Starting phenix.real_space_refine on Fri Jul 3 14:29:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wt7_37828/07_2026/8wt7_37828.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wt7_37828/07_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_37828/07_2026/8wt7_37828.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wt7_37828/07_2026/8wt7_37828.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8wt7_37828/07_2026/8wt7_37828.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wt7_37828/07_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-dev-6108/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: 4.55, 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: 1.05 Conformation dependent library (CDL) restraints added in 717.9 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: 1.63 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: 2.86 Time building geometry restraints manager: 1.47 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: 17316 1.48 - 2.96: 3977 2.96 - 4.43: 765 4.43 - 5.91: 87 5.91 - 7.39: 15 Bond angle restraints: 22160 Sorted by residual: 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=" O3' DA G 26 " pdb=" P DC G 27 " pdb=" O5' DC G 27 " ideal model delta sigma weight residual 104.00 96.61 7.39 1.50e+00 4.44e-01 2.43e+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 angle pdb=" O4' DC H 18 " pdb=" C4' DC H 18 " pdb=" C3' DC H 18 " ideal model delta sigma weight residual 106.00 103.13 2.87 6.00e-01 2.78e+00 2.28e+01 angle pdb=" O3' U F 132 " pdb=" P G F 133 " pdb=" O5' G F 133 " ideal model delta sigma weight residual 104.00 110.87 -6.87 1.50e+00 4.44e-01 2.10e+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: 2269 0.129 - 0.259: 295 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: 0.850 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: 0.020 Extract box with map and model: 0.170 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 16.170 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.630 ------------------------------------------------------------------------------- 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= 0.537 Angle : 1.304 7.391 22160 Z= 0.894 Chirality : 0.081 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 0.00814 / 0.54 (15620) covalent geometry : angle 1.30397 / 0.89 (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 : 0.517 Fit side-chains revert: symmetry clash REVERT: A 261 ARG cc_start: 0.8687 (OUTLIER) cc_final: 0.8458 (tpt-90) 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: 0.8466 time to fit residues: 85.1225 Evaluate side-chains 62 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 61 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 ARG 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: 20.0000 chunk 124 optimal weight: 10.0000 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: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 287 ASN C 287 ASN D 93 GLN D 99 ASN D 287 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.078449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2718 r_free = 0.2718 target = 0.051949 restraints weight = 64706.242| |-----------------------------------------------------------------------------| r_work (start): 0.2724 rms_B_bonded: 2.82 r_work: 0.2533 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.2533 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2533 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2533 r_free = 0.2533 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 = 0.2533 r_free = 0.2533 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.2533 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.1423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 15620 Z= 0.162 Angle : 0.601 6.932 22160 Z= 0.364 Chirality : 0.043 0.383 2570 Planarity : 0.004 0.034 1986 Dihedral : 21.943 163.243 4602 Min Nonbonded Distance : 1.781 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Rotamer: Outliers : 0.39 % Allowed : 4.94 % 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 : -0.64 (0.35), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 237 TYR 0.020 0.002 TYR A 215 PHE 0.010 0.001 PHE B 112 TRP 0.020 0.003 TRP D 46 HIS 0.005 0.001 HIS A 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.16 (15620) covalent geometry : angle 0.60148 / 0.36 (22160) hydrogen bonds : bond 0.06902 / 4.65 ( 905) hydrogen bonds : angle 4.23549 / 3.07 ( 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 67 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 63 time to evaluate : 0.409 Fit side-chains revert: symmetry clash REVERT: A 299 MET cc_start: 0.9128 (mtp) cc_final: 0.8893 (mtp) REVERT: B 107 ARG cc_start: 0.8665 (ttt90) cc_final: 0.8391 (ttm110) REVERT: B 298 MET cc_start: 0.9298 (tpt) cc_final: 0.8929 (tpt) REVERT: C 258 SER cc_start: 0.9352 (m) cc_final: 0.8901 (p) REVERT: D 108 MET cc_start: 0.8857 (tpp) cc_final: 0.8641 (mmt) REVERT: D 239 TYR cc_start: 0.9176 (t80) cc_final: 0.8870 (t80) outliers start: 4 outliers final: 0 residues processed: 64 average time/residue: 0.7218 time to fit residues: 50.1163 Evaluate side-chains 59 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 59 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.3980 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: 4.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 287 ASN B 93 GLN C 54 HIS D 6 HIS D 99 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.075180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2649 r_free = 0.2649 target = 0.048645 restraints weight = 76015.187| |-----------------------------------------------------------------------------| r_work (start): 0.2605 rms_B_bonded: 3.05 r_work: 0.2404 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.2404 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2421 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2421 r_free = 0.2421 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2421 r_free = 0.2421 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2421 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8677 moved from start: 0.1813 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 : 0.625 6.733 22160 Z= 0.361 Chirality : 0.045 0.254 2570 Planarity : 0.005 0.039 1986 Dihedral : 22.131 162.896 4598 Min Nonbonded Distance : 1.821 Molprobity Statistics. All-atom Clashscore : 2.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Rotamer: Outliers : 0.49 % Allowed : 5.63 % Favored : 93.88 % 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: 1.98 (0.24), residues: 1243 helix: 2.36 (0.18), residues: 808 sheet: -0.74 (0.36), residues: 171 loop : -0.54 (0.36), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 261 TYR 0.020 0.002 TYR A 215 PHE 0.018 0.002 PHE C 316 TRP 0.019 0.003 TRP D 46 HIS 0.006 0.001 HIS A 145 Details of bonding type rmsd/Z covalent geometry : bond 0.00728 / 0.34 (15620) covalent geometry : angle 0.62472 / 0.36 (22160) hydrogen bonds : bond 0.07030 / 4.71 ( 905) hydrogen bonds : angle 4.06989 / 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 64 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 59 time to evaluate : 0.422 Fit side-chains revert: symmetry clash REVERT: B 99 ASN cc_start: 0.8246 (m-40) cc_final: 0.7908 (m-40) REVERT: B 298 MET cc_start: 0.9218 (tpt) cc_final: 0.8915 (tpt) REVERT: D 99 ASN cc_start: 0.7867 (m-40) cc_final: 0.7603 (m-40) REVERT: D 261 ARG cc_start: 0.8902 (OUTLIER) cc_final: 0.8537 (ttm-80) outliers start: 5 outliers final: 0 residues processed: 62 average time/residue: 0.6658 time to fit residues: 45.2724 Evaluate side-chains 56 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 55 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.8980 chunk 46 optimal weight: 0.9980 chunk 61 optimal weight: 0.9990 chunk 77 optimal weight: 0.9990 chunk 78 optimal weight: 0.9990 chunk 8 optimal weight: 0.9990 chunk 90 optimal weight: 0.7980 chunk 136 optimal weight: 10.0000 chunk 59 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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 = 0.3255 r_free = 0.3255 target = 0.077840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2720 r_free = 0.2720 target = 0.051410 restraints weight = 71779.066| |-----------------------------------------------------------------------------| r_work (start): 0.2676 rms_B_bonded: 2.94 r_work: 0.2480 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.2480 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2513 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2513 r_free = 0.2513 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 = 0.2513 r_free = 0.2513 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: 0.2513 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 moved from start: 0.2080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15620 Z= 0.138 Angle : 0.502 5.194 22160 Z= 0.304 Chirality : 0.038 0.203 2570 Planarity : 0.004 0.037 1986 Dihedral : 22.117 165.278 4598 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Rotamer: Outliers : 0.49 % Allowed : 6.42 % Favored : 93.09 % 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: 2.35 (0.24), residues: 1243 helix: 2.63 (0.18), residues: 808 sheet: -0.20 (0.39), residues: 147 loop : -0.66 (0.34), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 261 TYR 0.016 0.001 TYR A 215 PHE 0.010 0.001 PHE B 112 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 0.00262 / 0.14 (15620) covalent geometry : angle 0.50211 / 0.30 (22160) hydrogen bonds : bond 0.05260 / 3.53 ( 905) hydrogen bonds : angle 3.80755 / 2.79 ( 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 70 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 65 time to evaluate : 0.428 Fit side-chains revert: symmetry clash REVERT: A 298 MET cc_start: 0.9219 (tpt) cc_final: 0.8979 (tpt) REVERT: B 99 ASN cc_start: 0.8096 (m-40) cc_final: 0.7710 (m-40) REVERT: B 107 ARG cc_start: 0.8855 (ttt90) cc_final: 0.8506 (ttm-80) REVERT: B 298 MET cc_start: 0.9190 (tpt) cc_final: 0.8977 (tpt) REVERT: C 304 GLN cc_start: 0.9018 (tt0) cc_final: 0.8815 (mt0) REVERT: D 99 ASN cc_start: 0.7856 (m-40) cc_final: 0.7596 (m-40) REVERT: D 261 ARG cc_start: 0.8760 (OUTLIER) cc_final: 0.8507 (ttm-80) outliers start: 5 outliers final: 0 residues processed: 67 average time/residue: 0.7199 time to fit residues: 52.4354 Evaluate side-chains 61 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 60 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 261 ARG 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: 4.9990 chunk 37 optimal weight: 0.9980 chunk 73 optimal weight: 3.9990 chunk 86 optimal weight: 0.8980 chunk 105 optimal weight: 0.9980 chunk 29 optimal weight: 6.9990 chunk 60 optimal weight: 6.9990 chunk 139 optimal weight: 20.0000 overall best weight: 2.1784 ------------------------------------------------------------------------------- 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 = 0.076744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2691 r_free = 0.2691 target = 0.050095 restraints weight = 69725.339| |-----------------------------------------------------------------------------| r_work (start): 0.2653 rms_B_bonded: 2.93 r_work: 0.2458 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.2458 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2491 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2491 r_free = 0.2491 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 = 0.2491 r_free = 0.2491 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: 0.2491 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 moved from start: 0.2191 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= 0.188 Angle : 0.512 6.039 22160 Z= 0.303 Chirality : 0.039 0.203 2570 Planarity : 0.004 0.051 1986 Dihedral : 22.137 166.185 4598 Min Nonbonded Distance : 1.831 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % Rotamer: Outliers : 0.59 % Allowed : 6.52 % Favored : 92.89 % 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: 2.74 (0.18), residues: 808 sheet: -0.06 (0.39), residues: 147 loop : -0.63 (0.34), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 261 TYR 0.015 0.001 TYR A 215 PHE 0.012 0.002 PHE B 112 TRP 0.013 0.002 TRP D 46 HIS 0.004 0.001 HIS C 166 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.19 (15620) covalent geometry : angle 0.51190 / 0.30 (22160) hydrogen bonds : bond 0.05451 / 3.66 ( 905) hydrogen bonds : angle 3.73495 / 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 66 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 60 time to evaluate : 0.472 Fit side-chains revert: symmetry clash REVERT: A 298 MET cc_start: 0.9213 (tpt) cc_final: 0.8878 (tpt) REVERT: B 99 ASN cc_start: 0.8122 (m-40) cc_final: 0.7728 (m-40) REVERT: B 107 ARG cc_start: 0.8888 (ttt90) cc_final: 0.8460 (ttm-80) REVERT: D 99 ASN cc_start: 0.7846 (m-40) cc_final: 0.7591 (m-40) REVERT: D 261 ARG cc_start: 0.8826 (OUTLIER) cc_final: 0.8493 (ttm-80) outliers start: 6 outliers final: 2 residues processed: 63 average time/residue: 0.7428 time to fit residues: 50.9208 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 : 0.480 ------------------------------------------------------------------------------- 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: 0.7980 chunk 71 optimal weight: 4.9990 chunk 97 optimal weight: 0.9990 chunk 115 optimal weight: 7.9990 chunk 57 optimal weight: 4.9990 chunk 131 optimal weight: 10.0000 chunk 114 optimal weight: 1.9990 chunk 122 optimal weight: 20.0000 overall best weight: 2.7588 ------------------------------------------------------------------------------- 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 = 0.3227 r_free = 0.3227 target = 0.076188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2675 r_free = 0.2675 target = 0.049395 restraints weight = 72430.308| |-----------------------------------------------------------------------------| r_work (start): 0.2625 rms_B_bonded: 3.00 r_work: 0.2422 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.2422 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2458 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2458 r_free = 0.2458 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 = 0.2458 r_free = 0.2458 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: 0.2458 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8671 moved from start: 0.2293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 15620 Z= 0.218 Angle : 0.526 8.367 22160 Z= 0.307 Chirality : 0.039 0.205 2570 Planarity : 0.004 0.036 1986 Dihedral : 22.200 165.390 4598 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Rotamer: Outliers : 0.69 % Allowed : 7.11 % Favored : 92.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.54 (0.24), residues: 1243 helix: 2.76 (0.18), residues: 808 sheet: -0.03 (0.39), residues: 148 loop : -0.60 (0.35), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 261 TYR 0.020 0.002 TYR D 215 PHE 0.013 0.002 PHE C 316 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 0.00470 / 0.22 (15620) covalent geometry : angle 0.52607 / 0.31 (22160) hydrogen bonds : bond 0.05532 / 3.71 ( 905) hydrogen bonds : angle 3.72664 / 2.72 ( 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 68 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 61 time to evaluate : 0.418 Fit side-chains revert: symmetry clash REVERT: A 298 MET cc_start: 0.9211 (tpt) cc_final: 0.8918 (tpt) REVERT: B 99 ASN cc_start: 0.8143 (m-40) cc_final: 0.7741 (m-40) REVERT: B 107 ARG cc_start: 0.8894 (ttt90) cc_final: 0.8484 (ttm-80) REVERT: D 99 ASN cc_start: 0.7833 (m-40) cc_final: 0.7566 (m-40) REVERT: D 206 GLU cc_start: 0.7949 (mp0) cc_final: 0.7701 (mm-30) REVERT: D 261 ARG cc_start: 0.8840 (OUTLIER) cc_final: 0.8482 (ttm-80) outliers start: 7 outliers final: 3 residues processed: 65 average time/residue: 0.6862 time to fit residues: 48.6100 Evaluate side-chains 63 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 59 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 157 GLU Chi-restraints excluded: chain C residue 191 MET Chi-restraints excluded: chain C residue 258 SER 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: 0.8980 chunk 29 optimal weight: 5.9990 chunk 60 optimal weight: 5.9990 chunk 107 optimal weight: 0.7980 chunk 93 optimal weight: 8.9990 chunk 33 optimal weight: 6.9990 chunk 75 optimal weight: 2.9990 chunk 92 optimal weight: 4.9990 chunk 135 optimal weight: 20.0000 chunk 122 optimal weight: 20.0000 chunk 130 optimal weight: 20.0000 overall best weight: 3.1386 ------------------------------------------------------------------------------- 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 = 0.3218 r_free = 0.3218 target = 0.075669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2664 r_free = 0.2664 target = 0.048905 restraints weight = 72161.903| |-----------------------------------------------------------------------------| r_work (start): 0.2614 rms_B_bonded: 3.01 r_work: 0.2410 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.2410 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2446 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2446 r_free = 0.2446 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 = 0.2446 r_free = 0.2446 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: 0.2446 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 moved from start: 0.2348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 15620 Z= 0.243 Angle : 0.536 7.051 22160 Z= 0.311 Chirality : 0.040 0.209 2570 Planarity : 0.004 0.036 1986 Dihedral : 22.257 165.465 4598 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Rotamer: Outliers : 0.59 % Allowed : 7.80 % 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: 2.55 (0.24), residues: 1243 helix: 2.76 (0.18), residues: 807 sheet: -0.01 (0.40), residues: 148 loop : -0.58 (0.35), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 261 TYR 0.014 0.001 TYR A 215 PHE 0.014 0.002 PHE C 316 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 0.00527 / 0.24 (15620) covalent geometry : angle 0.53630 / 0.31 (22160) hydrogen bonds : bond 0.05699 / 3.83 ( 905) hydrogen bonds : angle 3.75752 / 2.74 ( 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 : 0.402 Fit side-chains revert: symmetry clash REVERT: A 298 MET cc_start: 0.9223 (tpt) cc_final: 0.8929 (tpt) REVERT: B 99 ASN cc_start: 0.8119 (m-40) cc_final: 0.7695 (m-40) REVERT: B 107 ARG cc_start: 0.8904 (ttt90) cc_final: 0.8483 (ttm-80) REVERT: D 99 ASN cc_start: 0.7855 (m-40) cc_final: 0.7590 (m-40) REVERT: D 261 ARG cc_start: 0.8785 (OUTLIER) cc_final: 0.8497 (ttm-80) outliers start: 6 outliers final: 3 residues processed: 62 average time/residue: 0.7073 time to fit residues: 47.8723 Evaluate side-chains 63 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 59 time to evaluate : 0.506 ------------------------------------------------------------------------------- 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: 3.9990 chunk 136 optimal weight: 10.0000 chunk 66 optimal weight: 7.9990 chunk 104 optimal weight: 4.9990 chunk 91 optimal weight: 2.9990 chunk 128 optimal weight: 10.0000 chunk 67 optimal weight: 2.9990 chunk 132 optimal weight: 10.0000 chunk 65 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- 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 = 0.3225 r_free = 0.3225 target = 0.076005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2670 r_free = 0.2670 target = 0.049002 restraints weight = 96243.681| |-----------------------------------------------------------------------------| r_work (start): 0.2626 rms_B_bonded: 3.33 r_work: 0.2415 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.2415 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2438 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2438 r_free = 0.2438 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 = 0.2438 r_free = 0.2438 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2438 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8673 moved from start: 0.2410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 15620 Z= 0.220 Angle : 0.525 8.847 22160 Z= 0.306 Chirality : 0.039 0.203 2570 Planarity : 0.004 0.036 1986 Dihedral : 22.265 165.631 4598 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Rotamer: Outliers : 0.59 % Allowed : 7.80 % 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: 2.57 (0.24), residues: 1243 helix: 2.78 (0.18), residues: 807 sheet: 0.04 (0.40), residues: 148 loop : -0.57 (0.35), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 261 TYR 0.016 0.001 TYR D 215 PHE 0.012 0.002 PHE C 316 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 0.00473 / 0.22 (15620) covalent geometry : angle 0.52545 / 0.31 (22160) hydrogen bonds : bond 0.05486 / 3.68 ( 905) hydrogen bonds : angle 3.72139 / 2.71 ( 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 65 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 59 time to evaluate : 0.502 Fit side-chains REVERT: A 298 MET cc_start: 0.9209 (tpt) cc_final: 0.8951 (tpt) REVERT: B 99 ASN cc_start: 0.8137 (m-40) cc_final: 0.7710 (m-40) REVERT: B 107 ARG cc_start: 0.8897 (ttt90) cc_final: 0.8495 (ttm-80) REVERT: D 99 ASN cc_start: 0.7797 (m-40) cc_final: 0.7527 (m-40) outliers start: 6 outliers final: 4 residues processed: 62 average time/residue: 0.7186 time to fit residues: 48.6555 Evaluate side-chains 62 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 58 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 150 ASN 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 52 optimal weight: 0.7980 chunk 27 optimal weight: 3.9990 chunk 14 optimal weight: 0.8980 chunk 11 optimal weight: 0.9990 chunk 127 optimal weight: 20.0000 chunk 83 optimal weight: 0.7980 chunk 73 optimal weight: 1.9990 chunk 117 optimal weight: 1.9990 chunk 111 optimal weight: 0.8980 chunk 6 optimal weight: 4.9990 chunk 25 optimal weight: 5.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 = 0.3267 r_free = 0.3267 target = 0.078119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2731 r_free = 0.2731 target = 0.051427 restraints weight = 79001.660| |-----------------------------------------------------------------------------| r_work (start): 0.2682 rms_B_bonded: 3.11 r_work: 0.2481 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.2481 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2521 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2521 r_free = 0.2521 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 = 0.2521 r_free = 0.2521 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: 0.2521 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.2597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 15620 Z= 0.127 Angle : 0.474 8.430 22160 Z= 0.283 Chirality : 0.036 0.178 2570 Planarity : 0.004 0.041 1986 Dihedral : 22.177 168.369 4598 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Rotamer: Outliers : 0.49 % Allowed : 8.09 % Favored : 91.41 % 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: 2.66 (0.24), residues: 1243 helix: 2.88 (0.18), residues: 807 sheet: -0.08 (0.39), residues: 150 loop : -0.55 (0.36), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 27 TYR 0.012 0.001 TYR A 215 PHE 0.010 0.001 PHE A 280 TRP 0.013 0.002 TRP D 46 HIS 0.004 0.001 HIS B 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.13 (15620) covalent geometry : angle 0.47361 / 0.28 (22160) hydrogen bonds : bond 0.04576 / 3.07 ( 905) hydrogen bonds : angle 3.58545 / 2.62 ( 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: 5 poor density : 64 time to evaluate : 0.537 Fit side-chains REVERT: B 107 ARG cc_start: 0.8821 (ttt90) cc_final: 0.8471 (ttm-80) REVERT: D 99 ASN cc_start: 0.7687 (m-40) cc_final: 0.7414 (m-40) outliers start: 5 outliers final: 1 residues processed: 66 average time/residue: 0.7049 time to fit residues: 50.9666 Evaluate side-chains 62 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 61 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 258 SER 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: 7.9990 chunk 59 optimal weight: 4.9990 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: 0.9990 chunk 12 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 123 optimal weight: 10.0000 overall best weight: 2.7990 ------------------------------------------------------------------------------- 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 = 0.3231 r_free = 0.3231 target = 0.076266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2687 r_free = 0.2687 target = 0.049845 restraints weight = 62068.434| |-----------------------------------------------------------------------------| r_work (start): 0.2644 rms_B_bonded: 2.79 r_work: 0.2450 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.2450 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2493 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2493 r_free = 0.2493 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 = 0.2493 r_free = 0.2493 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: 0.2493 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8662 moved from start: 0.2532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 15620 Z= 0.220 Angle : 0.518 8.530 22160 Z= 0.301 Chirality : 0.039 0.196 2570 Planarity : 0.004 0.036 1986 Dihedral : 22.220 166.843 4598 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Rotamer: Outliers : 0.30 % Allowed : 8.59 % Favored : 91.12 % 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: 2.71 (0.24), residues: 1243 helix: 2.91 (0.18), residues: 806 sheet: 0.04 (0.39), residues: 152 loop : -0.56 (0.36), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 27 TYR 0.012 0.001 TYR D 307 PHE 0.014 0.002 PHE C 231 TRP 0.013 0.002 TRP C 46 HIS 0.004 0.001 HIS A 145 Details of bonding type rmsd/Z covalent geometry : bond 0.00475 / 0.22 (15620) covalent geometry : angle 0.51828 / 0.30 (22160) hydrogen bonds : bond 0.05355 / 3.60 ( 905) hydrogen bonds : angle 3.64741 / 2.66 ( 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 63 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 60 time to evaluate : 0.446 Fit side-chains REVERT: B 107 ARG cc_start: 0.8859 (ttt90) cc_final: 0.8436 (ttm-80) REVERT: D 99 ASN cc_start: 0.7756 (m-40) cc_final: 0.7492 (m-40) outliers start: 3 outliers final: 3 residues processed: 61 average time/residue: 0.6415 time to fit residues: 42.8181 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 : 0.300 ------------------------------------------------------------------------------- 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: 7.9990 chunk 30 optimal weight: 7.9990 chunk 73 optimal weight: 0.8980 chunk 29 optimal weight: 0.9980 chunk 34 optimal weight: 4.9990 chunk 86 optimal weight: 0.0980 chunk 125 optimal weight: 10.0000 chunk 3 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 21 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 93 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.078600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2748 r_free = 0.2748 target = 0.052088 restraints weight = 70054.206| |-----------------------------------------------------------------------------| r_work (start): 0.2702 rms_B_bonded: 2.96 r_work: 0.2508 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.2508 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2547 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2547 r_free = 0.2547 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2547 r_free = 0.2547 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2547 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.2711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 15620 Z= 0.122 Angle : 0.470 8.823 22160 Z= 0.280 Chirality : 0.035 0.174 2570 Planarity : 0.004 0.036 1986 Dihedral : 22.148 169.317 4598 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Rotamer: Outliers : 0.30 % Allowed : 8.59 % Favored : 91.12 % 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: 2.80 (0.24), residues: 1243 helix: 2.95 (0.18), residues: 807 sheet: 0.19 (0.40), residues: 146 loop : -0.51 (0.36), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 27 TYR 0.012 0.001 TYR A 215 PHE 0.010 0.001 PHE A 280 TRP 0.012 0.002 TRP D 46 HIS 0.003 0.001 HIS D 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00223 / 0.12 (15620) covalent geometry : angle 0.47011 / 0.28 (22160) hydrogen bonds : bond 0.04404 / 2.96 ( 905) hydrogen bonds : angle 3.53380 / 2.58 ( 2454) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4035.13 seconds wall clock time: 69 minutes 44.87 seconds (4184.87 seconds total)