Starting phenix.real_space_refine on Sun May 11 09:59:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b73_44299/05_2025/9b73_44299.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b73_44299/05_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_44299/05_2025/9b73_44299.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b73_44299/05_2025/9b73_44299.map" model { file = "/net/cci-nas-00/data/ceres_data/9b73_44299/05_2025/9b73_44299.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b73_44299/05_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-5687/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: 5.35, per 1000 atoms: 0.67 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: 2.36 Conformation dependent library (CDL) restraints added in 966.1 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: 0.76 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: 2.07 Time building geometry restraints manager: 2.70 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: 0.860 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: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 21.990 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.040 ------------------------------------------------------------------------------- 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 : 0.949 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: 1.2722 time to fit residues: 153.5354 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 : 0.946 ------------------------------------------------------------------------------- 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 = 0.100325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.069581 restraints weight = 12203.612| |-----------------------------------------------------------------------------| r_work (start): 0.2972 rms_B_bonded: 2.48 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: 0.8783 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 : 1.007 Fit side-chains REVERT: A 148 LYS cc_start: 0.8323 (ptpt) cc_final: 0.8008 (ptmm) REVERT: A 181 GLU cc_start: 0.8937 (mt-10) cc_final: 0.8317 (mp0) REVERT: A 271 ARG cc_start: 0.8603 (mtt180) cc_final: 0.8349 (mtt-85) REVERT: A 300 ASN cc_start: 0.8953 (t0) cc_final: 0.8449 (t0) REVERT: B 52 GLU cc_start: 0.9102 (mm-30) cc_final: 0.8890 (mm-30) REVERT: B 76 GLN cc_start: 0.8608 (tt0) cc_final: 0.7952 (tm-30) REVERT: B 148 LYS cc_start: 0.8221 (ptpp) cc_final: 0.7834 (ptmm) REVERT: B 181 GLU cc_start: 0.8897 (mt-10) cc_final: 0.8073 (mp0) REVERT: B 271 ARG cc_start: 0.8559 (mtt90) cc_final: 0.8257 (mtt-85) REVERT: B 300 ASN cc_start: 0.8944 (t0) cc_final: 0.8479 (t0) REVERT: C 148 LYS cc_start: 0.8442 (ptpt) cc_final: 0.8149 (ptmm) REVERT: C 181 GLU cc_start: 0.8893 (mt-10) cc_final: 0.8162 (mp0) REVERT: C 271 ARG cc_start: 0.8640 (mtt180) cc_final: 0.8360 (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: 1.1812 time to fit residues: 134.4986 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 : 0.870 ------------------------------------------------------------------------------- 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: 6.9990 chunk 6 optimal weight: 0.1980 chunk 54 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 chunk 95 optimal weight: 5.9990 chunk 32 optimal weight: 6.9990 chunk 44 optimal weight: 6.9990 chunk 94 optimal weight: 0.9980 chunk 71 optimal weight: 4.9990 chunk 67 optimal weight: 2.9990 chunk 59 optimal weight: 5.9990 overall best weight: 2.4386 ------------------------------------------------------------------------------- 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** C 76 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.097131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.065316 restraints weight = 12295.171| |-----------------------------------------------------------------------------| r_work (start): 0.2882 rms_B_bonded: 2.52 r_work: 0.2738 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2615 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8836 moved from start: 0.1343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 8181 Z= 0.271 Angle : 0.623 11.051 11145 Z= 0.313 Chirality : 0.046 0.183 1251 Planarity : 0.004 0.036 1386 Dihedral : 12.186 89.809 1335 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 1.30 % Allowed : 8.19 % Favored : 90.51 % 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: 0.49 (0.28), residues: 972 helix: 0.81 (0.34), residues: 243 sheet: -0.06 (0.30), residues: 291 loop : 0.54 (0.32), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP C 47 HIS 0.003 0.001 HIS B 120 PHE 0.014 0.002 PHE B 230 TYR 0.015 0.002 TYR A 90 ARG 0.005 0.001 ARG A 268 Details of bonding type rmsd link_NAG-ASN : bond 0.00206 ( 9) link_NAG-ASN : angle 2.70988 ( 27) hydrogen bonds : bond 0.03931 ( 232) hydrogen bonds : angle 5.25185 ( 579) SS BOND : bond 0.00302 ( 15) SS BOND : angle 1.06077 ( 30) covalent geometry : bond 0.00584 ( 8157) covalent geometry : angle 0.60776 (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 106 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 95 time to evaluate : 0.956 Fit side-chains REVERT: A 148 LYS cc_start: 0.8420 (ptpt) cc_final: 0.8047 (ptmm) REVERT: A 181 GLU cc_start: 0.8923 (mt-10) cc_final: 0.8201 (mp0) REVERT: A 271 ARG cc_start: 0.8638 (mtt180) cc_final: 0.8352 (mtt-85) REVERT: A 300 ASN cc_start: 0.8978 (t0) cc_final: 0.8407 (t0) REVERT: B 52 GLU cc_start: 0.9122 (mm-30) cc_final: 0.8903 (mm-30) REVERT: B 148 LYS cc_start: 0.8294 (ptpp) cc_final: 0.7854 (ptmm) REVERT: B 180 ARG cc_start: 0.8733 (ptt-90) cc_final: 0.8456 (ptt-90) REVERT: B 181 GLU cc_start: 0.8896 (mt-10) cc_final: 0.8102 (mp0) REVERT: B 258 ASP cc_start: 0.9136 (m-30) cc_final: 0.8870 (m-30) REVERT: B 271 ARG cc_start: 0.8530 (mtt90) cc_final: 0.8199 (mtt-85) REVERT: B 300 ASN cc_start: 0.8971 (t0) cc_final: 0.8484 (t0) REVERT: C 148 LYS cc_start: 0.8508 (ptpt) cc_final: 0.8167 (ptmm) REVERT: C 181 GLU cc_start: 0.8893 (mt-10) cc_final: 0.8172 (mp0) REVERT: C 271 ARG cc_start: 0.8686 (mtt180) cc_final: 0.8363 (mtt-85) REVERT: C 300 ASN cc_start: 0.9034 (t0) cc_final: 0.8517 (t0) outliers start: 11 outliers final: 7 residues processed: 102 average time/residue: 1.2525 time to fit residues: 135.5840 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 : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 285 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: 0.9980 chunk 28 optimal weight: 0.8980 chunk 26 optimal weight: 2.9990 chunk 85 optimal weight: 0.0060 chunk 94 optimal weight: 0.7980 chunk 70 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 chunk 34 optimal weight: 0.0010 chunk 93 optimal weight: 5.9990 chunk 73 optimal weight: 4.9990 chunk 30 optimal weight: 0.7980 overall best weight: 0.5002 ------------------------------------------------------------------------------- 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 213 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.100951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.070355 restraints weight = 12251.103| |-----------------------------------------------------------------------------| r_work (start): 0.2989 rms_B_bonded: 2.51 r_work: 0.2850 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2729 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8793 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 : 0.002 0.032 8181 Z= 0.115 Angle : 0.523 8.865 11145 Z= 0.265 Chirality : 0.043 0.136 1251 Planarity : 0.003 0.030 1386 Dihedral : 9.888 87.333 1335 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 1.30 % Allowed : 9.49 % Favored : 89.21 % 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: 0.39 (0.28), residues: 972 helix: 0.97 (0.34), residues: 243 sheet: -0.64 (0.30), residues: 270 loop : 0.67 (0.31), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 164 HIS 0.003 0.000 HIS C 306 PHE 0.010 0.001 PHE B 230 TYR 0.016 0.001 TYR C 90 ARG 0.006 0.001 ARG C 180 Details of bonding type rmsd link_NAG-ASN : bond 0.00354 ( 9) link_NAG-ASN : angle 3.33790 ( 27) hydrogen bonds : bond 0.03048 ( 232) hydrogen bonds : angle 4.99668 ( 579) SS BOND : bond 0.00201 ( 15) SS BOND : angle 0.88413 ( 30) covalent geometry : bond 0.00243 ( 8157) covalent geometry : angle 0.49583 (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: 11 poor density : 99 time to evaluate : 0.928 Fit side-chains REVERT: A 148 LYS cc_start: 0.8347 (ptpt) cc_final: 0.7991 (ptmm) REVERT: A 181 GLU cc_start: 0.8937 (mt-10) cc_final: 0.8251 (mp0) REVERT: A 271 ARG cc_start: 0.8605 (mtt180) cc_final: 0.8363 (mtt-85) REVERT: A 300 ASN cc_start: 0.8944 (t0) cc_final: 0.8356 (t0) REVERT: B 52 GLU cc_start: 0.9112 (mm-30) cc_final: 0.8891 (mm-30) REVERT: B 148 LYS cc_start: 0.8300 (ptpp) cc_final: 0.7873 (ptmm) REVERT: B 180 ARG cc_start: 0.8748 (ptt-90) cc_final: 0.8460 (ptt-90) REVERT: B 181 GLU cc_start: 0.8899 (mt-10) cc_final: 0.8118 (mp0) REVERT: B 271 ARG cc_start: 0.8489 (mtt90) cc_final: 0.8170 (mtt-85) REVERT: B 300 ASN cc_start: 0.8991 (t0) cc_final: 0.8502 (t0) REVERT: C 148 LYS cc_start: 0.8479 (ptpt) cc_final: 0.8143 (ptmm) REVERT: C 181 GLU cc_start: 0.8894 (mt-10) cc_final: 0.8134 (mp0) REVERT: C 271 ARG cc_start: 0.8619 (mtt180) cc_final: 0.8344 (mtt-85) REVERT: C 300 ASN cc_start: 0.9027 (t0) cc_final: 0.8527 (t0) outliers start: 11 outliers final: 5 residues processed: 105 average time/residue: 1.3064 time to fit residues: 145.1508 Evaluate side-chains 88 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 83 time to evaluate : 0.917 ------------------------------------------------------------------------------- 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 318 LEU Chi-restraints excluded: chain C residue 285 LEU 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: 0.0670 chunk 43 optimal weight: 0.7980 chunk 5 optimal weight: 7.9990 chunk 72 optimal weight: 5.9990 chunk 76 optimal weight: 2.9990 chunk 61 optimal weight: 0.0050 chunk 20 optimal weight: 0.9980 chunk 53 optimal weight: 0.0060 chunk 46 optimal weight: 5.9990 chunk 84 optimal weight: 5.9990 chunk 81 optimal weight: 0.0980 overall best weight: 0.1948 ------------------------------------------------------------------------------- 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 = 0.3573 r_free = 0.3573 target = 0.103166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.073149 restraints weight = 12241.686| |-----------------------------------------------------------------------------| r_work (start): 0.3046 rms_B_bonded: 2.51 r_work: 0.2913 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2795 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8744 moved from start: 0.1843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8181 Z= 0.093 Angle : 0.456 4.530 11145 Z= 0.240 Chirality : 0.042 0.137 1251 Planarity : 0.003 0.029 1386 Dihedral : 9.223 88.668 1335 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer: Outliers : 1.54 % Allowed : 10.32 % 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: 0.44 (0.28), residues: 972 helix: 1.21 (0.35), residues: 243 sheet: -0.63 (0.30), residues: 276 loop : 0.61 (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 A 306 PHE 0.007 0.001 PHE A 293 TYR 0.014 0.001 TYR C 90 ARG 0.006 0.000 ARG C 180 Details of bonding type rmsd link_NAG-ASN : bond 0.00227 ( 9) link_NAG-ASN : angle 1.93629 ( 27) hydrogen bonds : bond 0.02804 ( 232) hydrogen bonds : angle 4.88759 ( 579) SS BOND : bond 0.00239 ( 15) SS BOND : angle 0.72248 ( 30) covalent geometry : bond 0.00192 ( 8157) covalent geometry : angle 0.44509 (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 113 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 100 time to evaluate : 0.948 Fit side-chains revert: symmetry clash REVERT: A 128 GLU cc_start: 0.7725 (pm20) cc_final: 0.7439 (pm20) REVERT: A 148 LYS cc_start: 0.8334 (ptpt) cc_final: 0.7992 (ptmm) REVERT: A 181 GLU cc_start: 0.8910 (mt-10) cc_final: 0.8221 (mp0) REVERT: A 265 TRP cc_start: 0.8402 (m100) cc_final: 0.7894 (m-10) REVERT: A 271 ARG cc_start: 0.8590 (mtt180) cc_final: 0.8368 (mtt-85) REVERT: A 300 ASN cc_start: 0.8978 (t0) cc_final: 0.8375 (t0) REVERT: B 52 GLU cc_start: 0.9101 (mm-30) cc_final: 0.8887 (mm-30) REVERT: B 98 ASN cc_start: 0.8778 (m-40) cc_final: 0.8329 (m110) REVERT: B 148 LYS cc_start: 0.8317 (ptpp) cc_final: 0.7910 (ptmm) REVERT: B 180 ARG cc_start: 0.8740 (ptt-90) cc_final: 0.8438 (ptt-90) REVERT: B 181 GLU cc_start: 0.8916 (mt-10) cc_final: 0.8099 (mp0) REVERT: B 300 ASN cc_start: 0.8977 (t0) cc_final: 0.8500 (t0) REVERT: C 98 ASN cc_start: 0.8752 (m-40) cc_final: 0.8257 (m110) REVERT: C 128 GLU cc_start: 0.8031 (pm20) cc_final: 0.7795 (pm20) REVERT: C 148 LYS cc_start: 0.8426 (ptpt) cc_final: 0.8076 (ptmm) REVERT: C 149 CYS cc_start: 0.6647 (t) cc_final: 0.6435 (t) REVERT: C 181 GLU cc_start: 0.8903 (mt-10) cc_final: 0.8219 (mp0) REVERT: C 265 TRP cc_start: 0.8405 (m100) cc_final: 0.7898 (m-10) REVERT: C 271 ARG cc_start: 0.8568 (mtt180) cc_final: 0.8318 (mtt-85) REVERT: C 300 ASN cc_start: 0.8999 (t0) cc_final: 0.8507 (t0) outliers start: 13 outliers final: 1 residues processed: 106 average time/residue: 1.1681 time to fit residues: 131.8183 Evaluate side-chains 89 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 88 time to evaluate : 1.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 47 optimal weight: 1.9990 chunk 12 optimal weight: 4.9990 chunk 43 optimal weight: 3.9990 chunk 59 optimal weight: 5.9990 chunk 68 optimal weight: 2.9990 chunk 41 optimal weight: 0.1980 chunk 89 optimal weight: 0.9980 chunk 74 optimal weight: 1.9990 chunk 72 optimal weight: 0.5980 chunk 20 optimal weight: 0.5980 chunk 11 optimal weight: 5.9990 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 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 = 0.3539 r_free = 0.3539 target = 0.101020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.070270 restraints weight = 12262.895| |-----------------------------------------------------------------------------| r_work (start): 0.2991 rms_B_bonded: 2.54 r_work: 0.2855 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2735 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8795 moved from start: 0.1798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8181 Z= 0.133 Angle : 0.483 5.934 11145 Z= 0.254 Chirality : 0.043 0.137 1251 Planarity : 0.003 0.033 1386 Dihedral : 9.221 88.927 1335 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer: Outliers : 1.19 % Allowed : 11.86 % Favored : 86.95 % 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: 1.37 (0.35), residues: 243 sheet: -0.53 (0.30), residues: 276 loop : 0.73 (0.31), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 47 HIS 0.002 0.001 HIS C 120 PHE 0.012 0.001 PHE C 326 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 0.00122 ( 9) link_NAG-ASN : angle 2.03671 ( 27) hydrogen bonds : bond 0.02793 ( 232) hydrogen bonds : angle 4.89847 ( 579) SS BOND : bond 0.00209 ( 15) SS BOND : angle 0.77811 ( 30) covalent geometry : bond 0.00284 ( 8157) covalent geometry : angle 0.47184 (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: 10 poor density : 92 time to evaluate : 0.887 Fit side-chains REVERT: A 128 GLU cc_start: 0.7699 (pm20) cc_final: 0.7435 (pm20) REVERT: A 148 LYS cc_start: 0.8373 (ptpt) cc_final: 0.8020 (ptmm) REVERT: A 181 GLU cc_start: 0.8937 (mt-10) cc_final: 0.8260 (mp0) REVERT: A 265 TRP cc_start: 0.8449 (m100) cc_final: 0.7917 (m-10) REVERT: A 271 ARG cc_start: 0.8622 (mtt180) cc_final: 0.8387 (mtt-85) REVERT: A 300 ASN cc_start: 0.8982 (t0) cc_final: 0.8389 (t0) REVERT: B 52 GLU cc_start: 0.9109 (mm-30) cc_final: 0.8891 (mm-30) REVERT: B 98 ASN cc_start: 0.8794 (m-40) cc_final: 0.8341 (m110) REVERT: B 148 LYS cc_start: 0.8347 (ptpp) cc_final: 0.7948 (ptmm) REVERT: B 180 ARG cc_start: 0.8764 (ptt-90) cc_final: 0.8458 (ptt-90) REVERT: B 181 GLU cc_start: 0.8930 (mt-10) cc_final: 0.8134 (mp0) REVERT: B 300 ASN cc_start: 0.8975 (t0) cc_final: 0.8486 (t0) REVERT: C 98 ASN cc_start: 0.8784 (m-40) cc_final: 0.8290 (m110) REVERT: C 128 GLU cc_start: 0.8055 (pm20) cc_final: 0.7800 (pm20) REVERT: C 148 LYS cc_start: 0.8445 (ptpt) cc_final: 0.8086 (ptmm) REVERT: C 149 CYS cc_start: 0.6715 (t) cc_final: 0.6514 (t) REVERT: C 181 GLU cc_start: 0.8908 (mt-10) cc_final: 0.8233 (mp0) REVERT: C 265 TRP cc_start: 0.8447 (m100) cc_final: 0.7948 (m-10) REVERT: C 271 ARG cc_start: 0.8608 (mtt180) cc_final: 0.8332 (mtt-85) REVERT: C 300 ASN cc_start: 0.9023 (t0) cc_final: 0.8523 (t0) outliers start: 10 outliers final: 4 residues processed: 99 average time/residue: 1.1726 time to fit residues: 123.5739 Evaluate side-chains 88 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 84 time to evaluate : 0.929 ------------------------------------------------------------------------------- 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 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: 0.0270 chunk 94 optimal weight: 0.7980 chunk 17 optimal weight: 6.9990 chunk 72 optimal weight: 0.8980 chunk 89 optimal weight: 4.9990 chunk 76 optimal weight: 0.6980 chunk 16 optimal weight: 0.4980 chunk 26 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 51 optimal weight: 3.9990 overall best weight: 0.5838 ------------------------------------------------------------------------------- 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 = 0.3556 r_free = 0.3556 target = 0.101947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.071508 restraints weight = 12272.090| |-----------------------------------------------------------------------------| r_work (start): 0.3011 rms_B_bonded: 2.55 r_work: 0.2877 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2757 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8768 moved from start: 0.1896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 8181 Z= 0.110 Angle : 0.468 6.290 11145 Z= 0.248 Chirality : 0.043 0.167 1251 Planarity : 0.003 0.032 1386 Dihedral : 9.140 89.809 1335 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 1.07 % Allowed : 12.69 % Favored : 86.24 % 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: 0.62 (0.28), residues: 972 helix: 1.42 (0.36), residues: 243 sheet: -0.62 (0.30), residues: 276 loop : 0.76 (0.31), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 164 HIS 0.002 0.000 HIS C 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 0.00116 ( 9) link_NAG-ASN : angle 1.85432 ( 27) hydrogen bonds : bond 0.02713 ( 232) hydrogen bonds : angle 4.87273 ( 579) SS BOND : bond 0.00204 ( 15) SS BOND : angle 0.79894 ( 30) covalent geometry : bond 0.00232 ( 8157) covalent geometry : angle 0.45847 (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 98 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 89 time to evaluate : 1.025 Fit side-chains REVERT: A 128 GLU cc_start: 0.7732 (pm20) cc_final: 0.7473 (pm20) REVERT: A 148 LYS cc_start: 0.8349 (ptpt) cc_final: 0.7994 (ptmm) REVERT: A 181 GLU cc_start: 0.8934 (mt-10) cc_final: 0.8213 (mp0) REVERT: A 265 TRP cc_start: 0.8432 (m100) cc_final: 0.7884 (m-10) REVERT: A 271 ARG cc_start: 0.8602 (mtt180) cc_final: 0.8368 (mtt-85) REVERT: A 300 ASN cc_start: 0.8984 (t0) cc_final: 0.8371 (t0) REVERT: B 52 GLU cc_start: 0.9096 (mm-30) cc_final: 0.8867 (mm-30) REVERT: B 98 ASN cc_start: 0.8801 (m-40) cc_final: 0.8346 (m110) REVERT: B 148 LYS cc_start: 0.8317 (ptpp) cc_final: 0.7924 (ptmm) REVERT: B 180 ARG cc_start: 0.8747 (ptt-90) cc_final: 0.8429 (ptt-90) REVERT: B 181 GLU cc_start: 0.8920 (mt-10) cc_final: 0.8124 (mp0) REVERT: B 271 ARG cc_start: 0.8620 (mtt-85) cc_final: 0.8419 (mtt-85) REVERT: B 300 ASN cc_start: 0.8973 (t0) cc_final: 0.8474 (t0) REVERT: C 52 GLU cc_start: 0.9059 (mm-30) cc_final: 0.8755 (mm-30) REVERT: C 98 ASN cc_start: 0.8775 (m-40) cc_final: 0.8275 (m110) REVERT: C 128 GLU cc_start: 0.8058 (pm20) cc_final: 0.7794 (pm20) REVERT: C 148 LYS cc_start: 0.8373 (ptpt) cc_final: 0.8015 (ptmm) REVERT: C 181 GLU cc_start: 0.8906 (mt-10) cc_final: 0.8211 (mp0) REVERT: C 265 TRP cc_start: 0.8448 (m100) cc_final: 0.7962 (m-10) REVERT: C 271 ARG cc_start: 0.8604 (mtt180) cc_final: 0.8316 (mtt-85) REVERT: C 300 ASN cc_start: 0.9027 (t0) cc_final: 0.8507 (t0) outliers start: 9 outliers final: 8 residues processed: 96 average time/residue: 1.1605 time to fit residues: 118.7008 Evaluate side-chains 93 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 85 time to evaluate : 0.866 ------------------------------------------------------------------------------- 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 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: 0.0980 chunk 18 optimal weight: 4.9990 chunk 43 optimal weight: 0.0270 chunk 19 optimal weight: 0.3980 chunk 77 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 6 optimal weight: 0.7980 chunk 92 optimal weight: 1.9990 chunk 78 optimal weight: 0.9990 chunk 56 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 overall best weight: 0.4640 ------------------------------------------------------------------------------- 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 = 0.3563 r_free = 0.3563 target = 0.102430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.071976 restraints weight = 12330.595| |-----------------------------------------------------------------------------| r_work (start): 0.3027 rms_B_bonded: 2.52 r_work: 0.2893 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2773 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8764 moved from start: 0.1990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8181 Z= 0.102 Angle : 0.469 7.730 11145 Z= 0.245 Chirality : 0.043 0.166 1251 Planarity : 0.003 0.032 1386 Dihedral : 9.047 88.420 1335 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 1.19 % Allowed : 12.69 % 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: 0.67 (0.28), residues: 972 helix: 1.49 (0.36), residues: 243 sheet: -0.63 (0.30), residues: 276 loop : 0.80 (0.31), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 164 HIS 0.002 0.000 HIS A 306 PHE 0.011 0.001 PHE C 326 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 0.00112 ( 9) link_NAG-ASN : angle 1.77578 ( 27) hydrogen bonds : bond 0.02612 ( 232) hydrogen bonds : angle 4.82610 ( 579) SS BOND : bond 0.00216 ( 15) SS BOND : angle 0.92536 ( 30) covalent geometry : bond 0.00216 ( 8157) covalent geometry : angle 0.45907 (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: 10 poor density : 90 time to evaluate : 0.961 Fit side-chains REVERT: A 76 GLN cc_start: 0.8527 (tt0) cc_final: 0.8117 (tp40) REVERT: A 128 GLU cc_start: 0.7780 (pm20) cc_final: 0.7545 (pm20) REVERT: A 148 LYS cc_start: 0.8327 (ptpt) cc_final: 0.7971 (ptmm) REVERT: A 181 GLU cc_start: 0.8936 (mt-10) cc_final: 0.8240 (mp0) REVERT: A 265 TRP cc_start: 0.8420 (m100) cc_final: 0.7891 (m-10) REVERT: A 271 ARG cc_start: 0.8596 (mtt180) cc_final: 0.8375 (mtt-85) REVERT: A 300 ASN cc_start: 0.8995 (t0) cc_final: 0.8369 (t0) REVERT: B 52 GLU cc_start: 0.9082 (mm-30) cc_final: 0.8853 (mm-30) REVERT: B 98 ASN cc_start: 0.8799 (m-40) cc_final: 0.8352 (m110) REVERT: B 148 LYS cc_start: 0.8306 (ptpp) cc_final: 0.7925 (ptmm) REVERT: B 181 GLU cc_start: 0.8932 (mt-10) cc_final: 0.8106 (mp0) REVERT: B 265 TRP cc_start: 0.8197 (m100) cc_final: 0.7863 (m-10) REVERT: B 300 ASN cc_start: 0.8965 (t0) cc_final: 0.8474 (t0) REVERT: C 52 GLU cc_start: 0.9053 (mm-30) cc_final: 0.8469 (mp0) REVERT: C 98 ASN cc_start: 0.8771 (m-40) cc_final: 0.8286 (m110) REVERT: C 148 LYS cc_start: 0.8149 (ptpt) cc_final: 0.7919 (ptmm) REVERT: C 181 GLU cc_start: 0.8902 (mt-10) cc_final: 0.8205 (mp0) REVERT: C 265 TRP cc_start: 0.8408 (m100) cc_final: 0.7898 (m-10) REVERT: C 271 ARG cc_start: 0.8604 (mtt180) cc_final: 0.8327 (mtt-85) REVERT: C 300 ASN cc_start: 0.9024 (t0) cc_final: 0.8510 (t0) outliers start: 10 outliers final: 6 residues processed: 96 average time/residue: 1.1963 time to fit residues: 122.2380 Evaluate side-chains 94 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 88 time to evaluate : 0.928 ------------------------------------------------------------------------------- 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 20 optimal weight: 0.9990 chunk 8 optimal weight: 0.9980 chunk 91 optimal weight: 4.9990 chunk 38 optimal weight: 0.6980 chunk 33 optimal weight: 4.9990 chunk 25 optimal weight: 0.0980 chunk 14 optimal weight: 4.9990 chunk 55 optimal weight: 3.9990 chunk 37 optimal weight: 0.9980 chunk 32 optimal weight: 6.9990 chunk 73 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3554 r_free = 0.3554 target = 0.101797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.071125 restraints weight = 12512.019| |-----------------------------------------------------------------------------| r_work (start): 0.3004 rms_B_bonded: 2.56 r_work: 0.2869 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2750 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8775 moved from start: 0.2007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8181 Z= 0.122 Angle : 0.484 7.542 11145 Z= 0.254 Chirality : 0.043 0.161 1251 Planarity : 0.003 0.033 1386 Dihedral : 9.065 88.392 1335 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer: Outliers : 1.07 % Allowed : 12.93 % 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: 0.74 (0.28), residues: 972 helix: 1.53 (0.36), residues: 243 sheet: -0.65 (0.32), residues: 255 loop : 0.83 (0.31), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 259 HIS 0.001 0.000 HIS B 306 PHE 0.009 0.001 PHE B 230 TYR 0.013 0.001 TYR B 90 ARG 0.008 0.001 ARG A 180 Details of bonding type rmsd link_NAG-ASN : bond 0.00087 ( 9) link_NAG-ASN : angle 1.79028 ( 27) hydrogen bonds : bond 0.02671 ( 232) hydrogen bonds : angle 4.83453 ( 579) SS BOND : bond 0.00216 ( 15) SS BOND : angle 0.96352 ( 30) covalent geometry : bond 0.00260 ( 8157) covalent geometry : angle 0.47437 (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 103 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 94 time to evaluate : 1.013 Fit side-chains REVERT: A 76 GLN cc_start: 0.8557 (tt0) cc_final: 0.8154 (tp40) REVERT: A 128 GLU cc_start: 0.7791 (pm20) cc_final: 0.7554 (pm20) REVERT: A 148 LYS cc_start: 0.8305 (ptpt) cc_final: 0.7945 (ptmm) REVERT: A 181 GLU cc_start: 0.8943 (mt-10) cc_final: 0.8247 (mp0) REVERT: A 265 TRP cc_start: 0.8433 (m100) cc_final: 0.7906 (m-10) REVERT: A 271 ARG cc_start: 0.8605 (mtt180) cc_final: 0.8370 (mtt-85) REVERT: A 300 ASN cc_start: 0.9002 (t0) cc_final: 0.8378 (t0) REVERT: B 52 GLU cc_start: 0.9083 (mm-30) cc_final: 0.8837 (mm-30) REVERT: B 98 ASN cc_start: 0.8810 (m-40) cc_final: 0.8353 (m110) REVERT: B 148 LYS cc_start: 0.8287 (ptpp) cc_final: 0.7905 (ptmm) REVERT: B 180 ARG cc_start: 0.8717 (ptt-90) cc_final: 0.8434 (ptt-90) REVERT: B 181 GLU cc_start: 0.8936 (mt-10) cc_final: 0.8112 (mp0) REVERT: B 265 TRP cc_start: 0.8233 (m100) cc_final: 0.7863 (m-10) REVERT: B 300 ASN cc_start: 0.8966 (t0) cc_final: 0.8476 (t0) REVERT: C 52 GLU cc_start: 0.9054 (mm-30) cc_final: 0.8466 (mp0) REVERT: C 98 ASN cc_start: 0.8781 (m-40) cc_final: 0.8295 (m110) REVERT: C 148 LYS cc_start: 0.8134 (ptpt) cc_final: 0.7909 (ptmm) REVERT: C 181 GLU cc_start: 0.8908 (mt-10) cc_final: 0.8204 (mp0) REVERT: C 265 TRP cc_start: 0.8442 (m100) cc_final: 0.7926 (m-10) REVERT: C 271 ARG cc_start: 0.8610 (mtt180) cc_final: 0.8314 (mtt-85) REVERT: C 300 ASN cc_start: 0.9024 (t0) cc_final: 0.8504 (t0) outliers start: 9 outliers final: 7 residues processed: 101 average time/residue: 1.1989 time to fit residues: 129.0546 Evaluate side-chains 95 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 88 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 VAL 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 213 HIS Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain C residue 285 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 2 optimal weight: 0.6980 chunk 48 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 71 optimal weight: 4.9990 chunk 14 optimal weight: 4.9990 chunk 60 optimal weight: 5.9990 chunk 37 optimal weight: 0.2980 chunk 24 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 42 optimal weight: 6.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- 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 = 0.3535 r_free = 0.3535 target = 0.100775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.069804 restraints weight = 12234.360| |-----------------------------------------------------------------------------| r_work (start): 0.2981 rms_B_bonded: 2.53 r_work: 0.2844 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2724 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8787 moved from start: 0.1967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8181 Z= 0.143 Angle : 0.500 7.697 11145 Z= 0.260 Chirality : 0.043 0.157 1251 Planarity : 0.003 0.033 1386 Dihedral : 9.177 89.467 1335 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % 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: 0.84 (0.29), residues: 972 helix: 1.53 (0.36), residues: 243 sheet: -0.58 (0.30), residues: 282 loop : 1.03 (0.32), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 259 HIS 0.002 0.001 HIS B 120 PHE 0.010 0.001 PHE B 230 TYR 0.012 0.001 TYR C 90 ARG 0.007 0.001 ARG A 180 Details of bonding type rmsd link_NAG-ASN : bond 0.00074 ( 9) link_NAG-ASN : angle 1.84537 ( 27) hydrogen bonds : bond 0.02699 ( 232) hydrogen bonds : angle 4.85734 ( 579) SS BOND : bond 0.00227 ( 15) SS BOND : angle 0.96160 ( 30) covalent geometry : bond 0.00306 ( 8157) covalent geometry : angle 0.49072 (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 92 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 85 time to evaluate : 1.003 Fit side-chains REVERT: A 76 GLN cc_start: 0.8539 (tt0) cc_final: 0.8136 (tp40) REVERT: A 148 LYS cc_start: 0.8291 (ptpt) cc_final: 0.7917 (ptmm) REVERT: A 181 GLU cc_start: 0.8959 (mt-10) cc_final: 0.8265 (mp0) REVERT: A 265 TRP cc_start: 0.8430 (m100) cc_final: 0.7839 (m-10) REVERT: A 271 ARG cc_start: 0.8610 (mtt180) cc_final: 0.8363 (mtt-85) REVERT: A 300 ASN cc_start: 0.8976 (t0) cc_final: 0.8349 (t0) REVERT: B 52 GLU cc_start: 0.9082 (mm-30) cc_final: 0.8825 (mm-30) REVERT: B 148 LYS cc_start: 0.8287 (ptpp) cc_final: 0.7894 (ptmm) REVERT: B 180 ARG cc_start: 0.8719 (ptt-90) cc_final: 0.8460 (ptt-90) REVERT: B 181 GLU cc_start: 0.8927 (mt-10) cc_final: 0.8125 (mp0) REVERT: B 265 TRP cc_start: 0.8290 (m100) cc_final: 0.7893 (m-10) REVERT: B 300 ASN cc_start: 0.8967 (t0) cc_final: 0.8475 (t0) REVERT: C 52 GLU cc_start: 0.9060 (mm-30) cc_final: 0.8734 (mm-30) REVERT: C 98 ASN cc_start: 0.8789 (m-40) cc_final: 0.8273 (m110) REVERT: C 148 LYS cc_start: 0.8127 (ptpt) cc_final: 0.7900 (ptmm) REVERT: C 181 GLU cc_start: 0.8903 (mt-10) cc_final: 0.8201 (mp0) REVERT: C 265 TRP cc_start: 0.8443 (m100) cc_final: 0.7924 (m-10) REVERT: C 271 ARG cc_start: 0.8623 (mtt180) cc_final: 0.8305 (mtt-85) REVERT: C 300 ASN cc_start: 0.9015 (t0) cc_final: 0.8492 (t0) outliers start: 7 outliers final: 5 residues processed: 91 average time/residue: 1.0924 time to fit residues: 106.3830 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 : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 213 HIS Chi-restraints excluded: chain C residue 285 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 39 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 93 optimal weight: 9.9990 chunk 26 optimal weight: 3.9990 chunk 29 optimal weight: 9.9990 chunk 49 optimal weight: 0.8980 chunk 63 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 94 optimal weight: 0.9990 chunk 72 optimal weight: 0.0060 chunk 66 optimal weight: 0.0060 overall best weight: 0.5814 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.102023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.071525 restraints weight = 12288.395| |-----------------------------------------------------------------------------| r_work (start): 0.3016 rms_B_bonded: 2.52 r_work: 0.2880 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2761 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8764 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 0.033 8181 Z= 0.111 Angle : 0.481 7.510 11145 Z= 0.250 Chirality : 0.043 0.154 1251 Planarity : 0.003 0.031 1386 Dihedral : 9.016 89.054 1335 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 0.59 % Allowed : 13.40 % 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: 0.79 (0.29), residues: 972 helix: 1.56 (0.36), residues: 243 sheet: -0.66 (0.30), residues: 282 loop : 1.01 (0.32), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 259 HIS 0.002 0.000 HIS A 306 PHE 0.009 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 0.00113 ( 9) link_NAG-ASN : angle 1.70833 ( 27) hydrogen bonds : bond 0.02573 ( 232) hydrogen bonds : angle 4.77295 ( 579) SS BOND : bond 0.00207 ( 15) SS BOND : angle 0.93177 ( 30) covalent geometry : bond 0.00235 ( 8157) covalent geometry : angle 0.47185 (11088) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9548.17 seconds wall clock time: 164 minutes 1.00 seconds (9841.00 seconds total)