Starting phenix.real_space_refine on Tue Feb 11 20:16:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7jnc_22404/02_2025/7jnc_22404.cif Found real_map, /net/cci-nas-00/data/ceres_data/7jnc_22404/02_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_22404/02_2025/7jnc_22404.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7jnc_22404/02_2025/7jnc_22404.map" model { file = "/net/cci-nas-00/data/ceres_data/7jnc_22404/02_2025/7jnc_22404.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7jnc_22404/02_2025/7jnc_22404.cif" } resolution = 3.73 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 24 5.16 5 C 4287 2.51 5 N 1080 2.21 5 O 1182 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 6573 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2121 Classifications: {'peptide': 287} Incomplete info: {'truncation_to_alanine': 63} Link IDs: {'PTRANS': 13, 'TRANS': 273} Unresolved non-hydrogen bonds: 218 Unresolved non-hydrogen angles: 264 Unresolved non-hydrogen dihedrals: 186 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 7, 'TYR:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 5, 'PHE:plan': 2, 'GLU:plan': 4, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 118 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Restraints were copied for chains: C, B, D, F Time building chain proxies: 3.93, per 1000 atoms: 0.60 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=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 128 " - pdb=" SG CYS A 149 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG A 401 " - " ASN A 148 " " NAG A 402 " - " ASN A 162 " " NAG A 403 " - " ASN A 190 " " NAG B 401 " - " ASN B 148 " " NAG B 402 " - " ASN B 162 " " NAG B 403 " - " ASN B 190 " " NAG C 401 " - " ASN C 148 " " NAG C 402 " - " ASN C 162 " " NAG C 403 " - " ASN C 190 " " NAG D 1 " - " ASN A 155 " " NAG E 1 " - " ASN B 155 " " NAG F 1 " - " ASN C 155 " Time building additional restraints: 1.76 Conformation dependent library (CDL) restraints added in 1.1 seconds 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1662 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 12 sheets defined 37.0% alpha, 22.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.78 Creating SS restraints... Processing helix chain 'A' and resid 53 through 96 removed outlier: 4.215A pdb=" N PHE A 57 " --> pdb=" O SER A 53 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N ALA A 60 " --> pdb=" O ARG A 56 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N CYS A 61 " --> pdb=" O PHE A 57 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LYS A 95 " --> pdb=" O ASP A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 212 Processing helix chain 'A' and resid 215 through 226 Processing helix chain 'A' and resid 297 through 302 removed outlier: 3.777A pdb=" N ASN A 302 " --> pdb=" O ILE A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 339 removed outlier: 3.920A pdb=" N THR A 306 " --> pdb=" O ASN A 302 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA A 308 " --> pdb=" O TRP A 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 54 through 96 removed outlier: 4.443A pdb=" N ALA B 60 " --> pdb=" O ARG B 56 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N CYS B 61 " --> pdb=" O PHE B 57 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LYS B 95 " --> pdb=" O ASP B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 212 Processing helix chain 'B' and resid 215 through 226 Processing helix chain 'B' and resid 297 through 302 removed outlier: 3.777A pdb=" N ASN B 302 " --> pdb=" O ILE B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 339 removed outlier: 3.920A pdb=" N THR B 306 " --> pdb=" O ASN B 302 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA B 308 " --> pdb=" O TRP B 304 " (cutoff:3.500A) Processing helix chain 'C' and resid 54 through 96 removed outlier: 4.442A pdb=" N ALA C 60 " --> pdb=" O ARG C 56 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N CYS C 61 " --> pdb=" O PHE C 57 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LYS C 95 " --> pdb=" O ASP C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 212 Processing helix chain 'C' and resid 215 through 226 Processing helix chain 'C' and resid 297 through 302 removed outlier: 3.777A pdb=" N ASN C 302 " --> pdb=" O ILE C 298 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 339 removed outlier: 3.920A pdb=" N THR C 306 " --> pdb=" O ASN C 302 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA C 308 " --> pdb=" O TRP C 304 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 100 through 101 removed outlier: 5.519A pdb=" N LEU B 244 " --> pdb=" O PHE B 291 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 254 through 258 removed outlier: 5.519A pdb=" N LEU A 244 " --> pdb=" O PHE A 291 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 118 through 119 removed outlier: 4.023A pdb=" N ASP A 200 " --> pdb=" O TYR A 119 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ILE A 199 " --> pdb=" O PHE A 232 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N PHE A 232 " --> pdb=" O ILE A 199 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 124 through 131 removed outlier: 6.383A pdb=" N GLN A 186 " --> pdb=" O LEU A 126 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N CYS A 128 " --> pdb=" O PHE A 184 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N PHE A 184 " --> pdb=" O CYS A 128 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N HIS A 130 " --> pdb=" O LEU A 182 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N LEU A 182 " --> pdb=" O HIS A 130 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N PHE A 282 " --> pdb=" O PHE A 236 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LYS A 241 " --> pdb=" O GLU A 261 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLU A 261 " --> pdb=" O LYS A 241 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 151 through 157 removed outlier: 3.550A pdb=" N TYR A 156 " --> pdb=" O LYS A 166 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 100 through 101 removed outlier: 5.520A pdb=" N LEU C 244 " --> pdb=" O PHE C 291 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 118 through 119 removed outlier: 4.023A pdb=" N ASP B 200 " --> pdb=" O TYR B 119 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ILE B 199 " --> pdb=" O PHE B 232 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N PHE B 232 " --> pdb=" O ILE B 199 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 124 through 131 removed outlier: 6.383A pdb=" N GLN B 186 " --> pdb=" O LEU B 126 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N CYS B 128 " --> pdb=" O PHE B 184 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N PHE B 184 " --> pdb=" O CYS B 128 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N HIS B 130 " --> pdb=" O LEU B 182 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N LEU B 182 " --> pdb=" O HIS B 130 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N PHE B 282 " --> pdb=" O PHE B 236 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LYS B 241 " --> pdb=" O GLU B 261 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLU B 261 " --> pdb=" O LYS B 241 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 151 through 157 removed outlier: 3.550A pdb=" N TYR B 156 " --> pdb=" O LYS B 166 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 118 through 119 removed outlier: 4.023A pdb=" N ASP C 200 " --> pdb=" O TYR C 119 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ILE C 199 " --> pdb=" O PHE C 232 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N PHE C 232 " --> pdb=" O ILE C 199 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 124 through 131 removed outlier: 6.383A pdb=" N GLN C 186 " --> pdb=" O LEU C 126 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N CYS C 128 " --> pdb=" O PHE C 184 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N PHE C 184 " --> pdb=" O CYS C 128 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N HIS C 130 " --> pdb=" O LEU C 182 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N LEU C 182 " --> pdb=" O HIS C 130 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N PHE C 282 " --> pdb=" O PHE C 236 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LYS C 241 " --> pdb=" O GLU C 261 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLU C 261 " --> pdb=" O LYS C 241 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 151 through 157 removed outlier: 3.550A pdb=" N TYR C 156 " --> pdb=" O LYS C 166 " (cutoff:3.500A) 354 hydrogen bonds defined for protein. 1035 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.89 Time building geometry restraints manager: 2.05 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: 297 32.16 - 48.24: 64 48.24 - 64.32: 28 64.32 - 80.39: 3 Dihedral angle restraints: 4155 sinusoidal: 1605 harmonic: 2550 Sorted by residual: 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=" CA ALA B 198 " pdb=" C ALA B 198 " pdb=" N ILE B 199 " pdb=" CA ILE B 199 " ideal model delta harmonic sigma weight residual 180.00 159.64 20.36 0 5.00e+00 4.00e-02 1.66e+01 dihedral pdb=" CA ALA A 198 " pdb=" C ALA A 198 " pdb=" N ILE A 199 " pdb=" CA ILE A 199 " ideal model delta harmonic sigma weight residual 180.00 159.66 20.34 0 5.00e+00 4.00e-02 1.65e+01 ... (remaining 4152 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: 2.03 - 2.61: 64 2.61 - 3.18: 6042 3.18 - 3.75: 10149 3.75 - 4.33: 13647 4.33 - 4.90: 22429 Nonbonded interactions: 52331 Sorted by model distance: nonbonded pdb=" SG CYS C 128 " pdb=" SG CYS C 149 " model vdw 2.032 3.760 nonbonded pdb=" SG CYS B 128 " pdb=" SG CYS B 149 " model vdw 2.033 3.760 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 ... (remaining 52326 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' } ncs_group { reference = chain 'E' selection = chain 'D' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 18.870 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6644 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 6735 Z= 0.324 Angle : 0.682 5.468 9195 Z= 0.372 Chirality : 0.045 0.234 1107 Planarity : 0.003 0.028 1152 Dihedral : 13.562 80.394 2490 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 17.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 0.52 % Allowed : 6.74 % Favored : 92.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.01 (0.24), residues: 855 helix: -1.00 (0.24), residues: 291 sheet: -3.58 (0.25), residues: 255 loop : -3.22 (0.30), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 230 HIS 0.001 0.000 HIS C 98 PHE 0.022 0.002 PHE A 232 TYR 0.015 0.002 TYR A 267 ARG 0.002 0.000 ARG B 175 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 220 time to evaluate : 0.657 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: 0.2056 time to fit residues: 58.3957 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 : 0.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 70 optimal weight: 4.9990 chunk 63 optimal weight: 0.9980 chunk 35 optimal weight: 0.9990 chunk 21 optimal weight: 8.9990 chunk 42 optimal weight: 5.9990 chunk 34 optimal weight: 0.5980 chunk 65 optimal weight: 10.0000 chunk 25 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 49 optimal weight: 0.0980 chunk 76 optimal weight: 0.7980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 186 GLN B 186 GLN C 98 HIS C 186 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.163054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.140990 restraints weight = 8931.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.141504 restraints weight = 8648.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.141849 restraints weight = 7880.870| |-----------------------------------------------------------------------------| r_work (final): 0.3550 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3561 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3561 r_free = 0.3561 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 = 0.3558 r_free = 0.3558 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3558 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7032 moved from start: 0.2584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 6735 Z= 0.252 Angle : 0.651 7.026 9195 Z= 0.329 Chirality : 0.044 0.171 1107 Planarity : 0.004 0.027 1152 Dihedral : 8.666 57.913 1233 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 12.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.76 % Allowed : 21.24 % Favored : 75.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.56 (0.27), residues: 855 helix: 0.53 (0.28), residues: 297 sheet: -3.05 (0.25), residues: 309 loop : -2.26 (0.36), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 304 HIS 0.002 0.001 HIS C 98 PHE 0.026 0.002 PHE B 232 TYR 0.015 0.002 TYR A 201 ARG 0.009 0.001 ARG C 188 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 157 time to evaluate : 0.703 Fit side-chains REVERT: A 220 MET cc_start: 0.6966 (tpp) cc_final: 0.6575 (tpp) REVERT: B 153 ARG cc_start: 0.7527 (mtp-110) cc_final: 0.6848 (mmm160) REVERT: B 188 ARG cc_start: 0.7780 (ttm-80) cc_final: 0.7277 (ttm170) outliers start: 16 outliers final: 9 residues processed: 165 average time/residue: 0.1805 time to fit residues: 39.4016 Evaluate side-chains 153 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 144 time to evaluate : 0.743 ------------------------------------------------------------------------------- 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 317 LEU Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 317 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 46 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 77 optimal weight: 5.9990 chunk 83 optimal weight: 9.9990 chunk 51 optimal weight: 0.9990 chunk 42 optimal weight: 0.8980 chunk 82 optimal weight: 0.9980 chunk 2 optimal weight: 0.7980 chunk 13 optimal weight: 0.6980 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 = 0.3791 r_free = 0.3791 target = 0.162618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.140891 restraints weight = 9132.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.141506 restraints weight = 9000.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.141989 restraints weight = 8303.792| |-----------------------------------------------------------------------------| r_work (final): 0.3545 ------------------------------------------------------------------------------- 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: 2 | |-----------------------------------------------------------------------------| |-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: 0.7166 moved from start: 0.3368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 6735 Z= 0.242 Angle : 0.606 6.058 9195 Z= 0.304 Chirality : 0.044 0.231 1107 Planarity : 0.003 0.025 1152 Dihedral : 7.967 59.953 1233 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 5.53 % Allowed : 21.24 % Favored : 73.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.71 (0.28), residues: 855 helix: 1.22 (0.28), residues: 297 sheet: -2.45 (0.27), residues: 279 loop : -2.11 (0.38), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 304 HIS 0.001 0.000 HIS A 98 PHE 0.021 0.002 PHE C 232 TYR 0.021 0.002 TYR A 119 ARG 0.005 0.001 ARG C 253 *********************** 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 189 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 157 time to evaluate : 0.664 Fit side-chains REVERT: A 188 ARG cc_start: 0.7957 (ttm-80) cc_final: 0.7624 (ttm170) REVERT: A 220 MET cc_start: 0.6951 (tpp) cc_final: 0.6594 (tpp) REVERT: B 152 GLN cc_start: 0.6985 (mp10) cc_final: 0.6633 (tm-30) REVERT: C 152 GLN cc_start: 0.6933 (mp10) cc_final: 0.6679 (tm-30) REVERT: C 188 ARG cc_start: 0.7912 (ttm-80) cc_final: 0.7642 (ttm-80) outliers start: 32 outliers final: 16 residues processed: 177 average time/residue: 0.1797 time to fit residues: 43.2019 Evaluate side-chains 167 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 151 time to evaluate : 1.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 TYR Chi-restraints excluded: chain A residue 149 CYS Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 132 TYR Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 317 LEU 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 310 LEU Chi-restraints excluded: chain C residue 317 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 29 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 78 optimal weight: 0.9980 chunk 65 optimal weight: 20.0000 chunk 74 optimal weight: 0.8980 chunk 33 optimal weight: 0.9990 chunk 1 optimal weight: 4.9990 chunk 39 optimal weight: 0.9980 chunk 53 optimal weight: 0.9990 chunk 79 optimal weight: 0.8980 chunk 81 optimal weight: 0.8980 overall best weight: 0.9380 ------------------------------------------------------------------------------- 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 = 0.3912 r_free = 0.3912 target = 0.173296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.139684 restraints weight = 9276.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.141676 restraints weight = 7342.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.142482 restraints weight = 6361.834| |-----------------------------------------------------------------------------| r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3700 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3700 r_free = 0.3700 target_work(ls_wunit_k1) = 0.153 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3700 r_free = 0.3700 target_work(ls_wunit_k1) = 0.153 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3700 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7337 moved from start: 0.4222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 6735 Z= 0.237 Angle : 0.611 8.149 9195 Z= 0.302 Chirality : 0.043 0.158 1107 Planarity : 0.003 0.026 1152 Dihedral : 7.455 58.187 1233 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 7.25 % Allowed : 18.65 % Favored : 74.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.28), residues: 855 helix: 1.46 (0.28), residues: 297 sheet: -2.70 (0.26), residues: 285 loop : -1.62 (0.38), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 304 HIS 0.002 0.001 HIS B 130 PHE 0.025 0.002 PHE A 232 TYR 0.017 0.002 TYR C 227 ARG 0.005 0.001 ARG B 188 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 164 time to evaluate : 0.754 Fit side-chains REVERT: A 71 ILE cc_start: 0.7983 (OUTLIER) cc_final: 0.7720 (mm) REVERT: A 220 MET cc_start: 0.7016 (tpp) cc_final: 0.6635 (tpp) REVERT: A 286 GLU cc_start: 0.7515 (pt0) cc_final: 0.7298 (pt0) REVERT: B 152 GLN cc_start: 0.7167 (mp10) cc_final: 0.6724 (tm-30) REVERT: B 254 GLU cc_start: 0.7734 (pt0) cc_final: 0.7509 (pt0) REVERT: C 150 THR cc_start: 0.6501 (p) cc_final: 0.5786 (p) REVERT: C 152 GLN cc_start: 0.7087 (mp10) cc_final: 0.6667 (tm-30) REVERT: C 250 GLU cc_start: 0.6525 (OUTLIER) cc_final: 0.5988 (pt0) outliers start: 42 outliers final: 19 residues processed: 192 average time/residue: 0.2154 time to fit residues: 52.5394 Evaluate side-chains 180 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 159 time to evaluate : 0.662 ------------------------------------------------------------------------------- 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 217 VAL Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain B residue 132 TYR Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 250 GLU Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 317 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 72 optimal weight: 0.9990 chunk 42 optimal weight: 4.9990 chunk 15 optimal weight: 0.9990 chunk 71 optimal weight: 0.6980 chunk 64 optimal weight: 0.4980 chunk 69 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 80 optimal weight: 0.8980 chunk 56 optimal weight: 10.0000 chunk 32 optimal weight: 0.9980 chunk 59 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 HIS ** B 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.163840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.143365 restraints weight = 8982.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.143849 restraints weight = 8394.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.143849 restraints weight = 7983.976| |-----------------------------------------------------------------------------| r_work (final): 0.3545 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3548 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3548 r_free = 0.3548 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 = 0.3548 r_free = 0.3548 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3548 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7298 moved from start: 0.4678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6735 Z= 0.216 Angle : 0.613 11.088 9195 Z= 0.297 Chirality : 0.043 0.148 1107 Planarity : 0.003 0.026 1152 Dihedral : 7.084 55.879 1233 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 6.91 % Allowed : 21.59 % Favored : 71.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.28), residues: 855 helix: 1.36 (0.27), residues: 312 sheet: -2.61 (0.26), residues: 285 loop : -1.50 (0.40), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 304 HIS 0.002 0.000 HIS A 130 PHE 0.021 0.001 PHE A 232 TYR 0.022 0.002 TYR B 267 ARG 0.004 0.001 ARG B 188 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 172 time to evaluate : 0.720 Fit side-chains REVERT: A 220 MET cc_start: 0.6933 (tpp) cc_final: 0.6631 (tpp) REVERT: A 250 GLU cc_start: 0.6028 (OUTLIER) cc_final: 0.5745 (pt0) REVERT: B 152 GLN cc_start: 0.7289 (mp10) cc_final: 0.6848 (tm-30) REVERT: C 75 LEU cc_start: 0.7497 (OUTLIER) cc_final: 0.7296 (mm) REVERT: C 152 GLN cc_start: 0.7302 (mp10) cc_final: 0.7026 (tm-30) REVERT: C 182 LEU cc_start: 0.9328 (OUTLIER) cc_final: 0.9084 (pp) REVERT: C 259 ARG cc_start: 0.8226 (mtp85) cc_final: 0.7965 (mtp85) outliers start: 40 outliers final: 28 residues processed: 197 average time/residue: 0.2003 time to fit residues: 50.9554 Evaluate side-chains 196 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 165 time to evaluate : 0.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 132 TYR Chi-restraints excluded: chain A residue 149 CYS Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 250 GLU Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 132 TYR Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 223 CYS Chi-restraints excluded: chain B residue 233 SER 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 71 ILE Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain C residue 223 CYS Chi-restraints excluded: chain C residue 233 SER Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 310 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 9 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 chunk 35 optimal weight: 8.9990 chunk 7 optimal weight: 9.9990 chunk 62 optimal weight: 7.9990 chunk 70 optimal weight: 0.9990 chunk 13 optimal weight: 4.9990 chunk 82 optimal weight: 5.9990 chunk 17 optimal weight: 6.9990 chunk 44 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 305 ASN B 186 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.160416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.139812 restraints weight = 9118.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.137532 restraints weight = 13041.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.138156 restraints weight = 13782.409| |-----------------------------------------------------------------------------| r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3502 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3502 r_free = 0.3502 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3502 r_free = 0.3502 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3502 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7426 moved from start: 0.5384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 6735 Z= 0.315 Angle : 0.660 8.954 9195 Z= 0.327 Chirality : 0.045 0.165 1107 Planarity : 0.004 0.036 1152 Dihedral : 6.744 52.680 1233 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 12.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 7.60 % Allowed : 23.49 % Favored : 68.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.28), residues: 855 helix: 1.53 (0.27), residues: 297 sheet: -2.77 (0.25), residues: 291 loop : -1.46 (0.37), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 304 HIS 0.002 0.001 HIS C 130 PHE 0.033 0.002 PHE B 219 TYR 0.017 0.002 TYR B 267 ARG 0.004 0.001 ARG A 216 *********************** 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 206 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 162 time to evaluate : 0.717 Fit side-chains REVERT: A 75 LEU cc_start: 0.7583 (OUTLIER) cc_final: 0.7352 (mm) REVERT: A 94 GLU cc_start: 0.7404 (tm-30) cc_final: 0.7098 (tm-30) REVERT: A 156 TYR cc_start: 0.8580 (p90) cc_final: 0.8324 (p90) REVERT: A 220 MET cc_start: 0.7164 (tpp) cc_final: 0.6591 (tpp) REVERT: A 250 GLU cc_start: 0.6443 (OUTLIER) cc_final: 0.5998 (pt0) REVERT: B 94 GLU cc_start: 0.7469 (tm-30) cc_final: 0.7257 (tm-30) REVERT: B 152 GLN cc_start: 0.7440 (mp10) cc_final: 0.6762 (tm-30) REVERT: B 188 ARG cc_start: 0.8170 (ttm170) cc_final: 0.7832 (ttm-80) REVERT: B 250 GLU cc_start: 0.6469 (OUTLIER) cc_final: 0.5795 (pt0) REVERT: C 75 LEU cc_start: 0.7508 (OUTLIER) cc_final: 0.7267 (mm) REVERT: C 94 GLU cc_start: 0.7604 (tm-30) cc_final: 0.7320 (tm-30) REVERT: C 152 GLN cc_start: 0.7153 (mp10) cc_final: 0.6897 (tm-30) REVERT: C 182 LEU cc_start: 0.9416 (OUTLIER) cc_final: 0.9079 (pp) REVERT: C 250 GLU cc_start: 0.6740 (OUTLIER) cc_final: 0.6259 (pt0) outliers start: 44 outliers final: 30 residues processed: 196 average time/residue: 0.2073 time to fit residues: 51.9632 Evaluate side-chains 192 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 156 time to evaluate : 0.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 132 TYR Chi-restraints excluded: chain A residue 149 CYS Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 250 GLU Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 132 TYR Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 233 SER Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 250 GLU Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain C residue 223 CYS Chi-restraints excluded: chain C residue 233 SER Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 250 GLU Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 317 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 73 optimal weight: 5.9990 chunk 27 optimal weight: 10.0000 chunk 54 optimal weight: 0.9980 chunk 33 optimal weight: 0.7980 chunk 70 optimal weight: 0.9990 chunk 83 optimal weight: 6.9990 chunk 55 optimal weight: 10.0000 chunk 44 optimal weight: 0.0870 chunk 36 optimal weight: 3.9990 chunk 41 optimal weight: 0.8980 chunk 24 optimal weight: 0.7980 overall best weight: 0.7158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 293 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.161780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.137680 restraints weight = 8969.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.138675 restraints weight = 7487.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.139897 restraints weight = 6666.620| |-----------------------------------------------------------------------------| r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3506 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3506 r_free = 0.3506 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 = 0.3506 r_free = 0.3506 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3506 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7362 moved from start: 0.5669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6735 Z= 0.215 Angle : 0.630 10.312 9195 Z= 0.308 Chirality : 0.044 0.203 1107 Planarity : 0.004 0.040 1152 Dihedral : 6.267 51.940 1233 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 12.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 6.56 % Allowed : 26.42 % Favored : 67.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.28), residues: 855 helix: 1.49 (0.27), residues: 312 sheet: -2.67 (0.25), residues: 291 loop : -1.36 (0.39), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 304 HIS 0.001 0.000 HIS A 130 PHE 0.020 0.001 PHE C 232 TYR 0.031 0.002 TYR C 156 ARG 0.003 0.000 ARG B 188 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 165 time to evaluate : 0.662 Fit side-chains REVERT: A 94 GLU cc_start: 0.7562 (tm-30) cc_final: 0.7240 (tm-30) REVERT: A 309 LEU cc_start: 0.7234 (OUTLIER) cc_final: 0.6875 (tp) REVERT: B 94 GLU cc_start: 0.7573 (tm-30) cc_final: 0.7343 (tm-30) REVERT: B 152 GLN cc_start: 0.7088 (mp10) cc_final: 0.6560 (tm-30) REVERT: B 188 ARG cc_start: 0.8264 (ttm170) cc_final: 0.7893 (ttm-80) REVERT: B 233 SER cc_start: 0.8913 (OUTLIER) cc_final: 0.8618 (t) REVERT: B 250 GLU cc_start: 0.6466 (OUTLIER) cc_final: 0.5642 (pt0) REVERT: C 75 LEU cc_start: 0.7470 (OUTLIER) cc_final: 0.7237 (mm) REVERT: C 152 GLN cc_start: 0.6875 (mp10) cc_final: 0.6674 (tm-30) REVERT: C 182 LEU cc_start: 0.9376 (OUTLIER) cc_final: 0.9070 (pp) REVERT: C 250 GLU cc_start: 0.6760 (OUTLIER) cc_final: 0.6257 (pt0) outliers start: 38 outliers final: 21 residues processed: 191 average time/residue: 0.2161 time to fit residues: 52.9271 Evaluate side-chains 186 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 159 time to evaluate : 0.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 132 TYR Chi-restraints excluded: chain A residue 149 CYS Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 309 LEU 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 233 SER Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 250 GLU 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 154 ILE Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 233 SER Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 250 GLU Chi-restraints excluded: chain C residue 310 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 9 optimal weight: 10.0000 chunk 75 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 43 optimal weight: 0.3980 chunk 64 optimal weight: 5.9990 chunk 56 optimal weight: 10.0000 chunk 45 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 50 optimal weight: 0.6980 chunk 59 optimal weight: 2.9990 chunk 81 optimal weight: 0.9980 overall best weight: 1.2184 ------------------------------------------------------------------------------- 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 = 0.3762 r_free = 0.3762 target = 0.160419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.138887 restraints weight = 9006.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.137660 restraints weight = 8232.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.137740 restraints weight = 8247.787| |-----------------------------------------------------------------------------| r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3506 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3506 r_free = 0.3506 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3506 r_free = 0.3506 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3506 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7419 moved from start: 0.5978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 6735 Z= 0.262 Angle : 0.656 9.724 9195 Z= 0.319 Chirality : 0.044 0.291 1107 Planarity : 0.004 0.040 1152 Dihedral : 6.521 52.699 1233 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 14.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 5.70 % Allowed : 28.84 % Favored : 65.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.28), residues: 855 helix: 1.79 (0.27), residues: 297 sheet: -2.73 (0.25), residues: 291 loop : -1.42 (0.36), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 304 HIS 0.002 0.001 HIS A 98 PHE 0.039 0.002 PHE A 219 TYR 0.024 0.002 TYR C 156 ARG 0.003 0.001 ARG A 188 *********************** 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 196 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 163 time to evaluate : 0.746 Fit side-chains revert: symmetry clash REVERT: A 94 GLU cc_start: 0.7568 (tm-30) cc_final: 0.7260 (tm-30) REVERT: B 94 GLU cc_start: 0.7670 (tm-30) cc_final: 0.7412 (tm-30) REVERT: B 152 GLN cc_start: 0.7169 (mp10) cc_final: 0.6832 (tm-30) REVERT: B 188 ARG cc_start: 0.8232 (ttm170) cc_final: 0.7938 (ttm-80) REVERT: B 250 GLU cc_start: 0.6009 (OUTLIER) cc_final: 0.5384 (pt0) REVERT: C 75 LEU cc_start: 0.7470 (OUTLIER) cc_final: 0.7243 (mm) REVERT: C 94 GLU cc_start: 0.7709 (tm-30) cc_final: 0.7390 (tm-30) REVERT: C 152 GLN cc_start: 0.6993 (mp10) cc_final: 0.6730 (tm-30) REVERT: C 182 LEU cc_start: 0.9383 (OUTLIER) cc_final: 0.9049 (pp) REVERT: C 250 GLU cc_start: 0.6738 (OUTLIER) cc_final: 0.6251 (pt0) REVERT: C 259 ARG cc_start: 0.8138 (mtp85) cc_final: 0.7635 (mtt90) outliers start: 33 outliers final: 27 residues processed: 188 average time/residue: 0.2100 time to fit residues: 50.4278 Evaluate side-chains 190 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 159 time to evaluate : 0.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 132 TYR Chi-restraints excluded: chain A residue 149 CYS Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 132 TYR Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 250 GLU Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain C residue 233 SER Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 250 GLU Chi-restraints excluded: chain C residue 310 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 48 optimal weight: 3.9990 chunk 66 optimal weight: 0.8980 chunk 18 optimal weight: 2.9990 chunk 68 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 34 optimal weight: 0.0010 chunk 11 optimal weight: 0.9980 chunk 76 optimal weight: 0.9990 chunk 16 optimal weight: 0.8980 chunk 56 optimal weight: 10.0000 chunk 23 optimal weight: 0.8980 overall best weight: 0.7186 ------------------------------------------------------------------------------- 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 = 0.3811 r_free = 0.3811 target = 0.165096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.141295 restraints weight = 9112.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.141535 restraints weight = 8576.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.141990 restraints weight = 8192.238| |-----------------------------------------------------------------------------| r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3507 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3507 r_free = 0.3507 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 = 0.3507 r_free = 0.3507 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3507 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7426 moved from start: 0.6118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6735 Z= 0.212 Angle : 0.633 9.700 9195 Z= 0.310 Chirality : 0.044 0.285 1107 Planarity : 0.004 0.040 1152 Dihedral : 6.160 52.151 1233 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 6.04 % Allowed : 28.84 % Favored : 65.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.28), residues: 855 helix: 1.69 (0.27), residues: 312 sheet: -2.61 (0.26), residues: 291 loop : -1.36 (0.38), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 304 HIS 0.001 0.000 HIS B 98 PHE 0.030 0.002 PHE A 219 TYR 0.025 0.002 TYR C 156 ARG 0.003 0.000 ARG C 188 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 163 time to evaluate : 0.665 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 94 GLU cc_start: 0.7650 (tm-30) cc_final: 0.7376 (tm-30) REVERT: B 152 GLN cc_start: 0.7145 (mp10) cc_final: 0.6793 (tm-30) REVERT: B 188 ARG cc_start: 0.8328 (ttm170) cc_final: 0.7955 (ttm-80) REVERT: C 75 LEU cc_start: 0.7466 (OUTLIER) cc_final: 0.7264 (mm) REVERT: C 94 GLU cc_start: 0.7693 (tm-30) cc_final: 0.7388 (tm-30) REVERT: C 152 GLN cc_start: 0.6939 (mp10) cc_final: 0.6676 (tm-30) REVERT: C 182 LEU cc_start: 0.9390 (OUTLIER) cc_final: 0.9061 (pp) REVERT: C 250 GLU cc_start: 0.6655 (OUTLIER) cc_final: 0.6195 (pt0) REVERT: C 259 ARG cc_start: 0.8075 (mtp85) cc_final: 0.7619 (mtt90) REVERT: C 309 LEU cc_start: 0.7334 (OUTLIER) cc_final: 0.7101 (tp) outliers start: 35 outliers final: 26 residues processed: 189 average time/residue: 0.2179 time to fit residues: 52.0726 Evaluate side-chains 183 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 153 time to evaluate : 0.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 132 TYR Chi-restraints excluded: chain A residue 149 CYS Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 132 TYR Chi-restraints excluded: chain B residue 233 SER 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 75 LEU Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain C residue 233 SER Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 250 GLU Chi-restraints excluded: chain C residue 309 LEU Chi-restraints excluded: chain C residue 310 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 4 optimal weight: 4.9990 chunk 75 optimal weight: 0.9980 chunk 39 optimal weight: 0.7980 chunk 14 optimal weight: 0.5980 chunk 20 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 38 optimal weight: 0.8980 chunk 18 optimal weight: 0.7980 chunk 25 optimal weight: 0.4980 chunk 21 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.162703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.144079 restraints weight = 9033.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.142601 restraints weight = 10873.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.143445 restraints weight = 11361.200| |-----------------------------------------------------------------------------| r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3553 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3553 r_free = 0.3553 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3553 r_free = 0.3553 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3553 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7369 moved from start: 0.6241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6735 Z= 0.220 Angle : 0.641 9.521 9195 Z= 0.314 Chirality : 0.043 0.281 1107 Planarity : 0.004 0.039 1152 Dihedral : 6.472 52.449 1233 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 12.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 5.35 % Allowed : 30.05 % Favored : 64.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.28), residues: 855 helix: 1.77 (0.27), residues: 312 sheet: -2.55 (0.27), residues: 273 loop : -1.41 (0.36), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 304 HIS 0.001 0.000 HIS B 98 PHE 0.029 0.001 PHE A 219 TYR 0.026 0.002 TYR C 156 ARG 0.002 0.000 ARG C 188 ********************** 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 188 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 157 time to evaluate : 0.688 Fit side-chains REVERT: A 190 ASN cc_start: 0.5720 (m110) cc_final: 0.5315 (p0) REVERT: B 94 GLU cc_start: 0.7552 (tm-30) cc_final: 0.7310 (tm-30) REVERT: B 152 GLN cc_start: 0.7126 (mp10) cc_final: 0.6658 (tm-30) REVERT: B 188 ARG cc_start: 0.8305 (ttm170) cc_final: 0.7940 (ttm-80) REVERT: B 309 LEU cc_start: 0.7498 (OUTLIER) cc_final: 0.7191 (tp) REVERT: C 75 LEU cc_start: 0.7483 (OUTLIER) cc_final: 0.7272 (mm) REVERT: C 94 GLU cc_start: 0.7614 (tm-30) cc_final: 0.7312 (tm-30) REVERT: C 182 LEU cc_start: 0.9359 (OUTLIER) cc_final: 0.9039 (pp) REVERT: C 250 GLU cc_start: 0.6653 (OUTLIER) cc_final: 0.6202 (pt0) REVERT: C 259 ARG cc_start: 0.8145 (mtp85) cc_final: 0.7654 (mtt90) outliers start: 31 outliers final: 24 residues processed: 181 average time/residue: 0.2413 time to fit residues: 55.4972 Evaluate side-chains 182 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 154 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 132 TYR Chi-restraints excluded: chain A residue 149 CYS Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 265 VAL 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 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 309 LEU 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 165 VAL Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain C residue 233 SER Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 250 GLU Chi-restraints excluded: chain C residue 310 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 55 optimal weight: 20.0000 chunk 10 optimal weight: 0.7980 chunk 78 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 45 optimal weight: 6.9990 chunk 31 optimal weight: 2.9990 chunk 66 optimal weight: 0.7980 chunk 17 optimal weight: 0.9980 chunk 42 optimal weight: 0.6980 chunk 8 optimal weight: 2.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.161537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.137770 restraints weight = 9304.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.138195 restraints weight = 8696.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 19)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.138286 restraints weight = 8329.197| |-----------------------------------------------------------------------------| r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3487 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3487 r_free = 0.3487 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3487 r_free = 0.3487 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3487 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7459 moved from start: 0.6416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 6735 Z= 0.247 Angle : 0.641 8.465 9195 Z= 0.319 Chirality : 0.043 0.272 1107 Planarity : 0.004 0.038 1152 Dihedral : 6.422 57.678 1233 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 13.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 5.01 % Allowed : 29.71 % Favored : 65.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.28), residues: 855 helix: 2.07 (0.28), residues: 297 sheet: -2.65 (0.26), residues: 291 loop : -1.29 (0.36), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 304 HIS 0.001 0.000 HIS A 98 PHE 0.028 0.002 PHE A 219 TYR 0.019 0.002 TYR C 156 ARG 0.002 0.000 ARG B 188 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2453.84 seconds wall clock time: 44 minutes 49.33 seconds (2689.33 seconds total)