Starting phenix.real_space_refine on Wed Mar 4 01:12:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7q61_13849/03_2026/7q61_13849.cif Found real_map, /net/cci-nas-00/data/ceres_data/7q61_13849/03_2026/7q61_13849.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.88 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7q61_13849/03_2026/7q61_13849.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7q61_13849/03_2026/7q61_13849.map" model { file = "/net/cci-nas-00/data/ceres_data/7q61_13849/03_2026/7q61_13849.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7q61_13849/03_2026/7q61_13849.cif" } resolution = 2.88 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.005 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: 4 Type Number sf(0) Gaussians S 46 5.16 5 C 6095 2.51 5 N 1559 2.21 5 O 1835 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9535 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 9437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1210, 9437 Classifications: {'peptide': 1210} Link IDs: {'PCIS': 1, 'PTRANS': 61, 'TRANS': 1147} Chain breaks: 4 Chain: "X" 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: "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 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} 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 Time building chain proxies: 2.25, per 1000 atoms: 0.24 Number of scatterers: 9535 At special positions: 0 Unit cell: (89.286, 124.224, 124.224, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 46 16.00 O 1835 8.00 N 1559 7.00 C 6095 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 40 " - pdb=" SG CYS A 78 " distance=2.07 Simple disulfide: pdb=" SG CYS A 241 " - pdb=" SG CYS A 291 " distance=2.03 Simple disulfide: pdb=" SG CYS A 259 " - pdb=" SG CYS A 279 " distance=2.03 Simple disulfide: pdb=" SG CYS A 464 " - pdb=" SG CYS A 557 " distance=2.03 Simple disulfide: pdb=" SG CYS A 589 " - pdb=" SG CYS A 769 " distance=2.02 Simple disulfide: pdb=" SG CYS A 633 " - pdb=" SG CYS A 694 " distance=2.03 Simple disulfide: pdb=" SG CYS A 819 " - pdb=" SG CYS A 847 " distance=2.04 Simple disulfide: pdb=" SG CYS A 845 " - pdb=" SG CYS A 881 " distance=2.03 Simple disulfide: pdb=" SG CYS A 919 " - pdb=" SG CYS A1307 " distance=2.03 Simple disulfide: pdb=" SG CYS A1075 " - pdb=" SG CYS A1123 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG X 1 " - " NAG X 2 " NAG-ASN " NAG A1501 " - " ASN A 328 " " NAG A1502 " - " ASN A 609 " " NAG A1503 " - " ASN A 857 " " NAG B 1 " - " ASN A 867 " " NAG X 1 " - " ASN A 120 " Time building additional restraints: 0.63 Conformation dependent library (CDL) restraints added in 466.4 milliseconds 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2252 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 19 sheets defined 15.9% alpha, 36.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain 'A' and resid 508 through 512 removed outlier: 4.001A pdb=" N LYS A 511 " --> pdb=" O ASN A 508 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 602 removed outlier: 3.752A pdb=" N LEU A 601 " --> pdb=" O SER A 597 " (cutoff:3.500A) Processing helix chain 'A' and resid 608 through 615 Processing helix chain 'A' and resid 670 through 677 Processing helix chain 'A' and resid 837 through 839 No H-bonds generated for 'chain 'A' and resid 837 through 839' Processing helix chain 'A' and resid 970 through 973 Processing helix chain 'A' and resid 974 through 990 removed outlier: 4.031A pdb=" N ALA A 979 " --> pdb=" O MET A 975 " (cutoff:3.500A) Proline residue: A 980 - end of helix removed outlier: 4.145A pdb=" N TYR A 983 " --> pdb=" O ALA A 979 " (cutoff:3.500A) Processing helix chain 'A' and resid 995 through 1011 Processing helix chain 'A' and resid 1034 through 1046 Processing helix chain 'A' and resid 1047 through 1051 removed outlier: 4.044A pdb=" N LYS A1050 " --> pdb=" O GLN A1047 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N PHE A1051 " --> pdb=" O ALA A1048 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1047 through 1051' Processing helix chain 'A' and resid 1056 through 1070 removed outlier: 3.756A pdb=" N GLN A1060 " --> pdb=" O PRO A1056 " (cutoff:3.500A) Processing helix chain 'A' and resid 1093 through 1106 removed outlier: 3.930A pdb=" N LEU A1106 " --> pdb=" O THR A1102 " (cutoff:3.500A) Processing helix chain 'A' and resid 1114 through 1125 removed outlier: 4.078A pdb=" N GLN A1119 " --> pdb=" O PRO A1115 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N GLY A1120 " --> pdb=" O MET A1116 " (cutoff:3.500A) Processing helix chain 'A' and resid 1126 through 1131 removed outlier: 3.849A pdb=" N THR A1131 " --> pdb=" O SER A1127 " (cutoff:3.500A) Processing helix chain 'A' and resid 1134 through 1144 Processing helix chain 'A' and resid 1192 through 1205 Processing helix chain 'A' and resid 1211 through 1226 removed outlier: 3.645A pdb=" N TRP A1224 " --> pdb=" O SER A1220 " (cutoff:3.500A) Processing helix chain 'A' and resid 1239 through 1255 removed outlier: 3.640A pdb=" N VAL A1243 " --> pdb=" O GLN A1239 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 76 through 82 removed outlier: 8.357A pdb=" N LYS A 38 " --> pdb=" O PRO A 28 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 30 through 32 removed outlier: 6.822A pdb=" N PHE A 52 " --> pdb=" O GLU A 67 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N GLU A 67 " --> pdb=" O PHE A 52 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N VAL A 54 " --> pdb=" O LEU A 65 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 121 through 126 Processing sheet with id=AA4, first strand: chain 'A' and resid 130 through 131 removed outlier: 4.672A pdb=" N THR A 205 " --> pdb=" O VAL A 200 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N SER A 156 " --> pdb=" O GLU A 173 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 219 through 223 Processing sheet with id=AA6, first strand: chain 'A' and resid 229 through 230 removed outlier: 6.624A pdb=" N LEU A 229 " --> pdb=" O SER A 336 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N HIS A 310 " --> pdb=" O ILE A 335 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N GLN A 311 " --> pdb=" O LYS A 261 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N LYS A 261 " --> pdb=" O GLN A 311 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LYS A 278 " --> pdb=" O GLN A 260 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 398 through 403 removed outlier: 8.903A pdb=" N SER A 358 " --> pdb=" O THR A 347 " (cutoff:3.500A) removed outlier: 5.670A pdb=" N THR A 347 " --> pdb=" O SER A 358 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N LYS A 360 " --> pdb=" O GLU A 345 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N GLN A 436 " --> pdb=" O MET A 339 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N SER A 341 " --> pdb=" O GLN A 436 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 350 through 351 Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 455 Processing sheet with id=AB1, first strand: chain 'A' and resid 498 through 507 removed outlier: 5.220A pdb=" N LEU A 499 " --> pdb=" O GLY A 495 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N GLY A 495 " --> pdb=" O LEU A 499 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N SER A 488 " --> pdb=" O ILE A 539 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N ILE A 539 " --> pdb=" O SER A 488 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 563 through 567 Processing sheet with id=AB3, first strand: chain 'A' and resid 570 through 571 removed outlier: 3.507A pdb=" N GLN A 571 " --> pdb=" O THR A 785 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N ASP A 595 " --> pdb=" O THR A 736 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N THR A 736 " --> pdb=" O ASP A 595 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 570 through 571 removed outlier: 3.507A pdb=" N GLN A 571 " --> pdb=" O THR A 785 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 729 through 730 removed outlier: 3.505A pdb=" N ILE A 898 " --> pdb=" O ARG A 730 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 729 through 730 removed outlier: 3.505A pdb=" N ILE A 898 " --> pdb=" O ARG A 730 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 790 through 795 Processing sheet with id=AB8, first strand: chain 'A' and resid 908 through 918 Processing sheet with id=AB9, first strand: chain 'A' and resid 921 through 930 removed outlier: 5.040A pdb=" N LYS A 923 " --> pdb=" O GLY A1304 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N GLY A1304 " --> pdb=" O LYS A 923 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 1165 through 1166 401 hydrogen bonds defined for protein. 1110 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: 2.04 Time building geometry restraints manager: 0.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.36: 3076 1.36 - 1.50: 2688 1.50 - 1.64: 3914 1.64 - 1.78: 3 1.78 - 1.91: 66 Bond restraints: 9747 Sorted by residual: bond pdb=" CD GLU A 596 " pdb=" OE2 GLU A 596 " ideal model delta sigma weight residual 1.249 1.327 -0.078 1.90e-02 2.77e+03 1.69e+01 bond pdb=" CB CYS A 78 " pdb=" SG CYS A 78 " ideal model delta sigma weight residual 1.808 1.697 0.111 3.30e-02 9.18e+02 1.13e+01 bond pdb=" CB CYS A 40 " pdb=" SG CYS A 40 " ideal model delta sigma weight residual 1.808 1.915 -0.107 3.30e-02 9.18e+02 1.05e+01 bond pdb=" N SER A1024 " pdb=" CA SER A1024 " ideal model delta sigma weight residual 1.455 1.491 -0.036 1.25e-02 6.40e+03 8.37e+00 bond pdb=" N ARG A1029 " pdb=" CA ARG A1029 " ideal model delta sigma weight residual 1.456 1.488 -0.032 1.21e-02 6.83e+03 7.03e+00 ... (remaining 9742 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.58: 13173 5.58 - 11.15: 65 11.15 - 16.73: 4 16.73 - 22.30: 0 22.30 - 27.88: 1 Bond angle restraints: 13243 Sorted by residual: angle pdb=" CA CYS A 78 " pdb=" CB CYS A 78 " pdb=" SG CYS A 78 " ideal model delta sigma weight residual 114.40 142.28 -27.88 2.30e+00 1.89e-01 1.47e+02 angle pdb=" C ILE A 952 " pdb=" N MET A 953 " pdb=" CA MET A 953 " ideal model delta sigma weight residual 121.54 132.78 -11.24 1.91e+00 2.74e-01 3.46e+01 angle pdb=" CA TYR A1076 " pdb=" CB TYR A1076 " pdb=" CG TYR A1076 " ideal model delta sigma weight residual 113.90 123.65 -9.75 1.80e+00 3.09e-01 2.93e+01 angle pdb=" CA MET A 953 " pdb=" CB MET A 953 " pdb=" CG MET A 953 " ideal model delta sigma weight residual 114.10 124.83 -10.73 2.00e+00 2.50e-01 2.88e+01 angle pdb=" C ASN A 459 " pdb=" CA ASN A 459 " pdb=" CB ASN A 459 " ideal model delta sigma weight residual 117.23 110.43 6.80 1.36e+00 5.41e-01 2.50e+01 ... (remaining 13238 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.49: 5567 20.49 - 40.97: 288 40.97 - 61.46: 48 61.46 - 81.95: 20 81.95 - 102.43: 18 Dihedral angle restraints: 5941 sinusoidal: 2432 harmonic: 3509 Sorted by residual: dihedral pdb=" CA PHE A 616 " pdb=" C PHE A 616 " pdb=" N PRO A 617 " pdb=" CA PRO A 617 " ideal model delta harmonic sigma weight residual -180.00 -138.24 -41.76 0 5.00e+00 4.00e-02 6.98e+01 dihedral pdb=" CA PRO A1056 " pdb=" C PRO A1056 " pdb=" N LYS A1057 " pdb=" CA LYS A1057 " ideal model delta harmonic sigma weight residual -180.00 -155.10 -24.90 0 5.00e+00 4.00e-02 2.48e+01 dihedral pdb=" CA TYR A1256 " pdb=" C TYR A1256 " pdb=" N MET A1257 " pdb=" CA MET A1257 " ideal model delta harmonic sigma weight residual 180.00 156.00 24.00 0 5.00e+00 4.00e-02 2.30e+01 ... (remaining 5938 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 1181 0.066 - 0.131: 265 0.131 - 0.197: 54 0.197 - 0.263: 16 0.263 - 0.328: 5 Chirality restraints: 1521 Sorted by residual: chirality pdb=" CA CYS A 78 " pdb=" N CYS A 78 " pdb=" C CYS A 78 " pdb=" CB CYS A 78 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.69e+00 chirality pdb=" C1 NAG A1502 " pdb=" ND2 ASN A 609 " pdb=" C2 NAG A1502 " pdb=" O5 NAG A1502 " both_signs ideal model delta sigma weight residual False -2.40 -2.08 -0.32 2.00e-01 2.50e+01 2.54e+00 chirality pdb=" CB ILE A 952 " pdb=" CA ILE A 952 " pdb=" CG1 ILE A 952 " pdb=" CG2 ILE A 952 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.30 2.00e-01 2.50e+01 2.25e+00 ... (remaining 1518 not shown) Planarity restraints: 1699 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A 399 " 0.066 5.00e-02 4.00e+02 1.00e-01 1.60e+01 pdb=" N PRO A 400 " -0.173 5.00e-02 4.00e+02 pdb=" CA PRO A 400 " 0.053 5.00e-02 4.00e+02 pdb=" CD PRO A 400 " 0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 733 " 0.016 2.00e-02 2.50e+03 2.20e-02 8.43e+00 pdb=" CG PHE A 733 " -0.050 2.00e-02 2.50e+03 pdb=" CD1 PHE A 733 " 0.018 2.00e-02 2.50e+03 pdb=" CD2 PHE A 733 " 0.017 2.00e-02 2.50e+03 pdb=" CE1 PHE A 733 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 733 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE A 733 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP A1055 " 0.044 5.00e-02 4.00e+02 6.74e-02 7.27e+00 pdb=" N PRO A1056 " -0.117 5.00e-02 4.00e+02 pdb=" CA PRO A1056 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO A1056 " 0.038 5.00e-02 4.00e+02 ... (remaining 1696 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 2327 2.80 - 3.33: 7797 3.33 - 3.85: 15779 3.85 - 4.38: 17633 4.38 - 4.90: 31021 Nonbonded interactions: 74557 Sorted by model distance: nonbonded pdb=" OE2 GLU A 320 " pdb=" OG1 THR A 323 " model vdw 2.275 3.040 nonbonded pdb=" OD1 ASP A 127 " pdb=" OH TYR A 131 " model vdw 2.319 3.040 nonbonded pdb=" O CYS A 557 " pdb=" OH TYR A 613 " model vdw 2.329 3.040 nonbonded pdb=" O ALA A 827 " pdb=" OH TYR A 832 " model vdw 2.333 3.040 nonbonded pdb=" OE1 GLN A 161 " pdb=" OG1 THR A 955 " model vdw 2.339 3.040 ... (remaining 74552 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'X' } 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: 12.470 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: 0.260 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 10.260 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 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 : 0.006 0.111 9764 Z= 0.270 Angle : 1.114 27.881 13284 Z= 0.557 Chirality : 0.063 0.328 1521 Planarity : 0.009 0.100 1694 Dihedral : 14.479 102.431 3659 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.25 % Allowed : 4.50 % Favored : 95.25 % Rotamer: Outliers : 0.10 % Allowed : 0.19 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 1.61 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.84 (0.22), residues: 1200 helix: -3.00 (0.24), residues: 169 sheet: -0.23 (0.23), residues: 486 loop : -1.47 (0.24), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 730 TYR 0.040 0.003 TYR A1076 PHE 0.050 0.004 PHE A 733 TRP 0.038 0.002 TRP A1065 HIS 0.007 0.001 HIS A 75 Details of bonding type rmsd covalent geometry : bond 0.00583 ( 9747) covalent geometry : angle 1.09195 (13243) SS BOND : bond 0.01261 ( 10) SS BOND : angle 3.76198 ( 20) hydrogen bonds : bond 0.11416 ( 394) hydrogen bonds : angle 6.86483 ( 1110) link_BETA1-4 : bond 0.00678 ( 2) link_BETA1-4 : angle 5.96913 ( 6) link_NAG-ASN : bond 0.00682 ( 5) link_NAG-ASN : angle 3.64365 ( 15) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 111 time to evaluate : 0.303 Fit side-chains revert: symmetry clash REVERT: A 310 HIS cc_start: 0.7284 (m90) cc_final: 0.6932 (m90) REVERT: A 395 ASN cc_start: 0.9107 (p0) cc_final: 0.8902 (p0) REVERT: A 548 ASP cc_start: 0.7744 (t70) cc_final: 0.7307 (t70) REVERT: A 1015 MET cc_start: 0.7641 (pmm) cc_final: 0.7375 (pmm) REVERT: A 1045 PHE cc_start: 0.9227 (m-80) cc_final: 0.8761 (m-80) REVERT: A 1311 GLN cc_start: 0.7773 (tt0) cc_final: 0.7512 (tt0) outliers start: 1 outliers final: 0 residues processed: 112 average time/residue: 0.4229 time to fit residues: 51.6340 Evaluate side-chains 74 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 108 optimal weight: 0.8980 chunk 49 optimal weight: 0.8980 chunk 97 optimal weight: 10.0000 chunk 113 optimal weight: 0.9980 chunk 53 optimal weight: 0.5980 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.0980 chunk 51 optimal weight: 0.9990 chunk 117 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 GLN A 311 GLN A 313 ASN A 332 ASN A 384 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.119258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.083929 restraints weight = 22044.994| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 3.76 r_work: 0.3366 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.1302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 9764 Z= 0.143 Angle : 0.699 11.641 13284 Z= 0.343 Chirality : 0.046 0.291 1521 Planarity : 0.005 0.063 1694 Dihedral : 7.882 72.800 1438 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.83 % Favored : 96.00 % Rotamer: Outliers : 1.43 % Allowed : 9.82 % Favored : 88.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 1.61 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.23 (0.23), residues: 1200 helix: -1.41 (0.32), residues: 184 sheet: -0.15 (0.23), residues: 489 loop : -1.12 (0.26), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 602 TYR 0.021 0.001 TYR A1076 PHE 0.017 0.002 PHE A 107 TRP 0.019 0.002 TRP A1065 HIS 0.003 0.001 HIS A1018 Details of bonding type rmsd covalent geometry : bond 0.00313 ( 9747) covalent geometry : angle 0.68515 (13243) SS BOND : bond 0.00394 ( 10) SS BOND : angle 2.04384 ( 20) hydrogen bonds : bond 0.03725 ( 394) hydrogen bonds : angle 5.68203 ( 1110) link_BETA1-4 : bond 0.00283 ( 2) link_BETA1-4 : angle 2.93259 ( 6) link_NAG-ASN : bond 0.00481 ( 5) link_NAG-ASN : angle 2.94706 ( 15) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 83 time to evaluate : 0.366 Fit side-chains revert: symmetry clash REVERT: A 49 ASP cc_start: 0.8952 (p0) cc_final: 0.8641 (p0) REVERT: A 310 HIS cc_start: 0.7786 (m90) cc_final: 0.7235 (m90) REVERT: A 381 TYR cc_start: 0.8107 (m-10) cc_final: 0.7889 (m-10) REVERT: A 395 ASN cc_start: 0.9446 (p0) cc_final: 0.9180 (p0) REVERT: A 548 ASP cc_start: 0.8377 (t70) cc_final: 0.8002 (t70) REVERT: A 945 TYR cc_start: 0.8140 (OUTLIER) cc_final: 0.7039 (p90) REVERT: A 953 MET cc_start: 0.5423 (OUTLIER) cc_final: 0.5118 (ppp) REVERT: A 1005 PHE cc_start: 0.8253 (OUTLIER) cc_final: 0.7132 (m-80) REVERT: A 1015 MET cc_start: 0.7842 (pmm) cc_final: 0.7563 (pmm) REVERT: A 1045 PHE cc_start: 0.9404 (m-80) cc_final: 0.8856 (m-80) REVERT: A 1213 LYS cc_start: 0.8857 (mmpt) cc_final: 0.8501 (mmmt) REVERT: A 1311 GLN cc_start: 0.8399 (tt0) cc_final: 0.8047 (tt0) outliers start: 15 outliers final: 7 residues processed: 91 average time/residue: 0.3580 time to fit residues: 36.0508 Evaluate side-chains 80 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 70 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 682 ILE Chi-restraints excluded: chain A residue 790 PHE Chi-restraints excluded: chain A residue 945 TYR Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 953 MET Chi-restraints excluded: chain A residue 982 ILE Chi-restraints excluded: chain A residue 1005 PHE Chi-restraints excluded: chain A residue 1171 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 17 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 34 optimal weight: 9.9990 chunk 57 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 18 optimal weight: 0.9980 chunk 25 optimal weight: 3.9990 chunk 89 optimal weight: 5.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 441 HIS ** A 855 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 865 HIS A 914 HIS A 958 GLN A1246 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.115377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.080198 restraints weight = 21912.922| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 4.08 r_work: 0.3226 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.1875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 9764 Z= 0.220 Angle : 0.726 12.011 13284 Z= 0.354 Chirality : 0.047 0.294 1521 Planarity : 0.005 0.054 1694 Dihedral : 6.665 57.113 1438 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.42 % Favored : 95.42 % Rotamer: Outliers : 2.57 % Allowed : 12.39 % Favored : 85.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 1.61 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.73 (0.24), residues: 1200 helix: -0.41 (0.37), residues: 183 sheet: -0.13 (0.23), residues: 509 loop : -0.72 (0.28), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 610 TYR 0.024 0.002 TYR A1076 PHE 0.016 0.002 PHE A 733 TRP 0.009 0.002 TRP A1036 HIS 0.004 0.001 HIS A 75 Details of bonding type rmsd covalent geometry : bond 0.00500 ( 9747) covalent geometry : angle 0.71247 (13243) SS BOND : bond 0.00690 ( 10) SS BOND : angle 2.29024 ( 20) hydrogen bonds : bond 0.03718 ( 394) hydrogen bonds : angle 5.48021 ( 1110) link_BETA1-4 : bond 0.00281 ( 2) link_BETA1-4 : angle 3.14963 ( 6) link_NAG-ASN : bond 0.00545 ( 5) link_NAG-ASN : angle 2.69548 ( 15) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 68 time to evaluate : 0.402 Fit side-chains revert: symmetry clash REVERT: A 310 HIS cc_start: 0.7991 (m90) cc_final: 0.7402 (m90) REVERT: A 381 TYR cc_start: 0.8156 (m-10) cc_final: 0.7906 (m-10) REVERT: A 395 ASN cc_start: 0.9544 (p0) cc_final: 0.9270 (p0) REVERT: A 548 ASP cc_start: 0.8497 (t70) cc_final: 0.8179 (t0) REVERT: A 945 TYR cc_start: 0.8266 (OUTLIER) cc_final: 0.7002 (p90) REVERT: A 966 MET cc_start: -0.3070 (ttt) cc_final: -0.3479 (ttm) REVERT: A 1015 MET cc_start: 0.8024 (pmm) cc_final: 0.7700 (pmm) REVERT: A 1045 PHE cc_start: 0.9528 (m-80) cc_final: 0.9013 (m-80) REVERT: A 1213 LYS cc_start: 0.8881 (mmpt) cc_final: 0.8623 (mmpt) REVERT: A 1311 GLN cc_start: 0.8240 (tt0) cc_final: 0.7808 (tt0) outliers start: 27 outliers final: 17 residues processed: 84 average time/residue: 0.3838 time to fit residues: 35.9154 Evaluate side-chains 83 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 65 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 107 PHE Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 360 LYS Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 682 ILE Chi-restraints excluded: chain A residue 790 PHE Chi-restraints excluded: chain A residue 792 VAL Chi-restraints excluded: chain A residue 811 THR Chi-restraints excluded: chain A residue 945 TYR Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 982 ILE Chi-restraints excluded: chain A residue 1171 ILE Chi-restraints excluded: chain A residue 1280 SER Chi-restraints excluded: chain A residue 1307 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 108 optimal weight: 0.7980 chunk 64 optimal weight: 0.7980 chunk 101 optimal weight: 7.9990 chunk 81 optimal weight: 4.9990 chunk 97 optimal weight: 10.0000 chunk 106 optimal weight: 4.9990 chunk 42 optimal weight: 1.9990 chunk 111 optimal weight: 0.2980 chunk 77 optimal weight: 0.8980 chunk 104 optimal weight: 4.9990 chunk 7 optimal weight: 6.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 855 HIS ** 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 = 0.4067 r_free = 0.4067 target = 0.115743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.080632 restraints weight = 22111.179| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 4.04 r_work: 0.3241 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.2080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 9764 Z= 0.167 Angle : 0.666 12.930 13284 Z= 0.325 Chirality : 0.045 0.275 1521 Planarity : 0.004 0.055 1694 Dihedral : 5.625 40.972 1438 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.00 % Favored : 95.83 % Rotamer: Outliers : 2.86 % Allowed : 13.92 % Favored : 83.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 1.61 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.46 (0.25), residues: 1200 helix: 0.09 (0.38), residues: 181 sheet: 0.00 (0.23), residues: 511 loop : -0.64 (0.29), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 610 TYR 0.018 0.001 TYR A 620 PHE 0.016 0.001 PHE A 107 TRP 0.010 0.001 TRP A1036 HIS 0.003 0.001 HIS A 75 Details of bonding type rmsd covalent geometry : bond 0.00377 ( 9747) covalent geometry : angle 0.65308 (13243) SS BOND : bond 0.00456 ( 10) SS BOND : angle 2.11800 ( 20) hydrogen bonds : bond 0.03398 ( 394) hydrogen bonds : angle 5.31673 ( 1110) link_BETA1-4 : bond 0.00373 ( 2) link_BETA1-4 : angle 2.98664 ( 6) link_NAG-ASN : bond 0.00503 ( 5) link_NAG-ASN : angle 2.64456 ( 15) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 71 time to evaluate : 0.381 Fit side-chains revert: symmetry clash REVERT: A 310 HIS cc_start: 0.7968 (m90) cc_final: 0.7354 (m90) REVERT: A 381 TYR cc_start: 0.8151 (m-10) cc_final: 0.7846 (m-10) REVERT: A 395 ASN cc_start: 0.9532 (p0) cc_final: 0.9263 (p0) REVERT: A 548 ASP cc_start: 0.8465 (t70) cc_final: 0.8150 (t0) REVERT: A 945 TYR cc_start: 0.8250 (OUTLIER) cc_final: 0.6981 (p90) REVERT: A 966 MET cc_start: -0.2998 (ttt) cc_final: -0.3372 (ttm) REVERT: A 1015 MET cc_start: 0.7999 (pmm) cc_final: 0.7652 (pmm) REVERT: A 1045 PHE cc_start: 0.9499 (m-80) cc_final: 0.8997 (m-80) REVERT: A 1213 LYS cc_start: 0.8899 (mmpt) cc_final: 0.8636 (mmpt) REVERT: A 1301 GLU cc_start: 0.8837 (OUTLIER) cc_final: 0.8502 (pt0) REVERT: A 1311 GLN cc_start: 0.8218 (tt0) cc_final: 0.7787 (tt0) outliers start: 30 outliers final: 15 residues processed: 93 average time/residue: 0.3706 time to fit residues: 38.5121 Evaluate side-chains 82 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 65 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 PHE Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 682 ILE Chi-restraints excluded: chain A residue 760 ILE Chi-restraints excluded: chain A residue 790 PHE Chi-restraints excluded: chain A residue 792 VAL Chi-restraints excluded: chain A residue 822 VAL Chi-restraints excluded: chain A residue 945 TYR Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 982 ILE Chi-restraints excluded: chain A residue 1171 ILE Chi-restraints excluded: chain A residue 1301 GLU Chi-restraints excluded: chain A residue 1307 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 41 optimal weight: 4.9990 chunk 110 optimal weight: 0.8980 chunk 7 optimal weight: 6.9990 chunk 120 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 77 optimal weight: 0.5980 chunk 58 optimal weight: 0.8980 chunk 30 optimal weight: 6.9990 chunk 79 optimal weight: 5.9990 chunk 72 optimal weight: 0.6980 chunk 42 optimal weight: 0.7980 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 855 HIS ** 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 = 0.4071 r_free = 0.4071 target = 0.116028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.080842 restraints weight = 21962.298| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 4.01 r_work: 0.3246 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.2203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 9764 Z= 0.150 Angle : 0.664 12.459 13284 Z= 0.322 Chirality : 0.045 0.263 1521 Planarity : 0.004 0.054 1694 Dihedral : 5.270 35.165 1438 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.25 % Allowed : 4.17 % Favored : 95.58 % Rotamer: Outliers : 2.67 % Allowed : 15.06 % Favored : 82.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 1.61 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.25), residues: 1200 helix: 0.30 (0.38), residues: 182 sheet: 0.01 (0.23), residues: 515 loop : -0.53 (0.29), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 610 TYR 0.017 0.001 TYR A1076 PHE 0.016 0.001 PHE A 107 TRP 0.009 0.001 TRP A 619 HIS 0.002 0.001 HIS A 75 Details of bonding type rmsd covalent geometry : bond 0.00341 ( 9747) covalent geometry : angle 0.65140 (13243) SS BOND : bond 0.00495 ( 10) SS BOND : angle 2.00269 ( 20) hydrogen bonds : bond 0.03297 ( 394) hydrogen bonds : angle 5.21420 ( 1110) link_BETA1-4 : bond 0.00330 ( 2) link_BETA1-4 : angle 2.97872 ( 6) link_NAG-ASN : bond 0.00484 ( 5) link_NAG-ASN : angle 2.59342 ( 15) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 66 time to evaluate : 0.279 Fit side-chains revert: symmetry clash REVERT: A 310 HIS cc_start: 0.7948 (m90) cc_final: 0.7339 (m90) REVERT: A 381 TYR cc_start: 0.8129 (m-10) cc_final: 0.7874 (m-10) REVERT: A 395 ASN cc_start: 0.9552 (p0) cc_final: 0.9289 (p0) REVERT: A 548 ASP cc_start: 0.8440 (t70) cc_final: 0.8197 (t70) REVERT: A 945 TYR cc_start: 0.8239 (OUTLIER) cc_final: 0.7010 (p90) REVERT: A 966 MET cc_start: -0.2983 (ttt) cc_final: -0.3373 (ttm) REVERT: A 1015 MET cc_start: 0.7987 (pmm) cc_final: 0.7630 (pmm) REVERT: A 1045 PHE cc_start: 0.9485 (m-80) cc_final: 0.8961 (m-80) REVERT: A 1213 LYS cc_start: 0.8921 (mmpt) cc_final: 0.8644 (mmpt) REVERT: A 1301 GLU cc_start: 0.8835 (OUTLIER) cc_final: 0.8511 (pt0) outliers start: 28 outliers final: 18 residues processed: 89 average time/residue: 0.3395 time to fit residues: 33.9658 Evaluate side-chains 85 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 65 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 107 PHE Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 682 ILE Chi-restraints excluded: chain A residue 760 ILE Chi-restraints excluded: chain A residue 790 PHE Chi-restraints excluded: chain A residue 792 VAL Chi-restraints excluded: chain A residue 811 THR Chi-restraints excluded: chain A residue 945 TYR Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 982 ILE Chi-restraints excluded: chain A residue 1280 SER Chi-restraints excluded: chain A residue 1301 GLU Chi-restraints excluded: chain A residue 1307 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 114 optimal weight: 1.9990 chunk 73 optimal weight: 0.9980 chunk 21 optimal weight: 4.9990 chunk 78 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 15 optimal weight: 0.2980 chunk 7 optimal weight: 0.9980 chunk 18 optimal weight: 3.9990 chunk 32 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 728 GLN ** A 855 HIS ** 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 = 0.4069 r_free = 0.4069 target = 0.115825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.080408 restraints weight = 21884.909| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 4.16 r_work: 0.3230 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.2353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 9764 Z= 0.153 Angle : 0.658 11.633 13284 Z= 0.319 Chirality : 0.044 0.251 1521 Planarity : 0.004 0.053 1694 Dihedral : 5.066 34.805 1438 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.25 % Allowed : 4.00 % Favored : 95.75 % Rotamer: Outliers : 3.05 % Allowed : 15.16 % Favored : 81.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 1.61 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.24 (0.25), residues: 1200 helix: 0.39 (0.38), residues: 188 sheet: 0.04 (0.23), residues: 515 loop : -0.43 (0.29), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 610 TYR 0.014 0.001 TYR A1076 PHE 0.016 0.001 PHE A 107 TRP 0.010 0.001 TRP A 619 HIS 0.002 0.001 HIS A 75 Details of bonding type rmsd covalent geometry : bond 0.00348 ( 9747) covalent geometry : angle 0.64503 (13243) SS BOND : bond 0.00450 ( 10) SS BOND : angle 2.01995 ( 20) hydrogen bonds : bond 0.03247 ( 394) hydrogen bonds : angle 5.13453 ( 1110) link_BETA1-4 : bond 0.00316 ( 2) link_BETA1-4 : angle 3.00195 ( 6) link_NAG-ASN : bond 0.00432 ( 5) link_NAG-ASN : angle 2.57030 ( 15) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 71 time to evaluate : 0.362 Fit side-chains revert: symmetry clash REVERT: A 103 ASN cc_start: 0.8621 (m-40) cc_final: 0.8290 (t0) REVERT: A 310 HIS cc_start: 0.7937 (m90) cc_final: 0.7432 (m90) REVERT: A 381 TYR cc_start: 0.8109 (m-10) cc_final: 0.7845 (m-10) REVERT: A 395 ASN cc_start: 0.9560 (p0) cc_final: 0.9299 (p0) REVERT: A 471 LEU cc_start: 0.8896 (OUTLIER) cc_final: 0.8654 (tm) REVERT: A 548 ASP cc_start: 0.8459 (t70) cc_final: 0.8227 (t70) REVERT: A 945 TYR cc_start: 0.8239 (OUTLIER) cc_final: 0.7007 (p90) REVERT: A 966 MET cc_start: -0.2947 (ttt) cc_final: -0.3358 (ttm) REVERT: A 1015 MET cc_start: 0.8015 (pmm) cc_final: 0.7658 (pmm) REVERT: A 1045 PHE cc_start: 0.9453 (m-80) cc_final: 0.8941 (m-80) REVERT: A 1213 LYS cc_start: 0.8922 (mmpt) cc_final: 0.8646 (mmpt) REVERT: A 1301 GLU cc_start: 0.8849 (OUTLIER) cc_final: 0.8531 (pt0) outliers start: 32 outliers final: 19 residues processed: 99 average time/residue: 0.3232 time to fit residues: 35.9180 Evaluate side-chains 87 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 65 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 107 PHE Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 682 ILE Chi-restraints excluded: chain A residue 760 ILE Chi-restraints excluded: chain A residue 790 PHE Chi-restraints excluded: chain A residue 792 VAL Chi-restraints excluded: chain A residue 811 THR Chi-restraints excluded: chain A residue 822 VAL Chi-restraints excluded: chain A residue 945 TYR Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 982 ILE Chi-restraints excluded: chain A residue 1171 ILE Chi-restraints excluded: chain A residue 1280 SER Chi-restraints excluded: chain A residue 1301 GLU Chi-restraints excluded: chain A residue 1307 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 7 optimal weight: 0.9990 chunk 79 optimal weight: 0.0980 chunk 28 optimal weight: 4.9990 chunk 18 optimal weight: 0.8980 chunk 115 optimal weight: 0.8980 chunk 83 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 39 optimal weight: 4.9990 chunk 8 optimal weight: 0.6980 chunk 51 optimal weight: 0.9980 chunk 50 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 855 HIS ** 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 = 0.4077 r_free = 0.4077 target = 0.116387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.079917 restraints weight = 21964.049| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 3.86 r_work: 0.3259 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.2414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 9764 Z= 0.137 Angle : 0.671 12.743 13284 Z= 0.321 Chirality : 0.044 0.247 1521 Planarity : 0.004 0.052 1694 Dihedral : 4.943 34.022 1438 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.25 % Allowed : 4.17 % Favored : 95.58 % Rotamer: Outliers : 2.96 % Allowed : 16.21 % Favored : 80.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 1.61 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.25), residues: 1200 helix: 0.47 (0.39), residues: 188 sheet: 0.07 (0.23), residues: 505 loop : -0.41 (0.29), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 610 TYR 0.013 0.001 TYR A1076 PHE 0.016 0.001 PHE A 107 TRP 0.010 0.001 TRP A 619 HIS 0.002 0.000 HIS A 75 Details of bonding type rmsd covalent geometry : bond 0.00313 ( 9747) covalent geometry : angle 0.65876 (13243) SS BOND : bond 0.00560 ( 10) SS BOND : angle 1.94385 ( 20) hydrogen bonds : bond 0.03130 ( 394) hydrogen bonds : angle 5.08763 ( 1110) link_BETA1-4 : bond 0.00305 ( 2) link_BETA1-4 : angle 2.99439 ( 6) link_NAG-ASN : bond 0.00446 ( 5) link_NAG-ASN : angle 2.55457 ( 15) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 72 time to evaluate : 0.357 Fit side-chains revert: symmetry clash REVERT: A 103 ASN cc_start: 0.8577 (m-40) cc_final: 0.8271 (t0) REVERT: A 310 HIS cc_start: 0.7850 (m90) cc_final: 0.7592 (m90) REVERT: A 381 TYR cc_start: 0.8107 (m-10) cc_final: 0.7848 (m-10) REVERT: A 395 ASN cc_start: 0.9556 (p0) cc_final: 0.9288 (p0) REVERT: A 471 LEU cc_start: 0.8941 (OUTLIER) cc_final: 0.8698 (tm) REVERT: A 548 ASP cc_start: 0.8418 (t70) cc_final: 0.8212 (t70) REVERT: A 945 TYR cc_start: 0.8213 (OUTLIER) cc_final: 0.6990 (p90) REVERT: A 966 MET cc_start: -0.2988 (ttt) cc_final: -0.3370 (ttm) REVERT: A 978 PHE cc_start: 0.8997 (t80) cc_final: 0.8662 (t80) REVERT: A 1015 MET cc_start: 0.7962 (pmm) cc_final: 0.7606 (pmm) REVERT: A 1045 PHE cc_start: 0.9421 (m-80) cc_final: 0.8860 (m-80) REVERT: A 1213 LYS cc_start: 0.8927 (mmpt) cc_final: 0.8635 (mmpt) outliers start: 31 outliers final: 19 residues processed: 97 average time/residue: 0.3270 time to fit residues: 35.6276 Evaluate side-chains 90 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 69 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 PHE Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 320 GLU Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 682 ILE Chi-restraints excluded: chain A residue 760 ILE Chi-restraints excluded: chain A residue 790 PHE Chi-restraints excluded: chain A residue 792 VAL Chi-restraints excluded: chain A residue 811 THR Chi-restraints excluded: chain A residue 822 VAL Chi-restraints excluded: chain A residue 945 TYR Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 982 ILE Chi-restraints excluded: chain A residue 1171 ILE Chi-restraints excluded: chain A residue 1307 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 13 optimal weight: 0.9990 chunk 102 optimal weight: 0.9980 chunk 91 optimal weight: 9.9990 chunk 86 optimal weight: 7.9990 chunk 7 optimal weight: 4.9990 chunk 65 optimal weight: 0.0030 chunk 97 optimal weight: 6.9990 chunk 15 optimal weight: 0.0870 chunk 107 optimal weight: 3.9990 chunk 53 optimal weight: 0.9990 chunk 66 optimal weight: 0.9990 overall best weight: 0.6172 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 855 HIS ** 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 = 0.4077 r_free = 0.4077 target = 0.116390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.079986 restraints weight = 21887.539| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 3.85 r_work: 0.3262 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.2498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9764 Z= 0.135 Angle : 0.678 12.684 13284 Z= 0.323 Chirality : 0.044 0.240 1521 Planarity : 0.004 0.052 1694 Dihedral : 4.845 34.349 1438 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.17 % Favored : 95.67 % Rotamer: Outliers : 2.76 % Allowed : 16.49 % Favored : 80.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 1.61 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.25), residues: 1200 helix: 0.47 (0.39), residues: 190 sheet: 0.12 (0.23), residues: 505 loop : -0.35 (0.29), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 30 TYR 0.012 0.001 TYR A1076 PHE 0.016 0.001 PHE A 107 TRP 0.011 0.001 TRP A 619 HIS 0.002 0.000 HIS A 75 Details of bonding type rmsd covalent geometry : bond 0.00311 ( 9747) covalent geometry : angle 0.66672 (13243) SS BOND : bond 0.00512 ( 10) SS BOND : angle 1.88987 ( 20) hydrogen bonds : bond 0.03142 ( 394) hydrogen bonds : angle 5.04594 ( 1110) link_BETA1-4 : bond 0.00316 ( 2) link_BETA1-4 : angle 3.00397 ( 6) link_NAG-ASN : bond 0.00401 ( 5) link_NAG-ASN : angle 2.50583 ( 15) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 72 time to evaluate : 0.372 Fit side-chains revert: symmetry clash REVERT: A 103 ASN cc_start: 0.8547 (m-40) cc_final: 0.8245 (t0) REVERT: A 310 HIS cc_start: 0.7979 (m90) cc_final: 0.7617 (m-70) REVERT: A 381 TYR cc_start: 0.8104 (m-10) cc_final: 0.7844 (m-10) REVERT: A 395 ASN cc_start: 0.9556 (p0) cc_final: 0.9292 (p0) REVERT: A 462 LEU cc_start: 0.8692 (OUTLIER) cc_final: 0.8461 (mm) REVERT: A 471 LEU cc_start: 0.8936 (OUTLIER) cc_final: 0.8692 (tm) REVERT: A 548 ASP cc_start: 0.8379 (t70) cc_final: 0.8168 (t70) REVERT: A 945 TYR cc_start: 0.8201 (OUTLIER) cc_final: 0.6988 (p90) REVERT: A 966 MET cc_start: -0.2943 (ttt) cc_final: -0.3170 (ttt) REVERT: A 1015 MET cc_start: 0.7973 (pmm) cc_final: 0.7620 (pmm) REVERT: A 1045 PHE cc_start: 0.9412 (m-80) cc_final: 0.8846 (m-80) REVERT: A 1213 LYS cc_start: 0.8932 (mmpt) cc_final: 0.8639 (mmpt) REVERT: A 1301 GLU cc_start: 0.8841 (OUTLIER) cc_final: 0.8513 (pt0) outliers start: 29 outliers final: 20 residues processed: 96 average time/residue: 0.3720 time to fit residues: 39.7438 Evaluate side-chains 93 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 69 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 107 PHE Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 320 GLU Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 682 ILE Chi-restraints excluded: chain A residue 760 ILE Chi-restraints excluded: chain A residue 790 PHE Chi-restraints excluded: chain A residue 792 VAL Chi-restraints excluded: chain A residue 811 THR Chi-restraints excluded: chain A residue 822 VAL Chi-restraints excluded: chain A residue 945 TYR Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 982 ILE Chi-restraints excluded: chain A residue 1171 ILE Chi-restraints excluded: chain A residue 1301 GLU Chi-restraints excluded: chain A residue 1307 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 52 optimal weight: 0.6980 chunk 89 optimal weight: 4.9990 chunk 83 optimal weight: 3.9990 chunk 84 optimal weight: 0.9980 chunk 69 optimal weight: 0.5980 chunk 120 optimal weight: 0.9990 chunk 70 optimal weight: 0.3980 chunk 102 optimal weight: 0.7980 chunk 1 optimal weight: 0.8980 chunk 65 optimal weight: 0.0270 chunk 30 optimal weight: 4.9990 overall best weight: 0.5038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 855 HIS ** 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 = 0.4084 r_free = 0.4084 target = 0.116733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.080536 restraints weight = 21852.407| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 3.85 r_work: 0.3273 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.2560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9764 Z= 0.128 Angle : 0.698 12.578 13284 Z= 0.331 Chirality : 0.045 0.254 1521 Planarity : 0.004 0.050 1694 Dihedral : 4.771 33.625 1438 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.92 % Favored : 95.92 % Rotamer: Outliers : 2.48 % Allowed : 17.06 % Favored : 80.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 1.61 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.25), residues: 1200 helix: 0.55 (0.39), residues: 190 sheet: 0.17 (0.23), residues: 504 loop : -0.34 (0.29), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 610 TYR 0.014 0.001 TYR A1232 PHE 0.016 0.001 PHE A 107 TRP 0.013 0.001 TRP A 619 HIS 0.002 0.000 HIS A 75 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 9747) covalent geometry : angle 0.68779 (13243) SS BOND : bond 0.00485 ( 10) SS BOND : angle 1.82198 ( 20) hydrogen bonds : bond 0.03084 ( 394) hydrogen bonds : angle 5.00129 ( 1110) link_BETA1-4 : bond 0.00440 ( 2) link_BETA1-4 : angle 2.94329 ( 6) link_NAG-ASN : bond 0.00395 ( 5) link_NAG-ASN : angle 2.49564 ( 15) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 74 time to evaluate : 0.360 Fit side-chains REVERT: A 103 ASN cc_start: 0.8503 (m-40) cc_final: 0.8228 (t0) REVERT: A 310 HIS cc_start: 0.7907 (m90) cc_final: 0.7561 (m-70) REVERT: A 381 TYR cc_start: 0.8110 (m-10) cc_final: 0.7848 (m-10) REVERT: A 395 ASN cc_start: 0.9560 (p0) cc_final: 0.9285 (p0) REVERT: A 462 LEU cc_start: 0.8706 (OUTLIER) cc_final: 0.8484 (mm) REVERT: A 471 LEU cc_start: 0.8948 (OUTLIER) cc_final: 0.8645 (tm) REVERT: A 548 ASP cc_start: 0.8333 (t70) cc_final: 0.8126 (t70) REVERT: A 945 TYR cc_start: 0.8165 (OUTLIER) cc_final: 0.6974 (p90) REVERT: A 953 MET cc_start: 0.5963 (ptm) cc_final: 0.5325 (ptp) REVERT: A 1005 PHE cc_start: 0.8496 (m-80) cc_final: 0.7998 (m-80) REVERT: A 1015 MET cc_start: 0.7960 (pmm) cc_final: 0.7602 (pmm) REVERT: A 1045 PHE cc_start: 0.9390 (m-80) cc_final: 0.8828 (m-80) REVERT: A 1213 LYS cc_start: 0.8936 (mmpt) cc_final: 0.8644 (mmpt) REVERT: A 1301 GLU cc_start: 0.8844 (OUTLIER) cc_final: 0.8515 (pt0) outliers start: 26 outliers final: 17 residues processed: 95 average time/residue: 0.3651 time to fit residues: 38.7231 Evaluate side-chains 94 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 73 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 107 PHE Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 320 GLU Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 682 ILE Chi-restraints excluded: chain A residue 790 PHE Chi-restraints excluded: chain A residue 792 VAL Chi-restraints excluded: chain A residue 811 THR Chi-restraints excluded: chain A residue 822 VAL Chi-restraints excluded: chain A residue 945 TYR Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 982 ILE Chi-restraints excluded: chain A residue 1301 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 3 optimal weight: 5.9990 chunk 53 optimal weight: 1.9990 chunk 67 optimal weight: 0.7980 chunk 110 optimal weight: 0.9990 chunk 6 optimal weight: 0.9980 chunk 27 optimal weight: 4.9990 chunk 63 optimal weight: 0.4980 chunk 73 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 74 optimal weight: 8.9990 chunk 112 optimal weight: 2.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 855 HIS ** 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 = 0.4059 r_free = 0.4059 target = 0.115147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.078721 restraints weight = 21755.831| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 3.83 r_work: 0.3241 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.2686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 9764 Z= 0.184 Angle : 0.719 12.337 13284 Z= 0.346 Chirality : 0.046 0.253 1521 Planarity : 0.004 0.050 1694 Dihedral : 4.911 34.335 1438 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.67 % Favored : 95.17 % Rotamer: Outliers : 2.29 % Allowed : 17.64 % Favored : 80.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 1.61 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.25), residues: 1200 helix: 0.60 (0.40), residues: 190 sheet: 0.10 (0.23), residues: 504 loop : -0.39 (0.29), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 30 TYR 0.012 0.001 TYR A1076 PHE 0.016 0.002 PHE A 107 TRP 0.011 0.001 TRP A 619 HIS 0.002 0.001 HIS A 75 Details of bonding type rmsd covalent geometry : bond 0.00428 ( 9747) covalent geometry : angle 0.70920 (13243) SS BOND : bond 0.00560 ( 10) SS BOND : angle 1.80059 ( 20) hydrogen bonds : bond 0.03245 ( 394) hydrogen bonds : angle 5.09599 ( 1110) link_BETA1-4 : bond 0.00253 ( 2) link_BETA1-4 : angle 3.07394 ( 6) link_NAG-ASN : bond 0.00378 ( 5) link_NAG-ASN : angle 2.50834 ( 15) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 75 time to evaluate : 0.369 Fit side-chains revert: symmetry clash REVERT: A 103 ASN cc_start: 0.8519 (m-40) cc_final: 0.8245 (t0) REVERT: A 310 HIS cc_start: 0.7978 (m90) cc_final: 0.7511 (m90) REVERT: A 381 TYR cc_start: 0.8106 (m-10) cc_final: 0.7856 (m-10) REVERT: A 395 ASN cc_start: 0.9566 (p0) cc_final: 0.9297 (p0) REVERT: A 462 LEU cc_start: 0.8723 (OUTLIER) cc_final: 0.8499 (mm) REVERT: A 471 LEU cc_start: 0.8943 (OUTLIER) cc_final: 0.8682 (tm) REVERT: A 548 ASP cc_start: 0.8429 (t70) cc_final: 0.8203 (t70) REVERT: A 872 THR cc_start: 0.8224 (p) cc_final: 0.7803 (p) REVERT: A 945 TYR cc_start: 0.8224 (OUTLIER) cc_final: 0.7058 (p90) REVERT: A 953 MET cc_start: 0.5998 (ptm) cc_final: 0.5448 (ptp) REVERT: A 1015 MET cc_start: 0.7990 (pmm) cc_final: 0.7628 (pmm) REVERT: A 1045 PHE cc_start: 0.9398 (m-80) cc_final: 0.8855 (m-80) REVERT: A 1213 LYS cc_start: 0.8944 (mmpt) cc_final: 0.8648 (mmpt) REVERT: A 1301 GLU cc_start: 0.8858 (OUTLIER) cc_final: 0.8548 (pt0) outliers start: 24 outliers final: 18 residues processed: 94 average time/residue: 0.3455 time to fit residues: 36.2980 Evaluate side-chains 95 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 73 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 107 PHE Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 320 GLU Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 682 ILE Chi-restraints excluded: chain A residue 790 PHE Chi-restraints excluded: chain A residue 792 VAL Chi-restraints excluded: chain A residue 811 THR Chi-restraints excluded: chain A residue 822 VAL Chi-restraints excluded: chain A residue 945 TYR Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 982 ILE Chi-restraints excluded: chain A residue 1301 GLU Chi-restraints excluded: chain A residue 1307 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 27 optimal weight: 0.0570 chunk 22 optimal weight: 0.8980 chunk 66 optimal weight: 0.4980 chunk 59 optimal weight: 0.9980 chunk 71 optimal weight: 0.9990 chunk 96 optimal weight: 0.4980 chunk 6 optimal weight: 0.0070 chunk 8 optimal weight: 4.9990 chunk 56 optimal weight: 1.9990 chunk 76 optimal weight: 0.5980 chunk 116 optimal weight: 0.0050 overall best weight: 0.2130 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.117450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.081496 restraints weight = 21749.591| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 3.82 r_work: 0.3296 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.2683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 9764 Z= 0.115 Angle : 0.689 12.103 13284 Z= 0.328 Chirality : 0.044 0.242 1521 Planarity : 0.004 0.050 1694 Dihedral : 4.686 32.738 1438 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.58 % Favored : 96.25 % Rotamer: Outliers : 2.57 % Allowed : 17.45 % Favored : 79.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 1.61 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.25), residues: 1200 helix: 0.54 (0.39), residues: 191 sheet: 0.22 (0.23), residues: 504 loop : -0.36 (0.29), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 610 TYR 0.011 0.001 TYR A 620 PHE 0.023 0.001 PHE A 387 TRP 0.019 0.001 TRP A1065 HIS 0.002 0.000 HIS A 75 Details of bonding type rmsd covalent geometry : bond 0.00263 ( 9747) covalent geometry : angle 0.67890 (13243) SS BOND : bond 0.00491 ( 10) SS BOND : angle 1.61479 ( 20) hydrogen bonds : bond 0.02989 ( 394) hydrogen bonds : angle 4.97405 ( 1110) link_BETA1-4 : bond 0.00516 ( 2) link_BETA1-4 : angle 3.02261 ( 6) link_NAG-ASN : bond 0.00458 ( 5) link_NAG-ASN : angle 2.48160 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3131.40 seconds wall clock time: 54 minutes 10.75 seconds (3250.75 seconds total)