Starting phenix.real_space_refine on Thu Sep 18 06:28:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cp3_45798/09_2025/9cp3_45798.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cp3_45798/09_2025/9cp3_45798.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.94 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9cp3_45798/09_2025/9cp3_45798.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cp3_45798/09_2025/9cp3_45798.map" model { file = "/net/cci-nas-00/data/ceres_data/9cp3_45798/09_2025/9cp3_45798.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cp3_45798/09_2025/9cp3_45798.cif" } resolution = 2.94 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= 0.000 sd= 0.024 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 474 atoms to isotropic. 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: 6 Type Number sf(0) Gaussians P 45 5.49 5 S 41 5.16 5 C 8718 2.51 5 N 2311 2.21 5 O 2749 1.98 5 H 110 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13974 Number of models: 1 Model: "" Number of chains: 10 Chain: "B" Number of atoms: 2458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2458 Classifications: {'peptide': 317} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 303} Chain breaks: 1 Chain: "C" Number of atoms: 2458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2458 Classifications: {'peptide': 317} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 303} Chain breaks: 1 Chain: "E" Number of atoms: 1424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1424 Classifications: {'peptide': 183} Link IDs: {'PTRANS': 7, 'TRANS': 175} Chain breaks: 3 Chain: "D" Number of atoms: 2421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 2421 Classifications: {'peptide': 312} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 299} Chain breaks: 1 Chain: "A" Number of atoms: 2458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2458 Classifications: {'peptide': 317} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 303} Chain breaks: 1 Chain: "S" Number of atoms: 675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 675 Classifications: {'RNA': 32} Modifications used: {'5*END': 1, 'rna2p_pur': 7, 'rna2p_pyr': 10, 'rna3p_pur': 9, 'rna3p_pyr': 6} Link IDs: {'rna2p': 16, 'rna3p': 15} Chain: "G" Number of atoms: 1752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1752 Classifications: {'peptide': 204} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 193} Chain breaks: 6 Chain: "M" Number of atoms: 288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 288 Classifications: {'DNA': 14} Link IDs: {'rna3p': 13} Chain: "C" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'TRS': 1} Classifications: {'undetermined': 1} Chain: "S" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 32 Unusual residues: {'TRS': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 3.31, per 1000 atoms: 0.24 Number of scatterers: 13974 At special positions: 0 Unit cell: (83.78, 105.08, 166.14, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 41 16.00 P 45 15.00 O 2749 8.00 N 2311 7.00 C 8718 6.00 H 110 1.00 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: 1.25 Conformation dependent library (CDL) restraints added in 620.1 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3038 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 20 sheets defined 32.4% alpha, 17.0% beta 10 base pairs and 13 stacking pairs defined. Time for finding SS restraints: 1.46 Creating SS restraints... Processing helix chain 'B' and resid 49 through 69 removed outlier: 4.306A pdb=" N LEU B 53 " --> pdb=" O SER B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 78 removed outlier: 3.906A pdb=" N GLN B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 94 Processing helix chain 'B' and resid 103 through 115 Processing helix chain 'B' and resid 116 through 121 Processing helix chain 'B' and resid 207 through 225 removed outlier: 3.835A pdb=" N LEU B 211 " --> pdb=" O GLY B 207 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N ALA B 216 " --> pdb=" O GLU B 212 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N LYS B 217 " --> pdb=" O ARG B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 225 through 232 removed outlier: 4.351A pdb=" N LEU B 229 " --> pdb=" O ALA B 225 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 285 Processing helix chain 'B' and resid 310 through 321 removed outlier: 4.033A pdb=" N LEU B 314 " --> pdb=" O THR B 310 " (cutoff:3.500A) Processing helix chain 'C' and resid 50 through 69 Processing helix chain 'C' and resid 73 through 78 removed outlier: 3.899A pdb=" N GLN C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 86 through 94 Processing helix chain 'C' and resid 103 through 113 Processing helix chain 'C' and resid 116 through 121 Processing helix chain 'C' and resid 207 through 225 removed outlier: 3.794A pdb=" N LEU C 211 " --> pdb=" O GLY C 207 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N ALA C 216 " --> pdb=" O GLU C 212 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N LYS C 217 " --> pdb=" O ARG C 213 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 232 removed outlier: 4.331A pdb=" N LEU C 229 " --> pdb=" O ALA C 225 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 285 Processing helix chain 'C' and resid 310 through 321 removed outlier: 4.029A pdb=" N LEU C 314 " --> pdb=" O THR C 310 " (cutoff:3.500A) Processing helix chain 'E' and resid 49 through 67 removed outlier: 4.184A pdb=" N LEU E 53 " --> pdb=" O SER E 49 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LYS E 67 " --> pdb=" O ASP E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 73 through 78 removed outlier: 4.350A pdb=" N GLN E 78 " --> pdb=" O SER E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 94 removed outlier: 3.631A pdb=" N LEU E 90 " --> pdb=" O THR E 86 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 113 Processing helix chain 'E' and resid 116 through 122 Processing helix chain 'E' and resid 207 through 225 removed outlier: 3.583A pdb=" N LEU E 211 " --> pdb=" O GLY E 207 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N ALA E 216 " --> pdb=" O GLU E 212 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N LYS E 217 " --> pdb=" O ARG E 213 " (cutoff:3.500A) Processing helix chain 'E' and resid 226 through 232 Processing helix chain 'D' and resid 49 through 69 removed outlier: 4.403A pdb=" N LEU D 53 " --> pdb=" O SER D 49 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 78 removed outlier: 3.898A pdb=" N GLN D 78 " --> pdb=" O SER D 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 86 through 94 Processing helix chain 'D' and resid 103 through 115 Processing helix chain 'D' and resid 116 through 121 Processing helix chain 'D' and resid 207 through 225 removed outlier: 3.762A pdb=" N LEU D 211 " --> pdb=" O GLY D 207 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N ALA D 216 " --> pdb=" O GLU D 212 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N LYS D 217 " --> pdb=" O ARG D 213 " (cutoff:3.500A) Processing helix chain 'D' and resid 225 through 232 removed outlier: 4.349A pdb=" N LEU D 229 " --> pdb=" O ALA D 225 " (cutoff:3.500A) Processing helix chain 'D' and resid 270 through 285 Processing helix chain 'D' and resid 310 through 321 removed outlier: 4.059A pdb=" N LEU D 314 " --> pdb=" O THR D 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 69 removed outlier: 4.213A pdb=" N LEU A 53 " --> pdb=" O SER A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 94 removed outlier: 3.613A pdb=" N LEU A 90 " --> pdb=" O THR A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 115 Processing helix chain 'A' and resid 116 through 121 Processing helix chain 'A' and resid 192 through 195 Processing helix chain 'A' and resid 208 through 225 removed outlier: 4.805A pdb=" N ALA A 216 " --> pdb=" O GLU A 212 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N LYS A 217 " --> pdb=" O ARG A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 232 removed outlier: 4.017A pdb=" N LEU A 229 " --> pdb=" O ALA A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 285 removed outlier: 3.793A pdb=" N THR A 273 " --> pdb=" O TYR A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 321 removed outlier: 4.067A pdb=" N LEU A 314 " --> pdb=" O THR A 310 " (cutoff:3.500A) Processing helix chain 'G' and resid 32 through 42 removed outlier: 3.588A pdb=" N LEU G 36 " --> pdb=" O PRO G 32 " (cutoff:3.500A) Processing helix chain 'G' and resid 129 through 138 removed outlier: 3.689A pdb=" N LEU G 133 " --> pdb=" O SER G 129 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N TRP G 138 " --> pdb=" O GLU G 134 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 2 through 13 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 2 through 13 current: chain 'B' and resid 174 through 190 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 174 through 190 current: chain 'B' and resid 289 through 295 removed outlier: 4.113A pdb=" N THR B 306 " --> pdb=" O ALA B 291 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 29 through 36 Processing sheet with id=AA3, first strand: chain 'B' and resid 123 through 125 Processing sheet with id=AA4, first strand: chain 'C' and resid 2 through 13 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 2 through 13 current: chain 'C' and resid 174 through 190 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 174 through 190 current: chain 'C' and resid 289 through 295 removed outlier: 3.983A pdb=" N THR C 306 " --> pdb=" O ALA C 291 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 29 through 36 Processing sheet with id=AA6, first strand: chain 'C' and resid 123 through 125 Processing sheet with id=AA7, first strand: chain 'E' and resid 137 through 138 removed outlier: 4.182A pdb=" N GLY E 4 " --> pdb=" O PHE E 188 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 29 through 36 Processing sheet with id=AA9, first strand: chain 'E' and resid 123 through 125 Processing sheet with id=AB1, first strand: chain 'D' and resid 2 through 13 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 2 through 13 current: chain 'D' and resid 174 through 190 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 174 through 190 current: chain 'D' and resid 289 through 295 removed outlier: 4.131A pdb=" N THR D 306 " --> pdb=" O ALA D 291 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 29 through 36 Processing sheet with id=AB3, first strand: chain 'D' and resid 123 through 125 Processing sheet with id=AB4, first strand: chain 'A' and resid 2 through 13 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 2 through 13 current: chain 'A' and resid 174 through 182 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 174 through 182 current: chain 'A' and resid 289 through 295 removed outlier: 8.870A pdb=" N THR A 306 " --> pdb=" O ALA A 289 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N ALA A 291 " --> pdb=" O THR A 306 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 29 through 35 Processing sheet with id=AB6, first strand: chain 'G' and resid 69 through 73 removed outlier: 4.036A pdb=" N GLY G 117 " --> pdb=" O LEU G 10 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LEU G 10 " --> pdb=" O GLY G 117 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ASN G 154 " --> pdb=" O PHE G 7 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 13 through 14 Processing sheet with id=AB8, first strand: chain 'G' and resid 161 through 163 removed outlier: 3.563A pdb=" N VAL G 163 " --> pdb=" O ALA G 229 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ALA G 229 " --> pdb=" O VAL G 163 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N GLU G 228 " --> pdb=" O PHE G 239 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL G 232 " --> pdb=" O GLU G 235 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 167 through 169 Processing sheet with id=AC1, first strand: chain 'G' and resid 173 through 174 Processing sheet with id=AC2, first strand: chain 'G' and resid 212 through 213 removed outlier: 3.793A pdb=" N ALA G 218 " --> pdb=" O THR G 213 " (cutoff:3.500A) 426 hydrogen bonds defined for protein. 1206 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 24 hydrogen bonds 44 hydrogen bond angles 0 basepair planarities 10 basepair parallelities 13 stacking parallelities Total time for adding SS restraints: 2.07 Time building geometry restraints manager: 1.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 110 1.03 - 1.23: 19 1.23 - 1.42: 5834 1.42 - 1.61: 8259 1.61 - 1.81: 81 Bond restraints: 14303 Sorted by residual: bond pdb=" N ILE G 209 " pdb=" CA ILE G 209 " ideal model delta sigma weight residual 1.459 1.500 -0.041 1.19e-02 7.06e+03 1.17e+01 bond pdb=" N GLU G 221 " pdb=" CA GLU G 221 " ideal model delta sigma weight residual 1.453 1.497 -0.044 1.31e-02 5.83e+03 1.13e+01 bond pdb=" N GLU G 221 " pdb=" H GLU G 221 " ideal model delta sigma weight residual 0.860 0.924 -0.064 2.00e-02 2.50e+03 1.03e+01 bond pdb=" N LEU G 210 " pdb=" H LEU G 210 " ideal model delta sigma weight residual 0.860 0.921 -0.061 2.00e-02 2.50e+03 9.39e+00 bond pdb=" N ILE G 209 " pdb=" H ILE G 209 " ideal model delta sigma weight residual 0.860 0.918 -0.058 2.00e-02 2.50e+03 8.33e+00 ... (remaining 14298 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.13: 18847 1.13 - 2.26: 565 2.26 - 3.39: 166 3.39 - 4.53: 18 4.53 - 5.66: 7 Bond angle restraints: 19603 Sorted by residual: angle pdb=" N LEU G 210 " pdb=" CA LEU G 210 " pdb=" C LEU G 210 " ideal model delta sigma weight residual 109.04 103.80 5.24 1.52e+00 4.33e-01 1.19e+01 angle pdb=" CA GLU G 221 " pdb=" C GLU G 221 " pdb=" O GLU G 221 " ideal model delta sigma weight residual 121.81 117.78 4.03 1.18e+00 7.18e-01 1.17e+01 angle pdb=" CA ILE G 209 " pdb=" C ILE G 209 " pdb=" O ILE G 209 " ideal model delta sigma weight residual 120.65 116.67 3.98 1.17e+00 7.31e-01 1.16e+01 angle pdb=" CA LEU G 210 " pdb=" C LEU G 210 " pdb=" O LEU G 210 " ideal model delta sigma weight residual 119.32 115.56 3.76 1.12e+00 7.97e-01 1.13e+01 angle pdb=" CA TYR G 208 " pdb=" C TYR G 208 " pdb=" O TYR G 208 " ideal model delta sigma weight residual 120.28 116.79 3.49 1.23e+00 6.61e-01 8.06e+00 ... (remaining 19598 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.55: 8406 35.55 - 71.10: 186 71.10 - 106.65: 22 106.65 - 142.20: 0 142.20 - 177.76: 4 Dihedral angle restraints: 8618 sinusoidal: 3876 harmonic: 4742 Sorted by residual: dihedral pdb=" O4' U S 2 " pdb=" C1' U S 2 " pdb=" N1 U S 2 " pdb=" C2 U S 2 " ideal model delta sinusoidal sigma weight residual -128.00 49.76 -177.76 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' U S 32 " pdb=" C1' U S 32 " pdb=" N1 U S 32 " pdb=" C2 U S 32 " ideal model delta sinusoidal sigma weight residual 232.00 58.24 173.76 1 1.70e+01 3.46e-03 6.62e+01 dihedral pdb=" O4' C S 27 " pdb=" C1' C S 27 " pdb=" N1 C S 27 " pdb=" C2 C S 27 " ideal model delta sinusoidal sigma weight residual -128.00 -48.59 -79.41 1 1.70e+01 3.46e-03 2.71e+01 ... (remaining 8615 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 1652 0.042 - 0.084: 408 0.084 - 0.126: 154 0.126 - 0.168: 13 0.168 - 0.210: 4 Chirality restraints: 2231 Sorted by residual: chirality pdb=" CA LEU G 210 " pdb=" N LEU G 210 " pdb=" C LEU G 210 " pdb=" CB LEU G 210 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.11e+00 chirality pdb=" C1' U S 15 " pdb=" O4' U S 15 " pdb=" C2' U S 15 " pdb=" N1 U S 15 " both_signs ideal model delta sigma weight residual False 2.45 2.25 0.19 2.00e-01 2.50e+01 9.44e-01 chirality pdb=" CB ILE G 114 " pdb=" CA ILE G 114 " pdb=" CG1 ILE G 114 " pdb=" CG2 ILE G 114 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.18 2.00e-01 2.50e+01 7.79e-01 ... (remaining 2228 not shown) Planarity restraints: 2298 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' U S 15 " -0.018 2.00e-02 2.50e+03 2.49e-02 1.40e+01 pdb=" N1 U S 15 " 0.057 2.00e-02 2.50e+03 pdb=" C2 U S 15 " -0.041 2.00e-02 2.50e+03 pdb=" O2 U S 15 " 0.011 2.00e-02 2.50e+03 pdb=" N3 U S 15 " 0.006 2.00e-02 2.50e+03 pdb=" C4 U S 15 " -0.000 2.00e-02 2.50e+03 pdb=" O4 U S 15 " 0.002 2.00e-02 2.50e+03 pdb=" C5 U S 15 " -0.007 2.00e-02 2.50e+03 pdb=" C6 U S 15 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS G 220 " 0.016 2.00e-02 2.50e+03 3.23e-02 1.05e+01 pdb=" C LYS G 220 " -0.056 2.00e-02 2.50e+03 pdb=" O LYS G 220 " 0.021 2.00e-02 2.50e+03 pdb=" N GLU G 221 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT M 20 " 0.020 2.00e-02 2.50e+03 1.93e-02 9.30e+00 pdb=" N1 DT M 20 " -0.050 2.00e-02 2.50e+03 pdb=" C2 DT M 20 " 0.027 2.00e-02 2.50e+03 pdb=" O2 DT M 20 " -0.004 2.00e-02 2.50e+03 pdb=" N3 DT M 20 " -0.002 2.00e-02 2.50e+03 pdb=" C4 DT M 20 " -0.001 2.00e-02 2.50e+03 pdb=" O4 DT M 20 " -0.001 2.00e-02 2.50e+03 pdb=" C5 DT M 20 " 0.003 2.00e-02 2.50e+03 pdb=" C7 DT M 20 " 0.005 2.00e-02 2.50e+03 pdb=" C6 DT M 20 " 0.003 2.00e-02 2.50e+03 ... (remaining 2295 not shown) Histogram of nonbonded interaction distances: 1.85 - 2.40: 114 2.40 - 2.95: 6402 2.95 - 3.50: 15235 3.50 - 4.05: 24417 4.05 - 4.60: 34936 Nonbonded interactions: 81104 Sorted by model distance: nonbonded pdb=" CE1 TYR G 29 " pdb="HD21 LEU G 217 " model vdw 1.847 2.970 nonbonded pdb=" CD1 TYR G 29 " pdb="HD21 LEU G 217 " model vdw 1.917 2.970 nonbonded pdb=" H THR G 214 " pdb="HG22 THR G 214 " model vdw 1.931 2.270 nonbonded pdb=" OE2 GLU G 187 " pdb=" HB ILE G 212 " model vdw 2.026 2.620 nonbonded pdb=" HA TYR G 215 " pdb=" HA PRO G 216 " model vdw 2.046 2.440 ... (remaining 81099 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 163 or resid 173 through 321)) selection = (chain 'B' and (resid 1 through 163 or resid 173 through 321)) selection = (chain 'C' and (resid 1 through 163 or resid 173 through 321)) selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.130 Extract box with map and model: 0.170 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 14.400 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.040 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:9.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7453 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 : 0.003 0.063 14193 Z= 0.133 Angle : 0.483 5.658 19350 Z= 0.266 Chirality : 0.043 0.210 2231 Planarity : 0.004 0.064 2287 Dihedral : 15.669 177.756 5543 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 0.21 % Allowed : 0.00 % Favored : 99.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % 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 aren not related in a simple way. whole: 0.34 (0.21), residues: 1612 helix: 1.40 (0.25), residues: 472 sheet: 1.00 (0.27), residues: 364 loop : -0.92 (0.21), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 28 TYR 0.006 0.001 TYR C 141 PHE 0.014 0.001 PHE A 159 TRP 0.010 0.001 TRP G 12 HIS 0.003 0.001 HIS B 160 Details of bonding type rmsd covalent geometry : bond 0.00269 (14193) covalent geometry : angle 0.48342 (19350) hydrogen bonds : bond 0.14402 ( 450) hydrogen bonds : angle 6.02948 ( 1250) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 280 time to evaluate : 0.563 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: E 63 ASP cc_start: 0.8212 (m-30) cc_final: 0.7594 (t0) REVERT: E 78 GLN cc_start: 0.8426 (mp10) cc_final: 0.8218 (pm20) REVERT: E 190 LEU cc_start: 0.8602 (tp) cc_final: 0.8227 (tm) REVERT: A 132 ARG cc_start: 0.7051 (ttm170) cc_final: 0.6801 (mtt180) REVERT: G 129 SER cc_start: 0.7659 (t) cc_final: 0.7451 (t) REVERT: G 130 LYS cc_start: 0.6955 (mttt) cc_final: 0.6572 (tppt) REVERT: G 185 PHE cc_start: 0.7438 (m-80) cc_final: 0.7212 (m-80) REVERT: G 209 ILE cc_start: 0.8230 (mt) cc_final: 0.7968 (mp) REVERT: G 224 VAL cc_start: 0.8054 (t) cc_final: 0.7847 (t) outliers start: 3 outliers final: 1 residues processed: 282 average time/residue: 0.5748 time to fit residues: 177.7225 Evaluate side-chains 127 residues out of total 1397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 126 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 233 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 98 optimal weight: 0.0670 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 7.9990 chunk 77 optimal weight: 0.0770 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 4.9990 chunk 149 optimal weight: 4.9990 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 16 ASN B 265 HIS C 16 ASN C 265 HIS E 214 GLN D 16 ASN D 265 HIS A 16 ASN A 214 GLN A 295 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.124594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.099034 restraints weight = 29712.059| |-----------------------------------------------------------------------------| r_work (start): 0.3641 rms_B_bonded: 3.25 r_work: 0.3520 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.2167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 14193 Z= 0.100 Angle : 0.427 8.008 19350 Z= 0.227 Chirality : 0.039 0.134 2231 Planarity : 0.003 0.050 2287 Dihedral : 15.055 174.016 2423 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 18.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.29 % Allowed : 11.52 % Favored : 86.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % 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 aren not related in a simple way. whole: 0.71 (0.21), residues: 1612 helix: 2.04 (0.25), residues: 479 sheet: 1.10 (0.27), residues: 351 loop : -0.87 (0.21), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 207 TYR 0.011 0.001 TYR B 101 PHE 0.012 0.001 PHE C 159 TRP 0.006 0.001 TRP G 192 HIS 0.003 0.001 HIS B 160 Details of bonding type rmsd covalent geometry : bond 0.00223 (14193) covalent geometry : angle 0.42678 (19350) hydrogen bonds : bond 0.03511 ( 450) hydrogen bonds : angle 4.20734 ( 1250) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 120 time to evaluate : 0.496 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 101 TYR cc_start: 0.7451 (m-80) cc_final: 0.7234 (m-80) REVERT: E 63 ASP cc_start: 0.8181 (m-30) cc_final: 0.7568 (t0) REVERT: E 78 GLN cc_start: 0.8528 (mp10) cc_final: 0.8222 (pm20) REVERT: D 290 LYS cc_start: 0.8303 (mtpp) cc_final: 0.7960 (ttmm) REVERT: G 68 MET cc_start: 0.6318 (mmt) cc_final: 0.5559 (pmm) REVERT: G 179 VAL cc_start: 0.6138 (t) cc_final: 0.5761 (p) REVERT: G 224 VAL cc_start: 0.8153 (t) cc_final: 0.7761 (m) outliers start: 32 outliers final: 14 residues processed: 140 average time/residue: 0.5356 time to fit residues: 83.3194 Evaluate side-chains 119 residues out of total 1397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 105 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain C residue 63 ASP Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 134 THR Chi-restraints excluded: chain E residue 221 SER Chi-restraints excluded: chain D residue 224 LYS Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 311 VAL Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain G residue 215 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 90 optimal weight: 5.9990 chunk 63 optimal weight: 5.9990 chunk 72 optimal weight: 8.9990 chunk 74 optimal weight: 3.9990 chunk 95 optimal weight: 0.9990 chunk 41 optimal weight: 4.9990 chunk 7 optimal weight: 4.9990 chunk 16 optimal weight: 0.0470 chunk 100 optimal weight: 3.9990 chunk 115 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 overall best weight: 1.8086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 16 ASN B 176 ASN C 11 ASN C 16 ASN D 16 ASN A 16 ASN A 214 GLN A 296 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.118105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.092610 restraints weight = 30525.266| |-----------------------------------------------------------------------------| r_work (start): 0.3523 rms_B_bonded: 3.23 r_work: 0.3399 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.3096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 14193 Z= 0.210 Angle : 0.533 6.333 19350 Z= 0.284 Chirality : 0.042 0.143 2231 Planarity : 0.004 0.045 2287 Dihedral : 15.434 173.065 2421 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 24.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 3.72 % Allowed : 13.24 % Favored : 83.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % 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 aren not related in a simple way. whole: -0.08 (0.20), residues: 1612 helix: 1.42 (0.23), residues: 477 sheet: 0.62 (0.27), residues: 324 loop : -1.29 (0.20), residues: 811 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 132 TYR 0.039 0.002 TYR G 215 PHE 0.026 0.002 PHE A 186 TRP 0.006 0.002 TRP G 138 HIS 0.008 0.001 HIS B 160 Details of bonding type rmsd covalent geometry : bond 0.00475 (14193) covalent geometry : angle 0.53260 (19350) hydrogen bonds : bond 0.04799 ( 450) hydrogen bonds : angle 4.57806 ( 1250) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 107 time to evaluate : 0.530 Fit side-chains REVERT: B 16 ASN cc_start: 0.9077 (OUTLIER) cc_final: 0.8609 (t0) REVERT: B 275 MET cc_start: 0.7708 (OUTLIER) cc_final: 0.7270 (mpm) REVERT: C 101 TYR cc_start: 0.7602 (m-80) cc_final: 0.7353 (m-80) REVERT: C 247 LEU cc_start: 0.7987 (OUTLIER) cc_final: 0.7712 (mt) REVERT: E 63 ASP cc_start: 0.8301 (m-30) cc_final: 0.7706 (t0) REVERT: E 78 GLN cc_start: 0.8443 (mp10) cc_final: 0.8147 (pm20) REVERT: E 112 MET cc_start: 0.7501 (ttm) cc_final: 0.7131 (ttp) REVERT: E 184 TYR cc_start: 0.5195 (OUTLIER) cc_final: 0.4701 (m-10) REVERT: D 290 LYS cc_start: 0.8378 (mtpp) cc_final: 0.8059 (ttmm) REVERT: A 124 MET cc_start: 0.8276 (OUTLIER) cc_final: 0.7141 (tmm) REVERT: G 66 ASN cc_start: 0.5587 (m-40) cc_final: 0.4873 (t0) REVERT: G 68 MET cc_start: 0.6323 (mmt) cc_final: 0.5575 (pmm) REVERT: G 143 ILE cc_start: 0.6948 (OUTLIER) cc_final: 0.6702 (tt) REVERT: G 179 VAL cc_start: 0.7024 (t) cc_final: 0.6796 (p) REVERT: G 185 PHE cc_start: 0.7465 (m-80) cc_final: 0.7263 (m-80) REVERT: G 224 VAL cc_start: 0.8148 (t) cc_final: 0.7773 (m) outliers start: 52 outliers final: 27 residues processed: 142 average time/residue: 0.5164 time to fit residues: 81.7048 Evaluate side-chains 128 residues out of total 1397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 95 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 ASN Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 275 MET Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain C residue 16 ASN Chi-restraints excluded: chain C residue 63 ASP Chi-restraints excluded: chain C residue 247 LEU Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain C residue 313 ASP Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 134 THR Chi-restraints excluded: chain E residue 184 TYR Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain E residue 221 SER Chi-restraints excluded: chain D residue 78 GLN Chi-restraints excluded: chain D residue 88 GLU Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain D residue 221 SER Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain D residue 268 ASP Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 311 VAL Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 124 MET Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 121 VAL Chi-restraints excluded: chain G residue 137 CYS Chi-restraints excluded: chain G residue 143 ILE Chi-restraints excluded: chain G residue 157 VAL Chi-restraints excluded: chain G residue 238 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 57 optimal weight: 3.9990 chunk 96 optimal weight: 4.9990 chunk 157 optimal weight: 2.9990 chunk 95 optimal weight: 3.9990 chunk 114 optimal weight: 5.9990 chunk 103 optimal weight: 0.1980 chunk 145 optimal weight: 0.6980 chunk 27 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 93 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 160 HIS C 16 ASN C 160 HIS D 16 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.118172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.092927 restraints weight = 30608.090| |-----------------------------------------------------------------------------| r_work (start): 0.3528 rms_B_bonded: 3.20 r_work: 0.3403 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.3296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 14193 Z= 0.161 Angle : 0.468 6.050 19350 Z= 0.250 Chirality : 0.040 0.137 2231 Planarity : 0.004 0.043 2287 Dihedral : 15.405 172.467 2421 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 26.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 3.44 % Allowed : 14.75 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % 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 aren not related in a simple way. whole: -0.17 (0.20), residues: 1612 helix: 1.45 (0.23), residues: 477 sheet: 0.53 (0.28), residues: 321 loop : -1.39 (0.20), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG G 207 TYR 0.013 0.001 TYR A 292 PHE 0.014 0.001 PHE A 186 TRP 0.009 0.001 TRP G 12 HIS 0.004 0.001 HIS B 160 Details of bonding type rmsd covalent geometry : bond 0.00363 (14193) covalent geometry : angle 0.46832 (19350) hydrogen bonds : bond 0.04063 ( 450) hydrogen bonds : angle 4.36684 ( 1250) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 97 time to evaluate : 0.535 Fit side-chains revert: symmetry clash REVERT: C 101 TYR cc_start: 0.7671 (m-80) cc_final: 0.7387 (m-80) REVERT: E 63 ASP cc_start: 0.8292 (m-30) cc_final: 0.7706 (t0) REVERT: E 78 GLN cc_start: 0.8607 (mp10) cc_final: 0.8214 (pm20) REVERT: E 112 MET cc_start: 0.7425 (ttm) cc_final: 0.7184 (ttp) REVERT: D 290 LYS cc_start: 0.8438 (mtpp) cc_final: 0.8110 (ttmm) REVERT: A 124 MET cc_start: 0.8210 (OUTLIER) cc_final: 0.7138 (tmm) REVERT: G 66 ASN cc_start: 0.5368 (m-40) cc_final: 0.5104 (t0) REVERT: G 68 MET cc_start: 0.6337 (mmt) cc_final: 0.5581 (pmm) REVERT: G 224 VAL cc_start: 0.8261 (t) cc_final: 0.7888 (m) outliers start: 48 outliers final: 31 residues processed: 129 average time/residue: 0.5124 time to fit residues: 73.9528 Evaluate side-chains 121 residues out of total 1397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 89 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain C residue 16 ASN Chi-restraints excluded: chain C residue 63 ASP Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain C residue 313 ASP Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 134 THR Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain E residue 212 GLU Chi-restraints excluded: chain E residue 221 SER Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 78 GLN Chi-restraints excluded: chain D residue 88 GLU Chi-restraints excluded: chain D residue 142 MET Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain D residue 221 SER Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 311 VAL Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 124 MET Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 121 VAL Chi-restraints excluded: chain G residue 137 CYS Chi-restraints excluded: chain G residue 157 VAL Chi-restraints excluded: chain G residue 238 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 90 optimal weight: 7.9990 chunk 97 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 chunk 23 optimal weight: 0.0980 chunk 155 optimal weight: 5.9990 chunk 85 optimal weight: 2.9990 chunk 139 optimal weight: 0.9980 chunk 157 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 150 optimal weight: 6.9990 chunk 138 optimal weight: 2.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 16 ASN C 16 ASN D 16 ASN A 11 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.117434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.091922 restraints weight = 30646.947| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 3.22 r_work: 0.3393 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.3490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 14193 Z= 0.167 Angle : 0.470 5.066 19350 Z= 0.251 Chirality : 0.040 0.136 2231 Planarity : 0.004 0.045 2287 Dihedral : 15.399 171.847 2421 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 27.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 3.29 % Allowed : 16.25 % Favored : 80.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % 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 aren not related in a simple way. whole: -0.34 (0.20), residues: 1612 helix: 1.41 (0.23), residues: 477 sheet: 0.31 (0.28), residues: 323 loop : -1.51 (0.20), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG G 207 TYR 0.019 0.001 TYR E 227 PHE 0.018 0.001 PHE G 185 TRP 0.009 0.001 TRP G 12 HIS 0.003 0.001 HIS B 160 Details of bonding type rmsd covalent geometry : bond 0.00378 (14193) covalent geometry : angle 0.47032 (19350) hydrogen bonds : bond 0.04103 ( 450) hydrogen bonds : angle 4.36729 ( 1250) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 94 time to evaluate : 0.548 Fit side-chains revert: symmetry clash REVERT: B 16 ASN cc_start: 0.9197 (OUTLIER) cc_final: 0.8591 (t0) REVERT: C 101 TYR cc_start: 0.7718 (m-80) cc_final: 0.7440 (m-80) REVERT: E 63 ASP cc_start: 0.8302 (m-30) cc_final: 0.7717 (t0) REVERT: E 78 GLN cc_start: 0.8573 (mp10) cc_final: 0.8146 (pm20) REVERT: E 112 MET cc_start: 0.7452 (ttm) cc_final: 0.7205 (ttp) REVERT: D 1 MET cc_start: 0.8268 (mmm) cc_final: 0.7950 (mmm) REVERT: A 124 MET cc_start: 0.8060 (OUTLIER) cc_final: 0.6950 (tmm) REVERT: G 66 ASN cc_start: 0.5468 (m-40) cc_final: 0.5071 (t0) REVERT: G 68 MET cc_start: 0.6359 (mmt) cc_final: 0.5595 (pmm) REVERT: G 185 PHE cc_start: 0.7494 (m-10) cc_final: 0.7163 (m-80) REVERT: G 224 VAL cc_start: 0.8183 (t) cc_final: 0.7854 (m) outliers start: 46 outliers final: 31 residues processed: 126 average time/residue: 0.4864 time to fit residues: 69.1029 Evaluate side-chains 122 residues out of total 1397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 89 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 ASN Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain C residue 63 ASP Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain C residue 313 ASP Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 134 THR Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain E residue 221 SER Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 78 GLN Chi-restraints excluded: chain D residue 88 GLU Chi-restraints excluded: chain D residue 142 MET Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain D residue 221 SER Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain D residue 268 ASP Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 311 VAL Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 124 MET Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 121 VAL Chi-restraints excluded: chain G residue 137 CYS Chi-restraints excluded: chain G residue 157 VAL Chi-restraints excluded: chain G residue 238 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 76 optimal weight: 0.0470 chunk 116 optimal weight: 0.7980 chunk 137 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 127 optimal weight: 5.9990 chunk 124 optimal weight: 0.0870 chunk 66 optimal weight: 8.9990 chunk 68 optimal weight: 5.9990 chunk 78 optimal weight: 0.6980 chunk 5 optimal weight: 2.9990 chunk 110 optimal weight: 3.9990 overall best weight: 0.9258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 16 ASN C 16 ASN D 16 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.118011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.092698 restraints weight = 30427.883| |-----------------------------------------------------------------------------| r_work (start): 0.3537 rms_B_bonded: 3.20 r_work: 0.3414 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.3550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14193 Z= 0.118 Angle : 0.426 4.822 19350 Z= 0.227 Chirality : 0.039 0.135 2231 Planarity : 0.003 0.052 2287 Dihedral : 15.291 171.368 2421 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 27.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.93 % Allowed : 17.39 % Favored : 79.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % 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 aren not related in a simple way. whole: -0.10 (0.20), residues: 1612 helix: 1.76 (0.23), residues: 477 sheet: 0.39 (0.29), residues: 321 loop : -1.44 (0.20), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG G 207 TYR 0.010 0.001 TYR A 292 PHE 0.015 0.001 PHE G 185 TRP 0.010 0.001 TRP G 12 HIS 0.002 0.001 HIS A 27 Details of bonding type rmsd covalent geometry : bond 0.00268 (14193) covalent geometry : angle 0.42553 (19350) hydrogen bonds : bond 0.03620 ( 450) hydrogen bonds : angle 4.12378 ( 1250) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 90 time to evaluate : 0.536 Fit side-chains revert: symmetry clash REVERT: B 16 ASN cc_start: 0.9133 (OUTLIER) cc_final: 0.8562 (t0) REVERT: C 101 TYR cc_start: 0.7742 (m-80) cc_final: 0.7466 (m-80) REVERT: E 63 ASP cc_start: 0.8241 (m-30) cc_final: 0.7687 (t0) REVERT: E 78 GLN cc_start: 0.8591 (mp10) cc_final: 0.8154 (pm20) REVERT: D 1 MET cc_start: 0.8324 (mmm) cc_final: 0.7995 (mmm) REVERT: A 1 MET cc_start: 0.7933 (mtt) cc_final: 0.7149 (mpp) REVERT: A 124 MET cc_start: 0.7997 (OUTLIER) cc_final: 0.6829 (tmm) REVERT: G 68 MET cc_start: 0.6332 (mmt) cc_final: 0.5636 (pmm) outliers start: 41 outliers final: 29 residues processed: 120 average time/residue: 0.4611 time to fit residues: 62.7084 Evaluate side-chains 115 residues out of total 1397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 84 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 ASN Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain C residue 16 ASN Chi-restraints excluded: chain C residue 63 ASP Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain C residue 313 ASP Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 134 THR Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 78 GLN Chi-restraints excluded: chain D residue 88 GLU Chi-restraints excluded: chain D residue 142 MET Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain D residue 221 SER Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain D residue 268 ASP Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain A residue 124 MET Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 121 VAL Chi-restraints excluded: chain G residue 137 CYS Chi-restraints excluded: chain G residue 157 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 109 optimal weight: 4.9990 chunk 156 optimal weight: 8.9990 chunk 94 optimal weight: 5.9990 chunk 114 optimal weight: 7.9990 chunk 79 optimal weight: 9.9990 chunk 64 optimal weight: 7.9990 chunk 97 optimal weight: 2.9990 chunk 150 optimal weight: 5.9990 chunk 135 optimal weight: 5.9990 chunk 122 optimal weight: 4.9990 chunk 92 optimal weight: 5.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 16 ASN B 23 ASN B 160 HIS C 16 ASN D 16 ASN A 16 ASN G 52 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.111475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.086567 restraints weight = 31502.597| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 3.14 r_work: 0.3297 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.4481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.071 14193 Z= 0.534 Angle : 0.930 12.029 19350 Z= 0.489 Chirality : 0.054 0.247 2231 Planarity : 0.008 0.100 2287 Dihedral : 16.152 174.591 2421 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 42.03 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.30 % Favored : 89.64 % Rotamer: Outliers : 4.72 % Allowed : 17.97 % Favored : 77.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % 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 aren not related in a simple way. whole: -2.37 (0.19), residues: 1612 helix: -0.61 (0.21), residues: 489 sheet: -1.00 (0.29), residues: 305 loop : -2.46 (0.18), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG G 207 TYR 0.029 0.003 TYR G 42 PHE 0.031 0.004 PHE B 163 TRP 0.017 0.003 TRP G 199 HIS 0.009 0.003 HIS B 160 Details of bonding type rmsd covalent geometry : bond 0.01224 (14193) covalent geometry : angle 0.92977 (19350) hydrogen bonds : bond 0.07839 ( 450) hydrogen bonds : angle 6.10194 ( 1250) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 91 time to evaluate : 0.606 Fit side-chains REVERT: B 245 MET cc_start: 0.8138 (mtm) cc_final: 0.7772 (mtt) REVERT: B 275 MET cc_start: 0.7848 (OUTLIER) cc_final: 0.7540 (mpm) REVERT: C 247 LEU cc_start: 0.8402 (OUTLIER) cc_final: 0.8080 (mt) REVERT: E 63 ASP cc_start: 0.8209 (m-30) cc_final: 0.7616 (t0) REVERT: E 78 GLN cc_start: 0.8456 (mp10) cc_final: 0.7970 (pm20) REVERT: E 254 LYS cc_start: 0.8985 (tttt) cc_final: 0.8769 (ttpp) REVERT: D 1 MET cc_start: 0.8273 (mmm) cc_final: 0.8024 (mmm) REVERT: A 260 MET cc_start: 0.6998 (mmm) cc_final: 0.6668 (mmm) REVERT: A 269 TYR cc_start: 0.7364 (OUTLIER) cc_final: 0.6573 (p90) REVERT: G 68 MET cc_start: 0.6484 (mmt) cc_final: 0.6225 (pp-130) REVERT: G 142 ARG cc_start: 0.7492 (OUTLIER) cc_final: 0.6897 (ttt90) REVERT: G 145 CYS cc_start: 0.6972 (t) cc_final: 0.4482 (p) outliers start: 66 outliers final: 45 residues processed: 144 average time/residue: 0.4526 time to fit residues: 74.0097 Evaluate side-chains 135 residues out of total 1397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 86 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 112 MET Chi-restraints excluded: chain B residue 275 MET Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 313 ASP Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 63 ASP Chi-restraints excluded: chain C residue 191 ASP Chi-restraints excluded: chain C residue 247 LEU Chi-restraints excluded: chain C residue 266 ASP Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain C residue 313 ASP Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 134 THR Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain E residue 221 SER Chi-restraints excluded: chain D residue 6 VAL Chi-restraints excluded: chain D residue 10 VAL Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 78 GLN Chi-restraints excluded: chain D residue 88 GLU Chi-restraints excluded: chain D residue 142 MET Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain D residue 221 SER Chi-restraints excluded: chain D residue 245 MET Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain D residue 268 ASP Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 311 VAL Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 186 PHE Chi-restraints excluded: chain A residue 269 TYR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain G residue 2 ILE Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 80 THR Chi-restraints excluded: chain G residue 121 VAL Chi-restraints excluded: chain G residue 137 CYS Chi-restraints excluded: chain G residue 142 ARG Chi-restraints excluded: chain G residue 172 TYR Chi-restraints excluded: chain G residue 224 VAL Chi-restraints excluded: chain G residue 238 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 16 optimal weight: 0.8980 chunk 25 optimal weight: 0.7980 chunk 92 optimal weight: 0.7980 chunk 132 optimal weight: 1.9990 chunk 86 optimal weight: 0.8980 chunk 125 optimal weight: 0.8980 chunk 15 optimal weight: 0.9980 chunk 59 optimal weight: 5.9990 chunk 32 optimal weight: 0.7980 chunk 137 optimal weight: 0.6980 chunk 45 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 16 ASN C 23 ASN D 16 ASN A 16 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.116446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.091318 restraints weight = 30657.156| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 3.19 r_work: 0.3389 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.4095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14193 Z= 0.117 Angle : 0.466 6.214 19350 Z= 0.249 Chirality : 0.040 0.135 2231 Planarity : 0.004 0.043 2287 Dihedral : 15.656 173.437 2421 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 31.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 2.36 % Allowed : 20.47 % Favored : 77.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % 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 aren not related in a simple way. whole: -1.22 (0.20), residues: 1612 helix: 0.95 (0.22), residues: 477 sheet: -0.76 (0.28), residues: 336 loop : -1.98 (0.19), residues: 799 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 213 TYR 0.009 0.001 TYR A 292 PHE 0.020 0.001 PHE G 185 TRP 0.014 0.002 TRP G 12 HIS 0.002 0.001 HIS A 55 Details of bonding type rmsd covalent geometry : bond 0.00261 (14193) covalent geometry : angle 0.46594 (19350) hydrogen bonds : bond 0.03934 ( 450) hydrogen bonds : angle 4.55164 ( 1250) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 89 time to evaluate : 0.548 Fit side-chains REVERT: E 63 ASP cc_start: 0.8252 (m-30) cc_final: 0.7722 (t0) REVERT: E 78 GLN cc_start: 0.8435 (mp10) cc_final: 0.7990 (pm20) REVERT: E 254 LYS cc_start: 0.8915 (tttt) cc_final: 0.8701 (ttpp) REVERT: D 1 MET cc_start: 0.8236 (mmm) cc_final: 0.7869 (mmm) REVERT: G 68 MET cc_start: 0.6424 (mmt) cc_final: 0.6165 (pp-130) outliers start: 33 outliers final: 20 residues processed: 117 average time/residue: 0.5115 time to fit residues: 66.9521 Evaluate side-chains 106 residues out of total 1397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 86 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 6 VAL Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain C residue 63 ASP Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain C residue 313 ASP Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 134 THR Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain D residue 6 VAL Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 88 GLU Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain D residue 221 SER Chi-restraints excluded: chain D residue 268 ASP Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain G residue 51 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 30 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 112 optimal weight: 4.9990 chunk 117 optimal weight: 0.8980 chunk 132 optimal weight: 3.9990 chunk 159 optimal weight: 0.0010 chunk 55 optimal weight: 0.7980 chunk 43 optimal weight: 3.9990 chunk 129 optimal weight: 0.8980 chunk 123 optimal weight: 5.9990 chunk 58 optimal weight: 1.9990 overall best weight: 0.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 16 ASN C 16 ASN C 23 ASN D 16 ASN ** A 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.116690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.091644 restraints weight = 30660.012| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 3.17 r_work: 0.3399 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.4066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14193 Z= 0.124 Angle : 0.445 5.116 19350 Z= 0.236 Chirality : 0.039 0.133 2231 Planarity : 0.003 0.038 2287 Dihedral : 15.364 171.731 2421 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 31.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 2.08 % Allowed : 21.12 % Favored : 76.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % 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 aren not related in a simple way. whole: -0.70 (0.20), residues: 1612 helix: 1.66 (0.23), residues: 471 sheet: -0.35 (0.29), residues: 321 loop : -1.87 (0.19), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG G 207 TYR 0.016 0.001 TYR E 227 PHE 0.011 0.001 PHE A 159 TRP 0.012 0.002 TRP G 12 HIS 0.002 0.001 HIS B 160 Details of bonding type rmsd covalent geometry : bond 0.00282 (14193) covalent geometry : angle 0.44543 (19350) hydrogen bonds : bond 0.03691 ( 450) hydrogen bonds : angle 4.26301 ( 1250) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 91 time to evaluate : 0.550 Fit side-chains REVERT: B 275 MET cc_start: 0.7855 (mpm) cc_final: 0.7602 (mpm) REVERT: E 63 ASP cc_start: 0.8258 (m-30) cc_final: 0.7675 (t0) REVERT: E 78 GLN cc_start: 0.8416 (mp10) cc_final: 0.7967 (pm20) REVERT: D 1 MET cc_start: 0.8304 (mmm) cc_final: 0.7990 (mmm) REVERT: D 271 LYS cc_start: 0.8201 (ptmt) cc_final: 0.7972 (ptpp) REVERT: G 68 MET cc_start: 0.6445 (mmt) cc_final: 0.6171 (pp-130) outliers start: 29 outliers final: 22 residues processed: 117 average time/residue: 0.4920 time to fit residues: 64.8805 Evaluate side-chains 108 residues out of total 1397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 86 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 6 VAL Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 63 ASP Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain C residue 313 ASP Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 134 THR Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain D residue 6 VAL Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 88 GLU Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain D residue 221 SER Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain D residue 268 ASP Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain G residue 2 ILE Chi-restraints excluded: chain G residue 51 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 5 optimal weight: 0.7980 chunk 32 optimal weight: 0.0970 chunk 110 optimal weight: 5.9990 chunk 36 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 72 optimal weight: 7.9990 chunk 22 optimal weight: 0.0070 chunk 0 optimal weight: 4.9990 chunk 149 optimal weight: 6.9990 chunk 54 optimal weight: 0.9980 chunk 31 optimal weight: 3.9990 overall best weight: 0.7798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 16 ASN C 23 ASN D 16 ASN ** A 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.117359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.092345 restraints weight = 30733.244| |-----------------------------------------------------------------------------| r_work (start): 0.3532 rms_B_bonded: 3.18 r_work: 0.3414 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.4060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 14193 Z= 0.107 Angle : 0.427 5.287 19350 Z= 0.226 Chirality : 0.039 0.131 2231 Planarity : 0.003 0.051 2287 Dihedral : 15.273 171.001 2421 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 31.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 1.79 % Allowed : 21.40 % Favored : 76.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % 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 aren not related in a simple way. whole: -0.45 (0.21), residues: 1612 helix: 1.93 (0.24), residues: 473 sheet: -0.22 (0.29), residues: 331 loop : -1.78 (0.20), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG G 207 TYR 0.012 0.001 TYR G 123 PHE 0.009 0.001 PHE A 159 TRP 0.012 0.001 TRP G 12 HIS 0.002 0.001 HIS B 160 Details of bonding type rmsd covalent geometry : bond 0.00245 (14193) covalent geometry : angle 0.42694 (19350) hydrogen bonds : bond 0.03444 ( 450) hydrogen bonds : angle 4.07089 ( 1250) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 90 time to evaluate : 0.577 Fit side-chains revert: symmetry clash REVERT: E 63 ASP cc_start: 0.8241 (m-30) cc_final: 0.7663 (t0) REVERT: E 78 GLN cc_start: 0.8404 (mp10) cc_final: 0.7947 (pm20) REVERT: E 142 MET cc_start: 0.7024 (mpp) cc_final: 0.5563 (mtp) REVERT: E 254 LYS cc_start: 0.9022 (ttpp) cc_final: 0.8556 (ttmm) REVERT: D 1 MET cc_start: 0.8324 (mmm) cc_final: 0.8019 (mmm) REVERT: D 268 ASP cc_start: 0.7991 (OUTLIER) cc_final: 0.7275 (p0) REVERT: G 68 MET cc_start: 0.6527 (mmt) cc_final: 0.5731 (pmm) REVERT: G 239 PHE cc_start: 0.7836 (m-10) cc_final: 0.7487 (m-10) outliers start: 25 outliers final: 22 residues processed: 112 average time/residue: 0.5174 time to fit residues: 64.9168 Evaluate side-chains 108 residues out of total 1397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 85 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 6 VAL Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 88 GLU Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain C residue 16 ASN Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 63 ASP Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain C residue 313 ASP Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 134 THR Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain D residue 6 VAL Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 88 GLU Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain D residue 268 ASP Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain G residue 51 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 72 optimal weight: 7.9990 chunk 62 optimal weight: 20.0000 chunk 160 optimal weight: 6.9990 chunk 41 optimal weight: 4.9990 chunk 90 optimal weight: 6.9990 chunk 139 optimal weight: 5.9990 chunk 123 optimal weight: 0.7980 chunk 163 optimal weight: 0.9990 chunk 101 optimal weight: 0.8980 chunk 109 optimal weight: 7.9990 chunk 6 optimal weight: 3.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 16 ASN D 16 ASN A 16 ASN ** A 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.114025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.088911 restraints weight = 31022.021| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 3.19 r_work: 0.3346 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.4283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.033 14193 Z= 0.255 Angle : 0.586 7.352 19350 Z= 0.311 Chirality : 0.043 0.151 2231 Planarity : 0.005 0.068 2287 Dihedral : 15.462 171.225 2421 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 35.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.18 % Favored : 90.82 % Rotamer: Outliers : 2.15 % Allowed : 21.33 % Favored : 76.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % 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 aren not related in a simple way. whole: -1.16 (0.20), residues: 1612 helix: 1.03 (0.23), residues: 478 sheet: -0.75 (0.29), residues: 325 loop : -1.96 (0.19), residues: 809 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG G 207 TYR 0.014 0.002 TYR A 292 PHE 0.014 0.002 PHE B 163 TRP 0.008 0.002 TRP G 12 HIS 0.005 0.001 HIS C 27 Details of bonding type rmsd covalent geometry : bond 0.00580 (14193) covalent geometry : angle 0.58577 (19350) hydrogen bonds : bond 0.05065 ( 450) hydrogen bonds : angle 4.83917 ( 1250) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3816.33 seconds wall clock time: 66 minutes 22.73 seconds (3982.73 seconds total)