Starting phenix.real_space_refine on Sat Dec 28 05:59:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b73_44299/12_2024/9b73_44299.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b73_44299/12_2024/9b73_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_44299/12_2024/9b73_44299.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b73_44299/12_2024/9b73_44299.map" model { file = "/net/cci-nas-00/data/ceres_data/9b73_44299/12_2024/9b73_44299.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b73_44299/12_2024/9b73_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-5532/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: 5.17, per 1000 atoms: 0.64 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: 2.30 Conformation dependent library (CDL) restraints added in 981.9 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: 2.06 Time building geometry restraints manager: 2.58 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: 0.00 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: 0.640 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: 0.020 Extract box with map and model: 0.380 Check model and map are aligned: 0.080 Set scattering table: 0.150 Process input model: 20.970 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.020 ------------------------------------------------------------------------------- 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 8157 Z= 0.246 Angle : 0.502 5.215 11088 Z= 0.256 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 *********************** 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 : 0.925 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: 1.3648 time to fit residues: 164.4985 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 : 0.847 ------------------------------------------------------------------------------- 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: 0.0060 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: 0.9990 chunk 56 optimal weight: 5.9990 chunk 87 optimal weight: 1.9990 overall best weight: 0.5596 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8770 moved from start: 0.1048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 8157 Z= 0.186 Angle : 0.548 8.551 11088 Z= 0.281 Chirality : 0.046 0.221 1251 Planarity : 0.004 0.028 1386 Dihedral : 13.749 95.282 1335 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 1.19 % Allowed : 6.52 % Favored : 92.29 % 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: 0.14 (0.28), residues: 972 helix: 0.29 (0.34), residues: 261 sheet: -0.13 (0.30), residues: 303 loop : 0.40 (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 C 306 PHE 0.011 0.002 PHE B 230 TYR 0.018 0.001 TYR A 90 ARG 0.005 0.001 ARG A 180 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 101 time to evaluate : 0.914 Fit side-chains REVERT: A 148 LYS cc_start: 0.8317 (ptpt) cc_final: 0.8008 (ptmm) REVERT: A 181 GLU cc_start: 0.8792 (mt-10) cc_final: 0.8149 (mp0) REVERT: A 300 ASN cc_start: 0.8910 (t0) cc_final: 0.8406 (t0) REVERT: B 52 GLU cc_start: 0.8947 (mm-30) cc_final: 0.8675 (mm-30) REVERT: B 76 GLN cc_start: 0.8434 (tt0) cc_final: 0.7847 (tm-30) REVERT: B 148 LYS cc_start: 0.8233 (ptpp) cc_final: 0.7851 (ptmm) REVERT: B 181 GLU cc_start: 0.8791 (mt-10) cc_final: 0.7948 (mp0) REVERT: B 271 ARG cc_start: 0.8294 (mtt90) cc_final: 0.7983 (mtt-85) REVERT: B 300 ASN cc_start: 0.8879 (t0) cc_final: 0.8414 (t0) REVERT: C 148 LYS cc_start: 0.8376 (ptpt) cc_final: 0.8079 (ptmm) REVERT: C 181 GLU cc_start: 0.8759 (mt-10) cc_final: 0.8031 (mp0) REVERT: C 271 ARG cc_start: 0.8328 (mtt180) cc_final: 0.8121 (mtt-85) REVERT: C 300 ASN cc_start: 0.8959 (t0) cc_final: 0.8468 (t0) outliers start: 10 outliers final: 6 residues processed: 107 average time/residue: 1.2642 time to fit residues: 143.9172 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 : 0.870 ------------------------------------------------------------------------------- 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 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 48 optimal weight: 5.9990 chunk 27 optimal weight: 1.9990 chunk 72 optimal weight: 0.9990 chunk 59 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 87 optimal weight: 2.9990 chunk 94 optimal weight: 0.9990 chunk 77 optimal weight: 0.9990 chunk 86 optimal weight: 0.9990 chunk 29 optimal weight: 4.9990 chunk 70 optimal weight: 0.4980 overall best weight: 0.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN A 201 ASN A 237 GLN ** B 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 201 ASN C 76 GLN C 201 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8780 moved from start: 0.1371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8157 Z= 0.205 Angle : 0.544 11.038 11088 Z= 0.273 Chirality : 0.045 0.187 1251 Planarity : 0.004 0.032 1386 Dihedral : 11.893 89.383 1335 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer: Outliers : 1.19 % Allowed : 8.19 % Favored : 90.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.27), residues: 972 helix: 0.48 (0.34), residues: 261 sheet: -0.24 (0.31), residues: 276 loop : 0.31 (0.30), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 164 HIS 0.002 0.001 HIS C 213 PHE 0.011 0.001 PHE B 230 TYR 0.016 0.001 TYR A 90 ARG 0.007 0.001 ARG A 180 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 98 time to evaluate : 0.993 Fit side-chains REVERT: A 148 LYS cc_start: 0.8390 (ptpt) cc_final: 0.8072 (ptmm) REVERT: A 181 GLU cc_start: 0.8783 (mt-10) cc_final: 0.8057 (mp0) REVERT: A 300 ASN cc_start: 0.8891 (t0) cc_final: 0.8358 (t0) REVERT: B 76 GLN cc_start: 0.8447 (tt0) cc_final: 0.7852 (tm-30) REVERT: B 148 LYS cc_start: 0.8260 (ptpp) cc_final: 0.7867 (ptmm) REVERT: B 180 ARG cc_start: 0.8635 (ptt-90) cc_final: 0.8323 (ptt-90) REVERT: B 181 GLU cc_start: 0.8827 (mt-10) cc_final: 0.8041 (mp0) REVERT: B 271 ARG cc_start: 0.8282 (mtt90) cc_final: 0.7896 (mtt-85) REVERT: B 300 ASN cc_start: 0.8883 (t0) cc_final: 0.8386 (t0) REVERT: C 148 LYS cc_start: 0.8386 (ptpt) cc_final: 0.8065 (ptmm) REVERT: C 181 GLU cc_start: 0.8774 (mt-10) cc_final: 0.8048 (mp0) REVERT: C 300 ASN cc_start: 0.8936 (t0) cc_final: 0.8433 (t0) outliers start: 10 outliers final: 1 residues processed: 103 average time/residue: 1.2352 time to fit residues: 135.2507 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 : 1.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 86 optimal weight: 3.9990 chunk 65 optimal weight: 5.9990 chunk 45 optimal weight: 5.9990 chunk 9 optimal weight: 4.9990 chunk 41 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 87 optimal weight: 0.8980 chunk 92 optimal weight: 0.7980 chunk 83 optimal weight: 3.9990 chunk 25 optimal weight: 5.9990 chunk 77 optimal weight: 0.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 56 GLN ** B 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 76 GLN C 237 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8817 moved from start: 0.1520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 8157 Z= 0.340 Angle : 0.552 7.505 11088 Z= 0.291 Chirality : 0.045 0.143 1251 Planarity : 0.004 0.034 1386 Dihedral : 10.425 89.994 1335 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 1.07 % Allowed : 9.73 % 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: 0.59 (0.28), residues: 972 helix: 1.06 (0.34), residues: 243 sheet: -0.40 (0.29), residues: 297 loop : 0.86 (0.33), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 47 HIS 0.004 0.001 HIS C 213 PHE 0.015 0.002 PHE C 326 TYR 0.014 0.002 TYR A 90 ARG 0.007 0.001 ARG C 268 *********************** 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 99 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 90 time to evaluate : 1.026 Fit side-chains REVERT: A 148 LYS cc_start: 0.8463 (ptpt) cc_final: 0.8096 (ptmm) REVERT: A 181 GLU cc_start: 0.8763 (mt-10) cc_final: 0.8053 (mp0) REVERT: A 300 ASN cc_start: 0.8914 (t0) cc_final: 0.8324 (t0) REVERT: B 52 GLU cc_start: 0.8948 (mm-30) cc_final: 0.8689 (mm-30) REVERT: B 180 ARG cc_start: 0.8645 (ptt-90) cc_final: 0.8345 (ptt-90) REVERT: B 181 GLU cc_start: 0.8802 (mt-10) cc_final: 0.7985 (mp0) REVERT: B 258 ASP cc_start: 0.9089 (m-30) cc_final: 0.8828 (m-30) REVERT: B 271 ARG cc_start: 0.8265 (mtt90) cc_final: 0.7934 (mtt-85) REVERT: B 300 ASN cc_start: 0.8896 (t0) cc_final: 0.8400 (t0) REVERT: C 128 GLU cc_start: 0.7934 (pm20) cc_final: 0.7699 (pm20) REVERT: C 148 LYS cc_start: 0.8454 (ptpt) cc_final: 0.8094 (ptmm) REVERT: C 181 GLU cc_start: 0.8767 (mt-10) cc_final: 0.8026 (mp0) REVERT: C 300 ASN cc_start: 0.8948 (t0) cc_final: 0.8448 (t0) outliers start: 9 outliers final: 6 residues processed: 96 average time/residue: 1.2155 time to fit residues: 124.5776 Evaluate side-chains 88 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 82 time to evaluate : 0.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 285 LEU 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 52 optimal weight: 1.9990 chunk 1 optimal weight: 4.9990 chunk 69 optimal weight: 0.2980 chunk 38 optimal weight: 0.9990 chunk 79 optimal weight: 2.9990 chunk 64 optimal weight: 30.0000 chunk 0 optimal weight: 9.9990 chunk 47 optimal weight: 3.9990 chunk 83 optimal weight: 0.9980 chunk 23 optimal weight: 5.9990 chunk 31 optimal weight: 8.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8803 moved from start: 0.1647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8157 Z= 0.266 Angle : 0.505 5.180 11088 Z= 0.271 Chirality : 0.043 0.136 1251 Planarity : 0.003 0.031 1386 Dihedral : 9.963 89.384 1335 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 1.42 % Allowed : 10.32 % Favored : 88.26 % 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: 0.61 (0.28), residues: 972 helix: 1.14 (0.34), residues: 243 sheet: -0.53 (0.29), residues: 297 loop : 0.94 (0.33), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 259 HIS 0.002 0.001 HIS C 213 PHE 0.012 0.002 PHE B 230 TYR 0.014 0.001 TYR B 90 ARG 0.006 0.001 ARG C 180 *********************** 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 96 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 84 time to evaluate : 0.946 Fit side-chains REVERT: A 148 LYS cc_start: 0.8453 (ptpt) cc_final: 0.8124 (ptmm) REVERT: A 181 GLU cc_start: 0.8761 (mt-10) cc_final: 0.8023 (mp0) REVERT: A 300 ASN cc_start: 0.8889 (t0) cc_final: 0.8305 (t0) REVERT: B 52 GLU cc_start: 0.8973 (mm-30) cc_final: 0.8752 (mm-30) REVERT: B 148 LYS cc_start: 0.8334 (ptpp) cc_final: 0.7890 (ptmm) REVERT: B 181 GLU cc_start: 0.8801 (mt-10) cc_final: 0.7968 (mp0) REVERT: B 300 ASN cc_start: 0.8897 (t0) cc_final: 0.8413 (t0) REVERT: C 128 GLU cc_start: 0.7947 (pm20) cc_final: 0.7707 (pm20) REVERT: C 148 LYS cc_start: 0.8462 (ptpt) cc_final: 0.8057 (ptmm) REVERT: C 181 GLU cc_start: 0.8772 (mt-10) cc_final: 0.8000 (mp0) REVERT: C 300 ASN cc_start: 0.8951 (t0) cc_final: 0.8429 (t0) outliers start: 12 outliers final: 6 residues processed: 94 average time/residue: 1.0790 time to fit residues: 108.9376 Evaluate side-chains 84 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 78 time to evaluate : 0.957 ------------------------------------------------------------------------------- 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 285 LEU Chi-restraints excluded: chain C residue 318 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 83 optimal weight: 6.9990 chunk 18 optimal weight: 0.9980 chunk 54 optimal weight: 4.9990 chunk 22 optimal weight: 4.9990 chunk 92 optimal weight: 4.9990 chunk 77 optimal weight: 5.9990 chunk 43 optimal weight: 6.9990 chunk 7 optimal weight: 0.9990 chunk 30 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 chunk 89 optimal weight: 0.0770 overall best weight: 2.0144 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8818 moved from start: 0.1720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 8157 Z= 0.342 Angle : 0.532 5.252 11088 Z= 0.284 Chirality : 0.044 0.140 1251 Planarity : 0.004 0.031 1386 Dihedral : 10.074 89.218 1335 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 1.07 % Allowed : 11.39 % Favored : 87.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.28), residues: 972 helix: 1.24 (0.35), residues: 243 sheet: -0.47 (0.28), residues: 303 loop : 1.03 (0.34), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 259 HIS 0.003 0.001 HIS B 120 PHE 0.013 0.002 PHE B 230 TYR 0.013 0.001 TYR C 90 ARG 0.005 0.001 ARG C 180 *********************** 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 92 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 83 time to evaluate : 0.950 Fit side-chains REVERT: A 128 GLU cc_start: 0.7446 (pm20) cc_final: 0.7231 (pm20) REVERT: A 148 LYS cc_start: 0.8490 (ptpt) cc_final: 0.8137 (ptmm) REVERT: A 181 GLU cc_start: 0.8756 (mt-10) cc_final: 0.8048 (mp0) REVERT: A 268 ARG cc_start: 0.8323 (ptt90) cc_final: 0.8054 (ptt-90) REVERT: A 300 ASN cc_start: 0.8891 (t0) cc_final: 0.8292 (t0) REVERT: B 52 GLU cc_start: 0.8966 (mm-30) cc_final: 0.8712 (mm-30) REVERT: B 148 LYS cc_start: 0.8345 (ptpp) cc_final: 0.8004 (ptmm) REVERT: B 181 GLU cc_start: 0.8791 (mt-10) cc_final: 0.7944 (mp0) REVERT: B 300 ASN cc_start: 0.8910 (t0) cc_final: 0.8425 (t0) REVERT: C 52 GLU cc_start: 0.8978 (mm-30) cc_final: 0.8633 (mm-30) REVERT: C 128 GLU cc_start: 0.8005 (pm20) cc_final: 0.7783 (pm20) REVERT: C 148 LYS cc_start: 0.8324 (ptpt) cc_final: 0.7918 (ptmm) REVERT: C 181 GLU cc_start: 0.8773 (mt-10) cc_final: 0.7994 (mp0) REVERT: C 300 ASN cc_start: 0.8944 (t0) cc_final: 0.8417 (t0) outliers start: 9 outliers final: 7 residues processed: 89 average time/residue: 1.1392 time to fit residues: 108.7609 Evaluate side-chains 83 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 76 time to evaluate : 0.909 ------------------------------------------------------------------------------- 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 133 THR Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 318 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 10 optimal weight: 0.0370 chunk 52 optimal weight: 0.8980 chunk 67 optimal weight: 5.9990 chunk 78 optimal weight: 4.9990 chunk 51 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 57 optimal weight: 0.0370 chunk 56 optimal weight: 0.9990 chunk 42 optimal weight: 0.8980 chunk 36 optimal weight: 7.9990 chunk 55 optimal weight: 1.9990 overall best weight: 0.5738 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8778 moved from start: 0.1837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 8157 Z= 0.163 Angle : 0.471 6.364 11088 Z= 0.252 Chirality : 0.043 0.138 1251 Planarity : 0.003 0.031 1386 Dihedral : 9.470 89.262 1335 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 1.30 % Allowed : 11.15 % Favored : 87.54 % 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: 0.64 (0.28), residues: 972 helix: 1.34 (0.35), residues: 243 sheet: -0.65 (0.28), residues: 303 loop : 0.99 (0.34), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 259 HIS 0.002 0.000 HIS C 306 PHE 0.011 0.001 PHE B 230 TYR 0.014 0.001 TYR C 90 ARG 0.006 0.001 ARG B 180 *********************** 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 97 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 86 time to evaluate : 0.926 Fit side-chains REVERT: A 128 GLU cc_start: 0.7516 (pm20) cc_final: 0.7282 (pm20) REVERT: A 148 LYS cc_start: 0.8430 (ptpt) cc_final: 0.8095 (ptmm) REVERT: A 181 GLU cc_start: 0.8770 (mt-10) cc_final: 0.8021 (mp0) REVERT: A 265 TRP cc_start: 0.8307 (m100) cc_final: 0.7843 (m-10) REVERT: A 268 ARG cc_start: 0.8293 (ptt90) cc_final: 0.8017 (ptt-90) REVERT: A 300 ASN cc_start: 0.8878 (t0) cc_final: 0.8277 (t0) REVERT: B 52 GLU cc_start: 0.8970 (mm-30) cc_final: 0.8739 (mm-30) REVERT: B 128 GLU cc_start: 0.7466 (pm20) cc_final: 0.7245 (pm20) REVERT: B 148 LYS cc_start: 0.8321 (ptpp) cc_final: 0.7903 (ptmm) REVERT: B 181 GLU cc_start: 0.8811 (mt-10) cc_final: 0.7976 (mp0) REVERT: B 300 ASN cc_start: 0.8885 (t0) cc_final: 0.8391 (t0) REVERT: C 52 GLU cc_start: 0.8988 (mm-30) cc_final: 0.8662 (mm-30) REVERT: C 114 GLN cc_start: 0.8757 (OUTLIER) cc_final: 0.8253 (mt0) REVERT: C 148 LYS cc_start: 0.8194 (ptpt) cc_final: 0.7838 (ptmm) REVERT: C 181 GLU cc_start: 0.8769 (mt-10) cc_final: 0.7994 (mp0) REVERT: C 300 ASN cc_start: 0.8930 (t0) cc_final: 0.8402 (t0) REVERT: C 304 TYR cc_start: 0.8954 (m-80) cc_final: 0.8718 (m-80) outliers start: 11 outliers final: 6 residues processed: 92 average time/residue: 1.1336 time to fit residues: 111.7377 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 : 0.772 ------------------------------------------------------------------------------- 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 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 27 optimal weight: 5.9990 chunk 18 optimal weight: 1.9990 chunk 17 optimal weight: 6.9990 chunk 58 optimal weight: 3.9990 chunk 63 optimal weight: 4.9990 chunk 45 optimal weight: 5.9990 chunk 8 optimal weight: 0.8980 chunk 72 optimal weight: 4.9990 chunk 84 optimal weight: 5.9990 chunk 88 optimal weight: 0.8980 chunk 80 optimal weight: 4.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- 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** B 237 GLN C 76 GLN C 213 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8825 moved from start: 0.1811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.034 8157 Z= 0.409 Angle : 0.550 6.863 11088 Z= 0.294 Chirality : 0.045 0.142 1251 Planarity : 0.004 0.032 1386 Dihedral : 10.063 89.995 1335 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 0.95 % Allowed : 11.86 % Favored : 87.19 % 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: 1.34 (0.35), residues: 243 sheet: -0.46 (0.28), residues: 303 loop : 1.07 (0.34), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 47 HIS 0.003 0.001 HIS B 224 PHE 0.015 0.002 PHE C 326 TYR 0.013 0.002 TYR A 90 ARG 0.006 0.001 ARG B 180 *********************** 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 88 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 80 time to evaluate : 0.902 Fit side-chains REVERT: A 128 GLU cc_start: 0.7575 (pm20) cc_final: 0.7321 (pm20) REVERT: A 148 LYS cc_start: 0.8505 (ptpt) cc_final: 0.8123 (ptmm) REVERT: A 181 GLU cc_start: 0.8761 (mt-10) cc_final: 0.8060 (mp0) REVERT: A 268 ARG cc_start: 0.8313 (ptt90) cc_final: 0.8039 (ptt-90) REVERT: A 300 ASN cc_start: 0.8910 (t0) cc_final: 0.8313 (t0) REVERT: B 52 GLU cc_start: 0.8982 (mm-30) cc_final: 0.8765 (mm-30) REVERT: B 148 LYS cc_start: 0.8382 (ptpp) cc_final: 0.8039 (ptmm) REVERT: B 181 GLU cc_start: 0.8785 (mt-10) cc_final: 0.7937 (mp0) REVERT: B 258 ASP cc_start: 0.9120 (m-30) cc_final: 0.8888 (m-30) REVERT: B 300 ASN cc_start: 0.8919 (t0) cc_final: 0.8431 (t0) REVERT: C 52 GLU cc_start: 0.8970 (mm-30) cc_final: 0.8644 (mm-30) REVERT: C 114 GLN cc_start: 0.8895 (OUTLIER) cc_final: 0.8423 (mt0) REVERT: C 148 LYS cc_start: 0.8261 (ptpt) cc_final: 0.7849 (ptmm) REVERT: C 181 GLU cc_start: 0.8773 (mt-10) cc_final: 0.8017 (mp0) REVERT: C 300 ASN cc_start: 0.8943 (t0) cc_final: 0.8412 (t0) outliers start: 8 outliers final: 6 residues processed: 87 average time/residue: 1.1496 time to fit residues: 107.0701 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 : 0.894 ------------------------------------------------------------------------------- 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 285 LEU 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 86 optimal weight: 5.9990 chunk 88 optimal weight: 2.9990 chunk 51 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 chunk 67 optimal weight: 4.9990 chunk 26 optimal weight: 5.9990 chunk 77 optimal weight: 4.9990 chunk 81 optimal weight: 3.9990 chunk 85 optimal weight: 0.0970 chunk 56 optimal weight: 5.9990 chunk 91 optimal weight: 0.7980 overall best weight: 1.3382 ------------------------------------------------------------------------------- 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 213 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8805 moved from start: 0.1823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 8157 Z= 0.257 Angle : 0.507 7.502 11088 Z= 0.269 Chirality : 0.043 0.136 1251 Planarity : 0.003 0.031 1386 Dihedral : 9.822 89.879 1335 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 0.95 % Allowed : 12.10 % 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: 0.75 (0.29), residues: 972 helix: 1.34 (0.35), residues: 243 sheet: -0.58 (0.28), residues: 297 loop : 1.08 (0.34), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 259 HIS 0.002 0.001 HIS B 120 PHE 0.012 0.002 PHE B 230 TYR 0.014 0.001 TYR C 90 ARG 0.008 0.001 ARG B 180 *********************** 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 88 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 80 time to evaluate : 0.899 Fit side-chains REVERT: A 148 LYS cc_start: 0.8464 (ptpt) cc_final: 0.8083 (ptmm) REVERT: A 181 GLU cc_start: 0.8755 (mt-10) cc_final: 0.8042 (mp0) REVERT: A 265 TRP cc_start: 0.8350 (m100) cc_final: 0.7858 (m-10) REVERT: A 268 ARG cc_start: 0.8303 (ptt90) cc_final: 0.8025 (ptt-90) REVERT: A 300 ASN cc_start: 0.8892 (t0) cc_final: 0.8306 (t0) REVERT: B 52 GLU cc_start: 0.8988 (mm-30) cc_final: 0.8694 (mm-30) REVERT: B 148 LYS cc_start: 0.8353 (ptpp) cc_final: 0.8016 (ptmm) REVERT: B 181 GLU cc_start: 0.8773 (mt-10) cc_final: 0.7912 (mp0) REVERT: B 300 ASN cc_start: 0.8910 (t0) cc_final: 0.8437 (t0) REVERT: C 52 GLU cc_start: 0.8955 (mm-30) cc_final: 0.8634 (mm-30) REVERT: C 114 GLN cc_start: 0.8866 (OUTLIER) cc_final: 0.8366 (mt0) REVERT: C 148 LYS cc_start: 0.8226 (ptpt) cc_final: 0.8016 (ptmm) REVERT: C 181 GLU cc_start: 0.8780 (mt-10) cc_final: 0.8039 (mp0) REVERT: C 300 ASN cc_start: 0.8937 (t0) cc_final: 0.8406 (t0) outliers start: 8 outliers final: 5 residues processed: 87 average time/residue: 1.0692 time to fit residues: 99.8782 Evaluate side-chains 85 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 79 time to evaluate : 0.837 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 55 optimal weight: 3.9990 chunk 43 optimal weight: 6.9990 chunk 63 optimal weight: 4.9990 chunk 95 optimal weight: 5.9990 chunk 88 optimal weight: 2.9990 chunk 76 optimal weight: 6.9990 chunk 7 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 46 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- 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 213 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8827 moved from start: 0.1882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.035 8157 Z= 0.414 Angle : 0.559 7.369 11088 Z= 0.298 Chirality : 0.045 0.140 1251 Planarity : 0.004 0.032 1386 Dihedral : 10.164 89.612 1335 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 0.83 % Allowed : 12.69 % Favored : 86.48 % 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: 0.82 (0.29), residues: 972 helix: 1.34 (0.35), residues: 243 sheet: -0.44 (0.30), residues: 282 loop : 1.02 (0.33), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 259 HIS 0.003 0.001 HIS B 120 PHE 0.014 0.002 PHE B 230 TYR 0.014 0.002 TYR C 90 ARG 0.007 0.001 ARG B 180 ********************** 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 87 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 80 time to evaluate : 0.919 Fit side-chains REVERT: A 148 LYS cc_start: 0.8499 (ptpt) cc_final: 0.8095 (ptmm) REVERT: A 181 GLU cc_start: 0.8760 (mt-10) cc_final: 0.8056 (mp0) REVERT: A 268 ARG cc_start: 0.8347 (ptt90) cc_final: 0.8079 (ptt-90) REVERT: A 300 ASN cc_start: 0.8907 (t0) cc_final: 0.8312 (t0) REVERT: B 52 GLU cc_start: 0.8995 (mm-30) cc_final: 0.8732 (mm-30) REVERT: B 181 GLU cc_start: 0.8779 (mt-10) cc_final: 0.8108 (mp0) REVERT: B 300 ASN cc_start: 0.8927 (t0) cc_final: 0.8465 (t0) REVERT: C 52 GLU cc_start: 0.8951 (mm-30) cc_final: 0.8653 (mm-30) REVERT: C 114 GLN cc_start: 0.8900 (OUTLIER) cc_final: 0.8416 (mt0) REVERT: C 148 LYS cc_start: 0.8242 (ptpt) cc_final: 0.8016 (ptmm) REVERT: C 181 GLU cc_start: 0.8785 (mt-10) cc_final: 0.8030 (mp0) REVERT: C 300 ASN cc_start: 0.8956 (t0) cc_final: 0.8431 (t0) outliers start: 7 outliers final: 5 residues processed: 86 average time/residue: 1.0604 time to fit residues: 98.2037 Evaluate side-chains 83 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 77 time to evaluate : 0.866 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 23 optimal weight: 2.9990 chunk 70 optimal weight: 0.0970 chunk 11 optimal weight: 4.9990 chunk 21 optimal weight: 3.9990 chunk 76 optimal weight: 7.9990 chunk 31 optimal weight: 6.9990 chunk 78 optimal weight: 0.9990 chunk 9 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 66 optimal weight: 0.0670 chunk 4 optimal weight: 3.9990 overall best weight: 0.8120 ------------------------------------------------------------------------------- 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 = 0.3513 r_free = 0.3513 target = 0.099460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.068623 restraints weight = 12131.382| |-----------------------------------------------------------------------------| r_work (start): 0.2950 rms_B_bonded: 2.53 r_work: 0.2811 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2690 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8813 moved from start: 0.1916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8157 Z= 0.191 Angle : 0.493 7.917 11088 Z= 0.261 Chirality : 0.043 0.137 1251 Planarity : 0.003 0.030 1386 Dihedral : 9.603 87.678 1335 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 0.83 % Allowed : 12.93 % 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: 0.76 (0.29), residues: 972 helix: 1.36 (0.35), residues: 243 sheet: -0.60 (0.29), residues: 282 loop : 1.04 (0.33), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 259 HIS 0.002 0.001 HIS C 213 PHE 0.010 0.001 PHE B 230 TYR 0.015 0.001 TYR C 90 ARG 0.007 0.001 ARG B 180 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3240.41 seconds wall clock time: 58 minutes 53.15 seconds (3533.15 seconds total)