Starting phenix.real_space_refine on Mon Apr 28 18:00:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b73_44299/04_2025/9b73_44299.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b73_44299/04_2025/9b73_44299.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=1.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9b73_44299/04_2025/9b73_44299.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b73_44299/04_2025/9b73_44299.map" model { file = "/net/cci-nas-00/data/ceres_data/9b73_44299/04_2025/9b73_44299.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b73_44299/04_2025/9b73_44299.cif" } resolution = 1.96 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= 0.063 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: 6 Type Number sf(0) Gaussians P 9 5.49 5 Mg 3 5.21 5 S 42 5.16 5 C 5115 2.51 5 N 1338 2.21 5 O 1509 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-5669/modules/chem_data/mon_lib" Total number of atoms: 8016 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 2576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2576 Classifications: {'peptide': 326} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 310} Chain: "B" Number of atoms: 2576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2576 Classifications: {'peptide': 326} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 310} Chain: "C" Number of atoms: 2576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2576 Classifications: {'peptide': 326} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 310} Chain: "A" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 74 Unusual residues: {' MG': 1, 'ATP': 1, 'NAG': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 74 Unusual residues: {' MG': 1, 'ATP': 1, 'NAG': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 74 Unusual residues: {' MG': 1, 'ATP': 1, 'NAG': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 21 Classifications: {'water': 21} Link IDs: {None: 20} Chain: "B" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 23 Classifications: {'water': 23} Link IDs: {None: 22} Chain: "C" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 22 Classifications: {'water': 22} Link IDs: {None: 21} Time building chain proxies: 5.42, per 1000 atoms: 0.68 Number of scatterers: 8016 At special positions: 0 Unit cell: (86.92, 86.92, 114.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 42 16.00 P 9 15.00 Mg 3 11.99 O 1509 8.00 N 1338 7.00 C 5115 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 Simple disulfide: pdb=" SG CYS A 117 " - pdb=" SG CYS A 165 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 149 " distance=2.03 Simple disulfide: pdb=" SG CYS A 132 " - pdb=" SG CYS A 159 " distance=2.03 Simple disulfide: pdb=" SG CYS A 217 " - pdb=" SG CYS A 227 " distance=2.03 Simple disulfide: pdb=" SG CYS A 261 " - pdb=" SG CYS A 270 " distance=2.03 Simple disulfide: pdb=" SG CYS B 117 " - pdb=" SG CYS B 165 " distance=2.03 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 149 " distance=2.03 Simple disulfide: pdb=" SG CYS B 132 " - pdb=" SG CYS B 159 " distance=2.03 Simple disulfide: pdb=" SG CYS B 217 " - pdb=" SG CYS B 227 " distance=2.03 Simple disulfide: pdb=" SG CYS B 261 " - pdb=" SG CYS B 270 " distance=2.03 Simple disulfide: pdb=" SG CYS C 117 " - pdb=" SG CYS C 165 " distance=2.03 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 149 " distance=2.03 Simple disulfide: pdb=" SG CYS C 132 " - pdb=" SG CYS C 159 " distance=2.03 Simple disulfide: pdb=" SG CYS C 217 " - pdb=" SG CYS C 227 " distance=2.03 Simple disulfide: pdb=" SG CYS C 261 " - pdb=" SG CYS C 270 " 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 NAG-ASN " NAG A 401 " - " ASN A 153 " " NAG A 402 " - " ASN A 184 " " NAG A 403 " - " ASN A 242 " " NAG B 401 " - " ASN B 153 " " NAG B 402 " - " ASN B 184 " " NAG B 403 " - " ASN B 242 " " NAG C 403 " - " ASN C 153 " " NAG C 404 " - " ASN C 184 " " NAG C 405 " - " ASN C 242 " Time building additional restraints: 2.33 Conformation dependent library (CDL) restraints added in 967.3 milliseconds 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1776 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 9 sheets defined 28.3% alpha, 27.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.83 Creating SS restraints... Processing helix chain 'A' and resid 31 through 47 Processing helix chain 'A' and resid 86 through 90 Processing helix chain 'A' and resid 120 through 124 Processing helix chain 'A' and resid 179 through 184 Processing helix chain 'A' and resid 210 through 217 removed outlier: 3.548A pdb=" N THR A 216 " --> pdb=" O ALA A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 239 Processing helix chain 'A' and resid 242 through 250 removed outlier: 3.592A pdb=" N GLU A 248 " --> pdb=" O SER A 244 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LYS A 249 " --> pdb=" O THR A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 270 Processing helix chain 'A' and resid 327 through 356 Processing helix chain 'B' and resid 32 through 47 Processing helix chain 'B' and resid 86 through 90 Processing helix chain 'B' and resid 120 through 124 Processing helix chain 'B' and resid 179 through 184 Processing helix chain 'B' and resid 210 through 217 removed outlier: 3.551A pdb=" N THR B 216 " --> pdb=" O ALA B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 239 Processing helix chain 'B' and resid 242 through 250 removed outlier: 3.598A pdb=" N GLU B 248 " --> pdb=" O SER B 244 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LYS B 249 " --> pdb=" O THR B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 270 Processing helix chain 'B' and resid 327 through 356 Processing helix chain 'C' and resid 32 through 47 Processing helix chain 'C' and resid 86 through 90 Processing helix chain 'C' and resid 120 through 124 Processing helix chain 'C' and resid 179 through 184 Processing helix chain 'C' and resid 210 through 217 removed outlier: 3.554A pdb=" N THR C 216 " --> pdb=" O ALA C 212 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 239 Processing helix chain 'C' and resid 242 through 250 removed outlier: 3.600A pdb=" N GLU C 248 " --> pdb=" O SER C 244 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LYS C 249 " --> pdb=" O THR C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 266 through 270 Processing helix chain 'C' and resid 327 through 356 Processing sheet with id=AA1, first strand: chain 'A' and resid 56 through 60 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 56 through 60 current: chain 'A' and resid 99 through 118 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 99 through 118 current: chain 'A' and resid 144 through 151 removed outlier: 7.297A pdb=" N GLU A 160 " --> pdb=" O THR A 146 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N LYS A 148 " --> pdb=" O THR A 158 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N THR A 158 " --> pdb=" O LYS A 148 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 157 through 165 current: chain 'A' and resid 273 through 277 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 273 through 277 current: chain 'A' and resid 302 through 326 Processing sheet with id=AA2, first strand: chain 'A' and resid 62 through 70 Processing sheet with id=AA3, first strand: chain 'A' and resid 73 through 75 Processing sheet with id=AA4, first strand: chain 'B' and resid 56 through 60 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 56 through 60 current: chain 'B' and resid 99 through 118 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 99 through 118 current: chain 'B' and resid 144 through 151 removed outlier: 7.295A pdb=" N GLU B 160 " --> pdb=" O THR B 146 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N LYS B 148 " --> pdb=" O THR B 158 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N THR B 158 " --> pdb=" O LYS B 148 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 157 through 165 current: chain 'B' and resid 273 through 277 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 273 through 277 current: chain 'B' and resid 302 through 326 Processing sheet with id=AA5, first strand: chain 'B' and resid 62 through 70 Processing sheet with id=AA6, first strand: chain 'B' and resid 73 through 75 Processing sheet with id=AA7, first strand: chain 'C' and resid 56 through 60 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 56 through 60 current: chain 'C' and resid 99 through 118 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 99 through 118 current: chain 'C' and resid 144 through 151 removed outlier: 7.294A pdb=" N GLU C 160 " --> pdb=" O THR C 146 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N LYS C 148 " --> pdb=" O THR C 158 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N THR C 158 " --> pdb=" O LYS C 148 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 157 through 165 current: chain 'C' and resid 273 through 277 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 273 through 277 current: chain 'C' and resid 302 through 326 Processing sheet with id=AA8, first strand: chain 'C' and resid 62 through 70 Processing sheet with id=AA9, first strand: chain 'C' and resid 73 through 75 232 hydrogen bonds defined for protein. 579 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: 2.27 Time building geometry restraints manager: 2.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2508 1.34 - 1.46: 2030 1.46 - 1.58: 3562 1.58 - 1.70: 6 1.70 - 1.82: 51 Bond restraints: 8157 Sorted by residual: bond pdb=" C1 NAG C 404 " pdb=" O5 NAG C 404 " ideal model delta sigma weight residual 1.406 1.481 -0.075 2.00e-02 2.50e+03 1.42e+01 bond pdb=" C1 NAG A 402 " pdb=" O5 NAG A 402 " ideal model delta sigma weight residual 1.406 1.481 -0.075 2.00e-02 2.50e+03 1.42e+01 bond pdb=" C1 NAG B 402 " pdb=" O5 NAG B 402 " ideal model delta sigma weight residual 1.406 1.481 -0.075 2.00e-02 2.50e+03 1.41e+01 bond pdb=" C1 NAG A 401 " pdb=" O5 NAG A 401 " ideal model delta sigma weight residual 1.406 1.437 -0.031 2.00e-02 2.50e+03 2.42e+00 bond pdb=" C1 NAG B 401 " pdb=" O5 NAG B 401 " ideal model delta sigma weight residual 1.406 1.437 -0.031 2.00e-02 2.50e+03 2.41e+00 ... (remaining 8152 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.04: 10594 1.04 - 2.09: 382 2.09 - 3.13: 88 3.13 - 4.17: 9 4.17 - 5.21: 15 Bond angle restraints: 11088 Sorted by residual: angle pdb=" N GLY A 71 " pdb=" CA GLY A 71 " pdb=" C GLY A 71 " ideal model delta sigma weight residual 113.18 108.57 4.61 2.37e+00 1.78e-01 3.79e+00 angle pdb=" N GLY B 71 " pdb=" CA GLY B 71 " pdb=" C GLY B 71 " ideal model delta sigma weight residual 113.18 108.66 4.52 2.37e+00 1.78e-01 3.64e+00 angle pdb=" N GLY C 71 " pdb=" CA GLY C 71 " pdb=" C GLY C 71 " ideal model delta sigma weight residual 113.18 108.70 4.48 2.37e+00 1.78e-01 3.57e+00 angle pdb=" C1 NAG C 404 " pdb=" O5 NAG C 404 " pdb=" C5 NAG C 404 " ideal model delta sigma weight residual 113.21 118.42 -5.21 3.00e+00 1.11e-01 3.02e+00 angle pdb=" C1 NAG A 402 " pdb=" O5 NAG A 402 " pdb=" C5 NAG A 402 " ideal model delta sigma weight residual 113.21 118.42 -5.21 3.00e+00 1.11e-01 3.02e+00 ... (remaining 11083 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.15: 4711 23.15 - 46.30: 162 46.30 - 69.46: 56 69.46 - 92.61: 9 92.61 - 115.76: 9 Dihedral angle restraints: 4947 sinusoidal: 2169 harmonic: 2778 Sorted by residual: dihedral pdb=" C1 NAG B 402 " pdb=" C5 NAG B 402 " pdb=" O5 NAG B 402 " pdb=" C6 NAG B 402 " ideal model delta sinusoidal sigma weight residual 171.16 -73.08 -115.76 1 3.00e+01 1.11e-03 1.53e+01 dihedral pdb=" C1 NAG C 404 " pdb=" C5 NAG C 404 " pdb=" O5 NAG C 404 " pdb=" C6 NAG C 404 " ideal model delta sinusoidal sigma weight residual 171.16 -73.09 -115.75 1 3.00e+01 1.11e-03 1.53e+01 dihedral pdb=" C1 NAG A 402 " pdb=" C5 NAG A 402 " pdb=" O5 NAG A 402 " pdb=" C6 NAG A 402 " ideal model delta sinusoidal sigma weight residual 171.16 -73.09 -115.75 1 3.00e+01 1.11e-03 1.53e+01 ... (remaining 4944 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 1007 0.056 - 0.112: 221 0.112 - 0.168: 20 0.168 - 0.223: 0 0.223 - 0.279: 3 Chirality restraints: 1251 Sorted by residual: chirality pdb=" C1 NAG B 402 " pdb=" ND2 ASN B 184 " pdb=" C2 NAG B 402 " pdb=" O5 NAG B 402 " both_signs ideal model delta sigma weight residual False -2.40 -2.12 -0.28 2.00e-01 2.50e+01 1.95e+00 chirality pdb=" C1 NAG A 402 " pdb=" ND2 ASN A 184 " pdb=" C2 NAG A 402 " pdb=" O5 NAG A 402 " both_signs ideal model delta sigma weight residual False -2.40 -2.12 -0.28 2.00e-01 2.50e+01 1.91e+00 chirality pdb=" C1 NAG C 404 " pdb=" ND2 ASN C 184 " pdb=" C2 NAG C 404 " pdb=" O5 NAG C 404 " both_signs ideal model delta sigma weight residual False -2.40 -2.13 -0.27 2.00e-01 2.50e+01 1.88e+00 ... (remaining 1248 not shown) Planarity restraints: 1395 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 34 " 0.205 9.50e-02 1.11e+02 9.27e-02 6.79e+00 pdb=" NE ARG A 34 " -0.020 2.00e-02 2.50e+03 pdb=" CZ ARG A 34 " 0.020 2.00e-02 2.50e+03 pdb=" NH1 ARG A 34 " -0.009 2.00e-02 2.50e+03 pdb=" NH2 ARG A 34 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 34 " -0.205 9.50e-02 1.11e+02 9.28e-02 6.78e+00 pdb=" NE ARG B 34 " 0.020 2.00e-02 2.50e+03 pdb=" CZ ARG B 34 " -0.019 2.00e-02 2.50e+03 pdb=" NH1 ARG B 34 " 0.009 2.00e-02 2.50e+03 pdb=" NH2 ARG B 34 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 34 " -0.205 9.50e-02 1.11e+02 9.28e-02 6.75e+00 pdb=" NE ARG C 34 " 0.019 2.00e-02 2.50e+03 pdb=" CZ ARG C 34 " -0.019 2.00e-02 2.50e+03 pdb=" NH1 ARG C 34 " 0.009 2.00e-02 2.50e+03 pdb=" NH2 ARG C 34 " -0.000 2.00e-02 2.50e+03 ... (remaining 1392 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 120 2.53 - 3.12: 6303 3.12 - 3.71: 13296 3.71 - 4.31: 19717 4.31 - 4.90: 31513 Nonbonded interactions: 70949 Sorted by model distance: nonbonded pdb="MG MG A 404 " pdb=" O HOH A 507 " model vdw 1.936 2.170 nonbonded pdb="MG MG C 401 " pdb=" O HOH C 508 " model vdw 1.939 2.170 nonbonded pdb="MG MG B 404 " pdb=" O HOH B 510 " model vdw 1.949 2.170 nonbonded pdb="MG MG A 404 " pdb=" O HOH B 501 " model vdw 1.951 2.170 nonbonded pdb="MG MG B 404 " pdb=" O HOH C 501 " model vdw 1.953 2.170 ... (remaining 70944 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: 0.03 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 31 through 356 or resid 402 through 403)) selection = (chain 'B' and (resid 31 through 356 or resid 402 through 403)) selection = (chain 'C' and (resid 31 through 356 or resid 403 through 404)) } 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: 0.910 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: 0.000 Extract box with map and model: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 22.610 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8773 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 : 0.004 0.075 8181 Z= 0.178 Angle : 0.514 5.215 11145 Z= 0.258 Chirality : 0.046 0.279 1251 Planarity : 0.006 0.093 1386 Dihedral : 14.713 115.762 3126 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.36 % Allowed : 0.36 % Favored : 99.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % 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: 0.18 (0.28), residues: 972 helix: 0.35 (0.37), residues: 240 sheet: 0.33 (0.33), residues: 270 loop : 0.02 (0.29), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 259 HIS 0.003 0.001 HIS C 306 PHE 0.009 0.001 PHE B 276 TYR 0.014 0.001 TYR C 90 ARG 0.022 0.001 ARG A 34 Details of bonding type rmsd link_NAG-ASN : bond 0.00203 ( 9) link_NAG-ASN : angle 2.18057 ( 27) hydrogen bonds : bond 0.18708 ( 232) hydrogen bonds : angle 6.82595 ( 579) SS BOND : bond 0.00232 ( 15) SS BOND : angle 0.78909 ( 30) covalent geometry : bond 0.00367 ( 8157) covalent geometry : angle 0.50247 (11088) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 114 time to evaluate : 0.904 Fit side-chains REVERT: A 148 LYS cc_start: 0.8311 (ptpt) cc_final: 0.7995 (ptmm) REVERT: A 181 GLU cc_start: 0.8755 (mt-10) cc_final: 0.8284 (mp0) REVERT: A 271 ARG cc_start: 0.8214 (mtt180) cc_final: 0.7995 (mtt-85) REVERT: A 300 ASN cc_start: 0.8891 (t0) cc_final: 0.8415 (t0) REVERT: B 52 GLU cc_start: 0.8948 (mm-30) cc_final: 0.8725 (mm-30) REVERT: B 76 GLN cc_start: 0.8466 (tt0) cc_final: 0.7875 (tm-30) REVERT: B 181 GLU cc_start: 0.8698 (mt-10) cc_final: 0.8037 (mp0) REVERT: B 300 ASN cc_start: 0.8905 (t0) cc_final: 0.8464 (t0) REVERT: C 148 LYS cc_start: 0.8330 (ptpt) cc_final: 0.8026 (ptmm) REVERT: C 159 CYS cc_start: 0.6935 (m) cc_final: 0.6677 (m) REVERT: C 181 GLU cc_start: 0.8685 (mt-10) cc_final: 0.8214 (mp0) REVERT: C 271 ARG cc_start: 0.8268 (mtt180) cc_final: 0.8064 (mtt-85) REVERT: C 300 ASN cc_start: 0.8962 (t0) cc_final: 0.8479 (t0) outliers start: 3 outliers final: 0 residues processed: 114 average time/residue: 1.3183 time to fit residues: 159.1431 Evaluate side-chains 83 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 0.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 81 optimal weight: 3.9990 chunk 72 optimal weight: 0.6980 chunk 40 optimal weight: 0.6980 chunk 24 optimal weight: 0.3980 chunk 49 optimal weight: 0.6980 chunk 38 optimal weight: 0.9990 chunk 75 optimal weight: 0.9980 chunk 29 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 chunk 56 optimal weight: 5.9990 chunk 87 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN A 237 GLN ** B 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 76 GLN C 213 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.100335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.069487 restraints weight = 12203.266| |-----------------------------------------------------------------------------| r_work (start): 0.2971 rms_B_bonded: 2.50 r_work: 0.2832 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2711 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8782 moved from start: 0.1010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 8181 Z= 0.142 Angle : 0.556 8.507 11145 Z= 0.282 Chirality : 0.046 0.231 1251 Planarity : 0.004 0.029 1386 Dihedral : 13.821 95.353 1335 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 1.19 % Allowed : 6.64 % Favored : 92.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % 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: 0.14 (0.28), residues: 972 helix: 0.29 (0.34), residues: 261 sheet: -0.12 (0.30), residues: 303 loop : 0.38 (0.32), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 164 HIS 0.003 0.001 HIS B 306 PHE 0.011 0.002 PHE B 230 TYR 0.017 0.001 TYR A 90 ARG 0.005 0.001 ARG C 34 Details of bonding type rmsd link_NAG-ASN : bond 0.00226 ( 9) link_NAG-ASN : angle 2.04044 ( 27) hydrogen bonds : bond 0.04308 ( 232) hydrogen bonds : angle 5.33368 ( 579) SS BOND : bond 0.00229 ( 15) SS BOND : angle 0.96236 ( 30) covalent geometry : bond 0.00295 ( 8157) covalent geometry : angle 0.54591 (11088) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 101 time to evaluate : 0.852 Fit side-chains REVERT: A 148 LYS cc_start: 0.8322 (ptpt) cc_final: 0.8007 (ptmm) REVERT: A 181 GLU cc_start: 0.8938 (mt-10) cc_final: 0.8318 (mp0) REVERT: A 271 ARG cc_start: 0.8602 (mtt180) cc_final: 0.8348 (mtt-85) REVERT: A 300 ASN cc_start: 0.8953 (t0) cc_final: 0.8449 (t0) REVERT: B 52 GLU cc_start: 0.9101 (mm-30) cc_final: 0.8890 (mm-30) REVERT: B 76 GLN cc_start: 0.8607 (tt0) cc_final: 0.7951 (tm-30) REVERT: B 148 LYS cc_start: 0.8219 (ptpp) cc_final: 0.7832 (ptmm) REVERT: B 181 GLU cc_start: 0.8897 (mt-10) cc_final: 0.8074 (mp0) REVERT: B 271 ARG cc_start: 0.8559 (mtt90) cc_final: 0.8256 (mtt-85) REVERT: B 300 ASN cc_start: 0.8944 (t0) cc_final: 0.8478 (t0) REVERT: C 148 LYS cc_start: 0.8440 (ptpt) cc_final: 0.8147 (ptmm) REVERT: C 181 GLU cc_start: 0.8893 (mt-10) cc_final: 0.8163 (mp0) REVERT: C 271 ARG cc_start: 0.8639 (mtt180) cc_final: 0.8359 (mtt-85) REVERT: C 300 ASN cc_start: 0.9039 (t0) cc_final: 0.8548 (t0) outliers start: 10 outliers final: 6 residues processed: 107 average time/residue: 1.2278 time to fit residues: 139.8745 Evaluate side-chains 93 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 87 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 285 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 34 optimal weight: 0.0070 chunk 6 optimal weight: 0.9990 chunk 54 optimal weight: 0.1980 chunk 33 optimal weight: 0.8980 chunk 95 optimal weight: 5.9990 chunk 32 optimal weight: 5.9990 chunk 44 optimal weight: 6.9990 chunk 94 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 67 optimal weight: 0.0870 chunk 59 optimal weight: 6.9990 overall best weight: 0.4378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN A 201 ASN A 237 GLN ** B 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 201 ASN C 76 GLN C 201 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.101858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.071467 restraints weight = 12397.038| |-----------------------------------------------------------------------------| r_work (start): 0.3011 rms_B_bonded: 2.51 r_work: 0.2875 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2756 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8803 moved from start: 0.1435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8181 Z= 0.113 Angle : 0.542 11.101 11145 Z= 0.267 Chirality : 0.044 0.183 1251 Planarity : 0.004 0.032 1386 Dihedral : 11.709 86.965 1335 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 1.42 % Allowed : 7.95 % Favored : 90.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % 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: 0.18 (0.27), residues: 972 helix: 0.45 (0.34), residues: 261 sheet: -0.18 (0.30), residues: 294 loop : 0.38 (0.31), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 164 HIS 0.002 0.001 HIS C 306 PHE 0.010 0.001 PHE B 230 TYR 0.017 0.001 TYR A 90 ARG 0.006 0.001 ARG C 268 Details of bonding type rmsd link_NAG-ASN : bond 0.00160 ( 9) link_NAG-ASN : angle 2.41392 ( 27) hydrogen bonds : bond 0.03383 ( 232) hydrogen bonds : angle 5.07102 ( 579) SS BOND : bond 0.00232 ( 15) SS BOND : angle 0.85656 ( 30) covalent geometry : bond 0.00238 ( 8157) covalent geometry : angle 0.52871 (11088) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 100 time to evaluate : 0.918 Fit side-chains REVERT: A 148 LYS cc_start: 0.8384 (ptpt) cc_final: 0.8072 (ptmm) REVERT: A 181 GLU cc_start: 0.8936 (mt-10) cc_final: 0.8245 (mp0) REVERT: A 271 ARG cc_start: 0.8632 (mtt180) cc_final: 0.8419 (mtt-85) REVERT: A 300 ASN cc_start: 0.8994 (t0) cc_final: 0.8480 (t0) REVERT: B 76 GLN cc_start: 0.8590 (tt0) cc_final: 0.7990 (tm-30) REVERT: B 148 LYS cc_start: 0.8236 (ptpp) cc_final: 0.7867 (ptmm) REVERT: B 180 ARG cc_start: 0.8771 (ptt-90) cc_final: 0.8486 (ptt-90) REVERT: B 181 GLU cc_start: 0.8928 (mt-10) cc_final: 0.8203 (mp0) REVERT: B 271 ARG cc_start: 0.8574 (mtt90) cc_final: 0.8268 (mtt-85) REVERT: B 300 ASN cc_start: 0.8970 (t0) cc_final: 0.8485 (t0) REVERT: C 98 ASN cc_start: 0.8791 (m-40) cc_final: 0.8309 (m110) REVERT: C 148 LYS cc_start: 0.8458 (ptpt) cc_final: 0.8160 (ptmm) REVERT: C 181 GLU cc_start: 0.8909 (mt-10) cc_final: 0.8208 (mp0) REVERT: C 300 ASN cc_start: 0.9003 (t0) cc_final: 0.8506 (t0) outliers start: 12 outliers final: 4 residues processed: 106 average time/residue: 1.2390 time to fit residues: 139.7933 Evaluate side-chains 90 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 86 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 318 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 95 optimal weight: 5.9990 chunk 28 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 chunk 94 optimal weight: 0.9990 chunk 70 optimal weight: 0.0570 chunk 13 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 93 optimal weight: 0.8980 chunk 73 optimal weight: 0.7980 chunk 30 optimal weight: 4.9990 overall best weight: 0.7502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 56 GLN ** B 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 76 GLN C 237 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.100937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.070717 restraints weight = 12304.426| |-----------------------------------------------------------------------------| r_work (start): 0.2993 rms_B_bonded: 2.51 r_work: 0.2856 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2735 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8795 moved from start: 0.1589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8181 Z= 0.130 Angle : 0.521 9.142 11145 Z= 0.263 Chirality : 0.043 0.137 1251 Planarity : 0.004 0.033 1386 Dihedral : 9.848 89.404 1335 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 1.30 % Allowed : 9.73 % Favored : 88.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % 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: 0.48 (0.28), residues: 972 helix: 1.08 (0.35), residues: 243 sheet: -0.44 (0.31), residues: 270 loop : 0.61 (0.30), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 164 HIS 0.002 0.001 HIS C 213 PHE 0.010 0.001 PHE B 230 TYR 0.014 0.001 TYR A 90 ARG 0.006 0.001 ARG A 180 Details of bonding type rmsd link_NAG-ASN : bond 0.00411 ( 9) link_NAG-ASN : angle 3.48627 ( 27) hydrogen bonds : bond 0.03064 ( 232) hydrogen bonds : angle 4.96556 ( 579) SS BOND : bond 0.00252 ( 15) SS BOND : angle 0.78657 ( 30) covalent geometry : bond 0.00274 ( 8157) covalent geometry : angle 0.49192 (11088) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 97 time to evaluate : 0.851 Fit side-chains REVERT: A 148 LYS cc_start: 0.8385 (ptpt) cc_final: 0.8062 (ptmm) REVERT: A 181 GLU cc_start: 0.8918 (mt-10) cc_final: 0.8255 (mp0) REVERT: A 265 TRP cc_start: 0.8455 (m100) cc_final: 0.7961 (m-10) REVERT: A 271 ARG cc_start: 0.8626 (mtt180) cc_final: 0.8395 (mtt-85) REVERT: A 300 ASN cc_start: 0.8979 (t0) cc_final: 0.8394 (t0) REVERT: B 52 GLU cc_start: 0.9096 (mm-30) cc_final: 0.8849 (mm-30) REVERT: B 128 GLU cc_start: 0.7999 (OUTLIER) cc_final: 0.7791 (pm20) REVERT: B 148 LYS cc_start: 0.8314 (ptpp) cc_final: 0.7932 (ptmm) REVERT: B 180 ARG cc_start: 0.8765 (ptt-90) cc_final: 0.8473 (ptt-90) REVERT: B 181 GLU cc_start: 0.8918 (mt-10) cc_final: 0.8156 (mp0) REVERT: B 271 ARG cc_start: 0.8538 (mtt90) cc_final: 0.8158 (mtt-85) REVERT: B 300 ASN cc_start: 0.8976 (t0) cc_final: 0.8479 (t0) REVERT: C 98 ASN cc_start: 0.8780 (m-40) cc_final: 0.8301 (m110) REVERT: C 128 GLU cc_start: 0.8033 (pm20) cc_final: 0.7830 (pm20) REVERT: C 148 LYS cc_start: 0.8495 (ptpt) cc_final: 0.8188 (ptmm) REVERT: C 181 GLU cc_start: 0.8907 (mt-10) cc_final: 0.8176 (mp0) REVERT: C 300 ASN cc_start: 0.9005 (t0) cc_final: 0.8509 (t0) outliers start: 11 outliers final: 3 residues processed: 102 average time/residue: 1.1915 time to fit residues: 129.3046 Evaluate side-chains 91 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 87 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 ASP Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 318 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 17 optimal weight: 0.0060 chunk 43 optimal weight: 0.7980 chunk 5 optimal weight: 7.9990 chunk 72 optimal weight: 0.9990 chunk 76 optimal weight: 4.9990 chunk 61 optimal weight: 0.0370 chunk 20 optimal weight: 0.7980 chunk 53 optimal weight: 3.9990 chunk 46 optimal weight: 3.9990 chunk 84 optimal weight: 1.9990 chunk 81 optimal weight: 0.6980 overall best weight: 0.4674 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 76 GLN ** B 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 76 GLN C 237 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.102472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.072639 restraints weight = 12253.431| |-----------------------------------------------------------------------------| r_work (start): 0.3033 rms_B_bonded: 2.49 r_work: 0.2898 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2780 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8794 moved from start: 0.1782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8181 Z= 0.102 Angle : 0.463 5.101 11145 Z= 0.243 Chirality : 0.042 0.137 1251 Planarity : 0.003 0.030 1386 Dihedral : 9.369 89.886 1335 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 1.42 % Allowed : 10.79 % Favored : 87.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % 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: 0.55 (0.28), residues: 972 helix: 1.26 (0.35), residues: 243 sheet: -0.45 (0.30), residues: 276 loop : 0.62 (0.31), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 164 HIS 0.002 0.000 HIS C 213 PHE 0.011 0.001 PHE C 326 TYR 0.014 0.001 TYR C 90 ARG 0.008 0.001 ARG A 180 Details of bonding type rmsd link_NAG-ASN : bond 0.00142 ( 9) link_NAG-ASN : angle 2.19022 ( 27) hydrogen bonds : bond 0.02819 ( 232) hydrogen bonds : angle 4.85088 ( 579) SS BOND : bond 0.00200 ( 15) SS BOND : angle 0.75450 ( 30) covalent geometry : bond 0.00213 ( 8157) covalent geometry : angle 0.44957 (11088) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 96 time to evaluate : 0.810 Fit side-chains REVERT: A 148 LYS cc_start: 0.8396 (ptpt) cc_final: 0.8088 (ptmm) REVERT: A 181 GLU cc_start: 0.8929 (mt-10) cc_final: 0.8276 (mp0) REVERT: A 265 TRP cc_start: 0.8456 (m100) cc_final: 0.7945 (m-10) REVERT: A 271 ARG cc_start: 0.8621 (mtt180) cc_final: 0.8412 (mtt-85) REVERT: A 300 ASN cc_start: 0.9015 (t0) cc_final: 0.8402 (t0) REVERT: B 52 GLU cc_start: 0.9080 (mm-30) cc_final: 0.8840 (mm-30) REVERT: B 98 ASN cc_start: 0.8830 (m-40) cc_final: 0.8411 (m110) REVERT: B 128 GLU cc_start: 0.7962 (pm20) cc_final: 0.7756 (pm20) REVERT: B 148 LYS cc_start: 0.8312 (ptpp) cc_final: 0.7948 (ptmm) REVERT: B 181 GLU cc_start: 0.8924 (mt-10) cc_final: 0.8169 (mp0) REVERT: B 271 ARG cc_start: 0.8515 (mtt90) cc_final: 0.8177 (mtt-85) REVERT: B 300 ASN cc_start: 0.8975 (t0) cc_final: 0.8480 (t0) REVERT: C 98 ASN cc_start: 0.8764 (m-40) cc_final: 0.8329 (m110) REVERT: C 128 GLU cc_start: 0.8050 (pm20) cc_final: 0.7812 (pm20) REVERT: C 148 LYS cc_start: 0.8461 (ptpt) cc_final: 0.8150 (ptmm) REVERT: C 181 GLU cc_start: 0.8909 (mt-10) cc_final: 0.8283 (mp0) REVERT: C 265 TRP cc_start: 0.8408 (m100) cc_final: 0.7893 (m-10) REVERT: C 300 ASN cc_start: 0.9017 (t0) cc_final: 0.8510 (t0) outliers start: 12 outliers final: 7 residues processed: 104 average time/residue: 1.1533 time to fit residues: 128.1123 Evaluate side-chains 93 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 86 time to evaluate : 1.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 316 ASP Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 318 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 47 optimal weight: 2.9990 chunk 12 optimal weight: 5.9990 chunk 43 optimal weight: 3.9990 chunk 59 optimal weight: 0.9980 chunk 68 optimal weight: 0.9980 chunk 41 optimal weight: 0.0670 chunk 89 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 chunk 72 optimal weight: 0.9990 chunk 20 optimal weight: 0.5980 chunk 11 optimal weight: 7.9990 overall best weight: 0.7320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 237 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.101673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.071144 restraints weight = 12281.854| |-----------------------------------------------------------------------------| r_work (start): 0.3005 rms_B_bonded: 2.52 r_work: 0.2871 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2751 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8769 moved from start: 0.1834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8181 Z= 0.122 Angle : 0.472 5.641 11145 Z= 0.249 Chirality : 0.042 0.136 1251 Planarity : 0.003 0.032 1386 Dihedral : 9.268 89.694 1335 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer: Outliers : 1.19 % Allowed : 11.74 % Favored : 87.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % 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: 0.67 (0.28), residues: 972 helix: 1.41 (0.35), residues: 243 sheet: -0.46 (0.31), residues: 276 loop : 0.73 (0.31), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 164 HIS 0.002 0.000 HIS C 213 PHE 0.009 0.001 PHE B 230 TYR 0.013 0.001 TYR A 90 ARG 0.008 0.001 ARG A 180 Details of bonding type rmsd link_NAG-ASN : bond 0.00124 ( 9) link_NAG-ASN : angle 2.09800 ( 27) hydrogen bonds : bond 0.02829 ( 232) hydrogen bonds : angle 4.86877 ( 579) SS BOND : bond 0.00211 ( 15) SS BOND : angle 0.77136 ( 30) covalent geometry : bond 0.00256 ( 8157) covalent geometry : angle 0.46005 (11088) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 94 time to evaluate : 0.902 Fit side-chains REVERT: A 148 LYS cc_start: 0.8369 (ptpt) cc_final: 0.8047 (ptmm) REVERT: A 181 GLU cc_start: 0.8938 (mt-10) cc_final: 0.8258 (mp0) REVERT: A 265 TRP cc_start: 0.8459 (m100) cc_final: 0.7947 (m-10) REVERT: A 271 ARG cc_start: 0.8602 (mtt180) cc_final: 0.8363 (mtt-85) REVERT: A 300 ASN cc_start: 0.9001 (t0) cc_final: 0.8366 (t0) REVERT: B 52 GLU cc_start: 0.9092 (mm-30) cc_final: 0.8825 (mm-30) REVERT: B 98 ASN cc_start: 0.8817 (m-40) cc_final: 0.8379 (m110) REVERT: B 128 GLU cc_start: 0.8011 (pm20) cc_final: 0.7792 (pm20) REVERT: B 148 LYS cc_start: 0.8256 (ptpp) cc_final: 0.7894 (ptmm) REVERT: B 180 ARG cc_start: 0.8709 (ptt-90) cc_final: 0.8413 (ptt-90) REVERT: B 181 GLU cc_start: 0.8920 (mt-10) cc_final: 0.8101 (mp0) REVERT: B 271 ARG cc_start: 0.8494 (mtt90) cc_final: 0.8157 (mtt-85) REVERT: B 300 ASN cc_start: 0.8982 (t0) cc_final: 0.8461 (t0) REVERT: C 98 ASN cc_start: 0.8739 (m-40) cc_final: 0.8274 (m110) REVERT: C 128 GLU cc_start: 0.8081 (pm20) cc_final: 0.7854 (pm20) REVERT: C 148 LYS cc_start: 0.8428 (ptpt) cc_final: 0.8103 (ptmm) REVERT: C 149 CYS cc_start: 0.6663 (t) cc_final: 0.6447 (t) REVERT: C 181 GLU cc_start: 0.8905 (mt-10) cc_final: 0.8219 (mp0) REVERT: C 265 TRP cc_start: 0.8404 (m100) cc_final: 0.7857 (m-10) REVERT: C 300 ASN cc_start: 0.9015 (t0) cc_final: 0.8503 (t0) outliers start: 10 outliers final: 6 residues processed: 101 average time/residue: 1.1279 time to fit residues: 121.7941 Evaluate side-chains 93 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 87 time to evaluate : 0.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 316 ASP Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 285 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 27 optimal weight: 4.9990 chunk 93 optimal weight: 9.9990 chunk 94 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 chunk 72 optimal weight: 0.9980 chunk 89 optimal weight: 0.0870 chunk 76 optimal weight: 0.7980 chunk 16 optimal weight: 4.9990 chunk 26 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 51 optimal weight: 0.9980 overall best weight: 0.7758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 76 GLN ** B 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 76 GLN C 237 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.101638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.070988 restraints weight = 12289.099| |-----------------------------------------------------------------------------| r_work (start): 0.2999 rms_B_bonded: 2.54 r_work: 0.2865 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2744 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8791 moved from start: 0.1874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8181 Z= 0.124 Angle : 0.468 6.135 11145 Z= 0.248 Chirality : 0.043 0.137 1251 Planarity : 0.003 0.032 1386 Dihedral : 9.225 89.751 1335 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 1.19 % Allowed : 11.98 % Favored : 86.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % 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: 0.71 (0.28), residues: 972 helix: 1.48 (0.36), residues: 243 sheet: -0.55 (0.30), residues: 276 loop : 0.81 (0.32), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 259 HIS 0.002 0.000 HIS C 213 PHE 0.010 0.001 PHE B 230 TYR 0.013 0.001 TYR B 90 ARG 0.007 0.001 ARG A 180 Details of bonding type rmsd link_NAG-ASN : bond 0.00095 ( 9) link_NAG-ASN : angle 1.93627 ( 27) hydrogen bonds : bond 0.02751 ( 232) hydrogen bonds : angle 4.84641 ( 579) SS BOND : bond 0.00207 ( 15) SS BOND : angle 0.77409 ( 30) covalent geometry : bond 0.00263 ( 8157) covalent geometry : angle 0.45739 (11088) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 92 time to evaluate : 0.908 Fit side-chains REVERT: A 148 LYS cc_start: 0.8332 (ptpt) cc_final: 0.8000 (ptmm) REVERT: A 181 GLU cc_start: 0.8926 (mt-10) cc_final: 0.8243 (mp0) REVERT: A 265 TRP cc_start: 0.8472 (m100) cc_final: 0.7887 (m-10) REVERT: A 271 ARG cc_start: 0.8621 (mtt180) cc_final: 0.8387 (mtt-85) REVERT: A 300 ASN cc_start: 0.9005 (t0) cc_final: 0.8369 (t0) REVERT: B 52 GLU cc_start: 0.9094 (mm-30) cc_final: 0.8885 (mm-30) REVERT: B 98 ASN cc_start: 0.8827 (m-40) cc_final: 0.8385 (m110) REVERT: B 128 GLU cc_start: 0.8027 (pm20) cc_final: 0.7813 (pm20) REVERT: B 148 LYS cc_start: 0.8271 (ptpp) cc_final: 0.7899 (ptmm) REVERT: B 180 ARG cc_start: 0.8740 (ptt-90) cc_final: 0.8474 (ptt-90) REVERT: B 181 GLU cc_start: 0.8926 (mt-10) cc_final: 0.8143 (mp0) REVERT: B 265 TRP cc_start: 0.8250 (m100) cc_final: 0.7873 (m-10) REVERT: B 300 ASN cc_start: 0.8989 (t0) cc_final: 0.8482 (t0) REVERT: C 52 GLU cc_start: 0.9059 (mm-30) cc_final: 0.8756 (mm-30) REVERT: C 98 ASN cc_start: 0.8735 (m-40) cc_final: 0.8274 (m110) REVERT: C 128 GLU cc_start: 0.8099 (pm20) cc_final: 0.7877 (pm20) REVERT: C 148 LYS cc_start: 0.8420 (ptpt) cc_final: 0.8093 (ptmm) REVERT: C 149 CYS cc_start: 0.6710 (t) cc_final: 0.6503 (t) REVERT: C 181 GLU cc_start: 0.8911 (mt-10) cc_final: 0.8225 (mp0) REVERT: C 265 TRP cc_start: 0.8433 (m100) cc_final: 0.7885 (m-10) REVERT: C 300 ASN cc_start: 0.9024 (t0) cc_final: 0.8514 (t0) outliers start: 10 outliers final: 9 residues processed: 98 average time/residue: 1.1801 time to fit residues: 123.4364 Evaluate side-chains 97 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 88 time to evaluate : 0.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 316 ASP Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 213 HIS Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 318 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 38 optimal weight: 0.7980 chunk 18 optimal weight: 5.9990 chunk 43 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 77 optimal weight: 0.7980 chunk 10 optimal weight: 5.9990 chunk 6 optimal weight: 0.7980 chunk 92 optimal weight: 0.9980 chunk 78 optimal weight: 3.9990 chunk 56 optimal weight: 4.9990 chunk 53 optimal weight: 2.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 76 GLN ** B 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 237 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.100982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.070588 restraints weight = 12330.279| |-----------------------------------------------------------------------------| r_work (start): 0.2987 rms_B_bonded: 2.55 r_work: 0.2852 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2732 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8795 moved from start: 0.1887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 8181 Z= 0.133 Angle : 0.477 7.292 11145 Z= 0.251 Chirality : 0.043 0.136 1251 Planarity : 0.003 0.033 1386 Dihedral : 9.213 88.332 1335 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer: Outliers : 1.30 % Allowed : 12.34 % Favored : 86.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % 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: 0.71 (0.28), residues: 972 helix: 1.51 (0.36), residues: 243 sheet: -0.63 (0.31), residues: 270 loop : 0.83 (0.31), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 259 HIS 0.002 0.001 HIS C 213 PHE 0.010 0.001 PHE B 230 TYR 0.013 0.001 TYR A 90 ARG 0.006 0.001 ARG A 268 Details of bonding type rmsd link_NAG-ASN : bond 0.00084 ( 9) link_NAG-ASN : angle 1.90173 ( 27) hydrogen bonds : bond 0.02718 ( 232) hydrogen bonds : angle 4.86207 ( 579) SS BOND : bond 0.00244 ( 15) SS BOND : angle 0.81433 ( 30) covalent geometry : bond 0.00281 ( 8157) covalent geometry : angle 0.46728 (11088) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 90 time to evaluate : 0.838 Fit side-chains REVERT: A 148 LYS cc_start: 0.8309 (ptpt) cc_final: 0.7960 (ptmm) REVERT: A 181 GLU cc_start: 0.8948 (mt-10) cc_final: 0.8225 (mp0) REVERT: A 265 TRP cc_start: 0.8476 (m100) cc_final: 0.7898 (m-10) REVERT: A 271 ARG cc_start: 0.8615 (mtt180) cc_final: 0.8383 (mtt-85) REVERT: A 300 ASN cc_start: 0.9003 (t0) cc_final: 0.8375 (t0) REVERT: B 52 GLU cc_start: 0.9089 (mm-30) cc_final: 0.8866 (mm-30) REVERT: B 98 ASN cc_start: 0.8830 (m-40) cc_final: 0.8380 (m110) REVERT: B 148 LYS cc_start: 0.8252 (ptpp) cc_final: 0.7879 (ptmm) REVERT: B 180 ARG cc_start: 0.8738 (ptt-90) cc_final: 0.8471 (ptt-90) REVERT: B 181 GLU cc_start: 0.8930 (mt-10) cc_final: 0.8141 (mp0) REVERT: B 214 MET cc_start: 0.9076 (mmm) cc_final: 0.8732 (mmm) REVERT: B 300 ASN cc_start: 0.8975 (t0) cc_final: 0.8479 (t0) REVERT: C 52 GLU cc_start: 0.9061 (mm-30) cc_final: 0.8748 (mm-30) REVERT: C 98 ASN cc_start: 0.8758 (m-40) cc_final: 0.8286 (m110) REVERT: C 128 GLU cc_start: 0.8112 (pm20) cc_final: 0.7891 (pm20) REVERT: C 148 LYS cc_start: 0.8401 (ptpt) cc_final: 0.8061 (ptmm) REVERT: C 181 GLU cc_start: 0.8907 (mt-10) cc_final: 0.8210 (mp0) REVERT: C 265 TRP cc_start: 0.8443 (m100) cc_final: 0.7911 (m-10) REVERT: C 300 ASN cc_start: 0.9032 (t0) cc_final: 0.8530 (t0) outliers start: 11 outliers final: 5 residues processed: 97 average time/residue: 1.1516 time to fit residues: 119.3547 Evaluate side-chains 89 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 84 time to evaluate : 0.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 316 ASP Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 285 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 20 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 91 optimal weight: 5.9990 chunk 38 optimal weight: 0.9990 chunk 33 optimal weight: 3.9990 chunk 25 optimal weight: 10.0000 chunk 14 optimal weight: 4.9990 chunk 55 optimal weight: 3.9990 chunk 37 optimal weight: 0.9990 chunk 32 optimal weight: 7.9990 chunk 73 optimal weight: 0.8980 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 76 GLN ** B 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 237 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.100013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.069280 restraints weight = 12481.583| |-----------------------------------------------------------------------------| r_work (start): 0.2964 rms_B_bonded: 2.54 r_work: 0.2827 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2706 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8797 moved from start: 0.1891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8181 Z= 0.158 Angle : 0.498 7.453 11145 Z= 0.262 Chirality : 0.043 0.164 1251 Planarity : 0.004 0.035 1386 Dihedral : 9.299 86.737 1335 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer: Outliers : 1.07 % Allowed : 13.05 % Favored : 85.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % 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: 0.76 (0.29), residues: 972 helix: 1.49 (0.36), residues: 243 sheet: -0.61 (0.29), residues: 297 loop : 1.03 (0.33), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 259 HIS 0.002 0.001 HIS B 120 PHE 0.011 0.001 PHE B 230 TYR 0.013 0.001 TYR C 90 ARG 0.007 0.001 ARG A 180 Details of bonding type rmsd link_NAG-ASN : bond 0.00094 ( 9) link_NAG-ASN : angle 1.92581 ( 27) hydrogen bonds : bond 0.02820 ( 232) hydrogen bonds : angle 4.91772 ( 579) SS BOND : bond 0.00244 ( 15) SS BOND : angle 0.96229 ( 30) covalent geometry : bond 0.00337 ( 8157) covalent geometry : angle 0.48745 (11088) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 85 time to evaluate : 0.948 Fit side-chains REVERT: A 148 LYS cc_start: 0.8322 (ptpt) cc_final: 0.7953 (ptmm) REVERT: A 181 GLU cc_start: 0.8942 (mt-10) cc_final: 0.8258 (mp0) REVERT: A 265 TRP cc_start: 0.8498 (m100) cc_final: 0.7961 (m-10) REVERT: A 271 ARG cc_start: 0.8606 (mtt180) cc_final: 0.8350 (mtt-85) REVERT: A 300 ASN cc_start: 0.9008 (t0) cc_final: 0.8386 (t0) REVERT: B 52 GLU cc_start: 0.9093 (mm-30) cc_final: 0.8839 (mm-30) REVERT: B 148 LYS cc_start: 0.8273 (ptpp) cc_final: 0.7895 (ptmm) REVERT: B 180 ARG cc_start: 0.8725 (ptt-90) cc_final: 0.8447 (ptt-90) REVERT: B 181 GLU cc_start: 0.8918 (mt-10) cc_final: 0.8118 (mp0) REVERT: B 214 MET cc_start: 0.9059 (mmm) cc_final: 0.8720 (mmm) REVERT: B 265 TRP cc_start: 0.8182 (m100) cc_final: 0.7856 (m-10) REVERT: B 300 ASN cc_start: 0.8957 (t0) cc_final: 0.8450 (t0) REVERT: C 52 GLU cc_start: 0.9058 (mm-30) cc_final: 0.8724 (mm-30) REVERT: C 98 ASN cc_start: 0.8816 (m-40) cc_final: 0.8313 (m110) REVERT: C 148 LYS cc_start: 0.8188 (ptpt) cc_final: 0.7943 (ptmm) REVERT: C 181 GLU cc_start: 0.8901 (mt-10) cc_final: 0.8202 (mp0) REVERT: C 265 TRP cc_start: 0.8455 (m100) cc_final: 0.7921 (m-10) REVERT: C 300 ASN cc_start: 0.9017 (t0) cc_final: 0.8493 (t0) outliers start: 9 outliers final: 8 residues processed: 90 average time/residue: 1.2719 time to fit residues: 122.5799 Evaluate side-chains 90 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 82 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 316 ASP Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 213 HIS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 318 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 2 optimal weight: 0.8980 chunk 48 optimal weight: 0.8980 chunk 51 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 24 optimal weight: 5.9990 chunk 20 optimal weight: 2.9990 chunk 42 optimal weight: 4.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 76 GLN ** B 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 237 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.098509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.067651 restraints weight = 12193.351| |-----------------------------------------------------------------------------| r_work (start): 0.2930 rms_B_bonded: 2.50 r_work: 0.2791 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2669 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8813 moved from start: 0.1869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8181 Z= 0.196 Angle : 0.524 7.569 11145 Z= 0.276 Chirality : 0.044 0.179 1251 Planarity : 0.004 0.034 1386 Dihedral : 9.618 86.487 1335 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer: Outliers : 0.83 % Allowed : 13.17 % Favored : 86.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % 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 (0.29), residues: 972 helix: 1.41 (0.35), residues: 243 sheet: -0.61 (0.29), residues: 300 loop : 1.03 (0.34), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 85 HIS 0.002 0.001 HIS B 120 PHE 0.014 0.002 PHE B 230 TYR 0.013 0.001 TYR A 90 ARG 0.007 0.001 ARG A 180 Details of bonding type rmsd link_NAG-ASN : bond 0.00163 ( 9) link_NAG-ASN : angle 2.06115 ( 27) hydrogen bonds : bond 0.02886 ( 232) hydrogen bonds : angle 4.98808 ( 579) SS BOND : bond 0.00248 ( 15) SS BOND : angle 1.06874 ( 30) covalent geometry : bond 0.00421 ( 8157) covalent geometry : angle 0.51197 (11088) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 86 time to evaluate : 0.939 Fit side-chains REVERT: A 148 LYS cc_start: 0.8396 (ptpt) cc_final: 0.7999 (ptmm) REVERT: A 181 GLU cc_start: 0.8915 (mt-10) cc_final: 0.8238 (mp0) REVERT: A 265 TRP cc_start: 0.8549 (m100) cc_final: 0.8014 (m-10) REVERT: A 271 ARG cc_start: 0.8614 (mtt180) cc_final: 0.8347 (mtt-85) REVERT: A 300 ASN cc_start: 0.8972 (t0) cc_final: 0.8384 (t0) REVERT: B 52 GLU cc_start: 0.9102 (mm-30) cc_final: 0.8812 (mm-30) REVERT: B 181 GLU cc_start: 0.8905 (mt-10) cc_final: 0.8096 (mp0) REVERT: B 265 TRP cc_start: 0.8254 (m100) cc_final: 0.7891 (m-10) REVERT: B 300 ASN cc_start: 0.8960 (t0) cc_final: 0.8475 (t0) REVERT: C 52 GLU cc_start: 0.9077 (mm-30) cc_final: 0.8772 (mm-30) REVERT: C 148 LYS cc_start: 0.8191 (ptpt) cc_final: 0.7936 (ptmm) REVERT: C 181 GLU cc_start: 0.8893 (mt-10) cc_final: 0.8194 (mp0) REVERT: C 265 TRP cc_start: 0.8450 (m100) cc_final: 0.7887 (m-10) REVERT: C 300 ASN cc_start: 0.9026 (t0) cc_final: 0.8492 (t0) outliers start: 7 outliers final: 5 residues processed: 92 average time/residue: 1.0869 time to fit residues: 107.1699 Evaluate side-chains 85 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 80 time to evaluate : 0.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 318 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 39 optimal weight: 0.8980 chunk 4 optimal weight: 6.9990 chunk 93 optimal weight: 10.0000 chunk 26 optimal weight: 4.9990 chunk 29 optimal weight: 5.9990 chunk 49 optimal weight: 0.0980 chunk 63 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 94 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 76 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.098737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.067282 restraints weight = 12239.997| |-----------------------------------------------------------------------------| r_work (start): 0.2926 rms_B_bonded: 2.53 r_work: 0.2786 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2665 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8815 moved from start: 0.1913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8181 Z= 0.197 Angle : 0.527 7.230 11145 Z= 0.276 Chirality : 0.044 0.173 1251 Planarity : 0.004 0.034 1386 Dihedral : 9.740 88.832 1335 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 0.71 % Allowed : 13.64 % Favored : 85.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % 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: 0.70 (0.29), residues: 972 helix: 1.42 (0.35), residues: 243 sheet: -0.68 (0.29), residues: 300 loop : 1.06 (0.34), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 259 HIS 0.002 0.001 HIS C 120 PHE 0.013 0.002 PHE B 230 TYR 0.014 0.001 TYR A 90 ARG 0.007 0.001 ARG B 180 Details of bonding type rmsd link_NAG-ASN : bond 0.00143 ( 9) link_NAG-ASN : angle 2.02043 ( 27) hydrogen bonds : bond 0.02900 ( 232) hydrogen bonds : angle 4.99390 ( 579) SS BOND : bond 0.00246 ( 15) SS BOND : angle 1.03332 ( 30) covalent geometry : bond 0.00423 ( 8157) covalent geometry : angle 0.51595 (11088) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9113.21 seconds wall clock time: 155 minutes 4.63 seconds (9304.63 seconds total)