Starting phenix.real_space_refine on Thu Aug 6 09:35:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wt9_37830/08_2026/8wt9_37830.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wt9_37830/08_2026/8wt9_37830.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/8wt9_37830/08_2026/8wt9_37830.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wt9_37830/08_2026/8wt9_37830.map" model { file = "/net/cci-nas-00/data/ceres_data/8wt9_37830/08_2026/8wt9_37830.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wt9_37830/08_2026/8wt9_37830.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.028 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 241 5.49 5 Mg 2 5.21 5 S 48 5.16 5 C 8557 2.51 5 N 2771 2.21 5 O 3363 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 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: 14982 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 2530 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 319, 2515 Classifications: {'peptide': 319} Link IDs: {'PTRANS': 12, 'TRANS': 306} Conformer: "B" Number of residues, atoms: 319, 2515 Classifications: {'peptide': 319} Link IDs: {'PTRANS': 12, 'TRANS': 306} bond proxies already assigned to first conformer: 2547 Chain: "B" Number of atoms: 2449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2449 Classifications: {'peptide': 311} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 12, 'TRANS': 298} Chain breaks: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ARG:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "C" Number of atoms: 2517 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 318, 2506 Classifications: {'peptide': 318} Link IDs: {'PTRANS': 12, 'TRANS': 305} Conformer: "B" Number of residues, atoms: 318, 2506 Classifications: {'peptide': 318} Link IDs: {'PTRANS': 12, 'TRANS': 305} bond proxies already assigned to first conformer: 2543 Chain: "D" Number of atoms: 2456 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 310, 2447 Classifications: {'peptide': 310} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 297} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Conformer: "B" Number of residues, atoms: 310, 2447 Classifications: {'peptide': 310} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 297} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 bond proxies already assigned to first conformer: 2485 Chain: "E" Number of atoms: 1249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 1249 Classifications: {'RNA': 59} Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 11, 'rna3p_pur': 22, 'rna3p_pyr': 22} Link IDs: {'rna2p': 14, 'rna3p': 44} Chain: "F" Number of atoms: 1442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 1442 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: 580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 580 Classifications: {'DNA': 29} Link IDs: {'rna3p': 28} 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 breaks: 1 Chain: "I" Number of atoms: 555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 555 Classifications: {'DNA': 27} Link IDs: {'rna3p': 26} Chain: "J" Number of atoms: 643 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 29, 602 Classifications: {'DNA': 29} Link IDs: {'rna3p': 28} Conformer: "B" Number of residues, atoms: 29, 602 Classifications: {'DNA': 29} Link IDs: {'rna3p': 28} Chain breaks: 1 bond proxies already assigned to first conformer: 630 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "B" 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: 6 residue: pdb=" N AGLN A 139 " occ=0.50 ... (16 atoms not shown) pdb=" NE2BGLN A 139 " occ=0.50 residue: pdb=" N ASER A 241 " occ=0.50 ... (10 atoms not shown) pdb=" OG BSER A 241 " occ=0.50 residue: pdb=" N AARG C 237 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG C 237 " occ=0.50 residue: pdb=" N AGLN D 139 " occ=0.50 ... (16 atoms not shown) pdb=" NE2BGLN D 139 " occ=0.50 residue: pdb=" P A DT J 28 " occ=0.50 ... (38 atoms not shown) pdb=" C6 B DT J 28 " occ=0.50 residue: pdb=" P A DA J 29 " occ=0.50 ... (40 atoms not shown) pdb=" C4 B DA J 29 " occ=0.50 Time building chain proxies: 4.79, per 1000 atoms: 0.32 Number of scatterers: 14982 At special positions: 0 Unit cell: (122.84, 123.947, 116.2, 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 241 15.00 Mg 2 11.99 O 3363 8.00 N 2771 7.00 C 8557 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: 1.20 Conformation dependent library (CDL) restraints added in 766.5 milliseconds 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2364 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 8 sheets defined 67.2% alpha, 10.7% beta 87 base pairs and 148 stacking pairs defined. Time for finding SS restraints: 2.04 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: 3.627A pdb=" N GLY A 88 " --> pdb=" O ASN A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 117 Processing helix chain 'A' and resid 125 through 155 removed outlier: 4.162A pdb=" N GLU A 153 " --> pdb=" O LEU A 149 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N THR A 154 " --> pdb=" O ASN A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 188 removed outlier: 3.656A pdb=" N ASP A 188 " --> pdb=" O LEU A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 199 Processing helix chain 'A' and resid 205 through 217 Processing helix chain 'A' and resid 224 through 232 removed outlier: 3.671A pdb=" N PHE A 228 " --> pdb=" O HIS A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 263 removed outlier: 3.756A pdb=" N LEU A 263 " --> pdb=" O LEU A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 274 Processing helix chain 'A' and resid 274 through 287 removed outlier: 3.532A 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 removed outlier: 3.588A 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 63 through 65 No H-bonds generated for 'chain 'B' and resid 63 through 65' Processing helix chain 'B' and resid 66 through 77 Processing helix chain 'B' and resid 84 through 95 removed outlier: 3.532A pdb=" N GLY B 88 " --> pdb=" O ASN B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 117 Processing helix chain 'B' and resid 125 through 154 removed outlier: 3.810A pdb=" N GLU B 153 " --> pdb=" O LEU B 149 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N THR B 154 " --> pdb=" O ASN B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 188 removed outlier: 3.624A 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: 3.729A 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: 3.714A 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 96 removed outlier: 3.544A pdb=" N GLY C 88 " --> pdb=" O ASN C 84 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLY C 96 " --> pdb=" O ALA C 92 " (cutoff:3.500A) Processing helix chain 'C' and resid 105 through 117 Processing helix chain 'C' and resid 125 through 153 removed outlier: 3.912A pdb=" N GLU C 153 " --> pdb=" O LEU C 149 " (cutoff:3.500A) Processing helix chain 'C' and resid 159 through 188 removed outlier: 3.626A 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: 3.649A pdb=" N PHE C 228 " --> pdb=" O HIS C 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 256 through 262 removed outlier: 3.596A 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 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 49 Processing helix chain 'D' and resid 66 through 77 Processing helix chain 'D' and resid 84 through 95 Processing helix chain 'D' and resid 101 through 117 removed outlier: 3.511A pdb=" N ALA D 110 " --> pdb=" O ALA D 106 " (cutoff:3.500A) Processing helix chain 'D' and resid 125 through 152 Processing helix chain 'D' and resid 159 through 188 removed outlier: 3.653A pdb=" N ASP D 188 " --> pdb=" O LEU D 184 " (cutoff:3.500A) Processing helix chain 'D' and resid 188 through 200 Processing helix chain 'D' and resid 205 through 216 Processing helix chain 'D' and resid 224 through 232 removed outlier: 3.831A pdb=" N PHE D 228 " --> pdb=" O HIS D 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 256 through 262 removed outlier: 3.519A pdb=" N ALA D 262 " --> pdb=" O SER D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 263 through 274 Processing helix chain 'D' and resid 274 through 286 Processing helix chain 'D' and resid 290 through 313 Processing helix chain 'D' and resid 317 through 322 removed outlier: 3.633A pdb=" N ASN D 322 " --> pdb=" O SER D 319 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 34 removed outlier: 6.540A pdb=" N HIS A 6 " --> pdb=" O HIS A 56 " (cutoff:3.500A) removed outlier: 7.988A pdb=" N CYS A 58 " --> pdb=" O HIS A 6 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N ILE A 8 " --> pdb=" O CYS A 58 " (cutoff:3.500A) removed outlier: 8.517A pdb=" N GLU A 60 " --> pdb=" O ILE A 8 " (cutoff:3.500A) removed outlier: 8.357A pdb=" N ILE A 10 " --> pdb=" O GLU A 60 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 236 through 241 removed outlier: 3.685A pdb=" N ARG A 250 " --> pdb=" O ARG A 237 " (cutoff:3.500A) removed outlier: 5.855A pdb=" N TYR A 239 " --> pdb=" O ALA A 248 " (cutoff:3.500A) removed outlier: 5.490A pdb=" N ALA A 248 " --> pdb=" O TYR A 239 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N ASER A 241 " --> pdb=" O ARG A 246 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N ARG A 246 " --> pdb=" O ASER A 241 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 28 through 34 removed outlier: 4.434A pdb=" N GLU B 60 " --> pdb=" O ILE B 10 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N THR B 12 " --> pdb=" O GLU B 60 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 236 through 237 Processing sheet with id=AA5, first strand: chain 'C' and resid 28 through 34 removed outlier: 6.782A pdb=" N HIS C 6 " --> pdb=" O HIS C 56 " (cutoff:3.500A) removed outlier: 7.995A pdb=" N CYS C 58 " --> pdb=" O HIS C 6 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ILE C 8 " --> pdb=" O CYS C 58 " (cutoff:3.500A) removed outlier: 8.496A pdb=" N GLU C 60 " --> pdb=" O ILE C 8 " (cutoff:3.500A) removed outlier: 8.392A pdb=" N ILE C 10 " --> pdb=" O GLU C 60 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 236 through 241 removed outlier: 3.915A pdb=" N ARG C 250 " --> pdb=" O AARG C 237 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N TYR C 239 " --> pdb=" O ALA C 248 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N ALA C 248 " --> pdb=" O TYR C 239 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N SER C 241 " --> pdb=" O ARG C 246 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N ARG C 246 " --> pdb=" O SER C 241 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 28 through 34 removed outlier: 6.664A pdb=" N HIS D 6 " --> pdb=" O HIS D 56 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N CYS D 58 " --> pdb=" O HIS D 6 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ILE D 8 " --> pdb=" O CYS D 58 " (cutoff:3.500A) removed outlier: 8.576A pdb=" N GLU D 60 " --> pdb=" O ILE D 8 " (cutoff:3.500A) removed outlier: 8.372A pdb=" N ILE D 10 " --> pdb=" O GLU D 60 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 236 through 237 680 hydrogen bonds defined for protein. 2003 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 222 hydrogen bonds 438 hydrogen bond angles 0 basepair planarities 87 basepair parallelities 150 stacking parallelities Total time for adding SS restraints: 2.76 Time building geometry restraints manager: 1.60 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: 3485 1.34 - 1.46: 5386 1.46 - 1.58: 6336 1.58 - 1.69: 475 1.69 - 1.81: 84 Bond restraints: 15766 Sorted by residual: bond pdb=" P A F 110 " pdb=" O5' A F 110 " ideal model delta sigma weight residual 1.593 1.633 -0.040 1.00e-02 1.00e+04 1.59e+01 bond pdb=" P A F 110 " pdb=" OP2 A F 110 " ideal model delta sigma weight residual 1.485 1.560 -0.075 2.00e-02 2.50e+03 1.41e+01 bond pdb=" P A F 110 " pdb=" OP1 A F 110 " ideal model delta sigma weight residual 1.485 1.559 -0.074 2.00e-02 2.50e+03 1.37e+01 bond pdb=" P DG I 5 " pdb=" O5' DG I 5 " ideal model delta sigma weight residual 1.593 1.621 -0.028 1.00e-02 1.00e+04 7.60e+00 bond pdb=" P DT G 10 " pdb=" O5' DT G 10 " ideal model delta sigma weight residual 1.593 1.619 -0.026 1.00e-02 1.00e+04 6.67e+00 ... (remaining 15761 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.10: 19899 2.10 - 4.19: 2244 4.19 - 6.29: 210 6.29 - 8.38: 14 8.38 - 10.48: 2 Bond angle restraints: 22369 Sorted by residual: angle pdb=" O4' DC H 19 " pdb=" C4' DC H 19 " pdb=" C3' DC H 19 " ideal model delta sigma weight residual 106.00 102.61 3.39 6.00e-01 2.78e+00 3.19e+01 angle pdb=" C3' C E 42 " pdb=" C2' C E 42 " pdb=" C1' C E 42 " ideal model delta sigma weight residual 101.30 104.89 -3.59 7.00e-01 2.04e+00 2.63e+01 angle pdb=" O3' DC G 15 " pdb=" P DC G 16 " pdb=" O5' DC G 16 " ideal model delta sigma weight residual 104.00 94.68 9.32 1.90e+00 2.77e-01 2.40e+01 angle pdb=" CG MET D 108 " pdb=" SD MET D 108 " pdb=" CE MET D 108 " ideal model delta sigma weight residual 100.90 111.38 -10.48 2.20e+00 2.07e-01 2.27e+01 angle pdb=" C3' U E 84 " pdb=" C2' U E 84 " pdb=" C1' U E 84 " ideal model delta sigma weight residual 101.30 104.59 -3.29 7.00e-01 2.04e+00 2.20e+01 ... (remaining 22364 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.07: 8729 34.07 - 68.13: 676 68.13 - 102.20: 52 102.20 - 136.26: 0 136.26 - 170.33: 1 Dihedral angle restraints: 9458 sinusoidal: 5803 harmonic: 3655 Sorted by residual: dihedral pdb=" C5' C E 95 " pdb=" C4' C E 95 " pdb=" C3' C E 95 " pdb=" O3' C E 95 " ideal model delta sinusoidal sigma weight residual 147.00 86.35 60.65 1 8.00e+00 1.56e-02 7.65e+01 dihedral pdb=" O4' C E 95 " pdb=" C4' C E 95 " pdb=" C3' C E 95 " pdb=" C2' C E 95 " ideal model delta sinusoidal sigma weight residual 24.00 -32.53 56.53 1 8.00e+00 1.56e-02 6.73e+01 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 61.67 170.33 1 1.70e+01 3.46e-03 6.60e+01 ... (remaining 9455 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.148: 2417 0.148 - 0.297: 168 0.297 - 0.445: 0 0.445 - 0.594: 1 0.594 - 0.742: 5 Chirality restraints: 2591 Sorted by residual: chirality pdb=" P A F 110 " pdb=" OP1 A F 110 " pdb=" OP2 A F 110 " pdb=" O5' A F 110 " both_signs ideal model delta sigma weight residual True 2.41 -3.15 -0.74 2.00e-01 2.50e+01 1.38e+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 -0.66 2.00e-01 2.50e+01 1.08e+01 chirality pdb=" P DG I 5 " pdb=" OP1 DG I 5 " pdb=" OP2 DG I 5 " pdb=" O5' DG I 5 " both_signs ideal model delta sigma weight residual True 2.34 -2.96 -0.63 2.00e-01 2.50e+01 9.89e+00 ... (remaining 2588 not shown) Planarity restraints: 2007 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A F 157 " -0.037 2.00e-02 2.50e+03 1.49e-02 6.10e+00 pdb=" N9 A F 157 " 0.022 2.00e-02 2.50e+03 pdb=" C8 A F 157 " 0.008 2.00e-02 2.50e+03 pdb=" N7 A F 157 " 0.005 2.00e-02 2.50e+03 pdb=" C5 A F 157 " 0.005 2.00e-02 2.50e+03 pdb=" C6 A F 157 " -0.010 2.00e-02 2.50e+03 pdb=" N6 A F 157 " -0.014 2.00e-02 2.50e+03 pdb=" N1 A F 157 " -0.003 2.00e-02 2.50e+03 pdb=" C2 A F 157 " 0.007 2.00e-02 2.50e+03 pdb=" N3 A F 157 " 0.007 2.00e-02 2.50e+03 pdb=" C4 A F 157 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA J 35 " -0.031 2.00e-02 2.50e+03 1.31e-02 4.72e+00 pdb=" N9 DA J 35 " 0.027 2.00e-02 2.50e+03 pdb=" C8 DA J 35 " 0.004 2.00e-02 2.50e+03 pdb=" N7 DA J 35 " 0.000 2.00e-02 2.50e+03 pdb=" C5 DA J 35 " 0.000 2.00e-02 2.50e+03 pdb=" C6 DA J 35 " -0.005 2.00e-02 2.50e+03 pdb=" N6 DA J 35 " -0.010 2.00e-02 2.50e+03 pdb=" N1 DA J 35 " -0.001 2.00e-02 2.50e+03 pdb=" C2 DA J 35 " 0.004 2.00e-02 2.50e+03 pdb=" N3 DA J 35 " 0.006 2.00e-02 2.50e+03 pdb=" C4 DA J 35 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U F 168 " -0.024 2.00e-02 2.50e+03 1.35e-02 4.11e+00 pdb=" N1 U F 168 " 0.031 2.00e-02 2.50e+03 pdb=" C2 U F 168 " 0.003 2.00e-02 2.50e+03 pdb=" O2 U F 168 " 0.001 2.00e-02 2.50e+03 pdb=" N3 U F 168 " -0.004 2.00e-02 2.50e+03 pdb=" C4 U F 168 " -0.005 2.00e-02 2.50e+03 pdb=" O4 U F 168 " -0.003 2.00e-02 2.50e+03 pdb=" C5 U F 168 " -0.003 2.00e-02 2.50e+03 pdb=" C6 U F 168 " 0.004 2.00e-02 2.50e+03 ... (remaining 2004 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.27: 9 2.27 - 2.92: 5260 2.92 - 3.58: 22496 3.58 - 4.24: 40738 4.24 - 4.90: 62012 Nonbonded interactions: 130515 Sorted by model distance: nonbonded pdb=" OG SER C 241 " pdb=" P DC H 18 " model vdw 1.607 3.400 nonbonded pdb=" OG BSER A 241 " pdb=" P B DA J 29 " model vdw 1.608 3.400 nonbonded pdb="MG MG B 401 " pdb=" O HOH B 502 " model vdw 2.065 2.170 nonbonded pdb="MG MG B 401 " pdb=" O HOH B 501 " model vdw 2.072 2.170 nonbonded pdb=" OE1 GLU B 60 " pdb="MG MG B 401 " model vdw 2.086 2.170 ... (remaining 130510 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 138 or resid 140 through 236 or (resid 238 throu \ gh 239 and (name N or name CA or name C or name O or name CB )) or resid 248 thr \ ough 322)) selection = (chain 'B' and (resid 5 through 138 or resid 140 through 236 or resid 238 throug \ h 322)) selection = (chain 'C' and (resid 5 through 138 or resid 140 through 236 or (resid 238 throu \ gh 239 and (name N or name CA or name C or name O or name CB )) or resid 248 thr \ ough 322)) selection = (chain 'D' and (resid 5 through 138 or resid 140 through 236 or (resid 238 throu \ gh 248 and (name N or name CA or name C or name O or name CB )) or resid 249 thr \ ough 322)) } 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=0.99 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: 0.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 17.640 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8856 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 0.075 15766 Z= 0.549 Angle : 1.331 10.479 22369 Z= 0.901 Chirality : 0.078 0.742 2591 Planarity : 0.003 0.029 2007 Dihedral : 20.155 170.329 7094 Min Nonbonded Distance : 1.607 Molprobity Statistics. All-atom Clashscore : 0.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Rotamer: Outliers : 0.98 % Allowed : 2.44 % Favored : 96.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.58 (0.19), residues: 1258 helix: -0.66 (0.15), residues: 794 sheet: -1.40 (0.34), residues: 153 loop : -1.36 (0.29), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.002 ARG C 300 TYR 0.017 0.002 TYR B 78 PHE 0.017 0.003 PHE D 231 TRP 0.022 0.006 TRP B 169 HIS 0.006 0.002 HIS D 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00816 / 0.55 (15766) covalent geometry : angle 1.33146 / 0.90 (22369) hydrogen bonds : bond 0.20347 / 13.87 ( 902) hydrogen bonds : angle 6.71794 / 4.84 ( 2441) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 107 time to evaluate : 0.605 Fit side-chains REVERT: A 66 MET cc_start: 0.8236 (ppp) cc_final: 0.7997 (pp-130) REVERT: B 273 LYS cc_start: 0.8766 (OUTLIER) cc_final: 0.8496 (mttm) REVERT: C 298 MET cc_start: 0.8200 (tpt) cc_final: 0.7879 (tpt) REVERT: D 287 ASN cc_start: 0.8597 (OUTLIER) cc_final: 0.8324 (t0) outliers start: 10 outliers final: 0 residues processed: 112 average time/residue: 0.8610 time to fit residues: 103.5591 Evaluate side-chains 77 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 75 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 273 LYS Chi-restraints excluded: chain D residue 287 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 0.6980 chunk 55 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 139 GLN C 93 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 = 0.3266 r_free = 0.3266 target = 0.090586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2685 r_free = 0.2685 target = 0.057453 restraints weight = 78435.718| |-----------------------------------------------------------------------------| r_work (start): 0.2653 rms_B_bonded: 3.15 r_work: 0.2421 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.2421 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2434 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2434 r_free = 0.2434 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2433 r_free = 0.2433 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (8 function evaluations) r_final: 0.2433 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8769 moved from start: 0.1514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15766 Z= 0.164 Angle : 0.624 7.214 22369 Z= 0.369 Chirality : 0.044 0.199 2591 Planarity : 0.005 0.052 2007 Dihedral : 22.181 165.392 4647 Min Nonbonded Distance : 1.805 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 0.68 % Allowed : 5.87 % Favored : 93.45 % 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: 1.39 (0.23), residues: 1258 helix: 1.95 (0.17), residues: 798 sheet: -0.80 (0.37), residues: 150 loop : -0.85 (0.33), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 246 TYR 0.018 0.002 TYR A 74 PHE 0.012 0.002 PHE B 280 TRP 0.021 0.003 TRP D 276 HIS 0.005 0.001 HIS D 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.16 (15766) covalent geometry : angle 0.62425 / 0.37 (22369) hydrogen bonds : bond 0.06531 / 4.45 ( 902) hydrogen bonds : angle 4.18918 / 3.07 ( 2441) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 76 time to evaluate : 0.414 Fit side-chains REVERT: C 139 GLN cc_start: 0.8663 (OUTLIER) cc_final: 0.7229 (tm-30) REVERT: D 191 MET cc_start: 0.9073 (mmm) cc_final: 0.8810 (mtp) REVERT: D 287 ASN cc_start: 0.9016 (t0) cc_final: 0.8702 (m110) outliers start: 6 outliers final: 2 residues processed: 79 average time/residue: 0.7229 time to fit residues: 62.2325 Evaluate side-chains 66 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 63 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain C residue 139 GLN Chi-restraints excluded: chain D residue 38 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 20 optimal weight: 0.8980 chunk 45 optimal weight: 3.9990 chunk 126 optimal weight: 10.0000 chunk 67 optimal weight: 0.3980 chunk 11 optimal weight: 2.9990 chunk 32 optimal weight: 7.9990 chunk 106 optimal weight: 3.9990 chunk 33 optimal weight: 10.0000 chunk 21 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 66 optimal weight: 6.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 150 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.088792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2658 r_free = 0.2658 target = 0.055885 restraints weight = 87708.236| |-----------------------------------------------------------------------------| r_work (start): 0.2626 rms_B_bonded: 3.26 r_work: 0.2389 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.2389 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2447 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2447 r_free = 0.2447 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2447 r_free = 0.2447 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2447 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8804 moved from start: 0.1999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 15766 Z= 0.200 Angle : 0.573 7.375 22369 Z= 0.332 Chirality : 0.042 0.215 2591 Planarity : 0.004 0.045 2007 Dihedral : 22.377 169.574 4641 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Rotamer: Outliers : 1.27 % Allowed : 6.06 % Favored : 92.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.96 (0.24), residues: 1258 helix: 2.40 (0.18), residues: 804 sheet: -0.63 (0.37), residues: 163 loop : -0.69 (0.35), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 246 TYR 0.023 0.002 TYR A 74 PHE 0.014 0.002 PHE C 231 TRP 0.017 0.002 TRP C 46 HIS 0.007 0.001 HIS D 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00417 / 0.20 (15766) covalent geometry : angle 0.57324 / 0.33 (22369) hydrogen bonds : bond 0.05662 / 3.84 ( 902) hydrogen bonds : angle 3.82197 / 2.79 ( 2441) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 69 time to evaluate : 0.324 Fit side-chains REVERT: D 191 MET cc_start: 0.8977 (mmm) cc_final: 0.8724 (mtp) REVERT: D 287 ASN cc_start: 0.9034 (OUTLIER) cc_final: 0.8755 (m110) outliers start: 12 outliers final: 2 residues processed: 72 average time/residue: 0.6901 time to fit residues: 54.3118 Evaluate side-chains 66 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 63 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 258 SER Chi-restraints excluded: chain D residue 287 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 117 optimal weight: 3.9990 chunk 88 optimal weight: 2.9990 chunk 128 optimal weight: 10.0000 chunk 116 optimal weight: 0.9980 chunk 91 optimal weight: 0.6980 chunk 45 optimal weight: 0.7980 chunk 85 optimal weight: 6.9990 chunk 36 optimal weight: 3.9990 chunk 104 optimal weight: 0.4980 chunk 19 optimal weight: 0.4980 chunk 48 optimal weight: 3.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 139 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.091320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2718 r_free = 0.2718 target = 0.058426 restraints weight = 104644.879| |-----------------------------------------------------------------------------| r_work (start): 0.2683 rms_B_bonded: 3.46 r_work: 0.2445 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.2445 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2457 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2457 r_free = 0.2457 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2457 r_free = 0.2457 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2457 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8771 moved from start: 0.2262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 15766 Z= 0.123 Angle : 0.500 6.239 22369 Z= 0.298 Chirality : 0.037 0.151 2591 Planarity : 0.004 0.041 2007 Dihedral : 22.332 171.314 4641 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 0.68 % Allowed : 6.74 % Favored : 92.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.27 (0.24), residues: 1258 helix: 2.62 (0.18), residues: 806 sheet: -0.35 (0.40), residues: 147 loop : -0.62 (0.35), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 129 TYR 0.017 0.001 TYR A 74 PHE 0.010 0.001 PHE A 280 TRP 0.012 0.001 TRP A 46 HIS 0.004 0.001 HIS D 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.12 (15766) covalent geometry : angle 0.49980 / 0.30 (22369) hydrogen bonds : bond 0.04568 / 3.09 ( 902) hydrogen bonds : angle 3.66760 / 2.68 ( 2441) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 70 time to evaluate : 0.386 Fit side-chains REVERT: D 54 HIS cc_start: 0.8681 (m90) cc_final: 0.8458 (m90) REVERT: D 191 MET cc_start: 0.8951 (mmm) cc_final: 0.8664 (mtp) REVERT: D 287 ASN cc_start: 0.9100 (t0) cc_final: 0.8818 (m110) outliers start: 6 outliers final: 1 residues processed: 71 average time/residue: 0.6166 time to fit residues: 48.4378 Evaluate side-chains 68 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 67 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 218 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 107 optimal weight: 4.9990 chunk 35 optimal weight: 6.9990 chunk 67 optimal weight: 6.9990 chunk 130 optimal weight: 10.0000 chunk 83 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 chunk 5 optimal weight: 5.9990 chunk 85 optimal weight: 6.9990 chunk 15 optimal weight: 0.4980 chunk 96 optimal weight: 6.9990 chunk 36 optimal weight: 3.9990 overall best weight: 3.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 139 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.087384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2629 r_free = 0.2629 target = 0.054320 restraints weight = 104601.311| |-----------------------------------------------------------------------------| r_work (start): 0.2640 rms_B_bonded: 3.44 r_work: 0.2396 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.2396 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2408 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2408 r_free = 0.2408 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 = 0.2408 r_free = 0.2408 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.36 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: 0.8831 moved from start: 0.2188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.061 15766 Z= 0.294 Angle : 0.601 6.955 22369 Z= 0.338 Chirality : 0.044 0.176 2591 Planarity : 0.005 0.043 2007 Dihedral : 22.411 168.313 4641 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % Rotamer: Outliers : 0.88 % Allowed : 6.94 % Favored : 92.18 % 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: 2.14 (0.24), residues: 1258 helix: 2.57 (0.18), residues: 803 sheet: -0.75 (0.37), residues: 165 loop : -0.58 (0.36), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 246 TYR 0.015 0.002 TYR D 215 PHE 0.017 0.002 PHE C 112 TRP 0.016 0.002 TRP C 46 HIS 0.005 0.001 HIS B 145 Details of bonding type rmsd/Z covalent geometry : bond 0.00656 / 0.29 (15766) covalent geometry : angle 0.60116 / 0.34 (22369) hydrogen bonds : bond 0.05751 / 3.88 ( 902) hydrogen bonds : angle 3.77503 / 2.75 ( 2441) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 63 time to evaluate : 0.399 Fit side-chains REVERT: D 105 ASP cc_start: 0.7844 (OUTLIER) cc_final: 0.7604 (m-30) REVERT: D 191 MET cc_start: 0.8951 (mmm) cc_final: 0.8730 (mtp) REVERT: D 287 ASN cc_start: 0.9053 (OUTLIER) cc_final: 0.8792 (m110) outliers start: 8 outliers final: 1 residues processed: 66 average time/residue: 0.6219 time to fit residues: 45.2402 Evaluate side-chains 67 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 64 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain D residue 105 ASP Chi-restraints excluded: chain D residue 287 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 122 optimal weight: 0.7980 chunk 120 optimal weight: 1.9990 chunk 92 optimal weight: 0.7980 chunk 94 optimal weight: 0.8980 chunk 79 optimal weight: 0.7980 chunk 95 optimal weight: 2.9990 chunk 110 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 71 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 chunk 85 optimal weight: 5.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.090370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2701 r_free = 0.2701 target = 0.057640 restraints weight = 76947.568| |-----------------------------------------------------------------------------| r_work (start): 0.2670 rms_B_bonded: 3.12 r_work: 0.2441 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.2441 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2454 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2454 r_free = 0.2454 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2453 r_free = 0.2453 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2453 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8781 moved from start: 0.2385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 15766 Z= 0.127 Angle : 0.499 7.541 22369 Z= 0.296 Chirality : 0.037 0.158 2591 Planarity : 0.004 0.041 2007 Dihedral : 22.355 170.355 4641 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % Rotamer: Outliers : 0.49 % Allowed : 7.72 % Favored : 91.79 % 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: 2.39 (0.24), residues: 1258 helix: 2.72 (0.18), residues: 805 sheet: -0.49 (0.39), residues: 161 loop : -0.48 (0.36), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 129 TYR 0.012 0.001 TYR D 215 PHE 0.010 0.001 PHE A 280 TRP 0.013 0.002 TRP A 46 HIS 0.003 0.001 HIS D 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.13 (15766) covalent geometry : angle 0.49852 / 0.30 (22369) hydrogen bonds : bond 0.04594 / 3.10 ( 902) hydrogen bonds : angle 3.62132 / 2.65 ( 2441) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 72 time to evaluate : 0.280 Fit side-chains REVERT: D 54 HIS cc_start: 0.8675 (m90) cc_final: 0.8450 (m90) REVERT: D 191 MET cc_start: 0.8935 (mmm) cc_final: 0.8687 (mtp) REVERT: D 287 ASN cc_start: 0.9119 (t0) cc_final: 0.8842 (m110) outliers start: 4 outliers final: 1 residues processed: 73 average time/residue: 0.6470 time to fit residues: 52.1546 Evaluate side-chains 67 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 66 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 218 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 70 optimal weight: 3.9990 chunk 5 optimal weight: 6.9990 chunk 138 optimal weight: 10.0000 chunk 50 optimal weight: 6.9990 chunk 86 optimal weight: 10.0000 chunk 69 optimal weight: 0.6980 chunk 102 optimal weight: 0.8980 chunk 79 optimal weight: 1.9990 chunk 77 optimal weight: 0.7980 chunk 28 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.089794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2689 r_free = 0.2689 target = 0.057033 restraints weight = 80245.658| |-----------------------------------------------------------------------------| r_work (start): 0.2658 rms_B_bonded: 3.15 r_work: 0.2428 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.2428 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2440 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2440 r_free = 0.2440 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2440 r_free = 0.2440 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2440 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8793 moved from start: 0.2443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15766 Z= 0.159 Angle : 0.501 6.560 22369 Z= 0.292 Chirality : 0.038 0.168 2591 Planarity : 0.004 0.039 2007 Dihedral : 22.325 171.192 4641 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % Rotamer: Outliers : 0.78 % Allowed : 7.62 % Favored : 91.59 % 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: 2.48 (0.24), residues: 1258 helix: 2.78 (0.18), residues: 805 sheet: -0.46 (0.39), residues: 161 loop : -0.41 (0.36), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 129 TYR 0.018 0.001 TYR A 74 PHE 0.012 0.002 PHE D 112 TRP 0.013 0.002 TRP A 46 HIS 0.004 0.001 HIS D 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.16 (15766) covalent geometry : angle 0.50067 / 0.29 (22369) hydrogen bonds : bond 0.04703 / 3.18 ( 902) hydrogen bonds : angle 3.58326 / 2.62 ( 2441) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 67 time to evaluate : 0.446 Fit side-chains REVERT: D 54 HIS cc_start: 0.8694 (m90) cc_final: 0.8470 (m90) REVERT: D 105 ASP cc_start: 0.7830 (OUTLIER) cc_final: 0.7574 (m-30) REVERT: D 191 MET cc_start: 0.8935 (mmm) cc_final: 0.8695 (mtp) REVERT: D 287 ASN cc_start: 0.9123 (OUTLIER) cc_final: 0.8848 (m110) outliers start: 7 outliers final: 1 residues processed: 70 average time/residue: 0.5928 time to fit residues: 45.9101 Evaluate side-chains 68 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 65 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain D residue 105 ASP Chi-restraints excluded: chain D residue 287 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 61 optimal weight: 0.9980 chunk 106 optimal weight: 3.9990 chunk 31 optimal weight: 5.9990 chunk 133 optimal weight: 10.0000 chunk 42 optimal weight: 0.9990 chunk 48 optimal weight: 4.9990 chunk 13 optimal weight: 0.9990 chunk 44 optimal weight: 0.8980 chunk 110 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 96 optimal weight: 6.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.090402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2710 r_free = 0.2710 target = 0.057916 restraints weight = 77653.373| |-----------------------------------------------------------------------------| r_work (start): 0.2675 rms_B_bonded: 3.10 r_work: 0.2446 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.2446 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2459 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2459 r_free = 0.2459 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2459 r_free = 0.2459 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2459 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8782 moved from start: 0.2517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15766 Z= 0.140 Angle : 0.485 6.355 22369 Z= 0.286 Chirality : 0.037 0.162 2591 Planarity : 0.004 0.038 2007 Dihedral : 22.321 171.534 4641 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % Rotamer: Outliers : 0.29 % Allowed : 8.11 % Favored : 91.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.54 (0.24), residues: 1258 helix: 2.80 (0.18), residues: 806 sheet: -0.41 (0.39), residues: 161 loop : -0.33 (0.36), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 129 TYR 0.020 0.001 TYR A 74 PHE 0.010 0.002 PHE D 112 TRP 0.013 0.001 TRP A 46 HIS 0.003 0.001 HIS D 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.14 (15766) covalent geometry : angle 0.48534 / 0.29 (22369) hydrogen bonds : bond 0.04510 / 3.04 ( 902) hydrogen bonds : angle 3.55232 / 2.60 ( 2441) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 68 time to evaluate : 0.454 Fit side-chains REVERT: D 54 HIS cc_start: 0.8687 (m90) cc_final: 0.8465 (m90) REVERT: D 105 ASP cc_start: 0.7814 (OUTLIER) cc_final: 0.7567 (m-30) REVERT: D 191 MET cc_start: 0.8929 (mmm) cc_final: 0.8700 (mtp) REVERT: D 287 ASN cc_start: 0.9120 (t0) cc_final: 0.8865 (m110) outliers start: 2 outliers final: 1 residues processed: 69 average time/residue: 0.5569 time to fit residues: 42.4749 Evaluate side-chains 69 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 67 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain D residue 105 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 61 optimal weight: 0.5980 chunk 125 optimal weight: 10.0000 chunk 53 optimal weight: 2.9990 chunk 2 optimal weight: 0.6980 chunk 6 optimal weight: 4.9990 chunk 113 optimal weight: 0.7980 chunk 103 optimal weight: 6.9990 chunk 85 optimal weight: 5.9990 chunk 91 optimal weight: 2.9990 chunk 8 optimal weight: 4.9990 chunk 140 optimal weight: 10.0000 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 139 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.089818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2695 r_free = 0.2695 target = 0.057248 restraints weight = 76550.155| |-----------------------------------------------------------------------------| r_work (start): 0.2662 rms_B_bonded: 3.08 r_work: 0.2433 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.2433 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2486 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2486 r_free = 0.2486 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2486 r_free = 0.2486 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.2486 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8792 moved from start: 0.2546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 15766 Z= 0.165 Angle : 0.496 6.460 22369 Z= 0.289 Chirality : 0.038 0.166 2591 Planarity : 0.004 0.041 2007 Dihedral : 22.335 171.099 4641 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % Rotamer: Outliers : 0.49 % Allowed : 8.11 % Favored : 91.40 % 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: 2.56 (0.24), residues: 1258 helix: 2.82 (0.18), residues: 806 sheet: -0.47 (0.39), residues: 163 loop : -0.27 (0.37), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 129 TYR 0.021 0.002 TYR A 74 PHE 0.012 0.002 PHE D 112 TRP 0.013 0.002 TRP A 46 HIS 0.003 0.001 HIS D 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.16 (15766) covalent geometry : angle 0.49607 / 0.29 (22369) hydrogen bonds : bond 0.04676 / 3.15 ( 902) hydrogen bonds : angle 3.55236 / 2.60 ( 2441) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 68 time to evaluate : 0.420 Fit side-chains REVERT: D 105 ASP cc_start: 0.7806 (OUTLIER) cc_final: 0.7561 (m-30) REVERT: D 191 MET cc_start: 0.8926 (mmm) cc_final: 0.8711 (mtp) REVERT: D 287 ASN cc_start: 0.9084 (OUTLIER) cc_final: 0.8866 (m110) outliers start: 4 outliers final: 1 residues processed: 70 average time/residue: 0.5994 time to fit residues: 46.0678 Evaluate side-chains 69 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 66 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain D residue 105 ASP Chi-restraints excluded: chain D residue 287 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 17 optimal weight: 3.9990 chunk 37 optimal weight: 0.6980 chunk 104 optimal weight: 0.4980 chunk 106 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 chunk 57 optimal weight: 0.7980 chunk 43 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 24 optimal weight: 0.0970 chunk 127 optimal weight: 10.0000 chunk 125 optimal weight: 9.9990 overall best weight: 1.0180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.090579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2715 r_free = 0.2715 target = 0.058257 restraints weight = 68760.235| |-----------------------------------------------------------------------------| r_work (start): 0.2683 rms_B_bonded: 2.96 r_work: 0.2458 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.2458 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2468 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2468 r_free = 0.2468 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2468 r_free = 0.2468 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2468 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8776 moved from start: 0.2596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 15766 Z= 0.132 Angle : 0.480 7.034 22369 Z= 0.283 Chirality : 0.036 0.162 2591 Planarity : 0.004 0.041 2007 Dihedral : 22.327 171.632 4641 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % Rotamer: Outliers : 0.29 % Allowed : 8.21 % Favored : 91.50 % 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: 1258 helix: 2.84 (0.18), residues: 806 sheet: -0.43 (0.39), residues: 163 loop : -0.22 (0.37), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 129 TYR 0.019 0.001 TYR A 74 PHE 0.010 0.001 PHE D 112 TRP 0.013 0.002 TRP A 46 HIS 0.003 0.001 HIS D 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.13 (15766) covalent geometry : angle 0.48035 / 0.28 (22369) hydrogen bonds : bond 0.04455 / 3.01 ( 902) hydrogen bonds : angle 3.52314 / 2.58 ( 2441) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 67 time to evaluate : 0.467 Fit side-chains REVERT: D 191 MET cc_start: 0.8919 (mmm) cc_final: 0.8699 (mtp) REVERT: D 287 ASN cc_start: 0.9070 (OUTLIER) cc_final: 0.8759 (m110) outliers start: 2 outliers final: 1 residues processed: 67 average time/residue: 0.6201 time to fit residues: 45.9690 Evaluate side-chains 68 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 66 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain D residue 287 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 67 optimal weight: 4.9990 chunk 31 optimal weight: 6.9990 chunk 11 optimal weight: 0.7980 chunk 74 optimal weight: 0.0980 chunk 123 optimal weight: 0.0870 chunk 121 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 138 optimal weight: 10.0000 chunk 110 optimal weight: 2.9990 chunk 60 optimal weight: 4.9990 chunk 79 optimal weight: 2.9990 overall best weight: 1.3962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.090395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2708 r_free = 0.2708 target = 0.057923 restraints weight = 72390.133| |-----------------------------------------------------------------------------| r_work (start): 0.2677 rms_B_bonded: 3.01 r_work: 0.2450 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.2450 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2460 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2460 r_free = 0.2460 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2460 r_free = 0.2460 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2460 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8783 moved from start: 0.2628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 15766 Z= 0.148 Angle : 0.485 6.474 22369 Z= 0.284 Chirality : 0.037 0.166 2591 Planarity : 0.004 0.042 2007 Dihedral : 22.322 171.887 4641 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % Rotamer: Outliers : 0.29 % Allowed : 8.50 % Favored : 91.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.66 (0.24), residues: 1258 helix: 2.87 (0.18), residues: 807 sheet: -0.41 (0.39), residues: 163 loop : -0.17 (0.37), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 129 TYR 0.020 0.001 TYR A 74 PHE 0.011 0.002 PHE D 112 TRP 0.012 0.001 TRP A 46 HIS 0.003 0.001 HIS D 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.15 (15766) covalent geometry : angle 0.48533 / 0.28 (22369) hydrogen bonds : bond 0.04525 / 3.05 ( 902) hydrogen bonds : angle 3.50650 / 2.57 ( 2441) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4065.10 seconds wall clock time: 70 minutes 13.09 seconds (4213.09 seconds total)