Starting phenix.real_space_refine on Tue Aug 4 22:47:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/22cr_68177/08_2026/22cr_68177.cif Found real_map, /net/cci-nas-00/data/ceres_data/22cr_68177/08_2026/22cr_68177.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/22cr_68177/08_2026/22cr_68177.cif" } default_model = "/net/cci-nas-00/data/ceres_data/22cr_68177/08_2026/22cr_68177.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/22cr_68177/08_2026/22cr_68177.map" default_real_map = "/net/cci-nas-00/data/ceres_data/22cr_68177/08_2026/22cr_68177.map" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.016 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: 5 Type Number sf(0) Gaussians P 5 5.49 5 S 40 5.16 5 C 4496 2.51 5 N 1221 2.21 5 O 1309 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7071 Number of models: 1 Model: "" Number of chains: 5 Chain: "C" Number of atoms: 471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 471 Classifications: {'peptide': 70} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 1, 'TRANS': 68} Unresolved non-hydrogen bonds: 74 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 64 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 1, 'TYR:plan': 2, 'ARG:plan': 3, 'GLN:plan1': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 43 Chain: "R" Number of atoms: 2232 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 2232 Classifications: {'peptide': 297} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 279} Chain breaks: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 1, 'TPO:plan-1': 1} Unresolved non-hydrogen planarities: 4 Chain: "H" Number of atoms: 905 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 905 Classifications: {'peptide': 117} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 114} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "L" Number of atoms: 799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 799 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "A" Number of atoms: 2664 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2664 Classifications: {'peptide': 337} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 313} Chain breaks: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Time building chain proxies: 1.76, per 1000 atoms: 0.25 Number of scatterers: 7071 At special positions: 0 Unit cell: (79.05, 95.79, 165.54, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 40 16.00 P 5 15.00 O 1309 8.00 N 1221 7.00 C 4496 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS C 21 " - pdb=" SG CYS C 47 " distance=2.04 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 54 " distance=2.04 Simple disulfide: pdb=" SG CYS C 34 " - pdb=" SG CYS C 55 " distance=1.90 Simple disulfide: pdb=" SG CYS R 107 " - pdb=" SG CYS R 186 " distance=2.06 Simple disulfide: pdb=" SG CYS R 133 " - pdb=" SG CYS R 219 " distance=1.55 Simple disulfide: pdb=" SG CYS H 25 " - pdb=" SG CYS H 99 " distance=1.83 Simple disulfide: pdb=" SG CYS L 24 " - pdb=" SG CYS L 89 " distance=2.02 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 Time building additional restraints: 0.79 Conformation dependent library (CDL) restraints added in 358.7 milliseconds 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1738 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 12 sheets defined 30.7% alpha, 30.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'C' and resid 4 through 9 Processing helix chain 'C' and resid 16 through 21 removed outlier: 3.569A pdb=" N LYS C 20 " --> pdb=" O SER C 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 27 removed outlier: 3.787A pdb=" N GLY C 25 " --> pdb=" O CYS C 21 " (cutoff:3.500A) Processing helix chain 'C' and resid 32 through 36 Processing helix chain 'C' and resid 46 through 62 removed outlier: 4.242A pdb=" N ALA C 50 " --> pdb=" O ARG C 46 " (cutoff:3.500A) Processing helix chain 'R' and resid 32 through 37 Processing helix chain 'R' and resid 37 through 60 Proline residue: R 51 - end of helix Processing helix chain 'R' and resid 72 through 97 Proline residue: R 88 - end of helix Proline residue: R 93 - end of helix Processing helix chain 'R' and resid 103 through 134 removed outlier: 4.780A pdb=" N LEU R 110 " --> pdb=" O GLY R 106 " (cutoff:3.500A) Proline residue: R 111 - end of helix removed outlier: 3.897A pdb=" N PHE R 134 " --> pdb=" O ALA R 130 " (cutoff:3.500A) Processing helix chain 'R' and resid 135 through 138 removed outlier: 3.998A pdb=" N GLY R 138 " --> pdb=" O LEU R 135 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 135 through 138' Processing helix chain 'R' and resid 153 through 165 removed outlier: 4.244A pdb=" N TRP R 159 " --> pdb=" O CYS R 155 " (cutoff:3.500A) Processing helix chain 'R' and resid 166 through 171 Processing helix chain 'R' and resid 193 through 208 Processing helix chain 'R' and resid 211 through 227 Processing helix chain 'R' and resid 231 through 236 Processing helix chain 'R' and resid 237 through 259 Proline residue: R 248 - end of helix Processing helix chain 'R' and resid 263 through 282 removed outlier: 3.538A pdb=" N ALA R 267 " --> pdb=" O SER R 263 " (cutoff:3.500A) Proline residue: R 274 - end of helix Processing helix chain 'R' and resid 282 through 295 Proline residue: R 288 - end of helix removed outlier: 3.809A pdb=" N TYR R 293 " --> pdb=" O MET R 289 " (cutoff:3.500A) Processing helix chain 'R' and resid 296 through 299 Processing helix chain 'H' and resid 65 through 68 Processing helix chain 'H' and resid 90 through 94 Processing helix chain 'A' and resid 68 through 72 Processing helix chain 'A' and resid 90 through 94 Processing helix chain 'A' and resid 98 through 108 Processing helix chain 'A' and resid 159 through 161 No H-bonds generated for 'chain 'A' and resid 159 through 161' Processing sheet with id=AA1, first strand: chain 'R' and resid 173 through 178 Processing sheet with id=AA2, first strand: chain 'R' and resid 327 through 328 Processing sheet with id=AA3, first strand: chain 'H' and resid 6 through 10 Processing sheet with id=AA4, first strand: chain 'H' and resid 13 through 14 removed outlier: 8.572A pdb=" N SER H 35 " --> pdb=" O SER H 55 " (cutoff:3.500A) removed outlier: 5.773A pdb=" N SER H 55 " --> pdb=" O SER H 35 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N ILE H 37 " --> pdb=" O SER H 53 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N SER H 53 " --> pdb=" O ILE H 37 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N TRP H 39 " --> pdb=" O VAL H 51 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 13 through 14 Processing sheet with id=AA6, first strand: chain 'L' and resid 5 through 8 Processing sheet with id=AA7, first strand: chain 'L' and resid 11 through 13 removed outlier: 6.416A pdb=" N LEU L 12 " --> pdb=" O GLU L 106 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N VAL L 34 " --> pdb=" O TYR L 50 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N TYR L 50 " --> pdb=" O VAL L 34 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 11 through 13 removed outlier: 6.416A pdb=" N LEU L 12 " --> pdb=" O GLU L 106 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N THR L 98 " --> pdb=" O GLN L 91 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 26 through 28 removed outlier: 6.096A pdb=" N PHE A 27 " --> pdb=" O VAL A 171 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N TYR A 144 " --> pdb=" O ILE A 168 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N LYS A 170 " --> pdb=" O VAL A 142 " (cutoff:3.500A) removed outlier: 9.701A pdb=" N VAL A 142 " --> pdb=" O LYS A 170 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N VAL A 53 " --> pdb=" O SER A 86 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N PHE A 61 " --> pdb=" O ASP A 78 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N ASP A 78 " --> pdb=" O PHE A 61 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 26 through 28 removed outlier: 6.096A pdb=" N PHE A 27 " --> pdb=" O VAL A 171 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N TYR A 144 " --> pdb=" O ILE A 168 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N LYS A 170 " --> pdb=" O VAL A 142 " (cutoff:3.500A) removed outlier: 9.701A pdb=" N VAL A 142 " --> pdb=" O LYS A 170 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 183 through 190 removed outlier: 5.280A pdb=" N PHE A 190 " --> pdb=" O LYS A 195 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N LYS A 195 " --> pdb=" O PHE A 190 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 207 through 209 removed outlier: 4.026A pdb=" N TYR A 321 " --> pdb=" O PHE A 349 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N LEU A 351 " --> pdb=" O VAL A 319 " (cutoff:3.500A) removed outlier: 9.339A pdb=" N VAL A 319 " --> pdb=" O LEU A 351 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N ILE A 231 " --> pdb=" O GLU A 257 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N GLU A 257 " --> pdb=" O ILE A 231 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N ILE A 233 " --> pdb=" O MET A 255 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N MET A 255 " --> pdb=" O ILE A 233 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N VAL A 235 " --> pdb=" O VAL A 253 " (cutoff:3.500A) 345 hydrogen bonds defined for protein. 921 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: 1.18 Time building geometry restraints manager: 1.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1304 1.32 - 1.45: 2139 1.45 - 1.58: 3718 1.58 - 1.72: 15 1.72 - 1.85: 48 Bond restraints: 7224 Sorted by residual: bond pdb=" OG1 TPO R 327 " pdb=" P TPO R 327 " ideal model delta sigma weight residual 1.717 1.611 0.106 2.00e-02 2.50e+03 2.80e+01 bond pdb=" O2P SEP R 326 " pdb=" P SEP R 326 " ideal model delta sigma weight residual 1.610 1.508 0.102 2.00e-02 2.50e+03 2.62e+01 bond pdb=" O3P SEP R 328 " pdb=" P SEP R 328 " ideal model delta sigma weight residual 1.610 1.509 0.101 2.00e-02 2.50e+03 2.56e+01 bond pdb=" O3P SEP R 320 " pdb=" P SEP R 320 " ideal model delta sigma weight residual 1.610 1.509 0.101 2.00e-02 2.50e+03 2.56e+01 bond pdb=" O2P SEP R 328 " pdb=" P SEP R 328 " ideal model delta sigma weight residual 1.610 1.509 0.101 2.00e-02 2.50e+03 2.56e+01 ... (remaining 7219 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.26: 8575 2.26 - 4.51: 1038 4.51 - 6.77: 203 6.77 - 9.02: 17 9.02 - 11.28: 6 Bond angle restraints: 9839 Sorted by residual: angle pdb=" N VAL L 20 " pdb=" CA VAL L 20 " pdb=" C VAL L 20 " ideal model delta sigma weight residual 107.80 114.96 -7.16 1.45e+00 4.76e-01 2.44e+01 angle pdb=" N TYR R 102 " pdb=" CA TYR R 102 " pdb=" C TYR R 102 " ideal model delta sigma weight residual 112.94 106.10 6.84 1.41e+00 5.03e-01 2.35e+01 angle pdb=" N THR R 196 " pdb=" CA THR R 196 " pdb=" C THR R 196 " ideal model delta sigma weight residual 111.36 106.13 5.23 1.09e+00 8.42e-01 2.30e+01 angle pdb=" C TRP H 106 " pdb=" N TYR H 107 " pdb=" CA TYR H 107 " ideal model delta sigma weight residual 121.05 127.89 -6.84 1.43e+00 4.89e-01 2.29e+01 angle pdb=" C LEU A 347 " pdb=" N PRO A 348 " pdb=" CA PRO A 348 " ideal model delta sigma weight residual 119.85 124.64 -4.79 1.01e+00 9.80e-01 2.25e+01 ... (remaining 9834 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.29: 4163 16.29 - 32.59: 137 32.59 - 48.88: 31 48.88 - 65.17: 11 65.17 - 81.47: 5 Dihedral angle restraints: 4347 sinusoidal: 1651 harmonic: 2696 Sorted by residual: dihedral pdb=" CB CYS C 34 " pdb=" SG CYS C 34 " pdb=" SG CYS C 55 " pdb=" CB CYS C 55 " ideal model delta sinusoidal sigma weight residual 93.00 174.47 -81.47 1 1.00e+01 1.00e-02 8.18e+01 dihedral pdb=" CB CYS R 133 " pdb=" SG CYS R 133 " pdb=" SG CYS R 219 " pdb=" CB CYS R 219 " ideal model delta sinusoidal sigma weight residual -86.00 -21.57 -64.43 1 1.00e+01 1.00e-02 5.46e+01 dihedral pdb=" CA PHE R 180 " pdb=" C PHE R 180 " pdb=" N PRO R 181 " pdb=" CA PRO R 181 " ideal model delta harmonic sigma weight residual 0.00 -25.16 25.16 0 5.00e+00 4.00e-02 2.53e+01 ... (remaining 4344 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 799 0.073 - 0.146: 258 0.146 - 0.219: 71 0.219 - 0.292: 6 0.292 - 0.364: 3 Chirality restraints: 1137 Sorted by residual: chirality pdb=" CA MET R 55 " pdb=" N MET R 55 " pdb=" C MET R 55 " pdb=" CB MET R 55 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.32e+00 chirality pdb=" CB VAL H 5 " pdb=" CA VAL H 5 " pdb=" CG1 VAL H 5 " pdb=" CG2 VAL H 5 " both_signs ideal model delta sigma weight residual False -2.63 -2.98 0.35 2.00e-01 2.50e+01 3.13e+00 chirality pdb=" CA LYS A 284 " pdb=" N LYS A 284 " pdb=" C LYS A 284 " pdb=" CB LYS A 284 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.40e+00 ... (remaining 1134 not shown) Planarity restraints: 1247 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL H 51 " -0.018 2.00e-02 2.50e+03 3.63e-02 1.32e+01 pdb=" C VAL H 51 " 0.063 2.00e-02 2.50e+03 pdb=" O VAL H 51 " -0.024 2.00e-02 2.50e+03 pdb=" N ALA H 52 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP L 36 " -0.039 2.00e-02 2.50e+03 2.14e-02 1.15e+01 pdb=" CG TRP L 36 " 0.007 2.00e-02 2.50e+03 pdb=" CD1 TRP L 36 " 0.003 2.00e-02 2.50e+03 pdb=" CD2 TRP L 36 " 0.026 2.00e-02 2.50e+03 pdb=" NE1 TRP L 36 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP L 36 " 0.011 2.00e-02 2.50e+03 pdb=" CE3 TRP L 36 " 0.033 2.00e-02 2.50e+03 pdb=" CZ2 TRP L 36 " -0.013 2.00e-02 2.50e+03 pdb=" CZ3 TRP L 36 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP L 36 " -0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 249 " 0.042 2.00e-02 2.50e+03 2.16e-02 9.35e+00 pdb=" CG TYR A 249 " -0.021 2.00e-02 2.50e+03 pdb=" CD1 TYR A 249 " -0.018 2.00e-02 2.50e+03 pdb=" CD2 TYR A 249 " -0.019 2.00e-02 2.50e+03 pdb=" CE1 TYR A 249 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 TYR A 249 " -0.008 2.00e-02 2.50e+03 pdb=" CZ TYR A 249 " 0.008 2.00e-02 2.50e+03 pdb=" OH TYR A 249 " 0.025 2.00e-02 2.50e+03 ... (remaining 1244 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 2360 2.82 - 3.34: 6858 3.34 - 3.86: 12020 3.86 - 4.38: 14292 4.38 - 4.90: 23082 Nonbonded interactions: 58612 Sorted by model distance: nonbonded pdb=" O GLY R 208 " pdb=" N GLY R 211 " model vdw 2.304 3.120 nonbonded pdb=" O LYS C 19 " pdb=" N TYR C 23 " model vdw 2.355 3.120 nonbonded pdb=" O CYS R 219 " pdb=" N ALA R 222 " model vdw 2.363 3.120 nonbonded pdb=" OG SER R 193 " pdb=" OG1 THR R 196 " model vdw 2.378 3.040 nonbonded pdb=" NZ LYS A 95 " pdb=" O THR A 116 " model vdw 2.381 3.120 ... (remaining 58607 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 2.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.540 Find NCS groups from input model: 0.040 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:6.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7019 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 : 0.017 0.478 7231 Z= 0.932 Angle : 1.787 53.166 9853 Z= 1.099 Chirality : 0.078 0.364 1137 Planarity : 0.007 0.047 1247 Dihedral : 9.549 81.336 2588 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 15.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.31 % Favored : 92.69 % Rotamer: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.17 (0.27), residues: 903 helix: -2.32 (0.27), residues: 259 sheet: 1.15 (0.34), residues: 255 loop : -0.88 (0.30), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 51 TYR 0.042 0.006 TYR A 249 PHE 0.031 0.004 PHE L 99 TRP 0.039 0.007 TRP L 36 HIS 0.006 0.001 HIS R 283 Details of bonding type rmsd/Z covalent geometry : bond 0.01604 / 0.88 ( 7224) covalent geometry : angle 1.59330 / 1.03 ( 9839) SS BOND : bond 0.20150 / 14.65 ( 7) SS BOND : angle 21.54460 / 10.66 ( 14) hydrogen bonds : bond 0.19587 / 13.87 ( 332) hydrogen bonds : angle 8.72411 / 6.31 ( 921) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 243 time to evaluate : 0.243 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 73 LEU cc_start: 0.8381 (mm) cc_final: 0.8141 (pt) REVERT: R 270 LEU cc_start: 0.6988 (mt) cc_final: 0.6514 (mt) REVERT: R 283 HIS cc_start: 0.6490 (p-80) cc_final: 0.6199 (p-80) REVERT: H 112 TYR cc_start: 0.8219 (m-80) cc_final: 0.7960 (m-80) REVERT: H 115 GLN cc_start: 0.7161 (pm20) cc_final: 0.6916 (pm20) REVERT: L 4 GLN cc_start: 0.7345 (mm-40) cc_final: 0.6829 (mm-40) REVERT: L 64 SER cc_start: 0.8211 (p) cc_final: 0.8008 (m) REVERT: L 83 ASP cc_start: 0.7866 (m-30) cc_final: 0.7545 (m-30) REVERT: A 119 ILE cc_start: 0.8461 (mt) cc_final: 0.8080 (mt) REVERT: A 165 ARG cc_start: 0.6841 (ttp-170) cc_final: 0.6615 (ttp-170) REVERT: A 229 LYS cc_start: 0.8471 (pttt) cc_final: 0.8248 (pttt) REVERT: A 272 TYR cc_start: 0.8571 (m-80) cc_final: 0.8334 (m-80) outliers start: 0 outliers final: 0 residues processed: 243 average time/residue: 0.4640 time to fit residues: 119.6646 Evaluate side-chains 204 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 204 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 0.4980 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 0.5980 chunk 61 optimal weight: 0.7980 chunk 45 optimal weight: 0.9980 chunk 74 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 30 ASN R 179 HIS R 185 GLN ** R 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 317 GLN H 104 GLN A 30 HIS A 83 ASN A 181 GLN A 248 GLN A 281 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.172132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.148326 restraints weight = 12408.124| |-----------------------------------------------------------------------------| r_work (start): 0.3923 rms_B_bonded: 2.79 r_work: 0.3796 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7275 moved from start: 0.3136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 7231 Z= 0.223 Angle : 0.804 11.728 9853 Z= 0.413 Chirality : 0.048 0.210 1137 Planarity : 0.007 0.086 1247 Dihedral : 6.282 62.146 1020 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 4.03 % Allowed : 13.69 % Favored : 82.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.28), residues: 903 helix: -1.01 (0.30), residues: 256 sheet: 1.08 (0.33), residues: 267 loop : -0.46 (0.31), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG L 67 TYR 0.023 0.002 TYR H 107 PHE 0.026 0.002 PHE H 105 TRP 0.024 0.002 TRP H 106 HIS 0.013 0.002 HIS R 179 Details of bonding type rmsd/Z covalent geometry : bond 0.00488 / 0.22 ( 7224) covalent geometry : angle 0.79598 / 0.41 ( 9839) SS BOND : bond 0.00523 / 0.25 ( 7) SS BOND : angle 3.09958 / 1.65 ( 14) hydrogen bonds : bond 0.05524 / 3.90 ( 332) hydrogen bonds : angle 6.09838 / 4.31 ( 921) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 210 time to evaluate : 0.309 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 20 LYS cc_start: 0.8202 (tppt) cc_final: 0.7991 (tppt) REVERT: R 35 ARG cc_start: 0.7010 (mtp-110) cc_final: 0.6771 (mtp-110) REVERT: R 76 LEU cc_start: 0.8543 (tm) cc_final: 0.8021 (pp) REVERT: R 118 MET cc_start: 0.7588 (OUTLIER) cc_final: 0.7290 (mpp) REVERT: R 270 LEU cc_start: 0.6796 (mt) cc_final: 0.6374 (mm) REVERT: R 283 HIS cc_start: 0.6718 (p-80) cc_final: 0.6398 (p-80) REVERT: R 289 MET cc_start: 0.6116 (mtm) cc_final: 0.5765 (mtm) REVERT: H 10 SER cc_start: 0.8326 (OUTLIER) cc_final: 0.8082 (m) REVERT: H 63 TYR cc_start: 0.8658 (m-80) cc_final: 0.8264 (m-80) REVERT: L 83 ASP cc_start: 0.7761 (m-30) cc_final: 0.7526 (m-30) REVERT: A 9 PHE cc_start: 0.7886 (m-80) cc_final: 0.7311 (m-80) REVERT: A 21 TYR cc_start: 0.8389 (m-80) cc_final: 0.8121 (m-80) REVERT: A 54 TYR cc_start: 0.8420 (m-80) cc_final: 0.7974 (m-80) REVERT: A 99 ARG cc_start: 0.7925 (mmt180) cc_final: 0.7641 (mmt180) REVERT: A 126 SER cc_start: 0.8642 (m) cc_final: 0.8064 (p) REVERT: A 165 ARG cc_start: 0.7383 (ttp-170) cc_final: 0.7170 (ttp-170) REVERT: A 169 GLU cc_start: 0.7274 (mm-30) cc_final: 0.6724 (mm-30) REVERT: A 229 LYS cc_start: 0.8333 (pttt) cc_final: 0.8041 (pttt) REVERT: A 232 LYS cc_start: 0.7959 (mtpp) cc_final: 0.7650 (tttp) REVERT: A 236 ARG cc_start: 0.8577 (OUTLIER) cc_final: 0.8307 (mtp180) REVERT: A 260 ASP cc_start: 0.7007 (m-30) cc_final: 0.6794 (m-30) REVERT: A 285 ARG cc_start: 0.7908 (ttt-90) cc_final: 0.7437 (ttt-90) outliers start: 30 outliers final: 14 residues processed: 222 average time/residue: 0.4644 time to fit residues: 109.2706 Evaluate side-chains 212 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 195 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 72 LEU Chi-restraints excluded: chain R residue 117 THR Chi-restraints excluded: chain R residue 118 MET Chi-restraints excluded: chain R residue 125 LEU Chi-restraints excluded: chain R residue 167 VAL Chi-restraints excluded: chain R residue 243 PHE Chi-restraints excluded: chain R residue 265 LEU Chi-restraints excluded: chain R residue 276 ILE Chi-restraints excluded: chain H residue 10 SER Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 86 THR Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 202 SER Chi-restraints excluded: chain A residue 236 ARG Chi-restraints excluded: chain A residue 299 ASN Chi-restraints excluded: chain A residue 307 ARG Chi-restraints excluded: chain A residue 345 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 43 optimal weight: 0.9980 chunk 48 optimal weight: 0.0070 chunk 83 optimal weight: 0.9990 chunk 8 optimal weight: 0.0770 chunk 13 optimal weight: 0.6980 chunk 77 optimal weight: 0.9980 chunk 70 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 46 optimal weight: 0.6980 chunk 19 optimal weight: 0.8980 overall best weight: 0.4756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 64 ASN ** R 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 83 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.173036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.149327 restraints weight = 12229.742| |-----------------------------------------------------------------------------| r_work (start): 0.3923 rms_B_bonded: 2.78 r_work: 0.3790 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7286 moved from start: 0.3859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7231 Z= 0.169 Angle : 0.685 9.339 9853 Z= 0.350 Chirality : 0.046 0.183 1137 Planarity : 0.006 0.072 1247 Dihedral : 6.054 60.036 1020 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.32 % Favored : 95.57 % Rotamer: Outliers : 4.70 % Allowed : 16.24 % Favored : 79.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (0.28), residues: 903 helix: -0.55 (0.32), residues: 246 sheet: 1.29 (0.32), residues: 274 loop : -0.40 (0.31), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 188 TYR 0.017 0.002 TYR H 112 PHE 0.022 0.002 PHE R 243 TRP 0.017 0.001 TRP H 106 HIS 0.010 0.002 HIS R 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.17 ( 7224) covalent geometry : angle 0.67896 / 0.35 ( 9839) SS BOND : bond 0.00593 / 0.29 ( 7) SS BOND : angle 2.42803 / 1.19 ( 14) hydrogen bonds : bond 0.04463 / 3.12 ( 332) hydrogen bonds : angle 5.56747 / 3.92 ( 921) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 212 time to evaluate : 0.265 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 76 LEU cc_start: 0.8476 (tm) cc_final: 0.7940 (pp) REVERT: R 117 THR cc_start: 0.8028 (m) cc_final: 0.7590 (t) REVERT: R 118 MET cc_start: 0.7683 (OUTLIER) cc_final: 0.7362 (mpp) REVERT: R 187 VAL cc_start: 0.7484 (m) cc_final: 0.6989 (m) REVERT: R 257 THR cc_start: 0.7961 (m) cc_final: 0.7683 (t) REVERT: R 265 LEU cc_start: 0.7534 (OUTLIER) cc_final: 0.7206 (mt) REVERT: R 268 ARG cc_start: 0.7011 (mtm-85) cc_final: 0.6730 (mtm-85) REVERT: R 283 HIS cc_start: 0.6802 (p-80) cc_final: 0.6414 (p-80) REVERT: R 289 MET cc_start: 0.6126 (mtm) cc_final: 0.5854 (mtm) REVERT: H 120 THR cc_start: 0.8572 (m) cc_final: 0.8361 (t) REVERT: L 68 SER cc_start: 0.8163 (t) cc_final: 0.7957 (m) REVERT: L 83 ASP cc_start: 0.7735 (m-30) cc_final: 0.7501 (m-30) REVERT: A 54 TYR cc_start: 0.8381 (m-80) cc_final: 0.8037 (m-80) REVERT: A 77 LYS cc_start: 0.8228 (tptt) cc_final: 0.7955 (tptm) REVERT: A 97 LEU cc_start: 0.8032 (mt) cc_final: 0.7821 (mt) REVERT: A 99 ARG cc_start: 0.7857 (mmt180) cc_final: 0.7561 (mmt180) REVERT: A 126 SER cc_start: 0.8638 (m) cc_final: 0.8097 (p) REVERT: A 145 GLU cc_start: 0.7975 (mt-10) cc_final: 0.7687 (tt0) REVERT: A 165 ARG cc_start: 0.7346 (ttp-170) cc_final: 0.6883 (ttp-170) REVERT: A 169 GLU cc_start: 0.7364 (mm-30) cc_final: 0.6785 (mm-30) REVERT: A 170 LYS cc_start: 0.8617 (OUTLIER) cc_final: 0.8384 (tttp) REVERT: A 202 SER cc_start: 0.8348 (p) cc_final: 0.8067 (m) REVERT: A 229 LYS cc_start: 0.8242 (pttt) cc_final: 0.7958 (pttt) REVERT: A 232 LYS cc_start: 0.7969 (mtpp) cc_final: 0.7647 (tttp) REVERT: A 274 LEU cc_start: 0.8004 (mp) cc_final: 0.7768 (mt) REVERT: A 326 LYS cc_start: 0.8194 (ttpt) cc_final: 0.7851 (ttpt) outliers start: 35 outliers final: 13 residues processed: 227 average time/residue: 0.4784 time to fit residues: 114.8750 Evaluate side-chains 224 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 208 time to evaluate : 0.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 72 LEU Chi-restraints excluded: chain R residue 114 ILE Chi-restraints excluded: chain R residue 118 MET Chi-restraints excluded: chain R residue 167 VAL Chi-restraints excluded: chain R residue 243 PHE Chi-restraints excluded: chain R residue 265 LEU Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 170 LYS Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 206 GLU Chi-restraints excluded: chain A residue 299 ASN Chi-restraints excluded: chain A residue 302 SER Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 345 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 61 optimal weight: 0.1980 chunk 22 optimal weight: 0.6980 chunk 53 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 82 optimal weight: 3.9990 chunk 0 optimal weight: 0.7980 chunk 60 optimal weight: 0.9980 chunk 20 optimal weight: 5.9990 chunk 31 optimal weight: 0.0270 chunk 68 optimal weight: 0.3980 chunk 30 optimal weight: 0.6980 overall best weight: 0.4038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 64 ASN C 71 GLN R 185 GLN ** R 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 83 ASN A 281 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.173147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.149029 restraints weight = 12356.614| |-----------------------------------------------------------------------------| r_work (start): 0.3913 rms_B_bonded: 2.81 r_work: 0.3785 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7289 moved from start: 0.4266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 7231 Z= 0.156 Angle : 0.694 10.471 9853 Z= 0.348 Chirality : 0.045 0.228 1137 Planarity : 0.006 0.101 1247 Dihedral : 6.083 60.482 1020 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.65 % Favored : 96.23 % Rotamer: Outliers : 4.16 % Allowed : 18.12 % Favored : 77.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.28), residues: 903 helix: -0.44 (0.32), residues: 237 sheet: 1.25 (0.31), residues: 274 loop : -0.47 (0.32), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG R 108 TYR 0.015 0.001 TYR H 98 PHE 0.023 0.002 PHE R 205 TRP 0.014 0.001 TRP H 106 HIS 0.012 0.001 HIS R 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.16 ( 7224) covalent geometry : angle 0.68217 / 0.34 ( 9839) SS BOND : bond 0.00490 / 0.23 ( 7) SS BOND : angle 3.49325 / 1.76 ( 14) hydrogen bonds : bond 0.04019 / 2.82 ( 332) hydrogen bonds : angle 5.52775 / 3.88 ( 921) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 205 time to evaluate : 0.266 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 117 THR cc_start: 0.8036 (m) cc_final: 0.7664 (t) REVERT: R 118 MET cc_start: 0.7747 (OUTLIER) cc_final: 0.7452 (mpp) REVERT: R 265 LEU cc_start: 0.7524 (OUTLIER) cc_final: 0.7308 (tp) REVERT: R 268 ARG cc_start: 0.7109 (mtm-85) cc_final: 0.6785 (mtm-85) REVERT: R 283 HIS cc_start: 0.6819 (p-80) cc_final: 0.6417 (p-80) REVERT: R 285 CYS cc_start: 0.7055 (OUTLIER) cc_final: 0.6046 (m) REVERT: R 289 MET cc_start: 0.6114 (mtm) cc_final: 0.5880 (mtm) REVERT: H 8 VAL cc_start: 0.8476 (t) cc_final: 0.8164 (m) REVERT: H 120 THR cc_start: 0.8593 (m) cc_final: 0.8340 (t) REVERT: A 54 TYR cc_start: 0.8372 (m-80) cc_final: 0.8008 (m-80) REVERT: A 97 LEU cc_start: 0.8038 (mt) cc_final: 0.7828 (mt) REVERT: A 99 ARG cc_start: 0.7781 (mmt180) cc_final: 0.7494 (mmt180) REVERT: A 126 SER cc_start: 0.8616 (m) cc_final: 0.8088 (p) REVERT: A 145 GLU cc_start: 0.7952 (mt-10) cc_final: 0.7670 (tt0) REVERT: A 169 GLU cc_start: 0.7484 (mm-30) cc_final: 0.6847 (mm-30) REVERT: A 183 THR cc_start: 0.8520 (OUTLIER) cc_final: 0.8214 (p) REVERT: A 188 ARG cc_start: 0.7992 (tpp80) cc_final: 0.7773 (tpp80) REVERT: A 202 SER cc_start: 0.8337 (OUTLIER) cc_final: 0.8096 (m) REVERT: A 229 LYS cc_start: 0.8223 (pttt) cc_final: 0.7962 (pttt) REVERT: A 232 LYS cc_start: 0.7941 (mtpp) cc_final: 0.7587 (tttp) REVERT: A 274 LEU cc_start: 0.7971 (mp) cc_final: 0.7744 (mt) REVERT: A 285 ARG cc_start: 0.8072 (ttt180) cc_final: 0.7653 (ttt-90) REVERT: A 326 LYS cc_start: 0.8159 (ttpt) cc_final: 0.7817 (ttpt) outliers start: 31 outliers final: 16 residues processed: 219 average time/residue: 0.4497 time to fit residues: 104.5134 Evaluate side-chains 216 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 195 time to evaluate : 0.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 21 CYS Chi-restraints excluded: chain C residue 71 GLN Chi-restraints excluded: chain C residue 72 LEU Chi-restraints excluded: chain R residue 118 MET Chi-restraints excluded: chain R residue 167 VAL Chi-restraints excluded: chain R residue 200 VAL Chi-restraints excluded: chain R residue 243 PHE Chi-restraints excluded: chain R residue 265 LEU Chi-restraints excluded: chain R residue 276 ILE Chi-restraints excluded: chain R residue 285 CYS Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 86 THR Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 153 ASN Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 202 SER Chi-restraints excluded: chain A residue 299 ASN Chi-restraints excluded: chain A residue 302 SER Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 345 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 20 optimal weight: 5.9990 chunk 47 optimal weight: 0.9990 chunk 67 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 19 optimal weight: 0.5980 chunk 88 optimal weight: 0.8980 chunk 78 optimal weight: 2.9990 chunk 83 optimal weight: 0.5980 chunk 11 optimal weight: 0.9980 chunk 46 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 64 ASN C 71 GLN R 185 GLN R 220 HIS L 39 GLN A 172 GLN A 181 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.171515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.147456 restraints weight = 12390.829| |-----------------------------------------------------------------------------| r_work (start): 0.3880 rms_B_bonded: 2.78 r_work: 0.3749 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7340 moved from start: 0.4552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 7231 Z= 0.225 Angle : 0.745 14.145 9853 Z= 0.372 Chirality : 0.048 0.342 1137 Planarity : 0.008 0.210 1247 Dihedral : 6.205 61.919 1020 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.09 % Favored : 94.80 % Rotamer: Outliers : 4.97 % Allowed : 19.19 % Favored : 75.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.28), residues: 903 helix: -0.61 (0.31), residues: 253 sheet: 1.13 (0.31), residues: 279 loop : -0.53 (0.32), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 307 TYR 0.016 0.002 TYR H 107 PHE 0.019 0.002 PHE H 105 TRP 0.013 0.002 TRP H 106 HIS 0.010 0.001 HIS R 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00509 / 0.23 ( 7224) covalent geometry : angle 0.73814 / 0.37 ( 9839) SS BOND : bond 0.00667 / 0.32 ( 7) SS BOND : angle 2.84777 / 1.44 ( 14) hydrogen bonds : bond 0.04280 / 3.01 ( 332) hydrogen bonds : angle 5.62301 / 3.91 ( 921) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 202 time to evaluate : 0.201 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 117 THR cc_start: 0.8063 (m) cc_final: 0.7673 (t) REVERT: R 118 MET cc_start: 0.7760 (OUTLIER) cc_final: 0.7466 (mpp) REVERT: R 197 GLU cc_start: 0.6987 (tm-30) cc_final: 0.6634 (tm-30) REVERT: R 252 LEU cc_start: 0.8599 (tp) cc_final: 0.8360 (pp) REVERT: R 268 ARG cc_start: 0.7190 (mtm-85) cc_final: 0.6864 (mtm-85) REVERT: R 285 CYS cc_start: 0.7097 (OUTLIER) cc_final: 0.6175 (m) REVERT: R 289 MET cc_start: 0.6133 (mtm) cc_final: 0.5908 (mtm) REVERT: H 8 VAL cc_start: 0.8480 (t) cc_final: 0.8175 (m) REVERT: L 78 SER cc_start: 0.7781 (m) cc_final: 0.7533 (p) REVERT: A 54 TYR cc_start: 0.8399 (m-80) cc_final: 0.8055 (m-80) REVERT: A 97 LEU cc_start: 0.8057 (mt) cc_final: 0.7833 (mt) REVERT: A 99 ARG cc_start: 0.7843 (mmt180) cc_final: 0.7554 (mmt180) REVERT: A 116 THR cc_start: 0.8404 (OUTLIER) cc_final: 0.8068 (p) REVERT: A 126 SER cc_start: 0.8660 (m) cc_final: 0.7972 (p) REVERT: A 156 GLU cc_start: 0.6442 (mt-10) cc_final: 0.4388 (mt-10) REVERT: A 165 ARG cc_start: 0.7391 (ttp-170) cc_final: 0.6739 (ttp-170) REVERT: A 169 GLU cc_start: 0.7531 (mm-30) cc_final: 0.6940 (mm-30) REVERT: A 183 THR cc_start: 0.8533 (OUTLIER) cc_final: 0.8266 (p) REVERT: A 188 ARG cc_start: 0.7982 (tpp80) cc_final: 0.7744 (tpp80) REVERT: A 202 SER cc_start: 0.8372 (OUTLIER) cc_final: 0.8121 (m) REVERT: A 229 LYS cc_start: 0.8274 (pttt) cc_final: 0.7994 (pttt) REVERT: A 232 LYS cc_start: 0.7999 (mtpp) cc_final: 0.7493 (mtpt) REVERT: A 257 GLU cc_start: 0.7146 (OUTLIER) cc_final: 0.6691 (mt-10) REVERT: A 274 LEU cc_start: 0.8054 (mp) cc_final: 0.7790 (mt) REVERT: A 285 ARG cc_start: 0.8114 (ttt180) cc_final: 0.7776 (ttt-90) REVERT: A 326 LYS cc_start: 0.8165 (OUTLIER) cc_final: 0.7851 (ttpt) outliers start: 37 outliers final: 23 residues processed: 217 average time/residue: 0.4671 time to fit residues: 107.3566 Evaluate side-chains 228 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 198 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 21 CYS Chi-restraints excluded: chain C residue 71 GLN Chi-restraints excluded: chain C residue 72 LEU Chi-restraints excluded: chain R residue 35 ARG Chi-restraints excluded: chain R residue 113 ILE Chi-restraints excluded: chain R residue 118 MET Chi-restraints excluded: chain R residue 125 LEU Chi-restraints excluded: chain R residue 167 VAL Chi-restraints excluded: chain R residue 200 VAL Chi-restraints excluded: chain R residue 239 VAL Chi-restraints excluded: chain R residue 243 PHE Chi-restraints excluded: chain R residue 254 LEU Chi-restraints excluded: chain R residue 276 ILE Chi-restraints excluded: chain R residue 285 CYS Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 79 LEU Chi-restraints excluded: chain L residue 86 THR Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 202 SER Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 257 GLU Chi-restraints excluded: chain A residue 299 ASN Chi-restraints excluded: chain A residue 302 SER Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 326 LYS Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 346 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 50 optimal weight: 0.9980 chunk 82 optimal weight: 0.0670 chunk 42 optimal weight: 1.9990 chunk 70 optimal weight: 0.5980 chunk 21 optimal weight: 0.0040 chunk 33 optimal weight: 0.9980 chunk 79 optimal weight: 0.9990 chunk 43 optimal weight: 0.9980 chunk 41 optimal weight: 0.5980 chunk 53 optimal weight: 0.9990 chunk 37 optimal weight: 0.8980 overall best weight: 0.4330 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 71 GLN A 83 ASN A 172 GLN A 245 ASN A 281 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.172787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.148070 restraints weight = 12256.442| |-----------------------------------------------------------------------------| r_work (start): 0.3902 rms_B_bonded: 2.82 r_work: 0.3774 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7315 moved from start: 0.4753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 7231 Z= 0.162 Angle : 0.717 12.879 9853 Z= 0.353 Chirality : 0.046 0.320 1137 Planarity : 0.007 0.147 1247 Dihedral : 6.032 62.479 1020 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.54 % Favored : 95.35 % Rotamer: Outliers : 4.83 % Allowed : 20.94 % Favored : 74.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.28), residues: 903 helix: -0.55 (0.32), residues: 247 sheet: 1.36 (0.32), residues: 263 loop : -0.62 (0.31), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG R 271 TYR 0.015 0.001 TYR H 107 PHE 0.018 0.002 PHE R 243 TRP 0.012 0.001 TRP H 106 HIS 0.003 0.001 HIS R 283 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.16 ( 7224) covalent geometry : angle 0.71274 / 0.35 ( 9839) SS BOND : bond 0.00506 / 0.24 ( 7) SS BOND : angle 2.17985 / 1.08 ( 14) hydrogen bonds : bond 0.03950 / 2.75 ( 332) hydrogen bonds : angle 5.45354 / 3.79 ( 921) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 202 time to evaluate : 0.251 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 117 THR cc_start: 0.8043 (m) cc_final: 0.7706 (t) REVERT: R 118 MET cc_start: 0.7775 (OUTLIER) cc_final: 0.7459 (mpp) REVERT: R 252 LEU cc_start: 0.8605 (tp) cc_final: 0.8354 (pp) REVERT: R 268 ARG cc_start: 0.7301 (mtm-85) cc_final: 0.6903 (mtm-85) REVERT: R 285 CYS cc_start: 0.7141 (OUTLIER) cc_final: 0.6153 (m) REVERT: R 289 MET cc_start: 0.6225 (mtm) cc_final: 0.5947 (mtm) REVERT: H 8 VAL cc_start: 0.8486 (t) cc_final: 0.8183 (m) REVERT: H 98 TYR cc_start: 0.8554 (m-80) cc_final: 0.8335 (m-10) REVERT: L 78 SER cc_start: 0.7798 (m) cc_final: 0.7511 (p) REVERT: A 54 TYR cc_start: 0.8383 (m-80) cc_final: 0.8008 (m-80) REVERT: A 99 ARG cc_start: 0.7770 (mmt180) cc_final: 0.7481 (mmt180) REVERT: A 116 THR cc_start: 0.8411 (OUTLIER) cc_final: 0.8106 (p) REVERT: A 126 SER cc_start: 0.8644 (m) cc_final: 0.8103 (p) REVERT: A 145 GLU cc_start: 0.7878 (tt0) cc_final: 0.7669 (tm-30) REVERT: A 152 GLU cc_start: 0.6934 (mp0) cc_final: 0.6669 (mp0) REVERT: A 153 ASN cc_start: 0.7371 (p0) cc_final: 0.7169 (p0) REVERT: A 156 GLU cc_start: 0.6359 (mt-10) cc_final: 0.4452 (mt-10) REVERT: A 169 GLU cc_start: 0.7490 (mm-30) cc_final: 0.7054 (mm-30) REVERT: A 183 THR cc_start: 0.8539 (OUTLIER) cc_final: 0.8272 (p) REVERT: A 188 ARG cc_start: 0.7991 (tpp80) cc_final: 0.7717 (tpp80) REVERT: A 202 SER cc_start: 0.8364 (p) cc_final: 0.8129 (m) REVERT: A 229 LYS cc_start: 0.8230 (pttt) cc_final: 0.7949 (pttt) REVERT: A 232 LYS cc_start: 0.7983 (mtpp) cc_final: 0.7487 (mtpt) REVERT: A 285 ARG cc_start: 0.8119 (ttt180) cc_final: 0.7760 (ttt-90) REVERT: A 307 ARG cc_start: 0.7235 (OUTLIER) cc_final: 0.7029 (ppt90) REVERT: A 326 LYS cc_start: 0.8156 (ttpt) cc_final: 0.7811 (ttpp) outliers start: 36 outliers final: 27 residues processed: 217 average time/residue: 0.4591 time to fit residues: 105.6631 Evaluate side-chains 231 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 199 time to evaluate : 0.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 21 CYS Chi-restraints excluded: chain C residue 71 GLN Chi-restraints excluded: chain C residue 72 LEU Chi-restraints excluded: chain R residue 35 ARG Chi-restraints excluded: chain R residue 96 ARG Chi-restraints excluded: chain R residue 114 ILE Chi-restraints excluded: chain R residue 118 MET Chi-restraints excluded: chain R residue 125 LEU Chi-restraints excluded: chain R residue 167 VAL Chi-restraints excluded: chain R residue 200 VAL Chi-restraints excluded: chain R residue 220 HIS Chi-restraints excluded: chain R residue 239 VAL Chi-restraints excluded: chain R residue 243 PHE Chi-restraints excluded: chain R residue 244 VAL Chi-restraints excluded: chain R residue 276 ILE Chi-restraints excluded: chain R residue 285 CYS Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 79 LEU Chi-restraints excluded: chain L residue 86 THR Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 212 GLU Chi-restraints excluded: chain A residue 299 ASN Chi-restraints excluded: chain A residue 302 SER Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 307 ARG Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 346 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 45 optimal weight: 0.5980 chunk 76 optimal weight: 2.9990 chunk 69 optimal weight: 0.0870 chunk 31 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 chunk 53 optimal weight: 0.0970 chunk 3 optimal weight: 0.0030 chunk 36 optimal weight: 0.5980 chunk 63 optimal weight: 0.7980 chunk 27 optimal weight: 9.9990 chunk 86 optimal weight: 0.0870 overall best weight: 0.1744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 71 GLN A 83 ASN A 172 GLN A 281 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.174017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.149369 restraints weight = 12229.853| |-----------------------------------------------------------------------------| r_work (start): 0.3924 rms_B_bonded: 2.82 r_work: 0.3794 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7290 moved from start: 0.4921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7231 Z= 0.131 Angle : 0.698 12.058 9853 Z= 0.342 Chirality : 0.046 0.344 1137 Planarity : 0.006 0.122 1247 Dihedral : 5.791 62.242 1020 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.21 % Favored : 95.68 % Rotamer: Outliers : 4.30 % Allowed : 20.94 % Favored : 74.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.28), residues: 903 helix: -0.34 (0.32), residues: 242 sheet: 1.35 (0.32), residues: 262 loop : -0.60 (0.31), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG R 271 TYR 0.011 0.001 TYR H 107 PHE 0.034 0.002 PHE A 115 TRP 0.009 0.001 TRP H 106 HIS 0.002 0.000 HIS R 179 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 ( 7224) covalent geometry : angle 0.69609 / 0.34 ( 9839) SS BOND : bond 0.00332 / 0.16 ( 7) SS BOND : angle 1.63481 / 0.84 ( 14) hydrogen bonds : bond 0.03736 / 2.58 ( 332) hydrogen bonds : angle 5.21245 / 3.64 ( 921) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 192 time to evaluate : 0.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 96 ARG cc_start: 0.5486 (OUTLIER) cc_final: 0.4817 (mtp180) REVERT: R 117 THR cc_start: 0.8009 (m) cc_final: 0.7723 (t) REVERT: R 118 MET cc_start: 0.7706 (OUTLIER) cc_final: 0.7416 (mpp) REVERT: R 197 GLU cc_start: 0.7289 (tp30) cc_final: 0.6499 (tm-30) REVERT: R 252 LEU cc_start: 0.8475 (tp) cc_final: 0.8202 (pp) REVERT: R 256 LEU cc_start: 0.8432 (tt) cc_final: 0.8028 (tt) REVERT: R 257 THR cc_start: 0.7958 (p) cc_final: 0.7544 (t) REVERT: R 268 ARG cc_start: 0.7157 (mtm-85) cc_final: 0.6867 (mtm-85) REVERT: R 283 HIS cc_start: 0.6911 (p-80) cc_final: 0.6437 (p-80) REVERT: R 285 CYS cc_start: 0.7086 (OUTLIER) cc_final: 0.6098 (m) REVERT: R 289 MET cc_start: 0.6323 (mtm) cc_final: 0.5988 (mtm) REVERT: H 8 VAL cc_start: 0.8468 (t) cc_final: 0.8156 (m) REVERT: H 98 TYR cc_start: 0.8532 (m-80) cc_final: 0.8233 (m-80) REVERT: H 115 GLN cc_start: 0.7198 (pm20) cc_final: 0.6893 (pm20) REVERT: L 5 MET cc_start: 0.8315 (mtp) cc_final: 0.8049 (mmm) REVERT: A 54 TYR cc_start: 0.8358 (m-80) cc_final: 0.8009 (m-80) REVERT: A 99 ARG cc_start: 0.7789 (mmt180) cc_final: 0.7472 (mmt180) REVERT: A 116 THR cc_start: 0.8435 (OUTLIER) cc_final: 0.8161 (p) REVERT: A 126 SER cc_start: 0.8572 (m) cc_final: 0.8057 (p) REVERT: A 152 GLU cc_start: 0.6843 (mp0) cc_final: 0.6622 (mp0) REVERT: A 153 ASN cc_start: 0.7333 (p0) cc_final: 0.7100 (p0) REVERT: A 156 GLU cc_start: 0.6245 (mt-10) cc_final: 0.4406 (mt-10) REVERT: A 169 GLU cc_start: 0.7423 (mm-30) cc_final: 0.7037 (mm-30) REVERT: A 183 THR cc_start: 0.8502 (OUTLIER) cc_final: 0.8263 (p) REVERT: A 188 ARG cc_start: 0.7963 (tpp80) cc_final: 0.7675 (tpp80) REVERT: A 229 LYS cc_start: 0.8216 (pttt) cc_final: 0.7940 (pttt) REVERT: A 256 GLU cc_start: 0.7544 (tm-30) cc_final: 0.7097 (tm-30) REVERT: A 285 ARG cc_start: 0.8148 (ttt180) cc_final: 0.7781 (ttt-90) REVERT: A 326 LYS cc_start: 0.8167 (OUTLIER) cc_final: 0.7836 (ttpp) outliers start: 32 outliers final: 22 residues processed: 205 average time/residue: 0.4781 time to fit residues: 103.9496 Evaluate side-chains 215 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 187 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 21 CYS Chi-restraints excluded: chain C residue 71 GLN Chi-restraints excluded: chain C residue 72 LEU Chi-restraints excluded: chain R residue 35 ARG Chi-restraints excluded: chain R residue 72 TRP Chi-restraints excluded: chain R residue 96 ARG Chi-restraints excluded: chain R residue 114 ILE Chi-restraints excluded: chain R residue 118 MET Chi-restraints excluded: chain R residue 125 LEU Chi-restraints excluded: chain R residue 167 VAL Chi-restraints excluded: chain R residue 220 HIS Chi-restraints excluded: chain R residue 239 VAL Chi-restraints excluded: chain R residue 243 PHE Chi-restraints excluded: chain R residue 276 ILE Chi-restraints excluded: chain R residue 285 CYS Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 212 GLU Chi-restraints excluded: chain A residue 299 ASN Chi-restraints excluded: chain A residue 302 SER Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 326 LYS Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 346 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 50 optimal weight: 0.9980 chunk 42 optimal weight: 0.8980 chunk 70 optimal weight: 0.0770 chunk 64 optimal weight: 0.9980 chunk 85 optimal weight: 0.6980 chunk 61 optimal weight: 0.8980 chunk 33 optimal weight: 0.7980 chunk 56 optimal weight: 0.4980 chunk 20 optimal weight: 0.5980 chunk 49 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 71 GLN A 83 ASN A 281 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.165462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.140021 restraints weight = 12533.320| |-----------------------------------------------------------------------------| r_work (start): 0.3859 rms_B_bonded: 2.83 r_work: 0.3740 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7322 moved from start: 0.5043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 7231 Z= 0.173 Angle : 0.715 11.646 9853 Z= 0.354 Chirality : 0.046 0.311 1137 Planarity : 0.007 0.159 1247 Dihedral : 5.797 62.622 1020 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.76 % Favored : 95.13 % Rotamer: Outliers : 4.43 % Allowed : 21.07 % Favored : 74.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (0.28), residues: 903 helix: -0.26 (0.32), residues: 242 sheet: 1.34 (0.32), residues: 261 loop : -0.62 (0.31), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG R 271 TYR 0.014 0.001 TYR H 107 PHE 0.042 0.002 PHE R 205 TRP 0.008 0.001 TRP H 106 HIS 0.002 0.001 HIS R 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.17 ( 7224) covalent geometry : angle 0.71049 / 0.35 ( 9839) SS BOND : bond 0.00675 / 0.33 ( 7) SS BOND : angle 2.23866 / 1.09 ( 14) hydrogen bonds : bond 0.03856 / 2.68 ( 332) hydrogen bonds : angle 5.26250 / 3.66 ( 921) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 194 time to evaluate : 0.272 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 117 THR cc_start: 0.8030 (m) cc_final: 0.7710 (t) REVERT: R 118 MET cc_start: 0.7742 (OUTLIER) cc_final: 0.7448 (mpp) REVERT: R 197 GLU cc_start: 0.7290 (tp30) cc_final: 0.6747 (tm-30) REVERT: R 252 LEU cc_start: 0.8468 (tp) cc_final: 0.8220 (pp) REVERT: R 283 HIS cc_start: 0.6911 (p-80) cc_final: 0.6497 (p-80) REVERT: R 285 CYS cc_start: 0.7094 (OUTLIER) cc_final: 0.6118 (m) REVERT: R 289 MET cc_start: 0.6276 (mtm) cc_final: 0.5972 (mtm) REVERT: H 8 VAL cc_start: 0.8482 (t) cc_final: 0.8188 (m) REVERT: L 5 MET cc_start: 0.8295 (mtp) cc_final: 0.8027 (mmm) REVERT: L 78 SER cc_start: 0.7809 (m) cc_final: 0.7581 (p) REVERT: A 54 TYR cc_start: 0.8341 (m-80) cc_final: 0.7999 (m-80) REVERT: A 99 ARG cc_start: 0.7819 (mmt180) cc_final: 0.7521 (mmt180) REVERT: A 116 THR cc_start: 0.8482 (OUTLIER) cc_final: 0.8236 (p) REVERT: A 126 SER cc_start: 0.8585 (m) cc_final: 0.8002 (p) REVERT: A 152 GLU cc_start: 0.6883 (mp0) cc_final: 0.6557 (mp0) REVERT: A 156 GLU cc_start: 0.6525 (mt-10) cc_final: 0.4381 (mt-10) REVERT: A 169 GLU cc_start: 0.7373 (mm-30) cc_final: 0.7017 (mm-30) REVERT: A 183 THR cc_start: 0.8526 (OUTLIER) cc_final: 0.8289 (p) REVERT: A 188 ARG cc_start: 0.7978 (tpp80) cc_final: 0.7694 (tpp80) REVERT: A 229 LYS cc_start: 0.8222 (pttt) cc_final: 0.7950 (pttt) REVERT: A 256 GLU cc_start: 0.7466 (tm-30) cc_final: 0.7011 (tm-30) REVERT: A 285 ARG cc_start: 0.8102 (ttt180) cc_final: 0.7707 (ttt-90) REVERT: A 326 LYS cc_start: 0.8170 (OUTLIER) cc_final: 0.7937 (ttpt) outliers start: 33 outliers final: 23 residues processed: 210 average time/residue: 0.4847 time to fit residues: 107.7760 Evaluate side-chains 216 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 188 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 21 CYS Chi-restraints excluded: chain C residue 71 GLN Chi-restraints excluded: chain C residue 72 LEU Chi-restraints excluded: chain R residue 35 ARG Chi-restraints excluded: chain R residue 72 TRP Chi-restraints excluded: chain R residue 118 MET Chi-restraints excluded: chain R residue 125 LEU Chi-restraints excluded: chain R residue 167 VAL Chi-restraints excluded: chain R residue 173 ARG Chi-restraints excluded: chain R residue 220 HIS Chi-restraints excluded: chain R residue 239 VAL Chi-restraints excluded: chain R residue 243 PHE Chi-restraints excluded: chain R residue 244 VAL Chi-restraints excluded: chain R residue 276 ILE Chi-restraints excluded: chain R residue 285 CYS Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 212 GLU Chi-restraints excluded: chain A residue 299 ASN Chi-restraints excluded: chain A residue 302 SER Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 326 LYS Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 346 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 88 optimal weight: 0.5980 chunk 71 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 chunk 27 optimal weight: 9.9990 chunk 34 optimal weight: 3.9990 chunk 53 optimal weight: 0.9980 chunk 1 optimal weight: 0.3980 chunk 85 optimal weight: 0.7980 chunk 9 optimal weight: 0.9990 chunk 32 optimal weight: 0.6980 chunk 44 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 83 ASN A 172 GLN A 281 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.168558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.143482 restraints weight = 12421.323| |-----------------------------------------------------------------------------| r_work (start): 0.3851 rms_B_bonded: 2.86 r_work: 0.3723 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7344 moved from start: 0.5184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 7231 Z= 0.191 Angle : 0.752 11.556 9853 Z= 0.369 Chirality : 0.046 0.332 1137 Planarity : 0.007 0.143 1247 Dihedral : 5.834 63.895 1020 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.87 % Favored : 95.02 % Rotamer: Outliers : 4.30 % Allowed : 21.07 % Favored : 74.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.28), residues: 903 helix: -0.23 (0.32), residues: 242 sheet: 1.30 (0.33), residues: 263 loop : -0.65 (0.31), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG R 108 TYR 0.015 0.002 TYR H 98 PHE 0.028 0.002 PHE A 115 TRP 0.007 0.001 TRP R 100 HIS 0.002 0.001 HIS R 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00434 / 0.19 ( 7224) covalent geometry : angle 0.74839 / 0.37 ( 9839) SS BOND : bond 0.00618 / 0.30 ( 7) SS BOND : angle 2.19835 / 1.07 ( 14) hydrogen bonds : bond 0.03992 / 2.78 ( 332) hydrogen bonds : angle 5.32837 / 3.71 ( 921) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 181 time to evaluate : 0.180 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 117 THR cc_start: 0.8043 (m) cc_final: 0.7704 (t) REVERT: R 118 MET cc_start: 0.7761 (OUTLIER) cc_final: 0.7473 (mpp) REVERT: R 252 LEU cc_start: 0.8477 (tp) cc_final: 0.8226 (pp) REVERT: R 268 ARG cc_start: 0.7177 (mtm-85) cc_final: 0.6905 (mtm-85) REVERT: R 283 HIS cc_start: 0.6945 (p-80) cc_final: 0.6586 (p-80) REVERT: R 285 CYS cc_start: 0.7182 (OUTLIER) cc_final: 0.6225 (m) REVERT: R 289 MET cc_start: 0.6384 (mtm) cc_final: 0.6064 (mtm) REVERT: H 8 VAL cc_start: 0.8474 (t) cc_final: 0.8176 (m) REVERT: L 5 MET cc_start: 0.8306 (mtp) cc_final: 0.8039 (mmm) REVERT: L 78 SER cc_start: 0.7778 (m) cc_final: 0.7533 (p) REVERT: A 54 TYR cc_start: 0.8362 (m-80) cc_final: 0.8034 (m-80) REVERT: A 99 ARG cc_start: 0.7871 (mmt180) cc_final: 0.7573 (mmt180) REVERT: A 103 ARG cc_start: 0.8045 (mtt180) cc_final: 0.7758 (ttm-80) REVERT: A 116 THR cc_start: 0.8566 (OUTLIER) cc_final: 0.8315 (p) REVERT: A 126 SER cc_start: 0.8612 (m) cc_final: 0.8006 (p) REVERT: A 169 GLU cc_start: 0.7419 (mm-30) cc_final: 0.7042 (mm-30) REVERT: A 183 THR cc_start: 0.8515 (OUTLIER) cc_final: 0.8286 (p) REVERT: A 229 LYS cc_start: 0.8249 (pttt) cc_final: 0.7962 (pttt) REVERT: A 256 GLU cc_start: 0.7464 (tm-30) cc_final: 0.6974 (tm-30) REVERT: A 285 ARG cc_start: 0.8103 (ttt180) cc_final: 0.7712 (ttt-90) REVERT: A 326 LYS cc_start: 0.8175 (OUTLIER) cc_final: 0.7844 (ttpp) outliers start: 32 outliers final: 23 residues processed: 199 average time/residue: 0.4575 time to fit residues: 96.2169 Evaluate side-chains 207 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 179 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 21 CYS Chi-restraints excluded: chain R residue 72 TRP Chi-restraints excluded: chain R residue 118 MET Chi-restraints excluded: chain R residue 167 VAL Chi-restraints excluded: chain R residue 173 ARG Chi-restraints excluded: chain R residue 200 VAL Chi-restraints excluded: chain R residue 220 HIS Chi-restraints excluded: chain R residue 226 TRP Chi-restraints excluded: chain R residue 239 VAL Chi-restraints excluded: chain R residue 243 PHE Chi-restraints excluded: chain R residue 244 VAL Chi-restraints excluded: chain R residue 276 ILE Chi-restraints excluded: chain R residue 285 CYS Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 86 THR Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 212 GLU Chi-restraints excluded: chain A residue 299 ASN Chi-restraints excluded: chain A residue 302 SER Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 326 LYS Chi-restraints excluded: chain A residue 345 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 33 optimal weight: 0.9990 chunk 84 optimal weight: 0.4980 chunk 65 optimal weight: 0.3980 chunk 61 optimal weight: 0.4980 chunk 83 optimal weight: 0.5980 chunk 12 optimal weight: 2.9990 chunk 8 optimal weight: 0.0070 chunk 54 optimal weight: 1.9990 chunk 68 optimal weight: 0.9990 chunk 64 optimal weight: 0.9990 chunk 81 optimal weight: 0.9980 overall best weight: 0.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 71 GLN H 104 GLN A 122 ASN A 172 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.169928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.145011 restraints weight = 12383.529| |-----------------------------------------------------------------------------| r_work (start): 0.3857 rms_B_bonded: 2.85 r_work: 0.3732 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7316 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 : 0.004 0.043 7231 Z= 0.155 Angle : 0.749 12.520 9853 Z= 0.366 Chirality : 0.046 0.307 1137 Planarity : 0.006 0.136 1247 Dihedral : 5.711 64.425 1020 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.32 % Favored : 95.57 % Rotamer: Outliers : 3.62 % Allowed : 22.82 % Favored : 73.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (0.28), residues: 903 helix: -0.14 (0.32), residues: 241 sheet: 1.31 (0.33), residues: 262 loop : -0.67 (0.31), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG R 271 TYR 0.013 0.002 TYR H 98 PHE 0.040 0.002 PHE R 205 TRP 0.008 0.001 TRP R 72 HIS 0.002 0.001 HIS R 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.15 ( 7224) covalent geometry : angle 0.74666 / 0.36 ( 9839) SS BOND : bond 0.00511 / 0.24 ( 7) SS BOND : angle 1.81802 / 0.90 ( 14) hydrogen bonds : bond 0.03901 / 2.71 ( 332) hydrogen bonds : angle 5.23975 / 3.64 ( 921) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 187 time to evaluate : 0.160 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 117 THR cc_start: 0.7982 (m) cc_final: 0.7726 (t) REVERT: R 118 MET cc_start: 0.7739 (OUTLIER) cc_final: 0.7441 (mpp) REVERT: R 252 LEU cc_start: 0.8441 (tp) cc_final: 0.8208 (pp) REVERT: R 268 ARG cc_start: 0.7127 (mtm-85) cc_final: 0.6855 (mtm-85) REVERT: R 283 HIS cc_start: 0.6933 (p-80) cc_final: 0.6581 (p-80) REVERT: R 285 CYS cc_start: 0.7131 (OUTLIER) cc_final: 0.6159 (m) REVERT: R 289 MET cc_start: 0.6125 (mtm) cc_final: 0.5831 (mtm) REVERT: H 8 VAL cc_start: 0.8463 (t) cc_final: 0.8192 (m) REVERT: L 5 MET cc_start: 0.8284 (mtp) cc_final: 0.8036 (mmm) REVERT: L 78 SER cc_start: 0.7770 (m) cc_final: 0.7550 (p) REVERT: A 54 TYR cc_start: 0.8330 (m-80) cc_final: 0.7979 (m-80) REVERT: A 99 ARG cc_start: 0.7833 (mmt180) cc_final: 0.7543 (mmt180) REVERT: A 103 ARG cc_start: 0.7996 (mtt180) cc_final: 0.7747 (ttm-80) REVERT: A 116 THR cc_start: 0.8557 (OUTLIER) cc_final: 0.8321 (p) REVERT: A 126 SER cc_start: 0.8568 (m) cc_final: 0.8018 (p) REVERT: A 152 GLU cc_start: 0.6876 (mp0) cc_final: 0.6272 (pm20) REVERT: A 156 GLU cc_start: 0.6558 (mt-10) cc_final: 0.5145 (mt-10) REVERT: A 169 GLU cc_start: 0.7363 (mm-30) cc_final: 0.7007 (mm-30) REVERT: A 183 THR cc_start: 0.8503 (OUTLIER) cc_final: 0.8189 (p) REVERT: A 188 ARG cc_start: 0.7889 (tpp80) cc_final: 0.7662 (tpp80) REVERT: A 229 LYS cc_start: 0.8273 (pttt) cc_final: 0.7992 (pttt) REVERT: A 256 GLU cc_start: 0.7435 (tm-30) cc_final: 0.6934 (tm-30) REVERT: A 261 THR cc_start: 0.8344 (m) cc_final: 0.8013 (p) REVERT: A 285 ARG cc_start: 0.8057 (ttt180) cc_final: 0.7844 (ttt-90) REVERT: A 326 LYS cc_start: 0.8158 (ttpt) cc_final: 0.7889 (ttpp) outliers start: 27 outliers final: 20 residues processed: 202 average time/residue: 0.4749 time to fit residues: 101.4049 Evaluate side-chains 206 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 182 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 21 CYS Chi-restraints excluded: chain C residue 71 GLN Chi-restraints excluded: chain R residue 72 TRP Chi-restraints excluded: chain R residue 118 MET Chi-restraints excluded: chain R residue 167 VAL Chi-restraints excluded: chain R residue 173 ARG Chi-restraints excluded: chain R residue 200 VAL Chi-restraints excluded: chain R residue 220 HIS Chi-restraints excluded: chain R residue 226 TRP Chi-restraints excluded: chain R residue 243 PHE Chi-restraints excluded: chain R residue 244 VAL Chi-restraints excluded: chain R residue 285 CYS Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 212 GLU Chi-restraints excluded: chain A residue 299 ASN Chi-restraints excluded: chain A residue 302 SER Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 345 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 39 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 4 optimal weight: 0.7980 chunk 43 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 81 optimal weight: 1.9990 chunk 31 optimal weight: 0.1980 chunk 16 optimal weight: 0.5980 chunk 56 optimal weight: 0.9980 chunk 40 optimal weight: 0.9980 chunk 87 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 71 GLN A 83 ASN A 172 GLN A 248 GLN A 281 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.167596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.141593 restraints weight = 12251.151| |-----------------------------------------------------------------------------| r_work (start): 0.3844 rms_B_bonded: 2.85 r_work: 0.3720 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7361 moved from start: 0.5434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 7231 Z= 0.207 Angle : 0.783 12.214 9853 Z= 0.389 Chirality : 0.048 0.297 1137 Planarity : 0.007 0.134 1247 Dihedral : 5.860 64.872 1020 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.32 % Favored : 94.57 % Rotamer: Outliers : 3.62 % Allowed : 22.82 % Favored : 73.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.28), residues: 903 helix: -0.14 (0.33), residues: 240 sheet: 1.26 (0.33), residues: 263 loop : -0.74 (0.31), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG A 307 TYR 0.015 0.002 TYR H 107 PHE 0.027 0.002 PHE A 115 TRP 0.008 0.001 TRP R 72 HIS 0.003 0.001 HIS C 67 Details of bonding type rmsd/Z covalent geometry : bond 0.00469 / 0.21 ( 7224) covalent geometry : angle 0.77828 / 0.39 ( 9839) SS BOND : bond 0.00725 / 0.34 ( 7) SS BOND : angle 2.49766 / 1.26 ( 14) hydrogen bonds : bond 0.04168 / 2.92 ( 332) hydrogen bonds : angle 5.38031 / 3.74 ( 921) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2751.09 seconds wall clock time: 47 minutes 33.64 seconds (2853.64 seconds total)