Starting phenix.real_space_refine on Wed Mar 4 11:11:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6lcp_0872/03_2026/6lcp_0872.cif Found real_map, /net/cci-nas-00/data/ceres_data/6lcp_0872/03_2026/6lcp_0872.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.48 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6lcp_0872/03_2026/6lcp_0872.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6lcp_0872/03_2026/6lcp_0872.map" model { file = "/net/cci-nas-00/data/ceres_data/6lcp_0872/03_2026/6lcp_0872.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6lcp_0872/03_2026/6lcp_0872.cif" } resolution = 3.48 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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: 8 Type Number sf(0) Gaussians P 3 5.49 5 Mg 1 5.21 5 S 63 5.16 5 Be 1 3.05 5 C 7979 2.51 5 N 2058 2.21 5 O 2313 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 97 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12421 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 9082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1140, 9082 Classifications: {'peptide': 1140} Link IDs: {'PTRANS': 46, 'TRANS': 1093} Chain breaks: 3 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 2 Chain: "B" Number of atoms: 3061 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 3061 Classifications: {'peptide': 376} Link IDs: {'PTRANS': 26, 'TRANS': 349} Chain: "C" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {'MAN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "F" 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 111 Unusual residues: {' MG': 1, 'BEF': 1, 'POV': 2} Classifications: {'peptide': 1, 'undetermined': 4} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 52 Planarities with less than four sites: {'POV:plan-1': 2} Unresolved non-hydrogen planarities: 8 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 2.30, per 1000 atoms: 0.19 Number of scatterers: 12421 At special positions: 0 Unit cell: (147.7, 110.775, 128.71, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) S 63 16.00 P 3 15.00 Mg 1 11.99 F 3 9.00 O 2313 8.00 N 2058 7.00 C 7979 6.00 Be 1 4.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B 85 " - pdb=" SG CYS B 139 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Links applied ALPHA1-3 " MAN C 1 " - " MAN C 2 " " BMA E 3 " - " MAN E 4 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG B 501 " - " ASN B 131 " " NAG B 509 " - " ASN B 241 " " NAG D 1 " - " ASN B 189 " " NAG E 1 " - " ASN B 219 " " NAG F 1 " - " ASN B 314 " Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.11 Conformation dependent library (CDL) restraints added in 352.0 milliseconds 3012 Ramachandran restraints generated. 1506 Oldfield, 0 Emsley, 1506 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2860 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 10 sheets defined 44.9% alpha, 11.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.55 Creating SS restraints... Processing helix chain 'A' and resid 122 through 132 removed outlier: 3.674A pdb=" N LYS A 126 " --> pdb=" O SER A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 147 removed outlier: 3.727A pdb=" N PHE A 139 " --> pdb=" O ILE A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 191 Processing helix chain 'A' and resid 332 through 334 No H-bonds generated for 'chain 'A' and resid 332 through 334' Processing helix chain 'A' and resid 359 through 363 removed outlier: 3.896A pdb=" N GLY A 362 " --> pdb=" O ASP A 359 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ALA A 363 " --> pdb=" O PRO A 360 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 359 through 363' Processing helix chain 'A' and resid 440 through 442 No H-bonds generated for 'chain 'A' and resid 440 through 442' Processing helix chain 'A' and resid 484 through 515 Processing helix chain 'A' and resid 519 through 525 removed outlier: 4.070A pdb=" N TRP A 523 " --> pdb=" O ALA A 519 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N PHE A 524 " --> pdb=" O SER A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 532 through 548 Processing helix chain 'A' and resid 549 through 553 Proline residue: A 553 - end of helix Processing helix chain 'A' and resid 554 through 573 removed outlier: 4.377A pdb=" N ILE A 558 " --> pdb=" O ILE A 554 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 578 Processing helix chain 'A' and resid 595 through 599 Processing helix chain 'A' and resid 633 through 643 removed outlier: 4.210A pdb=" N ARG A 643 " --> pdb=" O MET A 639 " (cutoff:3.500A) Processing helix chain 'A' and resid 648 through 672 removed outlier: 3.850A pdb=" N LYS A 652 " --> pdb=" O GLU A 648 " (cutoff:3.500A) Processing helix chain 'A' and resid 687 through 696 Processing helix chain 'A' and resid 699 through 713 removed outlier: 3.762A pdb=" N GLN A 703 " --> pdb=" O GLY A 699 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLN A 704 " --> pdb=" O PRO A 700 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 748 Processing helix chain 'A' and resid 806 through 811 Processing helix chain 'A' and resid 819 through 836 Processing helix chain 'A' and resid 849 through 866 Processing helix chain 'A' and resid 869 through 878 Processing helix chain 'A' and resid 900 through 912 Processing helix chain 'A' and resid 922 through 933 removed outlier: 3.674A pdb=" N ILE A 927 " --> pdb=" O VAL A 923 " (cutoff:3.500A) Processing helix chain 'A' and resid 954 through 973 Processing helix chain 'A' and resid 979 through 984 removed outlier: 4.257A pdb=" N LYS A 983 " --> pdb=" O ASP A 979 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ARG A 984 " --> pdb=" O GLU A 980 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 979 through 984' Processing helix chain 'A' and resid 1002 through 1009 Processing helix chain 'A' and resid 1012 through 1024 removed outlier: 3.508A pdb=" N LYS A1016 " --> pdb=" O SER A1012 " (cutoff:3.500A) Processing helix chain 'A' and resid 1033 through 1048 removed outlier: 3.608A pdb=" N LEU A1048 " --> pdb=" O VAL A1044 " (cutoff:3.500A) Processing helix chain 'A' and resid 1058 through 1068 removed outlier: 3.544A pdb=" N GLU A1067 " --> pdb=" O ALA A1063 " (cutoff:3.500A) Processing helix chain 'A' and resid 1094 through 1103 removed outlier: 4.299A pdb=" N ARG A1098 " --> pdb=" O ARG A1094 " (cutoff:3.500A) Processing helix chain 'A' and resid 1104 through 1135 Processing helix chain 'A' and resid 1147 through 1152 Processing helix chain 'A' and resid 1157 through 1167 removed outlier: 3.952A pdb=" N VAL A1161 " --> pdb=" O THR A1157 " (cutoff:3.500A) Processing helix chain 'A' and resid 1174 through 1179 Processing helix chain 'A' and resid 1180 through 1182 No H-bonds generated for 'chain 'A' and resid 1180 through 1182' Processing helix chain 'A' and resid 1183 through 1188 Processing helix chain 'A' and resid 1195 through 1221 Proline residue: A1215 - end of helix Processing helix chain 'A' and resid 1236 through 1257 Proline residue: A1245 - end of helix Processing helix chain 'A' and resid 1263 through 1284 Processing helix chain 'A' and resid 1295 through 1300 Processing helix chain 'A' and resid 1302 through 1330 removed outlier: 4.254A pdb=" N TRP A1306 " --> pdb=" O GLU A1302 " (cutoff:3.500A) Proline residue: A1313 - end of helix Proline residue: A1319 - end of helix Processing helix chain 'A' and resid 1333 through 1345 removed outlier: 3.653A pdb=" N ILE A1337 " --> pdb=" O TYR A1333 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ARG A1344 " --> pdb=" O GLU A1340 " (cutoff:3.500A) Processing helix chain 'A' and resid 1347 through 1356 Processing helix chain 'B' and resid 49 through 75 removed outlier: 3.605A pdb=" N VAL B 75 " --> pdb=" O LEU B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 89 removed outlier: 4.549A pdb=" N LEU B 86 " --> pdb=" O TYR B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 181 removed outlier: 3.703A pdb=" N LEU B 178 " --> pdb=" O ASN B 174 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ASP B 181 " --> pdb=" O GLN B 177 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 216 removed outlier: 3.717A pdb=" N SER B 216 " --> pdb=" O LEU B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 256 removed outlier: 3.618A pdb=" N LYS B 253 " --> pdb=" O TRP B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 299 Processing helix chain 'B' and resid 334 through 338 Processing helix chain 'B' and resid 356 through 382 Processing sheet with id=AA1, first strand: chain 'A' and resid 86 through 89 Processing sheet with id=AA2, first strand: chain 'A' and resid 327 through 330 removed outlier: 3.961A pdb=" N HIS A 195 " --> pdb=" O ARG A 341 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 377 through 380 Processing sheet with id=AA4, first strand: chain 'A' and resid 587 through 588 removed outlier: 3.902A pdb=" N ILE A 587 " --> pdb=" O ALA A1089 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N SER A1054 " --> pdb=" O VAL A1072 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N ILE A1074 " --> pdb=" O SER A1054 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N GLY A1056 " --> pdb=" O ILE A1074 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N ILE A 603 " --> pdb=" O TRP A 916 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N LEU A 918 " --> pdb=" O ILE A 603 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N SER A 605 " --> pdb=" O LEU A 918 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N LEU A 915 " --> pdb=" O VAL A1027 " (cutoff:3.500A) removed outlier: 8.631A pdb=" N CYS A1029 " --> pdb=" O LEU A 915 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N VAL A 917 " --> pdb=" O CYS A1029 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N TYR A 996 " --> pdb=" O SER A1026 " (cutoff:3.500A) removed outlier: 8.357A pdb=" N LEU A1028 " --> pdb=" O TYR A 996 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N LEU A 998 " --> pdb=" O LEU A1028 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N CYS A1030 " --> pdb=" O LEU A 998 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ILE A1000 " --> pdb=" O CYS A1030 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N ASP A1001 " --> pdb=" O LEU A 945 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 626 through 627 removed outlier: 4.709A pdb=" N VAL A 615 " --> pdb=" O ARG A 896 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N ALA A 892 " --> pdb=" O LYS A 619 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N ALA A 621 " --> pdb=" O GLY A 890 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N GLY A 890 " --> pdb=" O ALA A 621 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N ILE A 623 " --> pdb=" O LEU A 888 " (cutoff:3.500A) removed outlier: 8.666A pdb=" N LEU A 888 " --> pdb=" O ILE A 623 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N LEU A 887 " --> pdb=" O GLU A 845 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N GLU A 845 " --> pdb=" O LEU A 887 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLY A 889 " --> pdb=" O ILE A 843 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N ARG A 793 " --> pdb=" O VAL A 775 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N VAL A 775 " --> pdb=" O ARG A 793 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 720 through 723 Processing sheet with id=AA7, first strand: chain 'A' and resid 753 through 755 removed outlier: 4.199A pdb=" N ASN A 763 " --> pdb=" O LEU A 755 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1260 through 1262 Processing sheet with id=AA9, first strand: chain 'B' and resid 102 through 105 removed outlier: 3.550A pdb=" N ARG B 340 " --> pdb=" O GLU B 160 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N ILE B 153 " --> pdb=" O LYS B 313 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N LYS B 313 " --> pdb=" O ILE B 153 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N PHE B 155 " --> pdb=" O TYR B 311 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N PHE B 307 " --> pdb=" O LEU B 159 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 95 through 96 removed outlier: 3.675A pdb=" N GLU B 95 " --> pdb=" O TRP B 120 " (cutoff:3.500A) 553 hydrogen bonds defined for protein. 1587 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: 1.92 Time building geometry restraints manager: 1.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.28: 2018 1.28 - 1.41: 3213 1.41 - 1.55: 7363 1.55 - 1.68: 11 1.68 - 1.81: 103 Bond restraints: 12708 Sorted by residual: bond pdb=" F3 BEF A2002 " pdb="BE BEF A2002 " ideal model delta sigma weight residual 1.476 1.765 -0.289 2.00e-02 2.50e+03 2.09e+02 bond pdb=" F2 BEF A2002 " pdb="BE BEF A2002 " ideal model delta sigma weight residual 1.476 1.764 -0.288 2.00e-02 2.50e+03 2.07e+02 bond pdb=" F1 BEF A2002 " pdb="BE BEF A2002 " ideal model delta sigma weight residual 1.476 1.761 -0.285 2.00e-02 2.50e+03 2.03e+02 bond pdb=" C ARG A1320 " pdb=" O ARG A1320 " ideal model delta sigma weight residual 1.236 1.144 0.093 1.26e-02 6.30e+03 5.41e+01 bond pdb=" C31 POV A2003 " pdb=" O31 POV A2003 " ideal model delta sigma weight residual 1.327 1.454 -0.127 2.00e-02 2.50e+03 4.04e+01 ... (remaining 12703 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.25: 16982 3.25 - 6.50: 224 6.50 - 9.75: 29 9.75 - 13.00: 8 13.00 - 16.25: 2 Bond angle restraints: 17245 Sorted by residual: angle pdb=" N GLY A 527 " pdb=" CA GLY A 527 " pdb=" C GLY A 527 " ideal model delta sigma weight residual 110.91 127.16 -16.25 1.49e+00 4.50e-01 1.19e+02 angle pdb=" C PRO B 151 " pdb=" N THR B 152 " pdb=" CA THR B 152 " ideal model delta sigma weight residual 121.54 135.35 -13.81 1.91e+00 2.74e-01 5.23e+01 angle pdb=" N ILE B 153 " pdb=" CA ILE B 153 " pdb=" CB ILE B 153 " ideal model delta sigma weight residual 110.82 103.29 7.53 1.11e+00 8.12e-01 4.60e+01 angle pdb=" CA GLY A 527 " pdb=" C GLY A 527 " pdb=" N SER A 528 " ideal model delta sigma weight residual 114.84 107.92 6.92 1.06e+00 8.90e-01 4.27e+01 angle pdb=" C ARG A1320 " pdb=" CA ARG A1320 " pdb=" CB ARG A1320 " ideal model delta sigma weight residual 110.67 99.03 11.64 1.92e+00 2.71e-01 3.67e+01 ... (remaining 17240 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.76: 7394 28.76 - 57.53: 306 57.53 - 86.29: 52 86.29 - 115.06: 14 115.06 - 143.82: 6 Dihedral angle restraints: 7772 sinusoidal: 3341 harmonic: 4431 Sorted by residual: dihedral pdb=" C PRO B 151 " pdb=" N PRO B 151 " pdb=" CA PRO B 151 " pdb=" CB PRO B 151 " ideal model delta harmonic sigma weight residual -120.70 -139.69 18.99 0 2.50e+00 1.60e-01 5.77e+01 dihedral pdb=" N PRO B 151 " pdb=" C PRO B 151 " pdb=" CA PRO B 151 " pdb=" CB PRO B 151 " ideal model delta harmonic sigma weight residual 115.10 133.88 -18.78 0 2.50e+00 1.60e-01 5.64e+01 dihedral pdb=" C THR B 152 " pdb=" N THR B 152 " pdb=" CA THR B 152 " pdb=" CB THR B 152 " ideal model delta harmonic sigma weight residual -122.00 -136.85 14.85 0 2.50e+00 1.60e-01 3.53e+01 ... (remaining 7769 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.230: 1929 0.230 - 0.460: 4 0.460 - 0.690: 2 0.690 - 0.920: 2 0.920 - 1.150: 2 Chirality restraints: 1939 Sorted by residual: chirality pdb=" C1 NAG D 2 " pdb=" O4 NAG D 1 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.63 -0.77 2.00e-02 2.50e+03 1.47e+03 chirality pdb=" C1 NAG E 2 " pdb=" O4 NAG E 1 " pdb=" C2 NAG E 2 " pdb=" O5 NAG E 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.90 -0.50 2.00e-02 2.50e+03 6.25e+02 chirality pdb=" C1 BMA D 3 " pdb=" O4 NAG D 2 " pdb=" C2 BMA D 3 " pdb=" O5 BMA D 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.68 0.28 2.00e-02 2.50e+03 1.92e+02 ... (remaining 1936 not shown) Planarity restraints: 2191 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 314 " -0.098 2.00e-02 2.50e+03 1.05e-01 1.39e+02 pdb=" CG ASN B 314 " 0.039 2.00e-02 2.50e+03 pdb=" OD1 ASN B 314 " 0.020 2.00e-02 2.50e+03 pdb=" ND2 ASN B 314 " 0.167 2.00e-02 2.50e+03 pdb=" C1 NAG F 1 " -0.127 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO B 269 " 0.093 5.00e-02 4.00e+02 1.42e-01 3.22e+01 pdb=" N PRO B 270 " -0.245 5.00e-02 4.00e+02 pdb=" CA PRO B 270 " 0.076 5.00e-02 4.00e+02 pdb=" CD PRO B 270 " 0.077 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR B 152 " 0.022 2.00e-02 2.50e+03 4.47e-02 2.00e+01 pdb=" C THR B 152 " -0.077 2.00e-02 2.50e+03 pdb=" O THR B 152 " 0.030 2.00e-02 2.50e+03 pdb=" N ILE B 153 " 0.025 2.00e-02 2.50e+03 ... (remaining 2188 not shown) Histogram of nonbonded interaction distances: 1.81 - 2.43: 68 2.43 - 3.04: 8278 3.04 - 3.66: 18513 3.66 - 4.28: 28266 4.28 - 4.90: 47365 Nonbonded interactions: 102490 Sorted by model distance: nonbonded pdb=" OD1 ASP A 606 " pdb=" F1 BEF A2002 " model vdw 1.807 2.990 nonbonded pdb=" OD2 ASP A 606 " pdb="MG MG A2001 " model vdw 1.968 2.170 nonbonded pdb=" O ASN A 948 " pdb=" N SER A 950 " model vdw 2.037 3.120 nonbonded pdb=" N ASP B 148 " pdb=" OD1 ASP B 148 " model vdw 2.073 3.120 nonbonded pdb=" OG SER A1289 " pdb=" O PHE A1292 " model vdw 2.073 3.040 ... (remaining 102485 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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 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: 1.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 11.240 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 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 0.736 12723 Z= 0.864 Angle : 1.087 38.492 17283 Z= 0.553 Chirality : 0.068 1.150 1939 Planarity : 0.007 0.142 2186 Dihedral : 17.331 143.820 4909 Min Nonbonded Distance : 1.807 Molprobity Statistics. All-atom Clashscore : 17.95 Ramachandran Plot: Outliers : 0.20 % Allowed : 9.83 % Favored : 89.97 % Rotamer: Outliers : 0.99 % Allowed : 8.72 % Favored : 90.29 % Cbeta Deviations : 0.35 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.12 (0.18), residues: 1506 helix: -1.91 (0.16), residues: 644 sheet: -2.63 (0.32), residues: 209 loop : -3.61 (0.20), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A1320 TYR 0.020 0.002 TYR A1293 PHE 0.028 0.002 PHE A 524 TRP 0.036 0.002 TRP B 120 HIS 0.003 0.001 HIS A 717 Details of bonding type rmsd covalent geometry : bond 0.00888 (12708) covalent geometry : angle 0.97083 (17245) SS BOND : bond 0.00284 ( 1) SS BOND : angle 0.26983 ( 2) hydrogen bonds : bond 0.15135 ( 553) hydrogen bonds : angle 6.72207 ( 1587) Misc. bond : bond 0.58095 ( 2) link_ALPHA1-3 : bond 0.00019 ( 2) link_ALPHA1-3 : angle 0.14172 ( 6) link_BETA1-4 : bond 0.04919 ( 5) link_BETA1-4 : angle 14.65951 ( 15) link_NAG-ASN : bond 0.01868 ( 5) link_NAG-ASN : angle 7.98334 ( 15) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3012 Ramachandran restraints generated. 1506 Oldfield, 0 Emsley, 1506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3012 Ramachandran restraints generated. 1506 Oldfield, 0 Emsley, 1506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 231 time to evaluate : 0.393 Fit side-chains revert: symmetry clash REVERT: A 326 PHE cc_start: 0.7832 (m-80) cc_final: 0.6867 (m-80) REVERT: A 399 GLN cc_start: 0.7329 (tt0) cc_final: 0.6768 (tp40) REVERT: A 441 ILE cc_start: 0.8437 (mm) cc_final: 0.8143 (mm) REVERT: A 476 ILE cc_start: 0.7330 (OUTLIER) cc_final: 0.7095 (mp) REVERT: A 501 ILE cc_start: 0.8193 (mm) cc_final: 0.7894 (mt) REVERT: A 788 MET cc_start: 0.7634 (tmm) cc_final: 0.7410 (tmm) REVERT: A 854 ARG cc_start: 0.6902 (ppt170) cc_final: 0.6696 (ppt170) REVERT: A 924 GLU cc_start: 0.5975 (mm-30) cc_final: 0.5700 (mm-30) REVERT: A 1145 GLU cc_start: 0.7145 (tm-30) cc_final: 0.6766 (tm-30) REVERT: A 1151 MET cc_start: 0.7816 (mtp) cc_final: 0.7566 (mtp) REVERT: B 135 ASN cc_start: 0.8142 (p0) cc_final: 0.7736 (p0) REVERT: B 270 PRO cc_start: 0.8577 (Cg_endo) cc_final: 0.8329 (Cg_exo) outliers start: 13 outliers final: 8 residues processed: 244 average time/residue: 0.1296 time to fit residues: 43.3813 Evaluate side-chains 180 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 171 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 ASN Chi-restraints excluded: chain A residue 476 ILE Chi-restraints excluded: chain A residue 478 PRO Chi-restraints excluded: chain A residue 592 ASN Chi-restraints excluded: chain A residue 950 SER Chi-restraints excluded: chain A residue 955 GLU Chi-restraints excluded: chain A residue 1060 ASN Chi-restraints excluded: chain B residue 148 ASP Chi-restraints excluded: chain B residue 153 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 0.0020 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 2.9990 overall best weight: 0.9594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 127 ASN A 344 ASN A 370 ASN A 408 GLN A 510 ASN A 613 GLN ** A 614 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 624 ASN A 646 ASN A 717 HIS A 990 ASN A1015 GLN A1023 GLN A1046 ASN A1251 ASN ** B 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 171 ASN ** B 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 397 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.144791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.113912 restraints weight = 16582.197| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 1.72 r_work: 0.3254 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3127 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.1404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 12723 Z= 0.187 Angle : 0.759 8.626 17283 Z= 0.387 Chirality : 0.046 0.183 1939 Planarity : 0.006 0.096 2186 Dihedral : 13.752 158.421 2031 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.30 % Favored : 92.56 % Rotamer: Outliers : 1.91 % Allowed : 15.21 % Favored : 82.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.94 (0.20), residues: 1506 helix: -0.78 (0.18), residues: 667 sheet: -2.17 (0.33), residues: 211 loop : -3.18 (0.22), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A1320 TYR 0.022 0.002 TYR A1293 PHE 0.034 0.002 PHE A 709 TRP 0.021 0.001 TRP B 120 HIS 0.004 0.001 HIS A 673 Details of bonding type rmsd covalent geometry : bond 0.00431 (12708) covalent geometry : angle 0.74438 (17245) SS BOND : bond 0.01075 ( 1) SS BOND : angle 0.66885 ( 2) hydrogen bonds : bond 0.05798 ( 553) hydrogen bonds : angle 5.40674 ( 1587) Misc. bond : bond 0.00233 ( 2) link_ALPHA1-3 : bond 0.01033 ( 2) link_ALPHA1-3 : angle 2.29498 ( 6) link_BETA1-4 : bond 0.00653 ( 5) link_BETA1-4 : angle 2.83474 ( 15) link_NAG-ASN : bond 0.00585 ( 5) link_NAG-ASN : angle 4.10428 ( 15) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3012 Ramachandran restraints generated. 1506 Oldfield, 0 Emsley, 1506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3012 Ramachandran restraints generated. 1506 Oldfield, 0 Emsley, 1506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 212 time to evaluate : 0.324 Fit side-chains revert: symmetry clash REVERT: A 164 LEU cc_start: 0.7938 (mm) cc_final: 0.7545 (tp) REVERT: A 326 PHE cc_start: 0.7539 (m-80) cc_final: 0.6902 (m-80) REVERT: A 501 ILE cc_start: 0.8520 (mm) cc_final: 0.8267 (mt) REVERT: A 709 PHE cc_start: 0.8604 (t80) cc_final: 0.8335 (t80) REVERT: A 779 ILE cc_start: 0.8543 (OUTLIER) cc_final: 0.8293 (pt) REVERT: A 788 MET cc_start: 0.8185 (tmm) cc_final: 0.7860 (tmm) REVERT: A 924 GLU cc_start: 0.6114 (mm-30) cc_final: 0.5757 (mm-30) REVERT: A 963 GLU cc_start: 0.8069 (tm-30) cc_final: 0.7814 (tm-30) REVERT: A 1145 GLU cc_start: 0.7837 (tm-30) cc_final: 0.7276 (tm-30) REVERT: A 1151 MET cc_start: 0.8278 (mtp) cc_final: 0.8065 (mtp) REVERT: A 1167 LEU cc_start: 0.9238 (OUTLIER) cc_final: 0.9006 (pp) REVERT: B 43 CYS cc_start: 0.8928 (p) cc_final: 0.8630 (p) REVERT: B 121 LYS cc_start: 0.8647 (OUTLIER) cc_final: 0.8381 (ptmt) REVERT: B 135 ASN cc_start: 0.8594 (p0) cc_final: 0.8137 (p0) REVERT: B 270 PRO cc_start: 0.8613 (Cg_endo) cc_final: 0.8328 (Cg_exo) outliers start: 25 outliers final: 13 residues processed: 231 average time/residue: 0.1141 time to fit residues: 37.3792 Evaluate side-chains 198 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 182 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 554 ILE Chi-restraints excluded: chain A residue 592 ASN Chi-restraints excluded: chain A residue 645 ILE Chi-restraints excluded: chain A residue 647 VAL Chi-restraints excluded: chain A residue 753 THR Chi-restraints excluded: chain A residue 766 VAL Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 918 LEU Chi-restraints excluded: chain A residue 939 ASP Chi-restraints excluded: chain A residue 954 THR Chi-restraints excluded: chain A residue 1167 LEU Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 93 ASP Chi-restraints excluded: chain B residue 121 LYS Chi-restraints excluded: chain B residue 129 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 1 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 chunk 111 optimal weight: 1.9990 chunk 55 optimal weight: 0.7980 chunk 18 optimal weight: 10.0000 chunk 71 optimal weight: 0.7980 chunk 133 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 119 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 399 GLN ** A 614 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 928 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.143408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.112609 restraints weight = 16742.016| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 1.77 r_work: 0.3217 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3084 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.1714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 12723 Z= 0.208 Angle : 0.744 9.627 17283 Z= 0.380 Chirality : 0.046 0.175 1939 Planarity : 0.006 0.093 2186 Dihedral : 12.860 154.035 2014 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.50 % Favored : 92.36 % Rotamer: Outliers : 2.75 % Allowed : 17.89 % Favored : 79.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.50 (0.20), residues: 1506 helix: -0.34 (0.19), residues: 670 sheet: -2.01 (0.33), residues: 211 loop : -3.02 (0.23), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 858 TYR 0.022 0.002 TYR A 853 PHE 0.030 0.002 PHE A 781 TRP 0.018 0.001 TRP B 120 HIS 0.003 0.001 HIS A 717 Details of bonding type rmsd covalent geometry : bond 0.00490 (12708) covalent geometry : angle 0.73140 (17245) SS BOND : bond 0.00777 ( 1) SS BOND : angle 0.80836 ( 2) hydrogen bonds : bond 0.05654 ( 553) hydrogen bonds : angle 5.26350 ( 1587) Misc. bond : bond 0.00302 ( 2) link_ALPHA1-3 : bond 0.00923 ( 2) link_ALPHA1-3 : angle 2.14049 ( 6) link_BETA1-4 : bond 0.00612 ( 5) link_BETA1-4 : angle 2.72559 ( 15) link_NAG-ASN : bond 0.00419 ( 5) link_NAG-ASN : angle 3.66786 ( 15) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3012 Ramachandran restraints generated. 1506 Oldfield, 0 Emsley, 1506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3012 Ramachandran restraints generated. 1506 Oldfield, 0 Emsley, 1506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 196 time to evaluate : 0.433 Fit side-chains revert: symmetry clash REVERT: A 164 LEU cc_start: 0.8022 (mm) cc_final: 0.7575 (tp) REVERT: A 326 PHE cc_start: 0.7449 (m-80) cc_final: 0.6821 (m-80) REVERT: A 501 ILE cc_start: 0.8573 (mm) cc_final: 0.8334 (mt) REVERT: A 648 GLU cc_start: 0.8085 (tp30) cc_final: 0.7855 (tp30) REVERT: A 709 PHE cc_start: 0.8671 (t80) cc_final: 0.8338 (t80) REVERT: A 713 LEU cc_start: 0.8622 (OUTLIER) cc_final: 0.8056 (mp) REVERT: A 779 ILE cc_start: 0.8636 (OUTLIER) cc_final: 0.8401 (pt) REVERT: A 788 MET cc_start: 0.8220 (tmm) cc_final: 0.7958 (tmm) REVERT: A 858 ARG cc_start: 0.8151 (mtm110) cc_final: 0.7920 (ptp90) REVERT: A 924 GLU cc_start: 0.6202 (mm-30) cc_final: 0.5953 (mm-30) REVERT: A 963 GLU cc_start: 0.8219 (tm-30) cc_final: 0.7911 (tm-30) REVERT: A 1145 GLU cc_start: 0.7956 (tm-30) cc_final: 0.7548 (tm-30) REVERT: A 1151 MET cc_start: 0.8338 (mtp) cc_final: 0.8127 (mtp) REVERT: A 1167 LEU cc_start: 0.9269 (OUTLIER) cc_final: 0.9019 (pp) REVERT: B 43 CYS cc_start: 0.8875 (p) cc_final: 0.8525 (p) REVERT: B 121 LYS cc_start: 0.8694 (OUTLIER) cc_final: 0.8424 (ptmt) REVERT: B 135 ASN cc_start: 0.8708 (p0) cc_final: 0.8230 (p0) outliers start: 36 outliers final: 23 residues processed: 220 average time/residue: 0.1178 time to fit residues: 36.8335 Evaluate side-chains 205 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 178 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 338 ASP Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 412 TYR Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain A residue 502 MET Chi-restraints excluded: chain A residue 508 ILE Chi-restraints excluded: chain A residue 526 TYR Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 554 ILE Chi-restraints excluded: chain A residue 592 ASN Chi-restraints excluded: chain A residue 645 ILE Chi-restraints excluded: chain A residue 647 VAL Chi-restraints excluded: chain A residue 713 LEU Chi-restraints excluded: chain A residue 753 THR Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 918 LEU Chi-restraints excluded: chain A residue 939 ASP Chi-restraints excluded: chain A residue 954 THR Chi-restraints excluded: chain A residue 1019 LEU Chi-restraints excluded: chain A residue 1062 VAL Chi-restraints excluded: chain A residue 1167 LEU Chi-restraints excluded: chain A residue 1307 MET Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 93 ASP Chi-restraints excluded: chain B residue 121 LYS Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 327 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 96 optimal weight: 1.9990 chunk 136 optimal weight: 0.8980 chunk 131 optimal weight: 0.9980 chunk 101 optimal weight: 0.7980 chunk 114 optimal weight: 0.5980 chunk 148 optimal weight: 1.9990 chunk 112 optimal weight: 0.5980 chunk 18 optimal weight: 0.6980 chunk 145 optimal weight: 0.5980 chunk 75 optimal weight: 2.9990 chunk 123 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 ASN A 399 GLN A 491 ASN ** A 614 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 928 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 271 ASN B 331 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.146764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.115130 restraints weight = 16588.054| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 1.90 r_work: 0.3278 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3149 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.2044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 12723 Z= 0.149 Angle : 0.684 8.528 17283 Z= 0.349 Chirality : 0.045 0.219 1939 Planarity : 0.005 0.099 2186 Dihedral : 11.852 151.078 2014 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.17 % Favored : 92.70 % Rotamer: Outliers : 3.82 % Allowed : 18.50 % Favored : 77.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.39 % 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 (0.21), residues: 1506 helix: 0.10 (0.20), residues: 662 sheet: -1.75 (0.33), residues: 224 loop : -2.81 (0.23), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 114 TYR 0.021 0.002 TYR A 853 PHE 0.031 0.001 PHE A 781 TRP 0.015 0.001 TRP B 120 HIS 0.002 0.000 HIS A 673 Details of bonding type rmsd covalent geometry : bond 0.00338 (12708) covalent geometry : angle 0.67362 (17245) SS BOND : bond 0.00366 ( 1) SS BOND : angle 0.73422 ( 2) hydrogen bonds : bond 0.05019 ( 553) hydrogen bonds : angle 5.05425 ( 1587) Misc. bond : bond 0.00716 ( 2) link_ALPHA1-3 : bond 0.00944 ( 2) link_ALPHA1-3 : angle 2.05120 ( 6) link_BETA1-4 : bond 0.00758 ( 5) link_BETA1-4 : angle 2.55222 ( 15) link_NAG-ASN : bond 0.00357 ( 5) link_NAG-ASN : angle 3.12516 ( 15) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3012 Ramachandran restraints generated. 1506 Oldfield, 0 Emsley, 1506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3012 Ramachandran restraints generated. 1506 Oldfield, 0 Emsley, 1506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 210 time to evaluate : 0.430 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 164 LEU cc_start: 0.7953 (OUTLIER) cc_final: 0.7527 (tp) REVERT: A 181 ARG cc_start: 0.6794 (mtt180) cc_final: 0.5759 (mmp80) REVERT: A 326 PHE cc_start: 0.7495 (m-80) cc_final: 0.7037 (m-80) REVERT: A 501 ILE cc_start: 0.8548 (mm) cc_final: 0.8287 (mt) REVERT: A 709 PHE cc_start: 0.8636 (t80) cc_final: 0.8217 (t80) REVERT: A 713 LEU cc_start: 0.8521 (OUTLIER) cc_final: 0.7909 (mp) REVERT: A 715 LEU cc_start: 0.8556 (mt) cc_final: 0.8353 (mt) REVERT: A 788 MET cc_start: 0.8250 (tmm) cc_final: 0.8033 (tmm) REVERT: A 924 GLU cc_start: 0.6107 (mm-30) cc_final: 0.5767 (mm-30) REVERT: A 963 GLU cc_start: 0.8126 (tm-30) cc_final: 0.7798 (tm-30) REVERT: A 974 ASN cc_start: 0.8772 (t0) cc_final: 0.8558 (t0) REVERT: A 1145 GLU cc_start: 0.7854 (tm-30) cc_final: 0.7449 (tm-30) REVERT: A 1151 MET cc_start: 0.8296 (mtp) cc_final: 0.8090 (mtp) REVERT: A 1167 LEU cc_start: 0.9182 (OUTLIER) cc_final: 0.8943 (pp) REVERT: A 1183 TYR cc_start: 0.8790 (t80) cc_final: 0.8552 (t80) REVERT: B 121 LYS cc_start: 0.8623 (OUTLIER) cc_final: 0.8382 (ptmt) REVERT: B 135 ASN cc_start: 0.8687 (p0) cc_final: 0.8300 (p0) outliers start: 50 outliers final: 27 residues processed: 243 average time/residue: 0.1197 time to fit residues: 41.3292 Evaluate side-chains 225 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 194 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 338 ASP Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 376 ASN Chi-restraints excluded: chain A residue 413 LYS Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 526 TYR Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 592 ASN Chi-restraints excluded: chain A residue 645 ILE Chi-restraints excluded: chain A residue 647 VAL Chi-restraints excluded: chain A residue 713 LEU Chi-restraints excluded: chain A residue 753 THR Chi-restraints excluded: chain A residue 918 LEU Chi-restraints excluded: chain A residue 939 ASP Chi-restraints excluded: chain A residue 954 THR Chi-restraints excluded: chain A residue 1019 LEU Chi-restraints excluded: chain A residue 1050 VAL Chi-restraints excluded: chain A residue 1146 TYR Chi-restraints excluded: chain A residue 1167 LEU Chi-restraints excluded: chain A residue 1172 SER Chi-restraints excluded: chain A residue 1333 TYR Chi-restraints excluded: chain B residue 93 ASP Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 121 LYS Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 299 MET Chi-restraints excluded: chain B residue 300 MET Chi-restraints excluded: chain B residue 344 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 115 optimal weight: 2.9990 chunk 99 optimal weight: 0.7980 chunk 47 optimal weight: 0.9980 chunk 145 optimal weight: 1.9990 chunk 56 optimal weight: 5.9990 chunk 104 optimal weight: 0.9990 chunk 107 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 71 optimal weight: 0.0980 chunk 29 optimal weight: 2.9990 chunk 93 optimal weight: 3.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 399 GLN ** A 614 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 928 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 164 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.145217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.113654 restraints weight = 16824.594| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 1.93 r_work: 0.3262 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3133 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.2186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 12723 Z= 0.173 Angle : 0.704 9.278 17283 Z= 0.359 Chirality : 0.046 0.201 1939 Planarity : 0.005 0.109 2186 Dihedral : 11.141 149.472 2014 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.30 % Favored : 92.56 % Rotamer: Outliers : 3.82 % Allowed : 21.02 % Favored : 75.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.39 % 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 (0.21), residues: 1506 helix: 0.25 (0.20), residues: 664 sheet: -1.62 (0.33), residues: 225 loop : -2.72 (0.23), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 114 TYR 0.020 0.002 TYR A1293 PHE 0.025 0.002 PHE A 781 TRP 0.014 0.001 TRP B 120 HIS 0.002 0.001 HIS A 673 Details of bonding type rmsd covalent geometry : bond 0.00400 (12708) covalent geometry : angle 0.69463 (17245) SS BOND : bond 0.00723 ( 1) SS BOND : angle 0.70874 ( 2) hydrogen bonds : bond 0.05122 ( 553) hydrogen bonds : angle 5.00409 ( 1587) Misc. bond : bond 0.00185 ( 2) link_ALPHA1-3 : bond 0.00870 ( 2) link_ALPHA1-3 : angle 2.04895 ( 6) link_BETA1-4 : bond 0.00618 ( 5) link_BETA1-4 : angle 2.49125 ( 15) link_NAG-ASN : bond 0.00313 ( 5) link_NAG-ASN : angle 3.01557 ( 15) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3012 Ramachandran restraints generated. 1506 Oldfield, 0 Emsley, 1506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3012 Ramachandran restraints generated. 1506 Oldfield, 0 Emsley, 1506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 208 time to evaluate : 0.452 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 164 LEU cc_start: 0.7971 (OUTLIER) cc_final: 0.7516 (tp) REVERT: A 173 ILE cc_start: 0.8633 (mm) cc_final: 0.8305 (mp) REVERT: A 181 ARG cc_start: 0.6814 (mtt180) cc_final: 0.5729 (mmp80) REVERT: A 326 PHE cc_start: 0.7255 (m-80) cc_final: 0.6701 (m-80) REVERT: A 501 ILE cc_start: 0.8551 (mm) cc_final: 0.8282 (mt) REVERT: A 709 PHE cc_start: 0.8626 (t80) cc_final: 0.8179 (t80) REVERT: A 713 LEU cc_start: 0.8522 (OUTLIER) cc_final: 0.7917 (mp) REVERT: A 788 MET cc_start: 0.8171 (tmm) cc_final: 0.7966 (tmm) REVERT: A 854 ARG cc_start: 0.7768 (ptm-80) cc_final: 0.7464 (ppt170) REVERT: A 924 GLU cc_start: 0.6201 (mm-30) cc_final: 0.5883 (mm-30) REVERT: A 963 GLU cc_start: 0.8202 (tm-30) cc_final: 0.7871 (tm-30) REVERT: A 974 ASN cc_start: 0.8762 (t0) cc_final: 0.8546 (t0) REVERT: A 1145 GLU cc_start: 0.7892 (tm-30) cc_final: 0.7513 (tm-30) REVERT: A 1167 LEU cc_start: 0.9203 (OUTLIER) cc_final: 0.8955 (pp) REVERT: B 135 ASN cc_start: 0.8745 (p0) cc_final: 0.8332 (p0) outliers start: 50 outliers final: 37 residues processed: 241 average time/residue: 0.1186 time to fit residues: 40.3646 Evaluate side-chains 229 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 189 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 338 ASP Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 376 ASN Chi-restraints excluded: chain A residue 412 TYR Chi-restraints excluded: chain A residue 413 LYS Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 502 MET Chi-restraints excluded: chain A residue 526 TYR Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 554 ILE Chi-restraints excluded: chain A residue 592 ASN Chi-restraints excluded: chain A residue 645 ILE Chi-restraints excluded: chain A residue 647 VAL Chi-restraints excluded: chain A residue 713 LEU Chi-restraints excluded: chain A residue 753 THR Chi-restraints excluded: chain A residue 918 LEU Chi-restraints excluded: chain A residue 939 ASP Chi-restraints excluded: chain A residue 954 THR Chi-restraints excluded: chain A residue 1019 LEU Chi-restraints excluded: chain A residue 1050 VAL Chi-restraints excluded: chain A residue 1146 TYR Chi-restraints excluded: chain A residue 1167 LEU Chi-restraints excluded: chain A residue 1172 SER Chi-restraints excluded: chain A residue 1292 PHE Chi-restraints excluded: chain A residue 1333 TYR Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 93 ASP Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 299 MET Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 351 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 32 optimal weight: 0.9980 chunk 88 optimal weight: 0.5980 chunk 35 optimal weight: 0.7980 chunk 92 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 73 optimal weight: 4.9990 chunk 145 optimal weight: 0.4980 chunk 77 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 47 optimal weight: 0.1980 chunk 133 optimal weight: 0.8980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 614 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 928 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1244 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.147640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.116148 restraints weight = 16634.455| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 1.88 r_work: 0.3290 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3160 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.2427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 12723 Z= 0.143 Angle : 0.675 8.408 17283 Z= 0.344 Chirality : 0.044 0.180 1939 Planarity : 0.006 0.128 2186 Dihedral : 10.502 148.603 2014 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.84 % Favored : 93.03 % Rotamer: Outliers : 3.67 % Allowed : 21.41 % Favored : 74.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.39 % 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: -1.57 (0.21), residues: 1506 helix: 0.48 (0.20), residues: 656 sheet: -1.41 (0.34), residues: 225 loop : -2.61 (0.23), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 858 TYR 0.029 0.002 TYR A 853 PHE 0.030 0.001 PHE A 781 TRP 0.013 0.001 TRP B 120 HIS 0.002 0.000 HIS A 673 Details of bonding type rmsd covalent geometry : bond 0.00322 (12708) covalent geometry : angle 0.66631 (17245) SS BOND : bond 0.00174 ( 1) SS BOND : angle 0.72057 ( 2) hydrogen bonds : bond 0.04774 ( 553) hydrogen bonds : angle 4.90167 ( 1587) Misc. bond : bond 0.00089 ( 2) link_ALPHA1-3 : bond 0.00981 ( 2) link_ALPHA1-3 : angle 1.98494 ( 6) link_BETA1-4 : bond 0.00584 ( 5) link_BETA1-4 : angle 2.31967 ( 15) link_NAG-ASN : bond 0.00280 ( 5) link_NAG-ASN : angle 2.74572 ( 15) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3012 Ramachandran restraints generated. 1506 Oldfield, 0 Emsley, 1506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3012 Ramachandran restraints generated. 1506 Oldfield, 0 Emsley, 1506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 212 time to evaluate : 0.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 164 LEU cc_start: 0.7938 (OUTLIER) cc_final: 0.7519 (tp) REVERT: A 173 ILE cc_start: 0.8620 (mm) cc_final: 0.8361 (mp) REVERT: A 181 ARG cc_start: 0.6695 (mtt180) cc_final: 0.5756 (mmp80) REVERT: A 326 PHE cc_start: 0.7224 (m-80) cc_final: 0.6797 (m-80) REVERT: A 471 MET cc_start: 0.7318 (mmt) cc_final: 0.7104 (mmt) REVERT: A 501 ILE cc_start: 0.8538 (mm) cc_final: 0.8261 (mt) REVERT: A 682 ASP cc_start: 0.8393 (t70) cc_final: 0.7967 (t0) REVERT: A 709 PHE cc_start: 0.8634 (t80) cc_final: 0.8183 (t80) REVERT: A 713 LEU cc_start: 0.8472 (OUTLIER) cc_final: 0.7880 (mp) REVERT: A 736 GLN cc_start: 0.7752 (tt0) cc_final: 0.7424 (tm-30) REVERT: A 847 GLU cc_start: 0.7728 (tm-30) cc_final: 0.7385 (tm-30) REVERT: A 853 TYR cc_start: 0.8143 (t80) cc_final: 0.7830 (t80) REVERT: A 857 ARG cc_start: 0.7393 (mmm-85) cc_final: 0.7153 (tpp-160) REVERT: A 924 GLU cc_start: 0.6155 (mm-30) cc_final: 0.5860 (mm-30) REVERT: A 963 GLU cc_start: 0.8233 (tm-30) cc_final: 0.7869 (tm-30) REVERT: A 974 ASN cc_start: 0.8766 (t0) cc_final: 0.8539 (t0) REVERT: A 1145 GLU cc_start: 0.7906 (OUTLIER) cc_final: 0.7485 (tm-30) REVERT: A 1167 LEU cc_start: 0.9165 (OUTLIER) cc_final: 0.8950 (pp) REVERT: A 1183 TYR cc_start: 0.8830 (t80) cc_final: 0.8593 (t80) REVERT: B 84 ASP cc_start: 0.7791 (m-30) cc_final: 0.6916 (t70) REVERT: B 135 ASN cc_start: 0.8738 (p0) cc_final: 0.8325 (p0) outliers start: 48 outliers final: 35 residues processed: 241 average time/residue: 0.1108 time to fit residues: 37.8411 Evaluate side-chains 231 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 192 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 338 ASP Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 376 ASN Chi-restraints excluded: chain A residue 412 TYR Chi-restraints excluded: chain A residue 413 LYS Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 502 MET Chi-restraints excluded: chain A residue 526 TYR Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 554 ILE Chi-restraints excluded: chain A residue 592 ASN Chi-restraints excluded: chain A residue 645 ILE Chi-restraints excluded: chain A residue 713 LEU Chi-restraints excluded: chain A residue 753 THR Chi-restraints excluded: chain A residue 762 ILE Chi-restraints excluded: chain A residue 918 LEU Chi-restraints excluded: chain A residue 1050 VAL Chi-restraints excluded: chain A residue 1062 VAL Chi-restraints excluded: chain A residue 1120 TYR Chi-restraints excluded: chain A residue 1134 CYS Chi-restraints excluded: chain A residue 1145 GLU Chi-restraints excluded: chain A residue 1146 TYR Chi-restraints excluded: chain A residue 1167 LEU Chi-restraints excluded: chain A residue 1172 SER Chi-restraints excluded: chain A residue 1292 PHE Chi-restraints excluded: chain A residue 1333 TYR Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 299 MET Chi-restraints excluded: chain B residue 300 MET Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 351 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 89 optimal weight: 2.9990 chunk 36 optimal weight: 0.6980 chunk 70 optimal weight: 0.9990 chunk 44 optimal weight: 0.7980 chunk 100 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 141 optimal weight: 0.0870 chunk 13 optimal weight: 4.9990 chunk 140 optimal weight: 0.0970 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 614 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 928 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 331 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.147924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.115521 restraints weight = 16429.793| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 1.86 r_work: 0.3294 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3162 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.2615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 12723 Z= 0.136 Angle : 0.664 9.421 17283 Z= 0.337 Chirality : 0.044 0.199 1939 Planarity : 0.005 0.111 2186 Dihedral : 9.938 149.989 2014 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.71 % Favored : 93.16 % Rotamer: Outliers : 3.75 % Allowed : 22.02 % Favored : 74.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.39 % 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: -1.36 (0.21), residues: 1506 helix: 0.60 (0.20), residues: 660 sheet: -1.24 (0.35), residues: 220 loop : -2.46 (0.23), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 858 TYR 0.019 0.001 TYR A1146 PHE 0.030 0.001 PHE A 781 TRP 0.013 0.001 TRP B 120 HIS 0.002 0.000 HIS A 673 Details of bonding type rmsd covalent geometry : bond 0.00304 (12708) covalent geometry : angle 0.65691 (17245) SS BOND : bond 0.00033 ( 1) SS BOND : angle 0.75456 ( 2) hydrogen bonds : bond 0.04602 ( 553) hydrogen bonds : angle 4.81547 ( 1587) Misc. bond : bond 0.00281 ( 2) link_ALPHA1-3 : bond 0.00995 ( 2) link_ALPHA1-3 : angle 1.90803 ( 6) link_BETA1-4 : bond 0.00498 ( 5) link_BETA1-4 : angle 1.98100 ( 15) link_NAG-ASN : bond 0.00279 ( 5) link_NAG-ASN : angle 2.61399 ( 15) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3012 Ramachandran restraints generated. 1506 Oldfield, 0 Emsley, 1506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3012 Ramachandran restraints generated. 1506 Oldfield, 0 Emsley, 1506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 217 time to evaluate : 0.452 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 164 LEU cc_start: 0.7955 (OUTLIER) cc_final: 0.7556 (tp) REVERT: A 173 ILE cc_start: 0.8658 (mm) cc_final: 0.8397 (mp) REVERT: A 181 ARG cc_start: 0.6585 (mtt180) cc_final: 0.5755 (mmp80) REVERT: A 326 PHE cc_start: 0.7174 (m-80) cc_final: 0.6681 (m-80) REVERT: A 501 ILE cc_start: 0.8499 (mm) cc_final: 0.8236 (mt) REVERT: A 682 ASP cc_start: 0.8349 (t70) cc_final: 0.7941 (t0) REVERT: A 709 PHE cc_start: 0.8635 (t80) cc_final: 0.8167 (t80) REVERT: A 713 LEU cc_start: 0.8431 (OUTLIER) cc_final: 0.7820 (mp) REVERT: A 736 GLN cc_start: 0.7758 (tt0) cc_final: 0.7421 (tm-30) REVERT: A 757 MET cc_start: 0.7819 (mmt) cc_final: 0.7585 (mpp) REVERT: A 853 TYR cc_start: 0.8089 (t80) cc_final: 0.7855 (t80) REVERT: A 854 ARG cc_start: 0.7561 (ptm-80) cc_final: 0.7092 (ppt170) REVERT: A 857 ARG cc_start: 0.7461 (mmm-85) cc_final: 0.7175 (tpp-160) REVERT: A 924 GLU cc_start: 0.6115 (mm-30) cc_final: 0.5643 (mm-30) REVERT: A 963 GLU cc_start: 0.8259 (tm-30) cc_final: 0.7888 (tm-30) REVERT: A 974 ASN cc_start: 0.8838 (t0) cc_final: 0.8588 (t0) REVERT: A 1145 GLU cc_start: 0.7980 (OUTLIER) cc_final: 0.7548 (tm-30) REVERT: A 1151 MET cc_start: 0.8063 (mtp) cc_final: 0.7826 (mtm) REVERT: A 1167 LEU cc_start: 0.9162 (OUTLIER) cc_final: 0.8942 (pp) REVERT: B 84 ASP cc_start: 0.7807 (m-30) cc_final: 0.6969 (t70) REVERT: B 135 ASN cc_start: 0.8694 (p0) cc_final: 0.8316 (p0) REVERT: B 238 ARG cc_start: 0.7981 (mmm160) cc_final: 0.7621 (mmm-85) outliers start: 49 outliers final: 32 residues processed: 246 average time/residue: 0.1111 time to fit residues: 38.8007 Evaluate side-chains 235 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 199 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 338 ASP Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 376 ASN Chi-restraints excluded: chain A residue 413 LYS Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 502 MET Chi-restraints excluded: chain A residue 526 TYR Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 554 ILE Chi-restraints excluded: chain A residue 645 ILE Chi-restraints excluded: chain A residue 647 VAL Chi-restraints excluded: chain A residue 713 LEU Chi-restraints excluded: chain A residue 753 THR Chi-restraints excluded: chain A residue 918 LEU Chi-restraints excluded: chain A residue 1050 VAL Chi-restraints excluded: chain A residue 1120 TYR Chi-restraints excluded: chain A residue 1134 CYS Chi-restraints excluded: chain A residue 1145 GLU Chi-restraints excluded: chain A residue 1146 TYR Chi-restraints excluded: chain A residue 1167 LEU Chi-restraints excluded: chain A residue 1172 SER Chi-restraints excluded: chain A residue 1333 TYR Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 299 MET Chi-restraints excluded: chain B residue 300 MET Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 351 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 51 optimal weight: 0.9990 chunk 70 optimal weight: 0.7980 chunk 124 optimal weight: 0.0870 chunk 8 optimal weight: 1.9990 chunk 100 optimal weight: 0.7980 chunk 45 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 chunk 121 optimal weight: 0.8980 chunk 83 optimal weight: 2.9990 chunk 50 optimal weight: 4.9990 chunk 113 optimal weight: 5.9990 overall best weight: 0.7160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 614 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 928 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1298 GLN ** 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 = 0.3798 r_free = 0.3798 target = 0.147170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.114840 restraints weight = 16409.742| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 1.85 r_work: 0.3285 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3156 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.2695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 12723 Z= 0.148 Angle : 0.680 9.889 17283 Z= 0.345 Chirality : 0.044 0.189 1939 Planarity : 0.005 0.090 2186 Dihedral : 9.605 151.680 2012 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.57 % Favored : 93.29 % Rotamer: Outliers : 2.98 % Allowed : 23.01 % Favored : 74.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.39 % 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: -1.28 (0.21), residues: 1506 helix: 0.62 (0.20), residues: 669 sheet: -1.17 (0.34), residues: 220 loop : -2.42 (0.24), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 854 TYR 0.020 0.001 TYR A1146 PHE 0.029 0.001 PHE A 781 TRP 0.013 0.001 TRP B 120 HIS 0.002 0.000 HIS A 673 Details of bonding type rmsd covalent geometry : bond 0.00340 (12708) covalent geometry : angle 0.67334 (17245) SS BOND : bond 0.00109 ( 1) SS BOND : angle 0.70937 ( 2) hydrogen bonds : bond 0.04718 ( 553) hydrogen bonds : angle 4.80673 ( 1587) Misc. bond : bond 0.00134 ( 2) link_ALPHA1-3 : bond 0.01003 ( 2) link_ALPHA1-3 : angle 1.89749 ( 6) link_BETA1-4 : bond 0.00487 ( 5) link_BETA1-4 : angle 1.73302 ( 15) link_NAG-ASN : bond 0.00264 ( 5) link_NAG-ASN : angle 2.59508 ( 15) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3012 Ramachandran restraints generated. 1506 Oldfield, 0 Emsley, 1506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3012 Ramachandran restraints generated. 1506 Oldfield, 0 Emsley, 1506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 211 time to evaluate : 0.374 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 164 LEU cc_start: 0.7977 (mm) cc_final: 0.7582 (tp) REVERT: A 173 ILE cc_start: 0.8661 (mm) cc_final: 0.8405 (mp) REVERT: A 181 ARG cc_start: 0.6699 (mtt180) cc_final: 0.5791 (mmp80) REVERT: A 326 PHE cc_start: 0.7201 (m-80) cc_final: 0.6648 (m-80) REVERT: A 435 MET cc_start: 0.7345 (mmp) cc_final: 0.7133 (mmp) REVERT: A 501 ILE cc_start: 0.8511 (mm) cc_final: 0.8255 (mt) REVERT: A 682 ASP cc_start: 0.8321 (t70) cc_final: 0.7967 (t0) REVERT: A 713 LEU cc_start: 0.8453 (OUTLIER) cc_final: 0.7845 (mp) REVERT: A 853 TYR cc_start: 0.8099 (t80) cc_final: 0.7824 (t80) REVERT: A 854 ARG cc_start: 0.7735 (ptm-80) cc_final: 0.7411 (ppt170) REVERT: A 888 LEU cc_start: 0.8765 (mt) cc_final: 0.8527 (mt) REVERT: A 924 GLU cc_start: 0.6109 (mm-30) cc_final: 0.5556 (mm-30) REVERT: A 963 GLU cc_start: 0.8288 (tm-30) cc_final: 0.7974 (tm-30) REVERT: A 1145 GLU cc_start: 0.7973 (tm-30) cc_final: 0.7541 (tm-30) REVERT: A 1151 MET cc_start: 0.8166 (mtp) cc_final: 0.7919 (mtm) REVERT: A 1167 LEU cc_start: 0.9167 (OUTLIER) cc_final: 0.8932 (pp) REVERT: B 84 ASP cc_start: 0.7785 (m-30) cc_final: 0.6957 (t70) REVERT: B 135 ASN cc_start: 0.8673 (p0) cc_final: 0.8294 (p0) REVERT: B 238 ARG cc_start: 0.7990 (mmm160) cc_final: 0.7701 (mmm-85) outliers start: 39 outliers final: 34 residues processed: 238 average time/residue: 0.1098 time to fit residues: 37.2148 Evaluate side-chains 237 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 201 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 338 ASP Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 376 ASN Chi-restraints excluded: chain A residue 412 TYR Chi-restraints excluded: chain A residue 413 LYS Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 502 MET Chi-restraints excluded: chain A residue 526 TYR Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 554 ILE Chi-restraints excluded: chain A residue 645 ILE Chi-restraints excluded: chain A residue 647 VAL Chi-restraints excluded: chain A residue 713 LEU Chi-restraints excluded: chain A residue 753 THR Chi-restraints excluded: chain A residue 918 LEU Chi-restraints excluded: chain A residue 939 ASP Chi-restraints excluded: chain A residue 1019 LEU Chi-restraints excluded: chain A residue 1050 VAL Chi-restraints excluded: chain A residue 1120 TYR Chi-restraints excluded: chain A residue 1134 CYS Chi-restraints excluded: chain A residue 1146 TYR Chi-restraints excluded: chain A residue 1167 LEU Chi-restraints excluded: chain A residue 1172 SER Chi-restraints excluded: chain A residue 1333 TYR Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 299 MET Chi-restraints excluded: chain B residue 300 MET Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 351 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 145 optimal weight: 2.9990 chunk 72 optimal weight: 0.2980 chunk 90 optimal weight: 1.9990 chunk 89 optimal weight: 0.6980 chunk 31 optimal weight: 0.0770 chunk 59 optimal weight: 0.9980 chunk 23 optimal weight: 6.9990 chunk 46 optimal weight: 5.9990 chunk 111 optimal weight: 0.8980 chunk 81 optimal weight: 5.9990 chunk 0 optimal weight: 8.9990 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 614 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 928 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 171 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.148741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.118374 restraints weight = 16422.938| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 1.79 r_work: 0.3320 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3193 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.2814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 12723 Z= 0.138 Angle : 0.667 10.353 17283 Z= 0.339 Chirality : 0.044 0.193 1939 Planarity : 0.005 0.098 2186 Dihedral : 9.344 153.142 2012 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.57 % Favored : 93.29 % Rotamer: Outliers : 3.21 % Allowed : 22.71 % Favored : 74.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.39 % 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: -1.16 (0.22), residues: 1506 helix: 0.71 (0.20), residues: 668 sheet: -1.08 (0.35), residues: 220 loop : -2.34 (0.24), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 854 TYR 0.020 0.001 TYR A1146 PHE 0.029 0.001 PHE A1278 TRP 0.016 0.001 TRP A1279 HIS 0.003 0.000 HIS A 103 Details of bonding type rmsd covalent geometry : bond 0.00314 (12708) covalent geometry : angle 0.66137 (17245) SS BOND : bond 0.00041 ( 1) SS BOND : angle 0.77694 ( 2) hydrogen bonds : bond 0.04597 ( 553) hydrogen bonds : angle 4.79454 ( 1587) Misc. bond : bond 0.00128 ( 2) link_ALPHA1-3 : bond 0.00924 ( 2) link_ALPHA1-3 : angle 1.80932 ( 6) link_BETA1-4 : bond 0.00473 ( 5) link_BETA1-4 : angle 1.53630 ( 15) link_NAG-ASN : bond 0.00272 ( 5) link_NAG-ASN : angle 2.52605 ( 15) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3012 Ramachandran restraints generated. 1506 Oldfield, 0 Emsley, 1506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3012 Ramachandran restraints generated. 1506 Oldfield, 0 Emsley, 1506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 211 time to evaluate : 0.363 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 164 LEU cc_start: 0.7932 (OUTLIER) cc_final: 0.7554 (tp) REVERT: A 173 ILE cc_start: 0.8636 (mm) cc_final: 0.8387 (mp) REVERT: A 181 ARG cc_start: 0.6546 (mtt180) cc_final: 0.5690 (mmp80) REVERT: A 326 PHE cc_start: 0.7098 (m-80) cc_final: 0.6631 (m-80) REVERT: A 435 MET cc_start: 0.7187 (mmp) cc_final: 0.6915 (mmp) REVERT: A 501 ILE cc_start: 0.8493 (mm) cc_final: 0.8250 (mt) REVERT: A 682 ASP cc_start: 0.8200 (t70) cc_final: 0.7943 (t0) REVERT: A 713 LEU cc_start: 0.8378 (OUTLIER) cc_final: 0.7769 (mp) REVERT: A 854 ARG cc_start: 0.7825 (ptm-80) cc_final: 0.7475 (ppt170) REVERT: A 888 LEU cc_start: 0.8693 (mt) cc_final: 0.8452 (mt) REVERT: A 924 GLU cc_start: 0.6041 (mm-30) cc_final: 0.5056 (mm-30) REVERT: A 963 GLU cc_start: 0.8251 (tm-30) cc_final: 0.7925 (tm-30) REVERT: A 1145 GLU cc_start: 0.7880 (tm-30) cc_final: 0.7443 (tm-30) REVERT: A 1167 LEU cc_start: 0.9142 (OUTLIER) cc_final: 0.8924 (pp) REVERT: B 84 ASP cc_start: 0.7745 (m-30) cc_final: 0.6937 (t70) REVERT: B 135 ASN cc_start: 0.8682 (p0) cc_final: 0.8315 (p0) REVERT: B 238 ARG cc_start: 0.8003 (mmm160) cc_final: 0.7710 (mmm-85) outliers start: 42 outliers final: 32 residues processed: 236 average time/residue: 0.1072 time to fit residues: 36.0146 Evaluate side-chains 235 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 200 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 338 ASP Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 376 ASN Chi-restraints excluded: chain A residue 413 LYS Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain A residue 502 MET Chi-restraints excluded: chain A residue 505 ILE Chi-restraints excluded: chain A residue 526 TYR Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 554 ILE Chi-restraints excluded: chain A residue 645 ILE Chi-restraints excluded: chain A residue 647 VAL Chi-restraints excluded: chain A residue 713 LEU Chi-restraints excluded: chain A residue 753 THR Chi-restraints excluded: chain A residue 918 LEU Chi-restraints excluded: chain A residue 939 ASP Chi-restraints excluded: chain A residue 1019 LEU Chi-restraints excluded: chain A residue 1050 VAL Chi-restraints excluded: chain A residue 1120 TYR Chi-restraints excluded: chain A residue 1134 CYS Chi-restraints excluded: chain A residue 1146 TYR Chi-restraints excluded: chain A residue 1167 LEU Chi-restraints excluded: chain A residue 1172 SER Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 85 CYS Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 299 MET Chi-restraints excluded: chain B residue 300 MET Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 351 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 15 optimal weight: 4.9990 chunk 77 optimal weight: 4.9990 chunk 8 optimal weight: 3.9990 chunk 45 optimal weight: 6.9990 chunk 35 optimal weight: 0.6980 chunk 94 optimal weight: 0.5980 chunk 21 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 16 optimal weight: 4.9990 chunk 130 optimal weight: 6.9990 chunk 71 optimal weight: 0.9980 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 613 GLN ** A 614 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 928 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.143885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.113292 restraints weight = 16606.525| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 1.74 r_work: 0.3251 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3126 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.2662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 12723 Z= 0.217 Angle : 0.734 10.511 17283 Z= 0.375 Chirality : 0.047 0.215 1939 Planarity : 0.006 0.129 2186 Dihedral : 9.508 152.105 2012 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.37 % Favored : 92.50 % Rotamer: Outliers : 2.75 % Allowed : 23.62 % Favored : 73.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.39 % 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: -1.31 (0.21), residues: 1506 helix: 0.53 (0.20), residues: 670 sheet: -1.18 (0.34), residues: 220 loop : -2.35 (0.24), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 114 TYR 0.025 0.002 TYR A 853 PHE 0.028 0.002 PHE A1278 TRP 0.013 0.002 TRP B 120 HIS 0.003 0.001 HIS A 103 Details of bonding type rmsd covalent geometry : bond 0.00517 (12708) covalent geometry : angle 0.72718 (17245) SS BOND : bond 0.00430 ( 1) SS BOND : angle 0.60018 ( 2) hydrogen bonds : bond 0.05361 ( 553) hydrogen bonds : angle 4.99317 ( 1587) Misc. bond : bond 0.00486 ( 2) link_ALPHA1-3 : bond 0.00793 ( 2) link_ALPHA1-3 : angle 1.98120 ( 6) link_BETA1-4 : bond 0.00464 ( 5) link_BETA1-4 : angle 1.49864 ( 15) link_NAG-ASN : bond 0.00326 ( 5) link_NAG-ASN : angle 2.87278 ( 15) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3012 Ramachandran restraints generated. 1506 Oldfield, 0 Emsley, 1506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3012 Ramachandran restraints generated. 1506 Oldfield, 0 Emsley, 1506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 201 time to evaluate : 0.441 Fit side-chains revert: symmetry clash REVERT: A 173 ILE cc_start: 0.8663 (mm) cc_final: 0.8339 (mp) REVERT: A 181 ARG cc_start: 0.6856 (mtt180) cc_final: 0.5858 (mmp80) REVERT: A 326 PHE cc_start: 0.7273 (m-80) cc_final: 0.6691 (m-80) REVERT: A 435 MET cc_start: 0.7235 (mmp) cc_final: 0.6959 (mmp) REVERT: A 481 ARG cc_start: 0.8026 (mtp-110) cc_final: 0.7504 (mtp-110) REVERT: A 501 ILE cc_start: 0.8477 (mm) cc_final: 0.8226 (mt) REVERT: A 682 ASP cc_start: 0.8208 (t70) cc_final: 0.7878 (t0) REVERT: A 854 ARG cc_start: 0.7829 (ptm-80) cc_final: 0.7486 (ppt170) REVERT: A 888 LEU cc_start: 0.8700 (mt) cc_final: 0.8465 (mt) REVERT: A 924 GLU cc_start: 0.6172 (mm-30) cc_final: 0.5594 (mm-30) REVERT: A 963 GLU cc_start: 0.8258 (tm-30) cc_final: 0.7967 (tm-30) REVERT: A 1145 GLU cc_start: 0.8024 (tm-30) cc_final: 0.7579 (tm-30) REVERT: A 1167 LEU cc_start: 0.9255 (OUTLIER) cc_final: 0.8966 (pp) REVERT: B 84 ASP cc_start: 0.7798 (m-30) cc_final: 0.6988 (t70) REVERT: B 86 LEU cc_start: 0.8110 (mp) cc_final: 0.7837 (mp) REVERT: B 135 ASN cc_start: 0.8774 (p0) cc_final: 0.8351 (p0) REVERT: B 238 ARG cc_start: 0.8008 (mmm160) cc_final: 0.7674 (mmm-85) outliers start: 36 outliers final: 29 residues processed: 224 average time/residue: 0.1134 time to fit residues: 35.6607 Evaluate side-chains 226 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 196 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 338 ASP Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 376 ASN Chi-restraints excluded: chain A residue 413 LYS Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain A residue 502 MET Chi-restraints excluded: chain A residue 505 ILE Chi-restraints excluded: chain A residue 526 TYR Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 554 ILE Chi-restraints excluded: chain A residue 645 ILE Chi-restraints excluded: chain A residue 647 VAL Chi-restraints excluded: chain A residue 753 THR Chi-restraints excluded: chain A residue 918 LEU Chi-restraints excluded: chain A residue 1019 LEU Chi-restraints excluded: chain A residue 1050 VAL Chi-restraints excluded: chain A residue 1134 CYS Chi-restraints excluded: chain A residue 1146 TYR Chi-restraints excluded: chain A residue 1167 LEU Chi-restraints excluded: chain A residue 1172 SER Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 300 MET Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 351 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 129 optimal weight: 0.9980 chunk 38 optimal weight: 0.8980 chunk 126 optimal weight: 2.9990 chunk 145 optimal weight: 1.9990 chunk 37 optimal weight: 0.0980 chunk 131 optimal weight: 0.2980 chunk 52 optimal weight: 0.7980 chunk 105 optimal weight: 0.9990 chunk 28 optimal weight: 0.0970 chunk 81 optimal weight: 2.9990 chunk 149 optimal weight: 0.0770 overall best weight: 0.2736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 613 GLN A 614 ASN ** A 928 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 974 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.150248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.118700 restraints weight = 16283.058| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 1.79 r_work: 0.3336 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3206 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.2999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 12723 Z= 0.127 Angle : 0.666 11.397 17283 Z= 0.339 Chirality : 0.043 0.194 1939 Planarity : 0.005 0.102 2186 Dihedral : 8.885 159.855 2012 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.91 % Favored : 93.96 % Rotamer: Outliers : 2.52 % Allowed : 23.85 % Favored : 73.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.39 % 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: -1.06 (0.22), residues: 1506 helix: 0.73 (0.20), residues: 669 sheet: -0.97 (0.34), residues: 220 loop : -2.24 (0.24), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 114 TYR 0.020 0.001 TYR A 853 PHE 0.028 0.001 PHE A 781 TRP 0.052 0.001 TRP A 542 HIS 0.002 0.001 HIS A1244 Details of bonding type rmsd covalent geometry : bond 0.00276 (12708) covalent geometry : angle 0.66128 (17245) SS BOND : bond 0.00145 ( 1) SS BOND : angle 0.87093 ( 2) hydrogen bonds : bond 0.04460 ( 553) hydrogen bonds : angle 4.78121 ( 1587) Misc. bond : bond 0.00242 ( 2) link_ALPHA1-3 : bond 0.00796 ( 2) link_ALPHA1-3 : angle 1.69406 ( 6) link_BETA1-4 : bond 0.00541 ( 5) link_BETA1-4 : angle 1.45422 ( 15) link_NAG-ASN : bond 0.00295 ( 5) link_NAG-ASN : angle 2.38440 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3091.26 seconds wall clock time: 53 minutes 38.58 seconds (3218.58 seconds total)