Starting phenix.real_space_refine on Thu Aug 6 08:44:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wt6_37827/08_2026/8wt6_37827.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wt6_37827/08_2026/8wt6_37827.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wt6_37827/08_2026/8wt6_37827.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wt6_37827/08_2026/8wt6_37827.map" model { file = "/net/cci-nas-00/data/ceres_data/8wt6_37827/08_2026/8wt6_37827.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wt6_37827/08_2026/8wt6_37827.cif" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.071 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 234 5.49 5 Mg 2 5.21 5 S 48 5.16 5 C 8431 2.51 5 N 2726 2.21 5 O 3302 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14743 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 2420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2420 Classifications: {'peptide': 306} Link IDs: {'PTRANS': 12, 'TRANS': 293} Chain breaks: 1 Chain: "B" Number of atoms: 2514 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: 2540 Chain: "C" Number of atoms: 2411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2411 Classifications: {'peptide': 305} Link IDs: {'PTRANS': 12, 'TRANS': 292} Chain breaks: 1 Chain: "D" Number of atoms: 2498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2498 Classifications: {'peptide': 317} Link IDs: {'PTRANS': 12, 'TRANS': 304} Chain: "E" Number of atoms: 1275 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 59, 1252 Classifications: {'RNA': 59} Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 12, 'rna3p_pur': 23, 'rna3p_pyr': 20} Link IDs: {'rna2p': 16, 'rna3p': 42} Conformer: "B" Number of residues, atoms: 59, 1252 Classifications: {'RNA': 59} Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 12, 'rna3p_pur': 23, 'rna3p_pyr': 20} Link IDs: {'rna2p': 16, 'rna3p': 42} bond proxies already assigned to first conformer: 1369 Chain: "F" Number of atoms: 1443 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 1443 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: 509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 509 Classifications: {'DNA': 25} Link IDs: {'rna3p': 24} Chain breaks: 2 Chain: "H" Number of atoms: 558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 558 Classifications: {'DNA': 27} Link IDs: {'rna3p': 26} Chain: "I" Number of atoms: 507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 507 Classifications: {'DNA': 25} Link IDs: {'rna3p': 24} Chain breaks: 2 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: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 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} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N AARG B 221 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG B 221 " occ=0.50 residue: pdb=" P A G E 75 " occ=0.50 ... (44 atoms not shown) pdb=" C4 B G E 75 " occ=0.50 Time building chain proxies: 4.05, per 1000 atoms: 0.27 Number of scatterers: 14743 At special positions: 0 Unit cell: (119.52, 123.314, 115.726, 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 234 15.00 Mg 2 11.99 O 3302 8.00 N 2726 7.00 C 8431 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: 1.78 Conformation dependent library (CDL) restraints added in 634.5 milliseconds 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2334 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 8 sheets defined 68.4% alpha, 9.3% beta 87 base pairs and 138 stacking pairs defined. Time for finding SS restraints: 2.11 Creating SS restraints... Processing helix chain 'A' and resid 36 through 50 Processing helix chain 'A' and resid 66 through 77 Processing helix chain 'A' and resid 84 through 95 removed outlier: 3.827A 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: 4.112A pdb=" N GLU A 153 " --> pdb=" O LEU A 149 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N THR A 154 " --> pdb=" O ASN A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 187 Processing helix chain 'A' and resid 188 through 200 Processing helix chain 'A' and resid 205 through 217 removed outlier: 3.539A pdb=" N ALA A 210 " --> pdb=" O GLU A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 232 removed outlier: 3.566A pdb=" N PHE A 228 " --> pdb=" O HIS A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 262 removed outlier: 3.591A 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 287 removed outlier: 3.715A pdb=" N ASN A 287 " --> pdb=" O ARG A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 313 Processing helix chain 'A' and resid 317 through 321 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 95 removed outlier: 3.714A pdb=" N GLY B 88 " --> pdb=" O ASN B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 117 Processing helix chain 'B' and resid 125 through 155 removed outlier: 3.769A pdb=" N GLU B 153 " --> pdb=" O LEU B 149 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N THR B 154 " --> pdb=" O ASN B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 158 No H-bonds generated for 'chain 'B' and resid 156 through 158' Processing helix chain 'B' and resid 159 through 188 removed outlier: 3.623A 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 removed outlier: 3.508A pdb=" N ALA B 210 " --> pdb=" O GLU B 206 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 233 removed outlier: 3.704A pdb=" N PHE B 228 " --> pdb=" O HIS B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 256 through 263 removed outlier: 3.567A pdb=" N ARG B 260 " --> pdb=" O HIS B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 274 Processing helix chain 'B' and resid 274 through 287 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 76 Processing helix chain 'C' and resid 84 through 95 removed outlier: 3.739A 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 153 removed outlier: 3.790A pdb=" N GLU C 153 " --> pdb=" O LEU C 149 " (cutoff:3.500A) Processing helix chain 'C' and resid 159 through 188 removed outlier: 3.558A 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: 3.723A pdb=" N PHE C 228 " --> pdb=" O HIS C 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 256 through 262 removed outlier: 3.576A 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 287 removed outlier: 3.600A pdb=" N ASN C 287 " --> pdb=" O ARG C 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 290 through 313 Processing helix chain 'C' and resid 317 through 321 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: 3.670A 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: 3.956A pdb=" N GLU D 153 " --> pdb=" O LEU D 149 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N THR D 154 " --> pdb=" O ASN D 150 " (cutoff:3.500A) Processing helix chain 'D' and resid 156 through 158 No H-bonds generated for 'chain 'D' and resid 156 through 158' Processing helix chain 'D' and resid 159 through 187 Processing helix chain 'D' and resid 188 through 199 Processing helix chain 'D' and resid 205 through 217 removed outlier: 3.570A pdb=" N ALA D 210 " --> pdb=" O GLU D 206 " (cutoff:3.500A) Processing helix chain 'D' and resid 224 through 233 removed outlier: 3.537A pdb=" N PHE D 228 " --> pdb=" O HIS D 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 256 through 263 removed outlier: 3.584A pdb=" N LEU D 263 " --> pdb=" O LEU D 259 " (cutoff:3.500A) Processing helix chain 'D' and resid 263 through 274 removed outlier: 3.549A pdb=" N SER D 272 " --> pdb=" O MET D 268 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N THR D 274 " --> pdb=" O ALA D 270 " (cutoff:3.500A) Processing helix chain 'D' and resid 274 through 287 Processing helix chain 'D' and resid 290 through 313 Processing helix chain 'D' and resid 317 through 321 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 34 removed outlier: 6.480A pdb=" N HIS A 6 " --> pdb=" O HIS A 56 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N CYS A 58 " --> pdb=" O HIS A 6 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N ILE A 8 " --> pdb=" O CYS A 58 " (cutoff:3.500A) removed outlier: 8.446A pdb=" N GLU A 60 " --> pdb=" O ILE A 8 " (cutoff:3.500A) removed outlier: 8.275A 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: 6.775A pdb=" N HIS B 6 " --> pdb=" O HIS B 56 " (cutoff:3.500A) removed outlier: 8.040A pdb=" N CYS B 58 " --> pdb=" O HIS B 6 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ILE B 8 " --> pdb=" O CYS B 58 " (cutoff:3.500A) removed outlier: 8.621A pdb=" N GLU B 60 " --> pdb=" O ILE B 8 " (cutoff:3.500A) removed outlier: 8.437A pdb=" N ILE B 10 " --> pdb=" O GLU B 60 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 236 through 237 removed outlier: 3.796A 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: 6.520A pdb=" N HIS C 6 " --> pdb=" O HIS C 56 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N CYS C 58 " --> pdb=" O HIS C 6 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N ILE C 8 " --> pdb=" O CYS C 58 " (cutoff:3.500A) removed outlier: 8.465A pdb=" N GLU C 60 " --> pdb=" O ILE C 8 " (cutoff:3.500A) removed outlier: 8.383A 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: 6.673A pdb=" N HIS D 6 " --> pdb=" O HIS D 56 " (cutoff:3.500A) removed outlier: 8.085A pdb=" N CYS D 58 " --> pdb=" O HIS D 6 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ILE D 8 " --> pdb=" O CYS D 58 " (cutoff:3.500A) removed outlier: 8.477A pdb=" N GLU D 60 " --> pdb=" O ILE D 8 " (cutoff:3.500A) removed outlier: 8.288A 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: 3.776A 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 241 672 hydrogen bonds defined for protein. 1974 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 220 hydrogen bonds 424 hydrogen bond angles 0 basepair planarities 87 basepair parallelities 140 stacking parallelities Total time for adding SS restraints: 3.18 Time building geometry restraints manager: 2.29 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: 3123 1.34 - 1.46: 5359 1.46 - 1.57: 6479 1.57 - 1.69: 459 1.69 - 1.81: 84 Bond restraints: 15504 Sorted by residual: bond pdb=" P DA I 18 " pdb=" O5' DA I 18 " ideal model delta sigma weight residual 1.593 1.622 -0.029 1.00e-02 1.00e+04 8.66e+00 bond pdb=" P DA H 3 " pdb=" O5' DA H 3 " ideal model delta sigma weight residual 1.593 1.622 -0.029 1.00e-02 1.00e+04 8.42e+00 bond pdb=" P DG J 12 " pdb=" O5' DG J 12 " ideal model delta sigma weight residual 1.593 1.619 -0.026 1.00e-02 1.00e+04 6.90e+00 bond pdb=" P DT G 10 " pdb=" O5' DT G 10 " ideal model delta sigma weight residual 1.593 1.618 -0.025 1.00e-02 1.00e+04 6.45e+00 bond pdb=" C ILE C 201 " pdb=" N PRO C 202 " ideal model delta sigma weight residual 1.333 1.359 -0.026 1.01e-02 9.80e+03 6.41e+00 ... (remaining 15499 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.01: 19361 2.01 - 4.02: 2347 4.02 - 6.03: 246 6.03 - 8.04: 22 8.04 - 10.05: 4 Bond angle restraints: 21980 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 106.00 101.94 4.06 6.00e-01 2.78e+00 4.58e+01 angle pdb=" O4' DG H 16 " pdb=" C4' DG H 16 " pdb=" C3' DG H 16 " ideal model delta sigma weight residual 106.00 102.76 3.24 6.00e-01 2.78e+00 2.92e+01 angle pdb=" O3' U F 132 " pdb=" P G F 133 " pdb=" O5' G F 133 " ideal model delta sigma weight residual 104.00 114.05 -10.05 1.90e+00 2.77e-01 2.80e+01 angle pdb=" O4' DT H 19 " pdb=" C4' DT H 19 " pdb=" C3' DT H 19 " ideal model delta sigma weight residual 106.00 102.96 3.04 6.00e-01 2.78e+00 2.57e+01 angle pdb=" O4' DC J 30 " pdb=" C4' DC J 30 " pdb=" C3' DC J 30 " ideal model delta sigma weight residual 106.00 102.96 3.04 6.00e-01 2.78e+00 2.57e+01 ... (remaining 21975 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.82: 8658 34.82 - 69.63: 606 69.63 - 104.45: 53 104.45 - 139.27: 0 139.27 - 174.09: 1 Dihedral angle restraints: 9318 sinusoidal: 5712 harmonic: 3606 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 -128.00 46.09 -174.09 1 1.70e+01 3.46e-03 6.63e+01 dihedral pdb=" O4' C E 42 " pdb=" C2' C E 42 " pdb=" C1' C E 42 " pdb=" C3' C E 42 " ideal model delta sinusoidal sigma weight residual 25.00 -9.61 34.61 1 8.00e+00 1.56e-02 2.65e+01 dihedral pdb=" C4' C E 42 " pdb=" O4' C E 42 " pdb=" C1' C E 42 " pdb=" C2' C E 42 " ideal model delta sinusoidal sigma weight residual 3.00 -29.14 32.14 1 8.00e+00 1.56e-02 2.30e+01 ... (remaining 9315 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.132: 2309 0.132 - 0.265: 232 0.265 - 0.397: 0 0.397 - 0.529: 0 0.529 - 0.662: 8 Chirality restraints: 2549 Sorted by residual: chirality pdb=" P DA I 18 " pdb=" OP1 DA I 18 " pdb=" OP2 DA I 18 " pdb=" O5' DA I 18 " both_signs ideal model delta sigma weight residual True 2.34 -3.00 -0.66 2.00e-01 2.50e+01 1.10e+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 -2.99 -0.66 2.00e-01 2.50e+01 1.07e+01 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 -2.99 -0.65 2.00e-01 2.50e+01 1.06e+01 ... (remaining 2546 not shown) Planarity restraints: 1975 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A F 157 " -0.071 2.00e-02 2.50e+03 2.87e-02 2.27e+01 pdb=" N9 A F 157 " 0.046 2.00e-02 2.50e+03 pdb=" C8 A F 157 " 0.016 2.00e-02 2.50e+03 pdb=" N7 A F 157 " 0.007 2.00e-02 2.50e+03 pdb=" C5 A F 157 " 0.005 2.00e-02 2.50e+03 pdb=" C6 A F 157 " -0.016 2.00e-02 2.50e+03 pdb=" N6 A F 157 " -0.028 2.00e-02 2.50e+03 pdb=" N1 A F 157 " 0.001 2.00e-02 2.50e+03 pdb=" C2 A F 157 " 0.006 2.00e-02 2.50e+03 pdb=" N3 A F 157 " 0.015 2.00e-02 2.50e+03 pdb=" C4 A F 157 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U F 132 " 0.040 2.00e-02 2.50e+03 2.08e-02 9.72e+00 pdb=" N1 U F 132 " -0.043 2.00e-02 2.50e+03 pdb=" C2 U F 132 " -0.012 2.00e-02 2.50e+03 pdb=" O2 U F 132 " -0.002 2.00e-02 2.50e+03 pdb=" N3 U F 132 " 0.007 2.00e-02 2.50e+03 pdb=" C4 U F 132 " 0.010 2.00e-02 2.50e+03 pdb=" O4 U F 132 " 0.008 2.00e-02 2.50e+03 pdb=" C5 U F 132 " -0.001 2.00e-02 2.50e+03 pdb=" C6 U F 132 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT I 26 " 0.040 2.00e-02 2.50e+03 1.96e-02 9.64e+00 pdb=" N1 DT I 26 " -0.042 2.00e-02 2.50e+03 pdb=" C2 DT I 26 " -0.009 2.00e-02 2.50e+03 pdb=" O2 DT I 26 " -0.004 2.00e-02 2.50e+03 pdb=" N3 DT I 26 " 0.001 2.00e-02 2.50e+03 pdb=" C4 DT I 26 " 0.008 2.00e-02 2.50e+03 pdb=" O4 DT I 26 " 0.015 2.00e-02 2.50e+03 pdb=" C5 DT I 26 " -0.001 2.00e-02 2.50e+03 pdb=" C7 DT I 26 " -0.006 2.00e-02 2.50e+03 pdb=" C6 DT I 26 " -0.002 2.00e-02 2.50e+03 ... (remaining 1972 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.27: 15 2.27 - 2.92: 5204 2.92 - 3.58: 21840 3.58 - 4.24: 39791 4.24 - 4.90: 60500 Nonbonded interactions: 127350 Sorted by model distance: nonbonded pdb=" OG SER B 241 " pdb=" P DT I 21 " model vdw 1.607 3.400 nonbonded pdb=" OG SER D 241 " pdb=" P DA G 26 " model vdw 1.609 3.400 nonbonded pdb=" OE2 GLU C 60 " pdb="MG MG C 401 " model vdw 1.856 2.170 nonbonded pdb="MG MG C 401 " pdb=" O HOH C 502 " model vdw 1.908 2.170 nonbonded pdb="MG MG A 401 " pdb=" O HOH G 101 " model vdw 1.965 2.170 ... (remaining 127345 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 220 or resid 222 through 321)) selection = (chain 'B' and (resid 5 through 220 or resid 222 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 220 or resid 222 through 321)) selection = (chain 'D' 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 220 or resid 222 through 238 or r \ esid 251 through 321)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 18.330 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8988 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 0.044 15504 Z= 0.558 Angle : 1.337 10.051 21980 Z= 0.908 Chirality : 0.081 0.662 2549 Planarity : 0.005 0.044 1975 Dihedral : 19.929 174.086 6984 Min Nonbonded Distance : 1.607 Molprobity Statistics. All-atom Clashscore : 0.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Rotamer: Outliers : 0.40 % Allowed : 2.47 % Favored : 97.13 % 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: -1.54 (0.20), residues: 1237 helix: -0.78 (0.15), residues: 786 sheet: -0.88 (0.37), residues: 160 loop : -1.21 (0.30), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.003 ARG A 300 TYR 0.024 0.003 TYR B 264 PHE 0.024 0.004 PHE A 231 TRP 0.037 0.009 TRP D 169 HIS 0.012 0.002 HIS D 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00817 / 0.56 (15504) covalent geometry : angle 1.33663 / 0.91 (21980) hydrogen bonds : bond 0.20172 / 13.52 ( 892) hydrogen bonds : angle 6.42089 / 4.60 ( 2398) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 104 time to evaluate : 0.434 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 51 LYS cc_start: 0.9418 (mttm) cc_final: 0.9211 (mtmm) REVERT: B 71 GLU cc_start: 0.8623 (mt-10) cc_final: 0.8372 (mt-10) REVERT: C 265 MET cc_start: 0.9357 (mmm) cc_final: 0.9029 (mmt) REVERT: D 105 ASP cc_start: 0.8265 (t70) cc_final: 0.8041 (p0) REVERT: D 287 ASN cc_start: 0.9065 (t0) cc_final: 0.8504 (t0) REVERT: D 307 TYR cc_start: 0.9076 (t80) cc_final: 0.8660 (t80) outliers start: 4 outliers final: 2 residues processed: 106 average time/residue: 0.9834 time to fit residues: 110.8953 Evaluate side-chains 77 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 75 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain C residue 60 GLU 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: 0.9980 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 20.0000 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 20.0000 chunk 91 optimal weight: 4.9990 chunk 55 optimal weight: 0.8980 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 139 GLN B 93 GLN B 99 ASN B 139 GLN D 99 ASN D 256 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.081850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2634 r_free = 0.2634 target = 0.054363 restraints weight = 46085.092| |-----------------------------------------------------------------------------| r_work (start): 0.2578 rms_B_bonded: 2.42 r_work: 0.2381 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.2381 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2418 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2418 r_free = 0.2418 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2418 r_free = 0.2418 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.2418 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.1478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15504 Z= 0.169 Angle : 0.613 7.155 21980 Z= 0.362 Chirality : 0.043 0.287 2549 Planarity : 0.005 0.041 1975 Dihedral : 22.039 175.050 4558 Min Nonbonded Distance : 1.769 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % Rotamer: Outliers : 0.79 % Allowed : 6.72 % Favored : 92.49 % 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: 1.72 (0.23), residues: 1237 helix: 2.02 (0.18), residues: 794 sheet: -0.27 (0.39), residues: 162 loop : -0.48 (0.34), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 160 TYR 0.020 0.002 TYR B 215 PHE 0.014 0.001 PHE C 280 TRP 0.026 0.003 TRP D 46 HIS 0.005 0.001 HIS D 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.17 (15504) covalent geometry : angle 0.61256 / 0.36 (21980) hydrogen bonds : bond 0.06417 / 4.28 ( 892) hydrogen bonds : angle 4.08096 / 2.95 ( 2398) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 78 time to evaluate : 0.410 Fit side-chains revert: symmetry clash REVERT: A 54 HIS cc_start: 0.8686 (m-70) cc_final: 0.8453 (m-70) REVERT: A 221 ARG cc_start: 0.8520 (ttp80) cc_final: 0.8232 (ttm-80) REVERT: A 258 SER cc_start: 0.9312 (m) cc_final: 0.8946 (t) REVERT: B 27 ARG cc_start: 0.8273 (mtm-85) cc_final: 0.7739 (mtm110) REVERT: B 51 LYS cc_start: 0.9398 (mttm) cc_final: 0.9196 (mtmm) REVERT: D 105 ASP cc_start: 0.7756 (t70) cc_final: 0.7184 (p0) REVERT: D 187 ASP cc_start: 0.8416 (m-30) cc_final: 0.8188 (t0) REVERT: D 287 ASN cc_start: 0.8830 (t0) cc_final: 0.8556 (t160) outliers start: 8 outliers final: 0 residues processed: 83 average time/residue: 0.8583 time to fit residues: 76.5622 Evaluate side-chains 75 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 75 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 128 optimal weight: 10.0000 chunk 127 optimal weight: 20.0000 chunk 28 optimal weight: 5.9990 chunk 31 optimal weight: 6.9990 chunk 100 optimal weight: 1.9990 chunk 63 optimal weight: 7.9990 chunk 79 optimal weight: 1.9990 chunk 132 optimal weight: 10.0000 chunk 47 optimal weight: 4.9990 chunk 71 optimal weight: 4.9990 chunk 121 optimal weight: 5.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 93 GLN B 139 GLN C 287 ASN D 99 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.078486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2564 r_free = 0.2564 target = 0.050841 restraints weight = 57861.152| |-----------------------------------------------------------------------------| r_work (start): 0.2536 rms_B_bonded: 2.62 r_work: 0.2328 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2328 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2338 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2338 r_free = 0.2338 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2338 r_free = 0.2338 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2338 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.1721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.051 15504 Z= 0.317 Angle : 0.639 7.397 21980 Z= 0.363 Chirality : 0.047 0.229 2549 Planarity : 0.005 0.047 1975 Dihedral : 22.067 173.722 4554 Min Nonbonded Distance : 1.721 Molprobity Statistics. All-atom Clashscore : 2.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Rotamer: Outliers : 0.89 % Allowed : 8.00 % Favored : 91.11 % 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: 2.03 (0.24), residues: 1237 helix: 2.29 (0.18), residues: 793 sheet: -0.36 (0.37), residues: 176 loop : -0.27 (0.36), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 98 TYR 0.015 0.002 TYR B 307 PHE 0.018 0.002 PHE B 231 TRP 0.021 0.003 TRP D 46 HIS 0.007 0.001 HIS D 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00689 / 0.32 (15504) covalent geometry : angle 0.63865 / 0.36 (21980) hydrogen bonds : bond 0.06961 / 4.62 ( 892) hydrogen bonds : angle 3.95373 / 2.87 ( 2398) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 77 time to evaluate : 0.437 Fit side-chains REVERT: A 54 HIS cc_start: 0.8740 (m-70) cc_final: 0.8531 (m-70) REVERT: A 221 ARG cc_start: 0.8578 (ttp80) cc_final: 0.8222 (ttm-80) REVERT: A 258 SER cc_start: 0.9309 (m) cc_final: 0.8949 (t) REVERT: B 27 ARG cc_start: 0.8284 (mtm-85) cc_final: 0.7917 (mtm110) REVERT: B 51 LYS cc_start: 0.9401 (mttm) cc_final: 0.9176 (mtmm) REVERT: D 105 ASP cc_start: 0.7945 (t0) cc_final: 0.7314 (p0) REVERT: D 187 ASP cc_start: 0.8457 (m-30) cc_final: 0.8244 (t0) REVERT: D 287 ASN cc_start: 0.8882 (t0) cc_final: 0.8550 (t160) outliers start: 9 outliers final: 2 residues processed: 81 average time/residue: 0.8293 time to fit residues: 72.3793 Evaluate side-chains 73 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 71 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 60 GLU Chi-restraints excluded: chain C residue 150 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 39 optimal weight: 6.9990 chunk 20 optimal weight: 0.9980 chunk 1 optimal weight: 2.9990 chunk 77 optimal weight: 0.7980 chunk 48 optimal weight: 2.9990 chunk 64 optimal weight: 4.9990 chunk 66 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 chunk 80 optimal weight: 0.8980 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 93 GLN B 139 GLN C 287 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.080719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2626 r_free = 0.2626 target = 0.053560 restraints weight = 42184.778| |-----------------------------------------------------------------------------| r_work (start): 0.2573 rms_B_bonded: 2.29 r_work: 0.2380 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.2242 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2242 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2280 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2280 r_free = 0.2280 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2280 r_free = 0.2280 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2280 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.1983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 15504 Z= 0.170 Angle : 0.529 6.661 21980 Z= 0.314 Chirality : 0.040 0.300 2549 Planarity : 0.004 0.047 1975 Dihedral : 22.053 174.771 4554 Min Nonbonded Distance : 1.795 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Rotamer: Outliers : 0.59 % Allowed : 8.99 % Favored : 90.42 % 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: 2.29 (0.24), residues: 1237 helix: 2.50 (0.18), residues: 794 sheet: -0.17 (0.38), residues: 162 loop : -0.31 (0.35), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 221 TYR 0.014 0.002 TYR B 215 PHE 0.012 0.002 PHE B 112 TRP 0.017 0.002 TRP D 46 HIS 0.004 0.001 HIS D 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.17 (15504) covalent geometry : angle 0.52860 / 0.31 (21980) hydrogen bonds : bond 0.05513 / 3.67 ( 892) hydrogen bonds : angle 3.80261 / 2.76 ( 2398) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 74 time to evaluate : 0.481 Fit side-chains REVERT: A 221 ARG cc_start: 0.8724 (ttp80) cc_final: 0.8307 (ttm-80) REVERT: A 258 SER cc_start: 0.9332 (m) cc_final: 0.8993 (t) REVERT: B 27 ARG cc_start: 0.8274 (mtm-85) cc_final: 0.7874 (mtm110) REVERT: B 51 LYS cc_start: 0.9402 (mttm) cc_final: 0.9193 (mtmm) REVERT: D 287 ASN cc_start: 0.8799 (t0) cc_final: 0.8457 (t160) outliers start: 6 outliers final: 1 residues processed: 76 average time/residue: 0.8091 time to fit residues: 66.3326 Evaluate side-chains 73 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 72 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 60 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 78 optimal weight: 3.9990 chunk 119 optimal weight: 5.9990 chunk 22 optimal weight: 0.9980 chunk 82 optimal weight: 6.9990 chunk 95 optimal weight: 0.9980 chunk 2 optimal weight: 2.9990 chunk 70 optimal weight: 0.6980 chunk 33 optimal weight: 6.9990 chunk 120 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 140 optimal weight: 10.0000 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 93 GLN B 139 GLN C 287 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.081258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2648 r_free = 0.2648 target = 0.054527 restraints weight = 36268.776| |-----------------------------------------------------------------------------| r_work (start): 0.2595 rms_B_bonded: 2.12 r_work: 0.2410 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2274 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2274 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2312 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2312 r_free = 0.2312 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2312 r_free = 0.2312 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2312 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.2165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15504 Z= 0.157 Angle : 0.512 6.830 21980 Z= 0.303 Chirality : 0.039 0.317 2549 Planarity : 0.004 0.047 1975 Dihedral : 21.970 174.872 4554 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Rotamer: Outliers : 0.69 % Allowed : 9.58 % Favored : 89.72 % 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: 2.47 (0.24), residues: 1237 helix: 2.63 (0.18), residues: 794 sheet: -0.12 (0.38), residues: 162 loop : -0.19 (0.36), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 27 TYR 0.023 0.002 TYR B 74 PHE 0.012 0.002 PHE B 112 TRP 0.014 0.002 TRP D 46 HIS 0.005 0.001 HIS D 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.16 (15504) covalent geometry : angle 0.51200 / 0.30 (21980) hydrogen bonds : bond 0.05175 / 3.44 ( 892) hydrogen bonds : angle 3.69513 / 2.68 ( 2398) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 76 time to evaluate : 0.425 Fit side-chains REVERT: A 221 ARG cc_start: 0.8738 (ttp80) cc_final: 0.8310 (ttm-80) REVERT: A 258 SER cc_start: 0.9269 (m) cc_final: 0.8936 (t) REVERT: B 27 ARG cc_start: 0.8202 (mtm-85) cc_final: 0.7758 (mtm110) REVERT: B 51 LYS cc_start: 0.9387 (mttm) cc_final: 0.9176 (mtmm) outliers start: 7 outliers final: 3 residues processed: 81 average time/residue: 0.7232 time to fit residues: 63.4915 Evaluate side-chains 75 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 72 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 60 GLU Chi-restraints excluded: chain C residue 150 ASN Chi-restraints excluded: chain D residue 84 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 2 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 chunk 90 optimal weight: 0.7980 chunk 1 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 31 optimal weight: 8.9990 chunk 36 optimal weight: 0.9980 chunk 8 optimal weight: 0.6980 chunk 3 optimal weight: 0.9980 chunk 138 optimal weight: 10.0000 chunk 64 optimal weight: 7.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 304 GLN B 93 GLN B 139 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 = 0.3173 r_free = 0.3173 target = 0.082454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2675 r_free = 0.2675 target = 0.055658 restraints weight = 36132.216| |-----------------------------------------------------------------------------| r_work (start): 0.2622 rms_B_bonded: 2.13 r_work: 0.2438 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2304 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2304 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2342 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2342 r_free = 0.2342 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2342 r_free = 0.2342 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.2342 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.2306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 15504 Z= 0.125 Angle : 0.483 7.192 21980 Z= 0.290 Chirality : 0.038 0.327 2549 Planarity : 0.004 0.048 1975 Dihedral : 21.942 175.054 4554 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Rotamer: Outliers : 0.49 % Allowed : 9.98 % Favored : 89.53 % 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: 2.61 (0.24), residues: 1237 helix: 2.73 (0.18), residues: 794 sheet: -0.07 (0.38), residues: 162 loop : -0.11 (0.36), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 27 TYR 0.013 0.001 TYR C 307 PHE 0.011 0.001 PHE B 112 TRP 0.013 0.001 TRP D 46 HIS 0.005 0.001 HIS D 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.13 (15504) covalent geometry : angle 0.48272 / 0.29 (21980) hydrogen bonds : bond 0.04738 / 3.15 ( 892) hydrogen bonds : angle 3.62257 / 2.63 ( 2398) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 76 time to evaluate : 0.384 Fit side-chains REVERT: A 221 ARG cc_start: 0.8750 (ttp80) cc_final: 0.8324 (ttm-80) REVERT: A 258 SER cc_start: 0.9281 (m) cc_final: 0.8956 (t) REVERT: B 27 ARG cc_start: 0.8220 (mtm-85) cc_final: 0.7728 (mtm110) REVERT: B 51 LYS cc_start: 0.9310 (mttm) cc_final: 0.9098 (mtmm) REVERT: D 105 ASP cc_start: 0.7905 (t0) cc_final: 0.7475 (m-30) outliers start: 5 outliers final: 2 residues processed: 79 average time/residue: 0.7186 time to fit residues: 61.4236 Evaluate side-chains 74 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 72 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 150 ASN Chi-restraints excluded: chain D residue 158 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 67 optimal weight: 1.9990 chunk 131 optimal weight: 10.0000 chunk 92 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 109 optimal weight: 0.9980 chunk 65 optimal weight: 2.9990 chunk 90 optimal weight: 4.9990 chunk 93 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 132 optimal weight: 10.0000 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 93 GLN B 139 GLN C 287 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.080888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2628 r_free = 0.2628 target = 0.053333 restraints weight = 52447.405| |-----------------------------------------------------------------------------| r_work (start): 0.2600 rms_B_bonded: 2.53 r_work: 0.2398 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2398 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2408 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2408 r_free = 0.2408 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2408 r_free = 0.2408 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2408 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.2284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 15504 Z= 0.191 Angle : 0.515 6.515 21980 Z= 0.301 Chirality : 0.040 0.292 2549 Planarity : 0.004 0.048 1975 Dihedral : 21.925 174.616 4554 Min Nonbonded Distance : 1.792 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % Rotamer: Outliers : 0.49 % Allowed : 10.77 % Favored : 88.74 % 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: 2.60 (0.24), residues: 1237 helix: 2.72 (0.18), residues: 794 sheet: -0.02 (0.38), residues: 162 loop : -0.11 (0.36), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 129 TYR 0.015 0.001 TYR B 74 PHE 0.014 0.002 PHE B 112 TRP 0.013 0.002 TRP D 46 HIS 0.006 0.001 HIS D 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.19 (15504) covalent geometry : angle 0.51482 / 0.30 (21980) hydrogen bonds : bond 0.05278 / 3.49 ( 892) hydrogen bonds : angle 3.64741 / 2.65 ( 2398) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 74 time to evaluate : 0.347 Fit side-chains REVERT: A 221 ARG cc_start: 0.8671 (ttp80) cc_final: 0.8302 (ttm-80) REVERT: A 258 SER cc_start: 0.9227 (m) cc_final: 0.8888 (t) REVERT: B 27 ARG cc_start: 0.8148 (mtm-85) cc_final: 0.7626 (mtm110) REVERT: B 51 LYS cc_start: 0.9304 (mttm) cc_final: 0.9083 (mtmm) REVERT: B 66 MET cc_start: 0.8941 (OUTLIER) cc_final: 0.7607 (ppp) REVERT: D 105 ASP cc_start: 0.7875 (t0) cc_final: 0.7505 (m-30) outliers start: 5 outliers final: 2 residues processed: 77 average time/residue: 0.7020 time to fit residues: 58.5775 Evaluate side-chains 75 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 72 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 MET Chi-restraints excluded: chain C residue 150 ASN Chi-restraints excluded: chain D residue 158 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 104 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 24 optimal weight: 0.7980 chunk 74 optimal weight: 2.9990 chunk 90 optimal weight: 3.9990 chunk 107 optimal weight: 0.6980 chunk 89 optimal weight: 2.9990 chunk 93 optimal weight: 3.9990 chunk 83 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 chunk 52 optimal weight: 0.8980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 93 GLN B 139 GLN C 287 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.081692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2652 r_free = 0.2652 target = 0.054439 restraints weight = 46318.864| |-----------------------------------------------------------------------------| r_work (start): 0.2594 rms_B_bonded: 2.39 r_work: 0.2398 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2398 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2437 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2437 r_free = 0.2437 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2437 r_free = 0.2437 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2437 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.2315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 15504 Z= 0.128 Angle : 0.492 6.603 21980 Z= 0.293 Chirality : 0.038 0.294 2549 Planarity : 0.004 0.048 1975 Dihedral : 21.941 174.826 4554 Min Nonbonded Distance : 1.794 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % Rotamer: Outliers : 0.40 % Allowed : 11.17 % Favored : 88.44 % 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: 2.68 (0.24), residues: 1237 helix: 2.79 (0.18), residues: 794 sheet: -0.05 (0.38), residues: 161 loop : -0.08 (0.36), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 129 TYR 0.015 0.002 TYR C 307 PHE 0.011 0.001 PHE B 112 TRP 0.011 0.001 TRP D 46 HIS 0.004 0.001 HIS D 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.13 (15504) covalent geometry : angle 0.49247 / 0.29 (21980) hydrogen bonds : bond 0.04962 / 3.29 ( 892) hydrogen bonds : angle 3.63176 / 2.63 ( 2398) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 74 time to evaluate : 0.401 Fit side-chains REVERT: A 221 ARG cc_start: 0.8652 (ttp80) cc_final: 0.8286 (ttm-80) REVERT: A 258 SER cc_start: 0.9207 (m) cc_final: 0.8869 (t) REVERT: B 27 ARG cc_start: 0.8120 (mtm-85) cc_final: 0.7567 (mtm110) REVERT: B 51 LYS cc_start: 0.9372 (mttm) cc_final: 0.9150 (mtmm) REVERT: B 66 MET cc_start: 0.8914 (OUTLIER) cc_final: 0.7545 (ppp) REVERT: D 105 ASP cc_start: 0.7792 (t0) cc_final: 0.7458 (m-30) outliers start: 4 outliers final: 2 residues processed: 76 average time/residue: 0.7073 time to fit residues: 58.2434 Evaluate side-chains 75 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 72 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 MET Chi-restraints excluded: chain C residue 150 ASN Chi-restraints excluded: chain D residue 158 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 41 optimal weight: 0.7980 chunk 1 optimal weight: 1.9990 chunk 121 optimal weight: 2.9990 chunk 140 optimal weight: 10.0000 chunk 110 optimal weight: 0.8980 chunk 59 optimal weight: 0.8980 chunk 81 optimal weight: 0.6980 chunk 50 optimal weight: 3.9990 chunk 79 optimal weight: 0.7980 chunk 109 optimal weight: 0.8980 chunk 123 optimal weight: 10.0000 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 93 GLN B 139 GLN C 287 ASN D 287 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.082704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2679 r_free = 0.2679 target = 0.055652 restraints weight = 43750.020| |-----------------------------------------------------------------------------| r_work (start): 0.2624 rms_B_bonded: 2.32 r_work: 0.2430 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work: 0.2292 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2292 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2301 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2301 r_free = 0.2301 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2301 r_free = 0.2301 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2301 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.2429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 15504 Z= 0.123 Angle : 0.483 6.632 21980 Z= 0.287 Chirality : 0.037 0.296 2549 Planarity : 0.004 0.048 1975 Dihedral : 21.913 175.106 4554 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Rotamer: Outliers : 0.59 % Allowed : 10.87 % Favored : 88.54 % 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: 2.72 (0.24), residues: 1237 helix: 2.82 (0.18), residues: 794 sheet: -0.06 (0.38), residues: 161 loop : -0.04 (0.36), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 129 TYR 0.014 0.001 TYR C 307 PHE 0.009 0.001 PHE C 280 TRP 0.013 0.001 TRP D 46 HIS 0.006 0.001 HIS D 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00224 / 0.12 (15504) covalent geometry : angle 0.48288 / 0.29 (21980) hydrogen bonds : bond 0.04666 / 3.09 ( 892) hydrogen bonds : angle 3.57775 / 2.60 ( 2398) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 75 time to evaluate : 0.450 Fit side-chains REVERT: A 221 ARG cc_start: 0.8783 (ttp80) cc_final: 0.8345 (ttm-80) REVERT: A 258 SER cc_start: 0.9275 (m) cc_final: 0.8958 (t) REVERT: B 51 LYS cc_start: 0.9388 (mttm) cc_final: 0.9176 (mtmm) REVERT: D 105 ASP cc_start: 0.7945 (t0) cc_final: 0.7550 (m-30) outliers start: 6 outliers final: 2 residues processed: 78 average time/residue: 0.7592 time to fit residues: 64.2091 Evaluate side-chains 76 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 74 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 150 ASN Chi-restraints excluded: chain D residue 158 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 89 optimal weight: 1.9990 chunk 122 optimal weight: 20.0000 chunk 67 optimal weight: 0.7980 chunk 75 optimal weight: 0.5980 chunk 133 optimal weight: 20.0000 chunk 14 optimal weight: 0.8980 chunk 119 optimal weight: 5.9990 chunk 58 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 102 optimal weight: 0.4980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 93 GLN B 139 GLN C 287 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.083480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2690 r_free = 0.2690 target = 0.055979 restraints weight = 54991.321| |-----------------------------------------------------------------------------| r_work (start): 0.2662 rms_B_bonded: 2.60 r_work: 0.2463 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2463 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2446 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2446 r_free = 0.2446 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2446 r_free = 0.2446 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.47 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: 0.8480 moved from start: 0.2601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 15504 Z= 0.127 Angle : 0.472 6.722 21980 Z= 0.280 Chirality : 0.036 0.277 2549 Planarity : 0.004 0.049 1975 Dihedral : 21.881 174.955 4554 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Rotamer: Outliers : 0.30 % Allowed : 11.46 % Favored : 88.24 % 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: 2.88 (0.24), residues: 1237 helix: 2.91 (0.18), residues: 794 sheet: 0.14 (0.38), residues: 160 loop : 0.03 (0.37), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 27 TYR 0.014 0.001 TYR B 307 PHE 0.012 0.001 PHE B 112 TRP 0.012 0.001 TRP D 46 HIS 0.006 0.001 HIS D 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.13 (15504) covalent geometry : angle 0.47237 / 0.28 (21980) hydrogen bonds : bond 0.04466 / 2.95 ( 892) hydrogen bonds : angle 3.48676 / 2.53 ( 2398) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 76 time to evaluate : 0.450 Fit side-chains REVERT: A 221 ARG cc_start: 0.8714 (ttp80) cc_final: 0.8330 (ttm-80) REVERT: A 258 SER cc_start: 0.9217 (m) cc_final: 0.8890 (t) REVERT: A 265 MET cc_start: 0.9245 (mmm) cc_final: 0.9023 (mmp) REVERT: B 27 ARG cc_start: 0.8319 (mtm-85) cc_final: 0.7982 (mtp-110) REVERT: D 105 ASP cc_start: 0.7878 (t0) cc_final: 0.7515 (m-30) outliers start: 3 outliers final: 1 residues processed: 77 average time/residue: 0.7173 time to fit residues: 60.0700 Evaluate side-chains 75 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 74 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 158 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 75 optimal weight: 0.6980 chunk 50 optimal weight: 4.9990 chunk 7 optimal weight: 2.9990 chunk 111 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 54 optimal weight: 6.9990 chunk 121 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 31 optimal weight: 7.9990 chunk 26 optimal weight: 5.9990 chunk 67 optimal weight: 0.8980 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 93 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.081852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2651 r_free = 0.2651 target = 0.054226 restraints weight = 53656.123| |-----------------------------------------------------------------------------| r_work (start): 0.2622 rms_B_bonded: 2.56 r_work: 0.2420 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2420 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2431 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2431 r_free = 0.2431 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2431 r_free = 0.2431 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2431 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.2494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 15504 Z= 0.176 Angle : 0.499 8.178 21980 Z= 0.290 Chirality : 0.038 0.210 2549 Planarity : 0.004 0.048 1975 Dihedral : 21.894 174.699 4554 Min Nonbonded Distance : 1.797 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Rotamer: Outliers : 0.20 % Allowed : 11.96 % Favored : 87.85 % 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: 1237 helix: 2.86 (0.18), residues: 793 sheet: 0.07 (0.38), residues: 162 loop : 0.01 (0.37), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 27 TYR 0.013 0.001 TYR C 307 PHE 0.013 0.002 PHE B 112 TRP 0.012 0.002 TRP C 46 HIS 0.006 0.001 HIS D 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.18 (15504) covalent geometry : angle 0.49923 / 0.29 (21980) hydrogen bonds : bond 0.04995 / 3.30 ( 892) hydrogen bonds : angle 3.53861 / 2.57 ( 2398) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5006.32 seconds wall clock time: 86 minutes 7.83 seconds (5167.83 seconds total)