Starting phenix.real_space_refine on Tue Nov 18 02:17:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5xlp_6731/11_2025/5xlp_6731.cif Found real_map, /net/cci-nas-00/data/ceres_data/5xlp_6731/11_2025/5xlp_6731.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/5xlp_6731/11_2025/5xlp_6731.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5xlp_6731/11_2025/5xlp_6731.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/5xlp_6731/11_2025/5xlp_6731.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5xlp_6731/11_2025/5xlp_6731.map" } resolution = 4.2 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= 0.010 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 24 5.49 5 S 11 5.16 5 C 6107 2.51 5 N 1737 2.21 5 O 2073 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9952 Number of models: 1 Model: "" Number of chains: 6 Chain: "C" Number of atoms: 2004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2004 Classifications: {'peptide': 287} Incomplete info: {'truncation_to_alanine': 43} Link IDs: {'PTRANS': 9, 'TRANS': 277} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 245 Unresolved non-hydrogen angles: 307 Unresolved non-hydrogen dihedrals: 228 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 14, 'ASP:plan': 1, 'TRP:plan': 4, 'TYR:plan': 4, 'GLN:plan1': 4, 'HIS:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 180 Chain: "D" Number of atoms: 2273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2273 Classifications: {'peptide': 326} Incomplete info: {'truncation_to_alanine': 50} Link IDs: {'PTRANS': 12, 'TRANS': 313} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 272 Unresolved non-hydrogen angles: 339 Unresolved non-hydrogen dihedrals: 250 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 15, 'ASP:plan': 2, 'TRP:plan': 4, 'ASN:plan1': 1, 'GLN:plan1': 5, 'TYR:plan': 4, 'HIS:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 195 Chain: "E" Number of atoms: 2273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2273 Classifications: {'peptide': 326} Incomplete info: {'truncation_to_alanine': 50} Link IDs: {'PTRANS': 12, 'TRANS': 313} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 272 Unresolved non-hydrogen angles: 339 Unresolved non-hydrogen dihedrals: 250 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 15, 'ASP:plan': 2, 'TRP:plan': 4, 'ASN:plan1': 1, 'GLN:plan1': 5, 'TYR:plan': 4, 'HIS:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 195 Chain: "F" Number of atoms: 2273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2273 Classifications: {'peptide': 326} Incomplete info: {'truncation_to_alanine': 50} Link IDs: {'PTRANS': 12, 'TRANS': 313} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 272 Unresolved non-hydrogen angles: 339 Unresolved non-hydrogen dihedrals: 250 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 15, 'ASP:plan': 2, 'TRP:plan': 4, 'ASN:plan1': 1, 'GLN:plan1': 5, 'TYR:plan': 4, 'HIS:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 195 Chain: "K" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 514 Classifications: {'RNA': 24} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 10, 'rna3p_pur': 6, 'rna3p_pyr': 1} Link IDs: {'rna2p': 16, 'rna3p': 7} Chain: "M" Number of atoms: 615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 615 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 75} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Time building chain proxies: 2.86, per 1000 atoms: 0.29 Number of scatterers: 9952 At special positions: 0 Unit cell: (110.04, 111.35, 127.07, 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 11 16.00 P 24 15.00 O 2073 8.00 N 1737 7.00 C 6107 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 1.17 Conformation dependent library (CDL) restraints added in 354.8 milliseconds 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2480 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 20 sheets defined 29.3% alpha, 6.0% beta 0 base pairs and 4 stacking pairs defined. Time for finding SS restraints: 1.44 Creating SS restraints... Processing helix chain 'C' and resid 121 through 138 Processing helix chain 'C' and resid 141 through 151 Processing helix chain 'C' and resid 159 through 163 removed outlier: 3.505A pdb=" N ILE C 162 " --> pdb=" O GLU C 159 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ASN C 163 " --> pdb=" O VAL C 160 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 159 through 163' Processing helix chain 'C' and resid 187 through 191 Processing helix chain 'C' and resid 199 through 214 removed outlier: 4.197A pdb=" N VAL C 214 " --> pdb=" O LEU C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 266 through 271 Processing helix chain 'C' and resid 272 through 274 No H-bonds generated for 'chain 'C' and resid 272 through 274' Processing helix chain 'C' and resid 293 through 297 removed outlier: 4.391A pdb=" N GLN C 297 " --> pdb=" O ALA C 294 " (cutoff:3.500A) Processing helix chain 'C' and resid 316 through 325 removed outlier: 4.900A pdb=" N GLN C 323 " --> pdb=" O ALA C 319 " (cutoff:3.500A) Processing helix chain 'C' and resid 331 through 336 Processing helix chain 'D' and resid 74 through 83 removed outlier: 3.933A pdb=" N THR D 78 " --> pdb=" O PRO D 74 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL D 79 " --> pdb=" O ASN D 75 " (cutoff:3.500A) Processing helix chain 'D' and resid 121 through 138 Processing helix chain 'D' and resid 141 through 151 Processing helix chain 'D' and resid 159 through 163 removed outlier: 3.505A pdb=" N ILE D 162 " --> pdb=" O GLU D 159 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ASN D 163 " --> pdb=" O VAL D 160 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 159 through 163' Processing helix chain 'D' and resid 187 through 191 Processing helix chain 'D' and resid 199 through 214 removed outlier: 4.198A pdb=" N VAL D 214 " --> pdb=" O LEU D 210 " (cutoff:3.500A) Processing helix chain 'D' and resid 266 through 271 Processing helix chain 'D' and resid 272 through 274 No H-bonds generated for 'chain 'D' and resid 272 through 274' Processing helix chain 'D' and resid 293 through 297 removed outlier: 4.390A pdb=" N GLN D 297 " --> pdb=" O ALA D 294 " (cutoff:3.500A) Processing helix chain 'D' and resid 316 through 325 removed outlier: 4.901A pdb=" N GLN D 323 " --> pdb=" O ALA D 319 " (cutoff:3.500A) Processing helix chain 'D' and resid 331 through 336 Processing helix chain 'E' and resid 75 through 83 removed outlier: 3.520A pdb=" N VAL E 79 " --> pdb=" O ASN E 75 " (cutoff:3.500A) Processing helix chain 'E' and resid 121 through 138 Processing helix chain 'E' and resid 141 through 151 Processing helix chain 'E' and resid 159 through 163 removed outlier: 3.504A pdb=" N ILE E 162 " --> pdb=" O GLU E 159 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ASN E 163 " --> pdb=" O VAL E 160 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 159 through 163' Processing helix chain 'E' and resid 187 through 191 Processing helix chain 'E' and resid 199 through 214 removed outlier: 4.198A pdb=" N VAL E 214 " --> pdb=" O LEU E 210 " (cutoff:3.500A) Processing helix chain 'E' and resid 266 through 271 Processing helix chain 'E' and resid 272 through 274 No H-bonds generated for 'chain 'E' and resid 272 through 274' Processing helix chain 'E' and resid 293 through 297 removed outlier: 4.391A pdb=" N GLN E 297 " --> pdb=" O ALA E 294 " (cutoff:3.500A) Processing helix chain 'E' and resid 316 through 325 removed outlier: 4.901A pdb=" N GLN E 323 " --> pdb=" O ALA E 319 " (cutoff:3.500A) Processing helix chain 'E' and resid 331 through 336 Processing helix chain 'F' and resid 73 through 81 removed outlier: 4.084A pdb=" N GLN F 77 " --> pdb=" O SER F 73 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N VAL F 79 " --> pdb=" O ASN F 75 " (cutoff:3.500A) Processing helix chain 'F' and resid 121 through 138 Processing helix chain 'F' and resid 141 through 151 Processing helix chain 'F' and resid 159 through 163 removed outlier: 3.505A pdb=" N ILE F 162 " --> pdb=" O GLU F 159 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ASN F 163 " --> pdb=" O VAL F 160 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 159 through 163' Processing helix chain 'F' and resid 187 through 191 Processing helix chain 'F' and resid 199 through 214 removed outlier: 4.198A pdb=" N VAL F 214 " --> pdb=" O LEU F 210 " (cutoff:3.500A) Processing helix chain 'F' and resid 266 through 271 Processing helix chain 'F' and resid 272 through 274 No H-bonds generated for 'chain 'F' and resid 272 through 274' Processing helix chain 'F' and resid 293 through 297 removed outlier: 4.391A pdb=" N GLN F 297 " --> pdb=" O ALA F 294 " (cutoff:3.500A) Processing helix chain 'F' and resid 316 through 325 removed outlier: 4.902A pdb=" N GLN F 323 " --> pdb=" O ALA F 319 " (cutoff:3.500A) Processing helix chain 'F' and resid 331 through 336 Processing helix chain 'M' and resid 46 through 56 removed outlier: 4.256A pdb=" N SER M 52 " --> pdb=" O GLU M 48 " (cutoff:3.500A) Processing helix chain 'M' and resid 61 through 74 removed outlier: 3.596A pdb=" N ILE M 65 " --> pdb=" O GLY M 61 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ARG M 74 " --> pdb=" O ASN M 70 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 36 through 37 removed outlier: 3.745A pdb=" N ARG C 50 " --> pdb=" O GLN C 37 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 107 through 108 removed outlier: 3.659A pdb=" N SER C 107 " --> pdb=" O ASP C 221 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 168 through 172 Processing sheet with id=AA4, first strand: chain 'C' and resid 174 through 175 Processing sheet with id=AA5, first strand: chain 'D' and resid 36 through 37 removed outlier: 3.745A pdb=" N ARG D 50 " --> pdb=" O GLN D 37 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 56 through 59 Processing sheet with id=AA7, first strand: chain 'D' and resid 107 through 108 removed outlier: 3.658A pdb=" N SER D 107 " --> pdb=" O ASP D 221 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 168 through 172 Processing sheet with id=AA9, first strand: chain 'D' and resid 174 through 175 Processing sheet with id=AB1, first strand: chain 'E' and resid 36 through 37 removed outlier: 3.746A pdb=" N ARG E 50 " --> pdb=" O GLN E 37 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 57 through 59 Processing sheet with id=AB3, first strand: chain 'E' and resid 107 through 108 removed outlier: 3.658A pdb=" N SER E 107 " --> pdb=" O ASP E 221 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 168 through 172 Processing sheet with id=AB5, first strand: chain 'E' and resid 174 through 175 Processing sheet with id=AB6, first strand: chain 'F' and resid 36 through 37 removed outlier: 3.744A pdb=" N ARG F 50 " --> pdb=" O GLN F 37 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 55 through 58 removed outlier: 3.626A pdb=" N ASN F 55 " --> pdb=" O LEU F 91 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 107 through 108 removed outlier: 3.658A pdb=" N SER F 107 " --> pdb=" O ASP F 221 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 168 through 172 Processing sheet with id=AC1, first strand: chain 'F' and resid 174 through 175 Processing sheet with id=AC2, first strand: chain 'M' and resid 19 through 21 248 hydrogen bonds defined for protein. 684 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 4 stacking parallelities Total time for adding SS restraints: 1.55 Time building geometry restraints manager: 1.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2658 1.33 - 1.45: 1827 1.45 - 1.57: 5592 1.57 - 1.69: 47 1.69 - 1.80: 18 Bond restraints: 10142 Sorted by residual: bond pdb=" C HIS E 164 " pdb=" N ILE E 165 " ideal model delta sigma weight residual 1.334 1.306 0.028 1.24e-02 6.50e+03 5.00e+00 bond pdb=" C HIS C 164 " pdb=" N ILE C 165 " ideal model delta sigma weight residual 1.334 1.306 0.028 1.24e-02 6.50e+03 4.94e+00 bond pdb=" C LEU M 12 " pdb=" N ASN M 13 " ideal model delta sigma weight residual 1.331 1.282 0.049 2.22e-02 2.03e+03 4.85e+00 bond pdb=" C HIS F 164 " pdb=" N ILE F 165 " ideal model delta sigma weight residual 1.334 1.307 0.027 1.24e-02 6.50e+03 4.77e+00 bond pdb=" C HIS D 164 " pdb=" N ILE D 165 " ideal model delta sigma weight residual 1.334 1.307 0.027 1.24e-02 6.50e+03 4.72e+00 ... (remaining 10137 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.05: 13457 3.05 - 6.10: 402 6.10 - 9.16: 80 9.16 - 12.21: 22 12.21 - 15.26: 2 Bond angle restraints: 13963 Sorted by residual: angle pdb=" N VAL E 42 " pdb=" CA VAL E 42 " pdb=" C VAL E 42 " ideal model delta sigma weight residual 111.88 101.65 10.23 1.06e+00 8.90e-01 9.32e+01 angle pdb=" N VAL D 42 " pdb=" CA VAL D 42 " pdb=" C VAL D 42 " ideal model delta sigma weight residual 111.88 101.66 10.22 1.06e+00 8.90e-01 9.29e+01 angle pdb=" N VAL C 42 " pdb=" CA VAL C 42 " pdb=" C VAL C 42 " ideal model delta sigma weight residual 111.88 101.67 10.21 1.06e+00 8.90e-01 9.28e+01 angle pdb=" N VAL F 42 " pdb=" CA VAL F 42 " pdb=" C VAL F 42 " ideal model delta sigma weight residual 111.88 101.67 10.21 1.06e+00 8.90e-01 9.27e+01 angle pdb=" N ILE D 280 " pdb=" CA ILE D 280 " pdb=" C ILE D 280 " ideal model delta sigma weight residual 111.88 102.37 9.51 1.06e+00 8.90e-01 8.06e+01 ... (remaining 13958 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.85: 5961 35.85 - 71.71: 106 71.71 - 107.56: 17 107.56 - 143.41: 1 143.41 - 179.27: 6 Dihedral angle restraints: 6091 sinusoidal: 2250 harmonic: 3841 Sorted by residual: dihedral pdb=" CA HIS M 11 " pdb=" C HIS M 11 " pdb=" N LEU M 12 " pdb=" CA LEU M 12 " ideal model delta harmonic sigma weight residual -180.00 -118.49 -61.51 0 5.00e+00 4.00e-02 1.51e+02 dihedral pdb=" C5' C K 12 " pdb=" C4' C K 12 " pdb=" C3' C K 12 " pdb=" O3' C K 12 " ideal model delta sinusoidal sigma weight residual 147.00 84.74 62.26 1 8.00e+00 1.56e-02 8.02e+01 dihedral pdb=" O4' C K 5 " pdb=" C1' C K 5 " pdb=" N1 C K 5 " pdb=" C2 C K 5 " ideal model delta sinusoidal sigma weight residual 200.00 48.73 151.27 1 1.50e+01 4.44e-03 8.01e+01 ... (remaining 6088 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 1424 0.083 - 0.165: 241 0.165 - 0.248: 21 0.248 - 0.330: 2 0.330 - 0.413: 3 Chirality restraints: 1691 Sorted by residual: chirality pdb=" C3' G K 18 " pdb=" C4' G K 18 " pdb=" O3' G K 18 " pdb=" C2' G K 18 " both_signs ideal model delta sigma weight residual False -2.74 -2.33 -0.41 2.00e-01 2.50e+01 4.26e+00 chirality pdb=" C3' A K 16 " pdb=" C4' A K 16 " pdb=" O3' A K 16 " pdb=" C2' A K 16 " both_signs ideal model delta sigma weight residual False -2.74 -2.36 -0.38 2.00e-01 2.50e+01 3.66e+00 chirality pdb=" C3' G K 9 " pdb=" C4' G K 9 " pdb=" O3' G K 9 " pdb=" C2' G K 9 " both_signs ideal model delta sigma weight residual False -2.48 -2.13 -0.35 2.00e-01 2.50e+01 3.09e+00 ... (remaining 1688 not shown) Planarity restraints: 1783 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA HIS M 11 " 0.023 2.00e-02 2.50e+03 4.63e-02 2.14e+01 pdb=" C HIS M 11 " -0.080 2.00e-02 2.50e+03 pdb=" O HIS M 11 " 0.029 2.00e-02 2.50e+03 pdb=" N LEU M 12 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR F 271 " -0.051 5.00e-02 4.00e+02 7.60e-02 9.24e+00 pdb=" N PRO F 272 " 0.131 5.00e-02 4.00e+02 pdb=" CA PRO F 272 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO F 272 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR E 271 " -0.051 5.00e-02 4.00e+02 7.60e-02 9.24e+00 pdb=" N PRO E 272 " 0.131 5.00e-02 4.00e+02 pdb=" CA PRO E 272 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO E 272 " -0.042 5.00e-02 4.00e+02 ... (remaining 1780 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.74: 1094 2.74 - 3.28: 9866 3.28 - 3.82: 15966 3.82 - 4.36: 18829 4.36 - 4.90: 30316 Nonbonded interactions: 76071 Sorted by model distance: nonbonded pdb=" OD1 ASP F 80 " pdb=" OH TYR M 6 " model vdw 2.194 3.040 nonbonded pdb=" O ASN E 75 " pdb=" OG1 THR E 78 " model vdw 2.232 3.040 nonbonded pdb=" OG1 THR D 90 " pdb=" O ALA D 254 " model vdw 2.258 3.040 nonbonded pdb=" OG1 THR C 105 " pdb=" OE1 GLN C 223 " model vdw 2.278 3.040 nonbonded pdb=" OG1 THR D 105 " pdb=" OE1 GLN D 223 " model vdw 2.279 3.040 ... (remaining 76066 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'C' selection = (chain 'D' and (resid 15 through 53 or resid 93 through 340)) selection = (chain 'E' and (resid 15 through 53 or resid 93 through 340)) selection = (chain 'F' and (resid 15 through 53 or resid 93 through 340)) } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.970 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5858 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 : 0.009 0.095 10142 Z= 0.419 Angle : 1.358 15.262 13963 Z= 0.748 Chirality : 0.064 0.413 1691 Planarity : 0.009 0.076 1783 Dihedral : 16.051 179.265 3611 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.45 % Allowed : 18.18 % Favored : 81.37 % Rotamer: Outliers : 0.57 % Allowed : 1.95 % Favored : 97.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.85 % 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: -5.53 (0.17), residues: 1331 helix: -3.73 (0.19), residues: 253 sheet: -3.98 (0.28), residues: 206 loop : -3.80 (0.16), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.002 ARG M 42 TYR 0.026 0.002 TYR M 20 PHE 0.035 0.004 PHE C 147 TRP 0.041 0.008 TRP C 174 HIS 0.007 0.003 HIS F 140 Details of bonding type rmsd covalent geometry : bond 0.00873 (10142) covalent geometry : angle 1.35814 (13963) hydrogen bonds : bond 0.16158 ( 248) hydrogen bonds : angle 13.70777 ( 684) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 314 time to evaluate : 0.287 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: symmetry clash 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 34 ASP cc_start: 0.6378 (m-30) cc_final: 0.5951 (t0) REVERT: C 237 ASP cc_start: 0.7657 (m-30) cc_final: 0.7368 (m-30) REVERT: C 284 PRO cc_start: 0.6843 (Cg_endo) cc_final: 0.6427 (Cg_exo) REVERT: C 321 GLU cc_start: 0.8239 (tt0) cc_final: 0.7844 (tm-30) REVERT: D 153 VAL cc_start: 0.7714 (t) cc_final: 0.7320 (p) REVERT: D 219 ILE cc_start: 0.7611 (mt) cc_final: 0.7284 (mt) REVERT: E 256 HIS cc_start: 0.7428 (m90) cc_final: 0.7188 (m90) REVERT: F 58 LYS cc_start: 0.6354 (mttt) cc_final: 0.5186 (mttt) REVERT: F 59 THR cc_start: 0.8927 (p) cc_final: 0.8650 (m) REVERT: F 314 ARG cc_start: 0.2850 (ttt-90) cc_final: 0.1939 (mmp80) REVERT: M 72 ILE cc_start: 0.8433 (mm) cc_final: 0.8070 (mm) outliers start: 5 outliers final: 1 residues processed: 318 average time/residue: 0.1283 time to fit residues: 53.6292 Evaluate side-chains 184 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 183 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 3.9990 chunk 55 optimal weight: 4.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 151 ASN D 83 ASN E 151 ASN E 223 GLN ** E 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 300 GLN ** F 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 151 ASN ** F 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 300 GLN M 32 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4545 r_free = 0.4545 target = 0.180921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.164635 restraints weight = 24717.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.164997 restraints weight = 21071.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4347 r_free = 0.4347 target = 0.165853 restraints weight = 19028.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4356 r_free = 0.4356 target = 0.166605 restraints weight = 15708.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4358 r_free = 0.4358 target = 0.166714 restraints weight = 14030.303| |-----------------------------------------------------------------------------| r_work (final): 0.4346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6185 moved from start: 0.4063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 10142 Z= 0.196 Angle : 0.907 10.040 13963 Z= 0.465 Chirality : 0.047 0.254 1691 Planarity : 0.007 0.075 1783 Dihedral : 18.705 172.976 1783 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 17.40 Ramachandran Plot: Outliers : 0.23 % Allowed : 12.70 % Favored : 87.08 % Rotamer: Outliers : 0.23 % Allowed : 5.27 % Favored : 94.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.73 (0.19), residues: 1331 helix: -2.07 (0.28), residues: 278 sheet: -3.73 (0.28), residues: 195 loop : -3.58 (0.17), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 184 TYR 0.020 0.002 TYR M 20 PHE 0.021 0.002 PHE D 147 TRP 0.030 0.003 TRP C 174 HIS 0.005 0.001 HIS E 256 Details of bonding type rmsd covalent geometry : bond 0.00411 (10142) covalent geometry : angle 0.90685 (13963) hydrogen bonds : bond 0.04030 ( 248) hydrogen bonds : angle 8.06100 ( 684) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 240 time to evaluate : 0.359 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 225 VAL cc_start: 0.7630 (t) cc_final: 0.7428 (t) REVERT: C 237 ASP cc_start: 0.6783 (m-30) cc_final: 0.6266 (p0) REVERT: C 274 GLU cc_start: 0.7993 (mp0) cc_final: 0.7655 (mm-30) REVERT: C 284 PRO cc_start: 0.6955 (Cg_endo) cc_final: 0.6717 (Cg_exo) REVERT: D 125 TYR cc_start: 0.5792 (t80) cc_final: 0.5549 (t80) REVERT: D 270 TRP cc_start: 0.6958 (t-100) cc_final: 0.6510 (t-100) REVERT: E 265 ARG cc_start: 0.7206 (mtp85) cc_final: 0.6918 (ttm110) REVERT: F 37 GLN cc_start: 0.5690 (mt0) cc_final: 0.5375 (mt0) REVERT: F 59 THR cc_start: 0.8790 (p) cc_final: 0.8580 (m) REVERT: F 169 GLU cc_start: 0.6126 (tt0) cc_final: 0.5693 (mt-10) REVERT: F 303 ASP cc_start: 0.5751 (m-30) cc_final: 0.5258 (t0) REVERT: F 314 ARG cc_start: 0.2367 (ttt-90) cc_final: 0.1473 (mmp80) outliers start: 2 outliers final: 0 residues processed: 241 average time/residue: 0.1357 time to fit residues: 42.8090 Evaluate side-chains 170 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 170 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 64 optimal weight: 0.9980 chunk 122 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 121 optimal weight: 4.9990 chunk 123 optimal weight: 5.9990 chunk 86 optimal weight: 2.9990 chunk 108 optimal weight: 10.0000 chunk 70 optimal weight: 5.9990 chunk 9 optimal weight: 6.9990 chunk 18 optimal weight: 7.9990 chunk 22 optimal weight: 5.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 208 HIS D 127 ASN E 144 ASN E 241 GLN E 300 GLN F 140 HIS F 208 HIS ** F 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4433 r_free = 0.4433 target = 0.169043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.152529 restraints weight = 25292.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.152808 restraints weight = 23513.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.154150 restraints weight = 21138.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.154646 restraints weight = 15474.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.154814 restraints weight = 15079.360| |-----------------------------------------------------------------------------| r_work (final): 0.4239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6450 moved from start: 0.5762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.091 10142 Z= 0.275 Angle : 0.987 10.744 13963 Z= 0.513 Chirality : 0.049 0.308 1691 Planarity : 0.008 0.079 1783 Dihedral : 18.766 171.953 1783 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 21.73 Ramachandran Plot: Outliers : 0.23 % Allowed : 17.05 % Favored : 82.72 % Rotamer: Outliers : 0.11 % Allowed : 6.19 % Favored : 93.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.31 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.66 (0.19), residues: 1331 helix: -2.01 (0.27), residues: 301 sheet: -3.66 (0.33), residues: 166 loop : -3.61 (0.18), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG E 161 TYR 0.023 0.003 TYR C 125 PHE 0.023 0.003 PHE C 226 TRP 0.023 0.003 TRP C 174 HIS 0.007 0.002 HIS D 324 Details of bonding type rmsd covalent geometry : bond 0.00595 (10142) covalent geometry : angle 0.98660 (13963) hydrogen bonds : bond 0.04428 ( 248) hydrogen bonds : angle 8.10170 ( 684) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 212 time to evaluate : 0.359 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 129 GLN cc_start: 0.7485 (pm20) cc_final: 0.7150 (mm-40) REVERT: C 140 HIS cc_start: 0.6696 (t-170) cc_final: 0.6278 (m170) REVERT: C 237 ASP cc_start: 0.6947 (m-30) cc_final: 0.5601 (p0) REVERT: D 67 LEU cc_start: 0.7771 (pt) cc_final: 0.7483 (pp) REVERT: D 251 ASP cc_start: 0.6011 (p0) cc_final: 0.5778 (p0) REVERT: E 43 THR cc_start: 0.7207 (OUTLIER) cc_final: 0.6852 (t) REVERT: E 279 PRO cc_start: 0.5678 (Cg_endo) cc_final: 0.5290 (Cg_exo) REVERT: E 295 TYR cc_start: 0.8121 (m-80) cc_final: 0.7892 (m-80) REVERT: F 37 GLN cc_start: 0.5829 (mt0) cc_final: 0.5560 (mt0) REVERT: F 169 GLU cc_start: 0.6341 (tt0) cc_final: 0.5633 (mt-10) REVERT: F 314 ARG cc_start: 0.2519 (ttt-90) cc_final: 0.1817 (mmp80) outliers start: 1 outliers final: 0 residues processed: 213 average time/residue: 0.1333 time to fit residues: 36.9040 Evaluate side-chains 161 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 160 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 15 optimal weight: 6.9990 chunk 23 optimal weight: 5.9990 chunk 101 optimal weight: 3.9990 chunk 132 optimal weight: 2.9990 chunk 11 optimal weight: 10.0000 chunk 92 optimal weight: 20.0000 chunk 20 optimal weight: 1.9990 chunk 40 optimal weight: 0.6980 chunk 21 optimal weight: 0.8980 chunk 73 optimal weight: 1.9990 chunk 112 optimal weight: 0.9980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 140 HIS ** D 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 140 HIS E 223 GLN F 110 ASN F 140 HIS F 223 GLN ** F 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 329 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4482 r_free = 0.4482 target = 0.173968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.157792 restraints weight = 24983.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4287 r_free = 0.4287 target = 0.158789 restraints weight = 21785.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.160007 restraints weight = 17894.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.160338 restraints weight = 13060.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.160458 restraints weight = 12637.054| |-----------------------------------------------------------------------------| r_work (final): 0.4313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6303 moved from start: 0.6472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 10142 Z= 0.158 Angle : 0.832 9.811 13963 Z= 0.430 Chirality : 0.045 0.263 1691 Planarity : 0.006 0.069 1783 Dihedral : 18.398 176.145 1783 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 15.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.12 % Favored : 85.88 % Rotamer: Outliers : 0.34 % Allowed : 2.98 % Favored : 96.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.32 (0.20), residues: 1331 helix: -1.47 (0.30), residues: 302 sheet: -3.36 (0.34), residues: 173 loop : -3.51 (0.18), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 161 TYR 0.022 0.001 TYR M 20 PHE 0.025 0.002 PHE C 131 TRP 0.019 0.002 TRP C 174 HIS 0.012 0.002 HIS E 140 Details of bonding type rmsd covalent geometry : bond 0.00336 (10142) covalent geometry : angle 0.83160 (13963) hydrogen bonds : bond 0.03281 ( 248) hydrogen bonds : angle 7.05235 ( 684) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 229 time to evaluate : 0.369 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 131 PHE cc_start: 0.7927 (m-80) cc_final: 0.7677 (m-80) REVERT: C 301 LYS cc_start: 0.7752 (mmtt) cc_final: 0.7545 (mmtt) REVERT: D 55 ASN cc_start: 0.7659 (t0) cc_final: 0.6838 (m110) REVERT: D 67 LEU cc_start: 0.7803 (pt) cc_final: 0.7433 (mt) REVERT: D 210 LEU cc_start: 0.7439 (tp) cc_final: 0.7201 (tp) REVERT: D 239 LYS cc_start: 0.8115 (tmmt) cc_final: 0.7641 (ttpt) REVERT: E 34 ASP cc_start: 0.7192 (t0) cc_final: 0.6856 (t0) REVERT: E 36 SER cc_start: 0.8877 (m) cc_final: 0.8340 (t) REVERT: E 53 ILE cc_start: 0.5988 (tp) cc_final: 0.5711 (tp) REVERT: E 94 ARG cc_start: 0.6736 (ttm170) cc_final: 0.6372 (mtm-85) REVERT: F 37 GLN cc_start: 0.5308 (mt0) cc_final: 0.5062 (mt0) REVERT: F 169 GLU cc_start: 0.6151 (tt0) cc_final: 0.5737 (mt-10) REVERT: F 314 ARG cc_start: 0.2165 (ttt-90) cc_final: 0.1828 (mmp80) outliers start: 3 outliers final: 1 residues processed: 230 average time/residue: 0.1358 time to fit residues: 40.5104 Evaluate side-chains 161 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 160 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 100 optimal weight: 8.9990 chunk 129 optimal weight: 7.9990 chunk 115 optimal weight: 10.0000 chunk 101 optimal weight: 9.9990 chunk 74 optimal weight: 0.0060 chunk 19 optimal weight: 20.0000 chunk 48 optimal weight: 8.9990 chunk 45 optimal weight: 4.9990 chunk 118 optimal weight: 0.5980 chunk 36 optimal weight: 7.9990 chunk 32 optimal weight: 0.9990 overall best weight: 2.9202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 140 HIS ** D 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4390 r_free = 0.4390 target = 0.165779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.151515 restraints weight = 25536.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.151306 restraints weight = 28951.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.152542 restraints weight = 25147.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.153094 restraints weight = 17400.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.153240 restraints weight = 16705.423| |-----------------------------------------------------------------------------| r_work (final): 0.4220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6519 moved from start: 0.7557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 10142 Z= 0.242 Angle : 0.953 10.038 13963 Z= 0.492 Chirality : 0.048 0.273 1691 Planarity : 0.006 0.066 1783 Dihedral : 18.524 170.996 1783 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 21.36 Ramachandran Plot: Outliers : 0.30 % Allowed : 17.73 % Favored : 81.97 % Rotamer: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.31 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.35 (0.20), residues: 1331 helix: -1.36 (0.30), residues: 297 sheet: -3.32 (0.34), residues: 176 loop : -3.59 (0.17), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 265 TYR 0.020 0.002 TYR M 20 PHE 0.026 0.003 PHE D 336 TRP 0.012 0.002 TRP D 174 HIS 0.009 0.002 HIS E 140 Details of bonding type rmsd covalent geometry : bond 0.00513 (10142) covalent geometry : angle 0.95321 (13963) hydrogen bonds : bond 0.04153 ( 248) hydrogen bonds : angle 7.53974 ( 684) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 211 time to evaluate : 0.369 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 141 ASN cc_start: 0.6100 (m-40) cc_final: 0.5872 (m110) REVERT: C 284 PRO cc_start: 0.6348 (Cg_endo) cc_final: 0.6077 (Cg_exo) REVERT: D 25 MET cc_start: 0.6851 (mmp) cc_final: 0.6448 (mpp) REVERT: D 55 ASN cc_start: 0.7638 (t0) cc_final: 0.7015 (m110) REVERT: D 67 LEU cc_start: 0.7829 (pt) cc_final: 0.7580 (mt) REVERT: F 169 GLU cc_start: 0.6463 (tt0) cc_final: 0.5859 (mt-10) REVERT: F 265 ARG cc_start: 0.6588 (mmp-170) cc_final: 0.5931 (mmp-170) REVERT: F 301 LYS cc_start: 0.6581 (pttp) cc_final: 0.6201 (pttm) REVERT: F 314 ARG cc_start: 0.2661 (ttt-90) cc_final: 0.1946 (mmp80) REVERT: M 1 MET cc_start: 0.7012 (tpp) cc_final: 0.6721 (tpp) REVERT: M 53 TRP cc_start: 0.7699 (p-90) cc_final: 0.7348 (p-90) outliers start: 0 outliers final: 0 residues processed: 211 average time/residue: 0.1304 time to fit residues: 36.0024 Evaluate side-chains 161 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 161 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 33 optimal weight: 0.4980 chunk 75 optimal weight: 3.9990 chunk 93 optimal weight: 9.9990 chunk 107 optimal weight: 10.0000 chunk 20 optimal weight: 8.9990 chunk 10 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 chunk 79 optimal weight: 9.9990 chunk 76 optimal weight: 4.9990 chunk 90 optimal weight: 2.9990 chunk 28 optimal weight: 9.9990 overall best weight: 2.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 144 ASN C 208 HIS ** C 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 324 HIS ** D 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 223 GLN E 322 GLN ** F 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 329 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4401 r_free = 0.4401 target = 0.167171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.152129 restraints weight = 26035.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.152558 restraints weight = 25467.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.153778 restraints weight = 23545.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.154287 restraints weight = 15965.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.154437 restraints weight = 15499.300| |-----------------------------------------------------------------------------| r_work (final): 0.4228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6499 moved from start: 0.8069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 10142 Z= 0.199 Angle : 0.898 12.025 13963 Z= 0.460 Chirality : 0.046 0.270 1691 Planarity : 0.006 0.060 1783 Dihedral : 18.370 177.151 1783 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 18.46 Ramachandran Plot: Outliers : 0.23 % Allowed : 16.08 % Favored : 83.70 % Rotamer: Outliers : 0.11 % Allowed : 2.75 % Favored : 97.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.26 (0.20), residues: 1331 helix: -1.32 (0.29), residues: 317 sheet: -3.47 (0.33), residues: 176 loop : -3.51 (0.18), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 184 TYR 0.018 0.002 TYR M 20 PHE 0.025 0.003 PHE E 95 TRP 0.012 0.002 TRP M 53 HIS 0.007 0.001 HIS E 208 Details of bonding type rmsd covalent geometry : bond 0.00425 (10142) covalent geometry : angle 0.89761 (13963) hydrogen bonds : bond 0.03464 ( 248) hydrogen bonds : angle 7.00658 ( 684) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 209 time to evaluate : 0.388 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 161 ARG cc_start: 0.7167 (mtp-110) cc_final: 0.6869 (mtp85) REVERT: C 235 LYS cc_start: 0.4740 (ptmt) cc_final: 0.4526 (ptmm) REVERT: C 284 PRO cc_start: 0.6340 (Cg_endo) cc_final: 0.6028 (Cg_exo) REVERT: D 25 MET cc_start: 0.6698 (mmp) cc_final: 0.6469 (mpp) REVERT: D 67 LEU cc_start: 0.7749 (pt) cc_final: 0.7518 (mt) REVERT: D 90 THR cc_start: 0.7984 (p) cc_final: 0.7685 (p) REVERT: D 270 TRP cc_start: 0.6828 (t-100) cc_final: 0.6378 (t-100) REVERT: F 37 GLN cc_start: 0.6104 (mt0) cc_final: 0.4950 (mt0) REVERT: F 89 ASP cc_start: 0.5666 (m-30) cc_final: 0.5465 (m-30) REVERT: F 169 GLU cc_start: 0.6179 (tt0) cc_final: 0.5535 (mt-10) REVERT: F 314 ARG cc_start: 0.2647 (ttt-90) cc_final: 0.1844 (mmp80) REVERT: M 53 TRP cc_start: 0.7608 (p-90) cc_final: 0.7334 (p-90) outliers start: 1 outliers final: 1 residues processed: 210 average time/residue: 0.1255 time to fit residues: 34.7114 Evaluate side-chains 165 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 164 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 113 optimal weight: 0.6980 chunk 110 optimal weight: 6.9990 chunk 5 optimal weight: 10.0000 chunk 124 optimal weight: 9.9990 chunk 24 optimal weight: 0.9980 chunk 73 optimal weight: 0.0570 chunk 21 optimal weight: 0.8980 chunk 63 optimal weight: 5.9990 chunk 89 optimal weight: 1.9990 chunk 3 optimal weight: 0.4980 chunk 20 optimal weight: 7.9990 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 129 GLN ** C 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 324 HIS D 140 HIS D 151 ASN ** D 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 324 HIS ** E 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 223 GLN F 110 ASN ** F 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4477 r_free = 0.4477 target = 0.173907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.159818 restraints weight = 25067.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.160110 restraints weight = 25242.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.161592 restraints weight = 20397.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.161986 restraints weight = 15019.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4324 r_free = 0.4324 target = 0.162277 restraints weight = 14999.897| |-----------------------------------------------------------------------------| r_work (final): 0.4327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6279 moved from start: 0.8313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10142 Z= 0.131 Angle : 0.797 11.034 13963 Z= 0.404 Chirality : 0.044 0.240 1691 Planarity : 0.005 0.058 1783 Dihedral : 18.037 179.072 1783 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 14.01 Ramachandran Plot: Outliers : 0.08 % Allowed : 14.35 % Favored : 85.57 % Rotamer: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.92 (0.21), residues: 1331 helix: -1.06 (0.30), residues: 332 sheet: -3.33 (0.35), residues: 170 loop : -3.29 (0.18), residues: 829 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 161 TYR 0.016 0.001 TYR M 20 PHE 0.014 0.002 PHE C 95 TRP 0.017 0.002 TRP E 174 HIS 0.009 0.001 HIS E 208 Details of bonding type rmsd covalent geometry : bond 0.00277 (10142) covalent geometry : angle 0.79676 (13963) hydrogen bonds : bond 0.02908 ( 248) hydrogen bonds : angle 6.43744 ( 684) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 225 time to evaluate : 0.393 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 129 GLN cc_start: 0.8078 (pt0) cc_final: 0.7709 (pt0) REVERT: C 284 PRO cc_start: 0.6076 (Cg_endo) cc_final: 0.5811 (Cg_exo) REVERT: D 67 LEU cc_start: 0.7817 (pt) cc_final: 0.7550 (mt) REVERT: D 90 THR cc_start: 0.7919 (p) cc_final: 0.7716 (p) REVERT: D 210 LEU cc_start: 0.7248 (mt) cc_final: 0.6986 (tp) REVERT: D 219 ILE cc_start: 0.8471 (mm) cc_final: 0.8261 (mm) REVERT: D 241 GLN cc_start: 0.5539 (pp30) cc_final: 0.4903 (pp30) REVERT: D 324 HIS cc_start: 0.6800 (m90) cc_final: 0.6556 (m-70) REVERT: E 34 ASP cc_start: 0.6795 (t0) cc_final: 0.6383 (t0) REVERT: E 36 SER cc_start: 0.8809 (m) cc_final: 0.8501 (t) REVERT: E 94 ARG cc_start: 0.6577 (ttp-170) cc_final: 0.6087 (mtm-85) REVERT: E 269 THR cc_start: 0.7859 (t) cc_final: 0.7655 (t) REVERT: F 37 GLN cc_start: 0.5540 (mt0) cc_final: 0.4414 (mt0) REVERT: F 169 GLU cc_start: 0.6071 (tt0) cc_final: 0.5630 (mt-10) REVERT: F 314 ARG cc_start: 0.2844 (ttt-90) cc_final: 0.2140 (mmt180) REVERT: M 54 PHE cc_start: 0.5666 (t80) cc_final: 0.5432 (t80) outliers start: 0 outliers final: 0 residues processed: 225 average time/residue: 0.1210 time to fit residues: 35.8115 Evaluate side-chains 176 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 176 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 50 optimal weight: 4.9990 chunk 25 optimal weight: 9.9990 chunk 84 optimal weight: 7.9990 chunk 115 optimal weight: 9.9990 chunk 49 optimal weight: 5.9990 chunk 79 optimal weight: 1.9990 chunk 83 optimal weight: 8.9990 chunk 122 optimal weight: 0.4980 chunk 33 optimal weight: 5.9990 chunk 2 optimal weight: 9.9990 chunk 91 optimal weight: 0.0060 overall best weight: 2.7002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 208 HIS C 324 HIS D 140 HIS ** D 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 256 HIS E 127 ASN E 144 ASN E 223 GLN E 322 GLN ** F 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 329 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4389 r_free = 0.4389 target = 0.166403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.152807 restraints weight = 25284.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.152513 restraints weight = 25465.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.153413 restraints weight = 25649.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.154072 restraints weight = 17892.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.154111 restraints weight = 17312.790| |-----------------------------------------------------------------------------| r_work (final): 0.4224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6512 moved from start: 0.8729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 10142 Z= 0.230 Angle : 0.947 11.018 13963 Z= 0.484 Chirality : 0.048 0.265 1691 Planarity : 0.006 0.072 1783 Dihedral : 18.233 172.623 1783 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 19.83 Ramachandran Plot: Outliers : 0.23 % Allowed : 17.73 % Favored : 82.04 % Rotamer: Outliers : 0.11 % Allowed : 2.06 % Favored : 97.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.12 (0.21), residues: 1331 helix: -1.20 (0.30), residues: 329 sheet: -3.37 (0.35), residues: 176 loop : -3.45 (0.18), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 150 TYR 0.023 0.002 TYR M 20 PHE 0.025 0.003 PHE F 131 TRP 0.026 0.003 TRP M 53 HIS 0.009 0.002 HIS C 208 Details of bonding type rmsd covalent geometry : bond 0.00495 (10142) covalent geometry : angle 0.94748 (13963) hydrogen bonds : bond 0.03892 ( 248) hydrogen bonds : angle 7.11033 ( 684) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 200 time to evaluate : 0.389 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: C 129 GLN cc_start: 0.7952 (pt0) cc_final: 0.7600 (pt0) REVERT: C 239 LYS cc_start: 0.7793 (mttp) cc_final: 0.7075 (tptp) REVERT: C 284 PRO cc_start: 0.6247 (Cg_endo) cc_final: 0.6006 (Cg_exo) REVERT: D 90 THR cc_start: 0.8053 (p) cc_final: 0.7770 (p) REVERT: D 301 LYS cc_start: 0.8114 (mmtt) cc_final: 0.7513 (tmtt) REVERT: F 169 GLU cc_start: 0.6149 (tt0) cc_final: 0.5793 (mt-10) REVERT: F 265 ARG cc_start: 0.6831 (mmp-170) cc_final: 0.5876 (mmp-170) REVERT: F 314 ARG cc_start: 0.3135 (ttt-90) cc_final: 0.2219 (mmp80) REVERT: M 51 GLU cc_start: 0.6421 (pm20) cc_final: 0.6165 (pm20) REVERT: M 74 ARG cc_start: 0.7390 (tmm160) cc_final: 0.7165 (ttp80) outliers start: 1 outliers final: 0 residues processed: 201 average time/residue: 0.1257 time to fit residues: 33.1792 Evaluate side-chains 161 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 161 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 66 optimal weight: 2.9990 chunk 94 optimal weight: 0.2980 chunk 15 optimal weight: 5.9990 chunk 62 optimal weight: 0.6980 chunk 6 optimal weight: 5.9990 chunk 58 optimal weight: 2.9990 chunk 89 optimal weight: 4.9990 chunk 132 optimal weight: 0.9990 chunk 113 optimal weight: 10.0000 chunk 52 optimal weight: 7.9990 chunk 121 optimal weight: 0.8980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 324 HIS ** D 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 324 HIS E 127 ASN E 144 ASN E 310 ASN E 322 GLN ** F 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 329 ASN M 32 ASN ** M 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4447 r_free = 0.4447 target = 0.170778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.158228 restraints weight = 25177.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.157510 restraints weight = 25305.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.158772 restraints weight = 24460.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.158998 restraints weight = 16581.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.159179 restraints weight = 17697.054| |-----------------------------------------------------------------------------| r_work (final): 0.4298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6368 moved from start: 0.8979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10142 Z= 0.149 Angle : 0.839 9.805 13963 Z= 0.427 Chirality : 0.045 0.247 1691 Planarity : 0.005 0.052 1783 Dihedral : 18.062 177.030 1783 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 15.34 Ramachandran Plot: Outliers : 0.08 % Allowed : 14.73 % Favored : 85.20 % Rotamer: Outliers : 0.11 % Allowed : 1.15 % Favored : 98.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -3.96 (0.21), residues: 1331 helix: -1.10 (0.30), residues: 341 sheet: -3.41 (0.35), residues: 170 loop : -3.32 (0.19), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 56 TYR 0.021 0.001 TYR M 20 PHE 0.013 0.002 PHE C 131 TRP 0.018 0.002 TRP M 53 HIS 0.008 0.002 HIS E 208 Details of bonding type rmsd covalent geometry : bond 0.00323 (10142) covalent geometry : angle 0.83875 (13963) hydrogen bonds : bond 0.03166 ( 248) hydrogen bonds : angle 6.62073 ( 684) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 203 time to evaluate : 0.292 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 129 GLN cc_start: 0.7813 (pt0) cc_final: 0.7377 (pt0) REVERT: C 161 ARG cc_start: 0.6918 (mtp85) cc_final: 0.6497 (mmm160) REVERT: C 284 PRO cc_start: 0.6187 (Cg_endo) cc_final: 0.5959 (Cg_exo) REVERT: C 336 PHE cc_start: 0.6814 (m-80) cc_final: 0.6609 (m-80) REVERT: D 25 MET cc_start: 0.6718 (mpp) cc_final: 0.6199 (mmt) REVERT: D 219 ILE cc_start: 0.8605 (mm) cc_final: 0.8311 (mm) REVERT: E 34 ASP cc_start: 0.6934 (t0) cc_final: 0.6726 (t0) REVERT: E 36 SER cc_start: 0.8975 (m) cc_final: 0.8635 (t) REVERT: E 94 ARG cc_start: 0.6584 (ttp-170) cc_final: 0.5912 (mtm-85) REVERT: E 211 LEU cc_start: 0.8461 (pp) cc_final: 0.8206 (mt) REVERT: F 169 GLU cc_start: 0.6005 (tt0) cc_final: 0.5643 (mt-10) REVERT: F 314 ARG cc_start: 0.2968 (ttt-90) cc_final: 0.2227 (mmp80) outliers start: 1 outliers final: 0 residues processed: 204 average time/residue: 0.1235 time to fit residues: 33.4640 Evaluate side-chains 169 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 169 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 67 optimal weight: 2.9990 chunk 34 optimal weight: 4.9990 chunk 128 optimal weight: 10.0000 chunk 6 optimal weight: 7.9990 chunk 81 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 chunk 47 optimal weight: 0.7980 chunk 54 optimal weight: 0.0000 chunk 25 optimal weight: 6.9990 chunk 15 optimal weight: 6.9990 chunk 95 optimal weight: 7.9990 overall best weight: 1.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 324 HIS D 140 HIS ** D 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 127 ASN E 144 ASN E 322 GLN ** F 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 329 ASN ** M 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4445 r_free = 0.4445 target = 0.170585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.156605 restraints weight = 24943.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.156805 restraints weight = 27184.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.157938 restraints weight = 24318.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4287 r_free = 0.4287 target = 0.158676 restraints weight = 17366.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.159030 restraints weight = 16616.121| |-----------------------------------------------------------------------------| r_work (final): 0.4294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6384 moved from start: 0.9155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10142 Z= 0.158 Angle : 0.861 10.484 13963 Z= 0.438 Chirality : 0.045 0.245 1691 Planarity : 0.006 0.100 1783 Dihedral : 18.029 176.340 1783 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 16.34 Ramachandran Plot: Outliers : 0.08 % Allowed : 16.90 % Favored : 83.02 % Rotamer: Outliers : 0.11 % Allowed : 0.23 % Favored : 99.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.83 (0.21), residues: 1331 helix: -0.93 (0.30), residues: 334 sheet: -3.28 (0.37), residues: 161 loop : -3.27 (0.19), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG M 74 TYR 0.021 0.001 TYR M 20 PHE 0.026 0.002 PHE F 131 TRP 0.018 0.002 TRP M 53 HIS 0.011 0.002 HIS C 324 Details of bonding type rmsd covalent geometry : bond 0.00346 (10142) covalent geometry : angle 0.86124 (13963) hydrogen bonds : bond 0.03157 ( 248) hydrogen bonds : angle 6.57880 ( 684) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 199 time to evaluate : 0.350 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 128 ASP cc_start: 0.7600 (m-30) cc_final: 0.6958 (m-30) REVERT: C 129 GLN cc_start: 0.7953 (pt0) cc_final: 0.7385 (pt0) REVERT: C 284 PRO cc_start: 0.6187 (Cg_endo) cc_final: 0.5945 (Cg_exo) REVERT: D 25 MET cc_start: 0.6642 (mpp) cc_final: 0.6071 (mmt) REVERT: E 36 SER cc_start: 0.9050 (m) cc_final: 0.8676 (t) REVERT: E 211 LEU cc_start: 0.8570 (pp) cc_final: 0.8245 (mt) REVERT: E 300 GLN cc_start: 0.7993 (mp10) cc_final: 0.7708 (mp10) REVERT: F 94 ARG cc_start: 0.7564 (mtt180) cc_final: 0.7060 (mtt180) REVERT: F 169 GLU cc_start: 0.5983 (tt0) cc_final: 0.5650 (mt-10) REVERT: F 314 ARG cc_start: 0.2978 (ttt-90) cc_final: 0.2395 (mmp80) outliers start: 1 outliers final: 0 residues processed: 200 average time/residue: 0.1164 time to fit residues: 31.1860 Evaluate side-chains 162 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 162 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 84 optimal weight: 5.9990 chunk 6 optimal weight: 9.9990 chunk 62 optimal weight: 2.9990 chunk 14 optimal weight: 10.0000 chunk 92 optimal weight: 30.0000 chunk 34 optimal weight: 1.9990 chunk 125 optimal weight: 4.9990 chunk 98 optimal weight: 7.9990 chunk 32 optimal weight: 10.0000 chunk 93 optimal weight: 7.9990 chunk 64 optimal weight: 2.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 141 ASN ** C 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 241 GLN C 324 HIS D 144 ASN ** D 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 262 ASN ** D 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 127 ASN E 144 ASN E 322 GLN F 329 ASN ** M 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.161590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.148167 restraints weight = 26406.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.147355 restraints weight = 30554.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.148553 restraints weight = 28830.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.148676 restraints weight = 20593.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.149602 restraints weight = 18921.964| |-----------------------------------------------------------------------------| r_work (final): 0.4167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6639 moved from start: 0.9719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.087 10142 Z= 0.300 Angle : 1.062 12.243 13963 Z= 0.546 Chirality : 0.053 0.286 1691 Planarity : 0.007 0.075 1783 Dihedral : 18.600 166.910 1783 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 25.22 Ramachandran Plot: Outliers : 0.30 % Allowed : 19.91 % Favored : 79.79 % Rotamer: Outliers : 0.23 % Allowed : 0.69 % Favored : 99.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.39 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.37 (0.21), residues: 1331 helix: -1.51 (0.28), residues: 339 sheet: -3.60 (0.33), residues: 192 loop : -3.53 (0.19), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.002 ARG M 74 TYR 0.029 0.003 TYR M 20 PHE 0.026 0.003 PHE E 147 TRP 0.024 0.003 TRP M 53 HIS 0.011 0.003 HIS E 208 Details of bonding type rmsd covalent geometry : bond 0.00641 (10142) covalent geometry : angle 1.06200 (13963) hydrogen bonds : bond 0.04659 ( 248) hydrogen bonds : angle 7.64833 ( 684) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1538.47 seconds wall clock time: 27 minutes 24.85 seconds (1644.85 seconds total)