Starting phenix.real_space_refine on Thu Jul 2 04:14:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7jnc_22404/07_2026/7jnc_22404.cif Found real_map, /net/cci-nas-00/data/ceres_data/7jnc_22404/07_2026/7jnc_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_22404/07_2026/7jnc_22404.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7jnc_22404/07_2026/7jnc_22404.map" model { file = "/net/cci-nas-00/data/ceres_data/7jnc_22404/07_2026/7jnc_22404.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7jnc_22404/07_2026/7jnc_22404.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7jnc_22404/07_2026/7jnc_22404.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7jnc_22404/07_2026/7jnc_22404.cif" } resolution = 3.73 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/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: {'ARG:plan': 5, 'PHE:plan': 2, 'ASN:plan1': 2, 'GLN:plan1': 7, 'GLU:plan': 4, 'ASP:plan': 5, 'TRP:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 118 Chain: "D" 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 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 chiralities: 3 Restraints were copied for chains: B, C, E, F Time building chain proxies: 1.23, per 1000 atoms: 0.19 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 B 128 " - pdb=" SG CYS B 149 " distance=2.03 Simple disulfide: pdb=" SG CYS C 128 " - pdb=" SG CYS C 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: 0.52 Conformation dependent library (CDL) restraints added in 277.8 milliseconds 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: 0.11 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: 0.91 Time building geometry restraints manager: 0.60 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: 3496 16.08 - 32.16: 281 32.16 - 48.24: 54 48.24 - 64.32: 12 64.32 - 80.39: 3 Dihedral angle restraints: 3846 sinusoidal: 1296 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 3843 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' 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: 0.500 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: 0.100 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.940 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6800 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 6753 Z= 0.236 Angle : 0.700 5.468 9246 Z= 0.376 Chirality : 0.045 0.234 1107 Planarity : 0.003 0.028 1152 Dihedral : 13.047 80.394 2175 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.002 0.000 ARG B 175 TYR 0.015 0.002 TYR A 267 PHE 0.022 0.002 PHE A 232 TRP 0.005 0.001 TRP C 230 HIS 0.001 0.000 HIS C 98 Details of bonding type rmsd/Z covalent geometry : bond 0.00488 / 0.24 ( 6735) covalent geometry : angle 0.68217 / 0.37 ( 9195) SS BOND : bond 0.00161 / 0.08 ( 3) SS BOND : angle 2.69178 / 1.51 ( 6) hydrogen bonds : bond 0.18701 / 12.46 ( 354) hydrogen bonds : angle 8.13157 / 5.59 ( 1035) link_BETA1-4 : bond 0.00166 / 0.08 ( 3) link_BETA1-4 : angle 2.69943 / 1.49 ( 9) link_NAG-ASN : bond 0.00444 / 0.30 ( 12) link_NAG-ASN : angle 2.02114 / 1.48 ( 36) *********************** 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 : 0.231 Fit side-chains REVERT: A 131 HIS cc_start: 0.8117 (m-70) cc_final: 0.7283 (m-70) REVERT: A 220 MET cc_start: 0.6992 (tpp) cc_final: 0.6720 (tpp) REVERT: A 286 GLU cc_start: 0.7175 (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: 0.0692 time to fit residues: 20.0037 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 : 0.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 49 optimal weight: 0.7980 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 8.9990 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 0.5980 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 0.6980 chunk 74 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3799 r_free = 0.3799 target = 0.163182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.139824 restraints weight = 9094.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.141059 restraints weight = 7591.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.141640 restraints weight = 6712.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.142644 restraints weight = 6244.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.142645 restraints weight = 5879.468| |-----------------------------------------------------------------------------| r_work (final): 0.3555 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3554 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3554 r_free = 0.3554 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 = 0.3550 r_free = 0.3550 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (9 function evaluations) r_final: 0.3550 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7169 moved from start: 0.2585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 6753 Z= 0.159 Angle : 0.662 9.768 9246 Z= 0.329 Chirality : 0.044 0.194 1107 Planarity : 0.004 0.026 1152 Dihedral : 4.707 15.763 918 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.94 % Allowed : 21.93 % Favored : 75.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.54 (0.27), residues: 855 helix: 0.55 (0.28), residues: 297 sheet: -3.05 (0.25), residues: 309 loop : -2.22 (0.36), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 188 TYR 0.015 0.002 TYR A 201 PHE 0.025 0.002 PHE B 232 TRP 0.016 0.001 TRP B 304 HIS 0.002 0.001 HIS C 98 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.16 ( 6735) covalent geometry : angle 0.63789 / 0.32 ( 9195) SS BOND : bond 0.00115 / 0.06 ( 3) SS BOND : angle 0.90181 / 0.50 ( 6) hydrogen bonds : bond 0.03919 / 2.66 ( 354) hydrogen bonds : angle 5.60990 / 3.91 ( 1035) link_BETA1-4 : bond 0.00429 / 0.22 ( 3) link_BETA1-4 : angle 2.12177 / 1.18 ( 9) link_NAG-ASN : bond 0.00626 / 0.46 ( 12) link_NAG-ASN : angle 2.68630 / 1.83 ( 36) *********************** 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 180 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 163 time to evaluate : 0.202 Fit side-chains REVERT: A 220 MET cc_start: 0.6966 (tpp) cc_final: 0.6572 (tpp) REVERT: B 153 ARG cc_start: 0.7516 (mtp-110) cc_final: 0.6893 (mmm160) outliers start: 17 outliers final: 11 residues processed: 172 average time/residue: 0.0649 time to fit residues: 15.3084 Evaluate side-chains 160 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 149 time to evaluate : 0.222 ------------------------------------------------------------------------------- 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 14 optimal weight: 4.9990 chunk 12 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 21 optimal weight: 5.9990 chunk 43 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 chunk 27 optimal weight: 10.0000 chunk 68 optimal weight: 2.9990 chunk 32 optimal weight: 0.7980 chunk 45 optimal weight: 0.9990 chunk 80 optimal weight: 0.2980 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 186 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.163413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.143718 restraints weight = 8989.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.144332 restraints weight = 8343.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.144422 restraints weight = 7916.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.144422 restraints weight = 7752.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.144422 restraints weight = 7752.617| |-----------------------------------------------------------------------------| r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3563 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3563 r_free = 0.3563 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3562 r_free = 0.3562 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (27 function evaluations) r_final: 0.3562 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7315 moved from start: 0.3378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6753 Z= 0.150 Angle : 0.604 5.889 9246 Z= 0.301 Chirality : 0.043 0.196 1107 Planarity : 0.003 0.022 1152 Dihedral : 4.542 17.268 918 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 6.74 % Allowed : 20.90 % Favored : 72.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.65 (0.28), residues: 855 helix: 1.26 (0.28), residues: 297 sheet: -2.43 (0.27), residues: 279 loop : -2.05 (0.38), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 188 TYR 0.020 0.002 TYR A 119 PHE 0.020 0.002 PHE C 232 TRP 0.014 0.001 TRP B 304 HIS 0.001 0.000 HIS A 98 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.15 ( 6735) covalent geometry : angle 0.59384 / 0.30 ( 9195) SS BOND : bond 0.00119 / 0.06 ( 3) SS BOND : angle 0.64192 / 0.32 ( 6) hydrogen bonds : bond 0.03661 / 2.49 ( 354) hydrogen bonds : angle 5.21115 / 3.65 ( 1035) link_BETA1-4 : bond 0.00438 / 0.23 ( 3) link_BETA1-4 : angle 1.73194 / 0.98 ( 9) link_NAG-ASN : bond 0.01111 / 0.73 ( 12) link_NAG-ASN : angle 1.63078 / 1.21 ( 36) *********************** 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 193 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 154 time to evaluate : 0.237 Fit side-chains REVERT: A 220 MET cc_start: 0.6899 (tpp) cc_final: 0.6553 (tpp) REVERT: B 152 GLN cc_start: 0.7025 (mp10) cc_final: 0.6591 (tm-30) REVERT: B 188 ARG cc_start: 0.7918 (ttm-80) cc_final: 0.7535 (ttm170) REVERT: C 152 GLN cc_start: 0.6792 (mp10) cc_final: 0.6519 (tm-30) REVERT: C 188 ARG cc_start: 0.7964 (ttm-80) cc_final: 0.7725 (ttm-80) outliers start: 39 outliers final: 21 residues processed: 178 average time/residue: 0.0632 time to fit residues: 15.5046 Evaluate side-chains 170 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 149 time to evaluate : 0.212 ------------------------------------------------------------------------------- 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 217 VAL Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain B residue 103 VAL 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 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 217 VAL 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 26 optimal weight: 0.8980 chunk 34 optimal weight: 10.0000 chunk 18 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 chunk 19 optimal weight: 2.9990 chunk 45 optimal weight: 4.9990 chunk 15 optimal weight: 4.9990 chunk 3 optimal weight: 0.9990 chunk 1 optimal weight: 4.9990 chunk 82 optimal weight: 5.9990 chunk 76 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 186 GLN A 305 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.161100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.140331 restraints weight = 9388.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.139282 restraints weight = 9116.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.139031 restraints weight = 9075.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.139090 restraints weight = 9210.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.139054 restraints weight = 9222.869| |-----------------------------------------------------------------------------| r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3467 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3467 r_free = 0.3467 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3467 r_free = 0.3467 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3467 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 0.4665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 6753 Z= 0.215 Angle : 0.694 8.258 9246 Z= 0.340 Chirality : 0.044 0.175 1107 Planarity : 0.004 0.031 1152 Dihedral : 4.713 16.498 918 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 8.98 % Allowed : 19.34 % Favored : 71.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.59 (0.28), residues: 855 helix: 1.32 (0.28), residues: 297 sheet: -2.69 (0.27), residues: 270 loop : -1.74 (0.35), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 188 TYR 0.020 0.002 TYR C 227 PHE 0.033 0.002 PHE A 232 TRP 0.028 0.002 TRP C 304 HIS 0.003 0.001 HIS B 130 Details of bonding type rmsd/Z covalent geometry : bond 0.00488 / 0.21 ( 6735) covalent geometry : angle 0.67950 / 0.34 ( 9195) SS BOND : bond 0.00205 / 0.10 ( 3) SS BOND : angle 0.70825 / 0.37 ( 6) hydrogen bonds : bond 0.03701 / 2.48 ( 354) hydrogen bonds : angle 5.30938 / 3.73 ( 1035) link_BETA1-4 : bond 0.00703 / 0.35 ( 3) link_BETA1-4 : angle 1.69375 / 0.94 ( 9) link_NAG-ASN : bond 0.00434 / 0.31 ( 12) link_NAG-ASN : angle 2.21299 / 1.57 ( 36) *********************** 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 214 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 162 time to evaluate : 0.274 Fit side-chains revert: symmetry clash REVERT: A 71 ILE cc_start: 0.8068 (OUTLIER) cc_final: 0.7818 (mm) REVERT: A 182 LEU cc_start: 0.9320 (OUTLIER) cc_final: 0.9090 (pp) REVERT: A 220 MET cc_start: 0.7139 (tpp) cc_final: 0.6850 (tpp) REVERT: A 221 GLN cc_start: 0.7137 (mt0) cc_final: 0.6931 (mt0) REVERT: A 309 LEU cc_start: 0.7699 (tp) cc_final: 0.7245 (tp) REVERT: B 124 GLN cc_start: 0.6781 (OUTLIER) cc_final: 0.6342 (pm20) REVERT: B 152 GLN cc_start: 0.7221 (mp10) cc_final: 0.6726 (tm-30) REVERT: B 188 ARG cc_start: 0.7994 (ttm-80) cc_final: 0.7653 (ttm-80) REVERT: B 221 GLN cc_start: 0.7531 (mt0) cc_final: 0.7313 (mt0) REVERT: B 238 THR cc_start: 0.9119 (t) cc_final: 0.8708 (p) REVERT: B 286 GLU cc_start: 0.7636 (pt0) cc_final: 0.7242 (pt0) REVERT: B 304 TRP cc_start: 0.7886 (m100) cc_final: 0.7576 (m100) REVERT: C 152 GLN cc_start: 0.7015 (mp10) cc_final: 0.6778 (tm-30) outliers start: 52 outliers final: 30 residues processed: 203 average time/residue: 0.0633 time to fit residues: 16.9998 Evaluate side-chains 186 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 153 time to evaluate : 0.190 ------------------------------------------------------------------------------- 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 150 THR Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 317 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 165 VAL Chi-restraints excluded: chain B residue 183 VAL 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 295 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 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 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 76 optimal weight: 3.9990 chunk 81 optimal weight: 2.9990 chunk 77 optimal weight: 0.9990 chunk 58 optimal weight: 2.9990 chunk 23 optimal weight: 0.5980 chunk 15 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 chunk 18 optimal weight: 0.7980 chunk 68 optimal weight: 5.9990 chunk 61 optimal weight: 0.9980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.163062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.138690 restraints weight = 9329.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.139406 restraints weight = 8324.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.140242 restraints weight = 7687.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.140242 restraints weight = 7309.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.140242 restraints weight = 7309.713| |-----------------------------------------------------------------------------| r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3519 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3519 r_free = 0.3519 target_work(ls_wunit_k1) = 0.139 | | 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) = 0.139 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3519 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7513 moved from start: 0.4998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6753 Z= 0.150 Angle : 0.617 9.905 9246 Z= 0.300 Chirality : 0.043 0.183 1107 Planarity : 0.004 0.040 1152 Dihedral : 4.552 16.071 918 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 7.43 % Allowed : 24.18 % Favored : 68.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.40 (0.28), residues: 855 helix: 1.57 (0.28), residues: 297 sheet: -2.66 (0.26), residues: 288 loop : -1.52 (0.38), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 188 TYR 0.020 0.002 TYR B 267 PHE 0.021 0.001 PHE A 232 TRP 0.017 0.002 TRP C 304 HIS 0.001 0.000 HIS B 98 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.15 ( 6735) covalent geometry : angle 0.60919 / 0.30 ( 9195) SS BOND : bond 0.00167 / 0.08 ( 3) SS BOND : angle 0.61057 / 0.33 ( 6) hydrogen bonds : bond 0.03484 / 2.35 ( 354) hydrogen bonds : angle 5.10204 / 3.59 ( 1035) link_BETA1-4 : bond 0.00499 / 0.25 ( 3) link_BETA1-4 : angle 1.56138 / 0.89 ( 9) link_NAG-ASN : bond 0.00223 / 0.14 ( 12) link_NAG-ASN : angle 1.48550 / 1.09 ( 36) *********************** 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 205 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 162 time to evaluate : 0.227 Fit side-chains REVERT: A 75 LEU cc_start: 0.7401 (OUTLIER) cc_final: 0.7145 (mm) REVERT: A 182 LEU cc_start: 0.9322 (OUTLIER) cc_final: 0.9096 (pp) REVERT: A 220 MET cc_start: 0.7137 (tpp) cc_final: 0.6804 (tpp) REVERT: A 309 LEU cc_start: 0.7549 (tp) cc_final: 0.7073 (tp) REVERT: B 152 GLN cc_start: 0.7138 (mp10) cc_final: 0.6638 (tm-30) REVERT: B 188 ARG cc_start: 0.8163 (ttm-80) cc_final: 0.7962 (ttm-80) REVERT: B 259 ARG cc_start: 0.8020 (mtp85) cc_final: 0.7772 (mtp-110) REVERT: B 304 TRP cc_start: 0.7880 (m100) cc_final: 0.7597 (m100) REVERT: C 75 LEU cc_start: 0.7394 (OUTLIER) cc_final: 0.7115 (mm) REVERT: C 152 GLN cc_start: 0.7080 (mp10) cc_final: 0.6673 (tm-30) REVERT: C 182 LEU cc_start: 0.9357 (OUTLIER) cc_final: 0.9068 (pp) REVERT: C 250 GLU cc_start: 0.6729 (OUTLIER) cc_final: 0.6181 (pt0) REVERT: C 259 ARG cc_start: 0.8288 (mtp85) cc_final: 0.8062 (mtp85) outliers start: 43 outliers final: 28 residues processed: 194 average time/residue: 0.0839 time to fit residues: 21.0125 Evaluate side-chains 184 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 151 time to evaluate : 0.340 ------------------------------------------------------------------------------- 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 182 LEU Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 245 VAL 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 165 VAL Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 295 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 149 CYS Chi-restraints excluded: chain C residue 150 THR 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 200 ASP 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 250 GLU Chi-restraints excluded: chain C residue 310 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 58 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 8 optimal weight: 4.9990 chunk 64 optimal weight: 7.9990 chunk 71 optimal weight: 2.9990 chunk 56 optimal weight: 10.0000 chunk 22 optimal weight: 0.9980 chunk 79 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3745 r_free = 0.3745 target = 0.158451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.134107 restraints weight = 9473.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.134687 restraints weight = 8607.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.134687 restraints weight = 8045.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.134687 restraints weight = 8045.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.134687 restraints weight = 8045.538| |-----------------------------------------------------------------------------| r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3451 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3451 r_free = 0.3451 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3451 r_free = 0.3451 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3451 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.5777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 6753 Z= 0.223 Angle : 0.715 11.525 9246 Z= 0.348 Chirality : 0.046 0.228 1107 Planarity : 0.004 0.039 1152 Dihedral : 4.858 18.875 918 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 13.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 9.50 % Allowed : 24.01 % Favored : 66.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.52 (0.28), residues: 855 helix: 1.44 (0.28), residues: 297 sheet: -2.77 (0.26), residues: 279 loop : -1.56 (0.36), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 216 TYR 0.019 0.002 TYR C 227 PHE 0.039 0.002 PHE B 219 TRP 0.018 0.002 TRP C 304 HIS 0.002 0.001 HIS C 130 Details of bonding type rmsd/Z covalent geometry : bond 0.00510 / 0.22 ( 6735) covalent geometry : angle 0.70561 / 0.35 ( 9195) SS BOND : bond 0.00230 / 0.11 ( 3) SS BOND : angle 0.86435 / 0.46 ( 6) hydrogen bonds : bond 0.03716 / 2.50 ( 354) hydrogen bonds : angle 5.28214 / 3.74 ( 1035) link_BETA1-4 : bond 0.00535 / 0.27 ( 3) link_BETA1-4 : angle 1.40496 / 0.80 ( 9) link_NAG-ASN : bond 0.00805 / 0.41 ( 12) link_NAG-ASN : angle 1.91372 / 1.43 ( 36) *********************** 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 202 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 147 time to evaluate : 0.157 Fit side-chains REVERT: A 250 GLU cc_start: 0.6359 (OUTLIER) cc_final: 0.5967 (pt0) REVERT: B 188 ARG cc_start: 0.8143 (ttm-80) cc_final: 0.7924 (ttm-80) REVERT: B 250 GLU cc_start: 0.6630 (OUTLIER) cc_final: 0.6139 (pt0) REVERT: B 259 ARG cc_start: 0.7947 (mtp85) cc_final: 0.7683 (mtp-110) REVERT: C 75 LEU cc_start: 0.7483 (OUTLIER) cc_final: 0.7273 (mm) REVERT: C 94 GLU cc_start: 0.7794 (tm-30) cc_final: 0.7494 (tm-30) REVERT: C 156 TYR cc_start: 0.8632 (p90) cc_final: 0.8378 (p90) REVERT: C 250 GLU cc_start: 0.6869 (OUTLIER) cc_final: 0.6372 (pt0) outliers start: 55 outliers final: 39 residues processed: 191 average time/residue: 0.0766 time to fit residues: 18.8318 Evaluate side-chains 190 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 147 time to evaluate : 0.202 ------------------------------------------------------------------------------- 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 157 THR Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 250 GLU 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 103 VAL 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 183 VAL Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 249 GLU 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 295 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 150 THR Chi-restraints excluded: chain C residue 154 ILE 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 250 GLU Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 311 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 47 optimal weight: 0.9990 chunk 41 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 33 optimal weight: 0.8980 chunk 8 optimal weight: 0.8980 chunk 15 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 chunk 64 optimal weight: 1.9990 chunk 7 optimal weight: 5.9990 chunk 21 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 130 HIS ** C 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.159078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.138173 restraints weight = 9230.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.138568 restraints weight = 8879.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.138568 restraints weight = 8681.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.138568 restraints weight = 8681.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.138568 restraints weight = 8681.706| |-----------------------------------------------------------------------------| r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3492 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3492 r_free = 0.3492 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3492 r_free = 0.3492 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3492 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.5984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6753 Z= 0.150 Angle : 0.645 11.004 9246 Z= 0.312 Chirality : 0.043 0.149 1107 Planarity : 0.004 0.039 1152 Dihedral : 4.637 18.431 918 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 12.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 6.74 % Allowed : 28.15 % Favored : 65.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.30 (0.28), residues: 855 helix: 1.65 (0.27), residues: 297 sheet: -2.61 (0.27), residues: 279 loop : -1.52 (0.35), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 188 TYR 0.024 0.002 TYR B 267 PHE 0.022 0.001 PHE C 232 TRP 0.019 0.002 TRP A 304 HIS 0.001 0.000 HIS B 98 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.15 ( 6735) covalent geometry : angle 0.63820 / 0.31 ( 9195) SS BOND : bond 0.00170 / 0.09 ( 3) SS BOND : angle 0.66557 / 0.35 ( 6) hydrogen bonds : bond 0.03466 / 2.33 ( 354) hydrogen bonds : angle 4.99246 / 3.52 ( 1035) link_BETA1-4 : bond 0.00479 / 0.24 ( 3) link_BETA1-4 : angle 1.44593 / 0.82 ( 9) link_NAG-ASN : bond 0.00561 / 0.30 ( 12) link_NAG-ASN : angle 1.46800 / 1.08 ( 36) *********************** 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 195 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 156 time to evaluate : 0.143 Fit side-chains revert: symmetry clash REVERT: A 250 GLU cc_start: 0.6344 (OUTLIER) cc_final: 0.5958 (pt0) REVERT: B 152 GLN cc_start: 0.7265 (tm-30) cc_final: 0.6801 (mp10) REVERT: B 188 ARG cc_start: 0.8183 (ttm-80) cc_final: 0.7944 (ttm-80) REVERT: B 250 GLU cc_start: 0.6746 (OUTLIER) cc_final: 0.6228 (pt0) REVERT: C 75 LEU cc_start: 0.7514 (OUTLIER) cc_final: 0.7290 (mm) REVERT: C 94 GLU cc_start: 0.7703 (tm-30) cc_final: 0.7405 (tm-30) REVERT: C 250 GLU cc_start: 0.6761 (OUTLIER) cc_final: 0.6307 (pt0) REVERT: C 259 ARG cc_start: 0.7720 (mtp85) cc_final: 0.7221 (mtt90) outliers start: 39 outliers final: 31 residues processed: 186 average time/residue: 0.0812 time to fit residues: 19.4213 Evaluate side-chains 181 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 146 time to evaluate : 0.229 ------------------------------------------------------------------------------- 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 124 GLN 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 233 SER 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 165 VAL 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 295 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 149 CYS Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 154 ILE 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 250 GLU 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 73 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 15 optimal weight: 0.0870 chunk 9 optimal weight: 10.0000 chunk 59 optimal weight: 1.9990 chunk 54 optimal weight: 0.7980 chunk 60 optimal weight: 3.9990 chunk 14 optimal weight: 0.7980 chunk 27 optimal weight: 20.0000 chunk 43 optimal weight: 0.7980 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 293 GLN ** C 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.162553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.141629 restraints weight = 9257.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.141922 restraints weight = 8841.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.141922 restraints weight = 8598.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.141922 restraints weight = 8598.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.141922 restraints weight = 8598.831| |-----------------------------------------------------------------------------| r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3527 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3527 r_free = 0.3527 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3527 r_free = 0.3527 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3527 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.6202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6753 Z= 0.138 Angle : 0.623 9.458 9246 Z= 0.304 Chirality : 0.043 0.231 1107 Planarity : 0.004 0.039 1152 Dihedral : 4.486 15.142 918 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 6.74 % Allowed : 28.50 % Favored : 64.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.11 (0.28), residues: 855 helix: 1.87 (0.27), residues: 297 sheet: -2.53 (0.26), residues: 297 loop : -1.33 (0.37), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 188 TYR 0.022 0.002 TYR B 267 PHE 0.041 0.002 PHE A 219 TRP 0.015 0.001 TRP B 304 HIS 0.001 0.000 HIS B 130 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 ( 6735) covalent geometry : angle 0.61812 / 0.30 ( 9195) SS BOND : bond 0.00084 / 0.04 ( 3) SS BOND : angle 0.63635 / 0.34 ( 6) hydrogen bonds : bond 0.03324 / 2.23 ( 354) hydrogen bonds : angle 4.83243 / 3.41 ( 1035) link_BETA1-4 : bond 0.00393 / 0.20 ( 3) link_BETA1-4 : angle 1.37923 / 0.78 ( 9) link_NAG-ASN : bond 0.00413 / 0.22 ( 12) link_NAG-ASN : angle 1.29784 / 0.95 ( 36) *********************** 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 203 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 164 time to evaluate : 0.235 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 250 GLU cc_start: 0.6337 (OUTLIER) cc_final: 0.5852 (pt0) REVERT: B 94 GLU cc_start: 0.7742 (tm-30) cc_final: 0.7473 (tm-30) REVERT: B 124 GLN cc_start: 0.7022 (OUTLIER) cc_final: 0.6551 (pm20) REVERT: B 152 GLN cc_start: 0.7191 (tm-30) cc_final: 0.6984 (mp10) REVERT: B 188 ARG cc_start: 0.8148 (ttm-80) cc_final: 0.7555 (ttm-80) REVERT: B 220 MET cc_start: 0.7004 (ttm) cc_final: 0.6793 (tpp) REVERT: B 250 GLU cc_start: 0.6304 (OUTLIER) cc_final: 0.5888 (pt0) REVERT: C 75 LEU cc_start: 0.7495 (OUTLIER) cc_final: 0.7265 (mm) REVERT: C 94 GLU cc_start: 0.7719 (tm-30) cc_final: 0.7417 (tm-30) REVERT: C 250 GLU cc_start: 0.6669 (OUTLIER) cc_final: 0.6205 (pt0) outliers start: 39 outliers final: 34 residues processed: 192 average time/residue: 0.0885 time to fit residues: 21.5027 Evaluate side-chains 190 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 151 time to evaluate : 0.237 ------------------------------------------------------------------------------- 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 118 LEU Chi-restraints excluded: chain A residue 124 GLN 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 245 VAL Chi-restraints excluded: chain A residue 250 GLU Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 266 ASN Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 103 VAL 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 165 VAL Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 249 GLU 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 149 CYS Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 154 ILE 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 250 GLU Chi-restraints excluded: chain C residue 266 ASN 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 61 optimal weight: 0.9990 chunk 15 optimal weight: 0.9990 chunk 69 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 chunk 25 optimal weight: 0.8980 chunk 62 optimal weight: 0.9980 chunk 24 optimal weight: 0.0670 chunk 45 optimal weight: 0.7980 chunk 17 optimal weight: 0.9990 chunk 81 optimal weight: 0.7980 overall best weight: 0.6718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.162542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.143424 restraints weight = 9222.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.141276 restraints weight = 8149.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.141100 restraints weight = 10094.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.141374 restraints weight = 9910.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.141405 restraints weight = 9074.643| |-----------------------------------------------------------------------------| r_work (final): 0.3522 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3521 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3521 r_free = 0.3521 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3521 r_free = 0.3521 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3521 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 moved from start: 0.6381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6753 Z= 0.138 Angle : 0.625 8.851 9246 Z= 0.307 Chirality : 0.042 0.216 1107 Planarity : 0.004 0.040 1152 Dihedral : 4.416 14.724 918 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 6.56 % Allowed : 29.53 % Favored : 63.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.88 (0.28), residues: 855 helix: 2.07 (0.27), residues: 297 sheet: -2.44 (0.28), residues: 279 loop : -1.31 (0.35), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 188 TYR 0.027 0.002 TYR C 156 PHE 0.031 0.002 PHE A 219 TRP 0.008 0.001 TRP B 304 HIS 0.001 0.000 HIS B 98 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.14 ( 6735) covalent geometry : angle 0.61988 / 0.31 ( 9195) SS BOND : bond 0.00089 / 0.04 ( 3) SS BOND : angle 0.65242 / 0.35 ( 6) hydrogen bonds : bond 0.03252 / 2.18 ( 354) hydrogen bonds : angle 4.74345 / 3.36 ( 1035) link_BETA1-4 : bond 0.00413 / 0.21 ( 3) link_BETA1-4 : angle 1.34785 / 0.76 ( 9) link_NAG-ASN : bond 0.00481 / 0.26 ( 12) link_NAG-ASN : angle 1.25472 / 0.91 ( 36) *********************** 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 192 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 154 time to evaluate : 0.185 Fit side-chains revert: symmetry clash REVERT: A 250 GLU cc_start: 0.6299 (OUTLIER) cc_final: 0.5832 (pt0) REVERT: B 94 GLU cc_start: 0.7746 (tm-30) cc_final: 0.7479 (tm-30) REVERT: B 165 VAL cc_start: 0.7284 (OUTLIER) cc_final: 0.6997 (m) REVERT: B 188 ARG cc_start: 0.8260 (ttm-80) cc_final: 0.7977 (ttm-80) REVERT: C 75 LEU cc_start: 0.7460 (OUTLIER) cc_final: 0.7238 (mm) REVERT: C 94 GLU cc_start: 0.7724 (tm-30) cc_final: 0.7411 (tm-30) REVERT: C 156 TYR cc_start: 0.8370 (p90) cc_final: 0.8103 (p90) REVERT: C 250 GLU cc_start: 0.6616 (OUTLIER) cc_final: 0.6132 (pt0) outliers start: 38 outliers final: 29 residues processed: 183 average time/residue: 0.0881 time to fit residues: 20.3370 Evaluate side-chains 185 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 152 time to evaluate : 0.230 ------------------------------------------------------------------------------- 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 124 GLN 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 A residue 266 ASN 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 165 VAL Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 249 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 149 CYS Chi-restraints excluded: chain C residue 154 ILE 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 250 GLU Chi-restraints excluded: chain C residue 266 ASN Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 311 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 33 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 6 optimal weight: 5.9990 chunk 13 optimal weight: 2.9990 chunk 1 optimal weight: 7.9990 chunk 16 optimal weight: 1.9990 chunk 73 optimal weight: 4.9990 chunk 45 optimal weight: 0.6980 chunk 56 optimal weight: 10.0000 chunk 48 optimal weight: 0.8980 chunk 62 optimal weight: 3.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.158593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.135592 restraints weight = 9348.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.134394 restraints weight = 9061.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.134525 restraints weight = 8873.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.134874 restraints weight = 8402.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.135077 restraints weight = 8137.745| |-----------------------------------------------------------------------------| r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3464 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3464 r_free = 0.3464 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3464 r_free = 0.3464 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3464 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.6633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 6753 Z= 0.227 Angle : 0.700 7.783 9246 Z= 0.347 Chirality : 0.045 0.243 1107 Planarity : 0.004 0.041 1152 Dihedral : 4.722 17.016 918 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 14.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 7.25 % Allowed : 28.50 % Favored : 64.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.16 (0.28), residues: 855 helix: 1.88 (0.28), residues: 297 sheet: -2.77 (0.26), residues: 279 loop : -1.31 (0.34), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 216 TYR 0.026 0.003 TYR C 156 PHE 0.030 0.002 PHE A 232 TRP 0.015 0.002 TRP B 304 HIS 0.002 0.001 HIS B 98 Details of bonding type rmsd/Z covalent geometry : bond 0.00523 / 0.23 ( 6735) covalent geometry : angle 0.69254 / 0.35 ( 9195) SS BOND : bond 0.00270 / 0.13 ( 3) SS BOND : angle 0.92483 / 0.51 ( 6) hydrogen bonds : bond 0.03575 / 2.40 ( 354) hydrogen bonds : angle 5.03505 / 3.56 ( 1035) link_BETA1-4 : bond 0.00519 / 0.26 ( 3) link_BETA1-4 : angle 1.24832 / 0.71 ( 9) link_NAG-ASN : bond 0.00420 / 0.23 ( 12) link_NAG-ASN : angle 1.62352 / 1.18 ( 36) ********************** 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 192 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 150 time to evaluate : 0.176 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 250 GLU cc_start: 0.6392 (OUTLIER) cc_final: 0.5981 (pt0) REVERT: A 318 PHE cc_start: 0.6479 (m-10) cc_final: 0.6249 (m-10) REVERT: B 94 GLU cc_start: 0.7901 (tm-30) cc_final: 0.7633 (tm-30) REVERT: B 124 GLN cc_start: 0.7072 (OUTLIER) cc_final: 0.6499 (pm20) REVERT: B 188 ARG cc_start: 0.8240 (ttm-80) cc_final: 0.7627 (ttm-80) REVERT: C 94 GLU cc_start: 0.7851 (tm-30) cc_final: 0.7503 (tm-30) REVERT: C 250 GLU cc_start: 0.6357 (OUTLIER) cc_final: 0.6016 (pt0) outliers start: 42 outliers final: 35 residues processed: 180 average time/residue: 0.0886 time to fit residues: 20.5112 Evaluate side-chains 187 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 149 time to evaluate : 0.143 ------------------------------------------------------------------------------- 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 124 GLN 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 217 VAL Chi-restraints excluded: chain A residue 233 SER 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 103 VAL 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 165 VAL Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 249 GLU Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 294 LYS Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 78 MET Chi-restraints excluded: chain C residue 149 CYS Chi-restraints excluded: chain C residue 154 ILE 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 245 VAL Chi-restraints excluded: chain C residue 250 GLU Chi-restraints excluded: chain C residue 265 VAL Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 311 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 9 optimal weight: 5.9990 chunk 47 optimal weight: 0.9980 chunk 27 optimal weight: 20.0000 chunk 38 optimal weight: 0.6980 chunk 8 optimal weight: 5.9990 chunk 51 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 65 optimal weight: 7.9990 chunk 42 optimal weight: 2.9990 chunk 44 optimal weight: 0.0040 chunk 61 optimal weight: 0.6980 overall best weight: 0.6792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.161244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.137985 restraints weight = 9291.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.138542 restraints weight = 9331.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.138916 restraints weight = 7783.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.138925 restraints weight = 7434.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.139059 restraints weight = 7501.194| |-----------------------------------------------------------------------------| r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3503 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3503 r_free = 0.3503 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3503 r_free = 0.3503 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3503 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 moved from start: 0.6801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6753 Z= 0.142 Angle : 0.631 8.435 9246 Z= 0.312 Chirality : 0.043 0.273 1107 Planarity : 0.004 0.041 1152 Dihedral : 4.488 15.165 918 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 12.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 5.35 % Allowed : 29.71 % Favored : 64.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.85 (0.29), residues: 855 helix: 2.17 (0.28), residues: 297 sheet: -2.48 (0.27), residues: 291 loop : -1.23 (0.36), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 188 TYR 0.026 0.002 TYR C 156 PHE 0.029 0.002 PHE A 219 TRP 0.011 0.001 TRP C 304 HIS 0.001 0.000 HIS A 130 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.14 ( 6735) covalent geometry : angle 0.62568 / 0.31 ( 9195) SS BOND : bond 0.00187 / 0.09 ( 3) SS BOND : angle 0.71428 / 0.38 ( 6) hydrogen bonds : bond 0.03312 / 2.24 ( 354) hydrogen bonds : angle 4.79701 / 3.41 ( 1035) link_BETA1-4 : bond 0.00376 / 0.19 ( 3) link_BETA1-4 : angle 1.29776 / 0.73 ( 9) link_NAG-ASN : bond 0.00423 / 0.24 ( 12) link_NAG-ASN : angle 1.30013 / 0.94 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1083.55 seconds wall clock time: 19 minutes 21.59 seconds (1161.59 seconds total)