Starting phenix.real_space_refine on Tue Mar 11 19:49:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7jnc_22404/03_2025/7jnc_22404.cif Found real_map, /net/cci-nas-00/data/ceres_data/7jnc_22404/03_2025/7jnc_22404.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.73 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7jnc_22404/03_2025/7jnc_22404.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7jnc_22404/03_2025/7jnc_22404.map" model { file = "/net/cci-nas-00/data/ceres_data/7jnc_22404/03_2025/7jnc_22404.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7jnc_22404/03_2025/7jnc_22404.cif" } resolution = 3.73 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= 0.000 sd= 0.005 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: 4 Type Number sf(0) Gaussians S 24 5.16 5 C 4287 2.51 5 N 1080 2.21 5 O 1182 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 6573 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2121 Classifications: {'peptide': 287} Incomplete info: {'truncation_to_alanine': 63} Link IDs: {'PTRANS': 13, 'TRANS': 273} Unresolved non-hydrogen bonds: 218 Unresolved non-hydrogen angles: 264 Unresolved non-hydrogen dihedrals: 186 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 7, 'TYR:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 5, 'PHE:plan': 2, 'GLU:plan': 4, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 118 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Restraints were copied for chains: C, B, D, F Time building chain proxies: 4.16, per 1000 atoms: 0.63 Number of scatterers: 6573 At special positions: 0 Unit cell: (84.132, 82.08, 126.198, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 24 16.00 O 1182 8.00 N 1080 7.00 C 4287 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 128 " - pdb=" SG CYS A 149 " distance=2.03 Simple disulfide: pdb=" SG CYS C 128 " - pdb=" SG CYS C 149 " distance=2.03 Simple disulfide: pdb=" SG CYS B 128 " - pdb=" SG CYS B 149 " 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 BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG A 401 " - " ASN A 148 " " NAG A 402 " - " ASN A 162 " " NAG A 403 " - " ASN A 190 " " NAG B 401 " - " ASN B 148 " " NAG B 402 " - " ASN B 162 " " NAG B 403 " - " ASN B 190 " " NAG C 401 " - " ASN C 148 " " NAG C 402 " - " ASN C 162 " " NAG C 403 " - " ASN C 190 " " NAG D 1 " - " ASN A 155 " " NAG E 1 " - " ASN B 155 " " NAG F 1 " - " ASN C 155 " Time building additional restraints: 1.97 Conformation dependent library (CDL) restraints added in 1.0 seconds 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1662 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 12 sheets defined 37.0% alpha, 22.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.85 Creating SS restraints... Processing helix chain 'A' and resid 53 through 96 removed outlier: 4.215A pdb=" N PHE A 57 " --> pdb=" O SER A 53 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N ALA A 60 " --> pdb=" O ARG A 56 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N CYS A 61 " --> pdb=" O PHE A 57 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LYS A 95 " --> pdb=" O ASP A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 212 Processing helix chain 'A' and resid 215 through 226 Processing helix chain 'A' and resid 297 through 302 removed outlier: 3.777A pdb=" N ASN A 302 " --> pdb=" O ILE A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 339 removed outlier: 3.920A pdb=" N THR A 306 " --> pdb=" O ASN A 302 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA A 308 " --> pdb=" O TRP A 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 54 through 96 removed outlier: 4.443A pdb=" N ALA B 60 " --> pdb=" O ARG B 56 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N CYS B 61 " --> pdb=" O PHE B 57 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LYS B 95 " --> pdb=" O ASP B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 212 Processing helix chain 'B' and resid 215 through 226 Processing helix chain 'B' and resid 297 through 302 removed outlier: 3.777A pdb=" N ASN B 302 " --> pdb=" O ILE B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 339 removed outlier: 3.920A pdb=" N THR B 306 " --> pdb=" O ASN B 302 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA B 308 " --> pdb=" O TRP B 304 " (cutoff:3.500A) Processing helix chain 'C' and resid 54 through 96 removed outlier: 4.442A pdb=" N ALA C 60 " --> pdb=" O ARG C 56 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N CYS C 61 " --> pdb=" O PHE C 57 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LYS C 95 " --> pdb=" O ASP C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 212 Processing helix chain 'C' and resid 215 through 226 Processing helix chain 'C' and resid 297 through 302 removed outlier: 3.777A pdb=" N ASN C 302 " --> pdb=" O ILE C 298 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 339 removed outlier: 3.920A pdb=" N THR C 306 " --> pdb=" O ASN C 302 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA C 308 " --> pdb=" O TRP C 304 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 100 through 101 removed outlier: 5.519A pdb=" N LEU B 244 " --> pdb=" O PHE B 291 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 254 through 258 removed outlier: 5.519A pdb=" N LEU A 244 " --> pdb=" O PHE A 291 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 118 through 119 removed outlier: 4.023A pdb=" N ASP A 200 " --> pdb=" O TYR A 119 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ILE A 199 " --> pdb=" O PHE A 232 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N PHE A 232 " --> pdb=" O ILE A 199 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 124 through 131 removed outlier: 6.383A pdb=" N GLN A 186 " --> pdb=" O LEU A 126 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N CYS A 128 " --> pdb=" O PHE A 184 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N PHE A 184 " --> pdb=" O CYS A 128 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N HIS A 130 " --> pdb=" O LEU A 182 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N LEU A 182 " --> pdb=" O HIS A 130 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N PHE A 282 " --> pdb=" O PHE A 236 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LYS A 241 " --> pdb=" O GLU A 261 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLU A 261 " --> pdb=" O LYS A 241 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 151 through 157 removed outlier: 3.550A pdb=" N TYR A 156 " --> pdb=" O LYS A 166 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 100 through 101 removed outlier: 5.520A pdb=" N LEU C 244 " --> pdb=" O PHE C 291 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 118 through 119 removed outlier: 4.023A pdb=" N ASP B 200 " --> pdb=" O TYR B 119 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ILE B 199 " --> pdb=" O PHE B 232 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N PHE B 232 " --> pdb=" O ILE B 199 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 124 through 131 removed outlier: 6.383A pdb=" N GLN B 186 " --> pdb=" O LEU B 126 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N CYS B 128 " --> pdb=" O PHE B 184 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N PHE B 184 " --> pdb=" O CYS B 128 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N HIS B 130 " --> pdb=" O LEU B 182 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N LEU B 182 " --> pdb=" O HIS B 130 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N PHE B 282 " --> pdb=" O PHE B 236 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LYS B 241 " --> pdb=" O GLU B 261 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLU B 261 " --> pdb=" O LYS B 241 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 151 through 157 removed outlier: 3.550A pdb=" N TYR B 156 " --> pdb=" O LYS B 166 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 118 through 119 removed outlier: 4.023A pdb=" N ASP C 200 " --> pdb=" O TYR C 119 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ILE C 199 " --> pdb=" O PHE C 232 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N PHE C 232 " --> pdb=" O ILE C 199 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 124 through 131 removed outlier: 6.383A pdb=" N GLN C 186 " --> pdb=" O LEU C 126 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N CYS C 128 " --> pdb=" O PHE C 184 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N PHE C 184 " --> pdb=" O CYS C 128 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N HIS C 130 " --> pdb=" O LEU C 182 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N LEU C 182 " --> pdb=" O HIS C 130 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N PHE C 282 " --> pdb=" O PHE C 236 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LYS C 241 " --> pdb=" O GLU C 261 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLU C 261 " --> pdb=" O LYS C 241 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 151 through 157 removed outlier: 3.550A pdb=" N TYR C 156 " --> pdb=" O LYS C 166 " (cutoff:3.500A) 354 hydrogen bonds defined for protein. 1035 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.89 Time building geometry restraints manager: 2.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2049 1.35 - 1.47: 1758 1.47 - 1.58: 2892 1.58 - 1.70: 0 1.70 - 1.82: 36 Bond restraints: 6735 Sorted by residual: bond pdb=" N LYS B 319 " pdb=" CA LYS B 319 " ideal model delta sigma weight residual 1.459 1.487 -0.028 1.20e-02 6.94e+03 5.52e+00 bond pdb=" N LYS C 319 " pdb=" CA LYS C 319 " ideal model delta sigma weight residual 1.459 1.487 -0.028 1.20e-02 6.94e+03 5.31e+00 bond pdb=" N LYS A 319 " pdb=" CA LYS A 319 " ideal model delta sigma weight residual 1.459 1.487 -0.027 1.20e-02 6.94e+03 5.22e+00 bond pdb=" N PHE A 318 " pdb=" CA PHE A 318 " ideal model delta sigma weight residual 1.459 1.485 -0.026 1.17e-02 7.31e+03 4.92e+00 bond pdb=" N PHE B 318 " pdb=" CA PHE B 318 " ideal model delta sigma weight residual 1.459 1.485 -0.026 1.17e-02 7.31e+03 4.87e+00 ... (remaining 6730 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.09: 8405 1.09 - 2.19: 619 2.19 - 3.28: 134 3.28 - 4.37: 17 4.37 - 5.47: 20 Bond angle restraints: 9195 Sorted by residual: angle pdb=" CA LYS B 319 " pdb=" C LYS B 319 " pdb=" O LYS B 319 " ideal model delta sigma weight residual 120.90 118.00 2.90 1.07e+00 8.73e-01 7.36e+00 angle pdb=" CA LYS A 319 " pdb=" C LYS A 319 " pdb=" O LYS A 319 " ideal model delta sigma weight residual 120.90 118.00 2.90 1.07e+00 8.73e-01 7.35e+00 angle pdb=" CA LYS C 319 " pdb=" C LYS C 319 " pdb=" O LYS C 319 " ideal model delta sigma weight residual 120.90 118.03 2.87 1.07e+00 8.73e-01 7.19e+00 angle pdb=" O PHE B 318 " pdb=" C PHE B 318 " pdb=" N LYS B 319 " ideal model delta sigma weight residual 122.03 124.55 -2.52 1.04e+00 9.25e-01 5.87e+00 angle pdb=" O PHE C 318 " pdb=" C PHE C 318 " pdb=" N LYS C 319 " ideal model delta sigma weight residual 122.03 124.50 -2.47 1.04e+00 9.25e-01 5.64e+00 ... (remaining 9190 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.08: 3763 16.08 - 32.16: 299 32.16 - 48.24: 66 48.24 - 64.32: 30 64.32 - 80.39: 3 Dihedral angle restraints: 4161 sinusoidal: 1611 harmonic: 2550 Sorted by residual: dihedral pdb=" CB CYS C 128 " pdb=" SG CYS C 128 " pdb=" SG CYS C 149 " pdb=" CB CYS C 149 " ideal model delta sinusoidal sigma weight residual 93.00 41.20 51.80 1 1.00e+01 1.00e-02 3.66e+01 dihedral pdb=" CB CYS A 128 " pdb=" SG CYS A 128 " pdb=" SG CYS A 149 " pdb=" CB CYS A 149 " ideal model delta sinusoidal sigma weight residual 93.00 41.23 51.77 1 1.00e+01 1.00e-02 3.66e+01 dihedral pdb=" CB CYS B 128 " pdb=" SG CYS B 128 " pdb=" SG CYS B 149 " pdb=" CB CYS B 149 " ideal model delta sinusoidal sigma weight residual 93.00 41.24 51.76 1 1.00e+01 1.00e-02 3.66e+01 ... (remaining 4158 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 837 0.047 - 0.094: 224 0.094 - 0.140: 40 0.140 - 0.187: 3 0.187 - 0.234: 3 Chirality restraints: 1107 Sorted by residual: chirality pdb=" CA PHE A 318 " pdb=" N PHE A 318 " pdb=" C PHE A 318 " pdb=" CB PHE A 318 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.37e+00 chirality pdb=" CA PHE B 318 " pdb=" N PHE B 318 " pdb=" C PHE B 318 " pdb=" CB PHE B 318 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" CA PHE C 318 " pdb=" N PHE C 318 " pdb=" C PHE C 318 " pdb=" CB PHE C 318 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.33e+00 ... (remaining 1104 not shown) Planarity restraints: 1164 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 232 " -0.014 2.00e-02 2.50e+03 1.02e-02 1.82e+00 pdb=" CG PHE A 232 " 0.022 2.00e-02 2.50e+03 pdb=" CD1 PHE A 232 " 0.000 2.00e-02 2.50e+03 pdb=" CD2 PHE A 232 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE A 232 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 232 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE A 232 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 232 " 0.014 2.00e-02 2.50e+03 1.02e-02 1.81e+00 pdb=" CG PHE B 232 " -0.022 2.00e-02 2.50e+03 pdb=" CD1 PHE B 232 " -0.000 2.00e-02 2.50e+03 pdb=" CD2 PHE B 232 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE B 232 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE B 232 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHE B 232 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 232 " 0.014 2.00e-02 2.50e+03 1.01e-02 1.79e+00 pdb=" CG PHE C 232 " -0.022 2.00e-02 2.50e+03 pdb=" CD1 PHE C 232 " -0.000 2.00e-02 2.50e+03 pdb=" CD2 PHE C 232 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE C 232 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE C 232 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHE C 232 " 0.006 2.00e-02 2.50e+03 ... (remaining 1161 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 1760 2.80 - 3.32: 6510 3.32 - 3.85: 10764 3.85 - 4.37: 12187 4.37 - 4.90: 21104 Nonbonded interactions: 52325 Sorted by model distance: nonbonded pdb=" O PRO A 174 " pdb=" NE1 TRP A 287 " model vdw 2.269 3.120 nonbonded pdb=" O PRO C 174 " pdb=" NE1 TRP C 287 " model vdw 2.269 3.120 nonbonded pdb=" O PRO B 174 " pdb=" NE1 TRP B 287 " model vdw 2.270 3.120 nonbonded pdb=" CG ARG A 259 " pdb=" OE2 GLU B 261 " model vdw 2.295 3.440 nonbonded pdb=" CG ARG B 259 " pdb=" OE2 GLU C 261 " model vdw 2.301 3.440 ... (remaining 52320 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' } ncs_group { reference = chain 'E' selection = chain 'D' selection = chain 'F' } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 0.340 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: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 19.940 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.020 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:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6644 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 : 0.005 0.043 6735 Z= 0.321 Angle : 0.682 5.468 9195 Z= 0.372 Chirality : 0.045 0.234 1107 Planarity : 0.003 0.028 1152 Dihedral : 13.562 80.394 2490 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 17.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 0.52 % Allowed : 6.74 % Favored : 92.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -4.01 (0.24), residues: 855 helix: -1.00 (0.24), residues: 291 sheet: -3.58 (0.25), residues: 255 loop : -3.22 (0.30), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 230 HIS 0.001 0.000 HIS C 98 PHE 0.022 0.002 PHE A 232 TYR 0.015 0.002 TYR A 267 ARG 0.002 0.000 ARG B 175 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 220 time to evaluate : 0.709 Fit side-chains REVERT: A 131 HIS cc_start: 0.8117 (m-70) cc_final: 0.7282 (m-70) REVERT: A 220 MET cc_start: 0.6991 (tpp) cc_final: 0.6719 (tpp) REVERT: A 286 GLU cc_start: 0.7176 (pt0) cc_final: 0.6612 (pt0) REVERT: B 286 GLU cc_start: 0.7102 (pt0) cc_final: 0.6692 (pt0) outliers start: 3 outliers final: 0 residues processed: 220 average time/residue: 0.2036 time to fit residues: 57.8772 Evaluate side-chains 163 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 163 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 70 optimal weight: 4.9990 chunk 63 optimal weight: 0.8980 chunk 35 optimal weight: 0.9990 chunk 21 optimal weight: 8.9990 chunk 42 optimal weight: 5.9990 chunk 34 optimal weight: 7.9990 chunk 65 optimal weight: 5.9990 chunk 25 optimal weight: 3.9990 chunk 40 optimal weight: 0.8980 chunk 49 optimal weight: 0.0980 chunk 76 optimal weight: 0.7980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 186 GLN B 186 GLN C 98 HIS C 186 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.164247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.144033 restraints weight = 8904.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.144277 restraints weight = 8388.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.144277 restraints weight = 8073.577| |-----------------------------------------------------------------------------| r_work (final): 0.3554 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3558 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3558 r_free = 0.3558 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3555 r_free = 0.3555 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3555 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7071 moved from start: 0.2761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 6735 Z= 0.234 Angle : 0.650 7.079 9195 Z= 0.329 Chirality : 0.045 0.179 1107 Planarity : 0.004 0.029 1152 Dihedral : 8.562 58.476 1233 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.94 % Allowed : 21.59 % Favored : 75.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.53 (0.27), residues: 855 helix: 0.53 (0.28), residues: 297 sheet: -3.02 (0.25), residues: 309 loop : -2.20 (0.37), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 304 HIS 0.003 0.001 HIS C 98 PHE 0.025 0.002 PHE B 232 TYR 0.016 0.002 TYR A 201 ARG 0.006 0.001 ARG C 188 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 161 time to evaluate : 0.940 Fit side-chains REVERT: A 220 MET cc_start: 0.6817 (tpp) cc_final: 0.6478 (tpp) REVERT: B 188 ARG cc_start: 0.7791 (ttm-80) cc_final: 0.7320 (ttm170) REVERT: B 286 GLU cc_start: 0.7445 (pt0) cc_final: 0.7232 (pt0) outliers start: 17 outliers final: 11 residues processed: 170 average time/residue: 0.1787 time to fit residues: 40.7004 Evaluate side-chains 163 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 152 time to evaluate : 0.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 TYR Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain B residue 132 TYR Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 317 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 46 optimal weight: 3.9990 chunk 15 optimal weight: 0.9980 chunk 58 optimal weight: 0.9990 chunk 39 optimal weight: 0.8980 chunk 77 optimal weight: 0.7980 chunk 83 optimal weight: 10.0000 chunk 51 optimal weight: 0.7980 chunk 42 optimal weight: 0.8980 chunk 82 optimal weight: 5.9990 chunk 2 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 186 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.165116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.138921 restraints weight = 8989.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.140332 restraints weight = 7118.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.141906 restraints weight = 6120.767| |-----------------------------------------------------------------------------| r_work (final): 0.3559 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3559 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3559 r_free = 0.3559 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3559 r_free = 0.3559 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3559 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7216 moved from start: 0.3539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6735 Z= 0.230 Angle : 0.594 5.939 9195 Z= 0.299 Chirality : 0.043 0.196 1107 Planarity : 0.003 0.019 1152 Dihedral : 7.834 59.999 1233 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 7.43 % Allowed : 18.83 % Favored : 73.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.59 (0.28), residues: 855 helix: 1.24 (0.28), residues: 297 sheet: -2.40 (0.28), residues: 258 loop : -2.03 (0.36), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 304 HIS 0.002 0.000 HIS B 130 PHE 0.020 0.002 PHE C 232 TYR 0.021 0.002 TYR A 119 ARG 0.007 0.001 ARG A 188 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 162 time to evaluate : 0.682 Fit side-chains REVERT: A 220 MET cc_start: 0.6970 (tpp) cc_final: 0.6600 (tpp) REVERT: A 304 TRP cc_start: 0.7199 (m100) cc_final: 0.6954 (m100) REVERT: B 188 ARG cc_start: 0.7917 (ttm-80) cc_final: 0.7481 (ttm170) REVERT: C 152 GLN cc_start: 0.6853 (mp10) cc_final: 0.6522 (tm-30) REVERT: C 188 ARG cc_start: 0.7925 (ttm-80) cc_final: 0.7677 (ttm-80) REVERT: C 304 TRP cc_start: 0.7453 (m100) cc_final: 0.7242 (m100) outliers start: 43 outliers final: 23 residues processed: 191 average time/residue: 0.1816 time to fit residues: 45.4771 Evaluate side-chains 179 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 156 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 TYR Chi-restraints excluded: chain A residue 149 CYS Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 132 TYR Chi-restraints excluded: chain B residue 149 CYS Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain C residue 149 CYS Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain C residue 223 CYS Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 317 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 29 optimal weight: 0.9990 chunk 17 optimal weight: 0.7980 chunk 78 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 chunk 39 optimal weight: 0.6980 chunk 53 optimal weight: 0.7980 chunk 79 optimal weight: 0.8980 chunk 81 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 HIS A 186 GLN A 305 ASN C 130 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.185282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.152154 restraints weight = 8737.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.154576 restraints weight = 6519.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.155803 restraints weight = 5466.023| |-----------------------------------------------------------------------------| r_work (final): 0.3648 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3795 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3795 r_free = 0.3795 target_work(ls_wunit_k1) = 0.161 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3795 r_free = 0.3795 target_work(ls_wunit_k1) = 0.161 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3795 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7313 moved from start: 0.4299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6735 Z= 0.209 Angle : 0.570 5.950 9195 Z= 0.287 Chirality : 0.042 0.149 1107 Planarity : 0.003 0.023 1152 Dihedral : 7.396 58.697 1233 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 7.60 % Allowed : 18.83 % Favored : 73.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.39 (0.28), residues: 855 helix: 1.54 (0.27), residues: 297 sheet: -2.59 (0.27), residues: 285 loop : -1.59 (0.38), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 304 HIS 0.002 0.001 HIS C 130 PHE 0.025 0.001 PHE A 232 TYR 0.017 0.002 TYR C 227 ARG 0.005 0.001 ARG C 188 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 160 time to evaluate : 0.702 Fit side-chains REVERT: A 71 ILE cc_start: 0.8019 (OUTLIER) cc_final: 0.7766 (mm) REVERT: A 220 MET cc_start: 0.7061 (tpp) cc_final: 0.6772 (tpp) REVERT: A 304 TRP cc_start: 0.7476 (m100) cc_final: 0.7118 (m100) REVERT: B 124 GLN cc_start: 0.6577 (OUTLIER) cc_final: 0.6204 (pm20) REVERT: B 188 ARG cc_start: 0.8118 (ttm-80) cc_final: 0.7854 (ttm170) REVERT: B 286 GLU cc_start: 0.7565 (pt0) cc_final: 0.7153 (pt0) REVERT: C 152 GLN cc_start: 0.6904 (mp10) cc_final: 0.6611 (tm-30) REVERT: C 250 GLU cc_start: 0.6649 (OUTLIER) cc_final: 0.6100 (pt0) REVERT: C 304 TRP cc_start: 0.7642 (m100) cc_final: 0.7366 (m100) outliers start: 44 outliers final: 23 residues processed: 190 average time/residue: 0.2095 time to fit residues: 51.0624 Evaluate side-chains 184 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 158 time to evaluate : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 132 TYR Chi-restraints excluded: chain A residue 149 CYS Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain B residue 124 GLN Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 132 TYR Chi-restraints excluded: chain B residue 149 CYS Chi-restraints excluded: chain B residue 223 CYS Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 149 CYS Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain C residue 223 CYS Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 250 GLU Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 311 CYS Chi-restraints excluded: chain C residue 317 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 72 optimal weight: 0.9980 chunk 42 optimal weight: 5.9990 chunk 15 optimal weight: 4.9990 chunk 71 optimal weight: 0.9980 chunk 64 optimal weight: 8.9990 chunk 69 optimal weight: 0.9990 chunk 48 optimal weight: 4.9990 chunk 80 optimal weight: 3.9990 chunk 56 optimal weight: 10.0000 chunk 32 optimal weight: 0.9990 chunk 59 optimal weight: 0.9980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 221 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.163271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.143783 restraints weight = 9164.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.141809 restraints weight = 11911.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.142439 restraints weight = 12562.956| |-----------------------------------------------------------------------------| r_work (final): 0.3557 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3552 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3552 r_free = 0.3552 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3552 r_free = 0.3552 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3552 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7309 moved from start: 0.4792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 6735 Z= 0.236 Angle : 0.585 6.130 9195 Z= 0.294 Chirality : 0.043 0.156 1107 Planarity : 0.003 0.026 1152 Dihedral : 7.034 54.171 1233 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 7.60 % Allowed : 21.07 % Favored : 71.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.34 (0.28), residues: 855 helix: 1.36 (0.27), residues: 312 sheet: -2.58 (0.27), residues: 273 loop : -1.49 (0.37), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 304 HIS 0.001 0.001 HIS A 98 PHE 0.029 0.002 PHE B 219 TYR 0.013 0.002 TYR A 201 ARG 0.004 0.001 ARG A 188 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 167 time to evaluate : 0.757 Fit side-chains revert: symmetry clash REVERT: A 75 LEU cc_start: 0.7589 (OUTLIER) cc_final: 0.7376 (mm) REVERT: A 220 MET cc_start: 0.7033 (tpp) cc_final: 0.6608 (tpp) REVERT: A 250 GLU cc_start: 0.6072 (OUTLIER) cc_final: 0.5671 (pt0) REVERT: A 309 LEU cc_start: 0.7858 (tp) cc_final: 0.7270 (tp) REVERT: B 188 ARG cc_start: 0.8130 (ttm-80) cc_final: 0.7849 (ttm-80) REVERT: B 304 TRP cc_start: 0.7839 (m100) cc_final: 0.7473 (m100) REVERT: C 75 LEU cc_start: 0.7663 (OUTLIER) cc_final: 0.7414 (mm) REVERT: C 152 GLN cc_start: 0.6889 (mp10) cc_final: 0.6670 (tm-30) REVERT: C 182 LEU cc_start: 0.9355 (OUTLIER) cc_final: 0.9064 (pp) REVERT: C 250 GLU cc_start: 0.6778 (OUTLIER) cc_final: 0.6235 (pt0) outliers start: 44 outliers final: 33 residues processed: 197 average time/residue: 0.2057 time to fit residues: 52.6106 Evaluate side-chains 200 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 162 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 132 TYR Chi-restraints excluded: chain A residue 149 CYS Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 250 GLU Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 132 TYR Chi-restraints excluded: chain B residue 149 CYS Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 149 CYS Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain C residue 223 CYS Chi-restraints excluded: chain C residue 233 SER Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 250 GLU Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 311 CYS Chi-restraints excluded: chain C residue 317 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 9 optimal weight: 5.9990 chunk 32 optimal weight: 2.9990 chunk 35 optimal weight: 0.0980 chunk 7 optimal weight: 6.9990 chunk 62 optimal weight: 4.9990 chunk 70 optimal weight: 0.5980 chunk 13 optimal weight: 0.9980 chunk 82 optimal weight: 5.9990 chunk 17 optimal weight: 3.9990 chunk 44 optimal weight: 0.7980 chunk 12 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.162879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.142616 restraints weight = 8943.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.142616 restraints weight = 8459.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.142616 restraints weight = 8459.200| |-----------------------------------------------------------------------------| r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3544 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3544 r_free = 0.3544 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3544 r_free = 0.3544 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3544 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7338 moved from start: 0.5208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6735 Z= 0.209 Angle : 0.571 5.859 9195 Z= 0.287 Chirality : 0.042 0.162 1107 Planarity : 0.004 0.038 1152 Dihedral : 6.704 52.468 1233 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 6.91 % Allowed : 24.35 % Favored : 68.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.23 (0.28), residues: 855 helix: 1.54 (0.27), residues: 312 sheet: -2.60 (0.26), residues: 291 loop : -1.31 (0.39), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 304 HIS 0.001 0.000 HIS C 130 PHE 0.024 0.001 PHE C 232 TYR 0.012 0.002 TYR C 201 ARG 0.003 0.000 ARG B 188 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 169 time to evaluate : 0.833 Fit side-chains revert: symmetry clash REVERT: A 220 MET cc_start: 0.7052 (tpp) cc_final: 0.6643 (tpp) REVERT: A 250 GLU cc_start: 0.6051 (OUTLIER) cc_final: 0.5635 (pt0) REVERT: A 309 LEU cc_start: 0.7678 (tp) cc_final: 0.7128 (tp) REVERT: B 94 GLU cc_start: 0.7393 (tm-30) cc_final: 0.7107 (tm-30) REVERT: B 188 ARG cc_start: 0.8191 (ttm-80) cc_final: 0.7849 (ttm-80) REVERT: B 250 GLU cc_start: 0.6468 (OUTLIER) cc_final: 0.5953 (pt0) REVERT: B 304 TRP cc_start: 0.7845 (m100) cc_final: 0.7527 (m100) REVERT: C 75 LEU cc_start: 0.7561 (OUTLIER) cc_final: 0.7329 (mm) REVERT: C 152 GLN cc_start: 0.6908 (mp10) cc_final: 0.6684 (tm-30) REVERT: C 182 LEU cc_start: 0.9366 (OUTLIER) cc_final: 0.9051 (pp) REVERT: C 241 LYS cc_start: 0.8879 (OUTLIER) cc_final: 0.8651 (mtmm) REVERT: C 259 ARG cc_start: 0.8035 (mtp85) cc_final: 0.7494 (mtt90) outliers start: 40 outliers final: 27 residues processed: 198 average time/residue: 0.2086 time to fit residues: 52.6539 Evaluate side-chains 193 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 161 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 132 TYR Chi-restraints excluded: chain A residue 149 CYS Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 250 GLU Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 132 TYR Chi-restraints excluded: chain B residue 149 CYS Chi-restraints excluded: chain B residue 233 SER Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 250 GLU Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 149 CYS Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain C residue 223 CYS Chi-restraints excluded: chain C residue 241 LYS Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 310 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 73 optimal weight: 0.7980 chunk 27 optimal weight: 10.0000 chunk 54 optimal weight: 0.7980 chunk 33 optimal weight: 0.0020 chunk 70 optimal weight: 1.9990 chunk 83 optimal weight: 0.9990 chunk 55 optimal weight: 10.0000 chunk 44 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 overall best weight: 0.6790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 130 HIS C 186 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.164735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.148187 restraints weight = 8914.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.146594 restraints weight = 9969.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.147016 restraints weight = 10871.459| |-----------------------------------------------------------------------------| r_work (final): 0.3599 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3601 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3601 r_free = 0.3601 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3601 r_free = 0.3601 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3601 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7283 moved from start: 0.5438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6735 Z= 0.205 Angle : 0.573 8.052 9195 Z= 0.287 Chirality : 0.042 0.164 1107 Planarity : 0.004 0.035 1152 Dihedral : 6.308 52.716 1233 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 12.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 6.04 % Allowed : 26.25 % Favored : 67.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.09 (0.28), residues: 855 helix: 1.65 (0.27), residues: 312 sheet: -2.51 (0.27), residues: 291 loop : -1.25 (0.39), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP C 304 HIS 0.001 0.000 HIS C 98 PHE 0.036 0.002 PHE A 219 TYR 0.020 0.002 TYR C 201 ARG 0.002 0.000 ARG A 188 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 175 time to evaluate : 0.681 Fit side-chains revert: symmetry clash REVERT: A 94 GLU cc_start: 0.7310 (tm-30) cc_final: 0.7033 (tm-30) REVERT: A 220 MET cc_start: 0.7003 (tpp) cc_final: 0.6553 (tpp) REVERT: A 250 GLU cc_start: 0.6196 (OUTLIER) cc_final: 0.5741 (pt0) REVERT: B 188 ARG cc_start: 0.8223 (ttm-80) cc_final: 0.7898 (ttm-80) REVERT: B 250 GLU cc_start: 0.6557 (OUTLIER) cc_final: 0.6053 (pt0) REVERT: C 75 LEU cc_start: 0.7579 (OUTLIER) cc_final: 0.7361 (mm) REVERT: C 152 GLN cc_start: 0.7021 (mp10) cc_final: 0.6692 (tm-30) REVERT: C 182 LEU cc_start: 0.9347 (OUTLIER) cc_final: 0.9025 (pp) REVERT: C 259 ARG cc_start: 0.7962 (mtp85) cc_final: 0.7448 (mtt90) outliers start: 35 outliers final: 25 residues processed: 203 average time/residue: 0.2163 time to fit residues: 56.5798 Evaluate side-chains 194 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 165 time to evaluate : 0.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 149 CYS Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 250 GLU Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 149 CYS Chi-restraints excluded: chain B residue 233 SER Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 250 GLU Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 149 CYS Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain C residue 223 CYS Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 310 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 9 optimal weight: 6.9990 chunk 75 optimal weight: 0.8980 chunk 70 optimal weight: 3.9990 chunk 43 optimal weight: 0.6980 chunk 64 optimal weight: 5.9990 chunk 56 optimal weight: 10.0000 chunk 45 optimal weight: 0.6980 chunk 41 optimal weight: 0.8980 chunk 50 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 81 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.163109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.144789 restraints weight = 8977.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.143873 restraints weight = 11205.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.144742 restraints weight = 10524.282| |-----------------------------------------------------------------------------| r_work (final): 0.3578 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3572 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3572 r_free = 0.3572 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3572 r_free = 0.3572 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3572 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7328 moved from start: 0.5754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6735 Z= 0.219 Angle : 0.613 11.523 9195 Z= 0.300 Chirality : 0.043 0.269 1107 Planarity : 0.004 0.037 1152 Dihedral : 5.953 52.374 1233 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 12.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 5.87 % Allowed : 28.32 % Favored : 65.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.00 (0.28), residues: 855 helix: 1.76 (0.27), residues: 312 sheet: -2.47 (0.27), residues: 291 loop : -1.22 (0.38), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP C 304 HIS 0.001 0.000 HIS B 98 PHE 0.024 0.002 PHE A 219 TYR 0.016 0.001 TYR C 201 ARG 0.003 0.000 ARG A 153 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 168 time to evaluate : 0.741 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 94 GLU cc_start: 0.7410 (tm-30) cc_final: 0.7108 (tm-30) REVERT: A 220 MET cc_start: 0.7084 (tpp) cc_final: 0.6718 (tpp) REVERT: A 250 GLU cc_start: 0.6329 (OUTLIER) cc_final: 0.5892 (pt0) REVERT: B 94 GLU cc_start: 0.7404 (tm-30) cc_final: 0.7110 (tm-30) REVERT: B 188 ARG cc_start: 0.8220 (ttm-80) cc_final: 0.7930 (ttm-80) REVERT: B 250 GLU cc_start: 0.6725 (OUTLIER) cc_final: 0.6226 (pt0) REVERT: C 75 LEU cc_start: 0.7567 (OUTLIER) cc_final: 0.7350 (mm) REVERT: C 94 GLU cc_start: 0.7587 (tm-30) cc_final: 0.7363 (tm-30) REVERT: C 152 GLN cc_start: 0.7052 (mp10) cc_final: 0.6711 (tm-30) REVERT: C 259 ARG cc_start: 0.7952 (mtp85) cc_final: 0.7436 (mtt90) outliers start: 34 outliers final: 27 residues processed: 193 average time/residue: 0.2105 time to fit residues: 51.8329 Evaluate side-chains 191 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 161 time to evaluate : 0.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 149 CYS Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 250 GLU Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 149 CYS Chi-restraints excluded: chain B residue 233 SER Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 250 GLU Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 149 CYS Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain C residue 233 SER Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 310 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 48 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 68 optimal weight: 0.0010 chunk 10 optimal weight: 3.9990 chunk 34 optimal weight: 0.0010 chunk 11 optimal weight: 1.9990 chunk 76 optimal weight: 3.9990 chunk 16 optimal weight: 0.0980 chunk 56 optimal weight: 10.0000 chunk 23 optimal weight: 1.9990 overall best weight: 0.6196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.164339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.144540 restraints weight = 9058.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.143333 restraints weight = 12182.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.144207 restraints weight = 11193.644| |-----------------------------------------------------------------------------| r_work (final): 0.3570 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3566 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3566 r_free = 0.3566 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3566 r_free = 0.3566 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3566 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7336 moved from start: 0.5918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6735 Z= 0.196 Angle : 0.596 11.269 9195 Z= 0.293 Chirality : 0.042 0.233 1107 Planarity : 0.003 0.037 1152 Dihedral : 5.647 52.213 1233 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 13.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 5.70 % Allowed : 28.50 % Favored : 65.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.89 (0.28), residues: 855 helix: 1.89 (0.27), residues: 312 sheet: -2.47 (0.27), residues: 291 loop : -1.16 (0.39), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP C 304 HIS 0.001 0.000 HIS A 98 PHE 0.045 0.002 PHE C 219 TYR 0.014 0.001 TYR C 201 ARG 0.002 0.000 ARG C 188 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 160 time to evaluate : 0.702 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 220 MET cc_start: 0.7240 (tpp) cc_final: 0.6963 (tpp) REVERT: A 250 GLU cc_start: 0.6326 (OUTLIER) cc_final: 0.5832 (pt0) REVERT: B 94 GLU cc_start: 0.7499 (tm-30) cc_final: 0.7223 (tm-30) REVERT: B 165 VAL cc_start: 0.7091 (OUTLIER) cc_final: 0.6779 (m) REVERT: B 188 ARG cc_start: 0.8226 (ttm-80) cc_final: 0.7891 (ttm-80) REVERT: B 250 GLU cc_start: 0.6439 (OUTLIER) cc_final: 0.5934 (pt0) REVERT: C 75 LEU cc_start: 0.7535 (OUTLIER) cc_final: 0.7325 (mm) REVERT: C 94 GLU cc_start: 0.7645 (tm-30) cc_final: 0.7417 (tm-30) REVERT: C 152 GLN cc_start: 0.6874 (mp10) cc_final: 0.6615 (tm-30) REVERT: C 259 ARG cc_start: 0.7968 (mtp85) cc_final: 0.7452 (mtt90) outliers start: 33 outliers final: 25 residues processed: 182 average time/residue: 0.2175 time to fit residues: 49.7796 Evaluate side-chains 186 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 157 time to evaluate : 0.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 149 CYS Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 250 GLU Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 149 CYS Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 233 SER Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 250 GLU Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 149 CYS Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain C residue 233 SER Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 310 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 4 optimal weight: 4.9990 chunk 75 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 14 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 18 optimal weight: 0.9990 chunk 25 optimal weight: 3.9990 chunk 21 optimal weight: 0.9990 overall best weight: 1.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.163796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.145612 restraints weight = 9137.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.144161 restraints weight = 13293.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.141992 restraints weight = 14996.432| |-----------------------------------------------------------------------------| r_work (final): 0.3523 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3519 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3519 r_free = 0.3519 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3519 r_free = 0.3519 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3519 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7425 moved from start: 0.6288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 6735 Z= 0.290 Angle : 0.649 8.452 9195 Z= 0.324 Chirality : 0.044 0.291 1107 Planarity : 0.004 0.038 1152 Dihedral : 5.777 53.113 1233 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 12.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 5.35 % Allowed : 29.36 % Favored : 65.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.11 (0.28), residues: 855 helix: 1.87 (0.27), residues: 312 sheet: -2.70 (0.26), residues: 297 loop : -1.28 (0.38), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP C 304 HIS 0.002 0.001 HIS B 98 PHE 0.034 0.002 PHE C 219 TYR 0.029 0.002 TYR C 201 ARG 0.003 0.000 ARG A 216 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 155 time to evaluate : 0.681 Fit side-chains revert: symmetry clash REVERT: A 250 GLU cc_start: 0.6314 (OUTLIER) cc_final: 0.5893 (pt0) REVERT: B 94 GLU cc_start: 0.7616 (tm-30) cc_final: 0.7326 (tm-30) REVERT: B 188 ARG cc_start: 0.8246 (ttm-80) cc_final: 0.7974 (ttm-80) REVERT: C 75 LEU cc_start: 0.7529 (OUTLIER) cc_final: 0.7308 (mm) REVERT: C 94 GLU cc_start: 0.7676 (tm-30) cc_final: 0.7437 (tm-30) REVERT: C 152 GLN cc_start: 0.7062 (mp10) cc_final: 0.6757 (tm-30) REVERT: C 259 ARG cc_start: 0.7957 (mtp85) cc_final: 0.7489 (mtt90) outliers start: 31 outliers final: 25 residues processed: 179 average time/residue: 0.2236 time to fit residues: 50.7245 Evaluate side-chains 178 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 151 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 149 CYS Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 250 GLU Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 149 CYS Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 149 CYS Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain C residue 233 SER Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 310 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 55 optimal weight: 20.0000 chunk 10 optimal weight: 0.9980 chunk 78 optimal weight: 0.5980 chunk 33 optimal weight: 0.0070 chunk 13 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 31 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 42 optimal weight: 0.6980 chunk 8 optimal weight: 3.9990 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.162971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.144073 restraints weight = 9136.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.142839 restraints weight = 10776.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.143659 restraints weight = 10728.478| |-----------------------------------------------------------------------------| r_work (final): 0.3566 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3558 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3558 r_free = 0.3558 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3558 r_free = 0.3558 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3558 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7369 moved from start: 0.6389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6735 Z= 0.208 Angle : 0.607 9.134 9195 Z= 0.300 Chirality : 0.043 0.279 1107 Planarity : 0.004 0.041 1152 Dihedral : 5.625 52.865 1233 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 12.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 4.84 % Allowed : 30.74 % Favored : 64.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.94 (0.29), residues: 855 helix: 1.97 (0.27), residues: 312 sheet: -2.60 (0.26), residues: 297 loop : -1.15 (0.39), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 304 HIS 0.001 0.000 HIS A 98 PHE 0.034 0.002 PHE C 219 TYR 0.021 0.002 TYR A 201 ARG 0.003 0.000 ARG C 188 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2471.69 seconds wall clock time: 43 minutes 34.89 seconds (2614.89 seconds total)