Starting phenix.real_space_refine on Sat Aug 23 04:30:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9fx3_50842/08_2025/9fx3_50842.cif Found real_map, /net/cci-nas-00/data/ceres_data/9fx3_50842/08_2025/9fx3_50842.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9fx3_50842/08_2025/9fx3_50842.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9fx3_50842/08_2025/9fx3_50842.map" model { file = "/net/cci-nas-00/data/ceres_data/9fx3_50842/08_2025/9fx3_50842.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9fx3_50842/08_2025/9fx3_50842.cif" } resolution = 3.2 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= -0.001 sd= 0.025 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 28 5.16 5 C 6090 2.51 5 N 1539 2.21 5 O 1854 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9511 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 9301 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1178, 9301 Classifications: {'peptide': 1178} Link IDs: {'PCIS': 2, 'PTRANS': 52, 'TRANS': 1123} Chain breaks: 4 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: "C" 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: "D" 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: "E" 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: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 2.44, per 1000 atoms: 0.26 Number of scatterers: 9511 At special positions: 0 Unit cell: (87.992, 119.048, 121.636, 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 28 16.00 O 1854 8.00 N 1539 7.00 C 6090 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 530 " - pdb=" SG CYS A 636 " 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 C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " NAG-ASN " NAG A1301 " - " ASN A 41 " " NAG A1302 " - " ASN A 118 " " NAG A1303 " - " ASN A 291 " " NAG A1304 " - " ASN A 337 " " NAG A1305 " - " ASN A 365 " " NAG A1306 " - " ASN A 419 " " NAG A1307 " - " ASN A 513 " " NAG B 1 " - " ASN A 247 " " NAG C 1 " - " ASN A1086 " " NAG D 1 " - " ASN A 279 " " NAG E 1 " - " ASN A1244 " Time building additional restraints: 0.95 Conformation dependent library (CDL) restraints added in 363.6 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2226 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 20 sheets defined 20.0% alpha, 38.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.47 Creating SS restraints... Processing helix chain 'A' and resid 301 through 306 Processing helix chain 'A' and resid 383 through 387 Processing helix chain 'A' and resid 522 through 526 removed outlier: 3.835A pdb=" N THR A 526 " --> pdb=" O ASN A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 594 through 598 Processing helix chain 'A' and resid 606 through 618 Processing helix chain 'A' and resid 629 through 635 Processing helix chain 'A' and resid 907 through 912 Processing helix chain 'A' and resid 913 through 915 No H-bonds generated for 'chain 'A' and resid 913 through 915' Processing helix chain 'A' and resid 921 through 928 Processing helix chain 'A' and resid 929 through 943 Processing helix chain 'A' and resid 946 through 966 Processing helix chain 'A' and resid 985 through 1000 Processing helix chain 'A' and resid 1006 through 1019 removed outlier: 3.575A pdb=" N LEU A1010 " --> pdb=" O ASP A1006 " (cutoff:3.500A) Processing helix chain 'A' and resid 1035 through 1040 Processing helix chain 'A' and resid 1044 through 1057 Processing helix chain 'A' and resid 1058 through 1062 removed outlier: 3.822A pdb=" N LYS A1061 " --> pdb=" O GLY A1058 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N TYR A1062 " --> pdb=" O TYR A1059 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1058 through 1062' Processing helix chain 'A' and resid 1068 through 1082 removed outlier: 3.920A pdb=" N GLY A1082 " --> pdb=" O GLU A1078 " (cutoff:3.500A) Processing helix chain 'A' and resid 1086 through 1100 Processing helix chain 'A' and resid 1103 through 1114 Processing helix chain 'A' and resid 1140 through 1155 Processing helix chain 'A' and resid 1161 through 1171 Processing helix chain 'A' and resid 1181 through 1198 removed outlier: 3.793A pdb=" N VAL A1186 " --> pdb=" O GLN A1182 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 85 through 89 removed outlier: 7.411A pdb=" N THR A 43 " --> pdb=" O PRO A 33 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 35 through 36 removed outlier: 6.565A pdb=" N GLY A 108 " --> pdb=" O LEU A 115 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N SER A 117 " --> pdb=" O VAL A 106 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N VAL A 106 " --> pdb=" O SER A 117 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N SER A 119 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N LEU A 104 " --> pdb=" O SER A 119 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N ARG A 121 " --> pdb=" O TYR A 102 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N TYR A 102 " --> pdb=" O ARG A 121 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ILE A 101 " --> pdb=" O THR A 65 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU A 74 " --> pdb=" O LEU A 62 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N LYS A 64 " --> pdb=" O SER A 72 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N SER A 72 " --> pdb=" O LYS A 64 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N ALA A 66 " --> pdb=" O THR A 70 " (cutoff:3.500A) removed outlier: 5.235A pdb=" N THR A 70 " --> pdb=" O ALA A 66 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 130 through 135 Processing sheet with id=AA4, first strand: chain 'A' and resid 139 through 140 removed outlier: 5.342A pdb=" N LEU A 164 " --> pdb=" O SER A 181 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 229 through 234 Processing sheet with id=AA6, first strand: chain 'A' and resid 238 through 240 removed outlier: 6.075A pdb=" N CYS A 239 " --> pdb=" O LYS A 345 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 349 through 354 Processing sheet with id=AA8, first strand: chain 'A' and resid 359 through 360 Processing sheet with id=AA9, first strand: chain 'A' and resid 413 through 420 Processing sheet with id=AB1, first strand: chain 'A' and resid 468 through 472 Processing sheet with id=AB2, first strand: chain 'A' and resid 505 through 512 removed outlier: 6.520A pdb=" N VAL A 500 " --> pdb=" O VAL A 507 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N VAL A 509 " --> pdb=" O TYR A 498 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N TYR A 498 " --> pdb=" O VAL A 509 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N LYS A 511 " --> pdb=" O LEU A 496 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N LEU A 496 " --> pdb=" O LYS A 511 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 559 through 563 Processing sheet with id=AB4, first strand: chain 'A' and resid 567 through 568 removed outlier: 6.860A pdb=" N ASP A 593 " --> pdb=" O THR A 693 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N THR A 693 " --> pdb=" O ASP A 593 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 567 through 568 Processing sheet with id=AB6, first strand: chain 'A' and resid 686 through 687 removed outlier: 6.047A pdb=" N ARG A 687 " --> pdb=" O THR A 846 " (cutoff:3.500A) removed outlier: 7.834A pdb=" N MET A 848 " --> pdb=" O ARG A 687 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N VAL A 758 " --> pdb=" O LYS A 852 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'A' and resid 686 through 687 removed outlier: 6.047A pdb=" N ARG A 687 " --> pdb=" O THR A 846 " (cutoff:3.500A) removed outlier: 7.834A pdb=" N MET A 848 " --> pdb=" O ARG A 687 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 748 through 753 removed outlier: 4.245A pdb=" N GLU A 767 " --> pdb=" O ASN A 753 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 856 through 868 removed outlier: 4.676A pdb=" N VAL A 895 " --> pdb=" O LEU A1235 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 875 through 882 Processing sheet with id=AC2, first strand: chain 'A' and resid 1116 through 1117 436 hydrogen bonds defined for protein. 1215 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.10 Time building geometry restraints manager: 1.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2967 1.34 - 1.46: 2266 1.46 - 1.58: 4428 1.58 - 1.70: 0 1.70 - 1.82: 49 Bond restraints: 9710 Sorted by residual: bond pdb=" C ILE A 280 " pdb=" N THR A 281 " ideal model delta sigma weight residual 1.330 1.228 0.102 1.44e-02 4.82e+03 5.06e+01 bond pdb=" C ILE A1162 " pdb=" N PRO A1163 " ideal model delta sigma weight residual 1.335 1.402 -0.068 1.28e-02 6.10e+03 2.81e+01 bond pdb=" C1 NAG C 1 " pdb=" O5 NAG C 1 " ideal model delta sigma weight residual 1.406 1.475 -0.069 2.00e-02 2.50e+03 1.20e+01 bond pdb=" N ASN A 279 " pdb=" CA ASN A 279 " ideal model delta sigma weight residual 1.455 1.491 -0.036 1.21e-02 6.83e+03 8.68e+00 bond pdb=" N ILE A 280 " pdb=" CA ILE A 280 " ideal model delta sigma weight residual 1.459 1.491 -0.032 1.19e-02 7.06e+03 7.18e+00 ... (remaining 9705 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.17: 13020 3.17 - 6.34: 136 6.34 - 9.51: 24 9.51 - 12.68: 7 12.68 - 15.84: 3 Bond angle restraints: 13190 Sorted by residual: angle pdb=" O ILE A 280 " pdb=" C ILE A 280 " pdb=" N THR A 281 " ideal model delta sigma weight residual 122.81 133.02 -10.21 1.11e+00 8.12e-01 8.46e+01 angle pdb=" CA ILE A 280 " pdb=" C ILE A 280 " pdb=" N THR A 281 " ideal model delta sigma weight residual 116.30 108.23 8.07 1.13e+00 7.83e-01 5.10e+01 angle pdb=" CG ARG A 872 " pdb=" CD ARG A 872 " pdb=" NE ARG A 872 " ideal model delta sigma weight residual 112.00 127.60 -15.60 2.20e+00 2.07e-01 5.03e+01 angle pdb=" C ILE A 280 " pdb=" N THR A 281 " pdb=" CA THR A 281 " ideal model delta sigma weight residual 122.94 112.45 10.49 1.50e+00 4.44e-01 4.89e+01 angle pdb=" C GLY A1161 " pdb=" N ILE A1162 " pdb=" CA ILE A1162 " ideal model delta sigma weight residual 120.24 124.49 -4.25 6.30e-01 2.52e+00 4.55e+01 ... (remaining 13185 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.09: 5309 17.09 - 34.17: 538 34.17 - 51.26: 134 51.26 - 68.34: 30 68.34 - 85.43: 8 Dihedral angle restraints: 6019 sinusoidal: 2578 harmonic: 3441 Sorted by residual: dihedral pdb=" CA ASP A1085 " pdb=" C ASP A1085 " pdb=" N ASN A1086 " pdb=" CA ASN A1086 " ideal model delta harmonic sigma weight residual -180.00 -141.60 -38.40 0 5.00e+00 4.00e-02 5.90e+01 dihedral pdb=" CB CYS A 530 " pdb=" SG CYS A 530 " pdb=" SG CYS A 636 " pdb=" CB CYS A 636 " ideal model delta sinusoidal sigma weight residual -86.00 -128.20 42.20 1 1.00e+01 1.00e-02 2.49e+01 dihedral pdb=" CA GLY A1041 " pdb=" C GLY A1041 " pdb=" N ASN A1042 " pdb=" CA ASN A1042 " ideal model delta harmonic sigma weight residual 180.00 158.37 21.63 0 5.00e+00 4.00e-02 1.87e+01 ... (remaining 6016 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.105: 1447 0.105 - 0.210: 120 0.210 - 0.315: 3 0.315 - 0.420: 2 0.420 - 0.525: 3 Chirality restraints: 1575 Sorted by residual: chirality pdb=" C1 NAG E 2 " pdb=" O4 NAG E 1 " pdb=" C2 NAG E 2 " pdb=" O5 NAG E 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.15 -0.25 2.00e-02 2.50e+03 1.60e+02 chirality pdb=" C1 NAG D 2 " pdb=" O4 NAG D 1 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.31 -0.09 2.00e-02 2.50e+03 1.85e+01 chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN A 279 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.88 -0.52 2.00e-01 2.50e+01 6.89e+00 ... (remaining 1572 not shown) Planarity restraints: 1660 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 1 " -0.172 2.00e-02 2.50e+03 1.46e-01 2.67e+02 pdb=" C7 NAG E 1 " 0.036 2.00e-02 2.50e+03 pdb=" C8 NAG E 1 " -0.118 2.00e-02 2.50e+03 pdb=" N2 NAG E 1 " 0.249 2.00e-02 2.50e+03 pdb=" O7 NAG E 1 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 2 " -0.142 2.00e-02 2.50e+03 1.19e-01 1.76e+02 pdb=" C7 NAG D 2 " 0.037 2.00e-02 2.50e+03 pdb=" C8 NAG D 2 " -0.104 2.00e-02 2.50e+03 pdb=" N2 NAG D 2 " 0.195 2.00e-02 2.50e+03 pdb=" O7 NAG D 2 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 1 " 0.127 2.00e-02 2.50e+03 1.04e-01 1.35e+02 pdb=" C7 NAG D 1 " -0.045 2.00e-02 2.50e+03 pdb=" C8 NAG D 1 " 0.098 2.00e-02 2.50e+03 pdb=" N2 NAG D 1 " -0.162 2.00e-02 2.50e+03 pdb=" O7 NAG D 1 " -0.018 2.00e-02 2.50e+03 ... (remaining 1657 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 2465 2.80 - 3.33: 7303 3.33 - 3.85: 16145 3.85 - 4.38: 17602 4.38 - 4.90: 31168 Nonbonded interactions: 74683 Sorted by model distance: nonbonded pdb=" O LEU A 936 " pdb=" OG1 THR A 940 " model vdw 2.280 3.040 nonbonded pdb=" O ARG A1114 " pdb=" C8 NAG C 2 " model vdw 2.298 3.460 nonbonded pdb=" OH TYR A 254 " pdb=" OE2 GLU A 329 " model vdw 2.326 3.040 nonbonded pdb=" O VAL A 331 " pdb=" OG1 THR A 817 " model vdw 2.328 3.040 nonbonded pdb=" OG SER A 502 " pdb=" O SER A 524 " model vdw 2.342 3.040 ... (remaining 74678 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 'C' selection = chain 'D' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.080 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: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.330 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 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 : 0.005 0.102 9726 Z= 0.259 Angle : 0.924 19.540 13237 Z= 0.460 Chirality : 0.059 0.525 1575 Planarity : 0.009 0.146 1649 Dihedral : 14.834 85.426 3790 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 0.57 % Allowed : 19.70 % Favored : 79.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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 aren not related in a simple way. whole: -0.71 (0.23), residues: 1168 helix: -1.99 (0.26), residues: 219 sheet: 0.74 (0.23), residues: 507 loop : -1.00 (0.27), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A1081 TYR 0.043 0.002 TYR A1059 PHE 0.022 0.002 PHE A 284 TRP 0.012 0.002 TRP A 204 HIS 0.002 0.000 HIS A 689 Details of bonding type rmsd covalent geometry : bond 0.00513 ( 9710) covalent geometry : angle 0.87389 (13190) SS BOND : bond 0.00574 ( 1) SS BOND : angle 2.86105 ( 2) hydrogen bonds : bond 0.12380 ( 429) hydrogen bonds : angle 6.28205 ( 1215) link_BETA1-4 : bond 0.03235 ( 4) link_BETA1-4 : angle 6.15674 ( 12) link_NAG-ASN : bond 0.00538 ( 11) link_NAG-ASN : angle 4.78345 ( 33) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 33 time to evaluate : 0.372 Fit side-chains REVERT: A 454 MET cc_start: 0.7900 (pmm) cc_final: 0.7333 (pmm) REVERT: A 1081 ARG cc_start: 0.8588 (mtt90) cc_final: 0.8220 (mtt90) outliers start: 6 outliers final: 1 residues processed: 39 average time/residue: 0.1030 time to fit residues: 6.1051 Evaluate side-chains 33 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 32 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 108 optimal weight: 2.9990 chunk 49 optimal weight: 0.5980 chunk 97 optimal weight: 0.9980 chunk 113 optimal weight: 0.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 100 optimal weight: 4.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 HIS A 174 ASN A 387 ASN A 469 GLN A 805 GLN ** A1122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1157 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.093405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.063669 restraints weight = 21550.256| |-----------------------------------------------------------------------------| r_work (start): 0.2964 rms_B_bonded: 3.60 r_work: 0.2823 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.0960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 9726 Z= 0.159 Angle : 0.529 8.252 13237 Z= 0.266 Chirality : 0.044 0.164 1575 Planarity : 0.004 0.053 1649 Dihedral : 5.233 54.127 1568 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.80 % Allowed : 17.80 % Favored : 80.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.26 (0.24), residues: 1168 helix: 0.03 (0.32), residues: 227 sheet: 0.90 (0.23), residues: 507 loop : -0.51 (0.29), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 872 TYR 0.011 0.001 TYR A1014 PHE 0.012 0.001 PHE A 764 TRP 0.007 0.001 TRP A 204 HIS 0.003 0.001 HIS A1035 Details of bonding type rmsd covalent geometry : bond 0.00355 ( 9710) covalent geometry : angle 0.51320 (13190) SS BOND : bond 0.00089 ( 1) SS BOND : angle 1.76518 ( 2) hydrogen bonds : bond 0.03106 ( 429) hydrogen bonds : angle 4.88925 ( 1215) link_BETA1-4 : bond 0.00623 ( 4) link_BETA1-4 : angle 3.51170 ( 12) link_NAG-ASN : bond 0.00200 ( 11) link_NAG-ASN : angle 1.52786 ( 33) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 39 time to evaluate : 0.389 Fit side-chains revert: symmetry clash REVERT: A 29 LEU cc_start: 0.9086 (OUTLIER) cc_final: 0.8878 (tt) REVERT: A 299 MET cc_start: 0.8486 (mpp) cc_final: 0.8100 (mpp) REVERT: A 352 GLU cc_start: 0.8102 (tm-30) cc_final: 0.7516 (tm-30) REVERT: A 545 ASP cc_start: 0.8693 (t0) cc_final: 0.8420 (t0) REVERT: A 599 MET cc_start: 0.9136 (mmm) cc_final: 0.8789 (mmm) REVERT: A 607 MET cc_start: 0.8737 (mmm) cc_final: 0.8493 (tpp) REVERT: A 627 MET cc_start: 0.4754 (tmm) cc_final: 0.4341 (tmm) REVERT: A 957 MET cc_start: 0.8250 (mmm) cc_final: 0.7991 (mmt) REVERT: A 1081 ARG cc_start: 0.8348 (mtt90) cc_final: 0.8029 (mtm180) outliers start: 19 outliers final: 13 residues processed: 57 average time/residue: 0.0849 time to fit residues: 7.4122 Evaluate side-chains 52 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 38 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 379 GLN Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 554 VAL Chi-restraints excluded: chain A residue 632 VAL Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain A residue 706 TYR Chi-restraints excluded: chain A residue 762 GLU Chi-restraints excluded: chain A residue 804 HIS Chi-restraints excluded: chain A residue 1047 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 0 optimal weight: 3.9990 chunk 60 optimal weight: 4.9990 chunk 72 optimal weight: 6.9990 chunk 44 optimal weight: 3.9990 chunk 116 optimal weight: 4.9990 chunk 23 optimal weight: 1.9990 chunk 31 optimal weight: 0.0980 chunk 98 optimal weight: 3.9990 chunk 94 optimal weight: 6.9990 chunk 65 optimal weight: 0.9980 chunk 104 optimal weight: 1.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1039 GLN A1073 HIS ** A1122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.089492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.058944 restraints weight = 21685.585| |-----------------------------------------------------------------------------| r_work (start): 0.2877 rms_B_bonded: 3.52 r_work: 0.2725 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.1756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.047 9726 Z= 0.284 Angle : 0.605 10.359 13237 Z= 0.303 Chirality : 0.046 0.220 1575 Planarity : 0.004 0.042 1649 Dihedral : 5.252 52.942 1567 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 3.12 % Allowed : 17.05 % Favored : 79.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.58 (0.25), residues: 1168 helix: 0.96 (0.35), residues: 227 sheet: 0.78 (0.23), residues: 507 loop : -0.29 (0.30), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 37 TYR 0.016 0.002 TYR A1014 PHE 0.016 0.002 PHE A 764 TRP 0.012 0.001 TRP A 525 HIS 0.004 0.001 HIS A1035 Details of bonding type rmsd covalent geometry : bond 0.00651 ( 9710) covalent geometry : angle 0.59257 (13190) SS BOND : bond 0.02463 ( 1) SS BOND : angle 2.90222 ( 2) hydrogen bonds : bond 0.03549 ( 429) hydrogen bonds : angle 5.03885 ( 1215) link_BETA1-4 : bond 0.00774 ( 4) link_BETA1-4 : angle 3.20871 ( 12) link_NAG-ASN : bond 0.00409 ( 11) link_NAG-ASN : angle 1.56093 ( 33) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 38 time to evaluate : 0.385 Fit side-chains REVERT: A 299 MET cc_start: 0.8709 (mpp) cc_final: 0.8401 (mpp) REVERT: A 352 GLU cc_start: 0.8233 (tm-30) cc_final: 0.7680 (tm-30) REVERT: A 545 ASP cc_start: 0.8728 (t0) cc_final: 0.8291 (t0) REVERT: A 599 MET cc_start: 0.9246 (mmm) cc_final: 0.8866 (mmm) REVERT: A 625 MET cc_start: 0.5262 (ppp) cc_final: 0.5041 (pmm) REVERT: A 627 MET cc_start: 0.4933 (tmm) cc_final: 0.4413 (tmm) REVERT: A 764 PHE cc_start: 0.8916 (OUTLIER) cc_final: 0.8307 (p90) REVERT: A 872 ARG cc_start: 0.8875 (mmp80) cc_final: 0.8631 (mmp80) REVERT: A 890 THR cc_start: 0.9578 (OUTLIER) cc_final: 0.9324 (p) REVERT: A 926 MET cc_start: 0.8023 (mmt) cc_final: 0.7568 (mmp) REVERT: A 1081 ARG cc_start: 0.8359 (mtt90) cc_final: 0.8089 (mtm180) REVERT: A 1121 MET cc_start: 0.7477 (mmt) cc_final: 0.6912 (mmt) outliers start: 33 outliers final: 18 residues processed: 68 average time/residue: 0.0743 time to fit residues: 7.9587 Evaluate side-chains 56 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 36 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 499 MET Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 554 VAL Chi-restraints excluded: chain A residue 586 ILE Chi-restraints excluded: chain A residue 632 VAL Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 706 TYR Chi-restraints excluded: chain A residue 762 GLU Chi-restraints excluded: chain A residue 764 PHE Chi-restraints excluded: chain A residue 804 HIS Chi-restraints excluded: chain A residue 890 THR Chi-restraints excluded: chain A residue 1047 THR Chi-restraints excluded: chain A residue 1168 LEU Chi-restraints excluded: chain A residue 1232 THR Chi-restraints excluded: chain A residue 1257 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 50 optimal weight: 0.8980 chunk 80 optimal weight: 1.9990 chunk 67 optimal weight: 0.8980 chunk 17 optimal weight: 0.0770 chunk 13 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 chunk 6 optimal weight: 0.8980 chunk 84 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 overall best weight: 0.7540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1122 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 = 0.3540 r_free = 0.3540 target = 0.090623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.059477 restraints weight = 21522.733| |-----------------------------------------------------------------------------| r_work (start): 0.2920 rms_B_bonded: 3.72 r_work: 0.2781 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.1766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9726 Z= 0.139 Angle : 0.502 8.285 13237 Z= 0.250 Chirality : 0.044 0.205 1575 Planarity : 0.004 0.038 1649 Dihedral : 5.025 51.757 1567 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 3.03 % Allowed : 17.90 % Favored : 79.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.74 (0.25), residues: 1168 helix: 1.21 (0.35), residues: 232 sheet: 0.83 (0.23), residues: 504 loop : -0.21 (0.30), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 872 TYR 0.011 0.001 TYR A1014 PHE 0.014 0.001 PHE A 284 TRP 0.007 0.001 TRP A 639 HIS 0.002 0.001 HIS A1035 Details of bonding type rmsd covalent geometry : bond 0.00307 ( 9710) covalent geometry : angle 0.48910 (13190) SS BOND : bond 0.00021 ( 1) SS BOND : angle 1.83873 ( 2) hydrogen bonds : bond 0.02855 ( 429) hydrogen bonds : angle 4.75113 ( 1215) link_BETA1-4 : bond 0.00779 ( 4) link_BETA1-4 : angle 3.21124 ( 12) link_NAG-ASN : bond 0.00254 ( 11) link_NAG-ASN : angle 1.28755 ( 33) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 38 time to evaluate : 0.305 Fit side-chains REVERT: A 29 LEU cc_start: 0.9105 (OUTLIER) cc_final: 0.8838 (tt) REVERT: A 299 MET cc_start: 0.8732 (mpp) cc_final: 0.8385 (mpp) REVERT: A 352 GLU cc_start: 0.8288 (OUTLIER) cc_final: 0.7667 (tm-30) REVERT: A 492 ARG cc_start: 0.8645 (OUTLIER) cc_final: 0.8027 (ttp80) REVERT: A 545 ASP cc_start: 0.8608 (t0) cc_final: 0.8295 (t0) REVERT: A 599 MET cc_start: 0.9328 (mmm) cc_final: 0.8936 (mmm) REVERT: A 627 MET cc_start: 0.4982 (tmm) cc_final: 0.4521 (tmm) REVERT: A 872 ARG cc_start: 0.8853 (mmp80) cc_final: 0.8615 (mmp80) REVERT: A 890 THR cc_start: 0.9577 (OUTLIER) cc_final: 0.9335 (p) REVERT: A 957 MET cc_start: 0.8227 (mmm) cc_final: 0.8017 (mmt) outliers start: 32 outliers final: 20 residues processed: 67 average time/residue: 0.0921 time to fit residues: 9.2447 Evaluate side-chains 61 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 37 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 352 GLU Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 492 ARG Chi-restraints excluded: chain A residue 554 VAL Chi-restraints excluded: chain A residue 586 ILE Chi-restraints excluded: chain A residue 632 VAL Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain A residue 706 TYR Chi-restraints excluded: chain A residue 762 GLU Chi-restraints excluded: chain A residue 804 HIS Chi-restraints excluded: chain A residue 845 VAL Chi-restraints excluded: chain A residue 890 THR Chi-restraints excluded: chain A residue 903 VAL Chi-restraints excluded: chain A residue 1047 THR Chi-restraints excluded: chain A residue 1057 LEU Chi-restraints excluded: chain A residue 1110 MET Chi-restraints excluded: chain A residue 1168 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 80 optimal weight: 0.9990 chunk 47 optimal weight: 3.9990 chunk 76 optimal weight: 1.9990 chunk 104 optimal weight: 0.5980 chunk 65 optimal weight: 1.9990 chunk 96 optimal weight: 0.9990 chunk 45 optimal weight: 0.9980 chunk 95 optimal weight: 0.9980 chunk 105 optimal weight: 0.5980 chunk 79 optimal weight: 0.9980 chunk 3 optimal weight: 3.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1122 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 = 0.3537 r_free = 0.3537 target = 0.090451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.059359 restraints weight = 21339.314| |-----------------------------------------------------------------------------| r_work (start): 0.2917 rms_B_bonded: 3.72 r_work: 0.2778 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.2778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.1866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9726 Z= 0.149 Angle : 0.503 9.011 13237 Z= 0.248 Chirality : 0.044 0.206 1575 Planarity : 0.003 0.037 1649 Dihedral : 4.926 52.376 1567 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.94 % Allowed : 18.09 % Favored : 78.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.81 (0.25), residues: 1168 helix: 1.24 (0.35), residues: 234 sheet: 0.84 (0.23), residues: 504 loop : -0.10 (0.30), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1081 TYR 0.010 0.001 TYR A1014 PHE 0.014 0.001 PHE A 284 TRP 0.005 0.001 TRP A 639 HIS 0.002 0.001 HIS A1035 Details of bonding type rmsd covalent geometry : bond 0.00335 ( 9710) covalent geometry : angle 0.49036 (13190) SS BOND : bond 0.00216 ( 1) SS BOND : angle 2.03105 ( 2) hydrogen bonds : bond 0.02838 ( 429) hydrogen bonds : angle 4.66323 ( 1215) link_BETA1-4 : bond 0.00700 ( 4) link_BETA1-4 : angle 3.12408 ( 12) link_NAG-ASN : bond 0.00254 ( 11) link_NAG-ASN : angle 1.31839 ( 33) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 39 time to evaluate : 0.262 Fit side-chains revert: symmetry clash REVERT: A 299 MET cc_start: 0.8762 (mpp) cc_final: 0.8430 (mpp) REVERT: A 352 GLU cc_start: 0.8325 (OUTLIER) cc_final: 0.7685 (tm-30) REVERT: A 435 LEU cc_start: 0.8856 (OUTLIER) cc_final: 0.8620 (mm) REVERT: A 492 ARG cc_start: 0.8622 (OUTLIER) cc_final: 0.8003 (ttp80) REVERT: A 545 ASP cc_start: 0.8593 (t0) cc_final: 0.8235 (t0) REVERT: A 599 MET cc_start: 0.9316 (mmm) cc_final: 0.8921 (mmm) REVERT: A 872 ARG cc_start: 0.8877 (mmp80) cc_final: 0.8652 (mmp80) outliers start: 31 outliers final: 20 residues processed: 67 average time/residue: 0.0819 time to fit residues: 8.5306 Evaluate side-chains 62 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 39 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 352 GLU Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 379 GLN Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 492 ARG Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 554 VAL Chi-restraints excluded: chain A residue 586 ILE Chi-restraints excluded: chain A residue 614 LEU Chi-restraints excluded: chain A residue 632 VAL Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain A residue 706 TYR Chi-restraints excluded: chain A residue 762 GLU Chi-restraints excluded: chain A residue 804 HIS Chi-restraints excluded: chain A residue 845 VAL Chi-restraints excluded: chain A residue 1047 THR Chi-restraints excluded: chain A residue 1057 LEU Chi-restraints excluded: chain A residue 1110 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 28 optimal weight: 6.9990 chunk 59 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 chunk 107 optimal weight: 0.8980 chunk 34 optimal weight: 6.9990 chunk 62 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1122 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 = 0.3501 r_free = 0.3501 target = 0.088575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.057824 restraints weight = 21755.396| |-----------------------------------------------------------------------------| r_work (start): 0.2868 rms_B_bonded: 3.50 r_work: 0.2724 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.2363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.050 9726 Z= 0.305 Angle : 0.619 8.735 13237 Z= 0.306 Chirality : 0.046 0.200 1575 Planarity : 0.004 0.040 1649 Dihedral : 5.250 52.954 1567 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 3.31 % Allowed : 17.99 % Favored : 78.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.66 (0.25), residues: 1168 helix: 1.33 (0.35), residues: 232 sheet: 0.63 (0.23), residues: 499 loop : -0.14 (0.30), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A1172 TYR 0.011 0.001 TYR A1014 PHE 0.016 0.002 PHE A 764 TRP 0.010 0.001 TRP A 525 HIS 0.005 0.001 HIS A 804 Details of bonding type rmsd covalent geometry : bond 0.00694 ( 9710) covalent geometry : angle 0.60708 (13190) SS BOND : bond 0.00434 ( 1) SS BOND : angle 3.26730 ( 2) hydrogen bonds : bond 0.03392 ( 429) hydrogen bonds : angle 5.05596 ( 1215) link_BETA1-4 : bond 0.00619 ( 4) link_BETA1-4 : angle 2.87184 ( 12) link_NAG-ASN : bond 0.00401 ( 11) link_NAG-ASN : angle 1.58400 ( 33) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 35 time to evaluate : 0.238 Fit side-chains revert: symmetry clash REVERT: A 352 GLU cc_start: 0.8321 (OUTLIER) cc_final: 0.7762 (tm-30) REVERT: A 435 LEU cc_start: 0.8833 (OUTLIER) cc_final: 0.8610 (mm) REVERT: A 492 ARG cc_start: 0.8647 (OUTLIER) cc_final: 0.7994 (ttp80) REVERT: A 545 ASP cc_start: 0.8653 (t0) cc_final: 0.8234 (t0) REVERT: A 599 MET cc_start: 0.9393 (mmm) cc_final: 0.8972 (mmm) REVERT: A 625 MET cc_start: 0.5530 (pmm) cc_final: 0.5323 (ppp) REVERT: A 764 PHE cc_start: 0.9017 (OUTLIER) cc_final: 0.8359 (p90) REVERT: A 890 THR cc_start: 0.9588 (OUTLIER) cc_final: 0.9349 (p) REVERT: A 1172 ARG cc_start: 0.6260 (OUTLIER) cc_final: 0.5394 (ptm-80) outliers start: 35 outliers final: 24 residues processed: 67 average time/residue: 0.0802 time to fit residues: 8.0432 Evaluate side-chains 63 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 33 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 352 GLU Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 492 ARG Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 554 VAL Chi-restraints excluded: chain A residue 586 ILE Chi-restraints excluded: chain A residue 614 LEU Chi-restraints excluded: chain A residue 632 VAL Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 706 TYR Chi-restraints excluded: chain A residue 762 GLU Chi-restraints excluded: chain A residue 764 PHE Chi-restraints excluded: chain A residue 804 HIS Chi-restraints excluded: chain A residue 845 VAL Chi-restraints excluded: chain A residue 890 THR Chi-restraints excluded: chain A residue 903 VAL Chi-restraints excluded: chain A residue 1013 THR Chi-restraints excluded: chain A residue 1047 THR Chi-restraints excluded: chain A residue 1057 LEU Chi-restraints excluded: chain A residue 1088 THR Chi-restraints excluded: chain A residue 1110 MET Chi-restraints excluded: chain A residue 1172 ARG Chi-restraints excluded: chain A residue 1263 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 99 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 75 optimal weight: 1.9990 chunk 69 optimal weight: 0.7980 chunk 86 optimal weight: 2.9990 chunk 114 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 34 optimal weight: 9.9990 chunk 57 optimal weight: 0.9980 chunk 92 optimal weight: 0.6980 chunk 50 optimal weight: 0.5980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1122 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 = 0.3514 r_free = 0.3514 target = 0.089357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.058062 restraints weight = 21509.778| |-----------------------------------------------------------------------------| r_work (start): 0.2892 rms_B_bonded: 3.72 r_work: 0.2749 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.2289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9726 Z= 0.149 Angle : 0.532 9.533 13237 Z= 0.264 Chirality : 0.045 0.212 1575 Planarity : 0.003 0.038 1649 Dihedral : 5.083 53.025 1567 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 3.12 % Allowed : 18.47 % Favored : 78.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.79 (0.25), residues: 1168 helix: 1.43 (0.35), residues: 232 sheet: 0.72 (0.23), residues: 498 loop : -0.09 (0.30), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 872 TYR 0.011 0.001 TYR A 756 PHE 0.016 0.001 PHE A 284 TRP 0.006 0.001 TRP A 639 HIS 0.002 0.001 HIS A 689 Details of bonding type rmsd covalent geometry : bond 0.00333 ( 9710) covalent geometry : angle 0.52035 (13190) SS BOND : bond 0.00050 ( 1) SS BOND : angle 1.94925 ( 2) hydrogen bonds : bond 0.02916 ( 429) hydrogen bonds : angle 4.83555 ( 1215) link_BETA1-4 : bond 0.00687 ( 4) link_BETA1-4 : angle 2.96739 ( 12) link_NAG-ASN : bond 0.00267 ( 11) link_NAG-ASN : angle 1.31145 ( 33) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 36 time to evaluate : 0.305 Fit side-chains REVERT: A 352 GLU cc_start: 0.8280 (OUTLIER) cc_final: 0.7659 (tm-30) REVERT: A 355 ASP cc_start: 0.8201 (m-30) cc_final: 0.7456 (t0) REVERT: A 435 LEU cc_start: 0.8863 (OUTLIER) cc_final: 0.8642 (mm) REVERT: A 492 ARG cc_start: 0.8662 (OUTLIER) cc_final: 0.7987 (ttp80) REVERT: A 545 ASP cc_start: 0.8648 (t0) cc_final: 0.8306 (t0) REVERT: A 599 MET cc_start: 0.9343 (mmm) cc_final: 0.9141 (mmm) REVERT: A 890 THR cc_start: 0.9567 (OUTLIER) cc_final: 0.9325 (p) REVERT: A 1172 ARG cc_start: 0.6195 (OUTLIER) cc_final: 0.5519 (ptm-80) outliers start: 33 outliers final: 22 residues processed: 65 average time/residue: 0.0674 time to fit residues: 6.7933 Evaluate side-chains 62 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 35 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 352 GLU Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 492 ARG Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 554 VAL Chi-restraints excluded: chain A residue 586 ILE Chi-restraints excluded: chain A residue 632 VAL Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 706 TYR Chi-restraints excluded: chain A residue 762 GLU Chi-restraints excluded: chain A residue 804 HIS Chi-restraints excluded: chain A residue 890 THR Chi-restraints excluded: chain A residue 1013 THR Chi-restraints excluded: chain A residue 1047 THR Chi-restraints excluded: chain A residue 1057 LEU Chi-restraints excluded: chain A residue 1088 THR Chi-restraints excluded: chain A residue 1110 MET Chi-restraints excluded: chain A residue 1168 LEU Chi-restraints excluded: chain A residue 1172 ARG Chi-restraints excluded: chain A residue 1213 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 115 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 90 optimal weight: 0.0770 chunk 41 optimal weight: 4.9990 chunk 51 optimal weight: 0.8980 chunk 18 optimal weight: 0.4980 chunk 59 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 77 optimal weight: 0.5980 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 959 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1122 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 = 0.3537 r_free = 0.3537 target = 0.090578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.060087 restraints weight = 21422.361| |-----------------------------------------------------------------------------| r_work (start): 0.2922 rms_B_bonded: 3.58 r_work: 0.2782 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.2285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9726 Z= 0.126 Angle : 0.539 11.730 13237 Z= 0.267 Chirality : 0.045 0.208 1575 Planarity : 0.003 0.037 1649 Dihedral : 4.969 53.159 1567 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 3.12 % Allowed : 18.37 % Favored : 78.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.89 (0.25), residues: 1168 helix: 1.48 (0.36), residues: 233 sheet: 0.83 (0.23), residues: 496 loop : -0.06 (0.30), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 872 TYR 0.011 0.001 TYR A 756 PHE 0.016 0.001 PHE A 284 TRP 0.006 0.001 TRP A 639 HIS 0.002 0.000 HIS A 804 Details of bonding type rmsd covalent geometry : bond 0.00281 ( 9710) covalent geometry : angle 0.52766 (13190) SS BOND : bond 0.00112 ( 1) SS BOND : angle 1.76221 ( 2) hydrogen bonds : bond 0.02820 ( 429) hydrogen bonds : angle 4.73667 ( 1215) link_BETA1-4 : bond 0.00703 ( 4) link_BETA1-4 : angle 2.96791 ( 12) link_NAG-ASN : bond 0.00259 ( 11) link_NAG-ASN : angle 1.30745 ( 33) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 38 time to evaluate : 0.347 Fit side-chains REVERT: A 29 LEU cc_start: 0.9133 (OUTLIER) cc_final: 0.8901 (tt) REVERT: A 303 MET cc_start: 0.5354 (pmm) cc_final: 0.4262 (tpt) REVERT: A 352 GLU cc_start: 0.8283 (OUTLIER) cc_final: 0.7724 (tm-30) REVERT: A 355 ASP cc_start: 0.8182 (m-30) cc_final: 0.7464 (t0) REVERT: A 435 LEU cc_start: 0.8838 (OUTLIER) cc_final: 0.8622 (mm) REVERT: A 492 ARG cc_start: 0.8657 (OUTLIER) cc_final: 0.7962 (ttp80) REVERT: A 599 MET cc_start: 0.9255 (mmm) cc_final: 0.9039 (mmm) REVERT: A 890 THR cc_start: 0.9550 (OUTLIER) cc_final: 0.9308 (p) REVERT: A 917 MET cc_start: 0.8671 (tpp) cc_final: 0.8406 (tpp) REVERT: A 957 MET cc_start: 0.8135 (mmm) cc_final: 0.7908 (mmt) REVERT: A 1172 ARG cc_start: 0.6340 (OUTLIER) cc_final: 0.5741 (ptm-80) outliers start: 33 outliers final: 26 residues processed: 66 average time/residue: 0.0882 time to fit residues: 8.7271 Evaluate side-chains 68 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 36 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 352 GLU Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 492 ARG Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 554 VAL Chi-restraints excluded: chain A residue 586 ILE Chi-restraints excluded: chain A residue 614 LEU Chi-restraints excluded: chain A residue 625 MET Chi-restraints excluded: chain A residue 632 VAL Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 706 TYR Chi-restraints excluded: chain A residue 762 GLU Chi-restraints excluded: chain A residue 804 HIS Chi-restraints excluded: chain A residue 890 THR Chi-restraints excluded: chain A residue 903 VAL Chi-restraints excluded: chain A residue 915 ILE Chi-restraints excluded: chain A residue 1013 THR Chi-restraints excluded: chain A residue 1047 THR Chi-restraints excluded: chain A residue 1057 LEU Chi-restraints excluded: chain A residue 1088 THR Chi-restraints excluded: chain A residue 1110 MET Chi-restraints excluded: chain A residue 1168 LEU Chi-restraints excluded: chain A residue 1172 ARG Chi-restraints excluded: chain A residue 1213 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 44 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 chunk 14 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 105 optimal weight: 0.9980 chunk 17 optimal weight: 0.9980 chunk 116 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 959 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1122 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 = 0.3518 r_free = 0.3518 target = 0.089707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.058904 restraints weight = 21534.404| |-----------------------------------------------------------------------------| r_work (start): 0.2882 rms_B_bonded: 3.59 r_work: 0.2740 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.2437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 9726 Z= 0.218 Angle : 0.572 9.834 13237 Z= 0.284 Chirality : 0.045 0.206 1575 Planarity : 0.004 0.039 1649 Dihedral : 5.067 53.278 1567 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 3.03 % Allowed : 18.28 % Favored : 78.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.84 (0.25), residues: 1168 helix: 1.55 (0.36), residues: 233 sheet: 0.75 (0.23), residues: 496 loop : -0.11 (0.30), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 872 TYR 0.009 0.001 TYR A 756 PHE 0.013 0.001 PHE A 284 TRP 0.006 0.001 TRP A 204 HIS 0.003 0.001 HIS A 804 Details of bonding type rmsd covalent geometry : bond 0.00501 ( 9710) covalent geometry : angle 0.56088 (13190) SS BOND : bond 0.00306 ( 1) SS BOND : angle 2.52933 ( 2) hydrogen bonds : bond 0.03017 ( 429) hydrogen bonds : angle 4.85949 ( 1215) link_BETA1-4 : bond 0.00616 ( 4) link_BETA1-4 : angle 2.83739 ( 12) link_NAG-ASN : bond 0.00282 ( 11) link_NAG-ASN : angle 1.40950 ( 33) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 38 time to evaluate : 0.318 Fit side-chains revert: symmetry clash REVERT: A 303 MET cc_start: 0.5346 (pmm) cc_final: 0.4269 (tpt) REVERT: A 352 GLU cc_start: 0.8258 (OUTLIER) cc_final: 0.7756 (tm-30) REVERT: A 355 ASP cc_start: 0.8200 (m-30) cc_final: 0.7489 (t0) REVERT: A 435 LEU cc_start: 0.8833 (OUTLIER) cc_final: 0.8614 (mm) REVERT: A 492 ARG cc_start: 0.8685 (OUTLIER) cc_final: 0.8002 (ttp80) REVERT: A 599 MET cc_start: 0.9301 (mmm) cc_final: 0.9086 (mmm) REVERT: A 890 THR cc_start: 0.9567 (OUTLIER) cc_final: 0.9328 (p) REVERT: A 917 MET cc_start: 0.8655 (tpp) cc_final: 0.8297 (tpp) REVERT: A 957 MET cc_start: 0.8136 (mmm) cc_final: 0.7912 (mmm) REVERT: A 1121 MET cc_start: 0.7989 (mmt) cc_final: 0.7137 (mmt) REVERT: A 1172 ARG cc_start: 0.6185 (OUTLIER) cc_final: 0.5520 (ptm-80) outliers start: 32 outliers final: 27 residues processed: 66 average time/residue: 0.0815 time to fit residues: 8.0935 Evaluate side-chains 70 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 38 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 352 GLU Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 492 ARG Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 554 VAL Chi-restraints excluded: chain A residue 586 ILE Chi-restraints excluded: chain A residue 614 LEU Chi-restraints excluded: chain A residue 632 VAL Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 706 TYR Chi-restraints excluded: chain A residue 762 GLU Chi-restraints excluded: chain A residue 804 HIS Chi-restraints excluded: chain A residue 890 THR Chi-restraints excluded: chain A residue 903 VAL Chi-restraints excluded: chain A residue 915 ILE Chi-restraints excluded: chain A residue 1013 THR Chi-restraints excluded: chain A residue 1047 THR Chi-restraints excluded: chain A residue 1057 LEU Chi-restraints excluded: chain A residue 1088 THR Chi-restraints excluded: chain A residue 1110 MET Chi-restraints excluded: chain A residue 1168 LEU Chi-restraints excluded: chain A residue 1172 ARG Chi-restraints excluded: chain A residue 1213 SER Chi-restraints excluded: chain A residue 1263 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 96 optimal weight: 2.9990 chunk 59 optimal weight: 0.9990 chunk 80 optimal weight: 2.9990 chunk 113 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 105 optimal weight: 3.9990 chunk 13 optimal weight: 0.9980 chunk 35 optimal weight: 6.9990 chunk 17 optimal weight: 0.6980 chunk 46 optimal weight: 0.8980 chunk 41 optimal weight: 3.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 959 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1122 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 = 0.3521 r_free = 0.3521 target = 0.089858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.058507 restraints weight = 21541.460| |-----------------------------------------------------------------------------| r_work (start): 0.2894 rms_B_bonded: 3.69 r_work: 0.2752 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.2436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9726 Z= 0.158 Angle : 0.552 9.870 13237 Z= 0.273 Chirality : 0.045 0.208 1575 Planarity : 0.003 0.040 1649 Dihedral : 5.012 53.503 1567 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 3.03 % Allowed : 18.37 % Favored : 78.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.85 (0.25), residues: 1168 helix: 1.60 (0.36), residues: 228 sheet: 0.77 (0.23), residues: 496 loop : -0.11 (0.30), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 872 TYR 0.010 0.001 TYR A 756 PHE 0.015 0.001 PHE A 284 TRP 0.005 0.001 TRP A 204 HIS 0.002 0.001 HIS A 804 Details of bonding type rmsd covalent geometry : bond 0.00357 ( 9710) covalent geometry : angle 0.54175 (13190) SS BOND : bond 0.00115 ( 1) SS BOND : angle 1.90114 ( 2) hydrogen bonds : bond 0.02871 ( 429) hydrogen bonds : angle 4.77848 ( 1215) link_BETA1-4 : bond 0.00646 ( 4) link_BETA1-4 : angle 2.88401 ( 12) link_NAG-ASN : bond 0.00255 ( 11) link_NAG-ASN : angle 1.31896 ( 33) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 38 time to evaluate : 0.405 Fit side-chains REVERT: A 29 LEU cc_start: 0.9113 (OUTLIER) cc_final: 0.8870 (tt) REVERT: A 303 MET cc_start: 0.5218 (pmm) cc_final: 0.4245 (tpt) REVERT: A 352 GLU cc_start: 0.8258 (OUTLIER) cc_final: 0.7719 (tm-30) REVERT: A 355 ASP cc_start: 0.8158 (m-30) cc_final: 0.7441 (t0) REVERT: A 435 LEU cc_start: 0.8837 (OUTLIER) cc_final: 0.8625 (mm) REVERT: A 492 ARG cc_start: 0.8686 (OUTLIER) cc_final: 0.8007 (ttp80) REVERT: A 599 MET cc_start: 0.9254 (mmm) cc_final: 0.9034 (mmm) REVERT: A 890 THR cc_start: 0.9552 (OUTLIER) cc_final: 0.9312 (p) REVERT: A 917 MET cc_start: 0.8640 (tpp) cc_final: 0.8396 (tpp) REVERT: A 927 ILE cc_start: 0.8664 (mt) cc_final: 0.8444 (mm) REVERT: A 957 MET cc_start: 0.8071 (mmm) cc_final: 0.7816 (mmm) REVERT: A 1172 ARG cc_start: 0.6190 (OUTLIER) cc_final: 0.5519 (ptm-80) outliers start: 32 outliers final: 26 residues processed: 66 average time/residue: 0.0828 time to fit residues: 8.4416 Evaluate side-chains 68 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 36 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 352 GLU Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 492 ARG Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 554 VAL Chi-restraints excluded: chain A residue 586 ILE Chi-restraints excluded: chain A residue 614 LEU Chi-restraints excluded: chain A residue 632 VAL Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 706 TYR Chi-restraints excluded: chain A residue 762 GLU Chi-restraints excluded: chain A residue 804 HIS Chi-restraints excluded: chain A residue 890 THR Chi-restraints excluded: chain A residue 903 VAL Chi-restraints excluded: chain A residue 915 ILE Chi-restraints excluded: chain A residue 1013 THR Chi-restraints excluded: chain A residue 1047 THR Chi-restraints excluded: chain A residue 1057 LEU Chi-restraints excluded: chain A residue 1088 THR Chi-restraints excluded: chain A residue 1110 MET Chi-restraints excluded: chain A residue 1168 LEU Chi-restraints excluded: chain A residue 1172 ARG Chi-restraints excluded: chain A residue 1213 SER Chi-restraints excluded: chain A residue 1263 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 45 optimal weight: 0.7980 chunk 4 optimal weight: 0.0050 chunk 31 optimal weight: 3.9990 chunk 38 optimal weight: 0.8980 chunk 85 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 chunk 53 optimal weight: 0.5980 chunk 83 optimal weight: 2.9990 chunk 92 optimal weight: 4.9990 overall best weight: 0.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 959 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1122 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 = 0.3534 r_free = 0.3534 target = 0.090443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.059574 restraints weight = 21491.838| |-----------------------------------------------------------------------------| r_work (start): 0.2919 rms_B_bonded: 3.61 r_work: 0.2781 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.2415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9726 Z= 0.123 Angle : 0.527 9.515 13237 Z= 0.261 Chirality : 0.044 0.213 1575 Planarity : 0.003 0.038 1649 Dihedral : 4.908 53.659 1567 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.94 % Allowed : 18.37 % Favored : 78.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.90 (0.25), residues: 1168 helix: 1.72 (0.36), residues: 227 sheet: 0.81 (0.23), residues: 500 loop : -0.15 (0.30), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 872 TYR 0.010 0.001 TYR A 756 PHE 0.014 0.001 PHE A 284 TRP 0.007 0.001 TRP A 639 HIS 0.001 0.000 HIS A 804 Details of bonding type rmsd covalent geometry : bond 0.00275 ( 9710) covalent geometry : angle 0.51584 (13190) SS BOND : bond 0.00040 ( 1) SS BOND : angle 1.65231 ( 2) hydrogen bonds : bond 0.02694 ( 429) hydrogen bonds : angle 4.64810 ( 1215) link_BETA1-4 : bond 0.00628 ( 4) link_BETA1-4 : angle 2.90080 ( 12) link_NAG-ASN : bond 0.00270 ( 11) link_NAG-ASN : angle 1.31179 ( 33) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1926.28 seconds wall clock time: 33 minutes 51.67 seconds (2031.67 seconds total)