Starting phenix.real_space_refine on Thu Aug 6 09:23:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wt7_37828/08_2026/8wt7_37828.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wt7_37828/08_2026/8wt7_37828.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8wt7_37828/08_2026/8wt7_37828.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wt7_37828/08_2026/8wt7_37828.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8wt7_37828/08_2026/8wt7_37828.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wt7_37828/08_2026/8wt7_37828.map" } resolution = 2.7 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= -0.002 sd= 0.082 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 239 5.49 5 Mg 2 5.21 5 S 48 5.16 5 C 8481 2.51 5 N 2743 2.21 5 O 3333 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 35 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: 14846 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 2429 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 306, 2420 Classifications: {'peptide': 306} Link IDs: {'PTRANS': 12, 'TRANS': 293} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 306, 2420 Classifications: {'peptide': 306} Link IDs: {'PTRANS': 12, 'TRANS': 293} Chain breaks: 1 bond proxies already assigned to first conformer: 2457 Chain: "B" Number of atoms: 2512 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 318, 2503 Classifications: {'peptide': 318} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 305} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Conformer: "B" Number of residues, atoms: 318, 2503 Classifications: {'peptide': 318} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 305} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 bond proxies already assigned to first conformer: 2542 Chain: "C" Number of atoms: 2420 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 305, 2411 Classifications: {'peptide': 305} Link IDs: {'PTRANS': 12, 'TRANS': 292} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 305, 2411 Classifications: {'peptide': 305} Link IDs: {'PTRANS': 12, 'TRANS': 292} Chain breaks: 1 bond proxies already assigned to first conformer: 2448 Chain: "D" Number of atoms: 2494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2494 Classifications: {'peptide': 317} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 304} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "E" Number of atoms: 1250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 1250 Classifications: {'RNA': 59} Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 11, 'rna3p_pur': 22, 'rna3p_pyr': 22} Link IDs: {'rna2p': 15, 'rna3p': 43} Chain: "F" Number of atoms: 1441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 1441 Classifications: {'RNA': 68} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 7, 'rna3p_pur': 27, 'rna3p_pyr': 28} Link IDs: {'rna2p': 13, 'rna3p': 54} Chain: "G" Number of atoms: 548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 548 Classifications: {'DNA': 27} Link IDs: {'rna3p': 26} Chain breaks: 1 Chain: "H" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 557 Classifications: {'DNA': 27} Link IDs: {'rna3p': 26} Chain: "I" Number of atoms: 587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 587 Classifications: {'DNA': 29} Link IDs: {'rna3p': 28} Chain breaks: 1 Chain: "J" Number of atoms: 602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 602 Classifications: {'DNA': 29} Link IDs: {'rna3p': 28} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 3 residue: pdb=" N AGLN A 139 " occ=0.50 ... (16 atoms not shown) pdb=" NE2BGLN A 139 " occ=0.50 residue: pdb=" N AGLN B 139 " occ=0.50 ... (16 atoms not shown) pdb=" NE2BGLN B 139 " occ=0.50 residue: pdb=" N AGLN C 139 " occ=0.50 ... (16 atoms not shown) pdb=" NE2BGLN C 139 " occ=0.50 Time building chain proxies: 4.57, per 1000 atoms: 0.31 Number of scatterers: 14846 At special positions: 0 Unit cell: (118.413, 125.053, 117.307, 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 48 16.00 P 239 15.00 Mg 2 11.99 O 3333 8.00 N 2743 7.00 C 8481 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.26 Conformation dependent library (CDL) restraints added in 670.1 milliseconds 2486 Ramachandran restraints generated. 1243 Oldfield, 0 Emsley, 1243 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2338 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 8 sheets defined 68.7% alpha, 9.3% beta 91 base pairs and 140 stacking pairs defined. Time for finding SS restraints: 1.90 Creating SS restraints... Processing helix chain 'A' and resid 36 through 49 Processing helix chain 'A' and resid 66 through 77 Processing helix chain 'A' and resid 84 through 95 removed outlier: 3.574A pdb=" N GLY A 88 " --> pdb=" O ASN A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 117 Processing helix chain 'A' and resid 125 through 155 removed outlier: 3.550A pdb=" N THR A 152 " --> pdb=" O GLU A 148 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N GLU A 153 " --> pdb=" O LEU A 149 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N THR A 154 " --> pdb=" O ASN A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 158 No H-bonds generated for 'chain 'A' and resid 156 through 158' Processing helix chain 'A' and resid 159 through 188 removed outlier: 3.839A pdb=" N ASP A 188 " --> pdb=" O LEU A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 200 Processing helix chain 'A' and resid 205 through 217 removed outlier: 3.531A pdb=" N ALA A 210 " --> pdb=" O GLU A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 233 removed outlier: 3.768A pdb=" N PHE A 228 " --> pdb=" O HIS A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 262 removed outlier: 3.642A pdb=" N ALA A 262 " --> pdb=" O SER A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 274 Processing helix chain 'A' and resid 274 through 288 Processing helix chain 'A' and resid 290 through 313 Processing helix chain 'A' and resid 317 through 321 removed outlier: 3.665A pdb=" N ARG A 320 " --> pdb=" O ASP A 317 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 50 Processing helix chain 'B' and resid 66 through 77 Processing helix chain 'B' and resid 84 through 96 removed outlier: 3.613A pdb=" N GLY B 88 " --> pdb=" O ASN B 84 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLY B 96 " --> pdb=" O ALA B 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 117 Processing helix chain 'B' and resid 125 through 155 removed outlier: 3.736A pdb=" N GLU B 153 " --> pdb=" O LEU B 149 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N THR B 154 " --> pdb=" O ASN B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 188 removed outlier: 3.613A pdb=" N ASP B 188 " --> pdb=" O LEU B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 188 through 200 Processing helix chain 'B' and resid 205 through 217 Processing helix chain 'B' and resid 224 through 232 removed outlier: 3.750A pdb=" N PHE B 228 " --> pdb=" O HIS B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 256 through 263 Processing helix chain 'B' and resid 263 through 274 Processing helix chain 'B' and resid 274 through 287 removed outlier: 3.565A pdb=" N ASN B 287 " --> pdb=" O ARG B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 313 Processing helix chain 'B' and resid 317 through 321 Processing helix chain 'C' and resid 36 through 50 Processing helix chain 'C' and resid 66 through 77 Processing helix chain 'C' and resid 84 through 95 removed outlier: 3.643A pdb=" N GLY C 88 " --> pdb=" O ASN C 84 " (cutoff:3.500A) Processing helix chain 'C' and resid 101 through 117 Processing helix chain 'C' and resid 125 through 155 removed outlier: 3.527A pdb=" N THR C 152 " --> pdb=" O GLU C 148 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLU C 153 " --> pdb=" O LEU C 149 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N THR C 154 " --> pdb=" O ASN C 150 " (cutoff:3.500A) Processing helix chain 'C' and resid 159 through 188 removed outlier: 3.633A pdb=" N ASP C 188 " --> pdb=" O LEU C 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 188 through 200 Processing helix chain 'C' and resid 205 through 217 Processing helix chain 'C' and resid 224 through 232 removed outlier: 3.677A pdb=" N PHE C 228 " --> pdb=" O HIS C 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 256 through 262 removed outlier: 3.566A pdb=" N ALA C 262 " --> pdb=" O SER C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 263 through 274 Processing helix chain 'C' and resid 274 through 288 Processing helix chain 'C' and resid 290 through 313 Processing helix chain 'C' and resid 317 through 321 removed outlier: 3.613A pdb=" N ARG C 320 " --> pdb=" O ASP C 317 " (cutoff:3.500A) Processing helix chain 'D' and resid 36 through 50 Processing helix chain 'D' and resid 66 through 77 Processing helix chain 'D' and resid 84 through 95 removed outlier: 3.794A pdb=" N GLY D 88 " --> pdb=" O ASN D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 105 through 117 Processing helix chain 'D' and resid 125 through 155 removed outlier: 4.086A pdb=" N GLU D 153 " --> pdb=" O LEU D 149 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N THR D 154 " --> pdb=" O ASN D 150 " (cutoff:3.500A) Processing helix chain 'D' and resid 159 through 188 removed outlier: 3.649A pdb=" N ASP D 188 " --> pdb=" O LEU D 184 " (cutoff:3.500A) Processing helix chain 'D' and resid 188 through 199 Processing helix chain 'D' and resid 205 through 217 Processing helix chain 'D' and resid 224 through 232 removed outlier: 3.610A pdb=" N PHE D 228 " --> pdb=" O HIS D 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 256 through 263 removed outlier: 3.558A pdb=" N LEU D 263 " --> pdb=" O LEU D 259 " (cutoff:3.500A) Processing helix chain 'D' and resid 263 through 274 Processing helix chain 'D' and resid 274 through 288 Processing helix chain 'D' and resid 290 through 313 Processing helix chain 'D' and resid 317 through 321 removed outlier: 3.505A pdb=" N ARG D 320 " --> pdb=" O ASP D 317 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 34 removed outlier: 6.522A pdb=" N HIS A 6 " --> pdb=" O HIS A 56 " (cutoff:3.500A) removed outlier: 7.995A pdb=" N CYS A 58 " --> pdb=" O HIS A 6 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ILE A 8 " --> pdb=" O CYS A 58 " (cutoff:3.500A) removed outlier: 8.527A pdb=" N GLU A 60 " --> pdb=" O ILE A 8 " (cutoff:3.500A) removed outlier: 8.336A pdb=" N ILE A 10 " --> pdb=" O GLU A 60 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 28 through 34 removed outlier: 6.831A pdb=" N HIS B 6 " --> pdb=" O HIS B 56 " (cutoff:3.500A) removed outlier: 8.074A pdb=" N CYS B 58 " --> pdb=" O HIS B 6 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N ILE B 8 " --> pdb=" O CYS B 58 " (cutoff:3.500A) removed outlier: 8.587A pdb=" N GLU B 60 " --> pdb=" O ILE B 8 " (cutoff:3.500A) removed outlier: 8.471A pdb=" N ILE B 10 " --> pdb=" O GLU B 60 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N ALA B 55 " --> pdb=" O ILE B 79 " (cutoff:3.500A) removed outlier: 7.953A pdb=" N SER B 81 " --> pdb=" O ALA B 55 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N ILE B 57 " --> pdb=" O SER B 81 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N ILE B 83 " --> pdb=" O ILE B 57 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ILE B 59 " --> pdb=" O ILE B 83 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 236 through 237 removed outlier: 3.751A pdb=" N ARG B 250 " --> pdb=" O ARG B 237 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 240 through 241 Processing sheet with id=AA5, first strand: chain 'C' and resid 28 through 34 removed outlier: 6.526A pdb=" N HIS C 6 " --> pdb=" O HIS C 56 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N CYS C 58 " --> pdb=" O HIS C 6 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N ILE C 8 " --> pdb=" O CYS C 58 " (cutoff:3.500A) removed outlier: 8.635A pdb=" N GLU C 60 " --> pdb=" O ILE C 8 " (cutoff:3.500A) removed outlier: 8.330A pdb=" N ILE C 10 " --> pdb=" O GLU C 60 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 28 through 34 removed outlier: 6.722A pdb=" N HIS D 6 " --> pdb=" O HIS D 56 " (cutoff:3.500A) removed outlier: 8.018A pdb=" N CYS D 58 " --> pdb=" O HIS D 6 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N ILE D 8 " --> pdb=" O CYS D 58 " (cutoff:3.500A) removed outlier: 8.759A pdb=" N GLU D 60 " --> pdb=" O ILE D 8 " (cutoff:3.500A) removed outlier: 8.390A pdb=" N ILE D 10 " --> pdb=" O GLU D 60 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 236 through 237 removed outlier: 3.755A pdb=" N ARG D 250 " --> pdb=" O ARG D 237 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 240 through 241 677 hydrogen bonds defined for protein. 2004 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 228 hydrogen bonds 450 hydrogen bond angles 0 basepair planarities 91 basepair parallelities 140 stacking parallelities Total time for adding SS restraints: 2.56 Time building geometry restraints manager: 1.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3274 1.34 - 1.46: 5506 1.46 - 1.58: 6286 1.58 - 1.69: 470 1.69 - 1.81: 84 Bond restraints: 15620 Sorted by residual: bond pdb=" C ILE B 201 " pdb=" N PRO B 202 " ideal model delta sigma weight residual 1.333 1.358 -0.025 1.01e-02 9.80e+03 6.09e+00 bond pdb=" C ILE A 201 " pdb=" N PRO A 202 " ideal model delta sigma weight residual 1.333 1.358 -0.024 1.01e-02 9.80e+03 5.81e+00 bond pdb=" P DT G 10 " pdb=" O5' DT G 10 " ideal model delta sigma weight residual 1.593 1.617 -0.024 1.00e-02 1.00e+04 5.80e+00 bond pdb=" P DG I 5 " pdb=" O5' DG I 5 " ideal model delta sigma weight residual 1.593 1.617 -0.024 1.00e-02 1.00e+04 5.76e+00 bond pdb=" C ILE C 201 " pdb=" N PRO C 202 " ideal model delta sigma weight residual 1.333 1.358 -0.024 1.01e-02 9.80e+03 5.67e+00 ... (remaining 15615 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.48: 17480 1.48 - 2.96: 3836 2.96 - 4.43: 742 4.43 - 5.91: 87 5.91 - 7.39: 15 Bond angle restraints: 22160 Sorted by residual: angle pdb=" O4' U F 159 " pdb=" C1' U F 159 " pdb=" N1 U F 159 " ideal model delta sigma weight residual 108.20 112.76 -4.56 8.00e-01 1.56e+00 3.24e+01 angle pdb=" C4' U F 159 " pdb=" O4' U F 159 " pdb=" C1' U F 159 " ideal model delta sigma weight residual 109.70 105.79 3.91 7.00e-01 2.04e+00 3.12e+01 angle pdb=" C3' C E 42 " pdb=" C2' C E 42 " pdb=" C1' C E 42 " ideal model delta sigma weight residual 101.30 105.10 -3.80 7.00e-01 2.04e+00 2.94e+01 angle pdb=" O4' DG H 15 " pdb=" C4' DG H 15 " pdb=" C3' DG H 15 " ideal model delta sigma weight residual 106.00 103.03 2.97 6.00e-01 2.78e+00 2.45e+01 angle pdb=" O4' DC H 19 " pdb=" C4' DC H 19 " pdb=" C3' DC H 19 " ideal model delta sigma weight residual 106.00 103.08 2.92 6.00e-01 2.78e+00 2.38e+01 ... (remaining 22155 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.43: 8684 34.43 - 68.86: 630 68.86 - 103.29: 52 103.29 - 137.72: 0 137.72 - 172.15: 1 Dihedral angle restraints: 9367 sinusoidal: 5753 harmonic: 3614 Sorted by residual: dihedral pdb=" O4' U F 159 " pdb=" C1' U F 159 " pdb=" N1 U F 159 " pdb=" C2 U F 159 " ideal model delta sinusoidal sigma weight residual 232.00 59.85 172.15 1 1.70e+01 3.46e-03 6.61e+01 dihedral pdb=" C5' U E 86 " pdb=" C4' U E 86 " pdb=" C3' U E 86 " pdb=" O3' U E 86 " ideal model delta sinusoidal sigma weight residual 147.00 102.18 44.82 1 8.00e+00 1.56e-02 4.36e+01 dihedral pdb=" O4' U E 86 " pdb=" C4' U E 86 " pdb=" C3' U E 86 " pdb=" C2' U E 86 " ideal model delta sinusoidal sigma weight residual 24.00 -16.12 40.12 1 8.00e+00 1.56e-02 3.53e+01 ... (remaining 9364 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.129: 2330 0.129 - 0.259: 234 0.259 - 0.388: 0 0.388 - 0.517: 0 0.517 - 0.647: 6 Chirality restraints: 2570 Sorted by residual: chirality pdb=" P DG J 12 " pdb=" OP1 DG J 12 " pdb=" OP2 DG J 12 " pdb=" O5' DG J 12 " both_signs ideal model delta sigma weight residual True 2.34 -2.98 -0.65 2.00e-01 2.50e+01 1.05e+01 chirality pdb=" P DA H 3 " pdb=" OP1 DA H 3 " pdb=" OP2 DA H 3 " pdb=" O5' DA H 3 " both_signs ideal model delta sigma weight residual True 2.34 -2.98 -0.65 2.00e-01 2.50e+01 1.04e+01 chirality pdb=" P DG I 5 " pdb=" OP1 DG I 5 " pdb=" OP2 DG I 5 " pdb=" O5' DG I 5 " both_signs ideal model delta sigma weight residual True 2.34 -2.96 -0.63 2.00e-01 2.50e+01 9.82e+00 ... (remaining 2567 not shown) Planarity restraints: 1986 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A F 157 " -0.035 2.00e-02 2.50e+03 1.42e-02 5.55e+00 pdb=" N9 A F 157 " 0.021 2.00e-02 2.50e+03 pdb=" C8 A F 157 " 0.008 2.00e-02 2.50e+03 pdb=" N7 A F 157 " 0.003 2.00e-02 2.50e+03 pdb=" C5 A F 157 " 0.006 2.00e-02 2.50e+03 pdb=" C6 A F 157 " -0.006 2.00e-02 2.50e+03 pdb=" N6 A F 157 " -0.016 2.00e-02 2.50e+03 pdb=" N1 A F 157 " -0.001 2.00e-02 2.50e+03 pdb=" C2 A F 157 " 0.003 2.00e-02 2.50e+03 pdb=" N3 A F 157 " 0.008 2.00e-02 2.50e+03 pdb=" C4 A F 157 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U F 159 " 0.027 2.00e-02 2.50e+03 1.39e-02 4.32e+00 pdb=" N1 U F 159 " -0.026 2.00e-02 2.50e+03 pdb=" C2 U F 159 " -0.001 2.00e-02 2.50e+03 pdb=" O2 U F 159 " -0.010 2.00e-02 2.50e+03 pdb=" N3 U F 159 " 0.010 2.00e-02 2.50e+03 pdb=" C4 U F 159 " 0.005 2.00e-02 2.50e+03 pdb=" O4 U F 159 " 0.005 2.00e-02 2.50e+03 pdb=" C5 U F 159 " -0.002 2.00e-02 2.50e+03 pdb=" C6 U F 159 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA I 27 " 0.027 2.00e-02 2.50e+03 1.22e-02 4.12e+00 pdb=" N9 DA I 27 " -0.028 2.00e-02 2.50e+03 pdb=" C8 DA I 27 " -0.004 2.00e-02 2.50e+03 pdb=" N7 DA I 27 " 0.002 2.00e-02 2.50e+03 pdb=" C5 DA I 27 " 0.001 2.00e-02 2.50e+03 pdb=" C6 DA I 27 " 0.003 2.00e-02 2.50e+03 pdb=" N6 DA I 27 " 0.008 2.00e-02 2.50e+03 pdb=" N1 DA I 27 " 0.002 2.00e-02 2.50e+03 pdb=" C2 DA I 27 " -0.003 2.00e-02 2.50e+03 pdb=" N3 DA I 27 " -0.005 2.00e-02 2.50e+03 pdb=" C4 DA I 27 " -0.002 2.00e-02 2.50e+03 ... (remaining 1983 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.27: 14 2.27 - 2.92: 5194 2.92 - 3.58: 21613 3.58 - 4.24: 39550 4.24 - 4.90: 60383 Nonbonded interactions: 126754 Sorted by model distance: nonbonded pdb=" OG SER D 241 " pdb=" P DA G 26 " model vdw 1.608 3.400 nonbonded pdb=" OG SER B 241 " pdb=" P DT I 21 " model vdw 1.608 3.400 nonbonded pdb=" OE2 GLU A 60 " pdb="MG MG A 401 " model vdw 1.884 2.170 nonbonded pdb="MG MG C 401 " pdb=" O HOH C 501 " model vdw 1.922 2.170 nonbonded pdb=" O3' DT G 25 " pdb="MG MG A 401 " model vdw 2.066 2.170 ... (remaining 126749 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 5 through 99 or (resid 100 and (name N or name CA or name \ C or name O or name CB )) or resid 101 through 138 or resid 140 through 321)) selection = (chain 'B' and (resid 5 through 138 or resid 140 through 238 or resid 251 throug \ h 321)) selection = (chain 'C' and (resid 5 through 99 or (resid 100 and (name N or name CA or name \ C or name O or name CB )) or resid 101 through 138 or resid 140 through 321)) selection = (chain 'D' and (resid 5 through 138 or resid 140 through 238 or resid 251 throug \ h 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=0.50 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: 1.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 17.350 Find NCS groups from input model: 0.270 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:6.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8846 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 : 0.008 0.039 15620 Z= 0.547 Angle : 1.286 7.391 22160 Z= 0.882 Chirality : 0.077 0.647 2570 Planarity : 0.004 0.052 1986 Dihedral : 19.845 172.147 7029 Min Nonbonded Distance : 1.608 Molprobity Statistics. All-atom Clashscore : 0.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Rotamer: Outliers : 0.49 % Allowed : 2.07 % Favored : 97.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.68 (0.20), residues: 1243 helix: -0.83 (0.15), residues: 805 sheet: -1.25 (0.36), residues: 162 loop : -1.19 (0.32), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.025 0.002 ARG D 238 TYR 0.017 0.002 TYR D 307 PHE 0.017 0.002 PHE C 228 TRP 0.021 0.005 TRP A 169 HIS 0.010 0.002 HIS D 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00812 / 0.55 (15620) covalent geometry : angle 1.28600 / 0.88 (22160) hydrogen bonds : bond 0.22277 / 15.17 ( 905) hydrogen bonds : angle 6.95784 / 5.05 ( 2454) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2486 Ramachandran restraints generated. 1243 Oldfield, 0 Emsley, 1243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2486 Ramachandran restraints generated. 1243 Oldfield, 0 Emsley, 1243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 91 time to evaluate : 0.464 Fit side-chains revert: symmetry clash REVERT: A 268 MET cc_start: 0.8680 (ttp) cc_final: 0.8458 (ttp) REVERT: A 299 MET cc_start: 0.9323 (mtp) cc_final: 0.9112 (mtp) REVERT: B 99 ASN cc_start: 0.8400 (m-40) cc_final: 0.8060 (m-40) REVERT: B 298 MET cc_start: 0.9398 (tpt) cc_final: 0.8624 (tpt) REVERT: C 268 MET cc_start: 0.8765 (mtm) cc_final: 0.8562 (mtm) REVERT: D 108 MET cc_start: 0.8901 (tpp) cc_final: 0.8671 (mmt) REVERT: D 239 TYR cc_start: 0.9156 (t80) cc_final: 0.8926 (t80) REVERT: D 268 MET cc_start: 0.8979 (ttp) cc_final: 0.8776 (ttm) outliers start: 5 outliers final: 0 residues processed: 94 average time/residue: 0.9423 time to fit residues: 94.8462 Evaluate side-chains 60 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.7980 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 30.0000 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 20.0000 chunk 91 optimal weight: 0.9990 chunk 55 optimal weight: 0.6980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 287 ASN C 93 GLN C 287 ASN D 93 GLN D 99 ASN D 287 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.078701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2725 r_free = 0.2725 target = 0.052214 restraints weight = 64815.376| |-----------------------------------------------------------------------------| r_work (start): 0.2731 rms_B_bonded: 2.82 r_work: 0.2541 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.2541 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2537 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2537 r_free = 0.2537 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2536 r_free = 0.2536 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.2536 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.1514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 15620 Z= 0.173 Angle : 0.616 6.877 22160 Z= 0.368 Chirality : 0.043 0.343 2570 Planarity : 0.005 0.053 1986 Dihedral : 21.865 164.170 4598 Min Nonbonded Distance : 1.779 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Rotamer: Outliers : 0.49 % Allowed : 4.84 % Favored : 94.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.49 (0.23), residues: 1243 helix: 1.93 (0.17), residues: 808 sheet: -0.78 (0.36), residues: 159 loop : -0.63 (0.35), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG A 261 TYR 0.018 0.002 TYR A 215 PHE 0.010 0.001 PHE A 280 TRP 0.019 0.003 TRP D 46 HIS 0.005 0.001 HIS A 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.17 (15620) covalent geometry : angle 0.61608 / 0.37 (22160) hydrogen bonds : bond 0.06732 / 4.53 ( 905) hydrogen bonds : angle 4.22102 / 3.06 ( 2454) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2486 Ramachandran restraints generated. 1243 Oldfield, 0 Emsley, 1243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2486 Ramachandran restraints generated. 1243 Oldfield, 0 Emsley, 1243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 63 time to evaluate : 0.458 Fit side-chains revert: symmetry clash REVERT: A 299 MET cc_start: 0.9120 (mtp) cc_final: 0.8880 (mtp) REVERT: B 107 ARG cc_start: 0.8661 (ttt90) cc_final: 0.8394 (ttm110) REVERT: B 261 ARG cc_start: 0.8864 (OUTLIER) cc_final: 0.8464 (ttm-80) REVERT: B 298 MET cc_start: 0.9298 (tpt) cc_final: 0.8925 (tpt) REVERT: C 258 SER cc_start: 0.9361 (m) cc_final: 0.8911 (p) REVERT: D 108 MET cc_start: 0.8857 (tpp) cc_final: 0.8628 (mmt) REVERT: D 219 LYS cc_start: 0.9231 (mtpt) cc_final: 0.9030 (mtmm) REVERT: D 239 TYR cc_start: 0.9169 (t80) cc_final: 0.8911 (t80) REVERT: D 261 ARG cc_start: 0.8804 (OUTLIER) cc_final: 0.8321 (ttt-90) outliers start: 5 outliers final: 0 residues processed: 65 average time/residue: 0.8080 time to fit residues: 56.9717 Evaluate side-chains 62 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 60 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 261 ARG Chi-restraints excluded: chain D residue 261 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 79 optimal weight: 7.9990 chunk 56 optimal weight: 4.9990 chunk 121 optimal weight: 6.9990 chunk 82 optimal weight: 7.9990 chunk 72 optimal weight: 4.9990 chunk 39 optimal weight: 8.9990 chunk 18 optimal weight: 0.5980 chunk 99 optimal weight: 4.9990 chunk 2 optimal weight: 6.9990 chunk 135 optimal weight: 20.0000 chunk 125 optimal weight: 10.0000 overall best weight: 4.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 287 ASN B 93 GLN D 6 HIS D 99 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.075009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2647 r_free = 0.2647 target = 0.048532 restraints weight = 76051.095| |-----------------------------------------------------------------------------| r_work (start): 0.2602 rms_B_bonded: 3.00 r_work: 0.2399 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.2399 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2425 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2425 r_free = 0.2425 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2425 r_free = 0.2425 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2425 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8685 moved from start: 0.1850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.103 15620 Z= 0.331 Angle : 0.650 6.684 22160 Z= 0.367 Chirality : 0.046 0.164 2570 Planarity : 0.005 0.039 1986 Dihedral : 22.107 164.605 4598 Min Nonbonded Distance : 1.814 Molprobity Statistics. All-atom Clashscore : 2.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Rotamer: Outliers : 0.69 % Allowed : 5.53 % Favored : 93.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.95 (0.24), residues: 1243 helix: 2.36 (0.18), residues: 808 sheet: -0.79 (0.35), residues: 174 loop : -0.59 (0.36), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 261 TYR 0.019 0.002 TYR A 215 PHE 0.019 0.002 PHE C 316 TRP 0.020 0.003 TRP D 46 HIS 0.006 0.002 HIS A 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00721 / 0.33 (15620) covalent geometry : angle 0.64974 / 0.37 (22160) hydrogen bonds : bond 0.07254 / 4.86 ( 905) hydrogen bonds : angle 4.07092 / 2.97 ( 2454) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2486 Ramachandran restraints generated. 1243 Oldfield, 0 Emsley, 1243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2486 Ramachandran restraints generated. 1243 Oldfield, 0 Emsley, 1243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 61 time to evaluate : 0.454 Fit side-chains revert: symmetry clash REVERT: B 99 ASN cc_start: 0.8303 (m-40) cc_final: 0.7981 (m-40) REVERT: B 261 ARG cc_start: 0.8987 (OUTLIER) cc_final: 0.8670 (ttm-80) REVERT: B 298 MET cc_start: 0.9226 (tpt) cc_final: 0.8926 (tpt) REVERT: C 54 HIS cc_start: 0.8638 (m-70) cc_final: 0.8324 (m90) REVERT: C 304 GLN cc_start: 0.9054 (tt0) cc_final: 0.8794 (mt0) REVERT: D 99 ASN cc_start: 0.7862 (m-40) cc_final: 0.7619 (m-40) REVERT: D 261 ARG cc_start: 0.8859 (OUTLIER) cc_final: 0.8543 (ttm-80) outliers start: 7 outliers final: 0 residues processed: 65 average time/residue: 0.7432 time to fit residues: 52.7684 Evaluate side-chains 58 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 56 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 261 ARG Chi-restraints excluded: chain D residue 261 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 129 optimal weight: 10.0000 chunk 44 optimal weight: 0.7980 chunk 46 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 78 optimal weight: 0.8980 chunk 8 optimal weight: 0.8980 chunk 90 optimal weight: 2.9990 chunk 136 optimal weight: 10.0000 chunk 59 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 287 ASN B 93 GLN C 93 GLN C 287 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.078206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2732 r_free = 0.2732 target = 0.051800 restraints weight = 71856.585| |-----------------------------------------------------------------------------| r_work (start): 0.2686 rms_B_bonded: 2.95 r_work: 0.2491 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.2491 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2525 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2525 r_free = 0.2525 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2525 r_free = 0.2525 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2525 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 moved from start: 0.2171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15620 Z= 0.140 Angle : 0.503 5.158 22160 Z= 0.302 Chirality : 0.037 0.144 2570 Planarity : 0.004 0.037 1986 Dihedral : 22.062 167.140 4598 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Rotamer: Outliers : 0.59 % Allowed : 5.82 % Favored : 93.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.34 (0.24), residues: 1243 helix: 2.64 (0.18), residues: 808 sheet: -0.30 (0.39), residues: 151 loop : -0.67 (0.34), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 261 TYR 0.014 0.001 TYR A 215 PHE 0.010 0.001 PHE A 280 TRP 0.014 0.002 TRP D 46 HIS 0.004 0.001 HIS D 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.14 (15620) covalent geometry : angle 0.50286 / 0.30 (22160) hydrogen bonds : bond 0.05211 / 3.50 ( 905) hydrogen bonds : angle 3.77641 / 2.76 ( 2454) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2486 Ramachandran restraints generated. 1243 Oldfield, 0 Emsley, 1243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2486 Ramachandran restraints generated. 1243 Oldfield, 0 Emsley, 1243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 66 time to evaluate : 0.431 Fit side-chains revert: symmetry clash REVERT: A 298 MET cc_start: 0.9199 (tpt) cc_final: 0.8961 (tpt) REVERT: B 99 ASN cc_start: 0.8080 (m-40) cc_final: 0.7684 (m-40) REVERT: B 107 ARG cc_start: 0.8844 (ttt90) cc_final: 0.8449 (ttm-80) REVERT: C 54 HIS cc_start: 0.8600 (m-70) cc_final: 0.8316 (m90) REVERT: D 99 ASN cc_start: 0.7856 (m-40) cc_final: 0.7595 (m-40) outliers start: 6 outliers final: 0 residues processed: 68 average time/residue: 0.7758 time to fit residues: 57.4725 Evaluate side-chains 60 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 116 optimal weight: 5.9990 chunk 75 optimal weight: 3.9990 chunk 128 optimal weight: 10.0000 chunk 85 optimal weight: 6.9990 chunk 37 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 chunk 86 optimal weight: 0.8980 chunk 105 optimal weight: 0.7980 chunk 29 optimal weight: 6.9990 chunk 60 optimal weight: 2.9990 chunk 139 optimal weight: 20.0000 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 287 ASN B 93 GLN B 139 GLN A Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.076719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2690 r_free = 0.2690 target = 0.050051 restraints weight = 69731.367| |-----------------------------------------------------------------------------| r_work (start): 0.2645 rms_B_bonded: 2.93 r_work: 0.2447 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.2447 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2484 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2484 r_free = 0.2484 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2484 r_free = 0.2484 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2484 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8655 moved from start: 0.2250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 15620 Z= 0.197 Angle : 0.522 5.405 22160 Z= 0.304 Chirality : 0.039 0.152 2570 Planarity : 0.004 0.037 1986 Dihedral : 22.097 167.936 4598 Min Nonbonded Distance : 1.830 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Rotamer: Outliers : 0.59 % Allowed : 6.81 % Favored : 92.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.50 (0.24), residues: 1243 helix: 2.75 (0.18), residues: 808 sheet: -0.08 (0.39), residues: 147 loop : -0.65 (0.34), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 261 TYR 0.015 0.001 TYR D 215 PHE 0.013 0.002 PHE C 231 TRP 0.013 0.002 TRP D 46 HIS 0.004 0.001 HIS D 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00418 / 0.20 (15620) covalent geometry : angle 0.52164 / 0.30 (22160) hydrogen bonds : bond 0.05554 / 3.73 ( 905) hydrogen bonds : angle 3.72745 / 2.72 ( 2454) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2486 Ramachandran restraints generated. 1243 Oldfield, 0 Emsley, 1243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2486 Ramachandran restraints generated. 1243 Oldfield, 0 Emsley, 1243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 61 time to evaluate : 0.459 Fit side-chains revert: symmetry clash REVERT: A 298 MET cc_start: 0.9220 (tpt) cc_final: 0.8915 (tpt) REVERT: B 99 ASN cc_start: 0.8131 (m-40) cc_final: 0.7734 (m-40) REVERT: B 107 ARG cc_start: 0.8894 (ttt90) cc_final: 0.8464 (ttm-80) REVERT: C 54 HIS cc_start: 0.8614 (m-70) cc_final: 0.8345 (m90) REVERT: D 99 ASN cc_start: 0.7833 (m-40) cc_final: 0.7562 (m-40) REVERT: D 261 ARG cc_start: 0.8850 (OUTLIER) cc_final: 0.8515 (ttm-80) outliers start: 6 outliers final: 2 residues processed: 64 average time/residue: 0.7651 time to fit residues: 53.4373 Evaluate side-chains 62 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 59 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 157 GLU Chi-restraints excluded: chain C residue 191 MET Chi-restraints excluded: chain D residue 261 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 31 optimal weight: 7.9990 chunk 51 optimal weight: 5.9990 chunk 137 optimal weight: 20.0000 chunk 17 optimal weight: 0.9980 chunk 71 optimal weight: 3.9990 chunk 97 optimal weight: 0.5980 chunk 115 optimal weight: 2.9990 chunk 57 optimal weight: 4.9990 chunk 131 optimal weight: 10.0000 chunk 114 optimal weight: 2.9990 chunk 122 optimal weight: 20.0000 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 287 ASN B 93 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.076732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2690 r_free = 0.2690 target = 0.049987 restraints weight = 72345.121| |-----------------------------------------------------------------------------| r_work (start): 0.2641 rms_B_bonded: 3.00 r_work: 0.2441 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.2441 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2483 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2483 r_free = 0.2483 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2483 r_free = 0.2483 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2483 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8659 moved from start: 0.2342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 15620 Z= 0.188 Angle : 0.512 7.819 22160 Z= 0.299 Chirality : 0.038 0.159 2570 Planarity : 0.004 0.037 1986 Dihedral : 22.115 167.696 4598 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Rotamer: Outliers : 0.59 % Allowed : 7.60 % Favored : 91.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.55 (0.24), residues: 1243 helix: 2.78 (0.18), residues: 808 sheet: -0.04 (0.39), residues: 148 loop : -0.62 (0.35), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 261 TYR 0.014 0.001 TYR A 215 PHE 0.011 0.002 PHE D 112 TRP 0.013 0.002 TRP D 46 HIS 0.004 0.001 HIS D 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.19 (15620) covalent geometry : angle 0.51213 / 0.30 (22160) hydrogen bonds : bond 0.05314 / 3.57 ( 905) hydrogen bonds : angle 3.69139 / 2.69 ( 2454) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2486 Ramachandran restraints generated. 1243 Oldfield, 0 Emsley, 1243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2486 Ramachandran restraints generated. 1243 Oldfield, 0 Emsley, 1243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 61 time to evaluate : 0.449 Fit side-chains revert: symmetry clash REVERT: A 298 MET cc_start: 0.9204 (tpt) cc_final: 0.8935 (tpt) REVERT: B 99 ASN cc_start: 0.8069 (m-40) cc_final: 0.7650 (m-40) REVERT: B 107 ARG cc_start: 0.8876 (ttt90) cc_final: 0.8477 (ttm-80) REVERT: C 54 HIS cc_start: 0.8661 (m-70) cc_final: 0.8400 (m90) REVERT: D 99 ASN cc_start: 0.7817 (m-40) cc_final: 0.7545 (m-40) REVERT: D 206 GLU cc_start: 0.7854 (mp0) cc_final: 0.7612 (mm-30) REVERT: D 261 ARG cc_start: 0.8798 (OUTLIER) cc_final: 0.8538 (ttm-80) outliers start: 6 outliers final: 2 residues processed: 64 average time/residue: 0.7583 time to fit residues: 53.0147 Evaluate side-chains 63 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 60 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 157 GLU Chi-restraints excluded: chain C residue 191 MET Chi-restraints excluded: chain D residue 261 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 22 optimal weight: 2.9990 chunk 29 optimal weight: 6.9990 chunk 60 optimal weight: 6.9990 chunk 107 optimal weight: 3.9990 chunk 93 optimal weight: 8.9990 chunk 33 optimal weight: 6.9990 chunk 75 optimal weight: 3.9990 chunk 92 optimal weight: 4.9990 chunk 135 optimal weight: 20.0000 chunk 122 optimal weight: 20.0000 chunk 130 optimal weight: 30.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 287 ASN B 93 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.074771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2647 r_free = 0.2647 target = 0.048241 restraints weight = 72256.997| |-----------------------------------------------------------------------------| r_work (start): 0.2607 rms_B_bonded: 2.93 r_work: 0.2408 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.2408 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2437 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2437 r_free = 0.2437 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2437 r_free = 0.2437 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2437 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8688 moved from start: 0.2318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.097 15620 Z= 0.335 Angle : 0.611 8.495 22160 Z= 0.340 Chirality : 0.044 0.183 2570 Planarity : 0.005 0.039 1986 Dihedral : 22.252 165.917 4598 Min Nonbonded Distance : 1.841 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Rotamer: Outliers : 0.59 % Allowed : 7.60 % Favored : 91.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.41 (0.24), residues: 1243 helix: 2.67 (0.18), residues: 808 sheet: -0.12 (0.39), residues: 148 loop : -0.64 (0.35), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 260 TYR 0.016 0.002 TYR D 215 PHE 0.018 0.002 PHE C 316 TRP 0.015 0.002 TRP C 46 HIS 0.006 0.001 HIS D 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00740 / 0.34 (15620) covalent geometry : angle 0.61066 / 0.34 (22160) hydrogen bonds : bond 0.06472 / 4.35 ( 905) hydrogen bonds : angle 3.85425 / 2.81 ( 2454) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2486 Ramachandran restraints generated. 1243 Oldfield, 0 Emsley, 1243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2486 Ramachandran restraints generated. 1243 Oldfield, 0 Emsley, 1243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 59 time to evaluate : 0.472 Fit side-chains revert: symmetry clash REVERT: B 99 ASN cc_start: 0.8217 (m-40) cc_final: 0.7836 (m-40) REVERT: C 54 HIS cc_start: 0.8683 (m-70) cc_final: 0.8432 (m90) REVERT: D 99 ASN cc_start: 0.7785 (m-40) cc_final: 0.7494 (m-40) REVERT: D 261 ARG cc_start: 0.8905 (OUTLIER) cc_final: 0.8549 (ttm-80) outliers start: 6 outliers final: 3 residues processed: 62 average time/residue: 0.7202 time to fit residues: 48.8808 Evaluate side-chains 61 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 57 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 191 MET Chi-restraints excluded: chain C residue 258 SER Chi-restraints excluded: chain D residue 191 MET Chi-restraints excluded: chain D residue 261 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 49 optimal weight: 0.9980 chunk 136 optimal weight: 10.0000 chunk 66 optimal weight: 2.9990 chunk 104 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 128 optimal weight: 10.0000 chunk 67 optimal weight: 0.6980 chunk 132 optimal weight: 10.0000 chunk 65 optimal weight: 4.9990 chunk 41 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 287 ASN B 93 GLN C 93 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.077323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2704 r_free = 0.2704 target = 0.050325 restraints weight = 96378.440| |-----------------------------------------------------------------------------| r_work (start): 0.2655 rms_B_bonded: 3.35 r_work: 0.2446 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.2446 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2488 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2488 r_free = 0.2488 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2488 r_free = 0.2488 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2488 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8642 moved from start: 0.2487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15620 Z= 0.140 Angle : 0.493 8.777 22160 Z= 0.292 Chirality : 0.036 0.158 2570 Planarity : 0.004 0.037 1986 Dihedral : 22.176 168.339 4598 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Rotamer: Outliers : 0.49 % Allowed : 8.00 % Favored : 91.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.63 (0.24), residues: 1243 helix: 2.84 (0.18), residues: 807 sheet: 0.06 (0.40), residues: 148 loop : -0.61 (0.35), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 261 TYR 0.013 0.001 TYR A 215 PHE 0.011 0.001 PHE A 280 TRP 0.014 0.002 TRP D 46 HIS 0.003 0.001 HIS B 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.14 (15620) covalent geometry : angle 0.49323 / 0.29 (22160) hydrogen bonds : bond 0.04993 / 3.35 ( 905) hydrogen bonds : angle 3.66036 / 2.67 ( 2454) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2486 Ramachandran restraints generated. 1243 Oldfield, 0 Emsley, 1243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2486 Ramachandran restraints generated. 1243 Oldfield, 0 Emsley, 1243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 62 time to evaluate : 0.436 Fit side-chains revert: symmetry clash REVERT: B 107 ARG cc_start: 0.8850 (ttt90) cc_final: 0.8471 (ttm-80) REVERT: C 54 HIS cc_start: 0.8741 (m-70) cc_final: 0.8498 (m90) REVERT: D 99 ASN cc_start: 0.7756 (m-40) cc_final: 0.7485 (m-40) outliers start: 5 outliers final: 2 residues processed: 64 average time/residue: 0.6956 time to fit residues: 48.6481 Evaluate side-chains 62 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 60 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 191 MET Chi-restraints excluded: chain C residue 258 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 52 optimal weight: 2.9990 chunk 27 optimal weight: 4.9990 chunk 14 optimal weight: 0.5980 chunk 11 optimal weight: 3.9990 chunk 127 optimal weight: 20.0000 chunk 83 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 117 optimal weight: 1.9990 chunk 111 optimal weight: 2.9990 chunk 6 optimal weight: 0.7980 chunk 25 optimal weight: 0.7980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 287 ASN B 93 GLN C 93 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.077832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2728 r_free = 0.2728 target = 0.051377 restraints weight = 78899.268| |-----------------------------------------------------------------------------| r_work (start): 0.2684 rms_B_bonded: 3.07 r_work: 0.2486 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.2486 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2522 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2522 r_free = 0.2522 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2522 r_free = 0.2522 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2522 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.2626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 15620 Z= 0.141 Angle : 0.481 8.757 22160 Z= 0.283 Chirality : 0.036 0.152 2570 Planarity : 0.004 0.036 1986 Dihedral : 22.104 171.595 4598 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % Rotamer: Outliers : 0.39 % Allowed : 8.00 % Favored : 91.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.76 (0.24), residues: 1243 helix: 2.95 (0.18), residues: 807 sheet: 0.12 (0.40), residues: 150 loop : -0.60 (0.35), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 261 TYR 0.014 0.001 TYR D 215 PHE 0.011 0.001 PHE B 112 TRP 0.012 0.001 TRP A 276 HIS 0.002 0.001 HIS A 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.14 (15620) covalent geometry : angle 0.48097 / 0.28 (22160) hydrogen bonds : bond 0.04749 / 3.19 ( 905) hydrogen bonds : angle 3.57452 / 2.61 ( 2454) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2486 Ramachandran restraints generated. 1243 Oldfield, 0 Emsley, 1243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2486 Ramachandran restraints generated. 1243 Oldfield, 0 Emsley, 1243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 65 time to evaluate : 0.400 Fit side-chains revert: symmetry clash REVERT: B 107 ARG cc_start: 0.8854 (ttt90) cc_final: 0.8478 (ttm-80) REVERT: C 54 HIS cc_start: 0.8705 (m-70) cc_final: 0.8468 (m90) REVERT: D 99 ASN cc_start: 0.7699 (m-40) cc_final: 0.7426 (m-40) REVERT: D 304 GLN cc_start: 0.9187 (tt0) cc_final: 0.8854 (mt0) outliers start: 4 outliers final: 3 residues processed: 66 average time/residue: 0.6100 time to fit residues: 43.9105 Evaluate side-chains 66 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 63 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 191 MET Chi-restraints excluded: chain C residue 258 SER Chi-restraints excluded: chain D residue 191 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 121 optimal weight: 6.9990 chunk 109 optimal weight: 6.9990 chunk 59 optimal weight: 0.7980 chunk 4 optimal weight: 6.9990 chunk 66 optimal weight: 9.9990 chunk 90 optimal weight: 5.9990 chunk 1 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 82 optimal weight: 3.9990 chunk 123 optimal weight: 10.0000 overall best weight: 2.1586 ------------------------------------------------------------------------------- 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 = 0.3246 r_free = 0.3246 target = 0.077018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2707 r_free = 0.2707 target = 0.050658 restraints weight = 62136.538| |-----------------------------------------------------------------------------| r_work (start): 0.2662 rms_B_bonded: 2.79 r_work: 0.2468 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2468 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2510 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2510 r_free = 0.2510 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2510 r_free = 0.2510 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2510 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.2594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 15620 Z= 0.181 Angle : 0.500 8.310 22160 Z= 0.291 Chirality : 0.037 0.165 2570 Planarity : 0.004 0.036 1986 Dihedral : 22.129 169.491 4598 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % Rotamer: Outliers : 0.30 % Allowed : 8.69 % Favored : 91.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.78 (0.24), residues: 1243 helix: 2.96 (0.18), residues: 806 sheet: 0.13 (0.39), residues: 150 loop : -0.58 (0.36), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 261 TYR 0.012 0.001 TYR D 307 PHE 0.012 0.002 PHE D 112 TRP 0.012 0.002 TRP C 46 HIS 0.004 0.001 HIS A 145 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.18 (15620) covalent geometry : angle 0.49992 / 0.29 (22160) hydrogen bonds : bond 0.05036 / 3.39 ( 905) hydrogen bonds : angle 3.60854 / 2.63 ( 2454) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2486 Ramachandran restraints generated. 1243 Oldfield, 0 Emsley, 1243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2486 Ramachandran restraints generated. 1243 Oldfield, 0 Emsley, 1243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 62 time to evaluate : 0.439 Fit side-chains revert: symmetry clash REVERT: A 144 MET cc_start: 0.9191 (ttm) cc_final: 0.8921 (mtp) REVERT: B 107 ARG cc_start: 0.8862 (ttt90) cc_final: 0.8473 (ttm-80) REVERT: C 54 HIS cc_start: 0.8709 (m-70) cc_final: 0.8466 (m90) REVERT: D 99 ASN cc_start: 0.7704 (m-40) cc_final: 0.7429 (m-40) outliers start: 3 outliers final: 3 residues processed: 63 average time/residue: 0.7378 time to fit residues: 50.9270 Evaluate side-chains 64 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 61 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 191 MET Chi-restraints excluded: chain C residue 258 SER Chi-restraints excluded: chain D residue 191 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 66 optimal weight: 8.9990 chunk 30 optimal weight: 7.9990 chunk 73 optimal weight: 0.8980 chunk 29 optimal weight: 5.9990 chunk 34 optimal weight: 4.9990 chunk 86 optimal weight: 0.9990 chunk 125 optimal weight: 10.0000 chunk 3 optimal weight: 0.8980 chunk 45 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 21 optimal weight: 2.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 93 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.077157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2708 r_free = 0.2708 target = 0.050620 restraints weight = 69949.374| |-----------------------------------------------------------------------------| r_work (start): 0.2671 rms_B_bonded: 2.93 r_work: 0.2474 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.2474 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2506 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2506 r_free = 0.2506 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2506 r_free = 0.2506 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2506 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8641 moved from start: 0.2624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 15620 Z= 0.168 Angle : 0.497 9.674 22160 Z= 0.288 Chirality : 0.037 0.164 2570 Planarity : 0.004 0.036 1986 Dihedral : 22.124 169.775 4598 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % Rotamer: Outliers : 0.59 % Allowed : 8.49 % Favored : 90.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.75 (0.24), residues: 1243 helix: 2.95 (0.18), residues: 807 sheet: 0.05 (0.40), residues: 148 loop : -0.59 (0.35), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 261 TYR 0.012 0.001 TYR D 215 PHE 0.011 0.002 PHE D 112 TRP 0.012 0.002 TRP C 46 HIS 0.005 0.001 HIS A 145 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.17 (15620) covalent geometry : angle 0.49690 / 0.29 (22160) hydrogen bonds : bond 0.04966 / 3.34 ( 905) hydrogen bonds : angle 3.59413 / 2.62 ( 2454) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4228.69 seconds wall clock time: 73 minutes 3.06 seconds (4383.06 seconds total)