Starting phenix.real_space_refine on Thu Jul 2 18:51:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7q61_13849/07_2026/7q61_13849.cif Found real_map, /net/cci-nas-00/data/ceres_data/7q61_13849/07_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/7q61_13849/07_2026/7q61_13849.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7q61_13849/07_2026/7q61_13849.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7q61_13849/07_2026/7q61_13849.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7q61_13849/07_2026/7q61_13849.map" model { file = "/net/cci-nas-00/data/ceres_data/7q61_13849/07_2026/7q61_13849.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7q61_13849/07_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-6108/lib/python3.11/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 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 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 chiralities: 3 Time building chain proxies: 1.70, per 1000 atoms: 0.18 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: 0.78 Conformation dependent library (CDL) restraints added in 308.0 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: 0.28 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: 1.56 Time building geometry restraints manager: 1.00 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 - 17.92: 5371 17.92 - 35.84: 329 35.84 - 53.76: 53 53.76 - 71.68: 21 71.68 - 89.60: 20 Dihedral angle restraints: 5794 sinusoidal: 2285 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 5791 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: 11.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.200 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.610 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 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:9.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 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 : 13.704 89.596 3512 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/Z covalent geometry : bond 0.00583 / 0.27 ( 9747) covalent geometry : angle 1.09195 / 0.55 (13243) SS BOND : bond 0.01261 / 0.68 ( 10) SS BOND : angle 3.76198 / 2.08 ( 20) hydrogen bonds : bond 0.11416 / 6.89 ( 394) hydrogen bonds : angle 6.86483 / 4.60 ( 1110) link_BETA1-4 : bond 0.00678 / 0.32 ( 2) link_BETA1-4 : angle 5.96913 / 3.29 ( 6) link_NAG-ASN : bond 0.00682 / 0.46 ( 5) link_NAG-ASN : angle 3.64365 / 1.94 ( 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 : 0.333 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: 0.4494 time to fit residues: 55.0658 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 : 0.286 ------------------------------------------------------------------------------- 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... 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 = 0.119319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.083916 restraints weight = 22257.423| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 3.81 r_work: 0.3366 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.1264 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 : 0.693 11.511 13284 Z= 0.343 Chirality : 0.046 0.303 1521 Planarity : 0.005 0.063 1694 Dihedral : 5.351 37.030 1291 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.83 % Favored : 96.00 % Rotamer: Outliers : 1.43 % Allowed : 9.72 % Favored : 88.85 % 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: -1.24 (0.23), residues: 1200 helix: -1.42 (0.32), residues: 184 sheet: -0.15 (0.23), residues: 489 loop : -1.14 (0.26), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 602 TYR 0.022 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/Z covalent geometry : bond 0.00312 / 0.14 ( 9747) covalent geometry : angle 0.67990 / 0.34 (13243) SS BOND : bond 0.00310 / 0.17 ( 10) SS BOND : angle 1.98608 / 1.09 ( 20) hydrogen bonds : bond 0.03778 / 2.44 ( 394) hydrogen bonds : angle 5.70881 / 3.84 ( 1110) link_BETA1-4 : bond 0.00348 / 0.17 ( 2) link_BETA1-4 : angle 2.82534 / 1.59 ( 6) link_NAG-ASN : bond 0.00413 / 0.22 ( 5) link_NAG-ASN : angle 3.00232 / 1.67 ( 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 96 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 81 time to evaluate : 0.333 Fit side-chains revert: symmetry clash REVERT: A 49 ASP cc_start: 0.8940 (p0) cc_final: 0.8624 (p0) REVERT: A 310 HIS cc_start: 0.7795 (m90) cc_final: 0.7250 (m90) REVERT: A 381 TYR cc_start: 0.8130 (m-10) cc_final: 0.7913 (m-10) REVERT: A 395 ASN cc_start: 0.9455 (p0) cc_final: 0.9192 (p0) REVERT: A 548 ASP cc_start: 0.8371 (t70) cc_final: 0.8002 (t70) REVERT: A 945 TYR cc_start: 0.8145 (OUTLIER) cc_final: 0.7047 (p90) REVERT: A 953 MET cc_start: 0.5424 (OUTLIER) cc_final: 0.5105 (ppp) REVERT: A 1005 PHE cc_start: 0.8257 (OUTLIER) cc_final: 0.7154 (m-80) REVERT: A 1015 MET cc_start: 0.7878 (pmm) cc_final: 0.7599 (pmm) REVERT: A 1045 PHE cc_start: 0.9442 (m-80) cc_final: 0.8891 (m-80) REVERT: A 1213 LYS cc_start: 0.8857 (mmpt) cc_final: 0.8504 (mmmt) REVERT: A 1311 GLN cc_start: 0.8399 (tt0) cc_final: 0.8044 (tt0) outliers start: 15 outliers final: 7 residues processed: 89 average time/residue: 0.3667 time to fit residues: 36.3911 Evaluate side-chains 81 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 71 time to evaluate : 0.359 ------------------------------------------------------------------------------- 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: 0.1980 chunk 10 optimal weight: 1.9990 chunk 34 optimal weight: 9.9990 chunk 57 optimal weight: 0.9980 chunk 60 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 chunk 25 optimal weight: 4.9990 chunk 89 optimal weight: 4.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 441 HIS ** A 855 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 865 HIS A 958 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.116414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.080926 restraints weight = 21855.337| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 4.15 r_work: 0.3248 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.1709 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= 0.179 Angle : 0.690 11.556 13284 Z= 0.338 Chirality : 0.046 0.274 1521 Planarity : 0.005 0.055 1694 Dihedral : 5.084 35.326 1291 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.25 % Favored : 95.58 % Rotamer: Outliers : 2.29 % Allowed : 11.92 % Favored : 85.80 % 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: -0.69 (0.24), residues: 1200 helix: -0.38 (0.37), residues: 181 sheet: -0.10 (0.23), residues: 515 loop : -0.71 (0.29), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 602 TYR 0.023 0.002 TYR A1076 PHE 0.016 0.002 PHE A 107 TRP 0.010 0.001 TRP A1036 HIS 0.003 0.001 HIS A 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.18 ( 9747) covalent geometry : angle 0.67760 / 0.33 (13243) SS BOND : bond 0.00619 / 0.34 ( 10) SS BOND : angle 2.15108 / 1.17 ( 20) hydrogen bonds : bond 0.03570 / 2.29 ( 394) hydrogen bonds : angle 5.42078 / 3.68 ( 1110) link_BETA1-4 : bond 0.00389 / 0.19 ( 2) link_BETA1-4 : angle 2.82421 / 1.57 ( 6) link_NAG-ASN : bond 0.00412 / 0.25 ( 5) link_NAG-ASN : angle 2.62896 / 1.50 ( 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 97 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 73 time to evaluate : 0.333 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 310 HIS cc_start: 0.7946 (m90) cc_final: 0.7354 (m90) REVERT: A 381 TYR cc_start: 0.8156 (m-10) cc_final: 0.7898 (m-10) REVERT: A 395 ASN cc_start: 0.9548 (p0) cc_final: 0.9272 (p0) REVERT: A 548 ASP cc_start: 0.8464 (t70) cc_final: 0.8170 (t0) REVERT: A 766 MET cc_start: 0.8684 (tmm) cc_final: 0.8456 (ppp) REVERT: A 945 TYR cc_start: 0.8236 (OUTLIER) cc_final: 0.6988 (p90) REVERT: A 966 MET cc_start: -0.3104 (ttt) cc_final: -0.3498 (ttm) REVERT: A 1015 MET cc_start: 0.7986 (pmm) cc_final: 0.7659 (pmm) REVERT: A 1045 PHE cc_start: 0.9517 (m-80) cc_final: 0.8989 (m-80) REVERT: A 1213 LYS cc_start: 0.8877 (mmpt) cc_final: 0.8624 (mmpt) REVERT: A 1311 GLN cc_start: 0.8231 (tt0) cc_final: 0.7822 (tt0) outliers start: 24 outliers final: 12 residues processed: 88 average time/residue: 0.3507 time to fit residues: 34.2471 Evaluate side-chains 80 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 67 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 1307 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 108 optimal weight: 0.6980 chunk 64 optimal weight: 0.9980 chunk 101 optimal weight: 6.9990 chunk 81 optimal weight: 5.9990 chunk 97 optimal weight: 9.9990 chunk 106 optimal weight: 0.0770 chunk 42 optimal weight: 1.9990 chunk 111 optimal weight: 0.0970 chunk 77 optimal weight: 0.5980 chunk 104 optimal weight: 0.9990 chunk 7 optimal weight: 6.9990 overall best weight: 0.4936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1246 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.117330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.082264 restraints weight = 22069.873| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 4.09 r_work: 0.3281 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.1862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 9764 Z= 0.122 Angle : 0.644 13.010 13284 Z= 0.313 Chirality : 0.044 0.255 1521 Planarity : 0.004 0.054 1694 Dihedral : 4.882 35.017 1291 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.00 % Favored : 95.83 % Rotamer: Outliers : 1.91 % Allowed : 14.01 % Favored : 84.08 % 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: -0.44 (0.25), residues: 1200 helix: -0.04 (0.37), residues: 182 sheet: 0.05 (0.23), residues: 513 loop : -0.61 (0.29), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 610 TYR 0.019 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/Z covalent geometry : bond 0.00271 / 0.12 ( 9747) covalent geometry : angle 0.63137 / 0.31 (13243) SS BOND : bond 0.00577 / 0.31 ( 10) SS BOND : angle 2.04337 / 1.11 ( 20) hydrogen bonds : bond 0.03287 / 2.12 ( 394) hydrogen bonds : angle 5.25807 / 3.59 ( 1110) link_BETA1-4 : bond 0.00395 / 0.20 ( 2) link_BETA1-4 : angle 2.75140 / 1.54 ( 6) link_NAG-ASN : bond 0.00400 / 0.24 ( 5) link_NAG-ASN : angle 2.50367 / 1.41 ( 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 91 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 71 time to evaluate : 0.380 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 310 HIS cc_start: 0.7870 (m90) cc_final: 0.7408 (m90) REVERT: A 381 TYR cc_start: 0.8174 (m-10) cc_final: 0.7931 (m-10) REVERT: A 395 ASN cc_start: 0.9530 (p0) cc_final: 0.9245 (p0) REVERT: A 548 ASP cc_start: 0.8385 (t70) cc_final: 0.8110 (t0) REVERT: A 766 MET cc_start: 0.8685 (tmm) cc_final: 0.8478 (ppp) REVERT: A 945 TYR cc_start: 0.8185 (OUTLIER) cc_final: 0.6958 (p90) REVERT: A 966 MET cc_start: -0.3195 (ttt) cc_final: -0.3582 (ttm) REVERT: A 1015 MET cc_start: 0.7947 (pmm) cc_final: 0.7610 (pmm) REVERT: A 1045 PHE cc_start: 0.9487 (m-80) cc_final: 0.8946 (m-80) REVERT: A 1213 LYS cc_start: 0.8892 (mmpt) cc_final: 0.8627 (mmpt) REVERT: A 1311 GLN cc_start: 0.8243 (tt0) cc_final: 0.7889 (tt0) outliers start: 20 outliers final: 10 residues processed: 86 average time/residue: 0.3606 time to fit residues: 34.7854 Evaluate side-chains 78 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 67 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU 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 682 ILE Chi-restraints excluded: chain A residue 790 PHE Chi-restraints excluded: chain A residue 792 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 1307 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 41 optimal weight: 1.9990 chunk 110 optimal weight: 0.6980 chunk 7 optimal weight: 5.9990 chunk 120 optimal weight: 2.9990 chunk 27 optimal weight: 0.0670 chunk 77 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 79 optimal weight: 0.0970 chunk 72 optimal weight: 0.7980 chunk 42 optimal weight: 1.9990 overall best weight: 0.7318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.4081 r_free = 0.4081 target = 0.116813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.081861 restraints weight = 21955.038| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 4.00 r_work: 0.3266 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.2047 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= 0.142 Angle : 0.648 12.101 13284 Z= 0.315 Chirality : 0.044 0.250 1521 Planarity : 0.004 0.053 1694 Dihedral : 4.786 34.910 1291 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.25 % Allowed : 4.08 % Favored : 95.67 % Rotamer: Outliers : 2.38 % Allowed : 14.39 % 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: -0.28 (0.25), residues: 1200 helix: 0.29 (0.38), residues: 181 sheet: 0.10 (0.23), residues: 517 loop : -0.54 (0.29), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 610 TYR 0.017 0.001 TYR A1076 PHE 0.015 0.001 PHE A 107 TRP 0.011 0.001 TRP A 619 HIS 0.002 0.001 HIS A 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 ( 9747) covalent geometry : angle 0.63617 / 0.31 (13243) SS BOND : bond 0.00463 / 0.25 ( 10) SS BOND : angle 1.94098 / 1.04 ( 20) hydrogen bonds : bond 0.03286 / 2.11 ( 394) hydrogen bonds : angle 5.12415 / 3.50 ( 1110) link_BETA1-4 : bond 0.00366 / 0.18 ( 2) link_BETA1-4 : angle 2.77204 / 1.54 ( 6) link_NAG-ASN : bond 0.00331 / 0.20 ( 5) link_NAG-ASN : angle 2.45656 / 1.38 ( 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 93 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 68 time to evaluate : 0.434 Fit side-chains revert: symmetry clash REVERT: A 310 HIS cc_start: 0.7835 (m90) cc_final: 0.7285 (m90) REVERT: A 381 TYR cc_start: 0.8178 (m-10) cc_final: 0.7854 (m-10) REVERT: A 395 ASN cc_start: 0.9544 (p0) cc_final: 0.9266 (p0) REVERT: A 548 ASP cc_start: 0.8446 (t70) cc_final: 0.8213 (t70) REVERT: A 945 TYR cc_start: 0.8197 (OUTLIER) cc_final: 0.6958 (p90) REVERT: A 966 MET cc_start: -0.3046 (ttt) cc_final: -0.3418 (ttm) REVERT: A 1015 MET cc_start: 0.7961 (pmm) cc_final: 0.7615 (pmm) REVERT: A 1045 PHE cc_start: 0.9475 (m-80) cc_final: 0.8941 (m-80) REVERT: A 1213 LYS cc_start: 0.8903 (mmpt) cc_final: 0.8635 (mmpt) REVERT: A 1301 GLU cc_start: 0.8813 (OUTLIER) cc_final: 0.8460 (pt0) REVERT: A 1311 GLN cc_start: 0.8207 (tt0) cc_final: 0.7847 (tt0) outliers start: 25 outliers final: 18 residues processed: 87 average time/residue: 0.3601 time to fit residues: 35.1892 Evaluate side-chains 83 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 63 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 78 CYS 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 330 THR 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 114 optimal weight: 1.9990 chunk 73 optimal weight: 3.9990 chunk 21 optimal weight: 4.9990 chunk 78 optimal weight: 8.9990 chunk 51 optimal weight: 0.9980 chunk 15 optimal weight: 0.8980 chunk 7 optimal weight: 0.7980 chunk 18 optimal weight: 0.5980 chunk 32 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 855 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 973 GLN A1084 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.116383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.079754 restraints weight = 21891.514| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 3.86 r_work: 0.3257 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.2250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 9764 Z= 0.156 Angle : 0.656 12.200 13284 Z= 0.319 Chirality : 0.045 0.246 1521 Planarity : 0.004 0.053 1694 Dihedral : 4.782 34.502 1291 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.25 % Allowed : 4.08 % Favored : 95.67 % Rotamer: Outliers : 3.05 % Allowed : 14.49 % Favored : 82.46 % 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: -0.24 (0.25), residues: 1200 helix: 0.38 (0.39), residues: 188 sheet: 0.14 (0.23), residues: 515 loop : -0.55 (0.29), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 610 TYR 0.015 0.001 TYR A1076 PHE 0.017 0.001 PHE A 107 TRP 0.011 0.001 TRP A 619 HIS 0.002 0.001 HIS A 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.16 ( 9747) covalent geometry : angle 0.64491 / 0.32 (13243) SS BOND : bond 0.00447 / 0.25 ( 10) SS BOND : angle 1.93963 / 1.05 ( 20) hydrogen bonds : bond 0.03271 / 2.11 ( 394) hydrogen bonds : angle 5.09616 / 3.48 ( 1110) link_BETA1-4 : bond 0.00307 / 0.15 ( 2) link_BETA1-4 : angle 2.82472 / 1.57 ( 6) link_NAG-ASN : bond 0.00327 / 0.20 ( 5) link_NAG-ASN : angle 2.44337 / 1.38 ( 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 101 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 69 time to evaluate : 0.405 Fit side-chains revert: symmetry clash REVERT: A 49 ASP cc_start: 0.9210 (p0) cc_final: 0.8906 (p0) REVERT: A 310 HIS cc_start: 0.7840 (m90) cc_final: 0.7398 (m-70) REVERT: A 381 TYR cc_start: 0.8144 (m-10) cc_final: 0.7881 (m-10) REVERT: A 395 ASN cc_start: 0.9546 (p0) cc_final: 0.9280 (p0) REVERT: A 548 ASP cc_start: 0.8446 (t70) cc_final: 0.8223 (t70) REVERT: A 945 TYR cc_start: 0.8209 (OUTLIER) cc_final: 0.6996 (p90) REVERT: A 966 MET cc_start: -0.2929 (ttt) cc_final: -0.3296 (ttm) REVERT: A 1015 MET cc_start: 0.7939 (pmm) cc_final: 0.7579 (pmm) REVERT: A 1045 PHE cc_start: 0.9433 (m-80) cc_final: 0.8924 (m-80) REVERT: A 1213 LYS cc_start: 0.8917 (mmpt) cc_final: 0.8634 (mmpt) REVERT: A 1301 GLU cc_start: 0.8838 (OUTLIER) cc_final: 0.8503 (pt0) outliers start: 32 outliers final: 19 residues processed: 96 average time/residue: 0.3293 time to fit residues: 35.8363 Evaluate side-chains 85 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 64 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 CYS 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 330 THR 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 1171 ILE 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: 3.9990 chunk 28 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 chunk 115 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 61 optimal weight: 0.5980 chunk 39 optimal weight: 2.9990 chunk 8 optimal weight: 4.9990 chunk 51 optimal weight: 0.8980 chunk 50 optimal weight: 0.6980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.4075 r_free = 0.4075 target = 0.116354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.079720 restraints weight = 21988.640| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 3.86 r_work: 0.3257 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.2324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 9764 Z= 0.150 Angle : 0.663 12.080 13284 Z= 0.319 Chirality : 0.045 0.240 1521 Planarity : 0.004 0.053 1694 Dihedral : 4.771 34.013 1291 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.17 % Favored : 95.67 % Rotamer: Outliers : 2.96 % Allowed : 15.16 % Favored : 81.89 % 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: -0.18 (0.25), residues: 1200 helix: 0.48 (0.38), residues: 188 sheet: 0.12 (0.23), residues: 516 loop : -0.46 (0.29), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 610 TYR 0.014 0.001 TYR A1076 PHE 0.015 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/Z covalent geometry : bond 0.00344 / 0.15 ( 9747) covalent geometry : angle 0.65231 / 0.32 (13243) SS BOND : bond 0.00452 / 0.25 ( 10) SS BOND : angle 1.90090 / 1.03 ( 20) hydrogen bonds : bond 0.03213 / 2.08 ( 394) hydrogen bonds : angle 5.07956 / 3.48 ( 1110) link_BETA1-4 : bond 0.00267 / 0.13 ( 2) link_BETA1-4 : angle 2.85180 / 1.59 ( 6) link_NAG-ASN : bond 0.00319 / 0.20 ( 5) link_NAG-ASN : angle 2.41391 / 1.36 ( 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 100 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 69 time to evaluate : 0.262 Fit side-chains revert: symmetry clash REVERT: A 310 HIS cc_start: 0.7832 (m90) cc_final: 0.7367 (m-70) REVERT: A 381 TYR cc_start: 0.8122 (m-10) cc_final: 0.7874 (m-10) REVERT: A 395 ASN cc_start: 0.9551 (p0) cc_final: 0.9282 (p0) REVERT: A 471 LEU cc_start: 0.8943 (OUTLIER) cc_final: 0.8661 (tm) REVERT: A 548 ASP cc_start: 0.8443 (t70) cc_final: 0.8237 (t70) REVERT: A 945 TYR cc_start: 0.8206 (OUTLIER) cc_final: 0.6999 (p90) REVERT: A 966 MET cc_start: -0.2871 (ttt) cc_final: -0.3173 (ttt) REVERT: A 1015 MET cc_start: 0.7952 (pmm) cc_final: 0.7594 (pmm) REVERT: A 1045 PHE cc_start: 0.9415 (m-80) cc_final: 0.8876 (m-80) REVERT: A 1213 LYS cc_start: 0.8929 (mmpt) cc_final: 0.8636 (mmpt) REVERT: A 1301 GLU cc_start: 0.8848 (OUTLIER) cc_final: 0.8506 (pt0) outliers start: 31 outliers final: 18 residues processed: 96 average time/residue: 0.3489 time to fit residues: 37.6387 Evaluate side-chains 86 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 65 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 CYS 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 13 optimal weight: 1.9990 chunk 102 optimal weight: 8.9990 chunk 91 optimal weight: 9.9990 chunk 86 optimal weight: 6.9990 chunk 7 optimal weight: 4.9990 chunk 65 optimal weight: 2.9990 chunk 97 optimal weight: 8.9990 chunk 15 optimal weight: 0.7980 chunk 107 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 728 GLN A 855 HIS A 914 HIS A 973 GLN A1084 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.113664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.078996 restraints weight = 21990.734| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 4.21 r_work: 0.3184 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.2653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 9764 Z= 0.247 Angle : 0.750 11.952 13284 Z= 0.361 Chirality : 0.047 0.255 1521 Planarity : 0.004 0.051 1694 Dihedral : 5.048 35.111 1291 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.25 % Allowed : 4.83 % Favored : 94.92 % Rotamer: Outliers : 3.34 % Allowed : 15.54 % Favored : 81.12 % 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: -0.28 (0.25), residues: 1200 helix: 0.65 (0.40), residues: 187 sheet: -0.04 (0.23), residues: 512 loop : -0.52 (0.29), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 610 TYR 0.014 0.002 TYR A 620 PHE 0.016 0.002 PHE A 518 TRP 0.008 0.002 TRP A 619 HIS 0.003 0.001 HIS A 855 Details of bonding type rmsd/Z covalent geometry : bond 0.00566 / 0.25 ( 9747) covalent geometry : angle 0.73774 / 0.36 (13243) SS BOND : bond 0.00540 / 0.31 ( 10) SS BOND : angle 2.28927 / 1.19 ( 20) hydrogen bonds : bond 0.03567 / 2.29 ( 394) hydrogen bonds : angle 5.31268 / 3.62 ( 1110) link_BETA1-4 : bond 0.00099 / 0.05 ( 2) link_BETA1-4 : angle 3.08316 / 1.72 ( 6) link_NAG-ASN : bond 0.00411 / 0.21 ( 5) link_NAG-ASN : angle 2.49195 / 1.42 ( 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 107 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 72 time to evaluate : 0.379 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 381 TYR cc_start: 0.8121 (m-10) cc_final: 0.7864 (m-10) REVERT: A 395 ASN cc_start: 0.9566 (p0) cc_final: 0.9308 (p0) REVERT: A 471 LEU cc_start: 0.8866 (OUTLIER) cc_final: 0.8600 (tm) REVERT: A 548 ASP cc_start: 0.8522 (t70) cc_final: 0.8273 (t70) REVERT: A 872 THR cc_start: 0.8232 (p) cc_final: 0.7832 (p) REVERT: A 945 TYR cc_start: 0.8293 (OUTLIER) cc_final: 0.7094 (p90) REVERT: A 1015 MET cc_start: 0.8017 (pmm) cc_final: 0.7656 (pmm) REVERT: A 1045 PHE cc_start: 0.9443 (m-80) cc_final: 0.8912 (m-80) REVERT: A 1213 LYS cc_start: 0.8942 (mmpt) cc_final: 0.8663 (mmpt) REVERT: A 1301 GLU cc_start: 0.8878 (OUTLIER) cc_final: 0.8521 (pt0) outliers start: 35 outliers final: 21 residues processed: 98 average time/residue: 0.3612 time to fit residues: 39.6845 Evaluate side-chains 92 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 68 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 CYS 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 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 1107 GLU 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: 0.8980 chunk 89 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 84 optimal weight: 0.7980 chunk 69 optimal weight: 0.6980 chunk 120 optimal weight: 0.8980 chunk 70 optimal weight: 0.7980 chunk 102 optimal weight: 0.9990 chunk 1 optimal weight: 0.6980 chunk 65 optimal weight: 0.0970 chunk 30 optimal weight: 0.9990 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.115606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.079159 restraints weight = 21838.560| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 3.82 r_work: 0.3242 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.2641 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= 0.141 Angle : 0.697 11.980 13284 Z= 0.333 Chirality : 0.045 0.233 1521 Planarity : 0.004 0.051 1694 Dihedral : 4.900 33.950 1291 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.25 % Favored : 95.58 % Rotamer: Outliers : 3.15 % Allowed : 16.49 % Favored : 80.36 % 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: -0.22 (0.25), residues: 1200 helix: 0.52 (0.39), residues: 190 sheet: 0.03 (0.23), residues: 514 loop : -0.45 (0.29), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 610 TYR 0.012 0.001 TYR A 620 PHE 0.016 0.001 PHE A 518 TRP 0.011 0.001 TRP A 619 HIS 0.002 0.000 HIS A 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 ( 9747) covalent geometry : angle 0.68682 / 0.33 (13243) SS BOND : bond 0.00497 / 0.27 ( 10) SS BOND : angle 1.75017 / 0.94 ( 20) hydrogen bonds : bond 0.03218 / 2.09 ( 394) hydrogen bonds : angle 5.18588 / 3.54 ( 1110) link_BETA1-4 : bond 0.00268 / 0.13 ( 2) link_BETA1-4 : angle 2.97748 / 1.67 ( 6) link_NAG-ASN : bond 0.00320 / 0.20 ( 5) link_NAG-ASN : angle 2.42069 / 1.35 ( 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 105 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 72 time to evaluate : 0.313 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 381 TYR cc_start: 0.8099 (m-10) cc_final: 0.7822 (m-10) REVERT: A 395 ASN cc_start: 0.9558 (p0) cc_final: 0.9300 (p0) REVERT: A 471 LEU cc_start: 0.8924 (OUTLIER) cc_final: 0.8603 (tm) REVERT: A 548 ASP cc_start: 0.8391 (t70) cc_final: 0.8165 (t70) REVERT: A 872 THR cc_start: 0.8276 (p) cc_final: 0.7844 (p) REVERT: A 945 TYR cc_start: 0.8217 (OUTLIER) cc_final: 0.7014 (p90) REVERT: A 953 MET cc_start: 0.5992 (ptm) cc_final: 0.5390 (ptp) REVERT: A 1005 PHE cc_start: 0.8505 (m-80) cc_final: 0.8160 (m-80) REVERT: A 1015 MET cc_start: 0.7981 (pmm) cc_final: 0.7618 (pmm) REVERT: A 1045 PHE cc_start: 0.9396 (m-80) cc_final: 0.8843 (m-80) REVERT: A 1213 LYS cc_start: 0.8941 (mmpt) cc_final: 0.8660 (mmpt) REVERT: A 1260 GLU cc_start: 0.7638 (OUTLIER) cc_final: 0.7237 (mm-30) REVERT: A 1301 GLU cc_start: 0.8856 (OUTLIER) cc_final: 0.8505 (pt0) outliers start: 33 outliers final: 20 residues processed: 95 average time/residue: 0.4038 time to fit residues: 42.5315 Evaluate side-chains 95 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 71 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 CYS 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 733 PHE Chi-restraints excluded: chain A residue 790 PHE 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 1107 GLU Chi-restraints excluded: chain A residue 1171 ILE Chi-restraints excluded: chain A residue 1260 GLU 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 3 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 110 optimal weight: 6.9990 chunk 6 optimal weight: 0.9980 chunk 27 optimal weight: 0.7980 chunk 63 optimal weight: 0.8980 chunk 73 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 chunk 112 optimal weight: 0.8980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.114451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.078127 restraints weight = 21754.653| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 3.72 r_work: 0.3226 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.2780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 9764 Z= 0.193 Angle : 0.725 12.213 13284 Z= 0.350 Chirality : 0.046 0.245 1521 Planarity : 0.004 0.050 1694 Dihedral : 4.950 34.123 1291 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.75 % Favored : 95.08 % Rotamer: Outliers : 2.76 % Allowed : 17.06 % Favored : 80.17 % 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: -0.23 (0.25), residues: 1200 helix: 0.70 (0.40), residues: 183 sheet: -0.04 (0.23), residues: 514 loop : -0.44 (0.29), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 610 TYR 0.012 0.001 TYR A 620 PHE 0.015 0.002 PHE A 518 TRP 0.011 0.001 TRP A 619 HIS 0.003 0.001 HIS A 855 Details of bonding type rmsd/Z covalent geometry : bond 0.00448 / 0.19 ( 9747) covalent geometry : angle 0.71519 / 0.35 (13243) SS BOND : bond 0.00524 / 0.29 ( 10) SS BOND : angle 1.88409 / 0.98 ( 20) hydrogen bonds : bond 0.03329 / 2.15 ( 394) hydrogen bonds : angle 5.22888 / 3.56 ( 1110) link_BETA1-4 : bond 0.00235 / 0.11 ( 2) link_BETA1-4 : angle 3.04051 / 1.69 ( 6) link_NAG-ASN : bond 0.00309 / 0.17 ( 5) link_NAG-ASN : angle 2.43813 / 1.36 ( 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 102 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 73 time to evaluate : 0.383 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 381 TYR cc_start: 0.8087 (m-10) cc_final: 0.7821 (m-10) REVERT: A 395 ASN cc_start: 0.9552 (p0) cc_final: 0.9292 (p0) REVERT: A 462 LEU cc_start: 0.8742 (OUTLIER) cc_final: 0.8528 (mm) REVERT: A 471 LEU cc_start: 0.8939 (OUTLIER) cc_final: 0.8690 (tm) REVERT: A 548 ASP cc_start: 0.8427 (t70) cc_final: 0.8206 (t70) REVERT: A 872 THR cc_start: 0.8348 (p) cc_final: 0.7916 (p) REVERT: A 945 TYR cc_start: 0.8234 (OUTLIER) cc_final: 0.7124 (p90) REVERT: A 953 MET cc_start: 0.6013 (ptm) cc_final: 0.5454 (ptp) REVERT: A 1015 MET cc_start: 0.8016 (pmm) cc_final: 0.7667 (pmm) REVERT: A 1045 PHE cc_start: 0.9393 (m-80) cc_final: 0.8840 (m-80) REVERT: A 1213 LYS cc_start: 0.8945 (mmpt) cc_final: 0.8661 (mmpt) REVERT: A 1260 GLU cc_start: 0.7686 (OUTLIER) cc_final: 0.7298 (mm-30) REVERT: A 1301 GLU cc_start: 0.8856 (OUTLIER) cc_final: 0.8487 (pt0) outliers start: 29 outliers final: 22 residues processed: 97 average time/residue: 0.3883 time to fit residues: 41.8626 Evaluate side-chains 98 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 71 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 CYS 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 733 PHE 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 1107 GLU Chi-restraints excluded: chain A residue 1171 ILE Chi-restraints excluded: chain A residue 1260 GLU 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: 0.0050 chunk 22 optimal weight: 0.7980 chunk 66 optimal weight: 0.5980 chunk 59 optimal weight: 0.5980 chunk 71 optimal weight: 1.9990 chunk 96 optimal weight: 8.9990 chunk 6 optimal weight: 0.0370 chunk 8 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 116 optimal weight: 3.9990 overall best weight: 0.4072 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.116377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.080310 restraints weight = 21768.416| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 3.81 r_work: 0.3276 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.2758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 9764 Z= 0.126 Angle : 0.702 12.640 13284 Z= 0.335 Chirality : 0.044 0.220 1521 Planarity : 0.004 0.050 1694 Dihedral : 4.784 32.602 1291 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.92 % Favored : 95.92 % Rotamer: Outliers : 2.86 % Allowed : 17.35 % Favored : 79.79 % 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: -0.17 (0.25), residues: 1200 helix: 0.60 (0.39), residues: 185 sheet: 0.11 (0.23), residues: 505 loop : -0.48 (0.29), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 610 TYR 0.011 0.001 TYR A 196 PHE 0.024 0.001 PHE A 387 TRP 0.020 0.001 TRP A1065 HIS 0.002 0.000 HIS A 855 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 ( 9747) covalent geometry : angle 0.69162 / 0.33 (13243) SS BOND : bond 0.00474 / 0.25 ( 10) SS BOND : angle 1.72326 / 0.91 ( 20) hydrogen bonds : bond 0.03062 / 2.00 ( 394) hydrogen bonds : angle 5.10487 / 3.48 ( 1110) link_BETA1-4 : bond 0.00156 / 0.07 ( 2) link_BETA1-4 : angle 3.00767 / 1.69 ( 6) link_NAG-ASN : bond 0.00333 / 0.20 ( 5) link_NAG-ASN : angle 2.43590 / 1.33 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3122.78 seconds wall clock time: 54 minutes 11.22 seconds (3251.22 seconds total)