Starting phenix.real_space_refine on Fri Jul 3 14:23:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wt8_37829/07_2026/8wt8_37829.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wt8_37829/07_2026/8wt8_37829.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8wt8_37829/07_2026/8wt8_37829.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wt8_37829/07_2026/8wt8_37829.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8wt8_37829/07_2026/8wt8_37829.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wt8_37829/07_2026/8wt8_37829.map" } resolution = 2.9 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= 0.026 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 1 5.21 5 S 48 5.16 5 C 8521 2.51 5 N 2759 2.21 5 O 3346 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14916 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 2429 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 306, 2420 Classifications: {'peptide': 306} Link IDs: {'PTRANS': 12, 'TRANS': 293} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 306, 2420 Classifications: {'peptide': 306} Link IDs: {'PTRANS': 12, 'TRANS': 293} Chain breaks: 1 bond proxies already assigned to first conformer: 2457 Chain: "B" Number of atoms: 2527 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 318, 2507 Classifications: {'peptide': 318} Link IDs: {'PTRANS': 12, 'TRANS': 305} Conformer: "B" Number of residues, atoms: 318, 2507 Classifications: {'peptide': 318} Link IDs: {'PTRANS': 12, 'TRANS': 305} bond proxies already assigned to first conformer: 2534 Chain: "C" Number of atoms: 2420 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 305, 2411 Classifications: {'peptide': 305} Link IDs: {'PTRANS': 12, 'TRANS': 292} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 305, 2411 Classifications: {'peptide': 305} Link IDs: {'PTRANS': 12, 'TRANS': 292} Chain breaks: 1 bond proxies already assigned to first conformer: 2448 Chain: "D" Number of atoms: 2513 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 317, 2498 Classifications: {'peptide': 317} Link IDs: {'PTRANS': 12, 'TRANS': 304} Conformer: "B" Number of residues, atoms: 317, 2498 Classifications: {'peptide': 317} Link IDs: {'PTRANS': 12, 'TRANS': 304} bond proxies already assigned to first conformer: 2530 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': 15, 'rna3p': 43} 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': 8, 'rna3p_pur': 27, 'rna3p_pyr': 27} 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: "I" Number of atoms: 596 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 27, 555 Classifications: {'DNA': 27} Link IDs: {'rna3p': 26} Conformer: "B" Number of residues, atoms: 27, 555 Classifications: {'DNA': 27} Link IDs: {'rna3p': 26} Chain breaks: 1 bond proxies already assigned to first conformer: 576 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: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "B" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 9 residue: pdb=" N AGLN A 139 " occ=0.50 ... (16 atoms not shown) pdb=" NE2BGLN A 139 " occ=0.50 residue: pdb=" N AGLN B 139 " occ=0.50 ... (16 atoms not shown) pdb=" NE2BGLN B 139 " occ=0.50 residue: pdb=" N AARG B 261 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG B 261 " occ=0.50 residue: pdb=" N AGLN C 139 " occ=0.50 ... (16 atoms not shown) pdb=" NE2BGLN C 139 " 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=" N ASER D 241 " occ=0.50 ... (10 atoms not shown) pdb=" OG BSER D 241 " occ=0.50 residue: pdb=" P A DT I 20 " occ=0.50 ... (38 atoms not shown) pdb=" C6 B DT I 20 " occ=0.50 residue: pdb=" P A DA I 21 " occ=0.50 ... (40 atoms not shown) pdb=" C4 B DA I 21 " occ=0.50 residue: pdb="MG B MG I 101 " occ=0.50 Time building chain proxies: 4.91, per 1000 atoms: 0.33 Number of scatterers: 14916 At special positions: 0 Unit cell: (119.52, 123.947, 110.667, 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 1 11.99 O 3346 8.00 N 2759 7.00 C 8521 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: 1.17 Conformation dependent library (CDL) restraints added in 806.2 milliseconds 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2344 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 7 sheets defined 68.6% alpha, 9.9% beta 89 base pairs and 149 stacking pairs defined. Time for finding SS restraints: 1.73 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: 3.668A 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 152 Processing helix chain 'A' and resid 153 through 155 No H-bonds generated for 'chain 'A' and resid 153 through 155' Processing helix chain 'A' and resid 159 through 188 removed outlier: 3.640A pdb=" N ASP A 188 " --> pdb=" O LEU A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 200 Processing helix chain 'A' and resid 205 through 217 Processing helix chain 'A' and resid 224 through 232 removed outlier: 3.672A pdb=" N PHE A 228 " --> pdb=" O HIS A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 262 removed outlier: 3.576A pdb=" N ALA A 262 " --> pdb=" O SER A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 274 Processing helix chain 'A' and resid 274 through 288 removed outlier: 3.508A 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: 3.521A pdb=" N ARG A 320 " --> pdb=" O ASP A 317 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 50 Processing helix chain 'B' and resid 66 through 76 Processing helix chain 'B' and resid 84 through 96 removed outlier: 3.589A pdb=" N GLY B 96 " --> pdb=" O ALA B 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 117 Processing helix chain 'B' and resid 125 through 154 removed outlier: 3.861A pdb=" N GLU B 153 " --> pdb=" O LEU B 149 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N THR B 154 " --> pdb=" O ASN B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 188 removed outlier: 3.639A 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: 3.654A pdb=" N ALA B 210 " --> pdb=" O GLU B 206 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 233 removed outlier: 3.766A 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 removed outlier: 3.501A pdb=" N SER B 272 " --> pdb=" O MET B 268 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 287 removed outlier: 3.876A pdb=" N ASN B 287 " --> pdb=" O ARG B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 313 removed outlier: 3.503A pdb=" N LEU B 310 " --> pdb=" O ALA B 306 " (cutoff:3.500A) 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 Processing helix chain 'C' and resid 101 through 117 removed outlier: 3.557A pdb=" N ARG C 107 " --> pdb=" O THR C 103 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ALA C 110 " --> pdb=" O ALA C 106 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 154 removed outlier: 3.800A pdb=" N GLU C 153 " --> pdb=" O LEU C 149 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N THR C 154 " --> pdb=" O ASN C 150 " (cutoff:3.500A) Processing helix chain 'C' and resid 159 through 188 removed outlier: 3.620A 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 removed outlier: 3.542A pdb=" N ALA C 210 " --> pdb=" O GLU C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 224 through 232 removed outlier: 3.746A pdb=" N PHE C 228 " --> pdb=" O HIS C 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 256 through 262 removed outlier: 3.501A pdb=" N ALA C 262 " --> pdb=" O SER C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 263 through 274 Processing helix chain 'C' and resid 274 through 288 Processing helix chain 'C' and resid 290 through 313 Processing helix chain 'C' and resid 317 through 321 removed outlier: 3.617A pdb=" N ARG C 320 " --> pdb=" O ASP C 317 " (cutoff:3.500A) Processing helix chain 'D' and resid 36 through 50 Processing helix chain 'D' and resid 66 through 77 Processing helix chain 'D' and resid 84 through 96 removed outlier: 3.589A pdb=" N GLY D 88 " --> pdb=" O ASN D 84 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLY D 96 " --> pdb=" O ALA D 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 105 through 117 Processing helix chain 'D' and resid 125 through 154 removed outlier: 3.990A pdb=" N GLU D 153 " --> pdb=" O LEU D 149 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N THR D 154 " --> pdb=" O ASN D 150 " (cutoff:3.500A) Processing helix chain 'D' and resid 159 through 188 removed outlier: 3.689A pdb=" N ASP D 188 " --> pdb=" O LEU D 184 " (cutoff:3.500A) Processing helix chain 'D' and resid 188 through 201 removed outlier: 3.803A pdb=" N ILE D 201 " --> pdb=" O LEU D 197 " (cutoff:3.500A) Processing helix chain 'D' and resid 205 through 217 removed outlier: 3.557A pdb=" N ALA D 210 " --> pdb=" O GLU D 206 " (cutoff:3.500A) Processing helix chain 'D' and resid 224 through 233 removed outlier: 3.606A pdb=" N PHE D 228 " --> pdb=" O HIS D 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 256 through 263 removed outlier: 3.595A pdb=" N LEU D 263 " --> pdb=" O LEU D 259 " (cutoff:3.500A) Processing helix chain 'D' and resid 263 through 274 Processing helix chain 'D' and resid 274 through 288 Processing helix chain 'D' and resid 290 through 313 Processing helix chain 'D' and resid 317 through 321 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 34 removed outlier: 6.576A pdb=" N HIS A 6 " --> pdb=" O HIS A 56 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N CYS A 58 " --> pdb=" O HIS A 6 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ILE A 8 " --> pdb=" O CYS A 58 " (cutoff:3.500A) removed outlier: 8.540A pdb=" N GLU A 60 " --> pdb=" O ILE A 8 " (cutoff:3.500A) removed outlier: 8.228A 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: 6.766A pdb=" N HIS B 6 " --> pdb=" O HIS B 56 " (cutoff:3.500A) removed outlier: 8.094A pdb=" N CYS B 58 " --> pdb=" O HIS B 6 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ILE B 8 " --> pdb=" O CYS B 58 " (cutoff:3.500A) removed outlier: 8.763A pdb=" N GLU B 60 " --> pdb=" O ILE B 8 " (cutoff:3.500A) removed outlier: 8.460A pdb=" N ILE B 10 " --> pdb=" O GLU B 60 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ALA B 55 " --> pdb=" O ILE B 79 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N SER B 81 " --> pdb=" O ALA B 55 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N ILE B 57 " --> pdb=" O SER B 81 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N ILE B 83 " --> pdb=" O ILE B 57 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ILE B 59 " --> pdb=" O ILE B 83 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 236 through 237 removed outlier: 3.853A 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: 6.290A pdb=" N HIS C 6 " --> pdb=" O HIS C 56 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N CYS C 58 " --> pdb=" O HIS C 6 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N ILE C 8 " --> pdb=" O CYS C 58 " (cutoff:3.500A) removed outlier: 8.538A pdb=" N GLU C 60 " --> pdb=" O ILE C 8 " (cutoff:3.500A) removed outlier: 8.495A 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: 4.462A pdb=" N GLU D 60 " --> pdb=" O ILE D 10 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N THR D 12 " --> pdb=" O GLU D 60 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N ALA D 55 " --> pdb=" O ILE D 79 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N SER D 81 " --> pdb=" O ALA D 55 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N ILE D 57 " --> pdb=" O SER D 81 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N ILE D 83 " --> pdb=" O ILE D 57 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N ILE D 59 " --> pdb=" O ILE D 83 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 236 through 241 removed outlier: 3.764A pdb=" N ARG D 250 " --> pdb=" O ARG D 237 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N TYR D 239 " --> pdb=" O ALA D 248 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N ALA D 248 " --> pdb=" O TYR D 239 " (cutoff:3.500A) removed outlier: 7.898A pdb=" N ASER D 241 " --> pdb=" O ARG D 246 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N ARG D 246 " --> pdb=" O ASER D 241 " (cutoff:3.500A) 674 hydrogen bonds defined for protein. 2000 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 227 hydrogen bonds 450 hydrogen bond angles 0 basepair planarities 89 basepair parallelities 152 stacking parallelities Total time for adding SS restraints: 2.69 Time building geometry restraints manager: 1.59 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: 3712 1.34 - 1.46: 5158 1.46 - 1.58: 6275 1.58 - 1.69: 476 1.69 - 1.81: 84 Bond restraints: 15705 Sorted by residual: 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 6.33e+00 bond pdb=" C ILE D 201 " pdb=" N PRO D 202 " ideal model delta sigma weight residual 1.335 1.356 -0.021 8.70e-03 1.32e+04 5.94e+00 bond pdb=" O5' A E 68 " pdb=" C5' A E 68 " ideal model delta sigma weight residual 1.420 1.456 -0.036 1.50e-02 4.44e+03 5.87e+00 bond pdb=" O5' G F 133 " pdb=" C5' G F 133 " ideal model delta sigma weight residual 1.420 1.456 -0.036 1.50e-02 4.44e+03 5.63e+00 bond pdb=" O5' G F 169 " pdb=" C5' G F 169 " ideal model delta sigma weight residual 1.420 1.456 -0.036 1.50e-02 4.44e+03 5.60e+00 ... (remaining 15700 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.47: 17179 1.47 - 2.94: 4234 2.94 - 4.42: 746 4.42 - 5.89: 110 5.89 - 7.36: 21 Bond angle restraints: 22290 Sorted by residual: angle pdb=" O4' DC J 30 " pdb=" C4' DC J 30 " pdb=" C3' DC J 30 " ideal model delta sigma weight residual 106.00 102.23 3.77 6.00e-01 2.78e+00 3.95e+01 angle pdb=" O4' DC H 19 " pdb=" C4' DC H 19 " pdb=" C3' DC H 19 " ideal model delta sigma weight residual 106.00 102.49 3.51 6.00e-01 2.78e+00 3.42e+01 angle pdb=" O3' DA G 32 " pdb=" P DT G 33 " pdb=" O5' DT G 33 " ideal model delta sigma weight residual 104.00 96.64 7.36 1.50e+00 4.44e-01 2.41e+01 angle pdb=" O4' DG J 26 " pdb=" C4' DG J 26 " pdb=" C3' DG J 26 " ideal model delta sigma weight residual 106.00 103.23 2.77 6.00e-01 2.78e+00 2.13e+01 angle pdb=" O4' DC H 18 " pdb=" C4' DC H 18 " pdb=" C3' DC H 18 " ideal model delta sigma weight residual 106.00 103.27 2.73 6.00e-01 2.78e+00 2.07e+01 ... (remaining 22285 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.61: 8697 35.61 - 71.21: 678 71.21 - 106.82: 49 106.82 - 142.42: 0 142.42 - 178.03: 2 Dihedral angle restraints: 9426 sinusoidal: 5800 harmonic: 3626 Sorted by residual: dihedral pdb=" O4' U F 159 " pdb=" C1' U F 159 " pdb=" N1 U F 159 " pdb=" C2 U F 159 " ideal model delta sinusoidal sigma weight residual 232.00 53.97 178.03 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" C5' U F 168 " pdb=" C4' U F 168 " pdb=" C3' U F 168 " pdb=" O3' U F 168 " ideal model delta sinusoidal sigma weight residual 147.00 98.77 48.23 1 8.00e+00 1.56e-02 5.01e+01 dihedral pdb=" O4' U F 168 " pdb=" C4' U F 168 " pdb=" C3' U F 168 " pdb=" C2' U F 168 " ideal model delta sinusoidal sigma weight residual 24.00 -14.47 38.47 1 8.00e+00 1.56e-02 3.26e+01 ... (remaining 9423 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.137: 2307 0.137 - 0.275: 267 0.275 - 0.412: 1 0.412 - 0.550: 0 0.550 - 0.687: 6 Chirality restraints: 2581 Sorted by residual: chirality pdb=" P DT G 10 " pdb=" OP1 DT G 10 " pdb=" OP2 DT G 10 " pdb=" O5' DT G 10 " both_signs ideal model delta sigma weight residual True 2.34 -3.02 -0.69 2.00e-01 2.50e+01 1.18e+01 chirality pdb=" P DA H 3 " pdb=" OP1 DA H 3 " pdb=" OP2 DA H 3 " pdb=" O5' DA H 3 " both_signs ideal model delta sigma weight residual True 2.34 -2.98 -0.65 2.00e-01 2.50e+01 1.05e+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 -2.98 -0.65 2.00e-01 2.50e+01 1.04e+01 ... (remaining 2578 not shown) Planarity restraints: 1996 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A F 157 " -0.024 2.00e-02 2.50e+03 9.85e-03 2.67e+00 pdb=" N9 A F 157 " 0.015 2.00e-02 2.50e+03 pdb=" C8 A F 157 " 0.006 2.00e-02 2.50e+03 pdb=" N7 A F 157 " 0.001 2.00e-02 2.50e+03 pdb=" C5 A F 157 " 0.002 2.00e-02 2.50e+03 pdb=" C6 A F 157 " -0.006 2.00e-02 2.50e+03 pdb=" N6 A F 157 " -0.007 2.00e-02 2.50e+03 pdb=" N1 A F 157 " -0.003 2.00e-02 2.50e+03 pdb=" C2 A F 157 " 0.004 2.00e-02 2.50e+03 pdb=" N3 A F 157 " 0.006 2.00e-02 2.50e+03 pdb=" C4 A F 157 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA G 29 " 0.020 2.00e-02 2.50e+03 8.85e-03 2.15e+00 pdb=" N9 DA G 29 " -0.020 2.00e-02 2.50e+03 pdb=" C8 DA G 29 " -0.001 2.00e-02 2.50e+03 pdb=" N7 DA G 29 " 0.001 2.00e-02 2.50e+03 pdb=" C5 DA G 29 " -0.000 2.00e-02 2.50e+03 pdb=" C6 DA G 29 " 0.001 2.00e-02 2.50e+03 pdb=" N6 DA G 29 " 0.007 2.00e-02 2.50e+03 pdb=" N1 DA G 29 " -0.001 2.00e-02 2.50e+03 pdb=" C2 DA G 29 " 0.000 2.00e-02 2.50e+03 pdb=" N3 DA G 29 " -0.002 2.00e-02 2.50e+03 pdb=" C4 DA G 29 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U E 74 " -0.021 2.00e-02 2.50e+03 9.59e-03 2.07e+00 pdb=" N1 U E 74 " 0.013 2.00e-02 2.50e+03 pdb=" C2 U E 74 " 0.005 2.00e-02 2.50e+03 pdb=" O2 U E 74 " 0.005 2.00e-02 2.50e+03 pdb=" N3 U E 74 " -0.002 2.00e-02 2.50e+03 pdb=" C4 U E 74 " -0.006 2.00e-02 2.50e+03 pdb=" O4 U E 74 " -0.005 2.00e-02 2.50e+03 pdb=" C5 U E 74 " 0.001 2.00e-02 2.50e+03 pdb=" C6 U E 74 " 0.010 2.00e-02 2.50e+03 ... (remaining 1993 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.27: 5 2.27 - 2.93: 5256 2.93 - 3.58: 22124 3.58 - 4.24: 40380 4.24 - 4.90: 61660 Nonbonded interactions: 129425 Sorted by model distance: nonbonded pdb=" OG BSER D 241 " pdb=" P B DA I 21 " model vdw 1.611 3.400 nonbonded pdb=" OE2 GLU A 60 " pdb="MG B MG I 101 " model vdw 2.078 2.170 nonbonded pdb=" O3'B DT I 20 " pdb="MG B MG I 101 " model vdw 2.085 2.170 nonbonded pdb=" OP1B DA I 21 " pdb="MG B MG I 101 " model vdw 2.091 2.170 nonbonded pdb=" OD1 ASP A 11 " pdb="MG B MG I 101 " model vdw 2.103 2.170 ... (remaining 129420 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 260 or resid 262 throug \ h 321)) selection = (chain 'B' and (resid 5 through 138 or resid 140 through 238 or resid 251 throug \ h 260 or resid 262 through 321)) selection = (chain 'C' and (resid 5 through 138 or resid 140 through 260 or resid 262 throug \ h 321)) selection = (chain 'D' and (resid 5 through 138 or resid 140 through 238 or resid 251 throug \ h 260 or resid 262 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=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: 0.990 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: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 17.100 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8831 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 0.047 15705 Z= 0.536 Angle : 1.320 7.360 22290 Z= 0.907 Chirality : 0.081 0.687 2581 Planarity : 0.003 0.026 1996 Dihedral : 20.482 178.027 7082 Min Nonbonded Distance : 1.611 Molprobity Statistics. All-atom Clashscore : 0.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 0.59 % Allowed : 2.46 % Favored : 96.95 % 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: -2.17 (0.19), residues: 1252 helix: -1.14 (0.14), residues: 807 sheet: -1.67 (0.35), residues: 150 loop : -1.49 (0.32), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.002 ARG D 300 TYR 0.017 0.002 TYR D 78 PHE 0.015 0.002 PHE A 231 TRP 0.016 0.004 TRP C 169 HIS 0.006 0.002 HIS D 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00817 / 0.54 (15705) covalent geometry : angle 1.31965 / 0.91 (22290) hydrogen bonds : bond 0.22488 / 15.21 ( 901) hydrogen bonds : angle 7.45544 / 5.42 ( 2450) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 116 time to evaluate : 0.433 Fit side-chains REVERT: A 268 MET cc_start: 0.8145 (mtm) cc_final: 0.7888 (mtp) outliers start: 5 outliers final: 0 residues processed: 120 average time/residue: 0.8285 time to fit residues: 106.4366 Evaluate side-chains 78 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 98 optimal weight: 0.7980 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 10.0000 chunk 91 optimal weight: 0.9980 chunk 55 optimal weight: 0.9980 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 99 ASN C 28 HIS C 54 HIS C 115 GLN D 54 HIS D 93 GLN D 287 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.091380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.059747 restraints weight = 88824.456| |-----------------------------------------------------------------------------| r_work (start): 0.2803 rms_B_bonded: 3.38 r_work: 0.2587 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.2587 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2593 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2593 r_free = 0.2593 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2593 r_free = 0.2593 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 7 (9 function evaluations) r_final: 0.2593 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8671 moved from start: 0.1642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15705 Z= 0.178 Angle : 0.632 7.667 22290 Z= 0.376 Chirality : 0.045 0.354 2581 Planarity : 0.005 0.039 1996 Dihedral : 22.672 169.799 4635 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 0.98 % Allowed : 7.27 % Favored : 91.75 % 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: 1.19 (0.23), residues: 1252 helix: 1.74 (0.17), residues: 812 sheet: -0.94 (0.37), residues: 138 loop : -0.88 (0.35), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 261 TYR 0.019 0.002 TYR D 215 PHE 0.011 0.002 PHE B 112 TRP 0.020 0.003 TRP A 46 HIS 0.004 0.001 HIS D 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.18 (15705) covalent geometry : angle 0.63213 / 0.38 (22290) hydrogen bonds : bond 0.06744 / 4.49 ( 901) hydrogen bonds : angle 4.30366 / 3.08 ( 2450) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 77 time to evaluate : 0.396 Fit side-chains REVERT: B 51 LYS cc_start: 0.9135 (mmtm) cc_final: 0.8820 (mmmm) REVERT: D 265 MET cc_start: 0.9211 (mmm) cc_final: 0.8181 (mmm) outliers start: 9 outliers final: 0 residues processed: 81 average time/residue: 0.6634 time to fit residues: 58.4944 Evaluate side-chains 72 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 140 optimal weight: 10.0000 chunk 41 optimal weight: 4.9990 chunk 61 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 chunk 75 optimal weight: 0.6980 chunk 52 optimal weight: 0.8980 chunk 30 optimal weight: 6.9990 chunk 2 optimal weight: 6.9990 chunk 121 optimal weight: 2.9990 chunk 118 optimal weight: 0.9990 chunk 67 optimal weight: 0.6980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 99 ASN C 6 HIS D 54 HIS D 93 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.092626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.061157 restraints weight = 98676.676| |-----------------------------------------------------------------------------| r_work (start): 0.2834 rms_B_bonded: 3.57 r_work: 0.2618 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.2618 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2619 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2619 r_free = 0.2619 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2618 r_free = 0.2618 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (9 function evaluations) r_final: 0.2618 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8651 moved from start: 0.2151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15705 Z= 0.140 Angle : 0.539 8.036 22290 Z= 0.323 Chirality : 0.039 0.197 2581 Planarity : 0.004 0.041 1996 Dihedral : 22.651 174.867 4635 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 0.59 % Allowed : 8.06 % Favored : 91.36 % 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: 1.82 (0.24), residues: 1252 helix: 2.23 (0.18), residues: 817 sheet: -0.72 (0.36), residues: 141 loop : -0.72 (0.37), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG C 27 TYR 0.018 0.002 TYR D 307 PHE 0.018 0.002 PHE C 33 TRP 0.014 0.002 TRP D 46 HIS 0.006 0.001 HIS C 28 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.14 (15705) covalent geometry : angle 0.53883 / 0.32 (22290) hydrogen bonds : bond 0.04996 / 3.33 ( 901) hydrogen bonds : angle 3.88411 / 2.78 ( 2450) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 78 time to evaluate : 0.387 Fit side-chains REVERT: D 265 MET cc_start: 0.9179 (mmm) cc_final: 0.8860 (mmt) outliers start: 5 outliers final: 0 residues processed: 79 average time/residue: 0.6110 time to fit residues: 52.9681 Evaluate side-chains 71 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 19 optimal weight: 0.8980 chunk 74 optimal weight: 1.9990 chunk 67 optimal weight: 0.9980 chunk 89 optimal weight: 5.9990 chunk 45 optimal weight: 0.6980 chunk 108 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 chunk 9 optimal weight: 7.9990 chunk 88 optimal weight: 5.9990 chunk 91 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 99 ASN D 54 HIS D 93 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.092265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.061027 restraints weight = 86878.211| |-----------------------------------------------------------------------------| r_work (start): 0.2841 rms_B_bonded: 3.37 r_work: 0.2630 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.2630 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2628 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2628 r_free = 0.2628 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2628 r_free = 0.2628 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.2628 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 moved from start: 0.2458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15705 Z= 0.143 Angle : 0.514 7.484 22290 Z= 0.303 Chirality : 0.038 0.190 2581 Planarity : 0.004 0.040 1996 Dihedral : 22.712 176.200 4635 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 0.59 % Allowed : 8.25 % Favored : 91.16 % 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: 2.16 (0.24), residues: 1252 helix: 2.46 (0.18), residues: 819 sheet: -0.39 (0.36), residues: 139 loop : -0.63 (0.37), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 27 TYR 0.020 0.001 TYR C 307 PHE 0.010 0.002 PHE B 112 TRP 0.013 0.002 TRP D 276 HIS 0.003 0.001 HIS A 166 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.14 (15705) covalent geometry : angle 0.51430 / 0.30 (22290) hydrogen bonds : bond 0.04569 / 3.03 ( 901) hydrogen bonds : angle 3.69656 / 2.64 ( 2450) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 78 time to evaluate : 0.326 Fit side-chains REVERT: C 107 ARG cc_start: 0.8626 (ttm-80) cc_final: 0.8263 (ttp80) outliers start: 5 outliers final: 0 residues processed: 78 average time/residue: 0.6893 time to fit residues: 58.5358 Evaluate side-chains 73 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 113 optimal weight: 0.9980 chunk 104 optimal weight: 0.8980 chunk 103 optimal weight: 2.9990 chunk 126 optimal weight: 10.0000 chunk 116 optimal weight: 4.9990 chunk 129 optimal weight: 9.9990 chunk 55 optimal weight: 4.9990 chunk 42 optimal weight: 3.9990 chunk 6 optimal weight: 5.9990 chunk 44 optimal weight: 2.9990 chunk 117 optimal weight: 3.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 99 ASN D 54 HIS D 93 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.090115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2813 r_free = 0.2813 target = 0.058652 restraints weight = 101040.932| |-----------------------------------------------------------------------------| r_work (start): 0.2792 rms_B_bonded: 3.55 r_work: 0.2574 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.2574 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2588 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2588 r_free = 0.2588 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2588 r_free = 0.2588 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.2588 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8697 moved from start: 0.2522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 15705 Z= 0.210 Angle : 0.547 7.822 22290 Z= 0.316 Chirality : 0.039 0.186 2581 Planarity : 0.004 0.049 1996 Dihedral : 22.761 175.577 4635 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 0.59 % Allowed : 9.14 % Favored : 90.28 % 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: 2.24 (0.24), residues: 1252 helix: 2.55 (0.18), residues: 818 sheet: -0.34 (0.34), residues: 143 loop : -0.68 (0.37), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 27 TYR 0.018 0.002 TYR C 307 PHE 0.011 0.002 PHE C 231 TRP 0.014 0.002 TRP A 46 HIS 0.004 0.001 HIS C 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00449 / 0.21 (15705) covalent geometry : angle 0.54687 / 0.32 (22290) hydrogen bonds : bond 0.04957 / 3.32 ( 901) hydrogen bonds : angle 3.75078 / 2.67 ( 2450) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 75 time to evaluate : 0.425 Fit side-chains REVERT: B 226 ARG cc_start: 0.8676 (mtp85) cc_final: 0.8456 (tpt-90) REVERT: B 238 ARG cc_start: 0.7622 (mtp180) cc_final: 0.6228 (tpt90) REVERT: C 107 ARG cc_start: 0.8662 (ttm-80) cc_final: 0.8321 (ttp80) REVERT: C 307 TYR cc_start: 0.8922 (t80) cc_final: 0.8670 (t80) outliers start: 5 outliers final: 1 residues processed: 78 average time/residue: 0.7227 time to fit residues: 61.1074 Evaluate side-chains 71 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 70 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 97 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 86 optimal weight: 1.9990 chunk 58 optimal weight: 7.9990 chunk 85 optimal weight: 3.9990 chunk 11 optimal weight: 0.3980 chunk 27 optimal weight: 0.9990 chunk 14 optimal weight: 0.9990 chunk 8 optimal weight: 0.9990 chunk 129 optimal weight: 10.0000 chunk 125 optimal weight: 10.0000 chunk 56 optimal weight: 2.9990 chunk 123 optimal weight: 6.9990 overall best weight: 1.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 99 ASN D 54 HIS D 93 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.092036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.060356 restraints weight = 107158.830| |-----------------------------------------------------------------------------| r_work (start): 0.2827 rms_B_bonded: 3.67 r_work: 0.2609 rms_B_bonded: 4.57 restraints_weight: 0.5000 r_work (final): 0.2609 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2627 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2627 r_free = 0.2627 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2627 r_free = 0.2627 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2627 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8673 moved from start: 0.2702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15705 Z= 0.132 Angle : 0.497 7.983 22290 Z= 0.293 Chirality : 0.036 0.185 2581 Planarity : 0.004 0.039 1996 Dihedral : 22.735 177.045 4635 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 0.79 % Allowed : 9.43 % Favored : 89.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.36 (0.24), residues: 1252 helix: 2.63 (0.18), residues: 819 sheet: -0.27 (0.35), residues: 139 loop : -0.61 (0.37), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 27 TYR 0.016 0.001 TYR C 307 PHE 0.009 0.001 PHE B 112 TRP 0.012 0.002 TRP C 46 HIS 0.003 0.001 HIS D 145 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.13 (15705) covalent geometry : angle 0.49701 / 0.29 (22290) hydrogen bonds : bond 0.04300 / 2.86 ( 901) hydrogen bonds : angle 3.63030 / 2.59 ( 2450) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 74 time to evaluate : 0.525 Fit side-chains REVERT: A 227 GLN cc_start: 0.9063 (mt0) cc_final: 0.8823 (mt0) REVERT: B 238 ARG cc_start: 0.7592 (mtp180) cc_final: 0.6219 (tpt90) REVERT: C 54 HIS cc_start: 0.8150 (t70) cc_final: 0.7865 (t70) REVERT: C 107 ARG cc_start: 0.8613 (ttm-80) cc_final: 0.8262 (ttp80) outliers start: 7 outliers final: 2 residues processed: 76 average time/residue: 0.7362 time to fit residues: 60.7316 Evaluate side-chains 74 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 72 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 268 MET Chi-restraints excluded: chain D residue 97 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 69 optimal weight: 0.0370 chunk 84 optimal weight: 0.7980 chunk 48 optimal weight: 0.0970 chunk 129 optimal weight: 10.0000 chunk 60 optimal weight: 0.6980 chunk 4 optimal weight: 4.9990 chunk 22 optimal weight: 4.9990 chunk 47 optimal weight: 0.8980 chunk 56 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 overall best weight: 0.5056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 99 ASN D 93 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.094584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.063325 restraints weight = 105669.656| |-----------------------------------------------------------------------------| r_work (start): 0.2891 rms_B_bonded: 3.65 r_work: 0.2676 rms_B_bonded: 4.61 restraints_weight: 0.5000 r_work (final): 0.2676 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2680 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2680 r_free = 0.2680 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2680 r_free = 0.2680 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2680 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.2990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 15705 Z= 0.113 Angle : 0.470 9.073 22290 Z= 0.278 Chirality : 0.035 0.174 2581 Planarity : 0.004 0.050 1996 Dihedral : 22.612 179.057 4635 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 0.79 % Allowed : 9.53 % Favored : 89.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.55 (0.24), residues: 1252 helix: 2.76 (0.18), residues: 820 sheet: -0.04 (0.35), residues: 137 loop : -0.62 (0.37), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG C 27 TYR 0.013 0.001 TYR D 239 PHE 0.009 0.001 PHE B 112 TRP 0.012 0.001 TRP B 46 HIS 0.003 0.001 HIS C 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00203 / 0.11 (15705) covalent geometry : angle 0.47019 / 0.28 (22290) hydrogen bonds : bond 0.03818 / 2.54 ( 901) hydrogen bonds : angle 3.48758 / 2.49 ( 2450) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 82 time to evaluate : 0.454 Fit side-chains REVERT: A 153 GLU cc_start: 0.9136 (tp30) cc_final: 0.8890 (tp30) REVERT: A 227 GLN cc_start: 0.9035 (mt0) cc_final: 0.8808 (mt0) REVERT: B 51 LYS cc_start: 0.8939 (OUTLIER) cc_final: 0.8487 (tppt) REVERT: B 238 ARG cc_start: 0.7589 (mtp180) cc_final: 0.6249 (tpt90) REVERT: C 54 HIS cc_start: 0.8127 (t70) cc_final: 0.7864 (t70) outliers start: 7 outliers final: 1 residues processed: 84 average time/residue: 0.6604 time to fit residues: 60.8222 Evaluate side-chains 75 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 73 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 51 LYS Chi-restraints excluded: chain D residue 97 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 117 optimal weight: 1.9990 chunk 136 optimal weight: 10.0000 chunk 1 optimal weight: 0.8980 chunk 82 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 74 optimal weight: 0.7980 chunk 137 optimal weight: 20.0000 chunk 79 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 chunk 65 optimal weight: 5.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 99 ASN A 150 ASN C 40 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.092798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.061342 restraints weight = 109814.017| |-----------------------------------------------------------------------------| r_work (start): 0.2849 rms_B_bonded: 3.70 r_work: 0.2630 rms_B_bonded: 4.62 restraints_weight: 0.5000 r_work (final): 0.2630 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2635 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2635 r_free = 0.2635 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2635 r_free = 0.2635 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.2635 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8667 moved from start: 0.2980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15705 Z= 0.144 Angle : 0.492 9.983 22290 Z= 0.282 Chirality : 0.036 0.173 2581 Planarity : 0.004 0.044 1996 Dihedral : 22.626 177.977 4635 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 0.49 % Allowed : 10.81 % Favored : 88.70 % 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: 2.62 (0.24), residues: 1252 helix: 2.81 (0.18), residues: 819 sheet: 0.06 (0.34), residues: 138 loop : -0.62 (0.37), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 27 TYR 0.015 0.001 TYR C 307 PHE 0.010 0.002 PHE B 112 TRP 0.011 0.001 TRP D 46 HIS 0.003 0.001 HIS D 145 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.14 (15705) covalent geometry : angle 0.49222 / 0.28 (22290) hydrogen bonds : bond 0.04134 / 2.75 ( 901) hydrogen bonds : angle 3.50393 / 2.49 ( 2450) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 77 time to evaluate : 0.456 Fit side-chains REVERT: A 153 GLU cc_start: 0.9145 (tp30) cc_final: 0.8893 (tp30) REVERT: A 227 GLN cc_start: 0.9063 (mt0) cc_final: 0.8828 (mt0) REVERT: B 238 ARG cc_start: 0.7635 (mtp180) cc_final: 0.6250 (tpt90) REVERT: C 54 HIS cc_start: 0.8116 (t70) cc_final: 0.7874 (t70) outliers start: 4 outliers final: 1 residues processed: 78 average time/residue: 0.6954 time to fit residues: 59.0648 Evaluate side-chains 74 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 73 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 97 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 16 optimal weight: 0.6980 chunk 59 optimal weight: 3.9990 chunk 89 optimal weight: 3.9990 chunk 131 optimal weight: 10.0000 chunk 53 optimal weight: 5.9990 chunk 25 optimal weight: 5.9990 chunk 103 optimal weight: 2.9990 chunk 4 optimal weight: 4.9990 chunk 87 optimal weight: 5.9990 chunk 1 optimal weight: 0.9990 chunk 58 optimal weight: 0.0060 overall best weight: 1.7402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 99 ASN D 93 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.091570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.059982 restraints weight = 111259.561| |-----------------------------------------------------------------------------| r_work (start): 0.2822 rms_B_bonded: 3.70 r_work: 0.2600 rms_B_bonded: 4.60 restraints_weight: 0.5000 r_work (final): 0.2600 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2605 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2605 r_free = 0.2605 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2605 r_free = 0.2605 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2605 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 moved from start: 0.2957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 15705 Z= 0.167 Angle : 0.509 8.683 22290 Z= 0.291 Chirality : 0.037 0.176 2581 Planarity : 0.004 0.048 1996 Dihedral : 22.605 177.461 4635 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 0.39 % Allowed : 10.90 % Favored : 88.70 % 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: 2.58 (0.24), residues: 1252 helix: 2.77 (0.18), residues: 819 sheet: 0.14 (0.35), residues: 138 loop : -0.64 (0.37), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG C 27 TYR 0.018 0.001 TYR C 307 PHE 0.009 0.002 PHE B 112 TRP 0.013 0.002 TRP D 46 HIS 0.003 0.001 HIS B 145 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.17 (15705) covalent geometry : angle 0.50938 / 0.29 (22290) hydrogen bonds : bond 0.04387 / 2.92 ( 901) hydrogen bonds : angle 3.55239 / 2.51 ( 2450) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 74 time to evaluate : 0.436 Fit side-chains REVERT: A 153 GLU cc_start: 0.9155 (tp30) cc_final: 0.8901 (tp30) REVERT: A 227 GLN cc_start: 0.9083 (mt0) cc_final: 0.8837 (mt0) REVERT: B 238 ARG cc_start: 0.7694 (mtp180) cc_final: 0.6260 (tpt90) REVERT: C 54 HIS cc_start: 0.8141 (t70) cc_final: 0.7898 (t70) REVERT: C 307 TYR cc_start: 0.8928 (t80) cc_final: 0.8721 (t80) outliers start: 3 outliers final: 1 residues processed: 74 average time/residue: 0.6617 time to fit residues: 53.5387 Evaluate side-chains 73 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 72 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 97 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 18 optimal weight: 3.9990 chunk 74 optimal weight: 0.9990 chunk 124 optimal weight: 10.0000 chunk 12 optimal weight: 0.9980 chunk 119 optimal weight: 0.9980 chunk 69 optimal weight: 0.4980 chunk 16 optimal weight: 0.9990 chunk 65 optimal weight: 0.0870 chunk 121 optimal weight: 0.9980 chunk 52 optimal weight: 0.6980 chunk 22 optimal weight: 3.9990 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 99 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.093825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.062065 restraints weight = 117276.359| |-----------------------------------------------------------------------------| r_work (start): 0.2868 rms_B_bonded: 3.83 r_work: 0.2647 rms_B_bonded: 4.71 restraints_weight: 0.5000 r_work (final): 0.2647 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2650 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2650 r_free = 0.2650 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2650 r_free = 0.2650 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2650 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8655 moved from start: 0.3126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 15705 Z= 0.113 Angle : 0.476 9.192 22290 Z= 0.276 Chirality : 0.034 0.172 2581 Planarity : 0.004 0.050 1996 Dihedral : 22.560 178.565 4635 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.08 % Allowed : 0.97 % Favored : 98.95 % Rotamer: Outliers : 0.49 % Allowed : 10.71 % Favored : 88.80 % 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: 1252 helix: 2.80 (0.18), residues: 819 sheet: 0.25 (0.35), residues: 138 loop : -0.55 (0.37), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG C 27 TYR 0.018 0.001 TYR C 307 PHE 0.010 0.001 PHE B 112 TRP 0.012 0.001 TRP A 276 HIS 0.003 0.000 HIS B 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00207 / 0.11 (15705) covalent geometry : angle 0.47605 / 0.28 (22290) hydrogen bonds : bond 0.03890 / 2.59 ( 901) hydrogen bonds : angle 3.47164 / 2.46 ( 2450) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 76 time to evaluate : 0.464 Fit side-chains REVERT: A 153 GLU cc_start: 0.9151 (tp30) cc_final: 0.8897 (tp30) REVERT: A 227 GLN cc_start: 0.9061 (mt0) cc_final: 0.8829 (mt0) REVERT: B 238 ARG cc_start: 0.7618 (mtp180) cc_final: 0.6219 (tpt90) REVERT: C 54 HIS cc_start: 0.8126 (t70) cc_final: 0.7887 (t70) outliers start: 4 outliers final: 2 residues processed: 76 average time/residue: 0.6557 time to fit residues: 54.5157 Evaluate side-chains 76 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 74 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 298 MET Chi-restraints excluded: chain D residue 97 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 96 optimal weight: 4.9990 chunk 139 optimal weight: 20.0000 chunk 43 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 137 optimal weight: 20.0000 chunk 97 optimal weight: 0.8980 chunk 85 optimal weight: 3.9990 chunk 135 optimal weight: 20.0000 chunk 95 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 93 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.090773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.059019 restraints weight = 115735.067| |-----------------------------------------------------------------------------| r_work (start): 0.2802 rms_B_bonded: 3.77 r_work: 0.2579 rms_B_bonded: 4.65 restraints_weight: 0.5000 r_work (final): 0.2579 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2584 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2584 r_free = 0.2584 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2584 r_free = 0.2584 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2584 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8703 moved from start: 0.2989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 15705 Z= 0.216 Angle : 0.538 8.857 22290 Z= 0.303 Chirality : 0.038 0.179 2581 Planarity : 0.004 0.053 1996 Dihedral : 22.587 176.491 4635 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.08 % Allowed : 1.05 % Favored : 98.87 % Rotamer: Outliers : 0.29 % Allowed : 10.81 % Favored : 88.90 % 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: 1252 helix: 2.77 (0.18), residues: 819 sheet: 0.27 (0.35), residues: 138 loop : -0.67 (0.37), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 27 TYR 0.022 0.002 TYR C 307 PHE 0.011 0.002 PHE D 316 TRP 0.013 0.002 TRP A 46 HIS 0.004 0.001 HIS A 145 Details of bonding type rmsd/Z covalent geometry : bond 0.00473 / 0.22 (15705) covalent geometry : angle 0.53805 / 0.30 (22290) hydrogen bonds : bond 0.04611 / 3.08 ( 901) hydrogen bonds : angle 3.56753 / 2.52 ( 2450) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3968.80 seconds wall clock time: 68 minutes 47.14 seconds (4127.14 seconds total)