Starting phenix.real_space_refine on Tue May 13 04:49:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9fx3_50842/05_2025/9fx3_50842.cif Found real_map, /net/cci-nas-00/data/ceres_data/9fx3_50842/05_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_50842/05_2025/9fx3_50842.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9fx3_50842/05_2025/9fx3_50842.map" model { file = "/net/cci-nas-00/data/ceres_data/9fx3_50842/05_2025/9fx3_50842.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9fx3_50842/05_2025/9fx3_50842.cif" } resolution = 3.2 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= -0.001 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-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 5.95, per 1000 atoms: 0.63 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: 2.59 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 1.27 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: 4.16 Time building geometry restraints manager: 3.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 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: 0.900 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: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 25.660 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.040 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:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.040 ------------------------------------------------------------------------------- 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 (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: -0.71 (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 TRP 0.012 0.002 TRP A 204 HIS 0.002 0.000 HIS A 689 PHE 0.022 0.002 PHE A 284 TYR 0.043 0.002 TYR A1059 ARG 0.015 0.001 ARG A1081 Details of bonding type rmsd link_NAG-ASN : bond 0.00538 ( 11) link_NAG-ASN : angle 4.78345 ( 33) link_BETA1-4 : bond 0.03235 ( 4) link_BETA1-4 : angle 6.15674 ( 12) hydrogen bonds : bond 0.12380 ( 429) hydrogen bonds : angle 6.28205 ( 1215) SS BOND : bond 0.00574 ( 1) SS BOND : angle 2.86105 ( 2) covalent geometry : bond 0.00513 ( 9710) covalent geometry : angle 0.87389 (13190) *********************** 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 : 1.133 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: 0.2170 time to fit residues: 13.0894 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 : 1.160 ------------------------------------------------------------------------------- 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 98 optimal weight: 0.0270 chunk 88 optimal weight: 0.5980 chunk 49 optimal weight: 0.5980 chunk 30 optimal weight: 2.9990 chunk 59 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 chunk 55 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 106 optimal weight: 2.9990 overall best weight: 0.8440 ------------------------------------------------------------------------------- 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 805 GLN ** A1122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1157 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.093549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.063910 restraints weight = 21189.620| |-----------------------------------------------------------------------------| r_work (start): 0.2972 rms_B_bonded: 3.55 r_work: 0.2832 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.0892 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= 0.153 Angle : 0.528 8.690 13237 Z= 0.264 Chirality : 0.044 0.166 1575 Planarity : 0.004 0.054 1649 Dihedral : 5.242 54.192 1568 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.80 % Allowed : 17.61 % Favored : 80.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.24), residues: 1168 helix: 0.03 (0.31), residues: 227 sheet: 0.87 (0.23), residues: 509 loop : -0.53 (0.29), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 204 HIS 0.003 0.001 HIS A1035 PHE 0.011 0.001 PHE A 764 TYR 0.012 0.001 TYR A1014 ARG 0.005 0.000 ARG A 872 Details of bonding type rmsd link_NAG-ASN : bond 0.00214 ( 11) link_NAG-ASN : angle 1.57790 ( 33) link_BETA1-4 : bond 0.00609 ( 4) link_BETA1-4 : angle 3.56871 ( 12) hydrogen bonds : bond 0.03108 ( 429) hydrogen bonds : angle 4.90786 ( 1215) SS BOND : bond 0.00048 ( 1) SS BOND : angle 1.65761 ( 2) covalent geometry : bond 0.00338 ( 9710) covalent geometry : angle 0.51090 (13190) *********************** 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 56 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 37 time to evaluate : 1.075 Fit side-chains REVERT: A 299 MET cc_start: 0.8485 (mpp) cc_final: 0.8075 (mpp) REVERT: A 352 GLU cc_start: 0.8107 (tm-30) cc_final: 0.7518 (tm-30) REVERT: A 599 MET cc_start: 0.9151 (mmm) cc_final: 0.8817 (mmm) REVERT: A 607 MET cc_start: 0.8788 (mmm) cc_final: 0.8542 (tpp) REVERT: A 627 MET cc_start: 0.5316 (tmm) cc_final: 0.4703 (tmm) REVERT: A 957 MET cc_start: 0.8246 (mmm) cc_final: 0.7986 (mmt) REVERT: A 1081 ARG cc_start: 0.8345 (mtt90) cc_final: 0.8027 (mtm180) outliers start: 19 outliers final: 12 residues processed: 55 average time/residue: 0.2010 time to fit residues: 17.1186 Evaluate side-chains 48 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 36 time to evaluate : 1.149 ------------------------------------------------------------------------------- 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 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 29 optimal weight: 0.5980 chunk 47 optimal weight: 0.0170 chunk 63 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 51 optimal weight: 0.5980 chunk 49 optimal weight: 0.7980 chunk 35 optimal weight: 5.9990 overall best weight: 0.8020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1039 GLN ** A1122 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 = 0.3589 r_free = 0.3589 target = 0.092483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.062535 restraints weight = 21395.584| |-----------------------------------------------------------------------------| r_work (start): 0.2951 rms_B_bonded: 3.58 r_work: 0.2809 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.1174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9726 Z= 0.142 Angle : 0.504 10.860 13237 Z= 0.250 Chirality : 0.044 0.198 1575 Planarity : 0.004 0.045 1649 Dihedral : 4.921 51.492 1567 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.08 % Allowed : 17.42 % Favored : 80.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.24), residues: 1168 helix: 0.87 (0.34), residues: 227 sheet: 0.94 (0.23), residues: 507 loop : -0.35 (0.29), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 204 HIS 0.003 0.001 HIS A1035 PHE 0.012 0.001 PHE A 284 TYR 0.012 0.001 TYR A1014 ARG 0.004 0.000 ARG A1081 Details of bonding type rmsd link_NAG-ASN : bond 0.00269 ( 11) link_NAG-ASN : angle 1.28078 ( 33) link_BETA1-4 : bond 0.00809 ( 4) link_BETA1-4 : angle 3.48715 ( 12) hydrogen bonds : bond 0.02894 ( 429) hydrogen bonds : angle 4.72330 ( 1215) SS BOND : bond 0.00111 ( 1) SS BOND : angle 2.04843 ( 2) covalent geometry : bond 0.00314 ( 9710) covalent geometry : angle 0.48911 (13190) *********************** 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 61 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 39 time to evaluate : 1.042 Fit side-chains revert: symmetry clash REVERT: A 299 MET cc_start: 0.8643 (mpp) cc_final: 0.8216 (mpp) REVERT: A 352 GLU cc_start: 0.8254 (tm-30) cc_final: 0.7686 (tm-30) REVERT: A 545 ASP cc_start: 0.8685 (t0) cc_final: 0.8382 (t0) REVERT: A 599 MET cc_start: 0.9212 (mmm) cc_final: 0.8794 (mmm) REVERT: A 607 MET cc_start: 0.8663 (mmm) cc_final: 0.8446 (tpp) REVERT: A 625 MET cc_start: 0.5150 (ppp) cc_final: 0.4908 (pmm) REVERT: A 627 MET cc_start: 0.4353 (tmm) cc_final: 0.3796 (tmm) REVERT: A 786 LYS cc_start: 0.8900 (OUTLIER) cc_final: 0.8655 (mtmt) REVERT: A 957 MET cc_start: 0.8164 (mmm) cc_final: 0.7919 (mmt) REVERT: A 1081 ARG cc_start: 0.8393 (mtt90) cc_final: 0.8032 (mtm-85) outliers start: 22 outliers final: 13 residues processed: 58 average time/residue: 0.2022 time to fit residues: 17.6546 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 : 1.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 176 ILE 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 380 LEU 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 786 LYS Chi-restraints excluded: chain A residue 804 HIS Chi-restraints excluded: chain A residue 1047 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 77 optimal weight: 2.9990 chunk 4 optimal weight: 4.9990 chunk 100 optimal weight: 6.9990 chunk 32 optimal weight: 0.7980 chunk 66 optimal weight: 1.9990 chunk 91 optimal weight: 5.9990 chunk 90 optimal weight: 7.9990 chunk 15 optimal weight: 2.9990 chunk 88 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 107 optimal weight: 0.6980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1073 HIS ** A1122 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 = 0.3524 r_free = 0.3524 target = 0.089721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.058651 restraints weight = 21282.491| |-----------------------------------------------------------------------------| r_work (start): 0.2912 rms_B_bonded: 3.69 r_work: 0.2756 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.1717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 9726 Z= 0.230 Angle : 0.551 8.831 13237 Z= 0.275 Chirality : 0.045 0.189 1575 Planarity : 0.004 0.041 1649 Dihedral : 5.065 52.620 1567 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 3.50 % Allowed : 17.23 % Favored : 79.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.25), residues: 1168 helix: 1.02 (0.34), residues: 232 sheet: 0.90 (0.23), residues: 504 loop : -0.24 (0.30), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 525 HIS 0.004 0.001 HIS A 689 PHE 0.013 0.002 PHE A 764 TYR 0.013 0.001 TYR A1014 ARG 0.003 0.000 ARG A 37 Details of bonding type rmsd link_NAG-ASN : bond 0.00287 ( 11) link_NAG-ASN : angle 1.40315 ( 33) link_BETA1-4 : bond 0.00699 ( 4) link_BETA1-4 : angle 3.14267 ( 12) hydrogen bonds : bond 0.03181 ( 429) hydrogen bonds : angle 4.84254 ( 1215) SS BOND : bond 0.00334 ( 1) SS BOND : angle 2.99185 ( 2) covalent geometry : bond 0.00529 ( 9710) covalent geometry : angle 0.53770 (13190) *********************** 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 75 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 38 time to evaluate : 1.126 Fit side-chains revert: symmetry clash REVERT: A 299 MET cc_start: 0.8860 (mpp) cc_final: 0.8658 (mpp) REVERT: A 352 GLU cc_start: 0.8288 (OUTLIER) cc_final: 0.7718 (tm-30) REVERT: A 545 ASP cc_start: 0.8670 (t0) cc_final: 0.8316 (t0) REVERT: A 599 MET cc_start: 0.9327 (mmm) cc_final: 0.8952 (mmm) REVERT: A 872 ARG cc_start: 0.8884 (mmp80) cc_final: 0.8635 (mmp80) REVERT: A 890 THR cc_start: 0.9587 (OUTLIER) cc_final: 0.9360 (p) REVERT: A 1121 MET cc_start: 0.7629 (mmt) cc_final: 0.7057 (mmt) outliers start: 37 outliers final: 22 residues processed: 70 average time/residue: 0.1832 time to fit residues: 19.9743 Evaluate side-chains 60 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 36 time to evaluate : 1.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 176 ILE 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 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 786 LYS 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 1168 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 111 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 116 optimal weight: 2.9990 chunk 95 optimal weight: 9.9990 chunk 89 optimal weight: 8.9990 chunk 2 optimal weight: 3.9990 chunk 22 optimal weight: 0.8980 chunk 44 optimal weight: 3.9990 chunk 102 optimal weight: 0.0070 chunk 100 optimal weight: 5.9990 chunk 28 optimal weight: 5.9990 overall best weight: 1.7804 ------------------------------------------------------------------------------- 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 = 0.3508 r_free = 0.3508 target = 0.088740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.057484 restraints weight = 21566.873| |-----------------------------------------------------------------------------| r_work (start): 0.2875 rms_B_bonded: 3.71 r_work: 0.2735 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.2735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.2130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 9726 Z= 0.267 Angle : 0.580 8.844 13237 Z= 0.291 Chirality : 0.046 0.211 1575 Planarity : 0.004 0.041 1649 Dihedral : 5.220 52.336 1567 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 3.22 % Allowed : 17.71 % 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 (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: 0.72 (0.25), residues: 1168 helix: 1.25 (0.35), residues: 233 sheet: 0.73 (0.23), residues: 500 loop : -0.11 (0.30), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 525 HIS 0.003 0.001 HIS A1035 PHE 0.013 0.002 PHE A 284 TYR 0.013 0.001 TYR A1014 ARG 0.006 0.001 ARG A1081 Details of bonding type rmsd link_NAG-ASN : bond 0.00333 ( 11) link_NAG-ASN : angle 1.46569 ( 33) link_BETA1-4 : bond 0.00657 ( 4) link_BETA1-4 : angle 2.97551 ( 12) hydrogen bonds : bond 0.03218 ( 429) hydrogen bonds : angle 4.92229 ( 1215) SS BOND : bond 0.00674 ( 1) SS BOND : angle 2.93414 ( 2) covalent geometry : bond 0.00611 ( 9710) covalent geometry : angle 0.56853 (13190) *********************** 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 74 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 40 time to evaluate : 1.099 Fit side-chains REVERT: A 352 GLU cc_start: 0.8324 (OUTLIER) cc_final: 0.7703 (tm-30) REVERT: A 492 ARG cc_start: 0.8639 (OUTLIER) cc_final: 0.7983 (ttp80) REVERT: A 545 ASP cc_start: 0.8590 (t0) cc_final: 0.8335 (t0) REVERT: A 599 MET cc_start: 0.9357 (mmm) cc_final: 0.8986 (mmm) REVERT: A 625 MET cc_start: 0.6116 (pmm) cc_final: 0.5908 (ppp) REVERT: A 764 PHE cc_start: 0.8926 (OUTLIER) cc_final: 0.8288 (p90) REVERT: A 872 ARG cc_start: 0.8858 (mmp80) cc_final: 0.8630 (mmp80) REVERT: A 890 THR cc_start: 0.9579 (OUTLIER) cc_final: 0.9336 (p) outliers start: 34 outliers final: 22 residues processed: 69 average time/residue: 0.2010 time to fit residues: 20.9509 Evaluate side-chains 64 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 38 time to evaluate : 1.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 ILE 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 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 890 THR 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 Chi-restraints excluded: chain A residue 1232 THR Chi-restraints excluded: chain A residue 1257 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 45 optimal weight: 0.6980 chunk 30 optimal weight: 2.9990 chunk 107 optimal weight: 0.7980 chunk 44 optimal weight: 0.6980 chunk 113 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 88 optimal weight: 0.4980 chunk 25 optimal weight: 6.9990 chunk 27 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3525 r_free = 0.3525 target = 0.090297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.059146 restraints weight = 21328.150| |-----------------------------------------------------------------------------| r_work (start): 0.2909 rms_B_bonded: 3.61 r_work: 0.2774 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.2086 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= 0.139 Angle : 0.517 9.370 13237 Z= 0.255 Chirality : 0.044 0.207 1575 Planarity : 0.003 0.039 1649 Dihedral : 5.018 52.787 1567 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.65 % Allowed : 18.47 % Favored : 78.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.25), residues: 1168 helix: 1.37 (0.35), residues: 233 sheet: 0.83 (0.23), residues: 498 loop : -0.03 (0.30), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 639 HIS 0.002 0.001 HIS A 804 PHE 0.015 0.001 PHE A 284 TYR 0.011 0.001 TYR A 756 ARG 0.004 0.000 ARG A1081 Details of bonding type rmsd link_NAG-ASN : bond 0.00256 ( 11) link_NAG-ASN : angle 1.28551 ( 33) link_BETA1-4 : bond 0.00741 ( 4) link_BETA1-4 : angle 3.02512 ( 12) hydrogen bonds : bond 0.02871 ( 429) hydrogen bonds : angle 4.74329 ( 1215) SS BOND : bond 0.00122 ( 1) SS BOND : angle 1.96733 ( 2) covalent geometry : bond 0.00307 ( 9710) covalent geometry : angle 0.50517 (13190) *********************** 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 65 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 37 time to evaluate : 1.163 Fit side-chains REVERT: A 352 GLU cc_start: 0.8258 (OUTLIER) cc_final: 0.7636 (tm-30) REVERT: A 435 LEU cc_start: 0.8863 (OUTLIER) cc_final: 0.8644 (mm) REVERT: A 492 ARG cc_start: 0.8652 (OUTLIER) cc_final: 0.7985 (ttp80) REVERT: A 545 ASP cc_start: 0.8604 (t0) cc_final: 0.8398 (t0) REVERT: A 599 MET cc_start: 0.9344 (mmm) cc_final: 0.9137 (mmm) REVERT: A 872 ARG cc_start: 0.8836 (mmp80) cc_final: 0.8632 (mmp80) REVERT: A 890 THR cc_start: 0.9568 (OUTLIER) cc_final: 0.9329 (p) REVERT: A 1172 ARG cc_start: 0.6294 (OUTLIER) cc_final: 0.5714 (ptm-80) outliers start: 28 outliers final: 19 residues processed: 61 average time/residue: 0.2004 time to fit residues: 18.8119 Evaluate side-chains 60 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 36 time to evaluate : 1.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 176 ILE 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 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 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 59 optimal weight: 0.6980 chunk 116 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 82 optimal weight: 0.6980 chunk 13 optimal weight: 0.0570 chunk 16 optimal weight: 0.8980 chunk 2 optimal weight: 4.9990 chunk 49 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 27 optimal weight: 0.7980 chunk 38 optimal weight: 0.5980 overall best weight: 0.5698 ------------------------------------------------------------------------------- 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 = 0.3543 r_free = 0.3543 target = 0.090720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.059729 restraints weight = 21415.806| |-----------------------------------------------------------------------------| r_work (start): 0.2920 rms_B_bonded: 3.70 r_work: 0.2782 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.2099 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= 0.118 Angle : 0.495 9.396 13237 Z= 0.244 Chirality : 0.044 0.209 1575 Planarity : 0.003 0.039 1649 Dihedral : 4.852 53.042 1567 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.94 % Allowed : 18.18 % Favored : 78.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.25), residues: 1168 helix: 1.54 (0.35), residues: 233 sheet: 0.89 (0.23), residues: 502 loop : -0.04 (0.30), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 639 HIS 0.001 0.000 HIS A1035 PHE 0.015 0.001 PHE A 284 TYR 0.010 0.001 TYR A 756 ARG 0.003 0.000 ARG A1081 Details of bonding type rmsd link_NAG-ASN : bond 0.00262 ( 11) link_NAG-ASN : angle 1.29978 ( 33) link_BETA1-4 : bond 0.00683 ( 4) link_BETA1-4 : angle 3.02846 ( 12) hydrogen bonds : bond 0.02671 ( 429) hydrogen bonds : angle 4.56709 ( 1215) SS BOND : bond 0.00082 ( 1) SS BOND : angle 1.65930 ( 2) covalent geometry : bond 0.00263 ( 9710) covalent geometry : angle 0.48269 (13190) *********************** 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 71 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 40 time to evaluate : 1.123 Fit side-chains REVERT: A 352 GLU cc_start: 0.8273 (OUTLIER) cc_final: 0.7747 (tm-30) REVERT: A 355 ASP cc_start: 0.8135 (m-30) cc_final: 0.7455 (t0) REVERT: A 435 LEU cc_start: 0.8885 (OUTLIER) cc_final: 0.8666 (mm) REVERT: A 492 ARG cc_start: 0.8670 (OUTLIER) cc_final: 0.7981 (ttp80) REVERT: A 599 MET cc_start: 0.9265 (mmm) cc_final: 0.9046 (mmm) REVERT: A 625 MET cc_start: 0.5381 (pmm) cc_final: 0.5141 (ppp) REVERT: A 872 ARG cc_start: 0.8874 (mmp80) cc_final: 0.8657 (mmp80) REVERT: A 890 THR cc_start: 0.9558 (OUTLIER) cc_final: 0.9318 (p) REVERT: A 957 MET cc_start: 0.8179 (mmm) cc_final: 0.7965 (mmt) REVERT: A 997 LEU cc_start: 0.8489 (OUTLIER) cc_final: 0.8279 (tt) REVERT: A 1172 ARG cc_start: 0.6313 (OUTLIER) cc_final: 0.5708 (ptm-80) outliers start: 31 outliers final: 19 residues processed: 67 average time/residue: 0.1932 time to fit residues: 19.9047 Evaluate side-chains 64 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 39 time to evaluate : 1.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 176 ILE 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 614 LEU 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 997 LEU 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 1172 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 50 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 72 optimal weight: 6.9990 chunk 16 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 30 optimal weight: 0.0770 chunk 70 optimal weight: 0.6980 chunk 102 optimal weight: 1.9990 chunk 29 optimal weight: 0.5980 chunk 31 optimal weight: 5.9990 overall best weight: 0.8740 ------------------------------------------------------------------------------- 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 = 0.3532 r_free = 0.3532 target = 0.090256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.059310 restraints weight = 21607.692| |-----------------------------------------------------------------------------| r_work (start): 0.2916 rms_B_bonded: 3.63 r_work: 0.2776 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.2198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9726 Z= 0.152 Angle : 0.514 9.649 13237 Z= 0.255 Chirality : 0.044 0.205 1575 Planarity : 0.003 0.046 1649 Dihedral : 4.850 53.247 1567 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 3.03 % Allowed : 18.18 % Favored : 78.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.25), residues: 1168 helix: 1.57 (0.35), residues: 233 sheet: 0.88 (0.23), residues: 502 loop : -0.05 (0.30), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 639 HIS 0.002 0.001 HIS A 804 PHE 0.013 0.001 PHE A 284 TYR 0.009 0.001 TYR A 756 ARG 0.003 0.000 ARG A1081 Details of bonding type rmsd link_NAG-ASN : bond 0.00251 ( 11) link_NAG-ASN : angle 1.31005 ( 33) link_BETA1-4 : bond 0.00634 ( 4) link_BETA1-4 : angle 2.94783 ( 12) hydrogen bonds : bond 0.02784 ( 429) hydrogen bonds : angle 4.60083 ( 1215) SS BOND : bond 0.00448 ( 1) SS BOND : angle 2.06452 ( 2) covalent geometry : bond 0.00344 ( 9710) covalent geometry : angle 0.50276 (13190) *********************** 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 73 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 41 time to evaluate : 1.045 Fit side-chains REVERT: A 303 MET cc_start: 0.5417 (pmm) cc_final: 0.4251 (tpt) REVERT: A 352 GLU cc_start: 0.8290 (OUTLIER) cc_final: 0.7765 (tm-30) REVERT: A 355 ASP cc_start: 0.8153 (m-30) cc_final: 0.7464 (t0) REVERT: A 435 LEU cc_start: 0.8824 (OUTLIER) cc_final: 0.8611 (mm) REVERT: A 492 ARG cc_start: 0.8652 (OUTLIER) cc_final: 0.7957 (ttp80) REVERT: A 599 MET cc_start: 0.9235 (mmm) cc_final: 0.9005 (mmm) REVERT: A 872 ARG cc_start: 0.8895 (mmp80) cc_final: 0.8666 (mmp80) REVERT: A 890 THR cc_start: 0.9545 (OUTLIER) cc_final: 0.9301 (p) REVERT: A 957 MET cc_start: 0.8260 (mmm) cc_final: 0.7951 (mmt) REVERT: A 1172 ARG cc_start: 0.6302 (OUTLIER) cc_final: 0.5734 (ptm-80) outliers start: 32 outliers final: 23 residues processed: 69 average time/residue: 0.1885 time to fit residues: 20.0199 Evaluate side-chains 68 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 40 time to evaluate : 1.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 176 ILE 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 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 1172 ARG Chi-restraints excluded: chain A residue 1232 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 16 optimal weight: 1.9990 chunk 76 optimal weight: 0.9980 chunk 11 optimal weight: 0.9990 chunk 58 optimal weight: 0.5980 chunk 91 optimal weight: 3.9990 chunk 56 optimal weight: 0.9980 chunk 44 optimal weight: 2.9990 chunk 50 optimal weight: 0.3980 chunk 24 optimal weight: 4.9990 chunk 88 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3532 r_free = 0.3532 target = 0.090248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.059309 restraints weight = 21337.648| |-----------------------------------------------------------------------------| r_work (start): 0.2918 rms_B_bonded: 3.69 r_work: 0.2776 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.2236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9726 Z= 0.138 Angle : 0.510 9.496 13237 Z= 0.253 Chirality : 0.044 0.209 1575 Planarity : 0.003 0.046 1649 Dihedral : 4.854 53.436 1567 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % 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 (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: 0.99 (0.25), residues: 1168 helix: 1.61 (0.35), residues: 233 sheet: 0.90 (0.23), residues: 505 loop : -0.06 (0.30), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 639 HIS 0.002 0.000 HIS A 804 PHE 0.014 0.001 PHE A 284 TYR 0.009 0.001 TYR A 756 ARG 0.004 0.000 ARG A1081 Details of bonding type rmsd link_NAG-ASN : bond 0.00250 ( 11) link_NAG-ASN : angle 1.29340 ( 33) link_BETA1-4 : bond 0.00653 ( 4) link_BETA1-4 : angle 2.92621 ( 12) hydrogen bonds : bond 0.02712 ( 429) hydrogen bonds : angle 4.56437 ( 1215) SS BOND : bond 0.00071 ( 1) SS BOND : angle 1.83042 ( 2) covalent geometry : bond 0.00311 ( 9710) covalent geometry : angle 0.49881 (13190) *********************** 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 73 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 42 time to evaluate : 1.083 Fit side-chains REVERT: A 303 MET cc_start: 0.5400 (pmm) cc_final: 0.4251 (tpt) REVERT: A 352 GLU cc_start: 0.8322 (OUTLIER) cc_final: 0.7831 (tm-30) REVERT: A 355 ASP cc_start: 0.8158 (m-30) cc_final: 0.7453 (t0) REVERT: A 435 LEU cc_start: 0.8879 (OUTLIER) cc_final: 0.8665 (mm) REVERT: A 492 ARG cc_start: 0.8659 (OUTLIER) cc_final: 0.7975 (ttp80) REVERT: A 599 MET cc_start: 0.9267 (mmm) cc_final: 0.9043 (mmm) REVERT: A 625 MET cc_start: 0.4615 (pmm) cc_final: 0.4301 (ppp) REVERT: A 872 ARG cc_start: 0.8887 (mmp80) cc_final: 0.8665 (mmp80) REVERT: A 890 THR cc_start: 0.9557 (OUTLIER) cc_final: 0.9315 (p) REVERT: A 927 ILE cc_start: 0.8542 (mt) cc_final: 0.8291 (mm) REVERT: A 957 MET cc_start: 0.8304 (mmm) cc_final: 0.8022 (mmt) REVERT: A 1172 ARG cc_start: 0.6305 (OUTLIER) cc_final: 0.5729 (ptm-80) outliers start: 31 outliers final: 24 residues processed: 69 average time/residue: 0.1880 time to fit residues: 20.0177 Evaluate side-chains 69 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 40 time to evaluate : 1.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 176 ILE 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 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 1172 ARG Chi-restraints excluded: chain A residue 1186 VAL 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 5 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 chunk 34 optimal weight: 9.9990 chunk 85 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 39 optimal weight: 3.9990 chunk 18 optimal weight: 0.5980 chunk 71 optimal weight: 0.0970 chunk 37 optimal weight: 7.9990 chunk 47 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 overall best weight: 1.2982 ------------------------------------------------------------------------------- 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 = 0.3509 r_free = 0.3509 target = 0.088992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.057796 restraints weight = 21686.674| |-----------------------------------------------------------------------------| r_work (start): 0.2887 rms_B_bonded: 3.72 r_work: 0.2747 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.2410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 9726 Z= 0.201 Angle : 0.545 9.867 13237 Z= 0.270 Chirality : 0.045 0.198 1575 Planarity : 0.003 0.039 1649 Dihedral : 4.972 53.508 1567 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.84 % Allowed : 18.09 % 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 (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: 0.99 (0.25), residues: 1168 helix: 1.77 (0.36), residues: 228 sheet: 0.83 (0.23), residues: 501 loop : -0.05 (0.30), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A1016 HIS 0.003 0.001 HIS A 804 PHE 0.014 0.001 PHE A 284 TYR 0.010 0.001 TYR A 756 ARG 0.003 0.000 ARG A1172 Details of bonding type rmsd link_NAG-ASN : bond 0.00253 ( 11) link_NAG-ASN : angle 1.36785 ( 33) link_BETA1-4 : bond 0.00594 ( 4) link_BETA1-4 : angle 2.79237 ( 12) hydrogen bonds : bond 0.02961 ( 429) hydrogen bonds : angle 4.71537 ( 1215) SS BOND : bond 0.00295 ( 1) SS BOND : angle 2.45432 ( 2) covalent geometry : bond 0.00459 ( 9710) covalent geometry : angle 0.53386 (13190) ********************** 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 72 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 42 time to evaluate : 1.025 Fit side-chains REVERT: A 303 MET cc_start: 0.5389 (pmm) cc_final: 0.4374 (tpt) REVERT: A 352 GLU cc_start: 0.8312 (OUTLIER) cc_final: 0.7787 (tm-30) REVERT: A 355 ASP cc_start: 0.8180 (m-30) cc_final: 0.7486 (t0) REVERT: A 435 LEU cc_start: 0.8872 (OUTLIER) cc_final: 0.8662 (mm) REVERT: A 492 ARG cc_start: 0.8686 (OUTLIER) cc_final: 0.8007 (ttp80) REVERT: A 599 MET cc_start: 0.9303 (mmm) cc_final: 0.9084 (mmm) REVERT: A 872 ARG cc_start: 0.8885 (mmp80) cc_final: 0.8674 (mmp80) REVERT: A 890 THR cc_start: 0.9570 (OUTLIER) cc_final: 0.9323 (p) REVERT: A 927 ILE cc_start: 0.8610 (mt) cc_final: 0.8382 (mm) REVERT: A 951 GLU cc_start: 0.9077 (mm-30) cc_final: 0.8764 (tp30) REVERT: A 957 MET cc_start: 0.8291 (mmm) cc_final: 0.8008 (mmm) REVERT: A 1172 ARG cc_start: 0.6167 (OUTLIER) cc_final: 0.5475 (ptm-80) outliers start: 30 outliers final: 24 residues processed: 68 average time/residue: 0.1979 time to fit residues: 20.5443 Evaluate side-chains 70 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 41 time to evaluate : 1.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 176 ILE 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 638 LEU Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 706 TYR 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 1172 ARG Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1232 THR 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 68 optimal weight: 2.9990 chunk 23 optimal weight: 0.0670 chunk 33 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 chunk 66 optimal weight: 0.7980 chunk 78 optimal weight: 0.8980 chunk 32 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 overall best weight: 0.7520 ------------------------------------------------------------------------------- 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 = 0.3530 r_free = 0.3530 target = 0.090116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.059030 restraints weight = 21470.453| |-----------------------------------------------------------------------------| r_work (start): 0.2909 rms_B_bonded: 3.73 r_work: 0.2767 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.2403 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= 0.137 Angle : 0.517 10.272 13237 Z= 0.255 Chirality : 0.044 0.212 1575 Planarity : 0.003 0.037 1649 Dihedral : 4.901 53.619 1567 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.84 % Allowed : 17.99 % Favored : 79.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.25), residues: 1168 helix: 1.73 (0.35), residues: 228 sheet: 0.85 (0.23), residues: 505 loop : -0.09 (0.30), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 639 HIS 0.002 0.001 HIS A 804 PHE 0.014 0.001 PHE A 284 TYR 0.010 0.001 TYR A 756 ARG 0.003 0.000 ARG A1081 Details of bonding type rmsd link_NAG-ASN : bond 0.00259 ( 11) link_NAG-ASN : angle 1.28866 ( 33) link_BETA1-4 : bond 0.00653 ( 4) link_BETA1-4 : angle 2.85295 ( 12) hydrogen bonds : bond 0.02739 ( 429) hydrogen bonds : angle 4.60806 ( 1215) SS BOND : bond 0.00030 ( 1) SS BOND : angle 1.64954 ( 2) covalent geometry : bond 0.00307 ( 9710) covalent geometry : angle 0.50614 (13190) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4279.16 seconds wall clock time: 75 minutes 8.57 seconds (4508.57 seconds total)