Starting phenix.real_space_refine on Tue Sep 24 02:04:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jnc_22404/09_2024/7jnc_22404.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jnc_22404/09_2024/7jnc_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jnc_22404/09_2024/7jnc_22404.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jnc_22404/09_2024/7jnc_22404.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jnc_22404/09_2024/7jnc_22404.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jnc_22404/09_2024/7jnc_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-5461/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: 3.91, per 1000 atoms: 0.59 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: 1.74 Conformation dependent library (CDL) restraints added in 929.7 milliseconds 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1662 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 12 sheets defined 37.0% alpha, 22.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.79 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: 1.78 Time building geometry restraints manager: 2.02 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 18.280 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.260 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 3 poor density : 220 time to evaluate : 0.725 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: 0.1966 time to fit residues: 55.7340 Evaluate side-chains 163 residues out of total 768 non-(ALA, GLY, PRO) need fitting. 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6868 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 : 12.85 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 fitting. rotamer outliers: 16 poor density : 157 time to evaluate : 0.797 Fit side-chains REVERT: A 220 MET cc_start: 0.7151 (tpp) cc_final: 0.6888 (tpp) REVERT: B 152 GLN cc_start: 0.6693 (mp10) cc_final: 0.6493 (mp10) REVERT: B 153 ARG cc_start: 0.7730 (mtp-110) cc_final: 0.6995 (mmm160) REVERT: B 188 ARG cc_start: 0.7573 (ttm-80) cc_final: 0.6860 (ttm170) REVERT: C 152 GLN cc_start: 0.6877 (mp10) cc_final: 0.6629 (mp10) REVERT: C 172 GLN cc_start: 0.7928 (tt0) cc_final: 0.7720 (tp40) outliers start: 16 outliers final: 9 residues processed: 165 average time/residue: 0.1754 time to fit residues: 38.5176 Evaluate side-chains 153 residues out of total 768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 144 time to evaluate : 0.747 ------------------------------------------------------------------------------- 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 42 optimal weight: 4.9990 chunk 23 optimal weight: 0.6980 chunk 63 optimal weight: 0.0670 chunk 51 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 chunk 76 optimal weight: 3.9990 chunk 82 optimal weight: 0.9980 chunk 68 optimal weight: 4.9990 chunk 75 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 61 optimal weight: 0.1980 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6913 moved from start: 0.3143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6735 Z= 0.201 Angle : 0.579 6.353 9195 Z= 0.290 Chirality : 0.042 0.254 1107 Planarity : 0.003 0.023 1152 Dihedral : 7.900 57.696 1233 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 5.01 % Allowed : 20.90 % 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: -1.73 (0.28), residues: 855 helix: 1.06 (0.27), residues: 312 sheet: -2.41 (0.27), residues: 279 loop : -2.20 (0.39), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 304 HIS 0.001 0.000 HIS A 98 PHE 0.018 0.001 PHE C 232 TYR 0.020 0.002 TYR A 119 ARG 0.006 0.001 ARG A 188 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 157 time to evaluate : 0.669 Fit side-chains REVERT: A 188 ARG cc_start: 0.7675 (ttm-80) cc_final: 0.7183 (ttm170) REVERT: A 220 MET cc_start: 0.7105 (tpp) cc_final: 0.6833 (tpp) REVERT: B 188 ARG cc_start: 0.7509 (ttm-80) cc_final: 0.6861 (ttm170) REVERT: C 111 TYR cc_start: 0.8572 (m-10) cc_final: 0.8324 (m-80) REVERT: C 188 ARG cc_start: 0.7611 (ttm-80) cc_final: 0.7343 (ttm-80) REVERT: C 304 TRP cc_start: 0.7760 (m100) cc_final: 0.7220 (m100) outliers start: 29 outliers final: 7 residues processed: 172 average time/residue: 0.1701 time to fit residues: 39.2805 Evaluate side-chains 161 residues out of total 768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 154 time to evaluate : 0.727 ------------------------------------------------------------------------------- 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 217 VAL Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain C residue 245 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 75 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 39 optimal weight: 0.8980 chunk 8 optimal weight: 4.9990 chunk 36 optimal weight: 8.9990 chunk 51 optimal weight: 1.9990 chunk 76 optimal weight: 0.9990 chunk 81 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 21 optimal weight: 0.4980 overall best weight: 1.2786 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7133 moved from start: 0.4438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 6735 Z= 0.275 Angle : 0.641 6.034 9195 Z= 0.320 Chirality : 0.045 0.181 1107 Planarity : 0.004 0.029 1152 Dihedral : 7.479 59.132 1233 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 8.29 % Allowed : 17.10 % Favored : 74.61 % 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: -1.61 (0.28), residues: 855 helix: 1.36 (0.27), residues: 297 sheet: -2.78 (0.26), residues: 288 loop : -1.57 (0.37), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 304 HIS 0.003 0.001 HIS C 130 PHE 0.032 0.002 PHE C 232 TYR 0.019 0.002 TYR C 227 ARG 0.005 0.001 ARG C 188 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 172 time to evaluate : 0.709 Fit side-chains REVERT: A 71 ILE cc_start: 0.7740 (OUTLIER) cc_final: 0.7517 (mm) REVERT: A 220 MET cc_start: 0.7192 (tpp) cc_final: 0.6984 (tpp) REVERT: A 221 GLN cc_start: 0.6554 (mt0) cc_final: 0.6288 (mt0) REVERT: A 241 LYS cc_start: 0.8849 (OUTLIER) cc_final: 0.8630 (mttm) REVERT: A 259 ARG cc_start: 0.8148 (mtm180) cc_final: 0.7891 (mtp-110) REVERT: A 304 TRP cc_start: 0.7639 (m100) cc_final: 0.7149 (m100) REVERT: A 309 LEU cc_start: 0.7581 (tp) cc_final: 0.7350 (tp) REVERT: B 124 GLN cc_start: 0.6383 (OUTLIER) cc_final: 0.6002 (pm20) REVERT: B 188 ARG cc_start: 0.7942 (ttm-80) cc_final: 0.7565 (ttm-80) REVERT: B 200 ASP cc_start: 0.8077 (OUTLIER) cc_final: 0.7875 (m-30) REVERT: B 221 GLN cc_start: 0.6970 (mt0) cc_final: 0.6697 (mt0) REVERT: B 286 GLU cc_start: 0.7721 (pt0) cc_final: 0.7217 (pt0) REVERT: B 304 TRP cc_start: 0.7951 (m100) cc_final: 0.7686 (m100) REVERT: C 75 LEU cc_start: 0.6780 (OUTLIER) cc_final: 0.6545 (mm) REVERT: C 94 GLU cc_start: 0.7031 (tm-30) cc_final: 0.6803 (tm-30) REVERT: C 250 GLU cc_start: 0.6463 (OUTLIER) cc_final: 0.5951 (pt0) REVERT: C 304 TRP cc_start: 0.7940 (m100) cc_final: 0.7438 (m100) outliers start: 48 outliers final: 21 residues processed: 211 average time/residue: 0.1987 time to fit residues: 53.9824 Evaluate side-chains 191 residues out of total 768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 164 time to evaluate : 0.733 ------------------------------------------------------------------------------- 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 183 VAL Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 241 LYS Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain B residue 124 GLN 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 200 ASP Chi-restraints excluded: chain B residue 223 CYS Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain C residue 75 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 311 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 67 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 1 optimal weight: 8.9990 chunk 60 optimal weight: 2.9990 chunk 33 optimal weight: 0.1980 chunk 69 optimal weight: 0.5980 chunk 56 optimal weight: 10.0000 chunk 0 optimal weight: 9.9990 chunk 41 optimal weight: 1.9990 chunk 72 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7204 moved from start: 0.5007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 6735 Z= 0.324 Angle : 0.621 5.694 9195 Z= 0.315 Chirality : 0.044 0.200 1107 Planarity : 0.004 0.037 1152 Dihedral : 7.038 52.384 1233 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 7.08 % Allowed : 21.93 % Favored : 70.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.55 (0.28), residues: 855 helix: 1.47 (0.28), residues: 297 sheet: -2.86 (0.25), residues: 294 loop : -1.43 (0.38), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 287 HIS 0.002 0.001 HIS B 98 PHE 0.027 0.002 PHE A 232 TYR 0.020 0.002 TYR B 267 ARG 0.004 0.001 ARG A 188 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 164 time to evaluate : 0.812 Fit side-chains revert: symmetry clash REVERT: A 75 LEU cc_start: 0.6916 (OUTLIER) cc_final: 0.6628 (mm) REVERT: A 124 GLN cc_start: 0.6284 (pm20) cc_final: 0.6062 (pm20) REVERT: A 156 TYR cc_start: 0.8558 (p90) cc_final: 0.8160 (p90) REVERT: A 188 ARG cc_start: 0.8118 (ttm-80) cc_final: 0.7780 (ttm110) REVERT: A 220 MET cc_start: 0.7321 (tpp) cc_final: 0.7041 (tpp) REVERT: A 221 GLN cc_start: 0.6750 (mt0) cc_final: 0.6410 (mt0) REVERT: A 241 LYS cc_start: 0.8943 (OUTLIER) cc_final: 0.8713 (mttm) REVERT: A 250 GLU cc_start: 0.5948 (OUTLIER) cc_final: 0.5601 (pt0) REVERT: A 259 ARG cc_start: 0.8169 (mtm180) cc_final: 0.7916 (mtp-110) REVERT: A 304 TRP cc_start: 0.7685 (m100) cc_final: 0.7238 (m100) REVERT: B 188 ARG cc_start: 0.8032 (ttm-80) cc_final: 0.7789 (ttm-80) REVERT: C 182 LEU cc_start: 0.9208 (OUTLIER) cc_final: 0.8878 (pp) REVERT: C 188 ARG cc_start: 0.7599 (ttm-80) cc_final: 0.7388 (ttm-80) REVERT: C 304 TRP cc_start: 0.7973 (m100) cc_final: 0.7623 (m100) outliers start: 41 outliers final: 24 residues processed: 194 average time/residue: 0.2164 time to fit residues: 53.5828 Evaluate side-chains 189 residues out of total 768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 161 time to evaluate : 0.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 132 TYR Chi-restraints excluded: chain A residue 149 CYS Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 241 LYS Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 250 GLU Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 103 VAL 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 245 VAL Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 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 245 VAL Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 311 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 27 optimal weight: 10.0000 chunk 73 optimal weight: 5.9990 chunk 16 optimal weight: 0.9980 chunk 47 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 chunk 81 optimal weight: 0.4980 chunk 67 optimal weight: 0.9990 chunk 37 optimal weight: 0.9990 chunk 6 optimal weight: 6.9990 chunk 26 optimal weight: 0.9980 chunk 42 optimal weight: 3.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7179 moved from start: 0.5315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6735 Z= 0.229 Angle : 0.580 5.434 9195 Z= 0.294 Chirality : 0.044 0.179 1107 Planarity : 0.004 0.037 1152 Dihedral : 6.808 51.886 1233 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 7.08 % Allowed : 22.97 % Favored : 69.95 % 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: -1.42 (0.28), residues: 855 helix: 1.40 (0.27), residues: 312 sheet: -2.70 (0.25), residues: 291 loop : -1.42 (0.39), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 304 HIS 0.001 0.000 HIS B 98 PHE 0.022 0.001 PHE C 232 TYR 0.018 0.002 TYR B 267 ARG 0.002 0.000 ARG C 93 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 168 time to evaluate : 0.843 Fit side-chains revert: symmetry clash REVERT: A 75 LEU cc_start: 0.6894 (OUTLIER) cc_final: 0.6682 (mm) REVERT: A 156 TYR cc_start: 0.8534 (p90) cc_final: 0.8246 (p90) REVERT: A 220 MET cc_start: 0.7394 (tpp) cc_final: 0.7188 (tpp) REVERT: A 221 GLN cc_start: 0.6833 (mt0) cc_final: 0.6549 (mt0) REVERT: A 241 LYS cc_start: 0.8961 (OUTLIER) cc_final: 0.8729 (mttm) REVERT: A 250 GLU cc_start: 0.5979 (OUTLIER) cc_final: 0.5597 (pt0) REVERT: A 304 TRP cc_start: 0.7680 (m100) cc_final: 0.7245 (m100) REVERT: B 94 GLU cc_start: 0.7066 (tm-30) cc_final: 0.6753 (tm-30) REVERT: B 188 ARG cc_start: 0.7979 (ttm-80) cc_final: 0.7712 (ttm-80) REVERT: B 221 GLN cc_start: 0.7327 (mt0) cc_final: 0.7113 (mt0) REVERT: B 259 ARG cc_start: 0.7970 (mtp85) cc_final: 0.7760 (mtp-110) REVERT: C 75 LEU cc_start: 0.6966 (OUTLIER) cc_final: 0.6665 (mm) REVERT: C 94 GLU cc_start: 0.7145 (tm-30) cc_final: 0.6842 (tm-30) REVERT: C 112 ASP cc_start: 0.9027 (m-30) cc_final: 0.8734 (m-30) REVERT: C 182 LEU cc_start: 0.9191 (OUTLIER) cc_final: 0.8854 (pp) REVERT: C 250 GLU cc_start: 0.6654 (OUTLIER) cc_final: 0.6177 (pt0) REVERT: C 304 TRP cc_start: 0.7948 (m100) cc_final: 0.7440 (m100) outliers start: 41 outliers final: 27 residues processed: 201 average time/residue: 0.2306 time to fit residues: 58.2646 Evaluate side-chains 193 residues out of total 768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 160 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 132 TYR Chi-restraints excluded: chain A residue 149 CYS Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 241 LYS Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 250 GLU 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 183 VAL 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 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 78 optimal weight: 1.9990 chunk 9 optimal weight: 4.9990 chunk 46 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 68 optimal weight: 0.7980 chunk 80 optimal weight: 3.9990 chunk 50 optimal weight: 0.5980 chunk 49 optimal weight: 0.7980 chunk 37 optimal weight: 2.9990 chunk 32 optimal weight: 0.8980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7191 moved from start: 0.5560 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 : 0.587 7.887 9195 Z= 0.300 Chirality : 0.044 0.215 1107 Planarity : 0.004 0.035 1152 Dihedral : 6.405 52.247 1233 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 7.08 % Allowed : 24.35 % Favored : 68.57 % 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: -1.37 (0.28), residues: 855 helix: 1.49 (0.27), residues: 312 sheet: -2.70 (0.25), residues: 297 loop : -1.39 (0.40), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 304 HIS 0.001 0.000 HIS B 98 PHE 0.032 0.002 PHE B 219 TYR 0.017 0.002 TYR B 267 ARG 0.005 0.001 ARG A 188 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 161 time to evaluate : 0.722 Fit side-chains REVERT: A 75 LEU cc_start: 0.6869 (OUTLIER) cc_final: 0.6656 (mm) REVERT: A 220 MET cc_start: 0.7261 (tpp) cc_final: 0.7039 (tpp) REVERT: A 221 GLN cc_start: 0.6902 (mt0) cc_final: 0.6645 (mt0) REVERT: A 250 GLU cc_start: 0.6095 (OUTLIER) cc_final: 0.5714 (pt0) REVERT: A 304 TRP cc_start: 0.7698 (m100) cc_final: 0.7259 (m100) REVERT: B 188 ARG cc_start: 0.8074 (ttm-80) cc_final: 0.7749 (ttm-80) REVERT: B 221 GLN cc_start: 0.7482 (mt0) cc_final: 0.7223 (mt0) REVERT: B 250 GLU cc_start: 0.6347 (OUTLIER) cc_final: 0.5869 (pt0) REVERT: B 259 ARG cc_start: 0.7950 (mtp85) cc_final: 0.7718 (mtp-110) REVERT: C 75 LEU cc_start: 0.6958 (OUTLIER) cc_final: 0.6707 (mm) REVERT: C 94 GLU cc_start: 0.7232 (tm-30) cc_final: 0.6862 (tm-30) REVERT: C 112 ASP cc_start: 0.9043 (m-30) cc_final: 0.8817 (m-30) REVERT: C 152 GLN cc_start: 0.7178 (tm-30) cc_final: 0.6764 (tm-30) REVERT: C 182 LEU cc_start: 0.9193 (OUTLIER) cc_final: 0.8860 (pp) REVERT: C 216 ARG cc_start: 0.7918 (mtt-85) cc_final: 0.7541 (mtt90) REVERT: C 250 GLU cc_start: 0.6722 (OUTLIER) cc_final: 0.6200 (pt0) REVERT: C 259 ARG cc_start: 0.8015 (mtp85) cc_final: 0.7284 (mtt90) REVERT: C 304 TRP cc_start: 0.7951 (m100) cc_final: 0.7430 (m100) outliers start: 41 outliers final: 30 residues processed: 195 average time/residue: 0.2164 time to fit residues: 53.0833 Evaluate side-chains 193 residues out of total 768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 157 time to evaluate : 0.895 ------------------------------------------------------------------------------- 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 265 VAL Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 132 TYR 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 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 310 LEU Chi-restraints excluded: chain C residue 317 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 48 optimal weight: 0.1980 chunk 24 optimal weight: 0.7980 chunk 15 optimal weight: 0.6980 chunk 51 optimal weight: 0.9990 chunk 55 optimal weight: 20.0000 chunk 40 optimal weight: 2.9990 chunk 7 optimal weight: 6.9990 chunk 63 optimal weight: 5.9990 chunk 73 optimal weight: 0.9980 chunk 77 optimal weight: 4.9990 chunk 70 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7182 moved from start: 0.5729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6735 Z= 0.215 Angle : 0.599 9.170 9195 Z= 0.301 Chirality : 0.043 0.167 1107 Planarity : 0.004 0.037 1152 Dihedral : 6.698 52.181 1233 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 6.56 % Allowed : 25.39 % Favored : 68.05 % 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: 1.58 (0.27), residues: 312 sheet: -2.67 (0.25), residues: 297 loop : -1.32 (0.40), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 230 HIS 0.001 0.000 HIS B 98 PHE 0.026 0.002 PHE B 219 TYR 0.016 0.002 TYR C 105 ARG 0.003 0.000 ARG C 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 205 residues out of total 768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 167 time to evaluate : 0.698 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 220 MET cc_start: 0.7325 (tpp) cc_final: 0.7076 (tpp) REVERT: A 221 GLN cc_start: 0.6877 (mt0) cc_final: 0.6642 (mt0) REVERT: A 250 GLU cc_start: 0.6182 (OUTLIER) cc_final: 0.5780 (pt0) REVERT: A 304 TRP cc_start: 0.7691 (m100) cc_final: 0.7255 (m100) REVERT: B 188 ARG cc_start: 0.8008 (ttm-80) cc_final: 0.7686 (ttm-80) REVERT: B 221 GLN cc_start: 0.7511 (mt0) cc_final: 0.7180 (mt0) REVERT: B 224 GLU cc_start: 0.6850 (tm-30) cc_final: 0.6436 (tm-30) REVERT: B 250 GLU cc_start: 0.6442 (OUTLIER) cc_final: 0.5945 (pt0) REVERT: B 304 TRP cc_start: 0.7767 (m100) cc_final: 0.7534 (m100) REVERT: C 75 LEU cc_start: 0.6989 (OUTLIER) cc_final: 0.6744 (mm) REVERT: C 94 GLU cc_start: 0.7197 (tm-30) cc_final: 0.6831 (tm-30) REVERT: C 112 ASP cc_start: 0.9062 (m-30) cc_final: 0.8852 (m-30) REVERT: C 152 GLN cc_start: 0.7217 (tm-30) cc_final: 0.6831 (tm-30) REVERT: C 172 GLN cc_start: 0.8189 (tp-100) cc_final: 0.7839 (tp40) REVERT: C 182 LEU cc_start: 0.9187 (OUTLIER) cc_final: 0.8847 (pp) REVERT: C 250 GLU cc_start: 0.6670 (OUTLIER) cc_final: 0.6173 (pt0) REVERT: C 259 ARG cc_start: 0.8016 (mtp85) cc_final: 0.7378 (mtt90) REVERT: C 304 TRP cc_start: 0.7932 (m100) cc_final: 0.7392 (m100) outliers start: 38 outliers final: 30 residues processed: 197 average time/residue: 0.2216 time to fit residues: 55.1331 Evaluate side-chains 191 residues out of total 768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 156 time to evaluate : 0.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 132 TYR Chi-restraints excluded: chain A residue 149 CYS Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 250 GLU Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 132 TYR 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 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 124 GLN 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 Chi-restraints excluded: chain C residue 317 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 75 optimal weight: 0.9990 chunk 77 optimal weight: 0.8980 chunk 45 optimal weight: 3.9990 chunk 32 optimal weight: 0.6980 chunk 59 optimal weight: 3.9990 chunk 23 optimal weight: 0.4980 chunk 68 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 chunk 49 optimal weight: 0.5980 chunk 79 optimal weight: 0.6980 chunk 48 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7175 moved from start: 0.5920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6735 Z= 0.206 Angle : 0.586 7.839 9195 Z= 0.298 Chirality : 0.043 0.196 1107 Planarity : 0.004 0.037 1152 Dihedral : 6.176 52.334 1233 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 6.39 % Allowed : 27.29 % Favored : 66.32 % 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: -1.10 (0.28), residues: 855 helix: 1.76 (0.26), residues: 312 sheet: -2.59 (0.26), residues: 297 loop : -1.27 (0.40), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 230 HIS 0.001 0.000 HIS B 98 PHE 0.043 0.002 PHE A 219 TYR 0.017 0.002 TYR C 267 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 189 residues out of total 768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 152 time to evaluate : 0.768 Fit side-chains revert: symmetry clash REVERT: A 94 GLU cc_start: 0.7122 (tm-30) cc_final: 0.6681 (tm-30) REVERT: A 207 PHE cc_start: 0.8008 (t80) cc_final: 0.7600 (t80) REVERT: A 220 MET cc_start: 0.7440 (tpp) cc_final: 0.7065 (tpp) REVERT: A 250 GLU cc_start: 0.6220 (OUTLIER) cc_final: 0.5725 (pt0) REVERT: A 304 TRP cc_start: 0.7685 (m100) cc_final: 0.7242 (m100) REVERT: B 188 ARG cc_start: 0.8061 (ttm-80) cc_final: 0.7762 (ttm-80) REVERT: B 221 GLN cc_start: 0.7667 (mt0) cc_final: 0.7439 (mt0) REVERT: C 75 LEU cc_start: 0.6962 (OUTLIER) cc_final: 0.6737 (mm) REVERT: C 94 GLU cc_start: 0.7193 (tm-30) cc_final: 0.6810 (tm-30) REVERT: C 124 GLN cc_start: 0.7493 (OUTLIER) cc_final: 0.6877 (pp30) REVERT: C 152 GLN cc_start: 0.7241 (tm-30) cc_final: 0.6838 (tm-30) REVERT: C 182 LEU cc_start: 0.9149 (OUTLIER) cc_final: 0.8833 (pp) REVERT: C 220 MET cc_start: 0.7164 (ttm) cc_final: 0.6714 (tpp) REVERT: C 250 GLU cc_start: 0.6584 (OUTLIER) cc_final: 0.6077 (pt0) REVERT: C 259 ARG cc_start: 0.8053 (mtp85) cc_final: 0.7368 (mtt90) REVERT: C 304 TRP cc_start: 0.7934 (m100) cc_final: 0.7371 (m100) outliers start: 37 outliers final: 29 residues processed: 181 average time/residue: 0.2093 time to fit residues: 48.5421 Evaluate side-chains 183 residues out of total 768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 149 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 149 CYS Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 250 GLU Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 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 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 124 GLN Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain C residue 233 SER Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 250 GLU Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 311 CYS Chi-restraints excluded: chain C residue 317 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 37 optimal weight: 0.8980 chunk 55 optimal weight: 20.0000 chunk 83 optimal weight: 0.9980 chunk 77 optimal weight: 0.9990 chunk 66 optimal weight: 2.9990 chunk 6 optimal weight: 0.0170 chunk 51 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 chunk 70 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 overall best weight: 0.7818 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7179 moved from start: 0.6151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6735 Z= 0.213 Angle : 0.585 8.945 9195 Z= 0.296 Chirality : 0.044 0.321 1107 Planarity : 0.004 0.037 1152 Dihedral : 5.918 52.608 1233 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 5.70 % Allowed : 29.19 % 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: -1.01 (0.28), residues: 855 helix: 1.88 (0.26), residues: 312 sheet: -2.54 (0.26), residues: 297 loop : -1.27 (0.39), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 304 HIS 0.001 0.000 HIS B 98 PHE 0.035 0.002 PHE A 219 TYR 0.017 0.002 TYR C 267 ARG 0.003 0.000 ARG B 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 193 residues out of total 768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 160 time to evaluate : 0.779 Fit side-chains revert: symmetry clash REVERT: A 94 GLU cc_start: 0.7136 (tm-30) cc_final: 0.6712 (tm-30) REVERT: A 207 PHE cc_start: 0.7977 (t80) cc_final: 0.7762 (t80) REVERT: A 220 MET cc_start: 0.7418 (tpp) cc_final: 0.7020 (tpp) REVERT: A 304 TRP cc_start: 0.7694 (m100) cc_final: 0.7246 (m100) REVERT: B 188 ARG cc_start: 0.7961 (ttm-80) cc_final: 0.7542 (ttm-80) REVERT: B 221 GLN cc_start: 0.7714 (mt0) cc_final: 0.7426 (mt0) REVERT: C 75 LEU cc_start: 0.6957 (OUTLIER) cc_final: 0.6740 (mm) REVERT: C 94 GLU cc_start: 0.7185 (tm-30) cc_final: 0.6802 (tm-30) REVERT: C 124 GLN cc_start: 0.7617 (OUTLIER) cc_final: 0.6962 (pp30) REVERT: C 152 GLN cc_start: 0.7246 (tm-30) cc_final: 0.6844 (tm-30) REVERT: C 182 LEU cc_start: 0.9163 (OUTLIER) cc_final: 0.8861 (pp) REVERT: C 220 MET cc_start: 0.7208 (ttm) cc_final: 0.6830 (tpp) REVERT: C 250 GLU cc_start: 0.6574 (OUTLIER) cc_final: 0.6058 (pt0) REVERT: C 259 ARG cc_start: 0.7960 (mtp85) cc_final: 0.7338 (mtt90) REVERT: C 304 TRP cc_start: 0.7928 (m100) cc_final: 0.7339 (m100) outliers start: 33 outliers final: 28 residues processed: 183 average time/residue: 0.1965 time to fit residues: 46.1645 Evaluate side-chains 189 residues out of total 768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 157 time to evaluate : 0.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 149 CYS Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 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 132 TYR Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 124 GLN 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 Chi-restraints excluded: chain C residue 311 CYS Chi-restraints excluded: chain C residue 317 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 61 optimal weight: 0.8980 chunk 9 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 27 optimal weight: 20.0000 chunk 68 optimal weight: 0.9990 chunk 8 optimal weight: 3.9990 chunk 12 optimal weight: 4.9990 chunk 58 optimal weight: 0.9990 chunk 3 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- 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 = 0.3798 r_free = 0.3798 target = 0.163869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.144969 restraints weight = 8893.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.142901 restraints weight = 12320.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.143131 restraints weight = 12617.299| |-----------------------------------------------------------------------------| r_work (final): 0.3511 ------------------------------------------------------------------------------- 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 = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3502 r_free = 0.3502 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3502 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 moved from start: 0.6429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 6735 Z= 0.310 Angle : 0.635 7.222 9195 Z= 0.323 Chirality : 0.045 0.312 1107 Planarity : 0.004 0.036 1152 Dihedral : 6.166 53.190 1233 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 13.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 6.04 % Allowed : 28.50 % 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: -1.01 (0.28), residues: 855 helix: 1.84 (0.27), residues: 312 sheet: -2.57 (0.27), residues: 261 loop : -1.45 (0.36), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 304 HIS 0.002 0.001 HIS B 98 PHE 0.034 0.002 PHE A 219 TYR 0.018 0.002 TYR C 201 ARG 0.003 0.001 ARG B 188 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1871.83 seconds wall clock time: 34 minutes 9.24 seconds (2049.24 seconds total)