Starting phenix.real_space_refine on Fri May 16 15:26:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wt7_37828/05_2025/8wt7_37828.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wt7_37828/05_2025/8wt7_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8wt7_37828/05_2025/8wt7_37828.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wt7_37828/05_2025/8wt7_37828.map" model { file = "/net/cci-nas-00/data/ceres_data/8wt7_37828/05_2025/8wt7_37828.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wt7_37828/05_2025/8wt7_37828.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 11.91, per 1000 atoms: 0.80 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: 3.67 Conformation dependent library (CDL) restraints added in 2.3 seconds 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: 6.62 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: 5.63 Time building geometry restraints manager: 4.30 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=" 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 bond pdb=" O5' G E 60 " pdb=" C5' G E 60 " ideal model delta sigma weight residual 1.420 1.455 -0.035 1.50e-02 4.44e+03 5.55e+00 bond pdb=" O5' G F 169 " pdb=" C5' G F 169 " ideal model delta sigma weight residual 1.420 1.455 -0.035 1.50e-02 4.44e+03 5.52e+00 ... (remaining 15615 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.48: 17312 1.48 - 2.96: 3967 2.96 - 4.43: 779 4.43 - 5.91: 87 5.91 - 7.39: 15 Bond angle restraints: 22160 Sorted by residual: 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=" 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 angle pdb=" CA ASP C 25 " pdb=" CB ASP C 25 " pdb=" CG ASP C 25 " ideal model delta sigma weight residual 112.60 117.05 -4.45 1.00e+00 1.00e+00 1.98e+01 angle pdb=" CA ASP C 11 " pdb=" CB ASP C 11 " pdb=" CG ASP C 11 " ideal model delta sigma weight residual 112.60 116.86 -4.26 1.00e+00 1.00e+00 1.82e+01 angle pdb=" CA ASP D 105 " pdb=" CB ASP D 105 " pdb=" CG ASP D 105 " ideal model delta sigma weight residual 112.60 116.81 -4.21 1.00e+00 1.00e+00 1.77e+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 - 0.127: 2266 0.127 - 0.255: 298 0.255 - 0.382: 0 0.382 - 0.509: 0 0.509 - 0.636: 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 2.35 -2.98 -0.64 2.00e-01 2.50e+01 1.01e+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 2.35 -2.98 -0.64 2.00e-01 2.50e+01 1.01e+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 2.35 -2.96 -0.62 2.00e-01 2.50e+01 9.50e+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: 0.670 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: 0.560 Check model and map are aligned: 0.100 Set scattering table: 0.140 Process input model: 44.410 Find NCS groups from input model: 0.610 Set up NCS constraints: 0.080 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:15.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 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= 0.475 Angle : 1.311 7.391 22160 Z= 0.851 Chirality : 0.078 0.636 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.021 0.005 TRP A 169 HIS 0.010 0.002 HIS D 256 PHE 0.017 0.002 PHE C 228 TYR 0.017 0.002 TYR D 307 ARG 0.025 0.002 ARG D 238 Details of bonding type rmsd hydrogen bonds : bond 0.22277 ( 905) hydrogen bonds : angle 6.95784 ( 2454) covalent geometry : bond 0.00790 (15620) covalent geometry : angle 1.31119 (22160) *********************** 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 : 1.245 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: 1.9317 time to fit residues: 194.6177 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 : 1.237 ------------------------------------------------------------------------------- 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 119 optimal weight: 3.9990 chunk 106 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 72 optimal weight: 4.9990 chunk 57 optimal weight: 2.9990 chunk 110 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 82 optimal weight: 0.0270 chunk 128 optimal weight: 5.9990 overall best weight: 1.4044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3252 r_free = 0.3252 target = 0.078156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2720 r_free = 0.2720 target = 0.051934 restraints weight = 62694.496| |-----------------------------------------------------------------------------| r_work (start): 0.2713 rms_B_bonded: 2.77 r_work: 0.2523 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.2523 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2530 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2530 r_free = 0.2530 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 = 0.2530 r_free = 0.2530 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2530 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.1627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 15620 Z= 0.174 Angle : 0.593 6.256 22160 Z= 0.331 Chirality : 0.039 0.195 2570 Planarity : 0.004 0.032 1986 Dihedral : 21.951 160.762 4602 Min Nonbonded Distance : 1.791 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Rotamer: Outliers : 0.59 % Allowed : 4.84 % Favored : 94.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.23), residues: 1243 helix: 1.94 (0.17), residues: 809 sheet: -0.85 (0.36), residues: 160 loop : -0.73 (0.35), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 276 HIS 0.005 0.001 HIS B 256 PHE 0.012 0.002 PHE B 112 TYR 0.020 0.002 TYR A 215 ARG 0.006 0.001 ARG C 237 Details of bonding type rmsd hydrogen bonds : bond 0.05864 ( 905) hydrogen bonds : angle 4.10488 ( 2454) covalent geometry : bond 0.00365 (15620) covalent geometry : angle 0.59291 (22160) *********************** 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 70 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 64 time to evaluate : 1.279 Fit side-chains revert: symmetry clash REVERT: B 107 ARG cc_start: 0.8673 (ttt90) cc_final: 0.8330 (ttm-80) REVERT: B 298 MET cc_start: 0.9316 (tpt) cc_final: 0.8972 (tpt) REVERT: C 258 SER cc_start: 0.9386 (m) cc_final: 0.8952 (p) REVERT: D 108 MET cc_start: 0.8855 (tpp) cc_final: 0.8634 (mmt) outliers start: 6 outliers final: 0 residues processed: 67 average time/residue: 1.6333 time to fit residues: 119.0651 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 : 1.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 43 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 33 optimal weight: 7.9990 chunk 136 optimal weight: 5.9990 chunk 9 optimal weight: 7.9990 chunk 72 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 67 optimal weight: 4.9990 chunk 30 optimal weight: 7.9990 chunk 38 optimal weight: 0.8980 chunk 84 optimal weight: 4.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 287 ASN B 93 GLN C 54 HIS C 93 GLN C 287 ASN D 6 HIS D 99 ASN D 287 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.078560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2729 r_free = 0.2729 target = 0.051779 restraints weight = 79953.810| |-----------------------------------------------------------------------------| r_work (start): 0.2685 rms_B_bonded: 3.16 r_work: 0.2488 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.2488 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2528 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2528 r_free = 0.2528 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 = 0.2528 r_free = 0.2528 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2528 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.2151 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= 0.154 Angle : 0.508 5.822 22160 Z= 0.285 Chirality : 0.036 0.174 2570 Planarity : 0.004 0.055 1986 Dihedral : 22.034 162.528 4598 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % Rotamer: Outliers : 0.59 % Allowed : 5.43 % Favored : 93.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.24 (0.24), residues: 1243 helix: 2.61 (0.18), residues: 807 sheet: -0.47 (0.38), residues: 151 loop : -0.75 (0.35), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 46 HIS 0.004 0.001 HIS B 256 PHE 0.011 0.001 PHE B 112 TYR 0.015 0.001 TYR A 215 ARG 0.007 0.000 ARG A 261 Details of bonding type rmsd hydrogen bonds : bond 0.04887 ( 905) hydrogen bonds : angle 3.71533 ( 2454) covalent geometry : bond 0.00331 (15620) covalent geometry : angle 0.50820 (22160) *********************** 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 75 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 69 time to evaluate : 1.272 Fit side-chains revert: symmetry clash REVERT: B 99 ASN cc_start: 0.8054 (m-40) cc_final: 0.7684 (m-40) REVERT: B 299 MET cc_start: 0.9346 (mtp) cc_final: 0.9074 (mtp) outliers start: 6 outliers final: 0 residues processed: 72 average time/residue: 1.5019 time to fit residues: 118.2918 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 : 1.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 100 optimal weight: 9.9990 chunk 104 optimal weight: 4.9990 chunk 58 optimal weight: 5.9990 chunk 5 optimal weight: 7.9990 chunk 54 optimal weight: 9.9990 chunk 79 optimal weight: 3.9990 chunk 117 optimal weight: 4.9990 chunk 28 optimal weight: 6.9990 chunk 107 optimal weight: 0.6980 chunk 77 optimal weight: 4.9990 chunk 47 optimal weight: 4.9990 overall best weight: 3.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 287 ASN B 93 GLN D 304 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.075291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2651 r_free = 0.2651 target = 0.048445 restraints weight = 80534.869| |-----------------------------------------------------------------------------| r_work (start): 0.2607 rms_B_bonded: 3.14 r_work: 0.2405 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.2405 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2444 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2444 r_free = 0.2444 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2444 r_free = 0.2444 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2444 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.2163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.087 15620 Z= 0.320 Angle : 0.590 6.221 22160 Z= 0.322 Chirality : 0.042 0.205 2570 Planarity : 0.005 0.035 1986 Dihedral : 22.209 160.213 4598 Min Nonbonded Distance : 1.810 Molprobity Statistics. All-atom Clashscore : 2.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Rotamer: Outliers : 0.59 % Allowed : 6.42 % Favored : 92.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.32 (0.24), residues: 1243 helix: 2.64 (0.18), residues: 808 sheet: -0.50 (0.36), residues: 162 loop : -0.60 (0.36), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 46 HIS 0.005 0.001 HIS D 256 PHE 0.016 0.002 PHE C 316 TYR 0.016 0.002 TYR A 215 ARG 0.005 0.000 ARG B 107 Details of bonding type rmsd hydrogen bonds : bond 0.05988 ( 905) hydrogen bonds : angle 3.83096 ( 2454) covalent geometry : bond 0.00721 (15620) covalent geometry : angle 0.58969 (22160) *********************** 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 66 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 60 time to evaluate : 1.427 Fit side-chains revert: symmetry clash REVERT: B 99 ASN cc_start: 0.8155 (m-40) cc_final: 0.7785 (m-40) REVERT: D 153 GLU cc_start: 0.8945 (OUTLIER) cc_final: 0.8740 (tm-30) REVERT: D 206 GLU cc_start: 0.7927 (mp0) cc_final: 0.7685 (mm-30) outliers start: 6 outliers final: 2 residues processed: 63 average time/residue: 1.5286 time to fit residues: 106.1016 Evaluate side-chains 60 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 57 time to evaluate : 1.321 ------------------------------------------------------------------------------- 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 153 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 131 optimal weight: 5.9990 chunk 35 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 104 optimal weight: 1.9990 chunk 94 optimal weight: 0.9990 chunk 9 optimal weight: 4.9990 chunk 52 optimal weight: 0.9990 chunk 49 optimal weight: 0.6980 chunk 66 optimal weight: 0.0870 chunk 125 optimal weight: 5.9990 chunk 89 optimal weight: 0.8980 overall best weight: 0.7362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 287 ASN B 93 GLN C 93 GLN D 99 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.079021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2754 r_free = 0.2754 target = 0.052451 restraints weight = 71485.910| |-----------------------------------------------------------------------------| r_work (start): 0.2714 rms_B_bonded: 2.99 r_work: 0.2520 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.2520 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2553 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2553 r_free = 0.2553 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 = 0.2553 r_free = 0.2553 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2553 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.2511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 15620 Z= 0.124 Angle : 0.489 6.031 22160 Z= 0.271 Chirality : 0.035 0.174 2570 Planarity : 0.004 0.035 1986 Dihedral : 22.137 161.581 4598 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Rotamer: Outliers : 0.89 % Allowed : 6.52 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.65 (0.24), residues: 1243 helix: 2.86 (0.18), residues: 807 sheet: -0.01 (0.39), residues: 148 loop : -0.56 (0.35), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 46 HIS 0.003 0.000 HIS B 256 PHE 0.009 0.001 PHE A 280 TYR 0.012 0.001 TYR A 215 ARG 0.004 0.000 ARG B 107 Details of bonding type rmsd hydrogen bonds : bond 0.04300 ( 905) hydrogen bonds : angle 3.58029 ( 2454) covalent geometry : bond 0.00258 (15620) covalent geometry : angle 0.48902 (22160) *********************** 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 70 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 61 time to evaluate : 1.501 Fit side-chains revert: symmetry clash REVERT: A 298 MET cc_start: 0.9225 (tpt) cc_final: 0.8932 (tpt) REVERT: C 237 ARG cc_start: 0.6801 (tmm160) cc_final: 0.6302 (tmm160) REVERT: D 99 ASN cc_start: 0.7427 (m110) cc_final: 0.7207 (m-40) outliers start: 9 outliers final: 1 residues processed: 67 average time/residue: 1.4267 time to fit residues: 105.3644 Evaluate side-chains 59 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 58 time to evaluate : 1.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 258 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 19 optimal weight: 4.9990 chunk 43 optimal weight: 4.9990 chunk 137 optimal weight: 8.9990 chunk 118 optimal weight: 7.9990 chunk 30 optimal weight: 7.9990 chunk 15 optimal weight: 0.7980 chunk 124 optimal weight: 7.9990 chunk 113 optimal weight: 0.4980 chunk 67 optimal weight: 0.9980 chunk 130 optimal weight: 10.0000 chunk 6 optimal weight: 5.9990 overall best weight: 2.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3239 r_free = 0.3239 target = 0.076691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2689 r_free = 0.2689 target = 0.049759 restraints weight = 84086.973| |-----------------------------------------------------------------------------| r_work (start): 0.2642 rms_B_bonded: 3.18 r_work: 0.2436 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.2436 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2472 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2472 r_free = 0.2472 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 = 0.2472 r_free = 0.2472 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2472 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.2452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 15620 Z= 0.216 Angle : 0.527 8.567 22160 Z= 0.288 Chirality : 0.037 0.190 2570 Planarity : 0.004 0.035 1986 Dihedral : 22.199 161.807 4598 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % Rotamer: Outliers : 0.49 % Allowed : 7.31 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.70 (0.24), residues: 1243 helix: 2.90 (0.18), residues: 807 sheet: 0.04 (0.39), residues: 148 loop : -0.59 (0.35), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 46 HIS 0.004 0.001 HIS D 256 PHE 0.013 0.002 PHE C 231 TYR 0.014 0.001 TYR D 215 ARG 0.003 0.000 ARG B 107 Details of bonding type rmsd hydrogen bonds : bond 0.05027 ( 905) hydrogen bonds : angle 3.63059 ( 2454) covalent geometry : bond 0.00483 (15620) covalent geometry : angle 0.52703 (22160) *********************** 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 64 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 59 time to evaluate : 1.147 Fit side-chains revert: symmetry clash REVERT: A 298 MET cc_start: 0.9276 (tpt) cc_final: 0.8956 (tpt) REVERT: C 237 ARG cc_start: 0.7017 (tmm160) cc_final: 0.6739 (tmm160) REVERT: D 99 ASN cc_start: 0.7232 (m110) cc_final: 0.6999 (m-40) outliers start: 5 outliers final: 3 residues processed: 61 average time/residue: 1.6016 time to fit residues: 107.5808 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 : 1.374 ------------------------------------------------------------------------------- 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 7 optimal weight: 4.9990 chunk 73 optimal weight: 2.9990 chunk 120 optimal weight: 1.9990 chunk 96 optimal weight: 7.9990 chunk 28 optimal weight: 4.9990 chunk 53 optimal weight: 4.9990 chunk 104 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 106 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3245 r_free = 0.3245 target = 0.077053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2697 r_free = 0.2697 target = 0.050154 restraints weight = 79992.216| |-----------------------------------------------------------------------------| r_work (start): 0.2652 rms_B_bonded: 3.11 r_work: 0.2452 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.2452 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2492 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2492 r_free = 0.2492 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 = 0.2492 r_free = 0.2492 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2492 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.2473 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= 0.174 Angle : 0.514 8.799 22160 Z= 0.281 Chirality : 0.036 0.183 2570 Planarity : 0.004 0.035 1986 Dihedral : 22.213 161.694 4598 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Rotamer: Outliers : 0.49 % Allowed : 7.31 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.73 (0.24), residues: 1243 helix: 2.92 (0.18), residues: 807 sheet: 0.07 (0.39), residues: 148 loop : -0.57 (0.35), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 46 HIS 0.003 0.001 HIS A 145 PHE 0.012 0.002 PHE B 112 TYR 0.015 0.001 TYR B 215 ARG 0.004 0.000 ARG B 107 Details of bonding type rmsd hydrogen bonds : bond 0.04825 ( 905) hydrogen bonds : angle 3.60519 ( 2454) covalent geometry : bond 0.00388 (15620) covalent geometry : angle 0.51416 (22160) *********************** 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 64 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 59 time to evaluate : 1.281 Fit side-chains revert: symmetry clash REVERT: A 298 MET cc_start: 0.9262 (tpt) cc_final: 0.8941 (tpt) REVERT: C 237 ARG cc_start: 0.6964 (tmm160) cc_final: 0.6709 (tmm160) REVERT: D 99 ASN cc_start: 0.7231 (m110) cc_final: 0.6993 (m-40) REVERT: D 206 GLU cc_start: 0.7784 (mp0) cc_final: 0.7524 (mm-30) outliers start: 5 outliers final: 3 residues processed: 61 average time/residue: 1.5163 time to fit residues: 101.7275 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 : 1.304 ------------------------------------------------------------------------------- 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 77 optimal weight: 0.9990 chunk 39 optimal weight: 9.9990 chunk 41 optimal weight: 0.3980 chunk 140 optimal weight: 5.9990 chunk 48 optimal weight: 0.9980 chunk 67 optimal weight: 1.9990 chunk 133 optimal weight: 10.0000 chunk 28 optimal weight: 4.9990 chunk 118 optimal weight: 6.9990 chunk 56 optimal weight: 0.9980 chunk 16 optimal weight: 0.7980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 GLN C 93 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.079322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2764 r_free = 0.2764 target = 0.052763 restraints weight = 76086.689| |-----------------------------------------------------------------------------| r_work (start): 0.2722 rms_B_bonded: 3.06 r_work: 0.2527 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.2527 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2568 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2568 r_free = 0.2568 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2568 r_free = 0.2568 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2568 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.2732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 15620 Z= 0.117 Angle : 0.479 8.126 22160 Z= 0.263 Chirality : 0.033 0.170 2570 Planarity : 0.003 0.035 1986 Dihedral : 22.156 163.297 4598 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Rotamer: Outliers : 0.49 % Allowed : 7.60 % Favored : 91.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.84 (0.24), residues: 1243 helix: 3.00 (0.18), residues: 808 sheet: 0.07 (0.40), residues: 146 loop : -0.47 (0.36), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 46 HIS 0.003 0.000 HIS B 256 PHE 0.009 0.001 PHE B 112 TYR 0.011 0.001 TYR A 215 ARG 0.004 0.000 ARG B 107 Details of bonding type rmsd hydrogen bonds : bond 0.04024 ( 905) hydrogen bonds : angle 3.47598 ( 2454) covalent geometry : bond 0.00247 (15620) covalent geometry : angle 0.47920 (22160) *********************** 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 68 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 63 time to evaluate : 1.409 Fit side-chains revert: symmetry clash REVERT: A 298 MET cc_start: 0.9229 (tpt) cc_final: 0.8967 (tpt) REVERT: D 99 ASN cc_start: 0.7311 (m110) cc_final: 0.7057 (m-40) outliers start: 5 outliers final: 2 residues processed: 65 average time/residue: 1.3890 time to fit residues: 100.2618 Evaluate side-chains 63 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 61 time to evaluate : 1.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 49 optimal weight: 3.9990 chunk 77 optimal weight: 5.9990 chunk 134 optimal weight: 6.9990 chunk 105 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 chunk 113 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 135 optimal weight: 7.9990 chunk 61 optimal weight: 8.9990 chunk 56 optimal weight: 0.8980 chunk 39 optimal weight: 9.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 GLN C 93 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.076526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2693 r_free = 0.2693 target = 0.050031 restraints weight = 64590.806| |-----------------------------------------------------------------------------| r_work (start): 0.2689 rms_B_bonded: 2.83 r_work: 0.2503 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.2503 ------------------------------------------------------------------------------- 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 = 0.30 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 = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2510 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.2575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 15620 Z= 0.251 Angle : 0.533 9.468 22160 Z= 0.289 Chirality : 0.038 0.192 2570 Planarity : 0.004 0.034 1986 Dihedral : 22.212 161.940 4598 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % Rotamer: Outliers : 0.39 % Allowed : 7.90 % Favored : 91.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.81 (0.24), residues: 1243 helix: 2.98 (0.18), residues: 807 sheet: 0.05 (0.39), residues: 150 loop : -0.51 (0.36), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 46 HIS 0.004 0.001 HIS A 145 PHE 0.014 0.002 PHE C 231 TYR 0.015 0.002 TYR B 215 ARG 0.004 0.000 ARG B 107 Details of bonding type rmsd hydrogen bonds : bond 0.05080 ( 905) hydrogen bonds : angle 3.60004 ( 2454) covalent geometry : bond 0.00562 (15620) covalent geometry : angle 0.53270 (22160) *********************** 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 62 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 58 time to evaluate : 1.264 Fit side-chains revert: symmetry clash REVERT: D 99 ASN cc_start: 0.7208 (m110) cc_final: 0.6956 (m-40) outliers start: 4 outliers final: 2 residues processed: 60 average time/residue: 1.3587 time to fit residues: 90.4315 Evaluate side-chains 59 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 57 time to evaluate : 1.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 67 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 97 optimal weight: 0.6980 chunk 83 optimal weight: 0.6980 chunk 6 optimal weight: 3.9990 chunk 137 optimal weight: 7.9990 chunk 37 optimal weight: 0.9980 chunk 99 optimal weight: 1.9990 chunk 114 optimal weight: 4.9990 chunk 12 optimal weight: 0.9980 chunk 91 optimal weight: 3.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.078695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2748 r_free = 0.2748 target = 0.052063 restraints weight = 81923.455| |-----------------------------------------------------------------------------| r_work (start): 0.2701 rms_B_bonded: 3.13 r_work: 0.2502 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.2502 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2533 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2533 r_free = 0.2533 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2533 r_free = 0.2533 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2533 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.2745 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= 0.131 Angle : 0.482 8.505 22160 Z= 0.265 Chirality : 0.034 0.175 2570 Planarity : 0.004 0.035 1986 Dihedral : 22.168 162.245 4598 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Rotamer: Outliers : 0.30 % Allowed : 8.29 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.90 (0.24), residues: 1243 helix: 3.02 (0.18), residues: 810 sheet: 0.14 (0.39), residues: 146 loop : -0.42 (0.36), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 46 HIS 0.003 0.000 HIS B 256 PHE 0.009 0.001 PHE B 112 TYR 0.011 0.001 TYR B 215 ARG 0.003 0.000 ARG B 107 Details of bonding type rmsd hydrogen bonds : bond 0.04199 ( 905) hydrogen bonds : angle 3.49342 ( 2454) covalent geometry : bond 0.00285 (15620) covalent geometry : angle 0.48194 (22160) ********************** 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 64 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 61 time to evaluate : 1.487 Fit side-chains revert: symmetry clash REVERT: A 144 MET cc_start: 0.9171 (mtm) cc_final: 0.8854 (mtp) REVERT: A 298 MET cc_start: 0.9248 (tpt) cc_final: 0.8920 (tpt) REVERT: D 99 ASN cc_start: 0.7278 (m110) cc_final: 0.7044 (m-40) outliers start: 3 outliers final: 2 residues processed: 62 average time/residue: 1.4951 time to fit residues: 102.4378 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 : 1.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 22 optimal weight: 6.9990 chunk 51 optimal weight: 5.9990 chunk 28 optimal weight: 4.9990 chunk 53 optimal weight: 0.0000 chunk 84 optimal weight: 0.5980 chunk 26 optimal weight: 2.9990 chunk 140 optimal weight: 6.9990 chunk 139 optimal weight: 6.9990 chunk 99 optimal weight: 2.9990 chunk 3 optimal weight: 0.9990 chunk 91 optimal weight: 6.9990 overall best weight: 1.5190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.078054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2735 r_free = 0.2735 target = 0.051693 restraints weight = 60558.229| |-----------------------------------------------------------------------------| r_work (start): 0.2732 rms_B_bonded: 2.76 r_work: 0.2550 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.2550 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2558 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2558 r_free = 0.2558 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2558 r_free = 0.2558 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2558 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.2760 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= 0.153 Angle : 0.485 8.870 22160 Z= 0.265 Chirality : 0.034 0.172 2570 Planarity : 0.004 0.034 1986 Dihedral : 22.154 162.841 4598 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % Rotamer: Outliers : 0.39 % Allowed : 8.39 % Favored : 91.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.94 (0.24), residues: 1243 helix: 3.06 (0.18), residues: 809 sheet: 0.18 (0.39), residues: 146 loop : -0.46 (0.36), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 46 HIS 0.003 0.001 HIS D 256 PHE 0.011 0.001 PHE B 112 TYR 0.012 0.001 TYR B 215 ARG 0.004 0.000 ARG B 107 Details of bonding type rmsd hydrogen bonds : bond 0.04365 ( 905) hydrogen bonds : angle 3.49873 ( 2454) covalent geometry : bond 0.00337 (15620) covalent geometry : angle 0.48506 (22160) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8473.06 seconds wall clock time: 146 minutes 55.23 seconds (8815.23 seconds total)