Starting phenix.real_space_refine on Wed Sep 17 07:15:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7jnc_22404/09_2025/7jnc_22404.cif Found real_map, /net/cci-nas-00/data/ceres_data/7jnc_22404/09_2025/7jnc_22404.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.73 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7jnc_22404/09_2025/7jnc_22404.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7jnc_22404/09_2025/7jnc_22404.map" model { file = "/net/cci-nas-00/data/ceres_data/7jnc_22404/09_2025/7jnc_22404.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7jnc_22404/09_2025/7jnc_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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Restraints were copied for chains: B, C, E, F Time building chain proxies: 1.37, per 1000 atoms: 0.21 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: 0.63 Conformation dependent library (CDL) restraints added in 381.0 milliseconds Enol-peptide restraints added in 1.2 microseconds 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: 0.27 Creating SS restraints... Processing helix chain 'A' and resid 53 through 96 removed outlier: 4.215A pdb=" N PHE A 57 " --> pdb=" O SER A 53 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N ALA A 60 " --> pdb=" O ARG A 56 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N CYS A 61 " --> pdb=" O PHE A 57 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LYS A 95 " --> pdb=" O ASP A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 212 Processing helix chain 'A' and resid 215 through 226 Processing helix chain 'A' and resid 297 through 302 removed outlier: 3.777A pdb=" N ASN A 302 " --> pdb=" O ILE A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 339 removed outlier: 3.920A pdb=" N THR A 306 " --> pdb=" O ASN A 302 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA A 308 " --> pdb=" O TRP A 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 54 through 96 removed outlier: 4.443A pdb=" N ALA B 60 " --> pdb=" O ARG B 56 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N CYS B 61 " --> pdb=" O PHE B 57 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LYS B 95 " --> pdb=" O ASP B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 212 Processing helix chain 'B' and resid 215 through 226 Processing helix chain 'B' and resid 297 through 302 removed outlier: 3.777A pdb=" N ASN B 302 " --> pdb=" O ILE B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 339 removed outlier: 3.920A pdb=" N THR B 306 " --> pdb=" O ASN B 302 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA B 308 " --> pdb=" O TRP B 304 " (cutoff:3.500A) Processing helix chain 'C' and resid 54 through 96 removed outlier: 4.442A pdb=" N ALA C 60 " --> pdb=" O ARG C 56 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N CYS C 61 " --> pdb=" O PHE C 57 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LYS C 95 " --> pdb=" O ASP C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 212 Processing helix chain 'C' and resid 215 through 226 Processing helix chain 'C' and resid 297 through 302 removed outlier: 3.777A pdb=" N ASN C 302 " --> pdb=" O ILE C 298 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 339 removed outlier: 3.920A pdb=" N THR C 306 " --> pdb=" O ASN C 302 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA C 308 " --> pdb=" O TRP C 304 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 100 through 101 removed outlier: 5.519A pdb=" N LEU B 244 " --> pdb=" O PHE B 291 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 254 through 258 removed outlier: 5.519A pdb=" N LEU A 244 " --> pdb=" O PHE A 291 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 118 through 119 removed outlier: 4.023A pdb=" N ASP A 200 " --> pdb=" O TYR A 119 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ILE A 199 " --> pdb=" O PHE A 232 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N PHE A 232 " --> pdb=" O ILE A 199 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 124 through 131 removed outlier: 6.383A pdb=" N GLN A 186 " --> pdb=" O LEU A 126 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N CYS A 128 " --> pdb=" O PHE A 184 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N PHE A 184 " --> pdb=" O CYS A 128 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N HIS A 130 " --> pdb=" O LEU A 182 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N LEU A 182 " --> pdb=" O HIS A 130 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N PHE A 282 " --> pdb=" O PHE A 236 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LYS A 241 " --> pdb=" O GLU A 261 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLU A 261 " --> pdb=" O LYS A 241 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 151 through 157 removed outlier: 3.550A pdb=" N TYR A 156 " --> pdb=" O LYS A 166 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 100 through 101 removed outlier: 5.520A pdb=" N LEU C 244 " --> pdb=" O PHE C 291 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 118 through 119 removed outlier: 4.023A pdb=" N ASP B 200 " --> pdb=" O TYR B 119 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ILE B 199 " --> pdb=" O PHE B 232 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N PHE B 232 " --> pdb=" O ILE B 199 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 124 through 131 removed outlier: 6.383A pdb=" N GLN B 186 " --> pdb=" O LEU B 126 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N CYS B 128 " --> pdb=" O PHE B 184 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N PHE B 184 " --> pdb=" O CYS B 128 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N HIS B 130 " --> pdb=" O LEU B 182 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N LEU B 182 " --> pdb=" O HIS B 130 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N PHE B 282 " --> pdb=" O PHE B 236 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LYS B 241 " --> pdb=" O GLU B 261 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLU B 261 " --> pdb=" O LYS B 241 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 151 through 157 removed outlier: 3.550A pdb=" N TYR B 156 " --> pdb=" O LYS B 166 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 118 through 119 removed outlier: 4.023A pdb=" N ASP C 200 " --> pdb=" O TYR C 119 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ILE C 199 " --> pdb=" O PHE C 232 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N PHE C 232 " --> pdb=" O ILE C 199 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 124 through 131 removed outlier: 6.383A pdb=" N GLN C 186 " --> pdb=" O LEU C 126 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N CYS C 128 " --> pdb=" O PHE C 184 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N PHE C 184 " --> pdb=" O CYS C 128 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N HIS C 130 " --> pdb=" O LEU C 182 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N LEU C 182 " --> pdb=" O HIS C 130 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N PHE C 282 " --> pdb=" O PHE C 236 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LYS C 241 " --> pdb=" O GLU C 261 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLU C 261 " --> pdb=" O LYS C 241 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 151 through 157 removed outlier: 3.550A pdb=" N TYR C 156 " --> pdb=" O LYS C 166 " (cutoff:3.500A) 354 hydrogen bonds defined for protein. 1035 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.16 Time building geometry restraints manager: 0.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2049 1.35 - 1.47: 1758 1.47 - 1.58: 2892 1.58 - 1.70: 0 1.70 - 1.82: 36 Bond restraints: 6735 Sorted by residual: bond pdb=" N LYS B 319 " pdb=" CA LYS B 319 " ideal model delta sigma weight residual 1.459 1.487 -0.028 1.20e-02 6.94e+03 5.52e+00 bond pdb=" N LYS C 319 " pdb=" CA LYS C 319 " ideal model delta sigma weight residual 1.459 1.487 -0.028 1.20e-02 6.94e+03 5.31e+00 bond pdb=" N LYS A 319 " pdb=" CA LYS A 319 " ideal model delta sigma weight residual 1.459 1.487 -0.027 1.20e-02 6.94e+03 5.22e+00 bond pdb=" N PHE A 318 " pdb=" CA PHE A 318 " ideal model delta sigma weight residual 1.459 1.485 -0.026 1.17e-02 7.31e+03 4.92e+00 bond pdb=" N PHE B 318 " pdb=" CA PHE B 318 " ideal model delta sigma weight residual 1.459 1.485 -0.026 1.17e-02 7.31e+03 4.87e+00 ... (remaining 6730 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.09: 8405 1.09 - 2.19: 619 2.19 - 3.28: 134 3.28 - 4.37: 17 4.37 - 5.47: 20 Bond angle restraints: 9195 Sorted by residual: angle pdb=" CA LYS B 319 " pdb=" C LYS B 319 " pdb=" O LYS B 319 " ideal model delta sigma weight residual 120.90 118.00 2.90 1.07e+00 8.73e-01 7.36e+00 angle pdb=" CA LYS A 319 " pdb=" C LYS A 319 " pdb=" O LYS A 319 " ideal model delta sigma weight residual 120.90 118.00 2.90 1.07e+00 8.73e-01 7.35e+00 angle pdb=" CA LYS C 319 " pdb=" C LYS C 319 " pdb=" O LYS C 319 " ideal model delta sigma weight residual 120.90 118.03 2.87 1.07e+00 8.73e-01 7.19e+00 angle pdb=" O PHE B 318 " pdb=" C PHE B 318 " pdb=" N LYS B 319 " ideal model delta sigma weight residual 122.03 124.55 -2.52 1.04e+00 9.25e-01 5.87e+00 angle pdb=" O PHE C 318 " pdb=" C PHE C 318 " pdb=" N LYS C 319 " ideal model delta sigma weight residual 122.03 124.50 -2.47 1.04e+00 9.25e-01 5.64e+00 ... (remaining 9190 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.08: 3763 16.08 - 32.16: 299 32.16 - 48.24: 66 48.24 - 64.32: 30 64.32 - 80.39: 3 Dihedral angle restraints: 4161 sinusoidal: 1611 harmonic: 2550 Sorted by residual: dihedral pdb=" CB CYS C 128 " pdb=" SG CYS C 128 " pdb=" SG CYS C 149 " pdb=" CB CYS C 149 " ideal model delta sinusoidal sigma weight residual 93.00 41.20 51.80 1 1.00e+01 1.00e-02 3.66e+01 dihedral pdb=" CB CYS A 128 " pdb=" SG CYS A 128 " pdb=" SG CYS A 149 " pdb=" CB CYS A 149 " ideal model delta sinusoidal sigma weight residual 93.00 41.23 51.77 1 1.00e+01 1.00e-02 3.66e+01 dihedral pdb=" CB CYS B 128 " pdb=" SG CYS B 128 " pdb=" SG CYS B 149 " pdb=" CB CYS B 149 " ideal model delta sinusoidal sigma weight residual 93.00 41.24 51.76 1 1.00e+01 1.00e-02 3.66e+01 ... (remaining 4158 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 837 0.047 - 0.094: 224 0.094 - 0.140: 40 0.140 - 0.187: 3 0.187 - 0.234: 3 Chirality restraints: 1107 Sorted by residual: chirality pdb=" CA PHE A 318 " pdb=" N PHE A 318 " pdb=" C PHE A 318 " pdb=" CB PHE A 318 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.37e+00 chirality pdb=" CA PHE B 318 " pdb=" N PHE B 318 " pdb=" C PHE B 318 " pdb=" CB PHE B 318 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" CA PHE C 318 " pdb=" N PHE C 318 " pdb=" C PHE C 318 " pdb=" CB PHE C 318 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.33e+00 ... (remaining 1104 not shown) Planarity restraints: 1164 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 232 " -0.014 2.00e-02 2.50e+03 1.02e-02 1.82e+00 pdb=" CG PHE A 232 " 0.022 2.00e-02 2.50e+03 pdb=" CD1 PHE A 232 " 0.000 2.00e-02 2.50e+03 pdb=" CD2 PHE A 232 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE A 232 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 232 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE A 232 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 232 " 0.014 2.00e-02 2.50e+03 1.02e-02 1.81e+00 pdb=" CG PHE B 232 " -0.022 2.00e-02 2.50e+03 pdb=" CD1 PHE B 232 " -0.000 2.00e-02 2.50e+03 pdb=" CD2 PHE B 232 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE B 232 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE B 232 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHE B 232 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 232 " 0.014 2.00e-02 2.50e+03 1.01e-02 1.79e+00 pdb=" CG PHE C 232 " -0.022 2.00e-02 2.50e+03 pdb=" CD1 PHE C 232 " -0.000 2.00e-02 2.50e+03 pdb=" CD2 PHE C 232 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE C 232 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE C 232 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHE C 232 " 0.006 2.00e-02 2.50e+03 ... (remaining 1161 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 1760 2.80 - 3.32: 6510 3.32 - 3.85: 10764 3.85 - 4.37: 12187 4.37 - 4.90: 21104 Nonbonded interactions: 52325 Sorted by model distance: nonbonded pdb=" O PRO A 174 " pdb=" NE1 TRP A 287 " model vdw 2.269 3.120 nonbonded pdb=" O PRO C 174 " pdb=" NE1 TRP C 287 " model vdw 2.269 3.120 nonbonded pdb=" O PRO B 174 " pdb=" NE1 TRP B 287 " model vdw 2.270 3.120 nonbonded pdb=" CG ARG A 259 " pdb=" OE2 GLU B 261 " model vdw 2.295 3.440 nonbonded pdb=" CG ARG B 259 " pdb=" OE2 GLU C 261 " model vdw 2.301 3.440 ... (remaining 52320 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 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: 0.770 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: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.170 Find NCS groups from input model: 0.050 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:1.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6644 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 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 : 13.562 80.394 2490 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 17.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 0.52 % Allowed : 6.74 % Favored : 92.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -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 covalent geometry : bond 0.00488 ( 6735) covalent geometry : angle 0.68217 ( 9195) SS BOND : bond 0.00161 ( 3) SS BOND : angle 2.69178 ( 6) hydrogen bonds : bond 0.18701 ( 354) hydrogen bonds : angle 8.13157 ( 1035) link_BETA1-4 : bond 0.00166 ( 3) link_BETA1-4 : angle 2.69943 ( 9) link_NAG-ASN : bond 0.00444 ( 12) link_NAG-ASN : angle 2.02114 ( 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 : 0.229 Fit side-chains REVERT: A 131 HIS cc_start: 0.8117 (m-70) cc_final: 0.7282 (m-70) REVERT: A 220 MET cc_start: 0.6991 (tpp) cc_final: 0.6719 (tpp) REVERT: A 286 GLU cc_start: 0.7176 (pt0) cc_final: 0.6612 (pt0) REVERT: B 286 GLU cc_start: 0.7102 (pt0) cc_final: 0.6692 (pt0) outliers start: 3 outliers final: 0 residues processed: 220 average time/residue: 0.0828 time to fit residues: 23.7104 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 : 0.199 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 186 GLN A 293 GLN B 186 GLN B 293 GLN C 98 HIS C 186 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.163123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.139680 restraints weight = 9083.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.140677 restraints weight = 7620.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.141715 restraints weight = 6783.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.142525 restraints weight = 6245.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.142526 restraints weight = 5869.581| |-----------------------------------------------------------------------------| r_work (final): 0.3550 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3552 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3552 r_free = 0.3552 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3548 r_free = 0.3548 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3548 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7021 moved from start: 0.2515 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= 0.166 Angle : 0.664 9.967 9246 Z= 0.331 Chirality : 0.044 0.194 1107 Planarity : 0.004 0.026 1152 Dihedral : 8.681 57.952 1233 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.94 % Allowed : 21.76 % Favored : 75.30 % 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 aren not related in a simple way. whole: -2.58 (0.27), residues: 855 helix: 0.53 (0.28), residues: 297 sheet: -3.08 (0.25), residues: 309 loop : -2.26 (0.36), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 188 TYR 0.014 0.002 TYR A 201 PHE 0.024 0.002 PHE B 232 TRP 0.014 0.001 TRP B 304 HIS 0.002 0.001 HIS C 98 Details of bonding type rmsd covalent geometry : bond 0.00384 ( 6735) covalent geometry : angle 0.63663 ( 9195) SS BOND : bond 0.00091 ( 3) SS BOND : angle 0.92648 ( 6) hydrogen bonds : bond 0.04197 ( 354) hydrogen bonds : angle 5.66948 ( 1035) link_BETA1-4 : bond 0.00682 ( 3) link_BETA1-4 : angle 2.24894 ( 9) link_NAG-ASN : bond 0.00276 ( 12) link_NAG-ASN : angle 2.85490 ( 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 176 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 159 time to evaluate : 0.171 Fit side-chains REVERT: A 220 MET cc_start: 0.6958 (tpp) cc_final: 0.6565 (tpp) REVERT: B 153 ARG cc_start: 0.7543 (mtp-110) cc_final: 0.6883 (mmm160) REVERT: B 188 ARG cc_start: 0.7784 (ttm-80) cc_final: 0.7213 (ttm170) outliers start: 17 outliers final: 11 residues processed: 168 average time/residue: 0.0729 time to fit residues: 16.4514 Evaluate side-chains 156 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 145 time to evaluate : 0.236 ------------------------------------------------------------------------------- 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: 3.9990 chunk 19 optimal weight: 0.6980 chunk 21 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 27 optimal weight: 10.0000 chunk 68 optimal weight: 2.9990 chunk 32 optimal weight: 0.8980 chunk 45 optimal weight: 0.5980 chunk 80 optimal weight: 0.0770 overall best weight: 1.0540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 293 GLN B 186 GLN B 293 GLN C 186 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.165268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.138860 restraints weight = 8824.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.140526 restraints weight = 7091.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.141194 restraints weight = 6142.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.142096 restraints weight = 5676.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.142527 restraints weight = 5340.765| |-----------------------------------------------------------------------------| r_work (final): 0.3553 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3553 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3553 r_free = 0.3553 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3553 r_free = 0.3553 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3553 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7222 moved from start: 0.3489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 6753 Z= 0.170 Angle : 0.645 5.985 9246 Z= 0.317 Chirality : 0.045 0.231 1107 Planarity : 0.004 0.033 1152 Dihedral : 7.967 59.644 1233 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 7.77 % Allowed : 21.07 % Favored : 71.16 % 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 aren not related in a simple way. whole: -1.68 (0.28), residues: 855 helix: 1.16 (0.28), residues: 297 sheet: -2.36 (0.28), residues: 273 loop : -2.11 (0.37), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 188 TYR 0.019 0.002 TYR A 119 PHE 0.022 0.002 PHE C 232 TRP 0.017 0.002 TRP B 304 HIS 0.001 0.000 HIS C 130 Details of bonding type rmsd covalent geometry : bond 0.00391 ( 6735) covalent geometry : angle 0.63310 ( 9195) SS BOND : bond 0.00104 ( 3) SS BOND : angle 0.78254 ( 6) hydrogen bonds : bond 0.03801 ( 354) hydrogen bonds : angle 5.26423 ( 1035) link_BETA1-4 : bond 0.00452 ( 3) link_BETA1-4 : angle 1.78092 ( 9) link_NAG-ASN : bond 0.00660 ( 12) link_NAG-ASN : angle 1.85718 ( 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 198 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 153 time to evaluate : 0.236 Fit side-chains REVERT: A 188 ARG cc_start: 0.7916 (ttm-80) cc_final: 0.7648 (ttm170) REVERT: A 220 MET cc_start: 0.6854 (tpp) cc_final: 0.6501 (tpp) REVERT: B 152 GLN cc_start: 0.7011 (mp10) cc_final: 0.6637 (tm-30) REVERT: B 188 ARG cc_start: 0.7918 (ttm-80) cc_final: 0.7505 (ttm170) REVERT: B 286 GLU cc_start: 0.7590 (pt0) cc_final: 0.7130 (pt0) REVERT: C 152 GLN cc_start: 0.6912 (mp10) cc_final: 0.6618 (tm-30) outliers start: 45 outliers final: 26 residues processed: 186 average time/residue: 0.0713 time to fit residues: 17.8463 Evaluate side-chains 175 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 149 time to evaluate : 0.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 TYR Chi-restraints excluded: chain A residue 149 CYS Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 315 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 150 THR 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 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 311 CYS 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: 0.9990 chunk 34 optimal weight: 6.9990 chunk 18 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 15 optimal weight: 0.7980 chunk 3 optimal weight: 1.9990 chunk 1 optimal weight: 5.9990 chunk 82 optimal weight: 4.9990 chunk 76 optimal weight: 4.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 186 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.158252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.141588 restraints weight = 9236.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.140252 restraints weight = 11453.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.140851 restraints weight = 12464.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.140704 restraints weight = 9845.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.141045 restraints weight = 9412.888| |-----------------------------------------------------------------------------| r_work (final): 0.3539 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3542 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3542 r_free = 0.3542 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3542 r_free = 0.3542 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3542 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7399 moved from start: 0.4859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 6753 Z= 0.260 Angle : 0.709 5.990 9246 Z= 0.354 Chirality : 0.047 0.186 1107 Planarity : 0.004 0.031 1152 Dihedral : 7.358 52.193 1233 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 13.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 9.15 % Allowed : 19.86 % Favored : 70.98 % 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 aren not related in a simple way. whole: -1.84 (0.28), residues: 855 helix: 1.12 (0.28), residues: 297 sheet: -2.87 (0.26), residues: 285 loop : -1.71 (0.37), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 188 TYR 0.023 0.002 TYR B 267 PHE 0.033 0.002 PHE A 232 TRP 0.033 0.003 TRP C 304 HIS 0.002 0.001 HIS C 130 Details of bonding type rmsd covalent geometry : bond 0.00599 ( 6735) covalent geometry : angle 0.69572 ( 9195) SS BOND : bond 0.00225 ( 3) SS BOND : angle 0.79886 ( 6) hydrogen bonds : bond 0.03996 ( 354) hydrogen bonds : angle 5.47993 ( 1035) link_BETA1-4 : bond 0.00865 ( 3) link_BETA1-4 : angle 1.92440 ( 9) link_NAG-ASN : bond 0.00694 ( 12) link_NAG-ASN : angle 2.13764 ( 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 210 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 157 time to evaluate : 0.206 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 156 TYR cc_start: 0.8527 (p90) cc_final: 0.8181 (p90) REVERT: A 220 MET cc_start: 0.6984 (tpp) cc_final: 0.6552 (tpp) REVERT: A 221 GLN cc_start: 0.7360 (mt0) cc_final: 0.7159 (mt0) REVERT: A 238 THR cc_start: 0.9086 (t) cc_final: 0.8874 (p) REVERT: A 254 GLU cc_start: 0.7700 (pt0) cc_final: 0.7479 (pt0) REVERT: B 124 GLN cc_start: 0.7016 (OUTLIER) cc_final: 0.6498 (pm20) REVERT: B 152 GLN cc_start: 0.7318 (mp10) cc_final: 0.6942 (tm-30) REVERT: B 188 ARG cc_start: 0.8134 (ttm-80) cc_final: 0.7597 (ttm-80) REVERT: B 238 THR cc_start: 0.9119 (t) cc_final: 0.8747 (p) outliers start: 53 outliers final: 31 residues processed: 199 average time/residue: 0.0807 time to fit residues: 21.0455 Evaluate side-chains 186 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 154 time to evaluate : 0.228 ------------------------------------------------------------------------------- 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 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 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 150 THR Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 149 CYS Chi-restraints excluded: chain C residue 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 245 VAL Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 311 CYS Chi-restraints excluded: chain C residue 317 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 76 optimal weight: 2.9990 chunk 81 optimal weight: 0.9990 chunk 77 optimal weight: 0.0670 chunk 58 optimal weight: 3.9990 chunk 23 optimal weight: 0.6980 chunk 15 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 67 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 chunk 68 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 overall best weight: 0.7524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.162392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.142513 restraints weight = 9118.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.141113 restraints weight = 11157.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.141634 restraints weight = 11144.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.141872 restraints weight = 9983.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.142160 restraints weight = 9106.570| |-----------------------------------------------------------------------------| r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3537 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3537 r_free = 0.3537 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3537 r_free = 0.3537 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3537 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7378 moved from start: 0.5152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6753 Z= 0.143 Angle : 0.616 7.381 9246 Z= 0.303 Chirality : 0.043 0.171 1107 Planarity : 0.004 0.037 1152 Dihedral : 6.667 52.015 1233 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 12.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 6.91 % Allowed : 25.73 % Favored : 67.36 % 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 aren not related in a simple way. whole: -1.40 (0.28), residues: 855 helix: 1.46 (0.28), residues: 297 sheet: -2.58 (0.27), residues: 270 loop : -1.59 (0.36), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 188 TYR 0.017 0.002 TYR C 227 PHE 0.018 0.001 PHE C 232 TRP 0.032 0.002 TRP C 304 HIS 0.001 0.001 HIS B 98 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 6735) covalent geometry : angle 0.60400 ( 9195) SS BOND : bond 0.00154 ( 3) SS BOND : angle 0.67676 ( 6) hydrogen bonds : bond 0.03611 ( 354) hydrogen bonds : angle 5.09106 ( 1035) link_BETA1-4 : bond 0.00441 ( 3) link_BETA1-4 : angle 1.65163 ( 9) link_NAG-ASN : bond 0.00632 ( 12) link_NAG-ASN : angle 1.86708 ( 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 203 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 163 time to evaluate : 0.246 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 75 LEU cc_start: 0.7574 (OUTLIER) cc_final: 0.7328 (mm) REVERT: A 156 TYR cc_start: 0.8530 (p90) cc_final: 0.8311 (p90) REVERT: A 220 MET cc_start: 0.7060 (tpp) cc_final: 0.6678 (tpp) REVERT: B 152 GLN cc_start: 0.7391 (mp10) cc_final: 0.6826 (tm-30) REVERT: B 188 ARG cc_start: 0.8206 (ttm-80) cc_final: 0.7885 (ttm-80) REVERT: C 75 LEU cc_start: 0.7568 (OUTLIER) cc_final: 0.7310 (mm) REVERT: C 94 GLU cc_start: 0.7611 (tm-30) cc_final: 0.7384 (tm-30) REVERT: C 207 PHE cc_start: 0.6958 (t80) cc_final: 0.6597 (t80) REVERT: C 220 MET cc_start: 0.7193 (ttm) cc_final: 0.6698 (tpp) outliers start: 40 outliers final: 26 residues processed: 191 average time/residue: 0.0887 time to fit residues: 21.4782 Evaluate side-chains 187 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 159 time to evaluate : 0.173 ------------------------------------------------------------------------------- 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 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 310 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 183 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 183 VAL Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain C residue 233 SER Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 310 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 58 optimal weight: 0.8980 chunk 48 optimal weight: 2.9990 chunk 8 optimal weight: 4.9990 chunk 64 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 56 optimal weight: 10.0000 chunk 22 optimal weight: 6.9990 chunk 79 optimal weight: 0.8980 chunk 24 optimal weight: 0.1980 chunk 60 optimal weight: 2.9990 chunk 80 optimal weight: 0.8980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.161807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.140446 restraints weight = 9098.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.139455 restraints weight = 11386.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.140081 restraints weight = 10859.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.140294 restraints weight = 9643.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.140521 restraints weight = 8909.692| |-----------------------------------------------------------------------------| r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3508 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3508 r_free = 0.3508 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3508 r_free = 0.3508 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3508 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7416 moved from start: 0.5525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 6753 Z= 0.161 Angle : 0.645 9.542 9246 Z= 0.311 Chirality : 0.043 0.165 1107 Planarity : 0.004 0.031 1152 Dihedral : 6.377 52.633 1233 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 6.74 % Allowed : 27.46 % Favored : 65.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.29 (0.28), residues: 855 helix: 1.57 (0.27), residues: 297 sheet: -2.57 (0.27), residues: 273 loop : -1.50 (0.36), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 188 TYR 0.015 0.002 TYR B 267 PHE 0.024 0.002 PHE C 232 TRP 0.031 0.002 TRP C 304 HIS 0.001 0.000 HIS A 131 Details of bonding type rmsd covalent geometry : bond 0.00367 ( 6735) covalent geometry : angle 0.62321 ( 9195) SS BOND : bond 0.00198 ( 3) SS BOND : angle 0.61938 ( 6) hydrogen bonds : bond 0.03492 ( 354) hydrogen bonds : angle 4.98417 ( 1035) link_BETA1-4 : bond 0.00524 ( 3) link_BETA1-4 : angle 1.57405 ( 9) link_NAG-ASN : bond 0.00580 ( 12) link_NAG-ASN : angle 2.62759 ( 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 198 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 159 time to evaluate : 0.185 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 152 GLN cc_start: 0.7290 (mp10) cc_final: 0.6794 (tm-30) REVERT: B 188 ARG cc_start: 0.8167 (ttm-80) cc_final: 0.7813 (ttm-80) REVERT: C 94 GLU cc_start: 0.7648 (tm-30) cc_final: 0.7392 (tm-30) REVERT: C 207 PHE cc_start: 0.6644 (t80) cc_final: 0.6425 (t80) REVERT: C 216 ARG cc_start: 0.8152 (mtt-85) cc_final: 0.7158 (mtt90) REVERT: C 220 MET cc_start: 0.7295 (ttm) cc_final: 0.6804 (tpp) outliers start: 39 outliers final: 30 residues processed: 190 average time/residue: 0.0988 time to fit residues: 23.6602 Evaluate side-chains 180 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 150 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 132 TYR Chi-restraints excluded: chain A residue 149 CYS 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 295 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 126 LEU Chi-restraints excluded: chain B residue 132 TYR Chi-restraints excluded: chain B residue 149 CYS Chi-restraints excluded: chain B residue 183 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 76 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 233 SER 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 47 optimal weight: 5.9990 chunk 41 optimal weight: 0.9990 chunk 5 optimal weight: 0.9980 chunk 51 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 8 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 64 optimal weight: 1.9990 chunk 7 optimal weight: 0.4980 chunk 21 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.161398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.138031 restraints weight = 8998.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.137086 restraints weight = 8148.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.137942 restraints weight = 8041.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.138262 restraints weight = 6985.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.138340 restraints weight = 6698.194| |-----------------------------------------------------------------------------| r_work (final): 0.3500 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3504 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3504 r_free = 0.3504 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 = 0.3504 r_free = 0.3504 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3504 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7428 moved from start: 0.5775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6753 Z= 0.155 Angle : 0.662 10.602 9246 Z= 0.316 Chirality : 0.043 0.146 1107 Planarity : 0.003 0.031 1152 Dihedral : 6.124 52.177 1233 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 13.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 6.22 % Allowed : 29.36 % Favored : 64.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.23 (0.28), residues: 855 helix: 1.70 (0.27), residues: 297 sheet: -2.55 (0.27), residues: 279 loop : -1.51 (0.36), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 216 TYR 0.019 0.002 TYR C 267 PHE 0.035 0.002 PHE A 219 TRP 0.028 0.002 TRP C 304 HIS 0.001 0.000 HIS B 98 Details of bonding type rmsd covalent geometry : bond 0.00358 ( 6735) covalent geometry : angle 0.63708 ( 9195) SS BOND : bond 0.00199 ( 3) SS BOND : angle 0.65052 ( 6) hydrogen bonds : bond 0.03431 ( 354) hydrogen bonds : angle 4.90135 ( 1035) link_BETA1-4 : bond 0.00466 ( 3) link_BETA1-4 : angle 1.52213 ( 9) link_NAG-ASN : bond 0.00857 ( 12) link_NAG-ASN : angle 2.86188 ( 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 190 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 154 time to evaluate : 0.234 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 94 GLU cc_start: 0.7621 (tm-30) cc_final: 0.7375 (tm-30) REVERT: B 103 VAL cc_start: 0.9198 (OUTLIER) cc_final: 0.8970 (m) REVERT: B 188 ARG cc_start: 0.8214 (ttm-80) cc_final: 0.7852 (ttm-80) REVERT: C 75 LEU cc_start: 0.7440 (OUTLIER) cc_final: 0.7208 (mm) REVERT: C 94 GLU cc_start: 0.7713 (tm-30) cc_final: 0.7443 (tm-30) REVERT: C 220 MET cc_start: 0.7304 (ttm) cc_final: 0.6811 (tpp) REVERT: C 241 LYS cc_start: 0.9030 (OUTLIER) cc_final: 0.8663 (mttp) REVERT: C 259 ARG cc_start: 0.7802 (mtp85) cc_final: 0.7295 (mtt90) outliers start: 36 outliers final: 28 residues processed: 181 average time/residue: 0.1052 time to fit residues: 23.6623 Evaluate side-chains 175 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 144 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 ILE 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 265 VAL Chi-restraints excluded: chain A residue 295 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 126 LEU Chi-restraints excluded: chain B residue 132 TYR Chi-restraints excluded: chain B residue 149 CYS Chi-restraints excluded: chain B residue 183 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 183 VAL Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain C residue 233 SER Chi-restraints excluded: chain C residue 241 LYS Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 265 VAL Chi-restraints excluded: chain C residue 310 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 73 optimal weight: 0.6980 chunk 61 optimal weight: 0.9980 chunk 3 optimal weight: 0.9990 chunk 15 optimal weight: 0.8980 chunk 9 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 54 optimal weight: 0.9980 chunk 60 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 27 optimal weight: 20.0000 chunk 43 optimal weight: 3.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.162384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.142905 restraints weight = 8963.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.141591 restraints weight = 10848.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.142226 restraints weight = 11483.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.142555 restraints weight = 9526.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.142567 restraints weight = 8663.657| |-----------------------------------------------------------------------------| r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3545 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3545 r_free = 0.3545 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3545 r_free = 0.3545 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3545 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7394 moved from start: 0.5998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 6753 Z= 0.156 Angle : 0.649 9.568 9246 Z= 0.317 Chirality : 0.044 0.262 1107 Planarity : 0.003 0.030 1152 Dihedral : 6.076 52.484 1233 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 13.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 6.22 % Allowed : 30.22 % Favored : 63.56 % 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 aren not related in a simple way. whole: -1.05 (0.28), residues: 855 helix: 1.84 (0.27), residues: 297 sheet: -2.34 (0.28), residues: 261 loop : -1.64 (0.35), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 188 TYR 0.015 0.002 TYR C 201 PHE 0.026 0.002 PHE A 219 TRP 0.024 0.002 TRP C 304 HIS 0.001 0.000 HIS B 98 Details of bonding type rmsd covalent geometry : bond 0.00361 ( 6735) covalent geometry : angle 0.63964 ( 9195) SS BOND : bond 0.00177 ( 3) SS BOND : angle 0.71269 ( 6) hydrogen bonds : bond 0.03420 ( 354) hydrogen bonds : angle 4.85452 ( 1035) link_BETA1-4 : bond 0.00528 ( 3) link_BETA1-4 : angle 1.45680 ( 9) link_NAG-ASN : bond 0.00758 ( 12) link_NAG-ASN : angle 1.70993 ( 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 191 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 155 time to evaluate : 0.188 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 127 SER cc_start: 0.7731 (p) cc_final: 0.7486 (p) REVERT: B 94 GLU cc_start: 0.7555 (tm-30) cc_final: 0.7314 (tm-30) REVERT: B 188 ARG cc_start: 0.8168 (ttm-80) cc_final: 0.7814 (ttm-80) REVERT: C 94 GLU cc_start: 0.7683 (tm-30) cc_final: 0.7417 (tm-30) REVERT: C 152 GLN cc_start: 0.7016 (tm-30) cc_final: 0.6755 (mp10) REVERT: C 220 MET cc_start: 0.7229 (ttm) cc_final: 0.6662 (tpp) REVERT: C 241 LYS cc_start: 0.8874 (OUTLIER) cc_final: 0.8645 (mttp) REVERT: C 259 ARG cc_start: 0.7718 (mtp85) cc_final: 0.7259 (mtt90) outliers start: 36 outliers final: 32 residues processed: 182 average time/residue: 0.1011 time to fit residues: 23.2428 Evaluate side-chains 182 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 149 time to evaluate : 0.270 ------------------------------------------------------------------------------- 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 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 265 VAL Chi-restraints excluded: chain A residue 295 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 126 LEU Chi-restraints excluded: chain B residue 132 TYR Chi-restraints excluded: chain B residue 149 CYS Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 112 ASP 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 241 LYS Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 265 VAL Chi-restraints excluded: chain C residue 310 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 61 optimal weight: 0.7980 chunk 15 optimal weight: 0.8980 chunk 69 optimal weight: 0.7980 chunk 21 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 62 optimal weight: 0.4980 chunk 24 optimal weight: 0.7980 chunk 45 optimal weight: 0.5980 chunk 17 optimal weight: 0.9990 chunk 81 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 152 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.163458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.144296 restraints weight = 8966.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.143289 restraints weight = 10765.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.143343 restraints weight = 11462.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.143716 restraints weight = 11708.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.143751 restraints weight = 9990.804| |-----------------------------------------------------------------------------| r_work (final): 0.3574 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3574 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3574 r_free = 0.3574 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3574 r_free = 0.3574 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3574 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7380 moved from start: 0.6091 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= 0.143 Angle : 0.669 12.027 9246 Z= 0.320 Chirality : 0.044 0.264 1107 Planarity : 0.003 0.035 1152 Dihedral : 6.533 59.707 1233 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 13.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 5.87 % Allowed : 31.09 % Favored : 63.04 % 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 aren not related in a simple way. whole: -0.98 (0.28), residues: 855 helix: 1.97 (0.27), residues: 297 sheet: -2.40 (0.27), residues: 279 loop : -1.46 (0.37), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 188 TYR 0.018 0.002 TYR C 267 PHE 0.025 0.002 PHE C 219 TRP 0.020 0.001 TRP C 304 HIS 0.001 0.000 HIS B 98 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 6735) covalent geometry : angle 0.65778 ( 9195) SS BOND : bond 0.00150 ( 3) SS BOND : angle 0.68314 ( 6) hydrogen bonds : bond 0.03318 ( 354) hydrogen bonds : angle 4.78911 ( 1035) link_BETA1-4 : bond 0.00467 ( 3) link_BETA1-4 : angle 1.44064 ( 9) link_NAG-ASN : bond 0.01096 ( 12) link_NAG-ASN : angle 2.00102 ( 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 184 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 150 time to evaluate : 0.195 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 127 SER cc_start: 0.7686 (p) cc_final: 0.7462 (p) REVERT: B 94 GLU cc_start: 0.7560 (tm-30) cc_final: 0.7271 (tm-30) REVERT: B 152 GLN cc_start: 0.7236 (tm-30) cc_final: 0.6953 (mp10) REVERT: B 165 VAL cc_start: 0.7183 (OUTLIER) cc_final: 0.6915 (m) REVERT: B 188 ARG cc_start: 0.8233 (ttm-80) cc_final: 0.7889 (ttm-80) REVERT: C 94 GLU cc_start: 0.7693 (tm-30) cc_final: 0.7411 (tm-30) REVERT: C 152 GLN cc_start: 0.7110 (tm130) cc_final: 0.6709 (mp10) REVERT: C 220 MET cc_start: 0.7030 (ttm) cc_final: 0.6546 (tpp) REVERT: C 241 LYS cc_start: 0.8748 (OUTLIER) cc_final: 0.8539 (mttp) REVERT: C 259 ARG cc_start: 0.7736 (mtp85) cc_final: 0.7255 (mtt90) outliers start: 34 outliers final: 29 residues processed: 175 average time/residue: 0.0911 time to fit residues: 20.3122 Evaluate side-chains 178 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 147 time to evaluate : 0.234 ------------------------------------------------------------------------------- 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 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 265 VAL Chi-restraints excluded: chain A residue 295 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 183 VAL Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain C residue 71 ILE 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 233 SER Chi-restraints excluded: chain C residue 241 LYS Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 265 VAL Chi-restraints excluded: chain C residue 310 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 33 optimal weight: 0.9990 chunk 47 optimal weight: 0.9980 chunk 6 optimal weight: 0.0570 chunk 13 optimal weight: 0.8980 chunk 1 optimal weight: 5.9990 chunk 16 optimal weight: 0.8980 chunk 73 optimal weight: 2.9990 chunk 45 optimal weight: 6.9990 chunk 56 optimal weight: 10.0000 chunk 48 optimal weight: 0.9990 chunk 62 optimal weight: 0.5980 overall best weight: 0.6898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.164554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.143071 restraints weight = 8941.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.143681 restraints weight = 8223.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.143681 restraints weight = 7787.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.143681 restraints weight = 7787.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.143681 restraints weight = 7787.465| |-----------------------------------------------------------------------------| r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3544 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3544 r_free = 0.3544 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3544 r_free = 0.3544 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3544 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7383 moved from start: 0.6237 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= 0.141 Angle : 0.643 8.915 9246 Z= 0.313 Chirality : 0.043 0.258 1107 Planarity : 0.003 0.035 1152 Dihedral : 6.146 52.528 1233 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 13.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 5.53 % Allowed : 31.78 % Favored : 62.69 % 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 aren not related in a simple way. whole: -0.92 (0.29), residues: 855 helix: 1.85 (0.27), residues: 312 sheet: -2.36 (0.27), residues: 279 loop : -1.41 (0.39), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 188 TYR 0.018 0.002 TYR C 267 PHE 0.022 0.002 PHE A 219 TRP 0.016 0.001 TRP C 304 HIS 0.001 0.000 HIS B 98 Details of bonding type rmsd covalent geometry : bond 0.00323 ( 6735) covalent geometry : angle 0.63532 ( 9195) SS BOND : bond 0.00138 ( 3) SS BOND : angle 0.75108 ( 6) hydrogen bonds : bond 0.03247 ( 354) hydrogen bonds : angle 4.70094 ( 1035) link_BETA1-4 : bond 0.00467 ( 3) link_BETA1-4 : angle 1.40236 ( 9) link_NAG-ASN : bond 0.00470 ( 12) link_NAG-ASN : angle 1.57627 ( 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: 32 poor density : 160 time to evaluate : 0.256 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 94 GLU cc_start: 0.7696 (tm-30) cc_final: 0.7373 (tm-30) REVERT: A 127 SER cc_start: 0.7625 (p) cc_final: 0.7373 (p) REVERT: B 94 GLU cc_start: 0.7661 (tm-30) cc_final: 0.7385 (tm-30) REVERT: B 152 GLN cc_start: 0.7280 (tm-30) cc_final: 0.7018 (mp10) REVERT: B 165 VAL cc_start: 0.7207 (OUTLIER) cc_final: 0.6921 (m) REVERT: B 188 ARG cc_start: 0.8179 (ttm-80) cc_final: 0.7799 (ttm-80) REVERT: B 220 MET cc_start: 0.7001 (ttm) cc_final: 0.6781 (tpp) REVERT: C 94 GLU cc_start: 0.7757 (tm-30) cc_final: 0.7458 (tm-30) REVERT: C 220 MET cc_start: 0.7056 (ttm) cc_final: 0.6783 (tpp) REVERT: C 241 LYS cc_start: 0.8760 (OUTLIER) cc_final: 0.8558 (mttp) REVERT: C 259 ARG cc_start: 0.7791 (mtp85) cc_final: 0.7321 (mtt90) outliers start: 32 outliers final: 29 residues processed: 185 average time/residue: 0.0970 time to fit residues: 22.8687 Evaluate side-chains 182 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 151 time to evaluate : 0.197 ------------------------------------------------------------------------------- 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 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 265 VAL Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 149 CYS Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 126 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 233 SER Chi-restraints excluded: chain C residue 241 LYS Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 265 VAL Chi-restraints excluded: chain C residue 310 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 9 optimal weight: 20.0000 chunk 47 optimal weight: 0.6980 chunk 27 optimal weight: 20.0000 chunk 38 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 51 optimal weight: 0.8980 chunk 36 optimal weight: 0.0570 chunk 65 optimal weight: 8.9990 chunk 42 optimal weight: 1.9990 chunk 44 optimal weight: 0.0040 chunk 61 optimal weight: 2.9990 overall best weight: 0.7312 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.163464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.144436 restraints weight = 9007.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.143046 restraints weight = 10188.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.143602 restraints weight = 10525.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.143845 restraints weight = 9257.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.143890 restraints weight = 8481.503| |-----------------------------------------------------------------------------| r_work (final): 0.3570 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3575 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3575 r_free = 0.3575 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3575 r_free = 0.3575 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3575 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7378 moved from start: 0.6392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6753 Z= 0.147 Angle : 0.639 8.359 9246 Z= 0.315 Chirality : 0.043 0.253 1107 Planarity : 0.003 0.036 1152 Dihedral : 5.920 52.633 1233 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 13.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 5.70 % Allowed : 32.30 % Favored : 62.00 % 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 aren not related in a simple way. whole: -0.79 (0.29), residues: 855 helix: 2.20 (0.27), residues: 297 sheet: -2.36 (0.28), residues: 279 loop : -1.38 (0.36), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 188 TYR 0.018 0.002 TYR C 267 PHE 0.022 0.001 PHE C 232 TRP 0.013 0.001 TRP C 304 HIS 0.001 0.000 HIS B 98 Details of bonding type rmsd covalent geometry : bond 0.00337 ( 6735) covalent geometry : angle 0.63377 ( 9195) SS BOND : bond 0.00151 ( 3) SS BOND : angle 0.68647 ( 6) hydrogen bonds : bond 0.03238 ( 354) hydrogen bonds : angle 4.69476 ( 1035) link_BETA1-4 : bond 0.00493 ( 3) link_BETA1-4 : angle 1.38027 ( 9) link_NAG-ASN : bond 0.00952 ( 12) link_NAG-ASN : angle 1.34610 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1205.70 seconds wall clock time: 21 minutes 29.78 seconds (1289.78 seconds total)