Starting phenix.real_space_refine on Thu Aug 6 00:15:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cp2_45797/08_2026/9cp2_45797.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cp2_45797/08_2026/9cp2_45797.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 { model { file = "/net/cci-nas-00/data/ceres_data/9cp2_45797/08_2026/9cp2_45797.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cp2_45797/08_2026/9cp2_45797.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9cp2_45797/08_2026/9cp2_45797.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cp2_45797/08_2026/9cp2_45797.map" } 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= 0.022 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 406 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: 5 Type Number sf(0) Gaussians P 37 5.49 5 S 36 5.16 5 C 7435 2.51 5 N 1963 2.21 5 O 2342 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11813 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: "D" Number of atoms: 1926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1926 Classifications: {'peptide': 247} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 236} Chain breaks: 4 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: "G" Number of atoms: 1688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1688 Classifications: {'peptide': 211} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 200} Chain breaks: 2 Chain: "S" Number of atoms: 572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 572 Classifications: {'RNA': 27} Modifications used: {'5*END': 1, 'rna2p_pur': 7, 'rna2p_pyr': 7, 'rna3p_pur': 8, 'rna3p_pyr': 5} Link IDs: {'rna2p': 13, 'rna3p': 13} Chain: "M" Number of atoms: 221 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 221 Classifications: {'DNA': 11} Link IDs: {'rna3p': 10} Chain: "B" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'TRS': 1} Classifications: {'undetermined': 1} 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: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {'TRS': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.12, per 1000 atoms: 0.18 Number of scatterers: 11813 At special positions: 0 Unit cell: (82.36, 102.24, 151.94, 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 36 16.00 P 37 15.00 O 2342 8.00 N 1963 7.00 C 7435 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: 0.89 Conformation dependent library (CDL) restraints added in 469.6 milliseconds 2762 Ramachandran restraints generated. 1381 Oldfield, 0 Emsley, 1381 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2598 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 20 sheets defined 33.8% alpha, 16.6% beta 8 base pairs and 11 stacking pairs defined. Time for finding SS restraints: 1.24 Creating SS restraints... Processing helix chain 'B' and resid 50 through 69 removed outlier: 4.004A pdb=" N ALA B 54 " --> pdb=" O GLY B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 78 removed outlier: 3.879A pdb=" N GLN B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 94 removed outlier: 3.588A pdb=" N LEU B 90 " --> pdb=" O THR B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 115 removed outlier: 3.575A pdb=" N ASP B 115 " --> pdb=" O VAL B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 121 Processing helix chain 'B' and resid 192 through 195 Processing helix chain 'B' and resid 207 through 214 removed outlier: 3.805A pdb=" N LEU B 211 " --> pdb=" O GLY B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 232 removed outlier: 3.945A pdb=" N LEU B 226 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N TYR B 227 " --> pdb=" O ILE B 223 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N SER B 228 " --> pdb=" O LYS B 224 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N LEU B 229 " --> pdb=" O ALA B 225 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 284 removed outlier: 3.858A pdb=" N GLY B 282 " --> pdb=" O GLY B 278 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 321 removed outlier: 4.020A pdb=" N LEU B 314 " --> pdb=" O THR B 310 " (cutoff:3.500A) Processing helix chain 'C' and resid 50 through 68 removed outlier: 3.801A pdb=" N ALA C 54 " --> pdb=" O GLY C 50 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 78 removed outlier: 3.796A pdb=" N GLN C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 86 through 94 removed outlier: 3.534A pdb=" N LEU C 90 " --> pdb=" O THR C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 115 removed outlier: 4.298A pdb=" N ARG C 105 " --> pdb=" O TYR C 101 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N ARG C 106 " --> pdb=" O ASN C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 116 through 121 Processing helix chain 'C' and resid 192 through 195 Processing helix chain 'C' and resid 207 through 214 removed outlier: 3.639A pdb=" N LEU C 211 " --> pdb=" O GLY C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 214 through 232 removed outlier: 3.831A pdb=" N LEU C 226 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N TYR C 227 " --> pdb=" O ILE C 223 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N SER C 228 " --> pdb=" O LYS C 224 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N LEU C 229 " --> pdb=" O ALA C 225 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 284 removed outlier: 3.755A pdb=" N THR C 273 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLY C 282 " --> pdb=" O GLY C 278 " (cutoff:3.500A) Processing helix chain 'C' and resid 310 through 321 removed outlier: 3.995A pdb=" N LEU C 314 " --> pdb=" O THR C 310 " (cutoff:3.500A) Processing helix chain 'D' and resid 53 through 68 Processing helix chain 'D' and resid 73 through 78 removed outlier: 3.980A 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 100 through 113 removed outlier: 4.335A pdb=" N ARG D 105 " --> pdb=" O TYR D 101 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N ARG D 106 " --> pdb=" O ASN D 102 " (cutoff:3.500A) Processing helix chain 'D' and resid 116 through 121 Processing helix chain 'D' and resid 192 through 195 Processing helix chain 'D' and resid 207 through 225 removed outlier: 3.532A pdb=" N LEU D 211 " --> pdb=" O GLY D 207 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N ALA D 216 " --> pdb=" O GLU D 212 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N LYS D 217 " --> pdb=" O ARG D 213 " (cutoff:3.500A) Processing helix chain 'D' and resid 225 through 231 removed outlier: 4.505A pdb=" N LEU D 229 " --> pdb=" O ALA D 225 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 284 removed outlier: 3.806A pdb=" N GLY D 278 " --> pdb=" O ILE D 274 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LYS D 279 " --> pdb=" O MET D 275 " (cutoff:3.500A) Processing helix chain 'D' and resid 310 through 321 Processing helix chain 'A' and resid 50 through 69 Processing helix chain 'A' and resid 73 through 78 removed outlier: 3.903A pdb=" N GLN A 78 " --> pdb=" O SER A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 94 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 207 through 225 removed outlier: 4.845A pdb=" N ALA A 216 " --> pdb=" O GLU A 212 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N LYS A 217 " --> pdb=" O ARG A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 232 removed outlier: 4.120A pdb=" N LEU A 229 " --> pdb=" O ALA A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 285 removed outlier: 3.731A pdb=" N THR A 273 " --> pdb=" O TYR A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 321 removed outlier: 3.802A pdb=" N LEU A 314 " --> pdb=" O THR A 310 " (cutoff:3.500A) Processing helix chain 'G' and resid 32 through 42 removed outlier: 3.583A pdb=" N LEU G 36 " --> pdb=" O PRO G 32 " (cutoff:3.500A) Processing helix chain 'G' and resid 129 through 138 Processing helix chain 'G' and resid 194 through 198 removed outlier: 3.951A pdb=" N ILE G 198 " --> pdb=" O ASN G 195 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 2 through 8 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 2 through 8 current: chain 'B' and resid 184 through 190 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 184 through 190 current: chain 'B' and resid 289 through 295 removed outlier: 3.809A pdb=" N THR B 306 " --> pdb=" O ALA B 291 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 10 through 13 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 10 through 13 current: chain 'B' and resid 24 through 27 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 24 through 27 current: chain 'B' and resid 174 through 182 No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 29 through 36 Processing sheet with id=AA4, first strand: chain 'B' and resid 123 through 125 Processing sheet with id=AA5, first strand: chain 'C' and resid 2 through 8 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 2 through 8 current: chain 'C' and resid 184 through 190 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 184 through 190 current: chain 'C' and resid 289 through 295 removed outlier: 3.778A pdb=" N THR C 306 " --> pdb=" O ALA C 291 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 10 through 13 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 10 through 13 current: chain 'C' and resid 24 through 27 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 24 through 27 current: chain 'C' and resid 174 through 182 No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'C' and resid 29 through 35 Processing sheet with id=AA8, first strand: chain 'C' and resid 123 through 125 Processing sheet with id=AA9, first strand: chain 'D' and resid 2 through 8 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 2 through 8 current: chain 'D' and resid 184 through 190 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 184 through 190 current: chain 'D' and resid 289 through 295 No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'D' and resid 29 through 36 Processing sheet with id=AB2, first strand: chain 'D' and resid 123 through 125 Processing sheet with id=AB3, 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 290 through 295 Processing sheet with id=AB4, first strand: chain 'A' and resid 29 through 35 Processing sheet with id=AB5, first strand: chain 'A' and resid 124 through 125 Processing sheet with id=AB6, first strand: chain 'G' and resid 68 through 73 removed outlier: 6.909A pdb=" N TYR G 3 " --> pdb=" O VAL G 157 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N VAL G 157 " --> pdb=" O TYR G 3 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N LYS G 5 " --> pdb=" O VAL G 155 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N VAL G 155 " --> pdb=" O LYS G 5 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N PHE G 7 " --> pdb=" O GLU G 153 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 13 through 14 removed outlier: 3.558A pdb=" N PHE G 14 " --> pdb=" O VAL G 112 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 161 through 163 removed outlier: 7.472A pdb=" N GLU G 228 " --> pdb=" O PHE G 239 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N PHE G 239 " --> pdb=" O GLU G 228 " (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: 3.559A pdb=" N ALA G 218 " --> pdb=" O THR G 213 " (cutoff:3.500A) 355 hydrogen bonds defined for protein. 990 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 19 hydrogen bonds 38 hydrogen bond angles 0 basepair planarities 8 basepair parallelities 11 stacking parallelities Total time for adding SS restraints: 1.63 Time building geometry restraints manager: 1.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 3210 1.33 - 1.45: 2030 1.45 - 1.57: 6712 1.57 - 1.69: 73 1.69 - 1.81: 69 Bond restraints: 12094 Sorted by residual: bond pdb=" C3' DT M 17 " pdb=" C2' DT M 17 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.93e+00 bond pdb=" C3' DA M 23 " pdb=" C2' DA M 23 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.05e+00 bond pdb=" C3' DC M 21 " pdb=" C2' DC M 21 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 7.92e+00 bond pdb=" C1' DT M 16 " pdb=" N1 DT M 16 " ideal model delta sigma weight residual 1.468 1.503 -0.035 1.40e-02 5.10e+03 6.38e+00 bond pdb=" C3' DC M 19 " pdb=" C2' DC M 19 " ideal model delta sigma weight residual 1.516 1.535 -0.019 8.00e-03 1.56e+04 5.88e+00 ... (remaining 12089 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.08: 15672 1.08 - 2.17: 614 2.17 - 3.25: 176 3.25 - 4.33: 22 4.33 - 5.41: 7 Bond angle restraints: 16491 Sorted by residual: angle pdb=" O2 U S 2 " pdb=" C2 U S 2 " pdb=" N3 U S 2 " ideal model delta sigma weight residual 122.20 118.91 3.29 7.00e-01 2.04e+00 2.21e+01 angle pdb=" N1 U S 2 " pdb=" C2 U S 2 " pdb=" O2 U S 2 " ideal model delta sigma weight residual 122.80 125.70 -2.90 7.00e-01 2.04e+00 1.72e+01 angle pdb=" N3 DT M 20 " pdb=" C4 DT M 20 " pdb=" O4 DT M 20 " ideal model delta sigma weight residual 119.90 122.36 -2.46 6.00e-01 2.78e+00 1.67e+01 angle pdb=" N3 DT M 16 " pdb=" C4 DT M 16 " pdb=" O4 DT M 16 " ideal model delta sigma weight residual 119.90 122.34 -2.44 6.00e-01 2.78e+00 1.65e+01 angle pdb=" N3 DT M 14 " pdb=" C4 DT M 14 " pdb=" O4 DT M 14 " ideal model delta sigma weight residual 119.90 122.29 -2.39 6.00e-01 2.78e+00 1.59e+01 ... (remaining 16486 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.28: 7007 29.28 - 58.56: 274 58.56 - 87.84: 33 87.84 - 117.13: 2 117.13 - 146.41: 1 Dihedral angle restraints: 7317 sinusoidal: 3264 harmonic: 4053 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 -23.46 -104.54 1 1.70e+01 3.46e-03 4.16e+01 dihedral pdb=" CA LEU C 12 " pdb=" C LEU C 12 " pdb=" N GLU C 13 " pdb=" CA GLU C 13 " ideal model delta harmonic sigma weight residual -180.00 -158.98 -21.02 0 5.00e+00 4.00e-02 1.77e+01 dihedral pdb=" O4' U S 15 " pdb=" C1' U S 15 " pdb=" N1 U S 15 " pdb=" C2 U S 15 " ideal model delta sinusoidal sigma weight residual -128.00 -66.12 -61.88 1 1.70e+01 3.46e-03 1.76e+01 ... (remaining 7314 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 1310 0.038 - 0.077: 393 0.077 - 0.115: 149 0.115 - 0.153: 49 0.153 - 0.192: 2 Chirality restraints: 1903 Sorted by residual: chirality pdb=" CB VAL B 18 " pdb=" CA VAL B 18 " pdb=" CG1 VAL B 18 " pdb=" CG2 VAL B 18 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.19 2.00e-01 2.50e+01 9.20e-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 2.48 0.17 2.00e-01 2.50e+01 7.16e-01 chirality pdb=" CB VAL C 18 " pdb=" CA VAL C 18 " pdb=" CG1 VAL C 18 " pdb=" CG2 VAL C 18 " both_signs ideal model delta sigma weight residual False -2.63 -2.49 -0.14 2.00e-01 2.50e+01 4.93e-01 ... (remaining 1900 not shown) Planarity restraints: 1956 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA D 30 " -0.029 5.00e-02 4.00e+02 4.31e-02 2.97e+00 pdb=" N PRO D 31 " 0.075 5.00e-02 4.00e+02 pdb=" CA PRO D 31 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO D 31 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU C 108 " -0.008 2.00e-02 2.50e+03 1.68e-02 2.82e+00 pdb=" C GLU C 108 " 0.029 2.00e-02 2.50e+03 pdb=" O GLU C 108 " -0.011 2.00e-02 2.50e+03 pdb=" N VAL C 109 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU B 108 " -0.008 2.00e-02 2.50e+03 1.53e-02 2.35e+00 pdb=" C GLU B 108 " 0.027 2.00e-02 2.50e+03 pdb=" O GLU B 108 " -0.010 2.00e-02 2.50e+03 pdb=" N VAL B 109 " -0.009 2.00e-02 2.50e+03 ... (remaining 1953 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 111 2.65 - 3.21: 10044 3.21 - 3.78: 16730 3.78 - 4.34: 23295 4.34 - 4.90: 39516 Nonbonded interactions: 89696 Sorted by model distance: nonbonded pdb=" O PHE B 159 " pdb=" NH2 ARG C 28 " model vdw 2.089 3.120 nonbonded pdb=" NH2 ARG B 28 " pdb=" O PHE A 159 " model vdw 2.193 3.120 nonbonded pdb=" OE1 GLU D 108 " pdb=" OG1 THR D 200 " model vdw 2.217 3.040 nonbonded pdb=" O THR A 134 " pdb=" NH1 ARG A 136 " model vdw 2.266 3.120 nonbonded pdb=" ND1 HIS C 55 " pdb=" OP2 A S 20 " model vdw 2.311 3.120 ... (remaining 89691 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and resid 1 through 321) selection = (chain 'C' and resid 1 through 321) } 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: 1.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.010 Extract box with map and model: 0.120 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 10.710 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 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 0.038 12094 Z= 0.183 Angle : 0.534 5.414 16491 Z= 0.349 Chirality : 0.045 0.192 1903 Planarity : 0.004 0.043 1956 Dihedral : 15.145 146.408 4719 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 0.25 % Allowed : 0.08 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.22), residues: 1381 helix: 0.55 (0.25), residues: 442 sheet: 0.70 (0.27), residues: 306 loop : -1.17 (0.23), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 46 TYR 0.015 0.001 TYR G 208 PHE 0.020 0.001 PHE B 159 TRP 0.010 0.001 TRP G 12 HIS 0.003 0.001 HIS C 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.18 (12094) covalent geometry : angle 0.53448 / 0.35 (16491) hydrogen bonds : bond 0.15178 / 10.52 ( 374) hydrogen bonds : angle 5.92528 / 4.17 ( 1028) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2762 Ramachandran restraints generated. 1381 Oldfield, 0 Emsley, 1381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2762 Ramachandran restraints generated. 1381 Oldfield, 0 Emsley, 1381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 194 time to evaluate : 0.410 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 101 TYR cc_start: 0.7248 (m-80) cc_final: 0.6977 (m-10) REVERT: C 233 ASN cc_start: 0.7692 (m-40) cc_final: 0.7233 (t0) REVERT: C 276 ARG cc_start: 0.7693 (mtp-110) cc_final: 0.7062 (mtm-85) REVERT: C 287 ASN cc_start: 0.8737 (t0) cc_final: 0.8443 (t0) REVERT: D 1 MET cc_start: 0.7640 (mtp) cc_final: 0.7429 (mtp) REVERT: D 78 GLN cc_start: 0.9123 (mp10) cc_final: 0.8891 (mp10) REVERT: D 193 ASP cc_start: 0.8832 (m-30) cc_final: 0.8600 (p0) REVERT: D 248 MET cc_start: 0.6266 (mmm) cc_final: 0.5440 (mmt) REVERT: D 260 MET cc_start: 0.8293 (mtm) cc_final: 0.8023 (ptp) REVERT: D 276 ARG cc_start: 0.7331 (mtp-110) cc_final: 0.7083 (ttm170) REVERT: A 96 LYS cc_start: 0.8908 (mmtt) cc_final: 0.8647 (mtpp) REVERT: G 118 ARG cc_start: 0.7666 (mtt180) cc_final: 0.7195 (mtt90) REVERT: G 209 ILE cc_start: 0.8308 (mt) cc_final: 0.7991 (mp) outliers start: 3 outliers final: 2 residues processed: 197 average time/residue: 0.5506 time to fit residues: 116.7063 Evaluate side-chains 95 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 93 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 ASN Chi-restraints excluded: chain A residue 201 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 8.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 8.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 0.7980 chunk 55 optimal weight: 3.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 11 ASN B 160 HIS C 11 ASN C 160 HIS C 265 HIS D 102 ASN A 160 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.106354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.083161 restraints weight = 24859.678| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 3.24 r_work: 0.3195 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.1844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.084 12094 Z= 0.327 Angle : 0.700 10.511 16491 Z= 0.370 Chirality : 0.048 0.151 1903 Planarity : 0.005 0.041 1956 Dihedral : 14.130 150.496 2055 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 2.42 % Allowed : 9.70 % Favored : 87.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.70 (0.21), residues: 1381 helix: 0.53 (0.25), residues: 443 sheet: 0.09 (0.27), residues: 304 loop : -1.46 (0.22), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 136 TYR 0.021 0.002 TYR G 172 PHE 0.018 0.002 PHE B 159 TRP 0.013 0.002 TRP G 138 HIS 0.009 0.002 HIS C 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00767 / 0.33 (12094) covalent geometry : angle 0.70010 / 0.37 (16491) hydrogen bonds : bond 0.06670 / 4.52 ( 374) hydrogen bonds : angle 4.87447 / 3.40 ( 1028) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2762 Ramachandran restraints generated. 1381 Oldfield, 0 Emsley, 1381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2762 Ramachandran restraints generated. 1381 Oldfield, 0 Emsley, 1381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 98 time to evaluate : 0.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 101 TYR cc_start: 0.7467 (m-80) cc_final: 0.7138 (m-80) REVERT: C 233 ASN cc_start: 0.8178 (m-40) cc_final: 0.7511 (t0) REVERT: C 287 ASN cc_start: 0.8872 (t0) cc_final: 0.8542 (t0) REVERT: D 78 GLN cc_start: 0.9125 (mp10) cc_final: 0.8885 (mp10) REVERT: D 80 GLU cc_start: 0.8448 (tt0) cc_final: 0.8230 (pp20) REVERT: D 248 MET cc_start: 0.5942 (mmm) cc_final: 0.5346 (mmt) REVERT: D 260 MET cc_start: 0.8238 (mtm) cc_final: 0.7956 (ptp) REVERT: D 275 MET cc_start: 0.9045 (ttp) cc_final: 0.8836 (ptm) REVERT: A 13 GLU cc_start: 0.7774 (tm-30) cc_final: 0.7455 (pp20) REVERT: A 96 LYS cc_start: 0.9032 (mmtt) cc_final: 0.8738 (mtpp) REVERT: A 115 ASP cc_start: 0.8235 (t0) cc_final: 0.8029 (t0) REVERT: A 124 MET cc_start: 0.8717 (OUTLIER) cc_final: 0.8329 (ttt) REVERT: G 118 ARG cc_start: 0.8073 (mtt180) cc_final: 0.7558 (mtt90) REVERT: G 209 ILE cc_start: 0.7729 (mt) cc_final: 0.7487 (mp) REVERT: G 212 ILE cc_start: 0.7024 (mm) cc_final: 0.6812 (mm) outliers start: 29 outliers final: 10 residues processed: 114 average time/residue: 0.4886 time to fit residues: 60.5040 Evaluate side-chains 91 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 80 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 174 ILE Chi-restraints excluded: chain C residue 204 LYS Chi-restraints excluded: chain D residue 90 LEU Chi-restraints excluded: chain D residue 223 ILE Chi-restraints excluded: chain A residue 124 MET Chi-restraints excluded: chain G residue 10 LEU Chi-restraints excluded: chain G residue 55 ASN Chi-restraints excluded: chain G residue 219 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 98 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 57 optimal weight: 0.8980 chunk 104 optimal weight: 0.5980 chunk 126 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 77 optimal weight: 5.9990 chunk 135 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 chunk 112 optimal weight: 0.9980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 214 GLN D 265 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.108693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.085466 restraints weight = 24742.715| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 3.27 r_work: 0.3243 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.2006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 12094 Z= 0.138 Angle : 0.526 7.385 16491 Z= 0.284 Chirality : 0.043 0.144 1903 Planarity : 0.004 0.043 1956 Dihedral : 13.859 151.525 2051 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 2.17 % Allowed : 11.87 % Favored : 85.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.22), residues: 1381 helix: 1.01 (0.25), residues: 444 sheet: 0.14 (0.28), residues: 312 loop : -1.36 (0.23), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 174 TYR 0.016 0.001 TYR D 227 PHE 0.019 0.001 PHE B 159 TRP 0.007 0.001 TRP G 12 HIS 0.003 0.001 HIS B 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.14 (12094) covalent geometry : angle 0.52591 / 0.28 (16491) hydrogen bonds : bond 0.04723 / 3.13 ( 374) hydrogen bonds : angle 4.18561 / 2.92 ( 1028) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2762 Ramachandran restraints generated. 1381 Oldfield, 0 Emsley, 1381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2762 Ramachandran restraints generated. 1381 Oldfield, 0 Emsley, 1381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 94 time to evaluate : 0.356 Fit side-chains revert: symmetry clash REVERT: B 13 GLU cc_start: 0.8515 (OUTLIER) cc_final: 0.8093 (pp20) REVERT: C 101 TYR cc_start: 0.7501 (m-80) cc_final: 0.7149 (m-80) REVERT: C 233 ASN cc_start: 0.7754 (m-40) cc_final: 0.7120 (t0) REVERT: C 287 ASN cc_start: 0.8902 (t0) cc_final: 0.8577 (t0) REVERT: D 248 MET cc_start: 0.5811 (mmm) cc_final: 0.5221 (mmt) REVERT: D 260 MET cc_start: 0.8271 (mtm) cc_final: 0.7865 (ptp) REVERT: D 275 MET cc_start: 0.9072 (ttp) cc_final: 0.8791 (ptm) REVERT: A 96 LYS cc_start: 0.8997 (mmtt) cc_final: 0.8700 (mtpp) REVERT: G 118 ARG cc_start: 0.8044 (mtt180) cc_final: 0.7473 (ttm110) REVERT: G 209 ILE cc_start: 0.7617 (mt) cc_final: 0.7380 (mp) outliers start: 26 outliers final: 8 residues processed: 111 average time/residue: 0.4404 time to fit residues: 53.6422 Evaluate side-chains 86 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 77 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 GLU Chi-restraints excluded: chain B residue 124 MET Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 174 ILE Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain D residue 90 LEU Chi-restraints excluded: chain D residue 223 ILE Chi-restraints excluded: chain G residue 55 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 139 optimal weight: 7.9990 chunk 59 optimal weight: 1.9990 chunk 72 optimal weight: 4.9990 chunk 17 optimal weight: 3.9990 chunk 98 optimal weight: 4.9990 chunk 39 optimal weight: 0.6980 chunk 78 optimal weight: 6.9990 chunk 5 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 127 optimal weight: 0.0970 chunk 19 optimal weight: 3.9990 overall best weight: 1.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.107657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.084210 restraints weight = 24751.707| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 3.26 r_work: 0.3219 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.2253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 12094 Z= 0.180 Angle : 0.543 7.789 16491 Z= 0.292 Chirality : 0.043 0.149 1903 Planarity : 0.004 0.034 1956 Dihedral : 13.782 152.174 2051 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.26 % Allowed : 14.38 % Favored : 83.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.34 (0.22), residues: 1381 helix: 1.05 (0.25), residues: 444 sheet: 0.13 (0.29), residues: 305 loop : -1.34 (0.23), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 65 TYR 0.014 0.001 TYR G 172 PHE 0.017 0.002 PHE B 159 TRP 0.010 0.002 TRP G 199 HIS 0.005 0.001 HIS B 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00419 / 0.18 (12094) covalent geometry : angle 0.54304 / 0.29 (16491) hydrogen bonds : bond 0.04909 / 3.29 ( 374) hydrogen bonds : angle 4.18848 / 2.91 ( 1028) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2762 Ramachandran restraints generated. 1381 Oldfield, 0 Emsley, 1381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2762 Ramachandran restraints generated. 1381 Oldfield, 0 Emsley, 1381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 79 time to evaluate : 0.362 Fit side-chains revert: symmetry clash REVERT: B 13 GLU cc_start: 0.8640 (OUTLIER) cc_final: 0.8296 (pp20) REVERT: C 101 TYR cc_start: 0.7516 (m-80) cc_final: 0.7047 (m-80) REVERT: C 233 ASN cc_start: 0.7848 (m-40) cc_final: 0.7279 (t0) REVERT: C 287 ASN cc_start: 0.8891 (t0) cc_final: 0.8594 (t0) REVERT: D 248 MET cc_start: 0.5706 (mmm) cc_final: 0.5106 (mmt) REVERT: D 260 MET cc_start: 0.8286 (mtm) cc_final: 0.8008 (mtm) REVERT: D 275 MET cc_start: 0.9107 (ttp) cc_final: 0.8855 (ptm) REVERT: A 96 LYS cc_start: 0.9006 (mmtt) cc_final: 0.8714 (mtpp) REVERT: A 124 MET cc_start: 0.8695 (OUTLIER) cc_final: 0.8171 (tmt) REVERT: G 118 ARG cc_start: 0.8029 (mtt180) cc_final: 0.7593 (ttm110) REVERT: G 209 ILE cc_start: 0.7624 (mt) cc_final: 0.7382 (mp) outliers start: 27 outliers final: 12 residues processed: 97 average time/residue: 0.4376 time to fit residues: 46.7985 Evaluate side-chains 86 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 72 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 GLU Chi-restraints excluded: chain B residue 124 MET Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 174 ILE Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain D residue 223 ILE Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 124 MET Chi-restraints excluded: chain A residue 142 MET Chi-restraints excluded: chain A residue 256 ASP Chi-restraints excluded: chain G residue 10 LEU Chi-restraints excluded: chain G residue 55 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 93 optimal weight: 2.9990 chunk 113 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 chunk 53 optimal weight: 0.7980 chunk 129 optimal weight: 4.9990 chunk 104 optimal weight: 0.6980 chunk 41 optimal weight: 2.9990 chunk 103 optimal weight: 0.9990 chunk 37 optimal weight: 0.6980 chunk 100 optimal weight: 0.8980 chunk 74 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.108890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.085403 restraints weight = 24711.443| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 3.25 r_work: 0.3242 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.2328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12094 Z= 0.123 Angle : 0.490 8.334 16491 Z= 0.265 Chirality : 0.042 0.151 1903 Planarity : 0.003 0.033 1956 Dihedral : 13.677 152.107 2051 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.42 % Allowed : 14.55 % Favored : 83.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.22), residues: 1381 helix: 1.28 (0.25), residues: 442 sheet: 0.25 (0.30), residues: 290 loop : -1.27 (0.23), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 65 TYR 0.012 0.001 TYR A 101 PHE 0.017 0.001 PHE B 159 TRP 0.008 0.001 TRP G 199 HIS 0.003 0.001 HIS B 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 (12094) covalent geometry : angle 0.49006 / 0.26 (16491) hydrogen bonds : bond 0.04197 / 2.76 ( 374) hydrogen bonds : angle 3.96223 / 2.75 ( 1028) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2762 Ramachandran restraints generated. 1381 Oldfield, 0 Emsley, 1381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2762 Ramachandran restraints generated. 1381 Oldfield, 0 Emsley, 1381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 81 time to evaluate : 0.366 Fit side-chains revert: symmetry clash REVERT: B 1 MET cc_start: 0.9002 (mtp) cc_final: 0.7985 (ttm) REVERT: B 13 GLU cc_start: 0.8473 (OUTLIER) cc_final: 0.8103 (pp20) REVERT: B 191 ASP cc_start: 0.7876 (OUTLIER) cc_final: 0.7656 (p0) REVERT: C 13 GLU cc_start: 0.8248 (OUTLIER) cc_final: 0.7852 (pp20) REVERT: C 101 TYR cc_start: 0.7547 (m-80) cc_final: 0.6962 (m-10) REVERT: C 142 MET cc_start: 0.8108 (OUTLIER) cc_final: 0.7814 (tpt) REVERT: C 233 ASN cc_start: 0.7717 (m-40) cc_final: 0.7274 (t0) REVERT: C 287 ASN cc_start: 0.8896 (t0) cc_final: 0.8594 (t0) REVERT: D 248 MET cc_start: 0.5621 (mmm) cc_final: 0.5096 (mmt) REVERT: D 260 MET cc_start: 0.8273 (mtm) cc_final: 0.8028 (mtm) REVERT: A 96 LYS cc_start: 0.8984 (mmtt) cc_final: 0.8706 (mtpp) REVERT: G 118 ARG cc_start: 0.8002 (mtt180) cc_final: 0.7460 (ttm110) REVERT: G 209 ILE cc_start: 0.7553 (mt) cc_final: 0.7315 (mp) outliers start: 29 outliers final: 13 residues processed: 101 average time/residue: 0.4362 time to fit residues: 48.6818 Evaluate side-chains 93 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 76 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 GLU Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 124 MET Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 191 ASP Chi-restraints excluded: chain C residue 13 GLU Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 142 MET Chi-restraints excluded: chain C residue 174 ILE Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain D residue 223 ILE Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 142 MET Chi-restraints excluded: chain A residue 256 ASP Chi-restraints excluded: chain G residue 10 LEU Chi-restraints excluded: chain G residue 55 ASN Chi-restraints excluded: chain G residue 219 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 63 optimal weight: 6.9990 chunk 89 optimal weight: 4.9990 chunk 101 optimal weight: 4.9990 chunk 22 optimal weight: 0.9990 chunk 20 optimal weight: 5.9990 chunk 25 optimal weight: 0.0170 chunk 121 optimal weight: 4.9990 chunk 59 optimal weight: 3.9990 chunk 82 optimal weight: 0.7980 chunk 125 optimal weight: 1.9990 chunk 131 optimal weight: 0.7980 overall best weight: 0.9222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.108413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.085320 restraints weight = 24710.763| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 3.21 r_work: 0.3241 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.2434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12094 Z= 0.134 Angle : 0.520 13.382 16491 Z= 0.275 Chirality : 0.043 0.167 1903 Planarity : 0.003 0.031 1956 Dihedral : 13.601 151.794 2051 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.34 % Allowed : 15.80 % Favored : 81.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.22), residues: 1381 helix: 1.35 (0.25), residues: 442 sheet: 0.11 (0.29), residues: 300 loop : -1.26 (0.23), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 166 TYR 0.011 0.001 TYR G 172 PHE 0.017 0.001 PHE B 159 TRP 0.009 0.001 TRP G 199 HIS 0.003 0.001 HIS B 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.13 (12094) covalent geometry : angle 0.51996 / 0.28 (16491) hydrogen bonds : bond 0.04177 / 2.77 ( 374) hydrogen bonds : angle 3.95152 / 2.74 ( 1028) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2762 Ramachandran restraints generated. 1381 Oldfield, 0 Emsley, 1381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2762 Ramachandran restraints generated. 1381 Oldfield, 0 Emsley, 1381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 81 time to evaluate : 0.307 Fit side-chains revert: symmetry clash REVERT: B 1 MET cc_start: 0.8984 (mtp) cc_final: 0.8010 (ttm) REVERT: B 13 GLU cc_start: 0.8520 (OUTLIER) cc_final: 0.8153 (pp20) REVERT: B 142 MET cc_start: 0.8778 (OUTLIER) cc_final: 0.8439 (ttt) REVERT: B 191 ASP cc_start: 0.7724 (OUTLIER) cc_final: 0.7514 (p0) REVERT: C 13 GLU cc_start: 0.8179 (OUTLIER) cc_final: 0.7790 (pp20) REVERT: C 101 TYR cc_start: 0.7618 (m-80) cc_final: 0.6985 (m-10) REVERT: C 142 MET cc_start: 0.8115 (OUTLIER) cc_final: 0.7846 (tpt) REVERT: C 233 ASN cc_start: 0.7753 (m-40) cc_final: 0.7274 (t0) REVERT: C 287 ASN cc_start: 0.8903 (t0) cc_final: 0.8620 (t0) REVERT: D 191 ASP cc_start: 0.7613 (p0) cc_final: 0.7027 (p0) REVERT: D 248 MET cc_start: 0.5684 (mmm) cc_final: 0.5066 (mmt) REVERT: D 260 MET cc_start: 0.8288 (mtm) cc_final: 0.8044 (mtm) REVERT: A 96 LYS cc_start: 0.9007 (mmtt) cc_final: 0.8735 (mtpp) REVERT: G 118 ARG cc_start: 0.7997 (mtt180) cc_final: 0.7446 (ttm110) REVERT: G 209 ILE cc_start: 0.7555 (mt) cc_final: 0.7318 (mp) REVERT: G 231 GLU cc_start: 0.8825 (tt0) cc_final: 0.8401 (tm-30) outliers start: 28 outliers final: 12 residues processed: 98 average time/residue: 0.4028 time to fit residues: 43.4633 Evaluate side-chains 96 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 79 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 GLU Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 124 MET Chi-restraints excluded: chain B residue 142 MET Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 191 ASP Chi-restraints excluded: chain C residue 13 GLU Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 142 MET Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 142 MET Chi-restraints excluded: chain A residue 256 ASP Chi-restraints excluded: chain G residue 10 LEU Chi-restraints excluded: chain G residue 55 ASN Chi-restraints excluded: chain G residue 219 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 101 optimal weight: 0.9990 chunk 112 optimal weight: 2.9990 chunk 130 optimal weight: 8.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.7980 chunk 5 optimal weight: 3.9990 chunk 15 optimal weight: 0.9990 chunk 43 optimal weight: 3.9990 chunk 59 optimal weight: 3.9990 chunk 119 optimal weight: 0.0470 chunk 7 optimal weight: 0.6980 overall best weight: 0.7082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.109005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.085824 restraints weight = 24608.176| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 3.23 r_work: 0.3251 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.2508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12094 Z= 0.114 Angle : 0.493 13.922 16491 Z= 0.262 Chirality : 0.042 0.152 1903 Planarity : 0.003 0.030 1956 Dihedral : 13.445 151.499 2051 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.26 % Allowed : 16.56 % Favored : 81.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.22), residues: 1381 helix: 1.43 (0.25), residues: 442 sheet: 0.18 (0.29), residues: 300 loop : -1.21 (0.23), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 166 TYR 0.010 0.001 TYR A 101 PHE 0.016 0.001 PHE B 159 TRP 0.008 0.001 TRP G 199 HIS 0.003 0.001 HIS B 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.11 (12094) covalent geometry : angle 0.49319 / 0.26 (16491) hydrogen bonds : bond 0.03838 / 2.52 ( 374) hydrogen bonds : angle 3.84390 / 2.67 ( 1028) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2762 Ramachandran restraints generated. 1381 Oldfield, 0 Emsley, 1381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2762 Ramachandran restraints generated. 1381 Oldfield, 0 Emsley, 1381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 84 time to evaluate : 0.387 Fit side-chains revert: symmetry clash REVERT: B 1 MET cc_start: 0.8974 (mtp) cc_final: 0.8012 (ttm) REVERT: B 13 GLU cc_start: 0.8463 (OUTLIER) cc_final: 0.8141 (pp20) REVERT: B 142 MET cc_start: 0.8747 (OUTLIER) cc_final: 0.8412 (ttt) REVERT: C 13 GLU cc_start: 0.8158 (OUTLIER) cc_final: 0.7777 (pp20) REVERT: C 101 TYR cc_start: 0.7601 (m-80) cc_final: 0.6912 (m-10) REVERT: C 142 MET cc_start: 0.8134 (OUTLIER) cc_final: 0.7865 (tpt) REVERT: C 233 ASN cc_start: 0.7694 (m-40) cc_final: 0.7262 (t0) REVERT: C 287 ASN cc_start: 0.8901 (t0) cc_final: 0.8621 (t0) REVERT: D 191 ASP cc_start: 0.7636 (p0) cc_final: 0.7040 (p0) REVERT: D 248 MET cc_start: 0.5690 (mmm) cc_final: 0.5097 (mmt) REVERT: D 260 MET cc_start: 0.8292 (mtm) cc_final: 0.8031 (mtm) REVERT: A 96 LYS cc_start: 0.9013 (mmtt) cc_final: 0.8746 (mtpp) REVERT: G 118 ARG cc_start: 0.8020 (mtt180) cc_final: 0.7436 (ttm110) REVERT: G 209 ILE cc_start: 0.7527 (mt) cc_final: 0.7292 (mp) REVERT: G 231 GLU cc_start: 0.8814 (tt0) cc_final: 0.8374 (tm-30) outliers start: 27 outliers final: 11 residues processed: 99 average time/residue: 0.3966 time to fit residues: 43.4601 Evaluate side-chains 95 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 80 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 GLU Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 124 MET Chi-restraints excluded: chain B residue 142 MET Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain C residue 13 GLU Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 142 MET Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 142 MET Chi-restraints excluded: chain A residue 256 ASP Chi-restraints excluded: chain G residue 10 LEU Chi-restraints excluded: chain G residue 55 ASN Chi-restraints excluded: chain G residue 219 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 86 optimal weight: 4.9990 chunk 140 optimal weight: 30.0000 chunk 59 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 20 optimal weight: 0.9980 chunk 56 optimal weight: 0.1980 chunk 9 optimal weight: 0.3980 chunk 17 optimal weight: 0.8980 chunk 84 optimal weight: 9.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.108632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.085386 restraints weight = 24542.011| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 3.27 r_work: 0.3245 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.2566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 12094 Z= 0.132 Angle : 0.522 12.720 16491 Z= 0.273 Chirality : 0.043 0.441 1903 Planarity : 0.003 0.030 1956 Dihedral : 13.407 151.283 2051 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 1.92 % Allowed : 17.22 % Favored : 80.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.22), residues: 1381 helix: 1.39 (0.25), residues: 443 sheet: 0.16 (0.29), residues: 300 loop : -1.21 (0.23), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 65 TYR 0.010 0.001 TYR G 172 PHE 0.016 0.001 PHE B 159 TRP 0.008 0.001 TRP G 199 HIS 0.003 0.001 HIS B 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.13 (12094) covalent geometry : angle 0.52205 / 0.27 (16491) hydrogen bonds : bond 0.04021 / 2.68 ( 374) hydrogen bonds : angle 3.92499 / 2.72 ( 1028) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2762 Ramachandran restraints generated. 1381 Oldfield, 0 Emsley, 1381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2762 Ramachandran restraints generated. 1381 Oldfield, 0 Emsley, 1381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 82 time to evaluate : 0.452 Fit side-chains revert: symmetry clash REVERT: B 1 MET cc_start: 0.8960 (mtp) cc_final: 0.7970 (ttm) REVERT: B 13 GLU cc_start: 0.8498 (OUTLIER) cc_final: 0.8105 (pp20) REVERT: B 142 MET cc_start: 0.8767 (OUTLIER) cc_final: 0.8488 (ttt) REVERT: C 13 GLU cc_start: 0.8176 (OUTLIER) cc_final: 0.7797 (pp20) REVERT: C 101 TYR cc_start: 0.7595 (m-80) cc_final: 0.6992 (m-80) REVERT: C 142 MET cc_start: 0.8217 (OUTLIER) cc_final: 0.7923 (tpt) REVERT: C 233 ASN cc_start: 0.7709 (m-40) cc_final: 0.7276 (t0) REVERT: C 287 ASN cc_start: 0.8904 (t0) cc_final: 0.8629 (t0) REVERT: D 191 ASP cc_start: 0.7597 (p0) cc_final: 0.7063 (p0) REVERT: D 223 ILE cc_start: 0.8655 (tp) cc_final: 0.8337 (pp) REVERT: D 248 MET cc_start: 0.5658 (mmm) cc_final: 0.5053 (mmt) REVERT: D 260 MET cc_start: 0.8311 (mtm) cc_final: 0.8060 (mtm) REVERT: A 96 LYS cc_start: 0.9027 (mmtt) cc_final: 0.8757 (mtpp) REVERT: G 118 ARG cc_start: 0.8031 (mtt180) cc_final: 0.7449 (ttm110) REVERT: G 209 ILE cc_start: 0.7647 (mt) cc_final: 0.7404 (mp) REVERT: G 231 GLU cc_start: 0.8818 (tt0) cc_final: 0.8379 (tm-30) outliers start: 23 outliers final: 12 residues processed: 96 average time/residue: 0.3951 time to fit residues: 42.1159 Evaluate side-chains 96 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 80 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 GLU Chi-restraints excluded: chain B residue 16 ASN Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 124 MET Chi-restraints excluded: chain B residue 142 MET Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain C residue 13 GLU Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 142 MET Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 142 MET Chi-restraints excluded: chain A residue 256 ASP Chi-restraints excluded: chain G residue 10 LEU Chi-restraints excluded: chain G residue 55 ASN Chi-restraints excluded: chain G residue 219 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 110 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 15 optimal weight: 0.0270 chunk 131 optimal weight: 0.0770 chunk 34 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 85 optimal weight: 10.0000 chunk 101 optimal weight: 0.0980 chunk 14 optimal weight: 0.3980 chunk 72 optimal weight: 4.9990 chunk 63 optimal weight: 3.9990 overall best weight: 0.7198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.109042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.085783 restraints weight = 24364.269| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 3.26 r_work: 0.3253 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.2617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 12094 Z= 0.118 Angle : 0.521 17.513 16491 Z= 0.271 Chirality : 0.043 0.400 1903 Planarity : 0.003 0.029 1956 Dihedral : 13.373 151.135 2051 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.92 % Allowed : 17.39 % Favored : 80.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.22), residues: 1381 helix: 1.43 (0.25), residues: 443 sheet: 0.18 (0.29), residues: 304 loop : -1.18 (0.23), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 65 TYR 0.009 0.001 TYR G 172 PHE 0.015 0.001 PHE B 159 TRP 0.009 0.001 TRP G 199 HIS 0.003 0.001 HIS B 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 (12094) covalent geometry : angle 0.52148 / 0.27 (16491) hydrogen bonds : bond 0.03834 / 2.54 ( 374) hydrogen bonds : angle 3.87289 / 2.69 ( 1028) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2762 Ramachandran restraints generated. 1381 Oldfield, 0 Emsley, 1381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2762 Ramachandran restraints generated. 1381 Oldfield, 0 Emsley, 1381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 84 time to evaluate : 0.436 Fit side-chains revert: symmetry clash REVERT: B 1 MET cc_start: 0.8936 (mtp) cc_final: 0.7926 (ttm) REVERT: B 13 GLU cc_start: 0.8408 (OUTLIER) cc_final: 0.8129 (pp20) REVERT: B 142 MET cc_start: 0.8750 (OUTLIER) cc_final: 0.8461 (ttt) REVERT: C 10 VAL cc_start: 0.7656 (OUTLIER) cc_final: 0.7452 (t) REVERT: C 13 GLU cc_start: 0.8178 (OUTLIER) cc_final: 0.7807 (pp20) REVERT: C 101 TYR cc_start: 0.7617 (m-80) cc_final: 0.6878 (m-10) REVERT: C 142 MET cc_start: 0.8184 (OUTLIER) cc_final: 0.7928 (tpt) REVERT: C 233 ASN cc_start: 0.7661 (m-40) cc_final: 0.7256 (t0) REVERT: C 287 ASN cc_start: 0.8899 (t0) cc_final: 0.8645 (t0) REVERT: D 191 ASP cc_start: 0.7552 (p0) cc_final: 0.7033 (p0) REVERT: D 223 ILE cc_start: 0.8661 (tp) cc_final: 0.8344 (pp) REVERT: D 248 MET cc_start: 0.5690 (mmm) cc_final: 0.5076 (mmt) REVERT: D 260 MET cc_start: 0.8295 (mtm) cc_final: 0.8030 (mtm) REVERT: A 96 LYS cc_start: 0.9025 (mmtt) cc_final: 0.8754 (mtpp) REVERT: G 114 ILE cc_start: 0.9084 (tt) cc_final: 0.8835 (pp) REVERT: G 118 ARG cc_start: 0.8020 (mtt180) cc_final: 0.7461 (ttm110) REVERT: G 209 ILE cc_start: 0.7639 (mt) cc_final: 0.7399 (mp) REVERT: G 231 GLU cc_start: 0.8809 (tt0) cc_final: 0.8375 (tm-30) outliers start: 23 outliers final: 14 residues processed: 98 average time/residue: 0.4041 time to fit residues: 43.9340 Evaluate side-chains 107 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 88 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 GLU Chi-restraints excluded: chain B residue 16 ASN Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 124 MET Chi-restraints excluded: chain B residue 142 MET Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain C residue 10 VAL Chi-restraints excluded: chain C residue 13 GLU Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 142 MET Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain D residue 124 MET Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 142 MET Chi-restraints excluded: chain A residue 256 ASP Chi-restraints excluded: chain G residue 10 LEU Chi-restraints excluded: chain G residue 55 ASN Chi-restraints excluded: chain G residue 219 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 9 optimal weight: 0.6980 chunk 10 optimal weight: 0.9980 chunk 36 optimal weight: 3.9990 chunk 93 optimal weight: 0.9980 chunk 51 optimal weight: 0.8980 chunk 114 optimal weight: 2.9990 chunk 106 optimal weight: 0.8980 chunk 44 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 62 optimal weight: 8.9990 chunk 32 optimal weight: 2.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.108735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.085282 restraints weight = 24814.489| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 3.26 r_work: 0.3242 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.2662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 12094 Z= 0.133 Angle : 0.529 13.629 16491 Z= 0.275 Chirality : 0.043 0.397 1903 Planarity : 0.003 0.030 1956 Dihedral : 13.362 150.848 2051 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 1.92 % Allowed : 17.73 % Favored : 80.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.22), residues: 1381 helix: 1.40 (0.25), residues: 443 sheet: 0.16 (0.29), residues: 298 loop : -1.21 (0.23), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 166 TYR 0.011 0.001 TYR G 172 PHE 0.018 0.001 PHE C 175 TRP 0.010 0.001 TRP G 199 HIS 0.003 0.001 HIS B 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.13 (12094) covalent geometry : angle 0.52942 / 0.28 (16491) hydrogen bonds : bond 0.03954 / 2.65 ( 374) hydrogen bonds : angle 3.92620 / 2.72 ( 1028) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2762 Ramachandran restraints generated. 1381 Oldfield, 0 Emsley, 1381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2762 Ramachandran restraints generated. 1381 Oldfield, 0 Emsley, 1381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 89 time to evaluate : 0.275 Fit side-chains revert: symmetry clash REVERT: B 1 MET cc_start: 0.8942 (mtp) cc_final: 0.7916 (ttm) REVERT: B 13 GLU cc_start: 0.8383 (OUTLIER) cc_final: 0.8064 (pp20) REVERT: B 142 MET cc_start: 0.8757 (OUTLIER) cc_final: 0.8482 (ttt) REVERT: C 10 VAL cc_start: 0.7729 (OUTLIER) cc_final: 0.7528 (t) REVERT: C 13 GLU cc_start: 0.8189 (OUTLIER) cc_final: 0.7817 (pp20) REVERT: C 101 TYR cc_start: 0.7614 (m-80) cc_final: 0.6746 (m-10) REVERT: C 142 MET cc_start: 0.8218 (OUTLIER) cc_final: 0.7936 (tpt) REVERT: C 233 ASN cc_start: 0.7674 (m-40) cc_final: 0.7261 (t0) REVERT: C 287 ASN cc_start: 0.8908 (t0) cc_final: 0.8668 (t0) REVERT: D 119 ASP cc_start: 0.8874 (t0) cc_final: 0.8647 (t0) REVERT: D 191 ASP cc_start: 0.7547 (p0) cc_final: 0.7044 (p0) REVERT: D 223 ILE cc_start: 0.8657 (tp) cc_final: 0.8334 (pp) REVERT: D 248 MET cc_start: 0.5630 (mmm) cc_final: 0.5031 (mmt) REVERT: D 260 MET cc_start: 0.8316 (mtm) cc_final: 0.8056 (mtm) REVERT: A 96 LYS cc_start: 0.9028 (mmtt) cc_final: 0.8751 (mtpp) REVERT: G 114 ILE cc_start: 0.9071 (tt) cc_final: 0.8837 (pp) REVERT: G 118 ARG cc_start: 0.8015 (mtt180) cc_final: 0.7448 (ttm110) REVERT: G 209 ILE cc_start: 0.7628 (mt) cc_final: 0.7384 (mp) REVERT: G 231 GLU cc_start: 0.8808 (tt0) cc_final: 0.8364 (tm-30) outliers start: 23 outliers final: 13 residues processed: 104 average time/residue: 0.4222 time to fit residues: 48.9007 Evaluate side-chains 101 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 83 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 GLU Chi-restraints excluded: chain B residue 16 ASN Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 124 MET Chi-restraints excluded: chain B residue 142 MET Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain C residue 10 VAL Chi-restraints excluded: chain C residue 13 GLU Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 142 MET Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain D residue 124 MET Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 142 MET Chi-restraints excluded: chain A residue 256 ASP Chi-restraints excluded: chain G residue 10 LEU Chi-restraints excluded: chain G residue 55 ASN Chi-restraints excluded: chain G residue 219 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 39 optimal weight: 0.7980 chunk 90 optimal weight: 0.7980 chunk 83 optimal weight: 10.0000 chunk 106 optimal weight: 0.3980 chunk 12 optimal weight: 3.9990 chunk 1 optimal weight: 0.5980 chunk 48 optimal weight: 0.0670 chunk 85 optimal weight: 4.9990 chunk 56 optimal weight: 0.2980 chunk 77 optimal weight: 0.5980 chunk 32 optimal weight: 0.9990 overall best weight: 0.3918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.110096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.086842 restraints weight = 24438.787| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 3.28 r_work: 0.3270 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.2722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.068 12094 Z= 0.099 Angle : 0.508 14.191 16491 Z= 0.265 Chirality : 0.042 0.381 1903 Planarity : 0.003 0.029 1956 Dihedral : 13.319 150.804 2051 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.34 % Allowed : 18.65 % Favored : 80.02 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.10 (0.23), residues: 1381 helix: 1.52 (0.26), residues: 443 sheet: 0.29 (0.29), residues: 302 loop : -1.10 (0.24), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 65 TYR 0.010 0.001 TYR A 101 PHE 0.016 0.001 PHE B 159 TRP 0.008 0.001 TRP G 199 HIS 0.003 0.001 HIS C 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00221 / 0.10 (12094) covalent geometry : angle 0.50809 / 0.27 (16491) hydrogen bonds : bond 0.03488 / 2.28 ( 374) hydrogen bonds : angle 3.80373 / 2.64 ( 1028) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2327.13 seconds wall clock time: 40 minutes 35.78 seconds (2435.78 seconds total)