Starting phenix.real_space_refine on Thu Jul 31 05:37:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6lcp_0872/07_2025/6lcp_0872.cif Found real_map, /net/cci-nas-00/data/ceres_data/6lcp_0872/07_2025/6lcp_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_0872/07_2025/6lcp_0872.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6lcp_0872/07_2025/6lcp_0872.map" model { file = "/net/cci-nas-00/data/ceres_data/6lcp_0872/07_2025/6lcp_0872.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6lcp_0872/07_2025/6lcp_0872.cif" } resolution = 3.48 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 8.28, per 1000 atoms: 0.67 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: 3.85 Conformation dependent library (CDL) restraints added in 1.7 seconds 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: 1.36 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: 4.59 Time building geometry restraints manager: 4.45 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: 2.270 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: 0.010 Extract box with map and model: 0.570 Check model and map are aligned: 0.100 Set scattering table: 0.140 Process input model: 33.120 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.450 ------------------------------------------------------------------------------- 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 : 17.99 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.036 0.002 TRP B 120 HIS 0.003 0.001 HIS A 717 PHE 0.028 0.002 PHE A 524 TYR 0.020 0.002 TYR A1293 ARG 0.009 0.001 ARG A1320 Details of bonding type rmsd link_NAG-ASN : bond 0.01868 ( 5) link_NAG-ASN : angle 7.98334 ( 15) link_BETA1-4 : bond 0.04919 ( 5) link_BETA1-4 : angle 14.65951 ( 15) link_ALPHA1-3 : bond 0.00019 ( 2) link_ALPHA1-3 : angle 0.14172 ( 6) hydrogen bonds : bond 0.15135 ( 553) hydrogen bonds : angle 6.72207 ( 1587) SS BOND : bond 0.00284 ( 1) SS BOND : angle 0.26983 ( 2) covalent geometry : bond 0.00888 (12708) covalent geometry : angle 0.97083 (17245) Misc. bond : bond 0.58095 ( 2) *********************** 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 : 2.078 Fit side-chains revert: symmetry clash REVERT: A 326 PHE cc_start: 0.7832 (m-80) cc_final: 0.6866 (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: 0.8142 (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: 0.7412 (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: 0.8141 (p0) cc_final: 0.7736 (p0) REVERT: B 270 PRO cc_start: 0.8578 (Cg_endo) cc_final: 0.8330 (Cg_exo) outliers start: 13 outliers final: 8 residues processed: 244 average time/residue: 0.3675 time to fit residues: 124.2082 Evaluate side-chains 181 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 172 time to evaluate : 1.322 ------------------------------------------------------------------------------- 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 127 optimal weight: 0.5980 chunk 114 optimal weight: 1.9990 chunk 63 optimal weight: 9.9990 chunk 39 optimal weight: 0.9990 chunk 77 optimal weight: 6.9990 chunk 61 optimal weight: 1.9990 chunk 118 optimal weight: 0.5980 chunk 45 optimal weight: 5.9990 chunk 71 optimal weight: 0.5980 chunk 88 optimal weight: 0.7980 chunk 137 optimal weight: 0.2980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 928 ASN 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: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.146703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.116330 restraints weight = 16305.588| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 1.73 r_work: 0.3278 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3150 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.1483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 12723 Z= 0.163 Angle : 0.742 8.744 17283 Z= 0.378 Chirality : 0.046 0.204 1939 Planarity : 0.006 0.095 2186 Dihedral : 13.671 159.431 2031 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.17 % Favored : 92.70 % Rotamer: Outliers : 1.83 % Allowed : 14.83 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.87 (0.20), residues: 1506 helix: -0.70 (0.19), residues: 667 sheet: -2.14 (0.33), residues: 212 loop : -3.17 (0.22), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 120 HIS 0.004 0.001 HIS A 673 PHE 0.035 0.002 PHE A 709 TYR 0.022 0.002 TYR A1293 ARG 0.007 0.000 ARG A1320 Details of bonding type rmsd link_NAG-ASN : bond 0.00607 ( 5) link_NAG-ASN : angle 3.93677 ( 15) link_BETA1-4 : bond 0.00648 ( 5) link_BETA1-4 : angle 2.76248 ( 15) link_ALPHA1-3 : bond 0.00924 ( 2) link_ALPHA1-3 : angle 2.20348 ( 6) hydrogen bonds : bond 0.05541 ( 553) hydrogen bonds : angle 5.35022 ( 1587) SS BOND : bond 0.02072 ( 1) SS BOND : angle 0.94781 ( 2) covalent geometry : bond 0.00361 (12708) covalent geometry : angle 0.72757 (17245) Misc. bond : bond 0.00119 ( 2) *********************** 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 244 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 220 time to evaluate : 1.783 Fit side-chains revert: symmetry clash REVERT: A 164 LEU cc_start: 0.7953 (mm) cc_final: 0.7560 (tp) REVERT: A 326 PHE cc_start: 0.7514 (m-80) cc_final: 0.6902 (m-80) REVERT: A 501 ILE cc_start: 0.8526 (mm) cc_final: 0.8275 (mt) REVERT: A 630 GLU cc_start: 0.7224 (mm-30) cc_final: 0.6924 (mm-30) REVERT: A 709 PHE cc_start: 0.8611 (t80) cc_final: 0.8402 (t80) REVERT: A 779 ILE cc_start: 0.8532 (OUTLIER) cc_final: 0.8295 (pt) REVERT: A 788 MET cc_start: 0.8176 (tmm) cc_final: 0.7867 (tmm) REVERT: A 924 GLU cc_start: 0.6026 (mm-30) cc_final: 0.5776 (mm-30) REVERT: A 963 GLU cc_start: 0.8041 (tm-30) cc_final: 0.7794 (tm-30) REVERT: A 1131 TRP cc_start: 0.8916 (m100) cc_final: 0.8693 (m100) REVERT: A 1145 GLU cc_start: 0.7787 (tm-30) cc_final: 0.7255 (tm-30) REVERT: A 1151 MET cc_start: 0.8283 (mtp) cc_final: 0.8053 (mtp) REVERT: A 1167 LEU cc_start: 0.9205 (OUTLIER) cc_final: 0.8996 (pp) REVERT: B 43 CYS cc_start: 0.8892 (p) cc_final: 0.8570 (p) REVERT: B 121 LYS cc_start: 0.8616 (OUTLIER) cc_final: 0.8395 (ptmt) REVERT: B 135 ASN cc_start: 0.8582 (p0) cc_final: 0.8106 (p0) REVERT: B 270 PRO cc_start: 0.8617 (Cg_endo) cc_final: 0.8301 (Cg_exo) outliers start: 24 outliers final: 11 residues processed: 237 average time/residue: 0.3381 time to fit residues: 116.6028 Evaluate side-chains 201 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 187 time to evaluate : 1.480 ------------------------------------------------------------------------------- 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 645 ILE Chi-restraints excluded: chain A residue 647 VAL 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 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 49 optimal weight: 1.9990 chunk 144 optimal weight: 1.9990 chunk 52 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 40 optimal weight: 0.6980 chunk 50 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 11 optimal weight: 5.9990 chunk 47 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 chunk 101 optimal weight: 0.3980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3766 r_free = 0.3766 target = 0.144202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.112845 restraints weight = 16652.644| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 1.83 r_work: 0.3233 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3102 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.1780 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= 0.199 Angle : 0.737 9.777 17283 Z= 0.377 Chirality : 0.046 0.175 1939 Planarity : 0.006 0.092 2186 Dihedral : 12.788 154.528 2012 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.30 % Favored : 92.56 % Rotamer: Outliers : 2.75 % Allowed : 17.74 % Favored : 79.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.43 (0.20), residues: 1506 helix: -0.28 (0.19), residues: 670 sheet: -1.96 (0.33), residues: 211 loop : -2.98 (0.23), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 120 HIS 0.003 0.001 HIS A 717 PHE 0.020 0.002 PHE A 538 TYR 0.033 0.002 TYR A 853 ARG 0.009 0.001 ARG A 858 Details of bonding type rmsd link_NAG-ASN : bond 0.00440 ( 5) link_NAG-ASN : angle 3.58542 ( 15) link_BETA1-4 : bond 0.00611 ( 5) link_BETA1-4 : angle 2.73483 ( 15) link_ALPHA1-3 : bond 0.00980 ( 2) link_ALPHA1-3 : angle 2.10950 ( 6) hydrogen bonds : bond 0.05566 ( 553) hydrogen bonds : angle 5.25080 ( 1587) SS BOND : bond 0.00062 ( 1) SS BOND : angle 0.63788 ( 2) covalent geometry : bond 0.00468 (12708) covalent geometry : angle 0.72461 (17245) Misc. bond : bond 0.00101 ( 2) *********************** 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 235 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 199 time to evaluate : 1.313 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 164 LEU cc_start: 0.8013 (mm) cc_final: 0.7569 (tp) REVERT: A 326 PHE cc_start: 0.7413 (m-80) cc_final: 0.6790 (m-80) REVERT: A 501 ILE cc_start: 0.8554 (mm) cc_final: 0.8306 (mt) REVERT: A 648 GLU cc_start: 0.8100 (tp30) cc_final: 0.7856 (tp30) REVERT: A 709 PHE cc_start: 0.8668 (t80) cc_final: 0.8282 (t80) REVERT: A 713 LEU cc_start: 0.8572 (OUTLIER) cc_final: 0.8002 (mp) REVERT: A 779 ILE cc_start: 0.8643 (OUTLIER) cc_final: 0.8422 (pt) REVERT: A 788 MET cc_start: 0.8240 (tmm) cc_final: 0.7976 (tmm) REVERT: A 924 GLU cc_start: 0.6158 (mm-30) cc_final: 0.5811 (mm-30) REVERT: A 963 GLU cc_start: 0.8178 (tm-30) cc_final: 0.7882 (tm-30) REVERT: A 1145 GLU cc_start: 0.7922 (tm-30) cc_final: 0.7505 (tm-30) REVERT: A 1164 MET cc_start: 0.8925 (ttp) cc_final: 0.8710 (ttp) REVERT: A 1167 LEU cc_start: 0.9248 (OUTLIER) cc_final: 0.9005 (pp) REVERT: B 29 PRO cc_start: 0.8362 (Cg_exo) cc_final: 0.8145 (Cg_endo) REVERT: B 43 CYS cc_start: 0.8848 (p) cc_final: 0.8476 (p) REVERT: B 121 LYS cc_start: 0.8687 (OUTLIER) cc_final: 0.8457 (ptmt) REVERT: B 135 ASN cc_start: 0.8697 (p0) cc_final: 0.8219 (p0) outliers start: 36 outliers final: 20 residues processed: 223 average time/residue: 0.2785 time to fit residues: 88.9517 Evaluate side-chains 205 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 181 time to evaluate : 1.332 ------------------------------------------------------------------------------- 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 526 TYR 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 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 1019 LEU 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 46 optimal weight: 4.9990 chunk 74 optimal weight: 2.9990 chunk 112 optimal weight: 3.9990 chunk 6 optimal weight: 4.9990 chunk 146 optimal weight: 0.7980 chunk 24 optimal weight: 4.9990 chunk 145 optimal weight: 0.9990 chunk 49 optimal weight: 0.9980 chunk 101 optimal weight: 0.9990 chunk 100 optimal weight: 0.6980 chunk 43 optimal weight: 3.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 ASN ** A 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.145794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.114053 restraints weight = 16564.180| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 1.87 r_work: 0.3261 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3128 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.2032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 12723 Z= 0.166 Angle : 0.701 8.618 17283 Z= 0.357 Chirality : 0.045 0.199 1939 Planarity : 0.005 0.091 2186 Dihedral : 11.886 150.871 2012 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.91 % Favored : 92.96 % Rotamer: Outliers : 3.98 % Allowed : 19.11 % Favored : 76.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.04 (0.21), residues: 1506 helix: 0.07 (0.19), residues: 663 sheet: -1.74 (0.33), residues: 224 loop : -2.82 (0.23), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 120 HIS 0.002 0.000 HIS A 673 PHE 0.019 0.001 PHE A 538 TYR 0.031 0.002 TYR A 853 ARG 0.011 0.000 ARG A 114 Details of bonding type rmsd link_NAG-ASN : bond 0.00325 ( 5) link_NAG-ASN : angle 3.12456 ( 15) link_BETA1-4 : bond 0.00630 ( 5) link_BETA1-4 : angle 2.56251 ( 15) link_ALPHA1-3 : bond 0.00992 ( 2) link_ALPHA1-3 : angle 2.11024 ( 6) hydrogen bonds : bond 0.05200 ( 553) hydrogen bonds : angle 5.10025 ( 1587) SS BOND : bond 0.01489 ( 1) SS BOND : angle 0.92182 ( 2) covalent geometry : bond 0.00381 (12708) covalent geometry : angle 0.69021 (17245) Misc. bond : bond 0.00431 ( 2) *********************** 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 251 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 199 time to evaluate : 1.183 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 164 LEU cc_start: 0.7974 (OUTLIER) cc_final: 0.7546 (tp) REVERT: A 181 ARG cc_start: 0.6861 (mtt180) cc_final: 0.5773 (mmp80) REVERT: A 326 PHE cc_start: 0.7362 (m-80) cc_final: 0.6808 (m-80) REVERT: A 472 MET cc_start: 0.7980 (ttt) cc_final: 0.7557 (ttm) REVERT: A 501 ILE cc_start: 0.8555 (mm) cc_final: 0.8304 (mt) REVERT: A 648 GLU cc_start: 0.8052 (tp30) cc_final: 0.7845 (tp30) REVERT: A 709 PHE cc_start: 0.8647 (t80) cc_final: 0.8243 (t80) REVERT: A 713 LEU cc_start: 0.8530 (OUTLIER) cc_final: 0.7919 (mp) REVERT: A 788 MET cc_start: 0.8228 (tmm) cc_final: 0.7999 (tmm) REVERT: A 858 ARG cc_start: 0.8039 (mtm110) cc_final: 0.7818 (ptp90) REVERT: A 924 GLU cc_start: 0.6191 (mm-30) cc_final: 0.5740 (mm-30) REVERT: A 963 GLU cc_start: 0.8161 (tm-30) cc_final: 0.7825 (tm-30) REVERT: A 974 ASN cc_start: 0.8771 (t0) cc_final: 0.8559 (t0) REVERT: A 1145 GLU cc_start: 0.7900 (tm-30) cc_final: 0.7498 (tm-30) REVERT: A 1167 LEU cc_start: 0.9206 (OUTLIER) cc_final: 0.8958 (pp) REVERT: B 43 CYS cc_start: 0.8801 (p) cc_final: 0.8412 (p) REVERT: B 121 LYS cc_start: 0.8642 (OUTLIER) cc_final: 0.8393 (ptmt) REVERT: B 135 ASN cc_start: 0.8694 (p0) cc_final: 0.8289 (p0) outliers start: 52 outliers final: 35 residues processed: 229 average time/residue: 0.2983 time to fit residues: 97.0458 Evaluate side-chains 223 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 184 time to evaluate : 1.344 ------------------------------------------------------------------------------- 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 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 547 VAL 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 623 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 801 LEU 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 1307 MET Chi-restraints excluded: chain A residue 1333 TYR 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 299 MET Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 351 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 84 optimal weight: 0.9980 chunk 139 optimal weight: 1.9990 chunk 140 optimal weight: 0.8980 chunk 20 optimal weight: 4.9990 chunk 129 optimal weight: 0.8980 chunk 113 optimal weight: 6.9990 chunk 114 optimal weight: 0.0060 chunk 85 optimal weight: 0.5980 chunk 36 optimal weight: 0.7980 chunk 71 optimal weight: 0.7980 chunk 90 optimal weight: 0.9990 overall best weight: 0.6196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 614 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 928 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1244 HIS B 164 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.147530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.116025 restraints weight = 16481.808| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 1.83 r_work: 0.3287 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3158 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.2267 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= 0.145 Angle : 0.683 9.200 17283 Z= 0.347 Chirality : 0.044 0.196 1939 Planarity : 0.005 0.099 2186 Dihedral : 11.027 149.213 2012 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.64 % Favored : 93.23 % Rotamer: Outliers : 3.29 % Allowed : 20.87 % Favored : 75.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.39 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.74 (0.21), residues: 1506 helix: 0.27 (0.20), residues: 670 sheet: -1.55 (0.33), residues: 225 loop : -2.64 (0.23), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 120 HIS 0.002 0.000 HIS A 673 PHE 0.029 0.001 PHE A 781 TYR 0.027 0.002 TYR A 853 ARG 0.005 0.000 ARG A 785 Details of bonding type rmsd link_NAG-ASN : bond 0.00296 ( 5) link_NAG-ASN : angle 2.86849 ( 15) link_BETA1-4 : bond 0.00601 ( 5) link_BETA1-4 : angle 2.48494 ( 15) link_ALPHA1-3 : bond 0.00985 ( 2) link_ALPHA1-3 : angle 2.02226 ( 6) hydrogen bonds : bond 0.04862 ( 553) hydrogen bonds : angle 4.95541 ( 1587) SS BOND : bond 0.00637 ( 1) SS BOND : angle 0.76083 ( 2) covalent geometry : bond 0.00327 (12708) covalent geometry : angle 0.67314 (17245) Misc. bond : bond 0.00277 ( 2) *********************** 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 261 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 218 time to evaluate : 1.485 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 164 LEU cc_start: 0.7937 (OUTLIER) cc_final: 0.7542 (tp) REVERT: A 173 ILE cc_start: 0.8623 (mm) cc_final: 0.8368 (mp) REVERT: A 181 ARG cc_start: 0.6695 (mtt180) cc_final: 0.5922 (mmp80) REVERT: A 326 PHE cc_start: 0.7305 (m-80) cc_final: 0.6732 (m-80) REVERT: A 501 ILE cc_start: 0.8540 (mm) cc_final: 0.8260 (mt) REVERT: A 682 ASP cc_start: 0.8342 (t70) cc_final: 0.7926 (t0) REVERT: A 683 MET cc_start: 0.8703 (ptm) cc_final: 0.8410 (ptp) REVERT: A 709 PHE cc_start: 0.8657 (t80) cc_final: 0.8209 (t80) REVERT: A 713 LEU cc_start: 0.8488 (OUTLIER) cc_final: 0.7890 (mp) REVERT: A 736 GLN cc_start: 0.7764 (tt0) cc_final: 0.7474 (tm-30) REVERT: A 788 MET cc_start: 0.8141 (tmm) cc_final: 0.7940 (tmm) REVERT: A 924 GLU cc_start: 0.6154 (mm-30) cc_final: 0.5831 (mm-30) REVERT: A 963 GLU cc_start: 0.8196 (tm-30) cc_final: 0.7851 (tm-30) REVERT: A 974 ASN cc_start: 0.8738 (t0) cc_final: 0.8517 (t0) REVERT: A 1145 GLU cc_start: 0.7873 (tm-30) cc_final: 0.7466 (tm-30) REVERT: A 1167 LEU cc_start: 0.9179 (OUTLIER) cc_final: 0.8961 (pp) REVERT: A 1183 TYR cc_start: 0.8809 (t80) cc_final: 0.8581 (t80) REVERT: B 135 ASN cc_start: 0.8702 (p0) cc_final: 0.8333 (p0) REVERT: B 168 ARG cc_start: 0.8821 (tpt170) cc_final: 0.8411 (ttt90) outliers start: 43 outliers final: 28 residues processed: 247 average time/residue: 0.3140 time to fit residues: 110.6641 Evaluate side-chains 229 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 198 time to evaluate : 1.415 ------------------------------------------------------------------------------- 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 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 801 LEU 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 1050 VAL Chi-restraints excluded: chain A residue 1120 TYR Chi-restraints excluded: chain A residue 1146 TYR Chi-restraints excluded: chain A residue 1167 LEU 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 129 VAL 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 48 optimal weight: 0.4980 chunk 9 optimal weight: 3.9990 chunk 134 optimal weight: 3.9990 chunk 139 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 42 optimal weight: 10.0000 chunk 22 optimal weight: 5.9990 chunk 74 optimal weight: 4.9990 chunk 118 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 chunk 45 optimal weight: 5.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 370 ASN A 613 GLN ** A 614 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 928 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.139476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.109547 restraints weight = 17034.473| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 1.67 r_work: 0.3183 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3058 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.2194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.055 12723 Z= 0.306 Angle : 0.818 9.127 17283 Z= 0.417 Chirality : 0.049 0.202 1939 Planarity : 0.006 0.132 2186 Dihedral : 11.078 147.773 2012 Min Nonbonded Distance : 1.822 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.70 % Favored : 91.17 % Rotamer: Outliers : 3.82 % Allowed : 21.33 % Favored : 74.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.39 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.05 (0.21), residues: 1506 helix: 0.01 (0.19), residues: 667 sheet: -1.72 (0.33), residues: 225 loop : -2.77 (0.23), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 120 HIS 0.003 0.001 HIS A 450 PHE 0.026 0.002 PHE A 781 TYR 0.027 0.003 TYR A 853 ARG 0.007 0.001 ARG A1109 Details of bonding type rmsd link_NAG-ASN : bond 0.00484 ( 5) link_NAG-ASN : angle 3.50610 ( 15) link_BETA1-4 : bond 0.00537 ( 5) link_BETA1-4 : angle 2.45146 ( 15) link_ALPHA1-3 : bond 0.00876 ( 2) link_ALPHA1-3 : angle 2.38127 ( 6) hydrogen bonds : bond 0.06229 ( 553) hydrogen bonds : angle 5.31192 ( 1587) SS BOND : bond 0.00566 ( 1) SS BOND : angle 0.50695 ( 2) covalent geometry : bond 0.00734 (12708) covalent geometry : angle 0.80805 (17245) Misc. bond : bond 0.00516 ( 2) *********************** 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 237 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 187 time to evaluate : 2.138 Fit side-chains revert: symmetry clash REVERT: A 110 ARG cc_start: 0.7650 (mmm160) cc_final: 0.6619 (mtp180) REVERT: A 181 ARG cc_start: 0.7106 (mtt180) cc_final: 0.6017 (mmp80) REVERT: A 326 PHE cc_start: 0.7340 (m-80) cc_final: 0.6706 (m-80) REVERT: A 501 ILE cc_start: 0.8533 (mm) cc_final: 0.8264 (mt) REVERT: A 713 LEU cc_start: 0.8548 (OUTLIER) cc_final: 0.7963 (mp) REVERT: A 782 ASN cc_start: 0.8407 (t0) cc_final: 0.8202 (m-40) REVERT: A 788 MET cc_start: 0.8128 (tmm) cc_final: 0.7805 (tmm) REVERT: A 854 ARG cc_start: 0.7614 (ptm-80) cc_final: 0.7345 (ppt170) REVERT: A 924 GLU cc_start: 0.6369 (mm-30) cc_final: 0.6058 (mm-30) REVERT: A 963 GLU cc_start: 0.8302 (tm-30) cc_final: 0.8063 (tm-30) REVERT: A 1145 GLU cc_start: 0.8070 (tm-30) cc_final: 0.7677 (tm-30) REVERT: A 1167 LEU cc_start: 0.9300 (OUTLIER) cc_final: 0.8979 (pp) REVERT: B 43 CYS cc_start: 0.8806 (p) cc_final: 0.8424 (p) REVERT: B 135 ASN cc_start: 0.8701 (p0) cc_final: 0.8271 (p0) outliers start: 50 outliers final: 38 residues processed: 219 average time/residue: 0.4775 time to fit residues: 154.1448 Evaluate side-chains 212 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 172 time to evaluate : 4.293 ------------------------------------------------------------------------------- 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 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 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 592 ASN Chi-restraints excluded: chain A residue 623 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 801 LEU 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 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 1292 PHE Chi-restraints excluded: chain A residue 1307 MET Chi-restraints excluded: chain A residue 1308 CYS 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 299 MET Chi-restraints excluded: chain B residue 344 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 46 optimal weight: 0.7980 chunk 18 optimal weight: 8.9990 chunk 80 optimal weight: 1.9990 chunk 129 optimal weight: 0.7980 chunk 135 optimal weight: 0.0970 chunk 99 optimal weight: 0.6980 chunk 150 optimal weight: 1.9990 chunk 41 optimal weight: 0.8980 chunk 138 optimal weight: 0.0170 chunk 95 optimal weight: 0.5980 chunk 113 optimal weight: 2.9990 overall best weight: 0.4416 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 GLN ** A 614 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 928 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 296 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 = 0.3785 r_free = 0.3785 target = 0.146146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.114834 restraints weight = 16466.793| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 1.96 r_work: 0.3270 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3138 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.2454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 12723 Z= 0.141 Angle : 0.686 9.154 17283 Z= 0.350 Chirality : 0.044 0.191 1939 Planarity : 0.006 0.135 2186 Dihedral : 10.295 146.922 2012 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.31 % Favored : 93.56 % Rotamer: Outliers : 3.36 % Allowed : 22.32 % Favored : 74.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.39 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.59 (0.21), residues: 1506 helix: 0.39 (0.20), residues: 666 sheet: -1.41 (0.33), residues: 220 loop : -2.56 (0.23), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP A 542 HIS 0.002 0.000 HIS A 860 PHE 0.031 0.001 PHE A 781 TYR 0.025 0.002 TYR A 853 ARG 0.015 0.001 ARG A 858 Details of bonding type rmsd link_NAG-ASN : bond 0.00283 ( 5) link_NAG-ASN : angle 2.75247 ( 15) link_BETA1-4 : bond 0.00522 ( 5) link_BETA1-4 : angle 2.10001 ( 15) link_ALPHA1-3 : bond 0.00997 ( 2) link_ALPHA1-3 : angle 2.04000 ( 6) hydrogen bonds : bond 0.04923 ( 553) hydrogen bonds : angle 4.94699 ( 1587) SS BOND : bond 0.00039 ( 1) SS BOND : angle 0.61024 ( 2) covalent geometry : bond 0.00319 (12708) covalent geometry : angle 0.67757 (17245) Misc. bond : bond 0.00074 ( 2) *********************** 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 248 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 204 time to evaluate : 1.406 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 173 ILE cc_start: 0.8626 (mm) cc_final: 0.8300 (mp) REVERT: A 181 ARG cc_start: 0.6866 (mtt180) cc_final: 0.5839 (mmp80) REVERT: A 326 PHE cc_start: 0.7234 (m-80) cc_final: 0.6810 (m-80) REVERT: A 501 ILE cc_start: 0.8451 (mm) cc_final: 0.8200 (mt) REVERT: A 682 ASP cc_start: 0.8443 (t70) cc_final: 0.8010 (t0) REVERT: A 683 MET cc_start: 0.8757 (ptm) cc_final: 0.8503 (ptp) REVERT: A 709 PHE cc_start: 0.8673 (t80) cc_final: 0.8185 (t80) REVERT: A 713 LEU cc_start: 0.8452 (OUTLIER) cc_final: 0.7865 (mp) REVERT: A 736 GLN cc_start: 0.7671 (tt0) cc_final: 0.7428 (tm-30) REVERT: A 782 ASN cc_start: 0.8492 (t0) cc_final: 0.8243 (m-40) REVERT: A 788 MET cc_start: 0.8191 (tmm) cc_final: 0.7780 (tmm) REVERT: A 847 GLU cc_start: 0.7676 (tm-30) cc_final: 0.7330 (tm-30) REVERT: A 854 ARG cc_start: 0.7802 (ptm-80) cc_final: 0.7069 (ppt170) REVERT: A 924 GLU cc_start: 0.6125 (mm-30) cc_final: 0.5841 (mm-30) REVERT: A 963 GLU cc_start: 0.8261 (tm-30) cc_final: 0.7923 (tm-30) REVERT: A 1145 GLU cc_start: 0.7988 (OUTLIER) cc_final: 0.7610 (tm-30) REVERT: A 1151 MET cc_start: 0.8134 (mtm) cc_final: 0.7873 (mtm) REVERT: A 1164 MET cc_start: 0.8863 (ttt) cc_final: 0.8511 (ttp) REVERT: A 1167 LEU cc_start: 0.9182 (OUTLIER) cc_final: 0.8966 (pp) REVERT: A 1183 TYR cc_start: 0.8845 (t80) cc_final: 0.8612 (t80) REVERT: B 84 ASP cc_start: 0.7891 (m-30) cc_final: 0.7045 (t70) REVERT: B 135 ASN cc_start: 0.8714 (p0) cc_final: 0.8265 (p0) outliers start: 44 outliers final: 32 residues processed: 231 average time/residue: 0.2805 time to fit residues: 92.2622 Evaluate side-chains 228 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 193 time to evaluate : 1.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 526 TYR Chi-restraints excluded: chain A residue 547 VAL 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 623 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 801 LEU 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 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 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 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 47 optimal weight: 1.9990 chunk 113 optimal weight: 7.9990 chunk 140 optimal weight: 1.9990 chunk 114 optimal weight: 0.0040 chunk 18 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 118 optimal weight: 0.8980 chunk 42 optimal weight: 10.0000 chunk 142 optimal weight: 1.9990 chunk 75 optimal weight: 0.5980 chunk 91 optimal weight: 1.9990 overall best weight: 0.8996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 296 GLN ** 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 = 0.3772 r_free = 0.3772 target = 0.145098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.114666 restraints weight = 16521.251| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 1.76 r_work: 0.3266 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3142 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.2497 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= 0.166 Angle : 0.697 9.841 17283 Z= 0.354 Chirality : 0.045 0.186 1939 Planarity : 0.005 0.092 2186 Dihedral : 10.042 149.275 2012 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.24 % Favored : 92.63 % Rotamer: Outliers : 3.52 % Allowed : 22.63 % Favored : 73.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.39 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.21), residues: 1506 helix: 0.48 (0.20), residues: 665 sheet: -1.40 (0.33), residues: 221 loop : -2.52 (0.23), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 542 HIS 0.002 0.001 HIS A 673 PHE 0.028 0.001 PHE A 781 TYR 0.021 0.002 TYR A 853 ARG 0.004 0.000 ARG A 419 Details of bonding type rmsd link_NAG-ASN : bond 0.00290 ( 5) link_NAG-ASN : angle 2.82974 ( 15) link_BETA1-4 : bond 0.00538 ( 5) link_BETA1-4 : angle 1.85525 ( 15) link_ALPHA1-3 : bond 0.00932 ( 2) link_ALPHA1-3 : angle 2.02949 ( 6) hydrogen bonds : bond 0.05048 ( 553) hydrogen bonds : angle 4.94587 ( 1587) SS BOND : bond 0.00433 ( 1) SS BOND : angle 0.63032 ( 2) covalent geometry : bond 0.00387 (12708) covalent geometry : angle 0.68913 (17245) Misc. bond : bond 0.00038 ( 2) *********************** 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 248 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 202 time to evaluate : 1.598 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 173 ILE cc_start: 0.8623 (mm) cc_final: 0.8292 (mp) REVERT: A 181 ARG cc_start: 0.6880 (mtt180) cc_final: 0.5872 (mmp80) REVERT: A 326 PHE cc_start: 0.7251 (m-80) cc_final: 0.6710 (m-80) REVERT: A 501 ILE cc_start: 0.8413 (mm) cc_final: 0.8158 (mt) REVERT: A 682 ASP cc_start: 0.8383 (t70) cc_final: 0.7976 (t0) REVERT: A 683 MET cc_start: 0.8758 (ptm) cc_final: 0.8516 (ptp) REVERT: A 709 PHE cc_start: 0.8686 (t80) cc_final: 0.8237 (t80) REVERT: A 713 LEU cc_start: 0.8425 (OUTLIER) cc_final: 0.7835 (mp) REVERT: A 782 ASN cc_start: 0.8447 (t0) cc_final: 0.8244 (m-40) REVERT: A 788 MET cc_start: 0.8183 (tmm) cc_final: 0.7734 (tmm) REVERT: A 841 LEU cc_start: 0.8233 (mp) cc_final: 0.7988 (mp) REVERT: A 851 GLU cc_start: 0.8869 (mp0) cc_final: 0.8556 (mp0) REVERT: A 854 ARG cc_start: 0.7636 (ptm-80) cc_final: 0.7287 (ppt170) REVERT: A 924 GLU cc_start: 0.6177 (mm-30) cc_final: 0.5888 (mm-30) REVERT: A 963 GLU cc_start: 0.8294 (tm-30) cc_final: 0.7972 (tm-30) REVERT: A 1145 GLU cc_start: 0.7958 (tm-30) cc_final: 0.7544 (tm-30) REVERT: A 1151 MET cc_start: 0.8186 (mtm) cc_final: 0.7899 (mtm) REVERT: A 1167 LEU cc_start: 0.9190 (OUTLIER) cc_final: 0.8940 (pp) REVERT: B 84 ASP cc_start: 0.7828 (m-30) cc_final: 0.7018 (t70) REVERT: B 135 ASN cc_start: 0.8672 (p0) cc_final: 0.8236 (p0) outliers start: 46 outliers final: 38 residues processed: 235 average time/residue: 0.2781 time to fit residues: 94.2727 Evaluate side-chains 230 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 190 time to evaluate : 1.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 LEU 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 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 526 TYR Chi-restraints excluded: chain A residue 547 VAL 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 623 ILE Chi-restraints excluded: chain A residue 645 ILE Chi-restraints excluded: chain A residue 647 VAL Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 713 LEU Chi-restraints excluded: chain A residue 753 THR Chi-restraints excluded: chain A residue 801 LEU Chi-restraints excluded: chain A residue 918 LEU Chi-restraints excluded: chain A residue 919 THR 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 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 37 optimal weight: 0.0370 chunk 128 optimal weight: 1.9990 chunk 67 optimal weight: 6.9990 chunk 42 optimal weight: 10.0000 chunk 19 optimal weight: 0.2980 chunk 11 optimal weight: 2.9990 chunk 60 optimal weight: 0.8980 chunk 122 optimal weight: 5.9990 chunk 14 optimal weight: 0.9980 chunk 134 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 overall best weight: 0.8460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 296 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 = 0.3782 r_free = 0.3782 target = 0.145891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.115562 restraints weight = 16482.039| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 1.82 r_work: 0.3271 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3144 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.2629 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= 0.159 Angle : 0.690 10.154 17283 Z= 0.352 Chirality : 0.044 0.180 1939 Planarity : 0.006 0.115 2186 Dihedral : 9.730 150.696 2012 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.71 % Favored : 93.16 % Rotamer: Outliers : 3.82 % Allowed : 22.55 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.41 (0.21), residues: 1506 helix: 0.52 (0.20), residues: 664 sheet: -1.30 (0.34), residues: 221 loop : -2.45 (0.23), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 120 HIS 0.002 0.001 HIS A 103 PHE 0.030 0.001 PHE A 781 TYR 0.021 0.002 TYR A1293 ARG 0.005 0.000 ARG A 114 Details of bonding type rmsd link_NAG-ASN : bond 0.00288 ( 5) link_NAG-ASN : angle 2.70868 ( 15) link_BETA1-4 : bond 0.00522 ( 5) link_BETA1-4 : angle 1.58404 ( 15) link_ALPHA1-3 : bond 0.00900 ( 2) link_ALPHA1-3 : angle 1.95868 ( 6) hydrogen bonds : bond 0.04944 ( 553) hydrogen bonds : angle 4.89844 ( 1587) SS BOND : bond 0.00204 ( 1) SS BOND : angle 0.66446 ( 2) covalent geometry : bond 0.00368 (12708) covalent geometry : angle 0.68354 (17245) Misc. bond : bond 0.00251 ( 2) *********************** 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 252 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 202 time to evaluate : 1.390 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 ILE cc_start: 0.8615 (mm) cc_final: 0.8291 (mp) REVERT: A 181 ARG cc_start: 0.6854 (mtt180) cc_final: 0.5833 (mmp80) REVERT: A 326 PHE cc_start: 0.7229 (m-80) cc_final: 0.6704 (m-80) REVERT: A 501 ILE cc_start: 0.8414 (mm) cc_final: 0.8155 (mt) REVERT: A 682 ASP cc_start: 0.8377 (t70) cc_final: 0.7949 (t0) REVERT: A 683 MET cc_start: 0.8738 (ptm) cc_final: 0.8508 (ptp) REVERT: A 709 PHE cc_start: 0.8639 (t80) cc_final: 0.8180 (t80) REVERT: A 713 LEU cc_start: 0.8408 (OUTLIER) cc_final: 0.7812 (mp) REVERT: A 782 ASN cc_start: 0.8448 (t0) cc_final: 0.8241 (m-40) REVERT: A 788 MET cc_start: 0.8233 (tmm) cc_final: 0.7823 (tmm) REVERT: A 841 LEU cc_start: 0.8214 (mp) cc_final: 0.7895 (mt) REVERT: A 851 GLU cc_start: 0.8944 (mp0) cc_final: 0.8694 (mp0) REVERT: A 924 GLU cc_start: 0.6144 (mm-30) cc_final: 0.5869 (mm-30) REVERT: A 963 GLU cc_start: 0.8292 (tm-30) cc_final: 0.7977 (tm-30) REVERT: A 1145 GLU cc_start: 0.7984 (tm-30) cc_final: 0.7564 (tm-30) REVERT: A 1167 LEU cc_start: 0.9174 (OUTLIER) cc_final: 0.8931 (pp) REVERT: B 84 ASP cc_start: 0.7855 (m-30) cc_final: 0.6988 (t70) REVERT: B 135 ASN cc_start: 0.8670 (p0) cc_final: 0.8257 (p0) REVERT: B 238 ARG cc_start: 0.7968 (mmm160) cc_final: 0.7650 (mmm-85) outliers start: 50 outliers final: 39 residues processed: 235 average time/residue: 0.2747 time to fit residues: 91.7694 Evaluate side-chains 235 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 194 time to evaluate : 1.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 LEU 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 412 TYR Chi-restraints excluded: chain A residue 413 LYS Chi-restraints excluded: chain A residue 439 ILE 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 623 ILE Chi-restraints excluded: chain A residue 645 ILE Chi-restraints excluded: chain A residue 647 VAL Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 713 LEU Chi-restraints excluded: chain A residue 753 THR Chi-restraints excluded: chain A residue 801 LEU Chi-restraints excluded: chain A residue 843 ILE Chi-restraints excluded: chain A residue 918 LEU Chi-restraints excluded: chain A residue 919 THR Chi-restraints excluded: chain A residue 939 ASP Chi-restraints excluded: chain A residue 948 ASN 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 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 8 optimal weight: 0.8980 chunk 14 optimal weight: 0.9980 chunk 86 optimal weight: 0.8980 chunk 49 optimal weight: 0.9990 chunk 133 optimal weight: 0.2980 chunk 27 optimal weight: 0.7980 chunk 60 optimal weight: 0.9990 chunk 15 optimal weight: 4.9990 chunk 67 optimal weight: 2.9990 chunk 122 optimal weight: 5.9990 chunk 64 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 195 HIS A 599 GLN ** A 614 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 928 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 974 ASN ** A1298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.146462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.116112 restraints weight = 16419.574| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 1.76 r_work: 0.3283 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3159 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.2742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 12723 Z= 0.155 Angle : 0.692 10.926 17283 Z= 0.353 Chirality : 0.045 0.236 1939 Planarity : 0.006 0.127 2186 Dihedral : 9.606 152.112 2012 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.10 % Favored : 92.76 % Rotamer: Outliers : 3.06 % Allowed : 23.47 % Favored : 73.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.39 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.21), residues: 1506 helix: 0.58 (0.20), residues: 665 sheet: -1.24 (0.34), residues: 221 loop : -2.43 (0.23), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 542 HIS 0.003 0.001 HIS A 673 PHE 0.029 0.001 PHE A 781 TYR 0.020 0.002 TYR A1146 ARG 0.009 0.000 ARG A 114 Details of bonding type rmsd link_NAG-ASN : bond 0.00260 ( 5) link_NAG-ASN : angle 2.63917 ( 15) link_BETA1-4 : bond 0.00497 ( 5) link_BETA1-4 : angle 1.49046 ( 15) link_ALPHA1-3 : bond 0.00861 ( 2) link_ALPHA1-3 : angle 1.91322 ( 6) hydrogen bonds : bond 0.04885 ( 553) hydrogen bonds : angle 4.90358 ( 1587) SS BOND : bond 0.00153 ( 1) SS BOND : angle 0.68478 ( 2) covalent geometry : bond 0.00357 (12708) covalent geometry : angle 0.68561 (17245) Misc. bond : bond 0.00297 ( 2) ********************** 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 241 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 201 time to evaluate : 1.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 GLU cc_start: 0.7157 (mp0) cc_final: 0.6936 (mp0) REVERT: A 173 ILE cc_start: 0.8642 (mm) cc_final: 0.8391 (mp) REVERT: A 181 ARG cc_start: 0.6746 (mtt180) cc_final: 0.5825 (mmp80) REVERT: A 326 PHE cc_start: 0.7224 (m-80) cc_final: 0.6812 (m-80) REVERT: A 501 ILE cc_start: 0.8408 (mm) cc_final: 0.8146 (mt) REVERT: A 682 ASP cc_start: 0.8325 (t70) cc_final: 0.7927 (t0) REVERT: A 683 MET cc_start: 0.8778 (ptm) cc_final: 0.8545 (ptp) REVERT: A 709 PHE cc_start: 0.8631 (t80) cc_final: 0.8189 (t80) REVERT: A 713 LEU cc_start: 0.8384 (OUTLIER) cc_final: 0.7796 (mp) REVERT: A 788 MET cc_start: 0.8211 (tmm) cc_final: 0.7814 (tmm) REVERT: A 851 GLU cc_start: 0.8891 (mp0) cc_final: 0.8664 (mp0) REVERT: A 888 LEU cc_start: 0.8748 (mt) cc_final: 0.8545 (mt) REVERT: A 924 GLU cc_start: 0.6104 (mm-30) cc_final: 0.5527 (mm-30) REVERT: A 963 GLU cc_start: 0.8247 (tm-30) cc_final: 0.7922 (tm-30) REVERT: A 1145 GLU cc_start: 0.7947 (tm-30) cc_final: 0.7519 (tm-30) REVERT: A 1167 LEU cc_start: 0.9168 (OUTLIER) cc_final: 0.8932 (pp) REVERT: B 84 ASP cc_start: 0.7800 (m-30) cc_final: 0.7009 (t70) REVERT: B 135 ASN cc_start: 0.8688 (p0) cc_final: 0.8270 (p0) REVERT: B 238 ARG cc_start: 0.7988 (mmm160) cc_final: 0.7673 (mmm-85) outliers start: 40 outliers final: 36 residues processed: 228 average time/residue: 0.2807 time to fit residues: 90.5891 Evaluate side-chains 233 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 195 time to evaluate : 1.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 338 ASP Chi-restraints excluded: chain A residue 364 CYS 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 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 623 ILE Chi-restraints excluded: chain A residue 645 ILE Chi-restraints excluded: chain A residue 647 VAL Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 713 LEU Chi-restraints excluded: chain A residue 753 THR Chi-restraints excluded: chain A residue 801 LEU Chi-restraints excluded: chain A residue 843 ILE Chi-restraints excluded: chain A residue 918 LEU Chi-restraints excluded: chain A residue 919 THR 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 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 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 22 optimal weight: 0.5980 chunk 70 optimal weight: 0.6980 chunk 55 optimal weight: 0.6980 chunk 7 optimal weight: 0.0770 chunk 8 optimal weight: 1.9990 chunk 116 optimal weight: 1.9990 chunk 146 optimal weight: 0.5980 chunk 128 optimal weight: 1.9990 chunk 110 optimal weight: 0.9990 chunk 41 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 195 HIS A 614 ASN ** A 928 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 171 ASN ** B 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 331 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.148232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.118111 restraints weight = 16501.759| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 1.75 r_work: 0.3311 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3187 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.2885 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= 0.137 Angle : 0.671 11.101 17283 Z= 0.342 Chirality : 0.044 0.176 1939 Planarity : 0.005 0.112 2186 Dihedral : 9.312 154.791 2012 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.51 % Favored : 93.36 % Rotamer: Outliers : 3.67 % Allowed : 23.17 % Favored : 73.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.39 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.21), residues: 1506 helix: 0.66 (0.20), residues: 671 sheet: -1.17 (0.34), residues: 223 loop : -2.36 (0.24), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 120 HIS 0.005 0.001 HIS A 103 PHE 0.029 0.001 PHE A 781 TYR 0.020 0.001 TYR A1146 ARG 0.007 0.000 ARG A 114 Details of bonding type rmsd link_NAG-ASN : bond 0.00277 ( 5) link_NAG-ASN : angle 2.51463 ( 15) link_BETA1-4 : bond 0.00491 ( 5) link_BETA1-4 : angle 1.44000 ( 15) link_ALPHA1-3 : bond 0.00837 ( 2) link_ALPHA1-3 : angle 1.79127 ( 6) hydrogen bonds : bond 0.04616 ( 553) hydrogen bonds : angle 4.80853 ( 1587) SS BOND : bond 0.00006 ( 1) SS BOND : angle 0.79251 ( 2) covalent geometry : bond 0.00308 (12708) covalent geometry : angle 0.66520 (17245) Misc. bond : bond 0.00523 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7451.78 seconds wall clock time: 134 minutes 43.75 seconds (8083.75 seconds total)