Starting phenix.real_space_refine on Fri Sep 11 15:51:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/5xlp_6731/09_2026/5xlp_6731.cif Found real_map, /net/cci-nas-00/data/ceres_data/5xlp_6731/09_2026/5xlp_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/5xlp_6731/09_2026/5xlp_6731.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/5xlp_6731/09_2026/5xlp_6731.cif" model { file = "/net/cci-nas-00/data/ceres_data/5xlp_6731/09_2026/5xlp_6731.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5xlp_6731/09_2026/5xlp_6731.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/5xlp_6731/09_2026/5xlp_6731.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5xlp_6731/09_2026/5xlp_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-2.2.1-6174/lib/python3.11/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: {'RNAv2': 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: 2.67, per 1000 atoms: 0.27 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: 0.88 Conformation dependent library (CDL) restraints added in 403.2 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: 1.12 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: 1.39 Time building geometry restraints manager: 1.18 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: 13400 3.05 - 6.10: 453 6.10 - 9.16: 84 9.16 - 12.21: 24 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: 5853 35.85 - 71.71: 123 71.71 - 107.56: 19 107.56 - 143.41: 1 143.41 - 179.27: 3 Dihedral angle restraints: 5999 sinusoidal: 2158 harmonic: 3841 Sorted by residual: dihedral pdb=" C4' U K 19 " pdb=" C3' U K 19 " pdb=" C2' U K 19 " pdb=" C1' U K 19 " ideal model delta sinusoidal sigma weight residual 36.34 -46.17 82.51 1 3.10e+00 1.04e-01 8.69e+02 dihedral pdb=" C4' A K 4 " pdb=" C3' A K 4 " pdb=" C2' A K 4 " pdb=" C1' A K 4 " ideal model delta sinusoidal sigma weight residual 36.34 -43.03 79.38 1 3.10e+00 1.04e-01 8.15e+02 dihedral pdb=" C4' G K 6 " pdb=" C3' G K 6 " pdb=" C2' G K 6 " pdb=" C1' G K 6 " ideal model delta sinusoidal sigma weight residual 36.35 -42.06 78.40 1 3.10e+00 1.04e-01 7.98e+02 ... (remaining 5996 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.097: 1464 0.097 - 0.193: 162 0.193 - 0.289: 42 0.289 - 0.386: 21 0.386 - 0.482: 2 Chirality restraints: 1691 Sorted by residual: chirality pdb=" P U K 13 " pdb=" OP1 U K 13 " pdb=" OP2 U K 13 " pdb=" O5' U K 13 " both_signs ideal model delta sigma weight residual True 2.17 -2.66 -0.48 2.00e-01 2.50e+01 5.82e+00 chirality pdb=" P G K 15 " pdb=" OP1 G K 15 " pdb=" OP2 G K 15 " pdb=" O5' G K 15 " both_signs ideal model delta sigma weight residual True 2.17 -2.63 -0.46 2.00e-01 2.50e+01 5.30e+00 chirality pdb=" P C K 20 " pdb=" OP1 C K 20 " pdb=" OP2 C K 20 " pdb=" O5' C K 20 " both_signs ideal model delta sigma weight residual True 2.17 -2.56 -0.39 2.00e-01 2.50e+01 3.71e+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: 0.500 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: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 11.600 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.030 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:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5809 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= 0.418 Angle : 1.402 15.262 13963 Z= 0.753 Chirality : 0.079 0.482 1691 Planarity : 0.009 0.076 1783 Dihedral : 16.114 179.265 3519 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/Z covalent geometry : bond 0.00878 / 0.42 (10142) covalent geometry : angle 1.40238 / 0.75 (13963) hydrogen bonds : bond 0.16158 / 11.19 ( 248) hydrogen bonds : angle 13.70777 / 9.40 ( 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 : 0.397 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: 0.7612 (mt) cc_final: 0.7285 (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: 0.8928 (p) cc_final: 0.8651 (m) REVERT: F 314 ARG cc_start: 0.2851 (ttt-90) cc_final: 0.1940 (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: 0.1253 time to fit residues: 53.1518 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 : 0.397 ------------------------------------------------------------------------------- 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: 0.8980 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: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 151 ASN D 83 ASN ** E 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 151 ASN E 223 GLN ** E 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 140 HIS 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 = 0.4598 r_free = 0.4598 target = 0.185679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4434 r_free = 0.4434 target = 0.172135 restraints weight = 24587.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4432 r_free = 0.4432 target = 0.172522 restraints weight = 23563.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4448 r_free = 0.4448 target = 0.173729 restraints weight = 20449.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4460 r_free = 0.4460 target = 0.174795 restraints weight = 14494.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4466 r_free = 0.4466 target = 0.175251 restraints weight = 13202.859| |-----------------------------------------------------------------------------| r_work (final): 0.4468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5855 moved from start: 0.3958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 10142 Z= 0.197 Angle : 1.098 13.187 13963 Z= 0.499 Chirality : 0.080 1.221 1691 Planarity : 0.006 0.069 1783 Dihedral : 17.614 174.116 1691 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 16.76 Ramachandran Plot: Outliers : 0.23 % Allowed : 12.17 % Favored : 87.60 % Rotamer: Outliers : 0.11 % Allowed : 4.81 % Favored : 95.07 % 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: -4.69 (0.19), residues: 1331 helix: -2.09 (0.28), residues: 277 sheet: -3.70 (0.29), residues: 189 loop : -3.54 (0.17), residues: 865 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG F 184 TYR 0.021 0.001 TYR M 20 PHE 0.015 0.002 PHE D 147 TRP 0.028 0.003 TRP C 174 HIS 0.005 0.001 HIS E 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00402 / 0.20 (10142) covalent geometry : angle 1.09760 / 0.50 (13963) hydrogen bonds : bond 0.03874 / 2.70 ( 248) hydrogen bonds : angle 8.07352 / 5.47 ( 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: 1 poor density : 241 time to evaluate : 0.396 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: D 270 TRP cc_start: 0.6810 (t-100) cc_final: 0.6393 (t-100) REVERT: E 165 ILE cc_start: 0.6534 (mt) cc_final: 0.5801 (mm) REVERT: F 59 THR cc_start: 0.8459 (p) cc_final: 0.8245 (p) REVERT: F 314 ARG cc_start: 0.2209 (ttt-90) cc_final: 0.1399 (mmt-90) outliers start: 1 outliers final: 0 residues processed: 242 average time/residue: 0.1250 time to fit residues: 40.1656 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 : 0.351 ------------------------------------------------------------------------------- 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: 3.9990 chunk 122 optimal weight: 0.5980 chunk 10 optimal weight: 0.0040 chunk 121 optimal weight: 0.8980 chunk 123 optimal weight: 4.9990 chunk 86 optimal weight: 6.9990 chunk 108 optimal weight: 7.9990 chunk 70 optimal weight: 10.0000 chunk 9 optimal weight: 6.9990 chunk 18 optimal weight: 10.0000 chunk 22 optimal weight: 0.9980 overall best weight: 1.2994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 140 HIS D 127 ASN D 322 GLN E 144 ASN E 229 GLN E 241 GLN ** F 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 229 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 = 0.4572 r_free = 0.4572 target = 0.182055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4384 r_free = 0.4384 target = 0.167103 restraints weight = 25074.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4381 r_free = 0.4381 target = 0.167258 restraints weight = 21767.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4400 r_free = 0.4400 target = 0.168747 restraints weight = 18595.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4410 r_free = 0.4410 target = 0.169597 restraints weight = 14245.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4412 r_free = 0.4412 target = 0.169781 restraints weight = 12927.729| |-----------------------------------------------------------------------------| r_work (final): 0.4404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6045 moved from start: 0.5275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10142 Z= 0.169 Angle : 0.920 11.748 13963 Z= 0.443 Chirality : 0.060 0.416 1691 Planarity : 0.006 0.063 1783 Dihedral : 17.063 179.388 1691 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 16.02 Ramachandran Plot: Outliers : 0.08 % Allowed : 12.85 % Favored : 87.08 % Rotamer: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % 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: -4.45 (0.20), residues: 1331 helix: -1.64 (0.29), residues: 301 sheet: -3.60 (0.28), residues: 232 loop : -3.45 (0.18), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG M 74 TYR 0.028 0.002 TYR F 305 PHE 0.014 0.002 PHE D 147 TRP 0.017 0.002 TRP D 174 HIS 0.006 0.001 HIS C 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.17 (10142) covalent geometry : angle 0.92002 / 0.44 (13963) hydrogen bonds : bond 0.03394 / 2.32 ( 248) hydrogen bonds : angle 7.21258 / 4.92 ( 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 224 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 224 time to evaluate : 0.346 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 129 GLN cc_start: 0.7566 (pm20) cc_final: 0.7324 (mm-40) REVERT: C 331 ILE cc_start: 0.8588 (tp) cc_final: 0.8387 (tt) REVERT: D 46 GLU cc_start: 0.6680 (pt0) cc_final: 0.6479 (pt0) REVERT: D 67 LEU cc_start: 0.7606 (pt) cc_final: 0.7322 (pp) REVERT: D 251 ASP cc_start: 0.5953 (p0) cc_final: 0.5591 (p0) REVERT: E 59 THR cc_start: 0.8955 (t) cc_final: 0.8330 (p) REVERT: E 210 LEU cc_start: 0.6924 (mt) cc_final: 0.6628 (mt) REVERT: F 59 THR cc_start: 0.8414 (p) cc_final: 0.8067 (m) outliers start: 0 outliers final: 0 residues processed: 224 average time/residue: 0.1159 time to fit residues: 34.6935 Evaluate side-chains 166 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 166 time to evaluate : 0.301 ------------------------------------------------------------------------------- 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: 10.0000 chunk 23 optimal weight: 1.9990 chunk 101 optimal weight: 3.9990 chunk 132 optimal weight: 5.9990 chunk 11 optimal weight: 10.0000 chunk 92 optimal weight: 30.0000 chunk 20 optimal weight: 20.0000 chunk 40 optimal weight: 5.9990 chunk 21 optimal weight: 7.9990 chunk 73 optimal weight: 1.9990 chunk 112 optimal weight: 0.8980 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 208 HIS C 256 HIS C 324 HIS D 208 HIS E 223 GLN ** E 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 208 HIS ** 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 = 0.4438 r_free = 0.4438 target = 0.169642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.154757 restraints weight = 25733.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.155813 restraints weight = 22481.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.156542 restraints weight = 21596.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.156741 restraints weight = 14987.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.157033 restraints weight = 14862.367| |-----------------------------------------------------------------------------| r_work (final): 0.4272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6355 moved from start: 0.6681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 10142 Z= 0.259 Angle : 1.066 12.735 13963 Z= 0.518 Chirality : 0.067 0.577 1691 Planarity : 0.007 0.072 1783 Dihedral : 17.115 177.314 1691 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 20.84 Ramachandran Plot: Outliers : 0.23 % Allowed : 16.53 % Favored : 83.25 % Rotamer: Outliers : 0.11 % Allowed : 4.70 % Favored : 95.19 % 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: -4.53 (0.20), residues: 1331 helix: -1.88 (0.27), residues: 332 sheet: -3.60 (0.31), residues: 185 loop : -3.54 (0.18), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 161 TYR 0.029 0.002 TYR D 125 PHE 0.029 0.003 PHE F 95 TRP 0.015 0.002 TRP C 174 HIS 0.007 0.002 HIS E 208 Details of bonding type rmsd/Z covalent geometry : bond 0.00558 / 0.26 (10142) covalent geometry : angle 1.06648 / 0.52 (13963) hydrogen bonds : bond 0.04213 / 2.87 ( 248) hydrogen bonds : angle 7.55675 / 5.19 ( 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 203 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 202 time to evaluate : 0.379 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 131 PHE cc_start: 0.7850 (m-80) cc_final: 0.7478 (m-80) REVERT: D 67 LEU cc_start: 0.7826 (pt) cc_final: 0.7427 (mt) REVERT: D 235 LYS cc_start: 0.6698 (mmmm) cc_final: 0.6439 (mmmm) REVERT: D 268 ASP cc_start: 0.6324 (p0) cc_final: 0.6124 (p0) REVERT: E 59 THR cc_start: 0.8871 (t) cc_final: 0.8538 (p) REVERT: E 111 ASP cc_start: 0.3883 (m-30) cc_final: 0.3562 (p0) REVERT: E 300 GLN cc_start: 0.8457 (mp10) cc_final: 0.8166 (mp10) REVERT: F 25 MET cc_start: 0.5038 (mmm) cc_final: 0.4827 (tpp) REVERT: M 15 MET cc_start: 0.5832 (tmm) cc_final: 0.5542 (tmm) REVERT: M 62 LEU cc_start: 0.7740 (mp) cc_final: 0.7445 (mt) outliers start: 1 outliers final: 0 residues processed: 203 average time/residue: 0.1200 time to fit residues: 32.7609 Evaluate side-chains 153 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 153 time to evaluate : 0.357 ------------------------------------------------------------------------------- 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: 1.9990 chunk 129 optimal weight: 9.9990 chunk 115 optimal weight: 0.9990 chunk 101 optimal weight: 7.9990 chunk 74 optimal weight: 0.6980 chunk 19 optimal weight: 20.0000 chunk 48 optimal weight: 0.9980 chunk 45 optimal weight: 0.8980 chunk 118 optimal weight: 8.9990 chunk 36 optimal weight: 7.9990 chunk 32 optimal weight: 7.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 208 HIS ** C 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 140 HIS ** E 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 110 ASN ** F 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 329 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4506 r_free = 0.4506 target = 0.175179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4328 r_free = 0.4328 target = 0.161023 restraints weight = 24968.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.162001 restraints weight = 20730.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4351 r_free = 0.4351 target = 0.163128 restraints weight = 17612.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4353 r_free = 0.4353 target = 0.163364 restraints weight = 12847.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4357 r_free = 0.4357 target = 0.163603 restraints weight = 12627.462| |-----------------------------------------------------------------------------| r_work (final): 0.4361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6183 moved from start: 0.7149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10142 Z= 0.159 Angle : 0.897 9.499 13963 Z= 0.435 Chirality : 0.059 0.422 1691 Planarity : 0.005 0.055 1783 Dihedral : 16.856 176.447 1691 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 15.81 Ramachandran Plot: Outliers : 0.08 % Allowed : 13.37 % Favored : 86.55 % Rotamer: Outliers : 0.11 % Allowed : 3.32 % Favored : 96.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.21 (0.20), residues: 1331 helix: -1.44 (0.30), residues: 305 sheet: -3.51 (0.33), residues: 168 loop : -3.36 (0.18), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG C 184 TYR 0.021 0.001 TYR M 20 PHE 0.023 0.002 PHE C 95 TRP 0.021 0.002 TRP M 53 HIS 0.014 0.002 HIS E 140 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.16 (10142) covalent geometry : angle 0.89728 / 0.44 (13963) hydrogen bonds : bond 0.03198 / 2.17 ( 248) hydrogen bonds : angle 6.80713 / 4.67 ( 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: 1 poor density : 210 time to evaluate : 0.294 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: C 25 MET cc_start: 0.6603 (mtt) cc_final: 0.6313 (mtm) REVERT: C 141 ASN cc_start: 0.6010 (m-40) cc_final: 0.5729 (m110) REVERT: C 301 LYS cc_start: 0.7706 (mmtt) cc_final: 0.7230 (mttm) REVERT: D 67 LEU cc_start: 0.7657 (pt) cc_final: 0.7247 (mt) REVERT: D 234 ASP cc_start: 0.6846 (m-30) cc_final: 0.6621 (m-30) REVERT: E 34 ASP cc_start: 0.7130 (t0) cc_final: 0.6807 (t0) REVERT: E 36 SER cc_start: 0.8640 (m) cc_final: 0.8238 (t) REVERT: E 53 ILE cc_start: 0.6294 (tp) cc_final: 0.6046 (tp) REVERT: E 338 GLU cc_start: 0.6951 (mp0) cc_final: 0.6572 (tp30) REVERT: M 62 LEU cc_start: 0.7393 (mp) cc_final: 0.7166 (mt) outliers start: 1 outliers final: 0 residues processed: 211 average time/residue: 0.1253 time to fit residues: 35.1702 Evaluate side-chains 156 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 156 time to evaluate : 0.347 ------------------------------------------------------------------------------- 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: 7.9990 chunk 75 optimal weight: 4.9990 chunk 93 optimal weight: 0.9980 chunk 107 optimal weight: 7.9990 chunk 20 optimal weight: 8.9990 chunk 10 optimal weight: 4.9990 chunk 21 optimal weight: 0.8980 chunk 79 optimal weight: 9.9990 chunk 76 optimal weight: 4.9990 chunk 90 optimal weight: 0.7980 chunk 28 optimal weight: 10.0000 overall best weight: 2.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 324 HIS D 140 HIS ** D 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 110 ASN ** F 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 329 ASN M 32 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4431 r_free = 0.4431 target = 0.169105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.153228 restraints weight = 25167.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.153275 restraints weight = 26640.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.155118 restraints weight = 23625.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.155228 restraints weight = 16169.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.155613 restraints weight = 16487.675| |-----------------------------------------------------------------------------| r_work (final): 0.4253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6424 moved from start: 0.7827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 10142 Z= 0.227 Angle : 1.002 10.722 13963 Z= 0.486 Chirality : 0.062 0.540 1691 Planarity : 0.006 0.060 1783 Dihedral : 16.990 174.280 1691 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 19.94 Ramachandran Plot: Outliers : 0.30 % Allowed : 17.05 % Favored : 82.64 % Rotamer: Outliers : 0.11 % Allowed : 4.47 % Favored : 95.42 % 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: -4.33 (0.20), residues: 1331 helix: -1.62 (0.28), residues: 321 sheet: -3.48 (0.35), residues: 167 loop : -3.46 (0.18), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 94 TYR 0.024 0.002 TYR M 20 PHE 0.018 0.002 PHE C 95 TRP 0.012 0.002 TRP M 53 HIS 0.008 0.002 HIS E 208 Details of bonding type rmsd/Z covalent geometry : bond 0.00490 / 0.23 (10142) covalent geometry : angle 1.00216 / 0.49 (13963) hydrogen bonds : bond 0.03887 / 2.65 ( 248) hydrogen bonds : angle 7.11565 / 4.90 ( 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 201 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 200 time to evaluate : 0.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 131 PHE cc_start: 0.8296 (m-10) cc_final: 0.7875 (m-80) REVERT: C 141 ASN cc_start: 0.5828 (m-40) cc_final: 0.5480 (m-40) REVERT: C 284 PRO cc_start: 0.6361 (Cg_endo) cc_final: 0.6101 (Cg_exo) REVERT: C 336 PHE cc_start: 0.7289 (m-80) cc_final: 0.7069 (m-80) REVERT: D 67 LEU cc_start: 0.7749 (pt) cc_final: 0.7418 (mt) REVERT: D 336 PHE cc_start: 0.6723 (m-10) cc_final: 0.6355 (m-80) REVERT: E 211 LEU cc_start: 0.8770 (pp) cc_final: 0.8365 (mt) REVERT: E 279 PRO cc_start: 0.6076 (Cg_endo) cc_final: 0.5709 (Cg_exo) REVERT: F 94 ARG cc_start: 0.7745 (mtt180) cc_final: 0.7144 (mtt180) REVERT: F 150 ARG cc_start: 0.5494 (mmt-90) cc_final: 0.4892 (mmt180) REVERT: F 203 LEU cc_start: 0.7483 (tp) cc_final: 0.7057 (tp) outliers start: 1 outliers final: 0 residues processed: 201 average time/residue: 0.1238 time to fit residues: 32.8795 Evaluate side-chains 152 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 152 time to evaluate : 0.254 ------------------------------------------------------------------------------- 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: 0.7980 chunk 110 optimal weight: 7.9990 chunk 5 optimal weight: 10.0000 chunk 124 optimal weight: 6.9990 chunk 24 optimal weight: 8.9990 chunk 73 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 89 optimal weight: 7.9990 chunk 3 optimal weight: 0.0170 chunk 20 optimal weight: 0.0670 overall best weight: 1.1760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 324 HIS D 262 ASN ** E 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 322 GLN ** F 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 329 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4468 r_free = 0.4468 target = 0.173256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.159955 restraints weight = 25248.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.160078 restraints weight = 24717.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.161327 restraints weight = 22816.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.161485 restraints weight = 16593.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.162456 restraints weight = 15994.396| |-----------------------------------------------------------------------------| r_work (final): 0.4328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6231 moved from start: 0.8125 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= 0.156 Angle : 0.907 12.207 13963 Z= 0.436 Chirality : 0.058 0.432 1691 Planarity : 0.005 0.067 1783 Dihedral : 16.839 177.654 1691 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 16.39 Ramachandran Plot: Outliers : 0.08 % Allowed : 14.27 % Favored : 85.65 % Rotamer: Outliers : 0.11 % Allowed : 1.95 % Favored : 97.94 % 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: -3.95 (0.21), residues: 1331 helix: -1.04 (0.30), residues: 314 sheet: -3.35 (0.35), residues: 165 loop : -3.30 (0.18), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 150 TYR 0.022 0.001 TYR M 20 PHE 0.021 0.002 PHE F 131 TRP 0.013 0.002 TRP D 174 HIS 0.011 0.002 HIS E 208 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.16 (10142) covalent geometry : angle 0.90711 / 0.44 (13963) hydrogen bonds : bond 0.03172 / 2.11 ( 248) hydrogen bonds : angle 6.57421 / 4.52 ( 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 215 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 214 time to evaluate : 0.361 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: C 125 TYR cc_start: 0.5640 (t80) cc_final: 0.5394 (t80) REVERT: C 129 GLN cc_start: 0.7948 (pt0) cc_final: 0.7140 (pt0) REVERT: C 284 PRO cc_start: 0.6296 (Cg_endo) cc_final: 0.6031 (Cg_exo) REVERT: D 67 LEU cc_start: 0.7755 (pt) cc_final: 0.7391 (mt) REVERT: D 165 ILE cc_start: 0.6650 (mm) cc_final: 0.6419 (mm) REVERT: D 219 ILE cc_start: 0.8212 (mm) cc_final: 0.7944 (mm) REVERT: E 34 ASP cc_start: 0.6983 (t0) cc_final: 0.6739 (t0) REVERT: E 36 SER cc_start: 0.8792 (m) cc_final: 0.8457 (t) REVERT: F 25 MET cc_start: 0.4972 (mmm) cc_final: 0.4717 (tpp) REVERT: F 301 LYS cc_start: 0.5974 (pttm) cc_final: 0.5729 (pttm) REVERT: M 24 SER cc_start: 0.8033 (p) cc_final: 0.7634 (p) outliers start: 1 outliers final: 0 residues processed: 215 average time/residue: 0.1140 time to fit residues: 33.0650 Evaluate side-chains 168 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 168 time to evaluate : 0.324 ------------------------------------------------------------------------------- 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: 0.5980 chunk 25 optimal weight: 9.9990 chunk 84 optimal weight: 0.5980 chunk 115 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 79 optimal weight: 4.9990 chunk 83 optimal weight: 5.9990 chunk 122 optimal weight: 5.9990 chunk 33 optimal weight: 8.9990 chunk 2 optimal weight: 8.9990 chunk 91 optimal weight: 6.9990 overall best weight: 2.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 324 HIS D 140 HIS ** E 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 223 GLN ** E 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 322 GLN ** F 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 329 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4407 r_free = 0.4407 target = 0.167882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.154047 restraints weight = 26174.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.154086 restraints weight = 28808.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.155214 restraints weight = 25290.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.155675 restraints weight = 17367.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.155889 restraints weight = 16127.364| |-----------------------------------------------------------------------------| r_work (final): 0.4245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6416 moved from start: 0.8574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 10142 Z= 0.221 Angle : 1.014 12.342 13963 Z= 0.493 Chirality : 0.061 0.522 1691 Planarity : 0.006 0.072 1783 Dihedral : 17.026 175.546 1691 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 20.62 Ramachandran Plot: Outliers : 0.23 % Allowed : 18.41 % Favored : 81.37 % Rotamer: Outliers : 0.11 % Allowed : 1.95 % Favored : 97.94 % 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: -4.08 (0.20), residues: 1331 helix: -1.18 (0.29), residues: 320 sheet: -3.29 (0.36), residues: 168 loop : -3.42 (0.18), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 150 TYR 0.019 0.002 TYR M 20 PHE 0.035 0.003 PHE C 131 TRP 0.043 0.003 TRP M 53 HIS 0.012 0.002 HIS E 208 Details of bonding type rmsd/Z covalent geometry : bond 0.00490 / 0.22 (10142) covalent geometry : angle 1.01434 / 0.49 (13963) hydrogen bonds : bond 0.03779 / 2.55 ( 248) hydrogen bonds : angle 6.89637 / 4.75 ( 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 197 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 196 time to evaluate : 0.363 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: 0.7891 (pt0) cc_final: 0.7545 (pt0) REVERT: C 265 ARG cc_start: 0.4819 (mtt180) cc_final: 0.4614 (mmt180) REVERT: C 284 PRO cc_start: 0.6234 (Cg_endo) cc_final: 0.5953 (Cg_exo) REVERT: D 67 LEU cc_start: 0.7779 (pt) cc_final: 0.7406 (mt) REVERT: D 210 LEU cc_start: 0.7149 (mt) cc_final: 0.6922 (tp) REVERT: D 219 ILE cc_start: 0.8536 (mm) cc_final: 0.8330 (mm) REVERT: D 241 GLN cc_start: 0.6970 (mt0) cc_final: 0.6714 (mt0) REVERT: E 211 LEU cc_start: 0.8688 (pp) cc_final: 0.8337 (mt) REVERT: E 270 TRP cc_start: 0.6053 (t-100) cc_final: 0.5399 (t-100) REVERT: E 338 GLU cc_start: 0.7713 (pm20) cc_final: 0.7411 (tt0) REVERT: F 76 LEU cc_start: 0.8386 (mt) cc_final: 0.7734 (mt) REVERT: F 94 ARG cc_start: 0.7982 (mtt180) cc_final: 0.7619 (mtt180) REVERT: F 279 PRO cc_start: 0.4774 (Cg_endo) cc_final: 0.4131 (Cg_exo) REVERT: M 69 MET cc_start: 0.7042 (tpt) cc_final: 0.6837 (tpp) REVERT: M 74 ARG cc_start: 0.7529 (tmm160) cc_final: 0.7228 (ttp80) outliers start: 1 outliers final: 1 residues processed: 197 average time/residue: 0.1245 time to fit residues: 32.4917 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 : 0.350 ------------------------------------------------------------------------------- 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: 0.5980 chunk 94 optimal weight: 8.9990 chunk 15 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 6 optimal weight: 0.2980 chunk 58 optimal weight: 0.7980 chunk 89 optimal weight: 6.9990 chunk 132 optimal weight: 1.9990 chunk 113 optimal weight: 0.9990 chunk 52 optimal weight: 5.9990 chunk 121 optimal weight: 0.9980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 127 ASN ** C 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 144 ASN C 324 HIS D 140 HIS E 223 GLN ** E 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 310 ASN E 322 GLN ** F 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4483 r_free = 0.4483 target = 0.174500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.161962 restraints weight = 25278.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.161906 restraints weight = 25511.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.163035 restraints weight = 22409.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.163381 restraints weight = 15518.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.163442 restraints weight = 14541.869| |-----------------------------------------------------------------------------| r_work (final): 0.4344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6188 moved from start: 0.8784 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= 0.146 Angle : 0.891 11.709 13963 Z= 0.430 Chirality : 0.057 0.409 1691 Planarity : 0.005 0.056 1783 Dihedral : 16.819 178.302 1691 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 15.07 Ramachandran Plot: Outliers : 0.08 % Allowed : 13.60 % Favored : 86.33 % Rotamer: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % 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: -3.70 (0.21), residues: 1331 helix: -0.67 (0.32), residues: 313 sheet: -3.16 (0.37), residues: 167 loop : -3.21 (0.18), residues: 851 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 56 TYR 0.017 0.001 TYR M 20 PHE 0.023 0.002 PHE F 131 TRP 0.033 0.003 TRP M 53 HIS 0.015 0.001 HIS E 208 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.15 (10142) covalent geometry : angle 0.89144 / 0.43 (13963) hydrogen bonds : bond 0.03000 / 2.01 ( 248) hydrogen bonds : angle 6.34432 / 4.39 ( 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 218 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 218 time to evaluate : 0.233 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: 0.7643 (pt0) cc_final: 0.6911 (pt0) REVERT: C 161 ARG cc_start: 0.6849 (mmm160) cc_final: 0.6554 (mmm160) REVERT: C 284 PRO cc_start: 0.6189 (Cg_endo) cc_final: 0.5937 (Cg_exo) REVERT: D 67 LEU cc_start: 0.7713 (pt) cc_final: 0.7456 (mt) REVERT: D 90 THR cc_start: 0.8155 (p) cc_final: 0.7936 (p) REVERT: D 322 GLN cc_start: 0.5445 (mm110) cc_final: 0.5055 (pm20) REVERT: E 36 SER cc_start: 0.8771 (m) cc_final: 0.8340 (t) REVERT: E 211 LEU cc_start: 0.8571 (pp) cc_final: 0.8248 (mt) REVERT: E 269 THR cc_start: 0.6869 (m) cc_final: 0.6615 (m) REVERT: E 338 GLU cc_start: 0.7177 (pm20) cc_final: 0.6701 (tt0) REVERT: F 25 MET cc_start: 0.5296 (mmm) cc_final: 0.4929 (tpp) REVERT: F 76 LEU cc_start: 0.7978 (mt) cc_final: 0.7592 (mt) REVERT: F 94 ARG cc_start: 0.7666 (mtt180) cc_final: 0.6948 (mtt180) REVERT: F 279 PRO cc_start: 0.4729 (Cg_endo) cc_final: 0.4129 (Cg_exo) outliers start: 0 outliers final: 0 residues processed: 218 average time/residue: 0.1219 time to fit residues: 35.2714 Evaluate side-chains 172 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 172 time to evaluate : 0.362 ------------------------------------------------------------------------------- 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: 3.9990 chunk 34 optimal weight: 0.9980 chunk 128 optimal weight: 0.9990 chunk 6 optimal weight: 0.7980 chunk 81 optimal weight: 0.6980 chunk 29 optimal weight: 7.9990 chunk 47 optimal weight: 0.9990 chunk 54 optimal weight: 0.0980 chunk 25 optimal weight: 7.9990 chunk 15 optimal weight: 5.9990 chunk 95 optimal weight: 2.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 229 GLN C 324 HIS E 223 GLN ** E 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 256 HIS E 322 GLN F 110 ASN ** F 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4490 r_free = 0.4490 target = 0.174818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.160936 restraints weight = 24802.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.161331 restraints weight = 25175.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.162469 restraints weight = 21653.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.163117 restraints weight = 15750.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.163288 restraints weight = 14675.328| |-----------------------------------------------------------------------------| r_work (final): 0.4344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6190 moved from start: 0.9020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10142 Z= 0.142 Angle : 0.881 11.787 13963 Z= 0.426 Chirality : 0.056 0.385 1691 Planarity : 0.005 0.056 1783 Dihedral : 16.717 177.455 1691 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 15.07 Ramachandran Plot: Outliers : 0.08 % Allowed : 15.10 % Favored : 84.82 % 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: -3.54 (0.22), residues: 1331 helix: -0.45 (0.32), residues: 312 sheet: -3.11 (0.38), residues: 161 loop : -3.13 (0.18), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG M 74 TYR 0.017 0.001 TYR M 20 PHE 0.011 0.001 PHE F 186 TRP 0.036 0.002 TRP C 270 HIS 0.013 0.001 HIS E 208 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 (10142) covalent geometry : angle 0.88088 / 0.43 (13963) hydrogen bonds : bond 0.02965 / 1.93 ( 248) hydrogen bonds : angle 6.13301 / 4.24 ( 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 203 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 202 time to evaluate : 0.330 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 284 PRO cc_start: 0.6114 (Cg_endo) cc_final: 0.5871 (Cg_exo) REVERT: E 36 SER cc_start: 0.8851 (m) cc_final: 0.8410 (t) REVERT: E 211 LEU cc_start: 0.8660 (pp) cc_final: 0.8307 (mt) REVERT: E 269 THR cc_start: 0.6892 (m) cc_final: 0.6605 (m) REVERT: F 76 LEU cc_start: 0.7954 (mt) cc_final: 0.7604 (mt) REVERT: M 1 MET cc_start: 0.6568 (tpp) cc_final: 0.6329 (tpp) REVERT: M 4 ILE cc_start: 0.7686 (pt) cc_final: 0.7371 (pt) REVERT: M 25 LYS cc_start: 0.6402 (ptmm) cc_final: 0.5621 (mmmt) outliers start: 1 outliers final: 0 residues processed: 203 average time/residue: 0.1122 time to fit residues: 30.8291 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 : 0.408 ------------------------------------------------------------------------------- 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: 3.9990 chunk 6 optimal weight: 0.9990 chunk 62 optimal weight: 3.9990 chunk 14 optimal weight: 5.9990 chunk 92 optimal weight: 30.0000 chunk 34 optimal weight: 0.5980 chunk 125 optimal weight: 4.9990 chunk 98 optimal weight: 5.9990 chunk 32 optimal weight: 3.9990 chunk 93 optimal weight: 20.0000 chunk 64 optimal weight: 5.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 324 HIS D 140 HIS D 324 HIS ** E 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 322 GLN ** F 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 329 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4389 r_free = 0.4389 target = 0.167337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.154873 restraints weight = 25956.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.155071 restraints weight = 25866.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.155733 restraints weight = 25472.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.156119 restraints weight = 16789.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.156120 restraints weight = 16803.967| |-----------------------------------------------------------------------------| r_work (final): 0.4240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6387 moved from start: 0.9386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 10142 Z= 0.229 Angle : 1.017 11.378 13963 Z= 0.494 Chirality : 0.062 0.518 1691 Planarity : 0.006 0.069 1783 Dihedral : 17.022 176.559 1691 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 21.05 Ramachandran Plot: Outliers : 0.15 % Allowed : 18.03 % Favored : 81.82 % Rotamer: Outliers : 0.11 % Allowed : 0.46 % Favored : 99.43 % 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: -3.92 (0.21), residues: 1331 helix: -1.05 (0.30), residues: 328 sheet: -3.30 (0.36), residues: 161 loop : -3.31 (0.18), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 56 TYR 0.019 0.002 TYR M 20 PHE 0.046 0.003 PHE C 131 TRP 0.018 0.003 TRP C 270 HIS 0.011 0.002 HIS E 208 Details of bonding type rmsd/Z covalent geometry : bond 0.00501 / 0.23 (10142) covalent geometry : angle 1.01715 / 0.49 (13963) hydrogen bonds : bond 0.03638 / 2.47 ( 248) hydrogen bonds : angle 6.78091 / 4.63 ( 684) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1545.92 seconds wall clock time: 27 minutes 27.95 seconds (1647.95 seconds total)