Starting phenix.real_space_refine on Sun Jul 27 22:30:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7q61_13849/07_2025/7q61_13849.cif Found real_map, /net/cci-nas-00/data/ceres_data/7q61_13849/07_2025/7q61_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_13849/07_2025/7q61_13849.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7q61_13849/07_2025/7q61_13849.map" model { file = "/net/cci-nas-00/data/ceres_data/7q61_13849/07_2025/7q61_13849.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7q61_13849/07_2025/7q61_13849.cif" } resolution = 2.88 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.005 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 9.17, per 1000 atoms: 0.96 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: 2.83 Conformation dependent library (CDL) restraints added in 1.9 seconds 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: 1.95 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: 5.63 Time building geometry restraints manager: 3.13 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: 209.980 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: 0.470 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 33.750 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.070 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:25.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 269.900 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.84 (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 TRP 0.038 0.002 TRP A1065 HIS 0.007 0.001 HIS A 75 PHE 0.050 0.004 PHE A 733 TYR 0.040 0.003 TYR A1076 ARG 0.006 0.001 ARG A 730 Details of bonding type rmsd link_NAG-ASN : bond 0.00682 ( 5) link_NAG-ASN : angle 3.64365 ( 15) link_BETA1-4 : bond 0.00678 ( 2) link_BETA1-4 : angle 5.96913 ( 6) hydrogen bonds : bond 0.11416 ( 394) hydrogen bonds : angle 6.86483 ( 1110) SS BOND : bond 0.01261 ( 10) SS BOND : angle 3.76198 ( 20) covalent geometry : bond 0.00583 ( 9747) covalent geometry : angle 1.09195 (13243) *********************** 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 : 1.026 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: 0.8975 time to fit residues: 110.9483 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 : 1.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 102 optimal weight: 4.9990 chunk 91 optimal weight: 5.9990 chunk 50 optimal weight: 0.5980 chunk 31 optimal weight: 5.9990 chunk 61 optimal weight: 0.9990 chunk 48 optimal weight: 7.9990 chunk 94 optimal weight: 4.9990 chunk 36 optimal weight: 4.9990 chunk 57 optimal weight: 0.6980 chunk 70 optimal weight: 2.9990 chunk 109 optimal weight: 0.0470 overall best weight: 1.0682 ------------------------------------------------------------------------------- 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 = 0.4111 r_free = 0.4111 target = 0.117685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.081798 restraints weight = 22023.818| |-----------------------------------------------------------------------------| r_work (start): 0.3480 rms_B_bonded: 3.78 r_work: 0.3329 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.1415 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= 0.189 Angle : 0.720 12.687 13284 Z= 0.355 Chirality : 0.047 0.297 1521 Planarity : 0.006 0.063 1694 Dihedral : 7.991 74.124 1438 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.08 % Favored : 95.75 % Rotamer: Outliers : 1.53 % Allowed : 10.10 % Favored : 88.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 1.61 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.23), residues: 1200 helix: -1.23 (0.33), residues: 182 sheet: -0.21 (0.23), residues: 494 loop : -1.08 (0.26), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A1065 HIS 0.003 0.001 HIS A1018 PHE 0.018 0.002 PHE A 107 TYR 0.021 0.002 TYR A1076 ARG 0.004 0.000 ARG A 602 Details of bonding type rmsd link_NAG-ASN : bond 0.00472 ( 5) link_NAG-ASN : angle 2.98634 ( 15) link_BETA1-4 : bond 0.00207 ( 2) link_BETA1-4 : angle 2.99733 ( 6) hydrogen bonds : bond 0.03811 ( 394) hydrogen bonds : angle 5.70390 ( 1110) SS BOND : bond 0.00412 ( 10) SS BOND : angle 2.11767 ( 20) covalent geometry : bond 0.00423 ( 9747) covalent geometry : angle 0.70654 (13243) *********************** 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 97 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 81 time to evaluate : 1.151 Fit side-chains revert: symmetry clash REVERT: A 49 ASP cc_start: 0.8992 (p0) cc_final: 0.8688 (p0) REVERT: A 310 HIS cc_start: 0.7864 (m90) cc_final: 0.7323 (m90) REVERT: A 381 TYR cc_start: 0.8143 (m-10) cc_final: 0.7930 (m-10) REVERT: A 395 ASN cc_start: 0.9455 (p0) cc_final: 0.9193 (p0) REVERT: A 548 ASP cc_start: 0.8383 (t70) cc_final: 0.7989 (t70) REVERT: A 945 TYR cc_start: 0.8197 (OUTLIER) cc_final: 0.7093 (p90) REVERT: A 953 MET cc_start: 0.5564 (OUTLIER) cc_final: 0.5205 (ppp) REVERT: A 1005 PHE cc_start: 0.8268 (OUTLIER) cc_final: 0.7162 (m-80) REVERT: A 1015 MET cc_start: 0.7914 (pmm) cc_final: 0.7632 (pmm) REVERT: A 1045 PHE cc_start: 0.9430 (m-80) cc_final: 0.8897 (m-80) REVERT: A 1213 LYS cc_start: 0.8863 (mmpt) cc_final: 0.8511 (mmmt) REVERT: A 1311 GLN cc_start: 0.8428 (tt0) cc_final: 0.8078 (tt0) outliers start: 16 outliers final: 7 residues processed: 89 average time/residue: 0.8815 time to fit residues: 87.2364 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 : 1.185 ------------------------------------------------------------------------------- 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 68 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 93 optimal weight: 20.0000 chunk 86 optimal weight: 0.0040 chunk 19 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 chunk 82 optimal weight: 0.1980 chunk 52 optimal weight: 1.9990 chunk 120 optimal weight: 2.9990 chunk 4 optimal weight: 0.7980 chunk 74 optimal weight: 9.9990 overall best weight: 0.9996 ------------------------------------------------------------------------------- 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 958 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.116252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.080663 restraints weight = 22012.447| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 4.09 r_work: 0.3250 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.1792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 9764 Z= 0.176 Angle : 0.697 11.760 13284 Z= 0.338 Chirality : 0.046 0.281 1521 Planarity : 0.005 0.055 1694 Dihedral : 6.587 58.492 1438 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.17 % Favored : 95.67 % Rotamer: Outliers : 2.57 % Allowed : 11.73 % Favored : 85.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 1.61 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.24), residues: 1200 helix: -0.30 (0.37), residues: 181 sheet: -0.14 (0.23), residues: 513 loop : -0.71 (0.28), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1036 HIS 0.003 0.001 HIS A 75 PHE 0.015 0.002 PHE A 107 TYR 0.023 0.002 TYR A1076 ARG 0.009 0.001 ARG A 610 Details of bonding type rmsd link_NAG-ASN : bond 0.00527 ( 5) link_NAG-ASN : angle 2.66717 ( 15) link_BETA1-4 : bond 0.00144 ( 2) link_BETA1-4 : angle 3.15115 ( 6) hydrogen bonds : bond 0.03541 ( 394) hydrogen bonds : angle 5.43228 ( 1110) SS BOND : bond 0.00397 ( 10) SS BOND : angle 2.11540 ( 20) covalent geometry : bond 0.00394 ( 9747) covalent geometry : angle 0.68398 (13243) *********************** 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 96 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 69 time to evaluate : 1.101 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 310 HIS cc_start: 0.7949 (m90) cc_final: 0.7378 (m90) REVERT: A 381 TYR cc_start: 0.8153 (m-10) cc_final: 0.7901 (m-10) REVERT: A 395 ASN cc_start: 0.9535 (p0) cc_final: 0.9260 (p0) REVERT: A 548 ASP cc_start: 0.8445 (t70) cc_final: 0.8175 (t0) REVERT: A 945 TYR cc_start: 0.8238 (OUTLIER) cc_final: 0.7013 (p90) REVERT: A 966 MET cc_start: -0.3028 (ttt) cc_final: -0.3427 (ttm) REVERT: A 1015 MET cc_start: 0.8001 (pmm) cc_final: 0.7679 (pmm) REVERT: A 1045 PHE cc_start: 0.9500 (m-80) cc_final: 0.8968 (m-80) REVERT: A 1213 LYS cc_start: 0.8884 (mmpt) cc_final: 0.8629 (mmpt) REVERT: A 1311 GLN cc_start: 0.8287 (tt0) cc_final: 0.7882 (tt0) outliers start: 27 outliers final: 14 residues processed: 86 average time/residue: 0.8105 time to fit residues: 78.4032 Evaluate side-chains 80 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 65 time to evaluate : 1.123 ------------------------------------------------------------------------------- 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 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 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 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 12 optimal weight: 1.9990 chunk 68 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 38 optimal weight: 0.3980 chunk 60 optimal weight: 2.9990 chunk 110 optimal weight: 1.9990 chunk 115 optimal weight: 0.9990 chunk 33 optimal weight: 6.9990 chunk 55 optimal weight: 1.9990 chunk 11 optimal weight: 0.0000 chunk 20 optimal weight: 2.9990 overall best weight: 0.8790 ------------------------------------------------------------------------------- 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** A1246 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.116045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.079491 restraints weight = 21771.020| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 3.86 r_work: 0.3251 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.2039 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= 0.160 Angle : 0.660 12.530 13284 Z= 0.323 Chirality : 0.045 0.268 1521 Planarity : 0.004 0.055 1694 Dihedral : 5.575 40.705 1438 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.17 % Favored : 95.67 % Rotamer: Outliers : 2.48 % Allowed : 13.82 % Favored : 83.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 1.61 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.24), residues: 1200 helix: 0.14 (0.38), residues: 181 sheet: -0.05 (0.23), residues: 517 loop : -0.62 (0.28), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1036 HIS 0.003 0.001 HIS A 75 PHE 0.019 0.001 PHE A 107 TYR 0.021 0.001 TYR A 620 ARG 0.005 0.000 ARG A 610 Details of bonding type rmsd link_NAG-ASN : bond 0.00497 ( 5) link_NAG-ASN : angle 2.63113 ( 15) link_BETA1-4 : bond 0.00395 ( 2) link_BETA1-4 : angle 2.90186 ( 6) hydrogen bonds : bond 0.03359 ( 394) hydrogen bonds : angle 5.27459 ( 1110) SS BOND : bond 0.00563 ( 10) SS BOND : angle 2.00616 ( 20) covalent geometry : bond 0.00361 ( 9747) covalent geometry : angle 0.64727 (13243) *********************** 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 98 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 72 time to evaluate : 1.119 Fit side-chains revert: symmetry clash REVERT: A 49 ASP cc_start: 0.9191 (p0) cc_final: 0.8872 (p0) REVERT: A 310 HIS cc_start: 0.7947 (m90) cc_final: 0.7344 (m90) REVERT: A 381 TYR cc_start: 0.8160 (m-10) cc_final: 0.7856 (m-10) REVERT: A 395 ASN cc_start: 0.9536 (p0) cc_final: 0.9271 (p0) REVERT: A 548 ASP cc_start: 0.8466 (t70) cc_final: 0.8176 (t0) REVERT: A 766 MET cc_start: 0.8699 (tmm) cc_final: 0.8481 (ppp) REVERT: A 945 TYR cc_start: 0.8235 (OUTLIER) cc_final: 0.7013 (p90) REVERT: A 966 MET cc_start: -0.3015 (ttt) cc_final: -0.3381 (ttm) REVERT: A 1015 MET cc_start: 0.7966 (pmm) cc_final: 0.7618 (pmm) REVERT: A 1045 PHE cc_start: 0.9489 (m-80) cc_final: 0.8973 (m-80) REVERT: A 1213 LYS cc_start: 0.8902 (mmpt) cc_final: 0.8642 (mmpt) REVERT: A 1301 GLU cc_start: 0.8813 (OUTLIER) cc_final: 0.8478 (pt0) REVERT: A 1311 GLN cc_start: 0.8266 (tt0) cc_final: 0.7858 (tt0) outliers start: 26 outliers final: 16 residues processed: 92 average time/residue: 0.7562 time to fit residues: 78.5887 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 : 1.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 257 SER 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 2 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 87 optimal weight: 9.9990 chunk 33 optimal weight: 6.9990 chunk 27 optimal weight: 0.3980 chunk 93 optimal weight: 0.8980 chunk 112 optimal weight: 0.8980 chunk 94 optimal weight: 5.9990 chunk 97 optimal weight: 0.0060 chunk 82 optimal weight: 1.9990 overall best weight: 0.6396 ------------------------------------------------------------------------------- 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 = 0.4079 r_free = 0.4079 target = 0.116602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.080297 restraints weight = 21690.853| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 3.81 r_work: 0.3266 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.2143 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= 0.134 Angle : 0.649 12.256 13284 Z= 0.314 Chirality : 0.044 0.260 1521 Planarity : 0.004 0.055 1694 Dihedral : 5.161 34.952 1438 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.25 % Allowed : 4.00 % Favored : 95.75 % Rotamer: Outliers : 2.67 % Allowed : 14.87 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.25), residues: 1200 helix: 0.35 (0.39), residues: 181 sheet: 0.07 (0.23), residues: 517 loop : -0.49 (0.29), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 619 HIS 0.002 0.001 HIS A 75 PHE 0.016 0.001 PHE A 107 TYR 0.016 0.001 TYR A1076 ARG 0.005 0.000 ARG A 610 Details of bonding type rmsd link_NAG-ASN : bond 0.00469 ( 5) link_NAG-ASN : angle 2.56414 ( 15) link_BETA1-4 : bond 0.00450 ( 2) link_BETA1-4 : angle 2.90986 ( 6) hydrogen bonds : bond 0.03197 ( 394) hydrogen bonds : angle 5.14224 ( 1110) SS BOND : bond 0.00442 ( 10) SS BOND : angle 1.91748 ( 20) covalent geometry : bond 0.00303 ( 9747) covalent geometry : angle 0.63714 (13243) *********************** 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 96 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 68 time to evaluate : 1.291 Fit side-chains revert: symmetry clash REVERT: A 310 HIS cc_start: 0.7908 (m90) cc_final: 0.7422 (m90) REVERT: A 381 TYR cc_start: 0.8124 (m-10) cc_final: 0.7880 (m-10) REVERT: A 395 ASN cc_start: 0.9545 (p0) cc_final: 0.9281 (p0) REVERT: A 548 ASP cc_start: 0.8403 (t70) cc_final: 0.8189 (t70) REVERT: A 945 TYR cc_start: 0.8221 (OUTLIER) cc_final: 0.7001 (p90) REVERT: A 966 MET cc_start: -0.2994 (ttt) cc_final: -0.3385 (ttm) REVERT: A 1015 MET cc_start: 0.7952 (pmm) cc_final: 0.7592 (pmm) REVERT: A 1045 PHE cc_start: 0.9459 (m-80) cc_final: 0.8915 (m-80) REVERT: A 1213 LYS cc_start: 0.8906 (mmpt) cc_final: 0.8642 (mmpt) REVERT: A 1311 GLN cc_start: 0.8255 (tt0) cc_final: 0.7825 (tt0) outliers start: 28 outliers final: 16 residues processed: 92 average time/residue: 0.9970 time to fit residues: 105.2582 Evaluate side-chains 79 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 62 time to evaluate : 1.052 ------------------------------------------------------------------------------- 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 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 1307 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 88 optimal weight: 6.9990 chunk 34 optimal weight: 10.0000 chunk 84 optimal weight: 6.9990 chunk 14 optimal weight: 0.9990 chunk 78 optimal weight: 0.9980 chunk 110 optimal weight: 0.7980 chunk 79 optimal weight: 0.5980 chunk 65 optimal weight: 0.5980 chunk 75 optimal weight: 2.9990 chunk 108 optimal weight: 0.9980 chunk 114 optimal weight: 4.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.4070 r_free = 0.4070 target = 0.116099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.079534 restraints weight = 21907.994| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 3.85 r_work: 0.3256 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.2329 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= 0.151 Angle : 0.660 12.113 13284 Z= 0.321 Chirality : 0.045 0.248 1521 Planarity : 0.004 0.053 1694 Dihedral : 5.030 34.651 1438 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.25 % Allowed : 4.00 % Favored : 95.75 % Rotamer: Outliers : 2.86 % Allowed : 15.63 % Favored : 81.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 1.61 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.25), residues: 1200 helix: 0.40 (0.38), residues: 187 sheet: 0.08 (0.23), residues: 515 loop : -0.39 (0.29), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 619 HIS 0.002 0.001 HIS A 75 PHE 0.018 0.001 PHE A 107 TYR 0.015 0.001 TYR A1076 ARG 0.004 0.000 ARG A 610 Details of bonding type rmsd link_NAG-ASN : bond 0.00427 ( 5) link_NAG-ASN : angle 2.54494 ( 15) link_BETA1-4 : bond 0.00319 ( 2) link_BETA1-4 : angle 2.95634 ( 6) hydrogen bonds : bond 0.03213 ( 394) hydrogen bonds : angle 5.11915 ( 1110) SS BOND : bond 0.00486 ( 10) SS BOND : angle 1.97733 ( 20) covalent geometry : bond 0.00345 ( 9747) covalent geometry : angle 0.64754 (13243) *********************** 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 96 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 66 time to evaluate : 1.281 Fit side-chains revert: symmetry clash REVERT: A 49 ASP cc_start: 0.9213 (p0) cc_final: 0.8877 (p0) REVERT: A 310 HIS cc_start: 0.7845 (m90) cc_final: 0.7286 (m90) REVERT: A 381 TYR cc_start: 0.8116 (m-10) cc_final: 0.7863 (m-10) REVERT: A 395 ASN cc_start: 0.9555 (p0) cc_final: 0.9295 (p0) REVERT: A 548 ASP cc_start: 0.8455 (t70) cc_final: 0.8232 (t70) REVERT: A 945 TYR cc_start: 0.8226 (OUTLIER) cc_final: 0.7001 (p90) REVERT: A 966 MET cc_start: -0.2947 (ttt) cc_final: -0.3335 (ttm) REVERT: A 1015 MET cc_start: 0.7960 (pmm) cc_final: 0.7602 (pmm) REVERT: A 1045 PHE cc_start: 0.9439 (m-80) cc_final: 0.8919 (m-80) REVERT: A 1213 LYS cc_start: 0.8921 (mmpt) cc_final: 0.8643 (mmpt) REVERT: A 1301 GLU cc_start: 0.8844 (OUTLIER) cc_final: 0.8496 (pt0) outliers start: 30 outliers final: 20 residues processed: 91 average time/residue: 1.0256 time to fit residues: 105.9372 Evaluate side-chains 86 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 64 time to evaluate : 2.187 ------------------------------------------------------------------------------- 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 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 73 optimal weight: 3.9990 chunk 74 optimal weight: 5.9990 chunk 111 optimal weight: 0.5980 chunk 83 optimal weight: 2.9990 chunk 65 optimal weight: 0.3980 chunk 50 optimal weight: 0.5980 chunk 29 optimal weight: 1.9990 chunk 48 optimal weight: 4.9990 chunk 54 optimal weight: 1.9990 chunk 21 optimal weight: 4.9990 chunk 82 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 855 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.114830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.078254 restraints weight = 21921.648| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 3.82 r_work: 0.3222 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.2505 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= 0.190 Angle : 0.695 12.142 13284 Z= 0.336 Chirality : 0.046 0.256 1521 Planarity : 0.004 0.052 1694 Dihedral : 5.070 34.839 1438 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.25 % Allowed : 4.33 % Favored : 95.42 % Rotamer: Outliers : 3.43 % Allowed : 15.92 % Favored : 80.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 1.61 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.25), residues: 1200 helix: 0.46 (0.39), residues: 190 sheet: 0.01 (0.23), residues: 516 loop : -0.40 (0.29), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 619 HIS 0.003 0.001 HIS A 855 PHE 0.016 0.002 PHE A 518 TYR 0.014 0.001 TYR A 620 ARG 0.004 0.000 ARG A 610 Details of bonding type rmsd link_NAG-ASN : bond 0.00427 ( 5) link_NAG-ASN : angle 2.56470 ( 15) link_BETA1-4 : bond 0.00310 ( 2) link_BETA1-4 : angle 3.07056 ( 6) hydrogen bonds : bond 0.03316 ( 394) hydrogen bonds : angle 5.18464 ( 1110) SS BOND : bond 0.00506 ( 10) SS BOND : angle 2.04724 ( 20) covalent geometry : bond 0.00436 ( 9747) covalent geometry : angle 0.68303 (13243) *********************** 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 109 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 73 time to evaluate : 1.883 Fit side-chains revert: symmetry clash REVERT: A 381 TYR cc_start: 0.8115 (m-10) cc_final: 0.7865 (m-10) REVERT: A 395 ASN cc_start: 0.9562 (p0) cc_final: 0.9302 (p0) REVERT: A 471 LEU cc_start: 0.8938 (OUTLIER) cc_final: 0.8578 (tm) REVERT: A 548 ASP cc_start: 0.8468 (t70) cc_final: 0.8239 (t70) REVERT: A 945 TYR cc_start: 0.8259 (OUTLIER) cc_final: 0.7033 (p90) REVERT: A 978 PHE cc_start: 0.9019 (t80) cc_final: 0.8688 (t80) REVERT: A 1015 MET cc_start: 0.7972 (pmm) cc_final: 0.7610 (pmm) REVERT: A 1045 PHE cc_start: 0.9426 (m-80) cc_final: 0.8880 (m-80) REVERT: A 1213 LYS cc_start: 0.8942 (mmpt) cc_final: 0.8656 (mmpt) REVERT: A 1301 GLU cc_start: 0.8868 (OUTLIER) cc_final: 0.8529 (pt0) outliers start: 36 outliers final: 20 residues processed: 101 average time/residue: 1.0419 time to fit residues: 121.1368 Evaluate side-chains 90 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 67 time to evaluate : 0.951 ------------------------------------------------------------------------------- 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 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 88 optimal weight: 6.9990 chunk 3 optimal weight: 6.9990 chunk 55 optimal weight: 1.9990 chunk 101 optimal weight: 7.9990 chunk 54 optimal weight: 2.9990 chunk 33 optimal weight: 5.9990 chunk 68 optimal weight: 0.6980 chunk 106 optimal weight: 0.0060 chunk 0 optimal weight: 2.9990 chunk 18 optimal weight: 0.4980 chunk 25 optimal weight: 3.9990 overall best weight: 1.2400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 728 GLN ** A1273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.114251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.079672 restraints weight = 22086.084| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 4.13 r_work: 0.3200 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.2718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 9764 Z= 0.206 Angle : 0.728 11.996 13284 Z= 0.351 Chirality : 0.046 0.266 1521 Planarity : 0.004 0.052 1694 Dihedral : 5.137 34.481 1438 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.25 % Allowed : 4.42 % Favored : 95.33 % Rotamer: Outliers : 3.15 % Allowed : 16.97 % Favored : 79.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 1.61 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.25), residues: 1200 helix: 0.57 (0.39), residues: 189 sheet: -0.04 (0.23), residues: 516 loop : -0.45 (0.29), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 619 HIS 0.003 0.001 HIS A 855 PHE 0.018 0.002 PHE A 107 TYR 0.014 0.002 TYR A1232 ARG 0.005 0.000 ARG A 30 Details of bonding type rmsd link_NAG-ASN : bond 0.00429 ( 5) link_NAG-ASN : angle 2.60338 ( 15) link_BETA1-4 : bond 0.00201 ( 2) link_BETA1-4 : angle 3.20995 ( 6) hydrogen bonds : bond 0.03401 ( 394) hydrogen bonds : angle 5.25134 ( 1110) SS BOND : bond 0.00489 ( 10) SS BOND : angle 2.09228 ( 20) covalent geometry : bond 0.00475 ( 9747) covalent geometry : angle 0.71624 (13243) *********************** 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 102 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 69 time to evaluate : 1.144 Fit side-chains revert: symmetry clash REVERT: A 49 ASP cc_start: 0.9294 (p0) cc_final: 0.8925 (p0) REVERT: A 381 TYR cc_start: 0.8109 (m-10) cc_final: 0.7853 (m-10) REVERT: A 395 ASN cc_start: 0.9570 (p0) cc_final: 0.9315 (p0) REVERT: A 462 LEU cc_start: 0.8687 (OUTLIER) cc_final: 0.8467 (mm) REVERT: A 471 LEU cc_start: 0.8909 (OUTLIER) cc_final: 0.8622 (tm) REVERT: A 548 ASP cc_start: 0.8465 (t70) cc_final: 0.8223 (t70) REVERT: A 945 TYR cc_start: 0.8256 (OUTLIER) cc_final: 0.7061 (p90) REVERT: A 953 MET cc_start: 0.6082 (ptm) cc_final: 0.5477 (ptp) REVERT: A 1005 PHE cc_start: 0.8533 (m-80) cc_final: 0.8048 (m-80) REVERT: A 1015 MET cc_start: 0.8029 (pmm) cc_final: 0.7664 (pmm) REVERT: A 1045 PHE cc_start: 0.9425 (m-80) cc_final: 0.8893 (m-80) REVERT: A 1213 LYS cc_start: 0.8936 (mmpt) cc_final: 0.8657 (mmpt) REVERT: A 1301 GLU cc_start: 0.8871 (OUTLIER) cc_final: 0.8527 (pt0) outliers start: 33 outliers final: 19 residues processed: 96 average time/residue: 0.8459 time to fit residues: 90.9239 Evaluate side-chains 91 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 68 time to evaluate : 1.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL 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 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 54 optimal weight: 1.9990 chunk 98 optimal weight: 7.9990 chunk 97 optimal weight: 8.9990 chunk 19 optimal weight: 1.9990 chunk 26 optimal weight: 6.9990 chunk 56 optimal weight: 0.9990 chunk 20 optimal weight: 0.5980 chunk 93 optimal weight: 5.9990 chunk 65 optimal weight: 1.9990 chunk 80 optimal weight: 0.9980 chunk 53 optimal weight: 0.7980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.114231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.079761 restraints weight = 21915.512| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 4.22 r_work: 0.3202 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.2766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 9764 Z= 0.189 Angle : 0.726 12.213 13284 Z= 0.349 Chirality : 0.046 0.267 1521 Planarity : 0.004 0.051 1694 Dihedral : 5.118 34.372 1438 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.25 % Allowed : 4.75 % Favored : 95.00 % Rotamer: Outliers : 2.67 % Allowed : 17.92 % Favored : 79.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 1.61 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.25), residues: 1200 helix: 0.65 (0.40), residues: 183 sheet: -0.05 (0.23), residues: 514 loop : -0.39 (0.29), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 619 HIS 0.003 0.001 HIS A 855 PHE 0.016 0.002 PHE A 107 TYR 0.013 0.001 TYR A1076 ARG 0.003 0.000 ARG A 30 Details of bonding type rmsd link_NAG-ASN : bond 0.00418 ( 5) link_NAG-ASN : angle 2.58681 ( 15) link_BETA1-4 : bond 0.00275 ( 2) link_BETA1-4 : angle 3.19331 ( 6) hydrogen bonds : bond 0.03268 ( 394) hydrogen bonds : angle 5.26669 ( 1110) SS BOND : bond 0.00616 ( 10) SS BOND : angle 1.88794 ( 20) covalent geometry : bond 0.00439 ( 9747) covalent geometry : angle 0.71543 (13243) *********************** 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: 28 poor density : 72 time to evaluate : 1.083 Fit side-chains revert: symmetry clash REVERT: A 381 TYR cc_start: 0.8122 (m-10) cc_final: 0.7863 (m-10) REVERT: A 395 ASN cc_start: 0.9565 (p0) cc_final: 0.9307 (p0) REVERT: A 462 LEU cc_start: 0.8637 (OUTLIER) cc_final: 0.8423 (mm) REVERT: A 471 LEU cc_start: 0.8890 (OUTLIER) cc_final: 0.8600 (tm) REVERT: A 548 ASP cc_start: 0.8463 (t70) cc_final: 0.8218 (t70) REVERT: A 945 TYR cc_start: 0.8258 (OUTLIER) cc_final: 0.7061 (p90) REVERT: A 953 MET cc_start: 0.6080 (ptm) cc_final: 0.5473 (ptp) REVERT: A 1015 MET cc_start: 0.8058 (pmm) cc_final: 0.7702 (pmm) REVERT: A 1045 PHE cc_start: 0.9413 (m-80) cc_final: 0.8864 (m-80) REVERT: A 1213 LYS cc_start: 0.8937 (mmpt) cc_final: 0.8664 (mmpt) REVERT: A 1301 GLU cc_start: 0.8863 (OUTLIER) cc_final: 0.8537 (pt0) outliers start: 28 outliers final: 20 residues processed: 93 average time/residue: 0.8542 time to fit residues: 89.2105 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 : 1.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL 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 863 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 9 optimal weight: 1.9990 chunk 79 optimal weight: 6.9990 chunk 22 optimal weight: 0.8980 chunk 36 optimal weight: 5.9990 chunk 105 optimal weight: 0.4980 chunk 0 optimal weight: 3.9990 chunk 100 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 47 optimal weight: 0.9980 chunk 109 optimal weight: 4.9990 chunk 14 optimal weight: 0.4980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.114389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.078886 restraints weight = 22154.472| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 4.12 r_work: 0.3203 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.2882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 9764 Z= 0.179 Angle : 0.728 12.399 13284 Z= 0.350 Chirality : 0.046 0.269 1521 Planarity : 0.004 0.051 1694 Dihedral : 5.061 33.834 1438 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.58 % Favored : 95.25 % Rotamer: Outliers : 2.57 % Allowed : 18.30 % Favored : 79.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 1.61 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.25), residues: 1200 helix: 0.65 (0.40), residues: 184 sheet: -0.05 (0.23), residues: 507 loop : -0.38 (0.29), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 619 HIS 0.003 0.001 HIS A 855 PHE 0.022 0.002 PHE A 387 TYR 0.012 0.001 TYR A1076 ARG 0.003 0.000 ARG A 30 Details of bonding type rmsd link_NAG-ASN : bond 0.00395 ( 5) link_NAG-ASN : angle 2.60270 ( 15) link_BETA1-4 : bond 0.00327 ( 2) link_BETA1-4 : angle 3.20922 ( 6) hydrogen bonds : bond 0.03210 ( 394) hydrogen bonds : angle 5.26118 ( 1110) SS BOND : bond 0.00572 ( 10) SS BOND : angle 1.78857 ( 20) covalent geometry : bond 0.00416 ( 9747) covalent geometry : angle 0.71766 (13243) ********************** 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: 27 poor density : 75 time to evaluate : 1.179 Fit side-chains revert: symmetry clash REVERT: A 49 ASP cc_start: 0.9307 (p0) cc_final: 0.8915 (p0) REVERT: A 381 TYR cc_start: 0.8115 (m-10) cc_final: 0.7855 (m-10) REVERT: A 395 ASN cc_start: 0.9571 (p0) cc_final: 0.9325 (p0) REVERT: A 462 LEU cc_start: 0.8659 (OUTLIER) cc_final: 0.8433 (mm) REVERT: A 471 LEU cc_start: 0.8905 (OUTLIER) cc_final: 0.8617 (tm) REVERT: A 548 ASP cc_start: 0.8419 (t70) cc_final: 0.8199 (t70) REVERT: A 945 TYR cc_start: 0.8241 (OUTLIER) cc_final: 0.7066 (p90) REVERT: A 953 MET cc_start: 0.6110 (ptm) cc_final: 0.5562 (ptp) REVERT: A 1001 ARG cc_start: 0.9328 (tpm170) cc_final: 0.8766 (tpm170) REVERT: A 1005 PHE cc_start: 0.8326 (OUTLIER) cc_final: 0.6785 (m-80) REVERT: A 1015 MET cc_start: 0.8078 (pmm) cc_final: 0.7721 (pmm) REVERT: A 1045 PHE cc_start: 0.9376 (m-80) cc_final: 0.8836 (m-80) REVERT: A 1213 LYS cc_start: 0.8943 (mmpt) cc_final: 0.8673 (mmpt) REVERT: A 1301 GLU cc_start: 0.8863 (OUTLIER) cc_final: 0.8535 (pt0) outliers start: 27 outliers final: 19 residues processed: 96 average time/residue: 0.8874 time to fit residues: 96.4927 Evaluate side-chains 96 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 72 time to evaluate : 1.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL 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 1005 PHE 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 104 optimal weight: 5.9990 chunk 89 optimal weight: 1.9990 chunk 81 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 chunk 65 optimal weight: 0.0000 chunk 99 optimal weight: 0.9990 chunk 106 optimal weight: 0.9990 chunk 84 optimal weight: 7.9990 chunk 28 optimal weight: 0.8980 chunk 88 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 overall best weight: 0.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1047 GLN ** A1273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.114997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.079584 restraints weight = 21953.752| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 4.11 r_work: 0.3218 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.2899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 9764 Z= 0.155 Angle : 0.711 12.205 13284 Z= 0.341 Chirality : 0.045 0.264 1521 Planarity : 0.004 0.051 1694 Dihedral : 4.945 33.261 1438 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.17 % Favored : 95.67 % Rotamer: Outliers : 2.48 % Allowed : 18.49 % Favored : 79.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 1.61 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.25), residues: 1200 helix: 0.62 (0.39), residues: 185 sheet: -0.01 (0.23), residues: 505 loop : -0.33 (0.29), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A1065 HIS 0.002 0.000 HIS A 855 PHE 0.017 0.001 PHE A 387 TYR 0.011 0.001 TYR A 196 ARG 0.003 0.000 ARG A 610 Details of bonding type rmsd link_NAG-ASN : bond 0.00383 ( 5) link_NAG-ASN : angle 2.59037 ( 15) link_BETA1-4 : bond 0.00276 ( 2) link_BETA1-4 : angle 3.22433 ( 6) hydrogen bonds : bond 0.03136 ( 394) hydrogen bonds : angle 5.19594 ( 1110) SS BOND : bond 0.00572 ( 10) SS BOND : angle 1.73959 ( 20) covalent geometry : bond 0.00361 ( 9747) covalent geometry : angle 0.70050 (13243) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8311.96 seconds wall clock time: 148 minutes 45.98 seconds (8925.98 seconds total)