Starting phenix.real_space_refine on Fri Jun 6 15:01:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b73_44299/06_2025/9b73_44299.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b73_44299/06_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_44299/06_2025/9b73_44299.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b73_44299/06_2025/9b73_44299.map" model { file = "/net/cci-nas-00/data/ceres_data/9b73_44299/06_2025/9b73_44299.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b73_44299/06_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-5710/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: 5.31, per 1000 atoms: 0.66 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: 2.17 Conformation dependent library (CDL) restraints added in 965.6 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: 1.17 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: 1.94 Time building geometry restraints manager: 2.52 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: 0.950 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: 0.070 Set scattering table: 0.070 Process input model: 21.570 Find NCS groups from input model: 0.400 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:13.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.410 ------------------------------------------------------------------------------- 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 : 0.932 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: 1.3101 time to fit residues: 158.0785 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 : 0.894 ------------------------------------------------------------------------------- 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: 4.9990 chunk 72 optimal weight: 0.6980 chunk 40 optimal weight: 0.6980 chunk 24 optimal weight: 0.3980 chunk 49 optimal weight: 0.9980 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: 0.7580 ------------------------------------------------------------------------------- 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 B 213 HIS C 76 GLN C 213 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.100282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.069488 restraints weight = 12216.850| |-----------------------------------------------------------------------------| r_work (start): 0.2970 rms_B_bonded: 2.51 r_work: 0.2832 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2710 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8797 moved from start: 0.1046 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= 0.145 Angle : 0.563 8.675 11145 Z= 0.286 Chirality : 0.046 0.230 1251 Planarity : 0.004 0.029 1386 Dihedral : 13.600 94.116 1335 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 1.19 % Allowed : 6.41 % Favored : 92.41 % 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: 0.27 (0.33), residues: 261 sheet: -0.13 (0.30), residues: 303 loop : 0.41 (0.33), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 164 HIS 0.003 0.001 HIS C 213 PHE 0.011 0.002 PHE B 230 TYR 0.018 0.001 TYR A 90 ARG 0.005 0.001 ARG A 180 Details of bonding type rmsd link_NAG-ASN : bond 0.00208 ( 9) link_NAG-ASN : angle 2.08461 ( 27) hydrogen bonds : bond 0.03773 ( 232) hydrogen bonds : angle 5.27682 ( 579) SS BOND : bond 0.00360 ( 15) SS BOND : angle 0.94250 ( 30) covalent geometry : bond 0.00305 ( 8157) covalent geometry : angle 0.55320 (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 110 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 100 time to evaluate : 0.838 Fit side-chains REVERT: A 148 LYS cc_start: 0.8340 (ptpt) cc_final: 0.8025 (ptmm) REVERT: A 181 GLU cc_start: 0.8946 (mt-10) cc_final: 0.8263 (mp0) REVERT: A 271 ARG cc_start: 0.8610 (mtt180) cc_final: 0.8355 (mtt-85) REVERT: A 300 ASN cc_start: 0.8954 (t0) cc_final: 0.8449 (t0) REVERT: B 52 GLU cc_start: 0.9108 (mm-30) cc_final: 0.8833 (mm-30) REVERT: B 76 GLN cc_start: 0.8612 (tt0) cc_final: 0.7965 (tm-30) REVERT: B 148 LYS cc_start: 0.8240 (ptpp) cc_final: 0.7855 (ptmm) REVERT: B 181 GLU cc_start: 0.8899 (mt-10) cc_final: 0.8104 (mp0) REVERT: B 271 ARG cc_start: 0.8559 (mtt90) cc_final: 0.8253 (mtt-85) REVERT: B 300 ASN cc_start: 0.8948 (t0) cc_final: 0.8481 (t0) REVERT: C 148 LYS cc_start: 0.8460 (ptpt) cc_final: 0.8168 (ptmm) REVERT: C 181 GLU cc_start: 0.8891 (mt-10) cc_final: 0.8187 (mp0) REVERT: C 271 ARG cc_start: 0.8659 (mtt180) cc_final: 0.8382 (mtt-85) REVERT: C 300 ASN cc_start: 0.9045 (t0) cc_final: 0.8552 (t0) outliers start: 10 outliers final: 5 residues processed: 106 average time/residue: 1.2319 time to fit residues: 138.8267 Evaluate side-chains 94 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 89 time to evaluate : 0.903 ------------------------------------------------------------------------------- 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 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: 5.9990 chunk 6 optimal weight: 0.7980 chunk 54 optimal weight: 0.0270 chunk 33 optimal weight: 1.9990 chunk 95 optimal weight: 5.9990 chunk 32 optimal weight: 8.9990 chunk 44 optimal weight: 6.9990 chunk 94 optimal weight: 0.7980 chunk 71 optimal weight: 4.9990 chunk 67 optimal weight: 3.9990 chunk 59 optimal weight: 5.9990 overall best weight: 1.5242 ------------------------------------------------------------------------------- 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 = 0.3502 r_free = 0.3502 target = 0.098800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.067533 restraints weight = 12319.409| |-----------------------------------------------------------------------------| r_work (start): 0.2928 rms_B_bonded: 2.52 r_work: 0.2785 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2663 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8814 moved from start: 0.1325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 8181 Z= 0.197 Angle : 0.583 11.104 11145 Z= 0.291 Chirality : 0.045 0.181 1251 Planarity : 0.004 0.029 1386 Dihedral : 11.908 89.874 1335 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 1.30 % Allowed : 7.83 % Favored : 90.87 % 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: 0.17 (0.27), residues: 972 helix: 0.46 (0.34), residues: 261 sheet: -0.28 (0.31), residues: 270 loop : 0.39 (0.30), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 47 HIS 0.002 0.001 HIS B 120 PHE 0.012 0.002 PHE B 230 TYR 0.015 0.001 TYR A 90 ARG 0.007 0.001 ARG A 180 Details of bonding type rmsd link_NAG-ASN : bond 0.00140 ( 9) link_NAG-ASN : angle 2.58836 ( 27) hydrogen bonds : bond 0.03598 ( 232) hydrogen bonds : angle 5.18461 ( 579) SS BOND : bond 0.00247 ( 15) SS BOND : angle 0.91405 ( 30) covalent geometry : bond 0.00419 ( 8157) covalent geometry : angle 0.56864 (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 108 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 97 time to evaluate : 0.824 Fit side-chains REVERT: A 148 LYS cc_start: 0.8413 (ptpt) cc_final: 0.8062 (ptmm) REVERT: A 181 GLU cc_start: 0.8941 (mt-10) cc_final: 0.8263 (mp0) REVERT: A 271 ARG cc_start: 0.8615 (mtt180) cc_final: 0.8353 (mtt-85) REVERT: A 300 ASN cc_start: 0.8966 (t0) cc_final: 0.8397 (t0) REVERT: B 148 LYS cc_start: 0.8261 (ptpp) cc_final: 0.7861 (ptmm) REVERT: B 180 ARG cc_start: 0.8741 (ptt-90) cc_final: 0.8437 (ptt-90) REVERT: B 181 GLU cc_start: 0.8909 (mt-10) cc_final: 0.8142 (mp0) REVERT: B 271 ARG cc_start: 0.8536 (mtt90) cc_final: 0.8205 (mtt-85) REVERT: B 300 ASN cc_start: 0.8960 (t0) cc_final: 0.8467 (t0) REVERT: C 114 GLN cc_start: 0.8887 (OUTLIER) cc_final: 0.8351 (mt0) REVERT: C 148 LYS cc_start: 0.8453 (ptpt) cc_final: 0.8127 (ptmm) REVERT: C 181 GLU cc_start: 0.8893 (mt-10) cc_final: 0.8167 (mp0) REVERT: C 271 ARG cc_start: 0.8655 (mtt180) cc_final: 0.8356 (mtt-85) REVERT: C 300 ASN cc_start: 0.9026 (t0) cc_final: 0.8529 (t0) outliers start: 11 outliers final: 3 residues processed: 102 average time/residue: 1.2242 time to fit residues: 132.6493 Evaluate side-chains 93 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 89 time to evaluate : 0.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain C residue 114 GLN Chi-restraints excluded: chain C residue 285 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: 0.0050 chunk 94 optimal weight: 0.9990 chunk 70 optimal weight: 0.8980 chunk 13 optimal weight: 0.9980 chunk 34 optimal weight: 0.0870 chunk 93 optimal weight: 1.9990 chunk 73 optimal weight: 0.9990 chunk 30 optimal weight: 3.9990 overall best weight: 0.5974 ------------------------------------------------------------------------------- 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 76 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.101280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.070935 restraints weight = 12260.245| |-----------------------------------------------------------------------------| r_work (start): 0.2998 rms_B_bonded: 2.50 r_work: 0.2860 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2740 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8814 moved from start: 0.1558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8181 Z= 0.122 Angle : 0.515 8.951 11145 Z= 0.261 Chirality : 0.043 0.136 1251 Planarity : 0.003 0.031 1386 Dihedral : 9.765 88.120 1335 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 1.07 % Allowed : 10.08 % Favored : 88.85 % 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: 0.46 (0.28), residues: 972 helix: 1.08 (0.35), residues: 243 sheet: -0.55 (0.30), residues: 270 loop : 0.65 (0.31), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 259 HIS 0.002 0.001 HIS C 306 PHE 0.013 0.001 PHE C 326 TYR 0.015 0.001 TYR B 90 ARG 0.007 0.001 ARG A 180 Details of bonding type rmsd link_NAG-ASN : bond 0.00362 ( 9) link_NAG-ASN : angle 3.36225 ( 27) hydrogen bonds : bond 0.03022 ( 232) hydrogen bonds : angle 4.96654 ( 579) SS BOND : bond 0.00209 ( 15) SS BOND : angle 0.85077 ( 30) covalent geometry : bond 0.00258 ( 8157) covalent geometry : angle 0.48701 (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 110 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 101 time to evaluate : 0.940 Fit side-chains REVERT: A 148 LYS cc_start: 0.8375 (ptpt) cc_final: 0.8040 (ptmm) REVERT: A 181 GLU cc_start: 0.8932 (mt-10) cc_final: 0.8280 (mp0) REVERT: A 271 ARG cc_start: 0.8623 (mtt180) cc_final: 0.8402 (mtt-85) REVERT: A 300 ASN cc_start: 0.8991 (t0) cc_final: 0.8401 (t0) REVERT: B 148 LYS cc_start: 0.8314 (ptpp) cc_final: 0.7917 (ptmm) REVERT: B 181 GLU cc_start: 0.8916 (mt-10) cc_final: 0.8169 (mp0) REVERT: B 271 ARG cc_start: 0.8544 (mtt90) cc_final: 0.8208 (mtt-85) REVERT: B 300 ASN cc_start: 0.8987 (t0) cc_final: 0.8493 (t0) REVERT: C 98 ASN cc_start: 0.8781 (m-40) cc_final: 0.8292 (m110) REVERT: C 114 GLN cc_start: 0.8784 (OUTLIER) cc_final: 0.8249 (mt0) REVERT: C 148 LYS cc_start: 0.8496 (ptpt) cc_final: 0.8178 (ptmm) REVERT: C 181 GLU cc_start: 0.8908 (mt-10) cc_final: 0.8159 (mp0) REVERT: C 271 ARG cc_start: 0.8629 (mtt180) cc_final: 0.8374 (mtt-85) REVERT: C 300 ASN cc_start: 0.9025 (t0) cc_final: 0.8532 (t0) outliers start: 9 outliers final: 3 residues processed: 105 average time/residue: 1.2641 time to fit residues: 140.7425 Evaluate side-chains 89 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 85 time to evaluate : 0.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 114 GLN Chi-restraints excluded: chain C 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: 0.3980 chunk 43 optimal weight: 0.7980 chunk 5 optimal weight: 7.9990 chunk 72 optimal weight: 0.7980 chunk 76 optimal weight: 6.9990 chunk 61 optimal weight: 0.2980 chunk 20 optimal weight: 0.9980 chunk 53 optimal weight: 3.9990 chunk 46 optimal weight: 3.9990 chunk 84 optimal weight: 0.8980 chunk 81 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 56 GLN 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.101360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.070857 restraints weight = 12230.086| |-----------------------------------------------------------------------------| r_work (start): 0.2997 rms_B_bonded: 2.53 r_work: 0.2860 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2741 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8790 moved from start: 0.1709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 8181 Z= 0.119 Angle : 0.476 5.153 11145 Z= 0.250 Chirality : 0.043 0.137 1251 Planarity : 0.003 0.034 1386 Dihedral : 9.438 89.683 1335 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer: Outliers : 1.78 % Allowed : 10.08 % Favored : 88.14 % 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: 0.54 (0.28), residues: 972 helix: 1.21 (0.35), residues: 243 sheet: -0.54 (0.31), residues: 270 loop : 0.69 (0.31), residues: 459 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 0.009 0.001 PHE B 230 TYR 0.014 0.001 TYR C 90 ARG 0.006 0.001 ARG C 268 Details of bonding type rmsd link_NAG-ASN : bond 0.00137 ( 9) link_NAG-ASN : angle 2.36089 ( 27) hydrogen bonds : bond 0.02884 ( 232) hydrogen bonds : angle 4.95175 ( 579) SS BOND : bond 0.00216 ( 15) SS BOND : angle 0.78028 ( 30) covalent geometry : bond 0.00248 ( 8157) covalent geometry : angle 0.46062 (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 114 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 99 time to evaluate : 0.891 Fit side-chains REVERT: A 128 GLU cc_start: 0.7727 (pm20) cc_final: 0.7467 (pm20) REVERT: A 148 LYS cc_start: 0.8363 (ptpt) cc_final: 0.8017 (ptmm) REVERT: A 181 GLU cc_start: 0.8926 (mt-10) cc_final: 0.8238 (mp0) REVERT: A 271 ARG cc_start: 0.8617 (mtt180) cc_final: 0.8384 (mtt-85) REVERT: A 300 ASN cc_start: 0.8985 (t0) cc_final: 0.8393 (t0) REVERT: B 98 ASN cc_start: 0.8835 (m-40) cc_final: 0.8376 (m110) REVERT: B 148 LYS cc_start: 0.8337 (ptpp) cc_final: 0.7933 (ptmm) REVERT: B 181 GLU cc_start: 0.8911 (mt-10) cc_final: 0.8108 (mp0) REVERT: B 271 ARG cc_start: 0.8514 (mtt90) cc_final: 0.8165 (mtt-85) REVERT: B 300 ASN cc_start: 0.8984 (t0) cc_final: 0.8492 (t0) REVERT: C 98 ASN cc_start: 0.8771 (m-40) cc_final: 0.8285 (m110) REVERT: C 114 GLN cc_start: 0.8729 (OUTLIER) cc_final: 0.8218 (mt0) REVERT: C 128 GLU cc_start: 0.8040 (pm20) cc_final: 0.7800 (pm20) REVERT: C 148 LYS cc_start: 0.8455 (ptpt) cc_final: 0.8109 (ptmm) REVERT: C 149 CYS cc_start: 0.6707 (t) cc_final: 0.6480 (t) REVERT: C 181 GLU cc_start: 0.8893 (mt-10) cc_final: 0.8226 (mp0) REVERT: C 271 ARG cc_start: 0.8619 (mtt180) cc_final: 0.8342 (mtt-85) REVERT: C 300 ASN cc_start: 0.9014 (t0) cc_final: 0.8519 (t0) outliers start: 15 outliers final: 4 residues processed: 108 average time/residue: 1.2216 time to fit residues: 140.1403 Evaluate side-chains 96 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 91 time to evaluate : 0.906 ------------------------------------------------------------------------------- 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 114 GLN 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: 5.9990 chunk 68 optimal weight: 1.9990 chunk 41 optimal weight: 0.6980 chunk 89 optimal weight: 6.9990 chunk 74 optimal weight: 1.9990 chunk 72 optimal weight: 0.0470 chunk 20 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 overall best weight: 1.1482 ------------------------------------------------------------------------------- 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 = 0.3517 r_free = 0.3517 target = 0.099805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.069481 restraints weight = 12233.367| |-----------------------------------------------------------------------------| r_work (start): 0.2965 rms_B_bonded: 2.47 r_work: 0.2826 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2706 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8833 moved from start: 0.1685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8181 Z= 0.158 Angle : 0.495 5.460 11145 Z= 0.261 Chirality : 0.043 0.137 1251 Planarity : 0.004 0.032 1386 Dihedral : 9.408 89.677 1335 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 1.07 % Allowed : 11.63 % Favored : 87.31 % 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: 0.66 (0.28), residues: 972 helix: 1.34 (0.35), residues: 243 sheet: -0.56 (0.31), residues: 270 loop : 0.80 (0.31), residues: 459 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 C 326 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 0.00148 ( 9) link_NAG-ASN : angle 2.19720 ( 27) hydrogen bonds : bond 0.02898 ( 232) hydrogen bonds : angle 4.96698 ( 579) SS BOND : bond 0.00225 ( 15) SS BOND : angle 0.80505 ( 30) covalent geometry : bond 0.00340 ( 8157) covalent geometry : angle 0.48218 (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 102 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 93 time to evaluate : 0.933 Fit side-chains REVERT: A 128 GLU cc_start: 0.7727 (pm20) cc_final: 0.7462 (pm20) REVERT: A 148 LYS cc_start: 0.8434 (ptpt) cc_final: 0.8077 (ptmm) REVERT: A 181 GLU cc_start: 0.8959 (mt-10) cc_final: 0.8287 (mp0) REVERT: A 271 ARG cc_start: 0.8637 (mtt180) cc_final: 0.8410 (mtt-85) REVERT: A 300 ASN cc_start: 0.8958 (t0) cc_final: 0.8359 (t0) REVERT: B 148 LYS cc_start: 0.8365 (ptpp) cc_final: 0.7945 (ptmm) REVERT: B 181 GLU cc_start: 0.8920 (mt-10) cc_final: 0.8137 (mp0) REVERT: B 300 ASN cc_start: 0.8973 (t0) cc_final: 0.8486 (t0) REVERT: C 98 ASN cc_start: 0.8803 (m-40) cc_final: 0.8309 (m110) REVERT: C 114 GLN cc_start: 0.8788 (OUTLIER) cc_final: 0.8284 (mt0) REVERT: C 128 GLU cc_start: 0.8037 (pm20) cc_final: 0.7741 (pm20) REVERT: C 148 LYS cc_start: 0.8517 (ptpt) cc_final: 0.8157 (ptmm) REVERT: C 149 CYS cc_start: 0.6740 (t) cc_final: 0.6524 (t) REVERT: C 181 GLU cc_start: 0.8895 (mt-10) cc_final: 0.8254 (mp0) REVERT: C 271 ARG cc_start: 0.8661 (mtt180) cc_final: 0.8380 (mtt-85) REVERT: C 300 ASN cc_start: 0.9002 (t0) cc_final: 0.8497 (t0) outliers start: 9 outliers final: 5 residues processed: 99 average time/residue: 1.2332 time to fit residues: 129.7771 Evaluate side-chains 95 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 89 time to evaluate : 0.815 ------------------------------------------------------------------------------- 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 114 GLN 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: 0.2980 chunk 94 optimal weight: 0.7980 chunk 17 optimal weight: 0.8980 chunk 72 optimal weight: 0.1980 chunk 89 optimal weight: 0.0010 chunk 76 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 overall best weight: 0.4386 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.102344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.071943 restraints weight = 12271.907| |-----------------------------------------------------------------------------| r_work (start): 0.3019 rms_B_bonded: 2.54 r_work: 0.2884 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2764 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8763 moved from start: 0.1880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 8181 Z= 0.101 Angle : 0.470 6.836 11145 Z= 0.247 Chirality : 0.043 0.137 1251 Planarity : 0.003 0.032 1386 Dihedral : 9.107 88.180 1335 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 0.95 % Allowed : 12.46 % Favored : 86.60 % 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: 0.63 (0.28), residues: 972 helix: 1.43 (0.36), residues: 243 sheet: -0.64 (0.30), residues: 276 loop : 0.78 (0.31), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 164 HIS 0.002 0.000 HIS A 306 PHE 0.009 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 0.00141 ( 9) link_NAG-ASN : angle 1.85987 ( 27) hydrogen bonds : bond 0.02629 ( 232) hydrogen bonds : angle 4.86249 ( 579) SS BOND : bond 0.00201 ( 15) SS BOND : angle 0.77327 ( 30) covalent geometry : bond 0.00212 ( 8157) covalent geometry : angle 0.46087 (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 101 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 93 time to evaluate : 0.897 Fit side-chains revert: symmetry clash REVERT: A 128 GLU cc_start: 0.7762 (pm20) cc_final: 0.7490 (pm20) REVERT: A 148 LYS cc_start: 0.8345 (ptpt) cc_final: 0.7989 (ptmm) REVERT: A 181 GLU cc_start: 0.8921 (mt-10) cc_final: 0.8228 (mp0) REVERT: A 213 HIS cc_start: 0.8071 (m-70) cc_final: 0.7671 (t70) REVERT: A 265 TRP cc_start: 0.8439 (m100) cc_final: 0.7902 (m-10) REVERT: A 271 ARG cc_start: 0.8602 (mtt180) cc_final: 0.8360 (mtt-85) REVERT: A 300 ASN cc_start: 0.8984 (t0) cc_final: 0.8374 (t0) REVERT: B 98 ASN cc_start: 0.8816 (m-40) cc_final: 0.8353 (m110) REVERT: B 148 LYS cc_start: 0.8320 (ptpp) cc_final: 0.7927 (ptmm) REVERT: B 181 GLU cc_start: 0.8929 (mt-10) cc_final: 0.8099 (mp0) REVERT: B 300 ASN cc_start: 0.8970 (t0) cc_final: 0.8483 (t0) REVERT: C 52 GLU cc_start: 0.9063 (mm-30) cc_final: 0.8798 (mm-30) REVERT: C 98 ASN cc_start: 0.8773 (m-40) cc_final: 0.8268 (m110) REVERT: C 114 GLN cc_start: 0.8691 (OUTLIER) cc_final: 0.8198 (mt0) REVERT: C 128 GLU cc_start: 0.8056 (pm20) cc_final: 0.7781 (pm20) REVERT: C 148 LYS cc_start: 0.8416 (ptpt) cc_final: 0.8054 (ptmm) REVERT: C 181 GLU cc_start: 0.8897 (mt-10) cc_final: 0.8199 (mp0) REVERT: C 265 TRP cc_start: 0.8415 (m100) cc_final: 0.7902 (m-10) REVERT: C 271 ARG cc_start: 0.8609 (mtt180) cc_final: 0.8321 (mtt-85) REVERT: C 300 ASN cc_start: 0.9024 (t0) cc_final: 0.8511 (t0) outliers start: 8 outliers final: 6 residues processed: 98 average time/residue: 1.2830 time to fit residues: 133.4617 Evaluate side-chains 92 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 85 time to evaluate : 0.824 ------------------------------------------------------------------------------- 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 318 LEU Chi-restraints excluded: chain C residue 114 GLN 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: 0.9990 chunk 18 optimal weight: 0.9990 chunk 43 optimal weight: 6.9990 chunk 19 optimal weight: 0.9990 chunk 77 optimal weight: 5.9990 chunk 10 optimal weight: 0.8980 chunk 6 optimal weight: 0.0980 chunk 92 optimal weight: 0.8980 chunk 78 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- 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 = 0.3544 r_free = 0.3544 target = 0.101432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.070780 restraints weight = 12301.901| |-----------------------------------------------------------------------------| r_work (start): 0.2996 rms_B_bonded: 2.52 r_work: 0.2861 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2741 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8774 moved from start: 0.1879 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= 0.126 Angle : 0.482 7.179 11145 Z= 0.253 Chirality : 0.043 0.177 1251 Planarity : 0.004 0.032 1386 Dihedral : 9.130 89.379 1335 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer: Outliers : 1.07 % Allowed : 12.81 % Favored : 86.12 % 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: 0.73 (0.28), residues: 972 helix: 1.47 (0.36), residues: 243 sheet: -0.57 (0.30), residues: 276 loop : 0.86 (0.32), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 164 HIS 0.001 0.000 HIS C 306 PHE 0.014 0.001 PHE C 326 TYR 0.013 0.001 TYR B 90 ARG 0.007 0.001 ARG B 180 Details of bonding type rmsd link_NAG-ASN : bond 0.00092 ( 9) link_NAG-ASN : angle 1.86947 ( 27) hydrogen bonds : bond 0.02716 ( 232) hydrogen bonds : angle 4.89332 ( 579) SS BOND : bond 0.00209 ( 15) SS BOND : angle 0.97878 ( 30) covalent geometry : bond 0.00269 ( 8157) covalent geometry : angle 0.47121 (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 100 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 91 time to evaluate : 0.834 Fit side-chains REVERT: A 128 GLU cc_start: 0.7808 (pm20) cc_final: 0.7523 (pm20) REVERT: A 148 LYS cc_start: 0.8336 (ptpt) cc_final: 0.7968 (ptmm) REVERT: A 181 GLU cc_start: 0.8936 (mt-10) cc_final: 0.8233 (mp0) REVERT: A 213 HIS cc_start: 0.8036 (m-70) cc_final: 0.7655 (t70) REVERT: A 265 TRP cc_start: 0.8442 (m100) cc_final: 0.7916 (m-10) REVERT: A 271 ARG cc_start: 0.8607 (mtt180) cc_final: 0.8363 (mtt-85) REVERT: A 300 ASN cc_start: 0.8963 (t0) cc_final: 0.8357 (t0) REVERT: B 98 ASN cc_start: 0.8825 (m-40) cc_final: 0.8356 (m110) REVERT: B 128 GLU cc_start: 0.7536 (pm20) cc_final: 0.7332 (pm20) REVERT: B 148 LYS cc_start: 0.8305 (ptpp) cc_final: 0.7916 (ptmm) REVERT: B 181 GLU cc_start: 0.8936 (mt-10) cc_final: 0.8288 (mp0) REVERT: B 300 ASN cc_start: 0.8976 (t0) cc_final: 0.8472 (t0) REVERT: C 52 GLU cc_start: 0.9066 (mm-30) cc_final: 0.8791 (mm-30) REVERT: C 98 ASN cc_start: 0.8785 (m-40) cc_final: 0.8274 (m110) REVERT: C 114 GLN cc_start: 0.8711 (OUTLIER) cc_final: 0.8212 (mt0) REVERT: C 148 LYS cc_start: 0.8252 (ptpt) cc_final: 0.7936 (ptmm) REVERT: C 181 GLU cc_start: 0.8902 (mt-10) cc_final: 0.8199 (mp0) REVERT: C 265 TRP cc_start: 0.8433 (m100) cc_final: 0.7919 (m-10) REVERT: C 271 ARG cc_start: 0.8617 (mtt180) cc_final: 0.8316 (mtt-85) REVERT: C 300 ASN cc_start: 0.9029 (t0) cc_final: 0.8502 (t0) outliers start: 9 outliers final: 3 residues processed: 96 average time/residue: 1.2836 time to fit residues: 130.7058 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 : 0.836 ------------------------------------------------------------------------------- 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 318 LEU Chi-restraints excluded: chain C residue 114 GLN 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: 0.7980 chunk 91 optimal weight: 5.9990 chunk 38 optimal weight: 0.9990 chunk 33 optimal weight: 3.9990 chunk 25 optimal weight: 0.0870 chunk 14 optimal weight: 4.9990 chunk 55 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 chunk 32 optimal weight: 5.9990 chunk 73 optimal weight: 0.7980 overall best weight: 0.9362 ------------------------------------------------------------------------------- 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 76 GLN C 237 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.100880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.069870 restraints weight = 12492.827| |-----------------------------------------------------------------------------| r_work (start): 0.2982 rms_B_bonded: 2.57 r_work: 0.2843 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2722 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8801 moved from start: 0.1915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8181 Z= 0.140 Angle : 0.498 7.537 11145 Z= 0.261 Chirality : 0.043 0.178 1251 Planarity : 0.004 0.034 1386 Dihedral : 9.161 87.368 1335 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer: Outliers : 0.71 % Allowed : 13.40 % 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: 0.75 (0.28), residues: 972 helix: 1.48 (0.36), residues: 243 sheet: -0.58 (0.30), residues: 276 loop : 0.90 (0.32), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 259 HIS 0.001 0.000 HIS B 120 PHE 0.010 0.001 PHE B 230 TYR 0.013 0.001 TYR B 90 ARG 0.007 0.001 ARG B 180 Details of bonding type rmsd link_NAG-ASN : bond 0.00080 ( 9) link_NAG-ASN : angle 1.87964 ( 27) hydrogen bonds : bond 0.02739 ( 232) hydrogen bonds : angle 4.90399 ( 579) SS BOND : bond 0.00243 ( 15) SS BOND : angle 0.96426 ( 30) covalent geometry : bond 0.00300 ( 8157) covalent geometry : angle 0.48792 (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 96 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 90 time to evaluate : 0.837 Fit side-chains REVERT: A 128 GLU cc_start: 0.7793 (pm20) cc_final: 0.7509 (pm20) REVERT: A 148 LYS cc_start: 0.8315 (ptpt) cc_final: 0.7943 (ptmm) REVERT: A 181 GLU cc_start: 0.8961 (mt-10) cc_final: 0.8284 (mp0) REVERT: A 213 HIS cc_start: 0.8024 (m-70) cc_final: 0.7676 (t70) REVERT: A 265 TRP cc_start: 0.8465 (m100) cc_final: 0.7908 (m-10) REVERT: A 271 ARG cc_start: 0.8610 (mtt180) cc_final: 0.8366 (mtt-85) REVERT: A 300 ASN cc_start: 0.8969 (t0) cc_final: 0.8363 (t0) REVERT: B 128 GLU cc_start: 0.7545 (pm20) cc_final: 0.7303 (pm20) REVERT: B 148 LYS cc_start: 0.8298 (ptpp) cc_final: 0.7901 (ptmm) REVERT: B 181 GLU cc_start: 0.8931 (mt-10) cc_final: 0.8283 (mp0) REVERT: B 265 TRP cc_start: 0.8193 (m100) cc_final: 0.7855 (m-10) REVERT: B 300 ASN cc_start: 0.8971 (t0) cc_final: 0.8468 (t0) REVERT: C 52 GLU cc_start: 0.9062 (mm-30) cc_final: 0.8785 (mm-30) REVERT: C 98 ASN cc_start: 0.8803 (m-40) cc_final: 0.8289 (m110) REVERT: C 114 GLN cc_start: 0.8740 (OUTLIER) cc_final: 0.8253 (mt0) REVERT: C 128 GLU cc_start: 0.7959 (pm20) cc_final: 0.7728 (pm20) REVERT: C 148 LYS cc_start: 0.8176 (ptpt) cc_final: 0.7939 (ptmm) REVERT: C 181 GLU cc_start: 0.8905 (mt-10) cc_final: 0.8215 (mp0) REVERT: C 265 TRP cc_start: 0.8432 (m100) cc_final: 0.7919 (m-10) REVERT: C 271 ARG cc_start: 0.8643 (mtt180) cc_final: 0.8324 (mtt-85) REVERT: C 300 ASN cc_start: 0.9035 (t0) cc_final: 0.8508 (t0) outliers start: 6 outliers final: 4 residues processed: 94 average time/residue: 1.3309 time to fit residues: 132.3788 Evaluate side-chains 91 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 86 time to evaluate : 0.850 ------------------------------------------------------------------------------- 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 114 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 2 optimal weight: 0.2980 chunk 48 optimal weight: 0.9980 chunk 51 optimal weight: 0.9980 chunk 45 optimal weight: 3.9990 chunk 71 optimal weight: 4.9990 chunk 14 optimal weight: 4.9990 chunk 60 optimal weight: 0.6980 chunk 37 optimal weight: 3.9990 chunk 24 optimal weight: 6.9990 chunk 20 optimal weight: 0.7980 chunk 42 optimal weight: 5.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3547 r_free = 0.3547 target = 0.101542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.070885 restraints weight = 12235.978| |-----------------------------------------------------------------------------| r_work (start): 0.2995 rms_B_bonded: 2.53 r_work: 0.2859 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2739 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8778 moved from start: 0.1972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8181 Z= 0.125 Angle : 0.491 7.797 11145 Z= 0.257 Chirality : 0.043 0.170 1251 Planarity : 0.004 0.032 1386 Dihedral : 9.048 86.916 1335 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 0.83 % Allowed : 13.29 % 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: 0.74 (0.29), residues: 972 helix: 1.49 (0.36), residues: 243 sheet: -0.63 (0.30), residues: 276 loop : 0.91 (0.32), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 259 HIS 0.001 0.000 HIS C 306 PHE 0.010 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 0.00086 ( 9) link_NAG-ASN : angle 1.79581 ( 27) hydrogen bonds : bond 0.02629 ( 232) hydrogen bonds : angle 4.86176 ( 579) SS BOND : bond 0.00219 ( 15) SS BOND : angle 0.93211 ( 30) covalent geometry : bond 0.00266 ( 8157) covalent geometry : angle 0.48156 (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 96 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 89 time to evaluate : 0.865 Fit side-chains REVERT: A 76 GLN cc_start: 0.8595 (tt0) cc_final: 0.8160 (tp40) REVERT: A 148 LYS cc_start: 0.8281 (ptpt) cc_final: 0.7903 (ptmm) REVERT: A 181 GLU cc_start: 0.8945 (mt-10) cc_final: 0.8268 (mp0) REVERT: A 213 HIS cc_start: 0.7966 (m-70) cc_final: 0.7667 (t70) REVERT: A 265 TRP cc_start: 0.8450 (m100) cc_final: 0.7902 (m-10) REVERT: A 271 ARG cc_start: 0.8592 (mtt180) cc_final: 0.8344 (mtt-85) REVERT: A 300 ASN cc_start: 0.8959 (t0) cc_final: 0.8351 (t0) REVERT: B 128 GLU cc_start: 0.7537 (pm20) cc_final: 0.7239 (pm20) REVERT: B 148 LYS cc_start: 0.8256 (ptpp) cc_final: 0.7864 (ptmm) REVERT: B 181 GLU cc_start: 0.8934 (mt-10) cc_final: 0.8281 (mp0) REVERT: B 265 TRP cc_start: 0.8249 (m100) cc_final: 0.7873 (m-10) REVERT: B 300 ASN cc_start: 0.8968 (t0) cc_final: 0.8468 (t0) REVERT: C 52 GLU cc_start: 0.9054 (mm-30) cc_final: 0.8773 (mm-30) REVERT: C 98 ASN cc_start: 0.8798 (m-40) cc_final: 0.8279 (m110) REVERT: C 128 GLU cc_start: 0.8024 (pm20) cc_final: 0.7805 (pm20) REVERT: C 148 LYS cc_start: 0.8131 (ptpt) cc_final: 0.7901 (ptmm) REVERT: C 181 GLU cc_start: 0.8899 (mt-10) cc_final: 0.8202 (mp0) REVERT: C 265 TRP cc_start: 0.8414 (m100) cc_final: 0.7923 (m-10) REVERT: C 271 ARG cc_start: 0.8629 (mtt180) cc_final: 0.8305 (mtt-85) REVERT: C 300 ASN cc_start: 0.9023 (t0) cc_final: 0.8498 (t0) outliers start: 7 outliers final: 5 residues processed: 94 average time/residue: 1.2297 time to fit residues: 123.0504 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 : 0.860 ------------------------------------------------------------------------------- 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 318 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 39 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 93 optimal weight: 5.9990 chunk 26 optimal weight: 0.9980 chunk 29 optimal weight: 7.9990 chunk 49 optimal weight: 0.0470 chunk 63 optimal weight: 5.9990 chunk 7 optimal weight: 0.7980 chunk 94 optimal weight: 0.6980 chunk 72 optimal weight: 0.0370 chunk 66 optimal weight: 1.9990 overall best weight: 0.5156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 76 GLN C 237 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.102293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.071787 restraints weight = 12275.966| |-----------------------------------------------------------------------------| r_work (start): 0.3016 rms_B_bonded: 2.54 r_work: 0.2882 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2762 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8762 moved from start: 0.2062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 8181 Z= 0.109 Angle : 0.487 7.446 11145 Z= 0.254 Chirality : 0.043 0.165 1251 Planarity : 0.004 0.034 1386 Dihedral : 8.889 86.270 1335 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % 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: 0.77 (0.29), residues: 972 helix: 1.71 (0.36), residues: 237 sheet: -0.63 (0.30), residues: 276 loop : 0.84 (0.32), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 259 HIS 0.002 0.000 HIS A 306 PHE 0.011 0.001 PHE C 326 TYR 0.012 0.001 TYR B 90 ARG 0.008 0.001 ARG A 180 Details of bonding type rmsd link_NAG-ASN : bond 0.00109 ( 9) link_NAG-ASN : angle 1.72977 ( 27) hydrogen bonds : bond 0.02623 ( 232) hydrogen bonds : angle 4.82394 ( 579) SS BOND : bond 0.00207 ( 15) SS BOND : angle 1.05617 ( 30) covalent geometry : bond 0.00232 ( 8157) covalent geometry : angle 0.47791 (11088) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9835.87 seconds wall clock time: 167 minutes 54.72 seconds (10074.72 seconds total)