 MET cc_start: 0.8246 (mtp) cc_final: 0.7840 (mtt) REVERT: A 402 GLU cc_start: 0.8032 (tt0) cc_final: 0.7703 (pt0) REVERT: A 668 GLU cc_start: 0.6314 (pt0) cc_final: 0.5923 (tt0) REVERT: A 1145 CYS cc_start: 0.8150 (m) cc_final: 0.7688 (m) REVERT: A 1315 ASP cc_start: 0.7415 (p0) cc_final: 0.6843 (p0) REVERT: A 1384 MET cc_start: 0.8721 (mtm) cc_final: 0.8385 (mtm) REVERT: A 1466 GLN cc_start: 0.6008 (mt0) cc_final: 0.5572 (mp10) outliers start: 18 outliers final: 6 residues processed: 133 average time/residue: 0.5063 time to fit residues: 72.8091 Evaluate side-chains 131 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 125 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 LYS Chi-restraints excluded: chain A residue 652 VAL Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain A residue 1211 LYS Chi-restraints excluded: chain A residue 1233 LEU Chi-restraints excluded: chain A residue 1291 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 10 optimal weight: 7.9990 chunk 42 optimal weight: 4.9990 chunk 77 optimal weight: 3.9990 chunk 90 optimal weight: 0.9980 chunk 49 optimal weight: 0.7980 chunk 29 optimal weight: 0.0470 chunk 97 optimal weight: 0.8980 chunk 98 optimal weight: 5.9990 chunk 84 optimal weight: 0.4980 chunk 96 optimal weight: 2.9990 chunk 19 optimal weight: 0.7980 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 404 ASN A 789 ASN A 878 ASN A1178 GLN A1463 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.144584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.112299 restraints weight = 18872.311| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 2.34 r_work: 0.3265 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3128 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3120 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3120 r_free = 0.3120 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3120 r_free = 0.3120 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (9 function evaluations) r_final: 0.3120 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.2502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 10043 Z= 0.115 Angle : 0.576 13.782 13583 Z= 0.286 Chirality : 0.038 0.155 1538 Planarity : 0.004 0.047 1571 Dihedral : 14.200 172.853 1656 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 1.83 % Allowed : 12.61 % Favored : 85.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.78 (0.26), residues: 1117 helix: 2.05 (0.19), residues: 775 sheet: -2.27 (0.85), residues: 24 loop : -0.71 (0.38), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 302 TYR 0.019 0.001 TYR A 164 PHE 0.020 0.001 PHE A 693 TRP 0.017 0.001 TRP A 191 HIS 0.003 0.001 HIS A 687 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.11 (10031) covalent geometry : angle 0.57006 / 0.28 (13552) SS BOND : bond 0.00416 / 0.31 ( 5) SS BOND : angle 1.20866 / 0.79 ( 10) hydrogen bonds : bond 0.03971 / 2.58 ( 597) hydrogen bonds : angle 3.91037 / 2.79 ( 1758) link_BETA1-4 : bond 0.00536 / 0.28 ( 2) link_BETA1-4 : angle 1.08882 / 0.59 ( 6) link_NAG-ASN : bond 0.00176 / 0.09 ( 5) link_NAG-ASN : angle 2.40625 / 1.71 ( 15) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 132 time to evaluate : 0.373 Fit side-chains REVERT: A 165 THR cc_start: 0.6708 (m) cc_final: 0.6370 (p) REVERT: A 295 PRO cc_start: 0.8468 (Cg_exo) cc_final: 0.8158 (Cg_endo) REVERT: A 398 MET cc_start: 0.8383 (mtp) cc_final: 0.7979 (mtt) REVERT: A 402 GLU cc_start: 0.7983 (tt0) cc_final: 0.7714 (pt0) REVERT: A 726 GLN cc_start: 0.6655 (OUTLIER) cc_final: 0.6422 (mt0) REVERT: A 882 LEU cc_start: 0.8661 (OUTLIER) cc_final: 0.8403 (tm) REVERT: A 1145 CYS cc_start: 0.8145 (m) cc_final: 0.7727 (m) REVERT: A 1147 ARG cc_start: 0.6229 (mtp180) cc_final: 0.5906 (mtm-85) REVERT: A 1315 ASP cc_start: 0.7499 (p0) cc_final: 0.6930 (p0) REVERT: A 1384 MET cc_start: 0.8817 (mtm) cc_final: 0.8484 (mtm) REVERT: A 1466 GLN cc_start: 0.6118 (mt0) cc_final: 0.5682 (mp10) outliers start: 18 outliers final: 6 residues processed: 141 average time/residue: 0.5527 time to fit residues: 84.0468 Evaluate side-chains 130 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 122 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 LYS Chi-restraints excluded: chain A residue 652 VAL Chi-restraints excluded: chain A residue 726 GLN Chi-restraints excluded: chain A residue 882 LEU Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain A residue 1211 LYS Chi-restraints excluded: chain A residue 1233 LEU Chi-restraints excluded: chain A residue 1291 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 85 optimal weight: 0.8980 chunk 89 optimal weight: 0.8980 chunk 46 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 86 optimal weight: 3.9990 chunk 91 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 chunk 103 optimal weight: 0.3980 chunk 49 optimal weight: 0.7980 chunk 92 optimal weight: 0.8980 chunk 100 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 789 ASN A 878 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.143938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.111539 restraints weight = 18869.503| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 2.34 r_work: 0.3253 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3119 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3070 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3070 r_free = 0.3070 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3070 r_free = 0.3070 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (9 function evaluations) r_final: 0.3070 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.2619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10043 Z= 0.121 Angle : 0.588 13.189 13583 Z= 0.291 Chirality : 0.038 0.151 1538 Planarity : 0.004 0.045 1571 Dihedral : 13.779 170.445 1656 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 1.53 % Allowed : 15.06 % Favored : 83.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.83 (0.26), residues: 1117 helix: 2.07 (0.19), residues: 776 sheet: -2.23 (0.89), residues: 24 loop : -0.68 (0.38), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 221 TYR 0.024 0.002 TYR A 164 PHE 0.019 0.001 PHE A 693 TRP 0.017 0.001 TRP A 191 HIS 0.003 0.001 HIS A 687 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 (10031) covalent geometry : angle 0.58228 / 0.29 (13552) SS BOND : bond 0.00308 / 0.22 ( 5) SS BOND : angle 1.20110 / 0.78 ( 10) hydrogen bonds : bond 0.04070 / 2.64 ( 597) hydrogen bonds : angle 3.87639 / 2.77 ( 1758) link_BETA1-4 : bond 0.00451 / 0.23 ( 2) link_BETA1-4 : angle 1.15896 / 0.62 ( 6) link_NAG-ASN : bond 0.00144 / 0.07 ( 5) link_NAG-ASN : angle 2.39657 / 1.71 ( 15) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 126 time to evaluate : 0.257 Fit side-chains REVERT: A 165 THR cc_start: 0.6705 (m) cc_final: 0.6363 (p) REVERT: A 295 PRO cc_start: 0.8490 (Cg_exo) cc_final: 0.8184 (Cg_endo) REVERT: A 398 MET cc_start: 0.8388 (mtp) cc_final: 0.8035 (mtt) REVERT: A 402 GLU cc_start: 0.8016 (tt0) cc_final: 0.7741 (pt0) REVERT: A 668 GLU cc_start: 0.6529 (OUTLIER) cc_final: 0.6190 (tt0) REVERT: A 726 GLN cc_start: 0.6686 (OUTLIER) cc_final: 0.6454 (mt0) REVERT: A 1145 CYS cc_start: 0.8197 (m) cc_final: 0.7761 (m) REVERT: A 1315 ASP cc_start: 0.7530 (p0) cc_final: 0.6935 (p0) REVERT: A 1384 MET cc_start: 0.8802 (mtm) cc_final: 0.8435 (mtm) REVERT: A 1393 TYR cc_start: 0.8705 (m-80) cc_final: 0.8055 (m-80) REVERT: A 1466 GLN cc_start: 0.6206 (mt0) cc_final: 0.5679 (mp10) outliers start: 15 outliers final: 7 residues processed: 131 average time/residue: 0.4942 time to fit residues: 69.9304 Evaluate side-chains 131 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 122 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 LYS Chi-restraints excluded: chain A residue 652 VAL Chi-restraints excluded: chain A residue 668 GLU Chi-restraints excluded: chain A residue 726 GLN Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain A residue 1211 LYS Chi-restraints excluded: chain A residue 1233 LEU Chi-restraints excluded: chain A residue 1249 LEU Chi-restraints excluded: chain A residue 1291 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 111 optimal weight: 0.7980 chunk 31 optimal weight: 0.9990 chunk 4 optimal weight: 4.9990 chunk 19 optimal weight: 0.5980 chunk 58 optimal weight: 5.9990 chunk 76 optimal weight: 0.7980 chunk 3 optimal weight: 0.7980 chunk 84 optimal weight: 0.7980 chunk 67 optimal weight: 0.6980 chunk 61 optimal weight: 4.9990 chunk 50 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 390 ASN A 789 ASN A 878 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.144003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.109997 restraints weight = 28670.811| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 2.89 r_work: 0.3216 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3194 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3194 r_free = 0.3194 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3194 r_free = 0.3194 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (9 function evaluations) r_final: 0.3194 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.2709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10043 Z= 0.119 Angle : 0.589 12.998 13583 Z= 0.291 Chirality : 0.038 0.154 1538 Planarity : 0.004 0.044 1571 Dihedral : 13.449 167.786 1656 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 1.93 % Allowed : 14.85 % Favored : 83.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.94 (0.26), residues: 1117 helix: 2.10 (0.19), residues: 778 sheet: -2.21 (0.92), residues: 20 loop : -0.53 (0.38), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 302 TYR 0.024 0.001 TYR A 164 PHE 0.018 0.001 PHE A 693 TRP 0.015 0.001 TRP A 191 HIS 0.002 0.001 HIS A 837 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 (10031) covalent geometry : angle 0.58021 / 0.29 (13552) SS BOND : bond 0.00431 / 0.31 ( 5) SS BOND : angle 2.54382 / 2.01 ( 10) hydrogen bonds : bond 0.03999 / 2.60 ( 597) hydrogen bonds : angle 3.85908 / 2.76 ( 1758) link_BETA1-4 : bond 0.00379 / 0.19 ( 2) link_BETA1-4 : angle 1.09528 / 0.59 ( 6) link_NAG-ASN : bond 0.00152 / 0.08 ( 5) link_NAG-ASN : angle 2.35181 / 1.68 ( 15) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 123 time to evaluate : 0.358 Fit side-chains REVERT: A 165 THR cc_start: 0.6530 (m) cc_final: 0.6202 (p) REVERT: A 295 PRO cc_start: 0.8423 (Cg_exo) cc_final: 0.8152 (Cg_endo) REVERT: A 398 MET cc_start: 0.8252 (mtp) cc_final: 0.7864 (mtt) REVERT: A 402 GLU cc_start: 0.8042 (tt0) cc_final: 0.7747 (pt0) REVERT: A 668 GLU cc_start: 0.6410 (OUTLIER) cc_final: 0.6097 (tt0) REVERT: A 726 GLN cc_start: 0.6632 (OUTLIER) cc_final: 0.6415 (mt0) REVERT: A 826 ASP cc_start: 0.8739 (t0) cc_final: 0.8465 (t0) REVERT: A 1145 CYS cc_start: 0.8185 (m) cc_final: 0.7731 (m) REVERT: A 1315 ASP cc_start: 0.7422 (p0) cc_final: 0.6946 (p0) REVERT: A 1317 GLU cc_start: 0.7687 (OUTLIER) cc_final: 0.7200 (mm-30) REVERT: A 1384 MET cc_start: 0.8691 (mtm) cc_final: 0.8312 (mtm) REVERT: A 1393 TYR cc_start: 0.8638 (m-80) cc_final: 0.7988 (m-80) REVERT: A 1466 GLN cc_start: 0.6043 (mt0) cc_final: 0.5541 (mp10) outliers start: 19 outliers final: 11 residues processed: 131 average time/residue: 0.5303 time to fit residues: 75.1313 Evaluate side-chains 134 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 120 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 224 LYS Chi-restraints excluded: chain A residue 652 VAL Chi-restraints excluded: chain A residue 668 GLU Chi-restraints excluded: chain A residue 690 SER Chi-restraints excluded: chain A residue 726 GLN Chi-restraints excluded: chain A residue 741 LEU Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain A residue 1211 LYS Chi-restraints excluded: chain A residue 1233 LEU Chi-restraints excluded: chain A residue 1249 LEU Chi-restraints excluded: chain A residue 1291 PHE Chi-restraints excluded: chain A residue 1317 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 46 optimal weight: 3.9990 chunk 63 optimal weight: 5.9990 chunk 66 optimal weight: 3.9990 chunk 104 optimal weight: 0.9990 chunk 94 optimal weight: 4.9990 chunk 68 optimal weight: 0.6980 chunk 42 optimal weight: 2.9990 chunk 103 optimal weight: 0.9990 chunk 98 optimal weight: 6.9990 chunk 55 optimal weight: 4.9990 chunk 6 optimal weight: 5.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 789 ASN A 878 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.138224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.105373 restraints weight = 19618.530| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 2.37 r_work: 0.3159 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3014 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3032 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3032 r_free = 0.3032 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3032 r_free = 0.3032 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (9 function evaluations) r_final: 0.3032 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.2794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 10043 Z= 0.197 Angle : 0.676 13.222 13583 Z= 0.339 Chirality : 0.041 0.170 1538 Planarity : 0.005 0.043 1571 Dihedral : 13.471 160.313 1656 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 2.34 % Allowed : 14.65 % Favored : 83.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.50 (0.26), residues: 1117 helix: 1.87 (0.19), residues: 780 sheet: -2.46 (0.82), residues: 22 loop : -0.99 (0.37), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A1250 TYR 0.027 0.002 TYR A 164 PHE 0.023 0.002 PHE A1701 TRP 0.022 0.002 TRP A 191 HIS 0.004 0.001 HIS A 687 Details of bonding type rmsd/Z covalent geometry : bond 0.00466 / 0.20 (10031) covalent geometry : angle 0.66439 / 0.34 (13552) SS BOND : bond 0.00583 / 0.39 ( 5) SS BOND : angle 2.91891 / 1.94 ( 10) hydrogen bonds : bond 0.05207 / 3.44 ( 597) hydrogen bonds : angle 4.02462 / 2.88 ( 1758) link_BETA1-4 : bond 0.00272 / 0.14 ( 2) link_BETA1-4 : angle 1.45649 / 0.77 ( 6) link_NAG-ASN : bond 0.00223 / 0.12 ( 5) link_NAG-ASN : angle 2.92881 / 2.21 ( 15) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 123 time to evaluate : 0.354 Fit side-chains REVERT: A 295 PRO cc_start: 0.8505 (Cg_exo) cc_final: 0.8254 (Cg_endo) REVERT: A 398 MET cc_start: 0.8688 (mtp) cc_final: 0.8325 (mtt) REVERT: A 402 GLU cc_start: 0.8286 (OUTLIER) cc_final: 0.7997 (pt0) REVERT: A 726 GLN cc_start: 0.6954 (OUTLIER) cc_final: 0.6740 (mt0) REVERT: A 728 LYS cc_start: 0.7958 (mtpt) cc_final: 0.7746 (mttm) REVERT: A 1145 CYS cc_start: 0.8440 (m) cc_final: 0.8025 (m) REVERT: A 1242 GLU cc_start: 0.7364 (OUTLIER) cc_final: 0.6731 (pm20) REVERT: A 1315 ASP cc_start: 0.7551 (p0) cc_final: 0.6963 (p0) REVERT: A 1384 MET cc_start: 0.8931 (mtm) cc_final: 0.8567 (mtm) REVERT: A 1466 GLN cc_start: 0.6573 (mt0) cc_final: 0.6029 (mp10) outliers start: 23 outliers final: 12 residues processed: 134 average time/residue: 0.5464 time to fit residues: 78.9494 Evaluate side-chains 134 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 119 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 224 LYS Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain A residue 652 VAL Chi-restraints excluded: chain A residue 690 SER Chi-restraints excluded: chain A residue 726 GLN Chi-restraints excluded: chain A residue 741 LEU Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain A residue 1211 LYS Chi-restraints excluded: chain A residue 1233 LEU Chi-restraints excluded: chain A residue 1242 GLU Chi-restraints excluded: chain A residue 1249 LEU Chi-restraints excluded: chain A residue 1291 PHE Chi-restraints excluded: chain A residue 1681 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 37 optimal weight: 0.9980 chunk 69 optimal weight: 3.9990 chunk 54 optimal weight: 4.9990 chunk 11 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 53 optimal weight: 0.6980 chunk 104 optimal weight: 0.7980 chunk 63 optimal weight: 5.9990 chunk 16 optimal weight: 0.0570 chunk 36 optimal weight: 3.9990 chunk 56 optimal weight: 0.5980 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 789 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.141781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.108394 restraints weight = 25466.497| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 2.75 r_work: 0.3186 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3202 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3202 r_free = 0.3202 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3202 r_free = 0.3202 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (8 function evaluations) r_final: 0.3202 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.2860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10043 Z= 0.118 Angle : 0.596 13.003 13583 Z= 0.295 Chirality : 0.038 0.163 1538 Planarity : 0.004 0.043 1571 Dihedral : 12.896 156.343 1656 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 1.12 % Allowed : 15.87 % Favored : 83.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.90 (0.26), residues: 1117 helix: 2.10 (0.19), residues: 776 sheet: -2.43 (0.87), residues: 20 loop : -0.57 (0.38), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A1250 TYR 0.023 0.002 TYR A 164 PHE 0.016 0.001 PHE A 693 TRP 0.015 0.001 TRP A 191 HIS 0.003 0.001 HIS A 687 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.12 (10031) covalent geometry : angle 0.58835 / 0.29 (13552) SS BOND : bond 0.00203 / 0.11 ( 5) SS BOND : angle 1.93872 / 1.27 ( 10) hydrogen bonds : bond 0.04056 / 2.64 ( 597) hydrogen bonds : angle 3.90785 / 2.79 ( 1758) link_BETA1-4 : bond 0.00436 / 0.22 ( 2) link_BETA1-4 : angle 1.07115 / 0.59 ( 6) link_NAG-ASN : bond 0.00225 / 0.11 ( 5) link_NAG-ASN : angle 2.38012 / 1.72 ( 15) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 121 time to evaluate : 0.369 Fit side-chains REVERT: A 165 THR cc_start: 0.6473 (m) cc_final: 0.6111 (p) REVERT: A 295 PRO cc_start: 0.8440 (Cg_exo) cc_final: 0.8216 (Cg_endo) REVERT: A 398 MET cc_start: 0.8462 (mtp) cc_final: 0.8094 (mtt) REVERT: A 402 GLU cc_start: 0.8157 (tt0) cc_final: 0.7865 (pt0) REVERT: A 668 GLU cc_start: 0.6815 (pt0) cc_final: 0.6494 (tt0) REVERT: A 1145 CYS cc_start: 0.8300 (m) cc_final: 0.7872 (m) REVERT: A 1315 ASP cc_start: 0.7419 (p0) cc_final: 0.6939 (p0) REVERT: A 1384 MET cc_start: 0.8745 (mtm) cc_final: 0.8366 (mtm) outliers start: 11 outliers final: 7 residues processed: 125 average time/residue: 0.5335 time to fit residues: 71.9828 Evaluate side-chains 124 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 117 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 224 LYS Chi-restraints excluded: chain A residue 690 SER Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain A residue 1211 LYS Chi-restraints excluded: chain A residue 1249 LEU Chi-restraints excluded: chain A residue 1291 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 65 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 42 optimal weight: 0.6980 chunk 12 optimal weight: 6.9990 chunk 61 optimal weight: 0.0370 chunk 80 optimal weight: 6.9990 chunk 17 optimal weight: 0.6980 chunk 82 optimal weight: 4.9990 chunk 37 optimal weight: 0.9990 chunk 66 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 overall best weight: 0.6860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 789 ASN A1178 GLN A1489 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.142381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.109164 restraints weight = 21454.728| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 2.50 r_work: 0.3210 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3223 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3223 r_free = 0.3223 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3223 r_free = 0.3223 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3223 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.2907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10043 Z= 0.121 Angle : 0.593 12.555 13583 Z= 0.295 Chirality : 0.038 0.230 1538 Planarity : 0.004 0.044 1571 Dihedral : 12.601 151.825 1656 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 1.02 % Allowed : 16.07 % Favored : 82.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.87 (0.26), residues: 1117 helix: 2.08 (0.19), residues: 785 sheet: -2.40 (1.15), residues: 10 loop : -0.78 (0.36), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 302 TYR 0.024 0.002 TYR A1442 PHE 0.016 0.001 PHE A 693 TRP 0.016 0.001 TRP A 191 HIS 0.002 0.001 HIS A 837 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 (10031) covalent geometry : angle 0.58591 / 0.29 (13552) SS BOND : bond 0.00204 / 0.10 ( 5) SS BOND : angle 2.03471 / 1.33 ( 10) hydrogen bonds : bond 0.03991 / 2.60 ( 597) hydrogen bonds : angle 3.87196 / 2.77 ( 1758) link_BETA1-4 : bond 0.00346 / 0.17 ( 2) link_BETA1-4 : angle 1.11923 / 0.61 ( 6) link_NAG-ASN : bond 0.00169 / 0.08 ( 5) link_NAG-ASN : angle 2.30143 / 1.66 ( 15) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 117 time to evaluate : 0.418 Fit side-chains REVERT: A 165 THR cc_start: 0.6724 (m) cc_final: 0.6363 (p) REVERT: A 398 MET cc_start: 0.8490 (mtp) cc_final: 0.8137 (mtt) REVERT: A 402 GLU cc_start: 0.8227 (tt0) cc_final: 0.7975 (pt0) REVERT: A 712 MET cc_start: 0.6551 (ttp) cc_final: 0.6270 (ttp) REVERT: A 826 ASP cc_start: 0.8652 (t0) cc_final: 0.8448 (t0) REVERT: A 1145 CYS cc_start: 0.8408 (m) cc_final: 0.8003 (m) REVERT: A 1315 ASP cc_start: 0.7419 (p0) cc_final: 0.6873 (p0) REVERT: A 1370 MET cc_start: 0.8775 (tpp) cc_final: 0.8369 (mmp) REVERT: A 1384 MET cc_start: 0.8749 (mtm) cc_final: 0.8387 (mtm) REVERT: A 1466 GLN cc_start: 0.6278 (mt0) cc_final: 0.5853 (mp10) outliers start: 10 outliers final: 8 residues processed: 121 average time/residue: 0.5538 time to fit residues: 72.2135 Evaluate side-chains 125 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 117 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 224 LYS Chi-restraints excluded: chain A residue 652 VAL Chi-restraints excluded: chain A residue 690 SER Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain A residue 1211 LYS Chi-restraints excluded: chain A residue 1249 LEU Chi-restraints excluded: chain A residue 1291 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 3.9990 chunk 111 optimal weight: 6.9990 chunk 97 optimal weight: 0.0000 chunk 94 optimal weight: 4.9990 chunk 33 optimal weight: 0.8980 chunk 98 optimal weight: 1.9990 chunk 90 optimal weight: 0.6980 chunk 88 optimal weight: 0.7980 chunk 24 optimal weight: 0.9990 chunk 17 optimal weight: 6.9990 overall best weight: 0.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 789 ASN A1476 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.143226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.112231 restraints weight = 13971.630| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 1.98 r_work: 0.3267 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3132 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3147 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3147 r_free = 0.3147 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3147 r_free = 0.3147 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3147 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.2964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10043 Z= 0.115 Angle : 0.582 12.251 13583 Z= 0.288 Chirality : 0.038 0.233 1538 Planarity : 0.004 0.044 1571 Dihedral : 12.364 147.415 1656 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 1.22 % Allowed : 16.07 % Favored : 82.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.02 (0.26), residues: 1117 helix: 2.16 (0.19), residues: 781 sheet: -2.43 (0.87), residues: 20 loop : -0.48 (0.38), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 302 TYR 0.027 0.002 TYR A1442 PHE 0.016 0.001 PHE A 693 TRP 0.016 0.001 TRP A 191 HIS 0.003 0.001 HIS A 687 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.12 (10031) covalent geometry : angle 0.57475 / 0.29 (13552) SS BOND : bond 0.00177 / 0.09 ( 5) SS BOND : angle 1.88862 / 1.24 ( 10) hydrogen bonds : bond 0.03853 / 2.51 ( 597) hydrogen bonds : angle 3.84551 / 2.75 ( 1758) link_BETA1-4 : bond 0.00395 / 0.20 ( 2) link_BETA1-4 : angle 1.10897 / 0.61 ( 6) link_NAG-ASN : bond 0.00190 / 0.10 ( 5) link_NAG-ASN : angle 2.23659 / 1.61 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3960.07 seconds wall clock time: 68 minutes 8.95 seconds (4088.95 seconds total)