Starting phenix.real_space_refine on Fri Aug 22 20:58:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b73_44299/08_2025/9b73_44299.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b73_44299/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/9b73_44299/08_2025/9b73_44299.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b73_44299/08_2025/9b73_44299.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9b73_44299/08_2025/9b73_44299.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b73_44299/08_2025/9b73_44299.map" } resolution = 1.96 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.063 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-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 2.15, per 1000 atoms: 0.27 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: 0.61 Conformation dependent library (CDL) restraints added in 462.6 milliseconds Enol-peptide restraints added in 1.2 microseconds 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: 0.29 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: 1.21 Time building geometry restraints manager: 0.85 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: 0.02 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: 0.160 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 8.960 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.010 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:6.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.630 ------------------------------------------------------------------------------- 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 : 5.96 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.18 (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 ARG 0.022 0.001 ARG A 34 TYR 0.014 0.001 TYR C 90 PHE 0.009 0.001 PHE B 276 TRP 0.008 0.001 TRP C 259 HIS 0.003 0.001 HIS C 306 Details of bonding type rmsd covalent geometry : bond 0.00367 ( 8157) covalent geometry : angle 0.50247 (11088) SS BOND : bond 0.00232 ( 15) SS BOND : angle 0.78909 ( 30) hydrogen bonds : bond 0.18708 ( 232) hydrogen bonds : angle 6.82595 ( 579) link_NAG-ASN : bond 0.00203 ( 9) link_NAG-ASN : angle 2.18057 ( 27) *********************** 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 : 0.311 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: 0.6246 time to fit residues: 75.2234 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 : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 49 optimal weight: 3.9990 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 6.9990 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 chunk 74 optimal weight: 9.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- 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** B 237 GLN C 76 GLN C 213 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.097742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.066482 restraints weight = 12295.382| |-----------------------------------------------------------------------------| r_work (start): 0.2906 rms_B_bonded: 2.49 r_work: 0.2764 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2642 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8820 moved from start: 0.1023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 8181 Z= 0.241 Angle : 0.607 8.814 11145 Z= 0.311 Chirality : 0.047 0.231 1251 Planarity : 0.004 0.030 1386 Dihedral : 13.796 93.413 1335 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 1.19 % Allowed : 6.17 % Favored : 92.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.14 (0.27), residues: 972 helix: 0.27 (0.33), residues: 261 sheet: 0.07 (0.30), residues: 288 loop : 0.21 (0.31), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 180 TYR 0.017 0.002 TYR A 90 PHE 0.013 0.002 PHE B 230 TRP 0.007 0.001 TRP C 259 HIS 0.003 0.001 HIS B 296 Details of bonding type rmsd covalent geometry : bond 0.00514 ( 8157) covalent geometry : angle 0.59570 (11088) SS BOND : bond 0.00252 ( 15) SS BOND : angle 1.01908 ( 30) hydrogen bonds : bond 0.04128 ( 232) hydrogen bonds : angle 5.38426 ( 579) link_NAG-ASN : bond 0.00142 ( 9) link_NAG-ASN : angle 2.23186 ( 27) *********************** 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 107 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 97 time to evaluate : 0.295 Fit side-chains REVERT: A 148 LYS cc_start: 0.8367 (ptpt) cc_final: 0.8017 (ptmm) REVERT: A 181 GLU cc_start: 0.8925 (mt-10) cc_final: 0.8235 (mp0) REVERT: A 271 ARG cc_start: 0.8637 (mtt180) cc_final: 0.8355 (mtt-85) REVERT: A 300 ASN cc_start: 0.8976 (t0) cc_final: 0.8463 (t0) REVERT: B 52 GLU cc_start: 0.9124 (mm-30) cc_final: 0.8868 (mm-30) REVERT: B 76 GLN cc_start: 0.8661 (tt0) cc_final: 0.7949 (tm-30) REVERT: B 148 LYS cc_start: 0.8244 (ptpp) cc_final: 0.7829 (ptmm) REVERT: B 181 GLU cc_start: 0.8890 (mt-10) cc_final: 0.8057 (mp0) REVERT: B 271 ARG cc_start: 0.8556 (mtt90) cc_final: 0.8144 (mtt-85) REVERT: B 300 ASN cc_start: 0.8975 (t0) cc_final: 0.8484 (t0) REVERT: C 148 LYS cc_start: 0.8471 (ptpt) cc_final: 0.8148 (ptmm) REVERT: C 181 GLU cc_start: 0.8880 (mt-10) cc_final: 0.8168 (mp0) REVERT: C 271 ARG cc_start: 0.8695 (mtt180) cc_final: 0.8386 (mtt-85) REVERT: C 300 ASN cc_start: 0.9060 (t0) cc_final: 0.8548 (t0) outliers start: 10 outliers final: 5 residues processed: 103 average time/residue: 0.5610 time to fit residues: 60.9745 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 : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain C residue 155 THR 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 38 optimal weight: 0.9980 chunk 83 optimal weight: 0.9980 chunk 50 optimal weight: 6.9990 chunk 64 optimal weight: 30.0000 chunk 89 optimal weight: 0.4980 chunk 9 optimal weight: 1.9990 chunk 65 optimal weight: 4.9990 chunk 60 optimal weight: 2.9990 chunk 28 optimal weight: 0.7980 chunk 34 optimal weight: 0.0570 chunk 33 optimal weight: 0.7980 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.100469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.069786 restraints weight = 12174.988| |-----------------------------------------------------------------------------| r_work (start): 0.2977 rms_B_bonded: 2.52 r_work: 0.2837 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2717 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8797 moved from start: 0.1335 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= 0.130 Angle : 0.556 11.306 11145 Z= 0.274 Chirality : 0.044 0.172 1251 Planarity : 0.003 0.030 1386 Dihedral : 11.629 89.453 1335 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 1.42 % Allowed : 7.47 % Favored : 91.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.37 (0.28), residues: 972 helix: 0.86 (0.34), residues: 243 sheet: -0.45 (0.31), residues: 270 loop : 0.57 (0.31), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 180 TYR 0.016 0.001 TYR A 90 PHE 0.011 0.001 PHE B 230 TRP 0.006 0.001 TRP C 164 HIS 0.002 0.001 HIS C 306 Details of bonding type rmsd covalent geometry : bond 0.00271 ( 8157) covalent geometry : angle 0.54072 (11088) SS BOND : bond 0.00469 ( 15) SS BOND : angle 0.88814 ( 30) hydrogen bonds : bond 0.03373 ( 232) hydrogen bonds : angle 5.09548 ( 579) link_NAG-ASN : bond 0.00153 ( 9) link_NAG-ASN : angle 2.56102 ( 27) *********************** 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 107 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 95 time to evaluate : 0.191 Fit side-chains REVERT: A 148 LYS cc_start: 0.8357 (ptpt) cc_final: 0.8017 (ptmm) REVERT: A 181 GLU cc_start: 0.8932 (mt-10) cc_final: 0.8219 (mp0) REVERT: A 271 ARG cc_start: 0.8612 (mtt180) cc_final: 0.8368 (mtt-85) REVERT: A 300 ASN cc_start: 0.8988 (t0) cc_final: 0.8414 (t0) REVERT: B 76 GLN cc_start: 0.8603 (tt0) cc_final: 0.7949 (tm-30) REVERT: B 148 LYS cc_start: 0.8260 (ptpp) cc_final: 0.7866 (ptmm) REVERT: B 180 ARG cc_start: 0.8742 (ptt-90) cc_final: 0.8426 (ptt-90) REVERT: B 181 GLU cc_start: 0.8914 (mt-10) cc_final: 0.8123 (mp0) REVERT: B 271 ARG cc_start: 0.8540 (mtt90) cc_final: 0.8150 (mtt-85) REVERT: B 300 ASN cc_start: 0.8978 (t0) cc_final: 0.8501 (t0) REVERT: C 148 LYS cc_start: 0.8450 (ptpt) cc_final: 0.8128 (ptmm) REVERT: C 181 GLU cc_start: 0.8891 (mt-10) cc_final: 0.8172 (mp0) REVERT: C 271 ARG cc_start: 0.8642 (mtt180) cc_final: 0.8384 (mtt-85) REVERT: C 300 ASN cc_start: 0.9036 (t0) cc_final: 0.8553 (t0) REVERT: C 326 PHE cc_start: 0.9226 (t80) cc_final: 0.8998 (t80) outliers start: 12 outliers final: 5 residues processed: 102 average time/residue: 0.5419 time to fit residues: 58.6227 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 : 0.234 ------------------------------------------------------------------------------- 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 79 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 75 optimal weight: 4.9990 chunk 31 optimal weight: 5.9990 chunk 20 optimal weight: 5.9990 chunk 30 optimal weight: 0.7980 chunk 9 optimal weight: 2.9990 chunk 8 optimal weight: 5.9990 chunk 81 optimal weight: 5.9990 chunk 57 optimal weight: 0.0270 chunk 47 optimal weight: 0.7980 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** C 76 GLN C 237 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.098392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.066782 restraints weight = 12438.547| |-----------------------------------------------------------------------------| r_work (start): 0.2915 rms_B_bonded: 2.55 r_work: 0.2772 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2650 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8819 moved from start: 0.1450 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= 0.200 Angle : 0.548 8.830 11145 Z= 0.282 Chirality : 0.044 0.138 1251 Planarity : 0.004 0.031 1386 Dihedral : 10.175 89.947 1335 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer: Outliers : 1.30 % Allowed : 9.37 % Favored : 89.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.51 (0.28), residues: 972 helix: 0.99 (0.34), residues: 243 sheet: -0.44 (0.31), residues: 270 loop : 0.70 (0.31), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 268 TYR 0.014 0.001 TYR C 90 PHE 0.012 0.002 PHE B 230 TRP 0.006 0.001 TRP C 259 HIS 0.002 0.001 HIS B 120 Details of bonding type rmsd covalent geometry : bond 0.00421 ( 8157) covalent geometry : angle 0.52159 (11088) SS BOND : bond 0.00259 ( 15) SS BOND : angle 0.92080 ( 30) hydrogen bonds : bond 0.03319 ( 232) hydrogen bonds : angle 5.09014 ( 579) link_NAG-ASN : bond 0.00515 ( 9) link_NAG-ASN : angle 3.37784 ( 27) *********************** 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 101 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 90 time to evaluate : 0.198 Fit side-chains REVERT: A 148 LYS cc_start: 0.8435 (ptpt) cc_final: 0.8062 (ptmm) REVERT: A 181 GLU cc_start: 0.8927 (mt-10) cc_final: 0.8243 (mp0) REVERT: A 271 ARG cc_start: 0.8610 (mtt180) cc_final: 0.8348 (mtt-85) REVERT: A 300 ASN cc_start: 0.8951 (t0) cc_final: 0.8372 (t0) REVERT: B 128 GLU cc_start: 0.8047 (OUTLIER) cc_final: 0.7841 (pm20) REVERT: B 180 ARG cc_start: 0.8726 (ptt-90) cc_final: 0.8428 (ptt-90) REVERT: B 181 GLU cc_start: 0.8905 (mt-10) cc_final: 0.8132 (mp0) REVERT: B 258 ASP cc_start: 0.9120 (m-30) cc_final: 0.8854 (m-30) REVERT: B 271 ARG cc_start: 0.8521 (mtt90) cc_final: 0.8169 (mtt-85) REVERT: B 300 ASN cc_start: 0.8963 (t0) cc_final: 0.8473 (t0) REVERT: C 114 GLN cc_start: 0.8876 (OUTLIER) cc_final: 0.8354 (mt0) REVERT: C 148 LYS cc_start: 0.8476 (ptpt) cc_final: 0.8130 (ptmm) REVERT: C 181 GLU cc_start: 0.8890 (mt-10) cc_final: 0.8129 (mp0) REVERT: C 271 ARG cc_start: 0.8665 (mtt180) cc_final: 0.8369 (mtt-85) REVERT: C 300 ASN cc_start: 0.9021 (t0) cc_final: 0.8518 (t0) outliers start: 11 outliers final: 3 residues processed: 97 average time/residue: 0.5947 time to fit residues: 60.9721 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 : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 114 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 61 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 chunk 70 optimal weight: 0.6980 chunk 45 optimal weight: 2.9990 chunk 64 optimal weight: 30.0000 chunk 47 optimal weight: 0.8980 chunk 35 optimal weight: 2.9990 chunk 40 optimal weight: 4.9990 chunk 68 optimal weight: 3.9990 chunk 65 optimal weight: 7.9990 chunk 55 optimal weight: 3.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- 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 = 0.3489 r_free = 0.3489 target = 0.097985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.066963 restraints weight = 12331.383| |-----------------------------------------------------------------------------| r_work (start): 0.2913 rms_B_bonded: 2.50 r_work: 0.2771 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2649 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8820 moved from start: 0.1578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8181 Z= 0.208 Angle : 0.531 5.234 11145 Z= 0.280 Chirality : 0.044 0.138 1251 Planarity : 0.004 0.039 1386 Dihedral : 9.962 89.854 1335 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 1.30 % Allowed : 11.03 % Favored : 87.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.58 (0.28), residues: 972 helix: 1.14 (0.34), residues: 243 sheet: -0.55 (0.30), residues: 270 loop : 0.80 (0.32), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 180 TYR 0.014 0.001 TYR B 90 PHE 0.012 0.002 PHE B 230 TRP 0.007 0.001 TRP C 259 HIS 0.003 0.001 HIS C 213 Details of bonding type rmsd covalent geometry : bond 0.00444 ( 8157) covalent geometry : angle 0.51648 (11088) SS BOND : bond 0.00241 ( 15) SS BOND : angle 0.91591 ( 30) hydrogen bonds : bond 0.03223 ( 232) hydrogen bonds : angle 5.07790 ( 579) link_NAG-ASN : bond 0.00209 ( 9) link_NAG-ASN : angle 2.45892 ( 27) *********************** 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 99 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 88 time to evaluate : 0.370 Fit side-chains REVERT: A 148 LYS cc_start: 0.8467 (ptpt) cc_final: 0.8124 (ptmm) REVERT: A 181 GLU cc_start: 0.8921 (mt-10) cc_final: 0.8225 (mp0) REVERT: A 271 ARG cc_start: 0.8598 (mtt180) cc_final: 0.8332 (mtt-85) REVERT: A 300 ASN cc_start: 0.8946 (t0) cc_final: 0.8348 (t0) REVERT: B 128 GLU cc_start: 0.8036 (pm20) cc_final: 0.7807 (pm20) REVERT: B 148 LYS cc_start: 0.8297 (ptpp) cc_final: 0.7843 (ptmm) REVERT: B 181 GLU cc_start: 0.8898 (mt-10) cc_final: 0.8070 (mp0) REVERT: B 300 ASN cc_start: 0.8973 (t0) cc_final: 0.8486 (t0) REVERT: C 114 GLN cc_start: 0.8872 (OUTLIER) cc_final: 0.8335 (mt0) REVERT: C 148 LYS cc_start: 0.8497 (ptpt) cc_final: 0.8105 (ptmm) REVERT: C 181 GLU cc_start: 0.8899 (mt-10) cc_final: 0.8121 (mp0) REVERT: C 271 ARG cc_start: 0.8652 (mtt180) cc_final: 0.8342 (mtt-85) REVERT: C 300 ASN cc_start: 0.9027 (t0) cc_final: 0.8499 (t0) outliers start: 11 outliers final: 6 residues processed: 97 average time/residue: 0.6200 time to fit residues: 63.8118 Evaluate side-chains 84 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 77 time to evaluate : 0.311 ------------------------------------------------------------------------------- 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 133 THR Chi-restraints excluded: chain B residue 285 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 82 optimal weight: 0.7980 chunk 0 optimal weight: 30.0000 chunk 57 optimal weight: 0.1980 chunk 9 optimal weight: 0.7980 chunk 75 optimal weight: 0.6980 chunk 70 optimal weight: 0.9990 chunk 79 optimal weight: 1.9990 chunk 34 optimal weight: 0.0040 chunk 12 optimal weight: 5.9990 chunk 6 optimal weight: 0.8980 chunk 69 optimal weight: 2.9990 overall best weight: 0.4992 ------------------------------------------------------------------------------- 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 = 0.3537 r_free = 0.3537 target = 0.100833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.070697 restraints weight = 12380.990| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 2.51 r_work: 0.2852 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2732 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8780 moved from start: 0.1712 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 : 0.483 6.188 11145 Z= 0.253 Chirality : 0.043 0.136 1251 Planarity : 0.003 0.031 1386 Dihedral : 9.346 89.732 1335 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 1.07 % Allowed : 11.86 % Favored : 87.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.55 (0.28), residues: 972 helix: 1.29 (0.35), residues: 243 sheet: -0.68 (0.30), residues: 276 loop : 0.78 (0.32), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 180 TYR 0.014 0.001 TYR C 90 PHE 0.010 0.001 PHE B 230 TRP 0.007 0.001 TRP B 164 HIS 0.002 0.000 HIS C 306 Details of bonding type rmsd covalent geometry : bond 0.00230 ( 8157) covalent geometry : angle 0.47251 (11088) SS BOND : bond 0.00225 ( 15) SS BOND : angle 0.83644 ( 30) hydrogen bonds : bond 0.02784 ( 232) hydrogen bonds : angle 4.95153 ( 579) link_NAG-ASN : bond 0.00141 ( 9) link_NAG-ASN : angle 2.00221 ( 27) *********************** 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 105 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 96 time to evaluate : 0.261 Fit side-chains REVERT: A 148 LYS cc_start: 0.8403 (ptpt) cc_final: 0.8032 (ptmm) REVERT: A 181 GLU cc_start: 0.8936 (mt-10) cc_final: 0.8222 (mp0) REVERT: A 265 TRP cc_start: 0.8507 (m100) cc_final: 0.7997 (m-10) REVERT: A 271 ARG cc_start: 0.8587 (mtt180) cc_final: 0.8337 (mtt-85) REVERT: A 300 ASN cc_start: 0.8930 (t0) cc_final: 0.8328 (t0) REVERT: B 148 LYS cc_start: 0.8257 (ptpp) cc_final: 0.7825 (ptmm) REVERT: B 181 GLU cc_start: 0.8917 (mt-10) cc_final: 0.8100 (mp0) REVERT: B 271 ARG cc_start: 0.8620 (mtt-85) cc_final: 0.8405 (mtt-85) REVERT: B 300 ASN cc_start: 0.8960 (t0) cc_final: 0.8483 (t0) REVERT: C 52 GLU cc_start: 0.9111 (mm-30) cc_final: 0.8811 (mm-30) REVERT: C 114 GLN cc_start: 0.8717 (OUTLIER) cc_final: 0.8207 (mt0) REVERT: C 148 LYS cc_start: 0.8474 (ptpt) cc_final: 0.8084 (ptmm) REVERT: C 181 GLU cc_start: 0.8896 (mt-10) cc_final: 0.8211 (mp0) REVERT: C 271 ARG cc_start: 0.8596 (mtt180) cc_final: 0.8302 (mtt-85) REVERT: C 300 ASN cc_start: 0.9022 (t0) cc_final: 0.8513 (t0) outliers start: 9 outliers final: 4 residues processed: 103 average time/residue: 0.7032 time to fit residues: 76.1969 Evaluate side-chains 86 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 81 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 114 GLN Chi-restraints excluded: chain C residue 318 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 86 optimal weight: 5.9990 chunk 17 optimal weight: 0.9990 chunk 89 optimal weight: 4.9990 chunk 94 optimal weight: 2.9990 chunk 95 optimal weight: 5.9990 chunk 90 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 87 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 75 optimal weight: 0.9990 chunk 59 optimal weight: 3.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- 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 = 0.3496 r_free = 0.3496 target = 0.098393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.067522 restraints weight = 12333.812| |-----------------------------------------------------------------------------| r_work (start): 0.2925 rms_B_bonded: 2.50 r_work: 0.2783 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2662 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8813 moved from start: 0.1744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8181 Z= 0.194 Angle : 0.521 5.925 11145 Z= 0.275 Chirality : 0.043 0.136 1251 Planarity : 0.004 0.033 1386 Dihedral : 9.577 89.023 1335 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 0.71 % Allowed : 12.57 % Favored : 86.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.77 (0.28), residues: 972 helix: 1.36 (0.35), residues: 243 sheet: -0.52 (0.29), residues: 297 loop : 1.06 (0.33), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 268 TYR 0.014 0.001 TYR C 90 PHE 0.011 0.002 PHE B 230 TRP 0.006 0.001 TRP C 47 HIS 0.002 0.001 HIS B 120 Details of bonding type rmsd covalent geometry : bond 0.00414 ( 8157) covalent geometry : angle 0.50849 (11088) SS BOND : bond 0.00234 ( 15) SS BOND : angle 1.00950 ( 30) hydrogen bonds : bond 0.03011 ( 232) hydrogen bonds : angle 5.00687 ( 579) link_NAG-ASN : bond 0.00171 ( 9) link_NAG-ASN : angle 2.13495 ( 27) *********************** 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 89 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 83 time to evaluate : 0.324 Fit side-chains REVERT: A 148 LYS cc_start: 0.8471 (ptpt) cc_final: 0.8112 (ptmm) REVERT: A 181 GLU cc_start: 0.8938 (mt-10) cc_final: 0.8253 (mp0) REVERT: A 265 TRP cc_start: 0.8484 (m100) cc_final: 0.7959 (m-10) REVERT: A 271 ARG cc_start: 0.8614 (mtt180) cc_final: 0.8346 (mtt-85) REVERT: A 300 ASN cc_start: 0.8949 (t0) cc_final: 0.8355 (t0) REVERT: B 148 LYS cc_start: 0.8284 (ptpp) cc_final: 0.7862 (ptmm) REVERT: B 181 GLU cc_start: 0.8919 (mt-10) cc_final: 0.8096 (mp0) REVERT: B 300 ASN cc_start: 0.8972 (t0) cc_final: 0.8490 (t0) REVERT: C 52 GLU cc_start: 0.9145 (mm-30) cc_final: 0.8799 (mm-30) REVERT: C 114 GLN cc_start: 0.8816 (OUTLIER) cc_final: 0.8321 (mt0) REVERT: C 148 LYS cc_start: 0.8331 (ptpt) cc_final: 0.8013 (ptmm) REVERT: C 181 GLU cc_start: 0.8891 (mt-10) cc_final: 0.8255 (mp0) REVERT: C 271 ARG cc_start: 0.8643 (mtt180) cc_final: 0.8312 (mtt-85) REVERT: C 300 ASN cc_start: 0.9014 (t0) cc_final: 0.8490 (t0) outliers start: 6 outliers final: 5 residues processed: 87 average time/residue: 0.6505 time to fit residues: 59.9478 Evaluate side-chains 87 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 81 time to evaluate : 0.305 ------------------------------------------------------------------------------- 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 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 79 optimal weight: 1.9990 chunk 27 optimal weight: 7.9990 chunk 89 optimal weight: 8.9990 chunk 15 optimal weight: 2.9990 chunk 71 optimal weight: 0.9990 chunk 6 optimal weight: 0.6980 chunk 26 optimal weight: 3.9990 chunk 82 optimal weight: 0.9980 chunk 92 optimal weight: 0.8980 chunk 21 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 = 0.3511 r_free = 0.3511 target = 0.099384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.068361 restraints weight = 12230.720| |-----------------------------------------------------------------------------| r_work (start): 0.2945 rms_B_bonded: 2.51 r_work: 0.2806 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2685 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8802 moved from start: 0.1768 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= 0.156 Angle : 0.506 6.701 11145 Z= 0.268 Chirality : 0.043 0.135 1251 Planarity : 0.004 0.030 1386 Dihedral : 9.523 89.319 1335 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer: Outliers : 1.07 % Allowed : 12.34 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.77 (0.28), residues: 972 helix: 1.39 (0.35), residues: 243 sheet: -0.59 (0.29), residues: 297 loop : 1.10 (0.33), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 180 TYR 0.013 0.001 TYR C 90 PHE 0.011 0.001 PHE B 230 TRP 0.006 0.001 TRP C 259 HIS 0.002 0.001 HIS B 120 Details of bonding type rmsd covalent geometry : bond 0.00334 ( 8157) covalent geometry : angle 0.49534 (11088) SS BOND : bond 0.00222 ( 15) SS BOND : angle 0.97362 ( 30) hydrogen bonds : bond 0.02836 ( 232) hydrogen bonds : angle 4.95971 ( 579) link_NAG-ASN : bond 0.00105 ( 9) link_NAG-ASN : angle 2.00047 ( 27) *********************** 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 94 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 85 time to evaluate : 0.347 Fit side-chains REVERT: A 148 LYS cc_start: 0.8443 (ptpt) cc_final: 0.8078 (ptmm) REVERT: A 181 GLU cc_start: 0.8915 (mt-10) cc_final: 0.8239 (mp0) REVERT: A 271 ARG cc_start: 0.8604 (mtt180) cc_final: 0.8337 (mtt-85) REVERT: A 300 ASN cc_start: 0.8941 (t0) cc_final: 0.8347 (t0) REVERT: B 181 GLU cc_start: 0.8888 (mt-10) cc_final: 0.8036 (mp0) REVERT: B 271 ARG cc_start: 0.8636 (OUTLIER) cc_final: 0.8417 (mtt-85) REVERT: B 300 ASN cc_start: 0.8966 (t0) cc_final: 0.8483 (t0) REVERT: C 52 GLU cc_start: 0.9143 (mm-30) cc_final: 0.8801 (mm-30) REVERT: C 114 GLN cc_start: 0.8798 (OUTLIER) cc_final: 0.8301 (mt0) REVERT: C 128 GLU cc_start: 0.7927 (pm20) cc_final: 0.7682 (pm20) REVERT: C 148 LYS cc_start: 0.8263 (ptpt) cc_final: 0.7991 (ptmm) REVERT: C 181 GLU cc_start: 0.8890 (mt-10) cc_final: 0.8187 (mp0) REVERT: C 271 ARG cc_start: 0.8614 (mtt180) cc_final: 0.8281 (mtt-85) REVERT: C 300 ASN cc_start: 0.9009 (t0) cc_final: 0.8471 (t0) outliers start: 9 outliers final: 5 residues processed: 92 average time/residue: 0.6471 time to fit residues: 63.0159 Evaluate side-chains 88 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 81 time to evaluate : 0.324 ------------------------------------------------------------------------------- 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 133 THR Chi-restraints excluded: chain B residue 271 ARG 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 13 optimal weight: 0.7980 chunk 78 optimal weight: 0.5980 chunk 18 optimal weight: 0.6980 chunk 56 optimal weight: 1.9990 chunk 80 optimal weight: 4.9990 chunk 31 optimal weight: 5.9990 chunk 26 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 47 optimal weight: 0.8980 chunk 14 optimal weight: 0.1980 chunk 94 optimal weight: 0.9990 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 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 = 0.3533 r_free = 0.3533 target = 0.100592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.070401 restraints weight = 12218.782| |-----------------------------------------------------------------------------| r_work (start): 0.2984 rms_B_bonded: 2.49 r_work: 0.2847 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2727 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8795 moved from start: 0.1888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8181 Z= 0.118 Angle : 0.504 9.139 11145 Z= 0.262 Chirality : 0.043 0.169 1251 Planarity : 0.003 0.030 1386 Dihedral : 9.315 88.832 1335 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer: Outliers : 1.30 % Allowed : 12.81 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.75 (0.29), residues: 972 helix: 1.41 (0.35), residues: 243 sheet: -0.60 (0.28), residues: 303 loop : 1.08 (0.34), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 180 TYR 0.013 0.001 TYR C 90 PHE 0.009 0.001 PHE B 230 TRP 0.006 0.001 TRP B 164 HIS 0.001 0.000 HIS C 306 Details of bonding type rmsd covalent geometry : bond 0.00252 ( 8157) covalent geometry : angle 0.49459 (11088) SS BOND : bond 0.00209 ( 15) SS BOND : angle 0.92519 ( 30) hydrogen bonds : bond 0.02679 ( 232) hydrogen bonds : angle 4.91211 ( 579) link_NAG-ASN : bond 0.00102 ( 9) link_NAG-ASN : angle 1.83522 ( 27) *********************** 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 97 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 86 time to evaluate : 0.325 Fit side-chains REVERT: A 76 GLN cc_start: 0.8598 (tt0) cc_final: 0.8203 (tp40) REVERT: A 148 LYS cc_start: 0.8410 (ptpt) cc_final: 0.8051 (ptmm) REVERT: A 181 GLU cc_start: 0.8924 (mt-10) cc_final: 0.8219 (mp0) REVERT: A 213 HIS cc_start: 0.8064 (m-70) cc_final: 0.7695 (t70) REVERT: A 271 ARG cc_start: 0.8580 (mtt180) cc_final: 0.8325 (mtt-85) REVERT: A 300 ASN cc_start: 0.8934 (t0) cc_final: 0.8337 (t0) REVERT: B 148 LYS cc_start: 0.8276 (ptpp) cc_final: 0.7797 (ptmm) REVERT: B 181 GLU cc_start: 0.8897 (mt-10) cc_final: 0.8082 (mp0) REVERT: B 300 ASN cc_start: 0.8965 (t0) cc_final: 0.8486 (t0) REVERT: C 52 GLU cc_start: 0.9118 (mm-30) cc_final: 0.8803 (mm-30) REVERT: C 114 GLN cc_start: 0.8721 (OUTLIER) cc_final: 0.8229 (mt0) REVERT: C 181 GLU cc_start: 0.8895 (mt-10) cc_final: 0.8215 (mp0) REVERT: C 265 TRP cc_start: 0.8437 (m100) cc_final: 0.7950 (m-10) REVERT: C 271 ARG cc_start: 0.8611 (mtt180) cc_final: 0.8293 (mtt-85) REVERT: C 300 ASN cc_start: 0.9020 (t0) cc_final: 0.8507 (t0) outliers start: 11 outliers final: 6 residues processed: 94 average time/residue: 0.6579 time to fit residues: 65.3728 Evaluate side-chains 91 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 84 time to evaluate : 0.310 ------------------------------------------------------------------------------- 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 133 THR Chi-restraints excluded: chain B residue 285 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 37 optimal weight: 0.0070 chunk 56 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 chunk 34 optimal weight: 0.0370 chunk 66 optimal weight: 0.0970 chunk 95 optimal weight: 0.9980 chunk 10 optimal weight: 5.9990 chunk 75 optimal weight: 0.6980 chunk 55 optimal weight: 0.7980 chunk 9 optimal weight: 0.1980 overall best weight: 0.2074 ------------------------------------------------------------------------------- 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 = 0.3573 r_free = 0.3573 target = 0.103074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.073003 restraints weight = 12367.708| |-----------------------------------------------------------------------------| r_work (start): 0.3042 rms_B_bonded: 2.64 r_work: 0.2907 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2789 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8762 moved from start: 0.2066 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= 0.093 Angle : 0.485 7.930 11145 Z= 0.252 Chirality : 0.043 0.178 1251 Planarity : 0.003 0.036 1386 Dihedral : 8.940 87.488 1335 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.70 (0.29), residues: 972 helix: 1.66 (0.36), residues: 237 sheet: -0.68 (0.30), residues: 276 loop : 0.79 (0.32), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 180 TYR 0.013 0.001 TYR B 90 PHE 0.007 0.001 PHE A 293 TRP 0.007 0.001 TRP B 164 HIS 0.002 0.000 HIS B 306 Details of bonding type rmsd covalent geometry : bond 0.00199 ( 8157) covalent geometry : angle 0.47730 (11088) SS BOND : bond 0.00208 ( 15) SS BOND : angle 0.91193 ( 30) hydrogen bonds : bond 0.02504 ( 232) hydrogen bonds : angle 4.81929 ( 579) link_NAG-ASN : bond 0.00174 ( 9) link_NAG-ASN : angle 1.66043 ( 27) ********************** 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 105 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 96 time to evaluate : 0.206 Fit side-chains REVERT: A 76 GLN cc_start: 0.8625 (tt0) cc_final: 0.8208 (tp40) REVERT: A 148 LYS cc_start: 0.8300 (ptpt) cc_final: 0.7909 (ptmm) REVERT: A 181 GLU cc_start: 0.8929 (mt-10) cc_final: 0.8204 (mp0) REVERT: A 213 HIS cc_start: 0.7957 (m-70) cc_final: 0.7729 (t70) REVERT: A 265 TRP cc_start: 0.8421 (m100) cc_final: 0.7884 (m-10) REVERT: A 271 ARG cc_start: 0.8580 (mtt180) cc_final: 0.8336 (mtt-85) REVERT: A 300 ASN cc_start: 0.8961 (t0) cc_final: 0.8339 (t0) REVERT: B 148 LYS cc_start: 0.8226 (ptpp) cc_final: 0.7762 (ptmm) REVERT: B 181 GLU cc_start: 0.8950 (mt-10) cc_final: 0.8302 (mp0) REVERT: B 213 HIS cc_start: 0.8148 (OUTLIER) cc_final: 0.7805 (t70) REVERT: B 265 TRP cc_start: 0.8170 (m100) cc_final: 0.7826 (m-10) REVERT: B 300 ASN cc_start: 0.8954 (t0) cc_final: 0.8472 (t0) REVERT: C 52 GLU cc_start: 0.9084 (mm-30) cc_final: 0.8790 (mm-30) REVERT: C 98 ASN cc_start: 0.8768 (m-40) cc_final: 0.8256 (m110) REVERT: C 181 GLU cc_start: 0.8910 (mt-10) cc_final: 0.8201 (mp0) REVERT: C 265 TRP cc_start: 0.8386 (m100) cc_final: 0.7908 (m-10) REVERT: C 271 ARG cc_start: 0.8587 (mtt180) cc_final: 0.8309 (mtt-85) REVERT: C 300 ASN cc_start: 0.9018 (t0) cc_final: 0.8489 (t0) REVERT: C 326 PHE cc_start: 0.9262 (t80) cc_final: 0.9043 (t80) outliers start: 9 outliers final: 4 residues processed: 100 average time/residue: 0.5872 time to fit residues: 62.3917 Evaluate side-chains 93 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 88 time to evaluate : 0.350 ------------------------------------------------------------------------------- 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 213 HIS Chi-restraints excluded: chain B residue 285 LEU 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 14 optimal weight: 5.9990 chunk 22 optimal weight: 4.9990 chunk 54 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 66 optimal weight: 5.9990 chunk 73 optimal weight: 0.6980 chunk 74 optimal weight: 5.9990 chunk 44 optimal weight: 0.9990 chunk 83 optimal weight: 4.9990 chunk 1 optimal weight: 4.9990 chunk 90 optimal weight: 4.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 237 GLN B 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 = 0.3470 r_free = 0.3470 target = 0.096828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.065124 restraints weight = 12192.058| |-----------------------------------------------------------------------------| r_work (start): 0.2875 rms_B_bonded: 2.51 r_work: 0.2731 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2608 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8838 moved from start: 0.1949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.050 8181 Z= 0.316 Angle : 0.607 7.026 11145 Z= 0.319 Chirality : 0.046 0.177 1251 Planarity : 0.004 0.036 1386 Dihedral : 9.897 83.098 1335 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 0.71 % Allowed : 13.64 % Favored : 85.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.88 (0.29), residues: 972 helix: 1.42 (0.35), residues: 243 sheet: -0.46 (0.29), residues: 303 loop : 1.17 (0.35), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 180 TYR 0.012 0.002 TYR C 90 PHE 0.015 0.002 PHE A 276 TRP 0.008 0.002 TRP C 47 HIS 0.005 0.001 HIS A 260 Details of bonding type rmsd covalent geometry : bond 0.00683 ( 8157) covalent geometry : angle 0.59436 (11088) SS BOND : bond 0.00312 ( 15) SS BOND : angle 1.12412 ( 30) hydrogen bonds : bond 0.03287 ( 232) hydrogen bonds : angle 5.11667 ( 579) link_NAG-ASN : bond 0.00337 ( 9) link_NAG-ASN : angle 2.37934 ( 27) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4924.63 seconds wall clock time: 84 minutes 21.96 seconds (5061.96 seconds total)