Starting phenix.real_space_refine on Wed Mar 12 12:58:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b73_44299/03_2025/9b73_44299.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b73_44299/03_2025/9b73_44299.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=1.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9b73_44299/03_2025/9b73_44299.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b73_44299/03_2025/9b73_44299.map" model { file = "/net/cci-nas-00/data/ceres_data/9b73_44299/03_2025/9b73_44299.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b73_44299/03_2025/9b73_44299.cif" } resolution = 1.96 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.063 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 9 5.49 5 Mg 3 5.21 5 S 42 5.16 5 C 5115 2.51 5 N 1338 2.21 5 O 1509 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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: 7.53, per 1000 atoms: 0.94 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: 2.41 Conformation dependent library (CDL) restraints added in 989.3 milliseconds 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1776 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 9 sheets defined 28.3% alpha, 27.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.84 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: 2.19 Time building geometry restraints manager: 2.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2508 1.34 - 1.46: 2030 1.46 - 1.58: 3562 1.58 - 1.70: 6 1.70 - 1.82: 51 Bond restraints: 8157 Sorted by residual: bond pdb=" C1 NAG C 404 " pdb=" O5 NAG C 404 " ideal model delta sigma weight residual 1.406 1.481 -0.075 2.00e-02 2.50e+03 1.42e+01 bond pdb=" C1 NAG A 402 " pdb=" O5 NAG A 402 " ideal model delta sigma weight residual 1.406 1.481 -0.075 2.00e-02 2.50e+03 1.42e+01 bond pdb=" C1 NAG B 402 " pdb=" O5 NAG B 402 " ideal model delta sigma weight residual 1.406 1.481 -0.075 2.00e-02 2.50e+03 1.41e+01 bond pdb=" C1 NAG A 401 " pdb=" O5 NAG A 401 " ideal model delta sigma weight residual 1.406 1.437 -0.031 2.00e-02 2.50e+03 2.42e+00 bond pdb=" C1 NAG B 401 " pdb=" O5 NAG B 401 " ideal model delta sigma weight residual 1.406 1.437 -0.031 2.00e-02 2.50e+03 2.41e+00 ... (remaining 8152 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.04: 10594 1.04 - 2.09: 382 2.09 - 3.13: 88 3.13 - 4.17: 9 4.17 - 5.21: 15 Bond angle restraints: 11088 Sorted by residual: angle pdb=" N GLY A 71 " pdb=" CA GLY A 71 " pdb=" C GLY A 71 " ideal model delta sigma weight residual 113.18 108.57 4.61 2.37e+00 1.78e-01 3.79e+00 angle pdb=" N GLY B 71 " pdb=" CA GLY B 71 " pdb=" C GLY B 71 " ideal model delta sigma weight residual 113.18 108.66 4.52 2.37e+00 1.78e-01 3.64e+00 angle pdb=" N GLY C 71 " pdb=" CA GLY C 71 " pdb=" C GLY C 71 " ideal model delta sigma weight residual 113.18 108.70 4.48 2.37e+00 1.78e-01 3.57e+00 angle pdb=" C1 NAG C 404 " pdb=" O5 NAG C 404 " pdb=" C5 NAG C 404 " ideal model delta sigma weight residual 113.21 118.42 -5.21 3.00e+00 1.11e-01 3.02e+00 angle pdb=" C1 NAG A 402 " pdb=" O5 NAG A 402 " pdb=" C5 NAG A 402 " ideal model delta sigma weight residual 113.21 118.42 -5.21 3.00e+00 1.11e-01 3.02e+00 ... (remaining 11083 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.15: 4711 23.15 - 46.30: 162 46.30 - 69.46: 56 69.46 - 92.61: 9 92.61 - 115.76: 9 Dihedral angle restraints: 4947 sinusoidal: 2169 harmonic: 2778 Sorted by residual: dihedral pdb=" C1 NAG B 402 " pdb=" C5 NAG B 402 " pdb=" O5 NAG B 402 " pdb=" C6 NAG B 402 " ideal model delta sinusoidal sigma weight residual 171.16 -73.08 -115.76 1 3.00e+01 1.11e-03 1.53e+01 dihedral pdb=" C1 NAG C 404 " pdb=" C5 NAG C 404 " pdb=" O5 NAG C 404 " pdb=" C6 NAG C 404 " ideal model delta sinusoidal sigma weight residual 171.16 -73.09 -115.75 1 3.00e+01 1.11e-03 1.53e+01 dihedral pdb=" C1 NAG A 402 " pdb=" C5 NAG A 402 " pdb=" O5 NAG A 402 " pdb=" C6 NAG A 402 " ideal model delta sinusoidal sigma weight residual 171.16 -73.09 -115.75 1 3.00e+01 1.11e-03 1.53e+01 ... (remaining 4944 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 1007 0.056 - 0.112: 221 0.112 - 0.168: 20 0.168 - 0.223: 0 0.223 - 0.279: 3 Chirality restraints: 1251 Sorted by residual: chirality pdb=" C1 NAG B 402 " pdb=" ND2 ASN B 184 " pdb=" C2 NAG B 402 " pdb=" O5 NAG B 402 " both_signs ideal model delta sigma weight residual False -2.40 -2.12 -0.28 2.00e-01 2.50e+01 1.95e+00 chirality pdb=" C1 NAG A 402 " pdb=" ND2 ASN A 184 " pdb=" C2 NAG A 402 " pdb=" O5 NAG A 402 " both_signs ideal model delta sigma weight residual False -2.40 -2.12 -0.28 2.00e-01 2.50e+01 1.91e+00 chirality pdb=" C1 NAG C 404 " pdb=" ND2 ASN C 184 " pdb=" C2 NAG C 404 " pdb=" O5 NAG C 404 " both_signs ideal model delta sigma weight residual False -2.40 -2.13 -0.27 2.00e-01 2.50e+01 1.88e+00 ... (remaining 1248 not shown) Planarity restraints: 1395 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 34 " 0.205 9.50e-02 1.11e+02 9.27e-02 6.79e+00 pdb=" NE ARG A 34 " -0.020 2.00e-02 2.50e+03 pdb=" CZ ARG A 34 " 0.020 2.00e-02 2.50e+03 pdb=" NH1 ARG A 34 " -0.009 2.00e-02 2.50e+03 pdb=" NH2 ARG A 34 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 34 " -0.205 9.50e-02 1.11e+02 9.28e-02 6.78e+00 pdb=" NE ARG B 34 " 0.020 2.00e-02 2.50e+03 pdb=" CZ ARG B 34 " -0.019 2.00e-02 2.50e+03 pdb=" NH1 ARG B 34 " 0.009 2.00e-02 2.50e+03 pdb=" NH2 ARG B 34 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 34 " -0.205 9.50e-02 1.11e+02 9.28e-02 6.75e+00 pdb=" NE ARG C 34 " 0.019 2.00e-02 2.50e+03 pdb=" CZ ARG C 34 " -0.019 2.00e-02 2.50e+03 pdb=" NH1 ARG C 34 " 0.009 2.00e-02 2.50e+03 pdb=" NH2 ARG C 34 " -0.000 2.00e-02 2.50e+03 ... (remaining 1392 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 120 2.53 - 3.12: 6303 3.12 - 3.71: 13296 3.71 - 4.31: 19717 4.31 - 4.90: 31513 Nonbonded interactions: 70949 Sorted by model distance: nonbonded pdb="MG MG A 404 " pdb=" O HOH A 507 " model vdw 1.936 2.170 nonbonded pdb="MG MG C 401 " pdb=" O HOH C 508 " model vdw 1.939 2.170 nonbonded pdb="MG MG B 404 " pdb=" O HOH B 510 " model vdw 1.949 2.170 nonbonded pdb="MG MG A 404 " pdb=" O HOH B 501 " model vdw 1.951 2.170 nonbonded pdb="MG MG B 404 " pdb=" O HOH C 501 " model vdw 1.953 2.170 ... (remaining 70944 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.03 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 31 through 356 or resid 402 through 403)) selection = (chain 'B' and (resid 31 through 356 or resid 402 through 403)) selection = (chain 'C' and (resid 31 through 356 or resid 403 through 404)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.220 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: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 25.310 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.050 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:12.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.460 ------------------------------------------------------------------------------- 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 : 0.821 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: 1.2880 time to fit residues: 155.2893 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 : 0.934 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.100740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.069991 restraints weight = 12212.404| |-----------------------------------------------------------------------------| r_work (start): 0.2982 rms_B_bonded: 2.51 r_work: 0.2843 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2723 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8778 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 : 0.939 Fit side-chains REVERT: A 148 LYS cc_start: 0.8302 (ptpt) cc_final: 0.7989 (ptmm) REVERT: A 181 GLU cc_start: 0.8943 (mt-10) cc_final: 0.8320 (mp0) REVERT: A 271 ARG cc_start: 0.8608 (mtt180) cc_final: 0.8356 (mtt-85) REVERT: A 300 ASN cc_start: 0.8977 (t0) cc_final: 0.8474 (t0) REVERT: B 52 GLU cc_start: 0.9098 (mm-30) cc_final: 0.8824 (mm-30) REVERT: B 76 GLN cc_start: 0.8613 (tt0) cc_final: 0.7955 (tm-30) REVERT: B 148 LYS cc_start: 0.8220 (ptpp) cc_final: 0.7834 (ptmm) REVERT: B 181 GLU cc_start: 0.8902 (mt-10) cc_final: 0.8078 (mp0) REVERT: B 271 ARG cc_start: 0.8561 (mtt90) cc_final: 0.8258 (mtt-85) REVERT: B 300 ASN cc_start: 0.8942 (t0) cc_final: 0.8477 (t0) REVERT: C 148 LYS cc_start: 0.8436 (ptpt) cc_final: 0.8146 (ptmm) REVERT: C 181 GLU cc_start: 0.8890 (mt-10) cc_final: 0.8160 (mp0) REVERT: C 271 ARG cc_start: 0.8639 (mtt180) cc_final: 0.8367 (mtt-85) REVERT: C 300 ASN cc_start: 0.9036 (t0) cc_final: 0.8546 (t0) outliers start: 10 outliers final: 6 residues processed: 107 average time/residue: 1.2031 time to fit residues: 136.8289 Evaluate side-chains 93 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 87 time to evaluate : 0.900 ------------------------------------------------------------------------------- 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 34 optimal weight: 4.9990 chunk 6 optimal weight: 0.8980 chunk 54 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 chunk 95 optimal weight: 6.9990 chunk 32 optimal weight: 5.9990 chunk 44 optimal weight: 8.9990 chunk 94 optimal weight: 0.9990 chunk 71 optimal weight: 4.9990 chunk 67 optimal weight: 0.0770 chunk 59 optimal weight: 3.9990 overall best weight: 1.5944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN A 201 ASN A 237 GLN ** B 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 201 ASN C 76 GLN C 201 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.098665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.067273 restraints weight = 12318.291| |-----------------------------------------------------------------------------| r_work (start): 0.2922 rms_B_bonded: 2.52 r_work: 0.2780 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2659 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8816 moved from start: 0.1325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8157 Z= 0.287 Angle : 0.574 11.075 11088 Z= 0.291 Chirality : 0.045 0.185 1251 Planarity : 0.004 0.035 1386 Dihedral : 12.002 89.433 1335 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 1.19 % Allowed : 8.42 % Favored : 90.39 % 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: 0.19 (0.27), residues: 972 helix: 0.48 (0.34), residues: 261 sheet: -0.28 (0.31), residues: 270 loop : 0.40 (0.30), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 47 HIS 0.002 0.001 HIS C 213 PHE 0.012 0.002 PHE B 230 TYR 0.016 0.002 TYR A 90 ARG 0.008 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 : 0.894 Fit side-chains REVERT: A 148 LYS cc_start: 0.8403 (ptpt) cc_final: 0.8048 (ptmm) REVERT: A 181 GLU cc_start: 0.8941 (mt-10) cc_final: 0.8265 (mp0) REVERT: A 271 ARG cc_start: 0.8614 (mtt180) cc_final: 0.8352 (mtt-85) REVERT: A 300 ASN cc_start: 0.8968 (t0) cc_final: 0.8400 (t0) REVERT: B 148 LYS cc_start: 0.8279 (ptpp) cc_final: 0.7847 (ptmm) REVERT: B 180 ARG cc_start: 0.8738 (ptt-90) cc_final: 0.8436 (ptt-90) REVERT: B 181 GLU cc_start: 0.8913 (mt-10) cc_final: 0.8144 (mp0) REVERT: B 271 ARG cc_start: 0.8540 (mtt90) cc_final: 0.8209 (mtt-85) REVERT: B 300 ASN cc_start: 0.8963 (t0) cc_final: 0.8472 (t0) REVERT: C 148 LYS cc_start: 0.8457 (ptpt) cc_final: 0.8129 (ptmm) REVERT: C 181 GLU cc_start: 0.8894 (mt-10) cc_final: 0.8171 (mp0) REVERT: C 271 ARG cc_start: 0.8657 (mtt180) cc_final: 0.8356 (mtt-85) REVERT: C 300 ASN cc_start: 0.9023 (t0) cc_final: 0.8519 (t0) outliers start: 10 outliers final: 3 residues processed: 103 average time/residue: 1.2398 time to fit residues: 135.6906 Evaluate side-chains 91 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 88 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain C residue 285 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 95 optimal weight: 5.9990 chunk 28 optimal weight: 4.9990 chunk 26 optimal weight: 5.9990 chunk 85 optimal weight: 0.0030 chunk 94 optimal weight: 0.8980 chunk 70 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 93 optimal weight: 8.9990 chunk 73 optimal weight: 4.9990 chunk 30 optimal weight: 4.9990 overall best weight: 0.9392 ------------------------------------------------------------------------------- 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 = 0.3525 r_free = 0.3525 target = 0.100179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.069234 restraints weight = 12238.226| |-----------------------------------------------------------------------------| r_work (start): 0.2964 rms_B_bonded: 2.52 r_work: 0.2825 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2704 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8807 moved from start: 0.1526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8157 Z= 0.207 Angle : 0.501 6.940 11088 Z= 0.263 Chirality : 0.043 0.136 1251 Planarity : 0.004 0.032 1386 Dihedral : 9.968 89.616 1335 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % 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: 0.49 (0.28), residues: 972 helix: 1.04 (0.34), residues: 243 sheet: -0.53 (0.31), residues: 270 loop : 0.71 (0.31), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 259 HIS 0.002 0.001 HIS C 306 PHE 0.010 0.001 PHE B 230 TYR 0.015 0.001 TYR B 90 ARG 0.008 0.001 ARG A 180 *********************** 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 109 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 100 time to evaluate : 0.987 Fit side-chains REVERT: A 148 LYS cc_start: 0.8391 (ptpt) cc_final: 0.8042 (ptmm) REVERT: A 181 GLU cc_start: 0.8929 (mt-10) cc_final: 0.8259 (mp0) REVERT: A 271 ARG cc_start: 0.8619 (mtt180) cc_final: 0.8374 (mtt-85) REVERT: A 300 ASN cc_start: 0.8960 (t0) cc_final: 0.8358 (t0) REVERT: B 52 GLU cc_start: 0.9101 (mm-30) cc_final: 0.8881 (mm-30) REVERT: B 148 LYS cc_start: 0.8294 (ptpp) cc_final: 0.7868 (ptmm) REVERT: B 180 ARG cc_start: 0.8742 (ptt-90) cc_final: 0.8458 (ptt-90) REVERT: B 181 GLU cc_start: 0.8917 (mt-10) cc_final: 0.8152 (mp0) REVERT: B 271 ARG cc_start: 0.8526 (mtt90) cc_final: 0.8177 (mtt-85) REVERT: B 300 ASN cc_start: 0.8985 (t0) cc_final: 0.8495 (t0) REVERT: C 148 LYS cc_start: 0.8487 (ptpt) cc_final: 0.8152 (ptmm) REVERT: C 181 GLU cc_start: 0.8897 (mt-10) cc_final: 0.8137 (mp0) REVERT: C 271 ARG cc_start: 0.8627 (mtt180) cc_final: 0.8340 (mtt-85) REVERT: C 300 ASN cc_start: 0.9030 (t0) cc_final: 0.8533 (t0) outliers start: 9 outliers final: 5 residues processed: 106 average time/residue: 1.2814 time to fit residues: 144.2083 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 : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 318 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 17 optimal weight: 0.4980 chunk 43 optimal weight: 2.9990 chunk 5 optimal weight: 7.9990 chunk 72 optimal weight: 4.9990 chunk 76 optimal weight: 3.9990 chunk 61 optimal weight: 0.6980 chunk 20 optimal weight: 0.1980 chunk 53 optimal weight: 0.7980 chunk 46 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 81 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 237 GLN B 56 GLN B 76 GLN ** B 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 76 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.101122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.070577 restraints weight = 12208.869| |-----------------------------------------------------------------------------| r_work (start): 0.2991 rms_B_bonded: 2.52 r_work: 0.2852 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2733 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8816 moved from start: 0.1677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 8157 Z= 0.164 Angle : 0.462 5.027 11088 Z= 0.247 Chirality : 0.043 0.137 1251 Planarity : 0.003 0.030 1386 Dihedral : 9.479 89.431 1335 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer: Outliers : 1.42 % Allowed : 10.91 % 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 (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: 0.52 (0.28), residues: 972 helix: 1.21 (0.35), residues: 243 sheet: -0.61 (0.31), residues: 270 loop : 0.71 (0.31), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 164 HIS 0.002 0.000 HIS C 306 PHE 0.014 0.001 PHE C 326 TYR 0.014 0.001 TYR C 90 ARG 0.007 0.001 ARG A 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 111 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 99 time to evaluate : 1.019 Fit side-chains REVERT: A 128 GLU cc_start: 0.7652 (pm20) cc_final: 0.7401 (pm20) REVERT: A 148 LYS cc_start: 0.8407 (ptpt) cc_final: 0.8063 (ptmm) REVERT: A 181 GLU cc_start: 0.8928 (mt-10) cc_final: 0.8260 (mp0) REVERT: A 265 TRP cc_start: 0.8471 (m100) cc_final: 0.7954 (m-10) REVERT: A 271 ARG cc_start: 0.8625 (mtt180) cc_final: 0.8398 (mtt-85) REVERT: A 300 ASN cc_start: 0.8995 (t0) cc_final: 0.8403 (t0) REVERT: B 52 GLU cc_start: 0.9106 (mm-30) cc_final: 0.8883 (mm-30) REVERT: B 98 ASN cc_start: 0.8849 (m-40) cc_final: 0.8391 (m110) REVERT: B 148 LYS cc_start: 0.8359 (ptpp) cc_final: 0.7938 (ptmm) REVERT: B 180 ARG cc_start: 0.8769 (ptt-90) cc_final: 0.8456 (ptt-90) REVERT: B 181 GLU cc_start: 0.8925 (mt-10) cc_final: 0.8146 (mp0) REVERT: B 271 ARG cc_start: 0.8529 (mtt90) cc_final: 0.8183 (mtt-85) REVERT: B 300 ASN cc_start: 0.8991 (t0) cc_final: 0.8511 (t0) REVERT: C 98 ASN cc_start: 0.8779 (m-40) cc_final: 0.8288 (m110) REVERT: C 114 GLN cc_start: 0.8744 (OUTLIER) cc_final: 0.8229 (mt0) REVERT: C 128 GLU cc_start: 0.8062 (pm20) cc_final: 0.7826 (pm20) REVERT: C 148 LYS cc_start: 0.8537 (ptpt) cc_final: 0.8192 (ptmm) REVERT: C 149 CYS cc_start: 0.6698 (t) cc_final: 0.6475 (t) REVERT: C 181 GLU cc_start: 0.8902 (mt-10) cc_final: 0.8253 (mp0) REVERT: C 271 ARG cc_start: 0.8624 (mtt180) cc_final: 0.8343 (mtt-85) REVERT: C 300 ASN cc_start: 0.9021 (t0) cc_final: 0.8529 (t0) outliers start: 12 outliers final: 4 residues processed: 107 average time/residue: 1.2453 time to fit residues: 141.4159 Evaluate side-chains 97 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 92 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 316 ASP Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 114 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 47 optimal weight: 1.9990 chunk 12 optimal weight: 4.9990 chunk 43 optimal weight: 0.8980 chunk 59 optimal weight: 5.9990 chunk 68 optimal weight: 4.9990 chunk 41 optimal weight: 0.9990 chunk 89 optimal weight: 0.0980 chunk 74 optimal weight: 2.9990 chunk 72 optimal weight: 0.9980 chunk 20 optimal weight: 0.8980 chunk 11 optimal weight: 5.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 = 0.3532 r_free = 0.3532 target = 0.100703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.069985 restraints weight = 12255.242| |-----------------------------------------------------------------------------| r_work (start): 0.2983 rms_B_bonded: 2.51 r_work: 0.2846 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2726 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8786 moved from start: 0.1760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8157 Z= 0.181 Angle : 0.473 5.937 11088 Z= 0.253 Chirality : 0.043 0.137 1251 Planarity : 0.003 0.033 1386 Dihedral : 9.329 89.985 1335 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 1.19 % Allowed : 11.15 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.28), residues: 972 helix: 1.38 (0.35), residues: 243 sheet: -0.64 (0.31), residues: 270 loop : 0.77 (0.31), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 164 HIS 0.002 0.001 HIS C 213 PHE 0.009 0.001 PHE B 230 TYR 0.013 0.001 TYR B 90 ARG 0.007 0.001 ARG A 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 105 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 95 time to evaluate : 0.918 Fit side-chains REVERT: A 128 GLU cc_start: 0.7674 (pm20) cc_final: 0.7416 (pm20) REVERT: A 148 LYS cc_start: 0.8373 (ptpt) cc_final: 0.8015 (ptmm) REVERT: A 181 GLU cc_start: 0.8940 (mt-10) cc_final: 0.8240 (mp0) REVERT: A 265 TRP cc_start: 0.8452 (m100) cc_final: 0.7947 (m-10) REVERT: A 271 ARG cc_start: 0.8621 (mtt180) cc_final: 0.8371 (mtt-85) REVERT: A 300 ASN cc_start: 0.8979 (t0) cc_final: 0.8384 (t0) REVERT: B 52 GLU cc_start: 0.9111 (mm-30) cc_final: 0.8868 (mm-30) REVERT: B 98 ASN cc_start: 0.8836 (m-40) cc_final: 0.8366 (m110) REVERT: B 148 LYS cc_start: 0.8325 (ptpp) cc_final: 0.7901 (ptmm) REVERT: B 181 GLU cc_start: 0.8915 (mt-10) cc_final: 0.8099 (mp0) REVERT: B 300 ASN cc_start: 0.8968 (t0) cc_final: 0.8478 (t0) REVERT: C 98 ASN cc_start: 0.8768 (m-40) cc_final: 0.8268 (m110) REVERT: C 114 GLN cc_start: 0.8724 (OUTLIER) cc_final: 0.8220 (mt0) REVERT: C 128 GLU cc_start: 0.8033 (pm20) cc_final: 0.7808 (pm20) REVERT: C 148 LYS cc_start: 0.8458 (ptpt) cc_final: 0.8098 (ptmm) REVERT: C 149 CYS cc_start: 0.6659 (t) cc_final: 0.6459 (t) REVERT: C 181 GLU cc_start: 0.8897 (mt-10) cc_final: 0.8215 (mp0) REVERT: C 265 TRP cc_start: 0.8457 (m100) cc_final: 0.7983 (m-10) REVERT: C 271 ARG cc_start: 0.8617 (mtt180) cc_final: 0.8325 (mtt-85) REVERT: C 300 ASN cc_start: 0.9022 (t0) cc_final: 0.8514 (t0) outliers start: 10 outliers final: 6 residues processed: 101 average time/residue: 1.2309 time to fit residues: 132.0034 Evaluate side-chains 97 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 90 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 316 ASP Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 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 27 optimal weight: 6.9990 chunk 93 optimal weight: 0.5980 chunk 94 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 chunk 72 optimal weight: 0.2980 chunk 89 optimal weight: 0.0980 chunk 76 optimal weight: 7.9990 chunk 16 optimal weight: 0.8980 chunk 26 optimal weight: 0.9990 chunk 41 optimal weight: 0.1980 chunk 51 optimal weight: 0.9980 overall best weight: 0.4180 ------------------------------------------------------------------------------- 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 = 0.3562 r_free = 0.3562 target = 0.102530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.072286 restraints weight = 12280.593| |-----------------------------------------------------------------------------| r_work (start): 0.3028 rms_B_bonded: 2.52 r_work: 0.2896 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2777 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8754 moved from start: 0.1910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 8157 Z= 0.140 Angle : 0.454 6.278 11088 Z= 0.241 Chirality : 0.043 0.136 1251 Planarity : 0.003 0.034 1386 Dihedral : 9.064 87.920 1335 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 1.30 % Allowed : 11.63 % Favored : 87.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.28), residues: 972 helix: 1.50 (0.36), residues: 243 sheet: -0.64 (0.30), residues: 276 loop : 0.78 (0.31), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 164 HIS 0.002 0.000 HIS B 306 PHE 0.014 0.001 PHE C 326 TYR 0.014 0.001 TYR C 90 ARG 0.008 0.001 ARG A 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 105 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 94 time to evaluate : 0.821 Fit side-chains REVERT: A 128 GLU cc_start: 0.7746 (pm20) cc_final: 0.7513 (pm20) REVERT: A 148 LYS cc_start: 0.8344 (ptpt) cc_final: 0.7989 (ptmm) REVERT: A 181 GLU cc_start: 0.8927 (mt-10) cc_final: 0.8238 (mp0) REVERT: A 213 HIS cc_start: 0.8095 (m-70) cc_final: 0.7693 (t70) REVERT: A 265 TRP cc_start: 0.8454 (m100) cc_final: 0.7930 (m-10) REVERT: A 271 ARG cc_start: 0.8582 (mtt180) cc_final: 0.8339 (mtt-85) REVERT: A 300 ASN cc_start: 0.8991 (t0) cc_final: 0.8375 (t0) REVERT: B 52 GLU cc_start: 0.9089 (mm-30) cc_final: 0.8863 (mm-30) REVERT: B 98 ASN cc_start: 0.8810 (m-40) cc_final: 0.8356 (m110) REVERT: B 148 LYS cc_start: 0.8319 (ptpp) cc_final: 0.7927 (ptmm) REVERT: B 180 ARG cc_start: 0.8703 (ptt-90) cc_final: 0.8433 (ptt-90) REVERT: B 181 GLU cc_start: 0.8927 (mt-10) cc_final: 0.8118 (mp0) REVERT: B 300 ASN cc_start: 0.8965 (t0) cc_final: 0.8467 (t0) REVERT: C 98 ASN cc_start: 0.8749 (m-40) cc_final: 0.8261 (m110) REVERT: C 128 GLU cc_start: 0.8023 (pm20) cc_final: 0.7804 (pm20) REVERT: C 148 LYS cc_start: 0.8400 (ptpt) cc_final: 0.8042 (ptmm) REVERT: C 181 GLU cc_start: 0.8896 (mt-10) cc_final: 0.8194 (mp0) REVERT: C 265 TRP cc_start: 0.8432 (m100) cc_final: 0.7945 (m-10) REVERT: C 271 ARG cc_start: 0.8592 (mtt180) cc_final: 0.8305 (mtt-85) REVERT: C 300 ASN cc_start: 0.9023 (t0) cc_final: 0.8500 (t0) outliers start: 11 outliers final: 7 residues processed: 99 average time/residue: 1.2087 time to fit residues: 127.3778 Evaluate side-chains 96 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 89 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 316 ASP Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 213 HIS Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 318 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 38 optimal weight: 0.0470 chunk 18 optimal weight: 4.9990 chunk 43 optimal weight: 3.9990 chunk 19 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 92 optimal weight: 0.7980 chunk 78 optimal weight: 0.7980 chunk 56 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 overall best weight: 0.6878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 76 GLN ** B 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 237 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.101703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.071263 restraints weight = 12330.132| |-----------------------------------------------------------------------------| r_work (start): 0.3006 rms_B_bonded: 2.53 r_work: 0.2870 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2751 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8774 moved from start: 0.1965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8157 Z= 0.168 Angle : 0.465 7.070 11088 Z= 0.249 Chirality : 0.043 0.165 1251 Planarity : 0.003 0.032 1386 Dihedral : 9.082 87.036 1335 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 5.07 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 (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: 1.51 (0.36), residues: 243 sheet: -0.58 (0.30), residues: 276 loop : 0.83 (0.32), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 259 HIS 0.001 0.000 HIS C 213 PHE 0.009 0.001 PHE B 230 TYR 0.013 0.001 TYR A 90 ARG 0.008 0.001 ARG A 180 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 92 time to evaluate : 0.859 Fit side-chains REVERT: A 128 GLU cc_start: 0.7769 (pm20) cc_final: 0.7533 (pm20) REVERT: A 148 LYS cc_start: 0.8312 (ptpt) cc_final: 0.7945 (ptmm) REVERT: A 181 GLU cc_start: 0.8935 (mt-10) cc_final: 0.8239 (mp0) REVERT: A 213 HIS cc_start: 0.8060 (m-70) cc_final: 0.7626 (t70) REVERT: A 265 TRP cc_start: 0.8460 (m100) cc_final: 0.7918 (m-10) REVERT: A 271 ARG cc_start: 0.8587 (mtt180) cc_final: 0.8339 (mtt-85) REVERT: A 300 ASN cc_start: 0.9004 (t0) cc_final: 0.8376 (t0) REVERT: B 52 GLU cc_start: 0.9097 (mm-30) cc_final: 0.8847 (mm-30) REVERT: B 98 ASN cc_start: 0.8818 (m-40) cc_final: 0.8365 (m110) REVERT: B 128 GLU cc_start: 0.7510 (pm20) cc_final: 0.7308 (pm20) REVERT: B 148 LYS cc_start: 0.8282 (ptpp) cc_final: 0.7902 (ptmm) REVERT: B 180 ARG cc_start: 0.8727 (ptt-90) cc_final: 0.8444 (ptt-90) REVERT: B 181 GLU cc_start: 0.8925 (mt-10) cc_final: 0.8125 (mp0) REVERT: B 265 TRP cc_start: 0.8180 (m100) cc_final: 0.7839 (m-10) REVERT: B 271 ARG cc_start: 0.8450 (mtt-85) cc_final: 0.8178 (mtt-85) REVERT: B 300 ASN cc_start: 0.8976 (t0) cc_final: 0.8479 (t0) REVERT: C 98 ASN cc_start: 0.8759 (m-40) cc_final: 0.8277 (m110) REVERT: C 148 LYS cc_start: 0.8226 (ptpt) cc_final: 0.7904 (ptmm) REVERT: C 181 GLU cc_start: 0.8908 (mt-10) cc_final: 0.8200 (mp0) REVERT: C 265 TRP cc_start: 0.8397 (m100) cc_final: 0.7871 (m-10) REVERT: C 271 ARG cc_start: 0.8615 (mtt180) cc_final: 0.8316 (mtt-85) REVERT: C 300 ASN cc_start: 0.9029 (t0) cc_final: 0.8514 (t0) outliers start: 9 outliers final: 5 residues processed: 97 average time/residue: 1.2461 time to fit residues: 128.2720 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 : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 ASP Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 213 HIS Chi-restraints excluded: chain B residue 285 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 20 optimal weight: 0.8980 chunk 8 optimal weight: 0.9980 chunk 91 optimal weight: 6.9990 chunk 38 optimal weight: 0.0570 chunk 33 optimal weight: 5.9990 chunk 25 optimal weight: 8.9990 chunk 14 optimal weight: 4.9990 chunk 55 optimal weight: 0.8980 chunk 37 optimal weight: 3.9990 chunk 32 optimal weight: 6.9990 chunk 73 optimal weight: 0.8980 overall best weight: 0.7498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 76 GLN C 237 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.101495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.070956 restraints weight = 12512.744| |-----------------------------------------------------------------------------| r_work (start): 0.3001 rms_B_bonded: 2.54 r_work: 0.2865 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2745 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8772 moved from start: 0.1971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8157 Z= 0.179 Angle : 0.477 7.512 11088 Z= 0.254 Chirality : 0.043 0.181 1251 Planarity : 0.003 0.034 1386 Dihedral : 9.051 88.452 1335 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % 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: 0.74 (0.28), residues: 972 helix: 1.53 (0.36), residues: 243 sheet: -0.64 (0.32), residues: 255 loop : 0.82 (0.31), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 259 HIS 0.001 0.000 HIS A 306 PHE 0.013 0.001 PHE C 326 TYR 0.013 0.001 TYR B 90 ARG 0.008 0.001 ARG A 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 97 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 90 time to evaluate : 0.901 Fit side-chains REVERT: A 76 GLN cc_start: 0.8598 (tt0) cc_final: 0.8162 (tp40) REVERT: A 148 LYS cc_start: 0.8274 (ptpt) cc_final: 0.7908 (ptmm) REVERT: A 181 GLU cc_start: 0.8922 (mt-10) cc_final: 0.8237 (mp0) REVERT: A 213 HIS cc_start: 0.8018 (m-70) cc_final: 0.7614 (t70) REVERT: A 265 TRP cc_start: 0.8463 (m100) cc_final: 0.7921 (m-10) REVERT: A 271 ARG cc_start: 0.8592 (mtt180) cc_final: 0.8334 (mtt-85) REVERT: A 300 ASN cc_start: 0.9001 (t0) cc_final: 0.8375 (t0) REVERT: B 52 GLU cc_start: 0.9084 (mm-30) cc_final: 0.8836 (mm-30) REVERT: B 98 ASN cc_start: 0.8809 (m-40) cc_final: 0.8352 (m110) REVERT: B 128 GLU cc_start: 0.7495 (pm20) cc_final: 0.7225 (pm20) REVERT: B 148 LYS cc_start: 0.8271 (ptpp) cc_final: 0.7884 (ptmm) REVERT: B 180 ARG cc_start: 0.8729 (ptt-90) cc_final: 0.8431 (ptt-90) REVERT: B 181 GLU cc_start: 0.8928 (mt-10) cc_final: 0.8097 (mp0) REVERT: B 265 TRP cc_start: 0.8231 (m100) cc_final: 0.7851 (m-10) REVERT: B 300 ASN cc_start: 0.8971 (t0) cc_final: 0.8475 (t0) REVERT: C 52 GLU cc_start: 0.9079 (mm-30) cc_final: 0.8760 (mm-30) REVERT: C 98 ASN cc_start: 0.8769 (m-40) cc_final: 0.8269 (m110) REVERT: C 128 GLU cc_start: 0.7917 (pm20) cc_final: 0.7687 (pm20) REVERT: C 148 LYS cc_start: 0.8163 (ptpt) cc_final: 0.7937 (ptmm) REVERT: C 181 GLU cc_start: 0.8898 (mt-10) cc_final: 0.8200 (mp0) REVERT: C 265 TRP cc_start: 0.8422 (m100) cc_final: 0.7893 (m-10) REVERT: C 271 ARG cc_start: 0.8617 (mtt180) cc_final: 0.8308 (mtt-85) REVERT: C 300 ASN cc_start: 0.9027 (t0) cc_final: 0.8517 (t0) outliers start: 7 outliers final: 6 residues processed: 95 average time/residue: 1.2216 time to fit residues: 123.6663 Evaluate side-chains 93 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 87 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 316 ASP Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 213 HIS Chi-restraints excluded: chain B residue 285 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 2 optimal weight: 0.5980 chunk 48 optimal weight: 0.9990 chunk 51 optimal weight: 7.9990 chunk 45 optimal weight: 2.9990 chunk 71 optimal weight: 0.5980 chunk 14 optimal weight: 3.9990 chunk 60 optimal weight: 0.8980 chunk 37 optimal weight: 4.9990 chunk 24 optimal weight: 1.9990 chunk 20 optimal weight: 0.0970 chunk 42 optimal weight: 5.9990 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 237 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.101823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.071380 restraints weight = 12212.583| |-----------------------------------------------------------------------------| r_work (start): 0.3011 rms_B_bonded: 2.52 r_work: 0.2875 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2756 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8765 moved from start: 0.2043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 8157 Z= 0.165 Angle : 0.472 7.761 11088 Z= 0.251 Chirality : 0.043 0.167 1251 Planarity : 0.003 0.031 1386 Dihedral : 9.001 88.885 1335 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer: Outliers : 0.71 % Allowed : 12.93 % Favored : 86.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.28), residues: 972 helix: 1.55 (0.36), residues: 243 sheet: -0.65 (0.32), residues: 255 loop : 0.83 (0.31), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 259 HIS 0.002 0.000 HIS A 306 PHE 0.009 0.001 PHE B 230 TYR 0.013 0.001 TYR C 90 ARG 0.007 0.001 ARG A 180 ********************** 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 95 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 89 time to evaluate : 0.847 Fit side-chains REVERT: A 76 GLN cc_start: 0.8536 (tt0) cc_final: 0.8125 (tp40) REVERT: A 148 LYS cc_start: 0.8261 (ptpt) cc_final: 0.7892 (ptmm) REVERT: A 181 GLU cc_start: 0.8930 (mt-10) cc_final: 0.8245 (mp0) REVERT: A 213 HIS cc_start: 0.7987 (m-70) cc_final: 0.7626 (t70) REVERT: A 265 TRP cc_start: 0.8448 (m100) cc_final: 0.7902 (m-10) REVERT: A 271 ARG cc_start: 0.8582 (mtt180) cc_final: 0.8328 (mtt-85) REVERT: A 300 ASN cc_start: 0.8997 (t0) cc_final: 0.8370 (t0) REVERT: B 52 GLU cc_start: 0.9064 (mm-30) cc_final: 0.8815 (mm-30) REVERT: B 98 ASN cc_start: 0.8800 (m-40) cc_final: 0.8339 (m110) REVERT: B 148 LYS cc_start: 0.7954 (ptpp) cc_final: 0.7665 (ptmt) REVERT: B 180 ARG cc_start: 0.8726 (ptt-90) cc_final: 0.8431 (ptt-90) REVERT: B 181 GLU cc_start: 0.8931 (mt-10) cc_final: 0.8101 (mp0) REVERT: B 265 TRP cc_start: 0.8257 (m100) cc_final: 0.7865 (m-10) REVERT: B 300 ASN cc_start: 0.8966 (t0) cc_final: 0.8473 (t0) REVERT: C 52 GLU cc_start: 0.9075 (mm-30) cc_final: 0.8755 (mm-30) REVERT: C 98 ASN cc_start: 0.8760 (m-40) cc_final: 0.8256 (m110) REVERT: C 148 LYS cc_start: 0.8107 (ptpt) cc_final: 0.7881 (ptmm) REVERT: C 181 GLU cc_start: 0.8900 (mt-10) cc_final: 0.8196 (mp0) REVERT: C 265 TRP cc_start: 0.8406 (m100) cc_final: 0.7901 (m-10) REVERT: C 271 ARG cc_start: 0.8607 (mtt180) cc_final: 0.8299 (mtt-85) REVERT: C 300 ASN cc_start: 0.9023 (t0) cc_final: 0.8501 (t0) outliers start: 6 outliers final: 5 residues processed: 93 average time/residue: 1.1464 time to fit residues: 113.8784 Evaluate side-chains 95 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 90 time to evaluate : 0.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 316 ASP Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 285 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 39 optimal weight: 2.9990 chunk 4 optimal weight: 0.8980 chunk 93 optimal weight: 5.9990 chunk 26 optimal weight: 0.9990 chunk 29 optimal weight: 0.1980 chunk 49 optimal weight: 4.9990 chunk 63 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 94 optimal weight: 0.9990 chunk 72 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 overall best weight: 0.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 76 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.101303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.070658 restraints weight = 12279.063| |-----------------------------------------------------------------------------| r_work (start): 0.2994 rms_B_bonded: 2.54 r_work: 0.2859 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2739 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8781 moved from start: 0.2027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8157 Z= 0.186 Angle : 0.475 7.316 11088 Z= 0.254 Chirality : 0.043 0.166 1251 Planarity : 0.003 0.031 1386 Dihedral : 9.021 89.344 1335 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 0.83 % Allowed : 13.05 % Favored : 86.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.29), residues: 972 helix: 1.55 (0.36), residues: 243 sheet: -0.60 (0.30), residues: 282 loop : 1.04 (0.32), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 259 HIS 0.001 0.000 HIS C 306 PHE 0.014 0.001 PHE C 326 TYR 0.012 0.001 TYR B 90 ARG 0.007 0.001 ARG A 180 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9609.81 seconds wall clock time: 163 minutes 31.49 seconds (9811.49 seconds total)