Starting phenix.real_space_refine on Thu Aug 6 09:18:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wt8_37829/08_2026/8wt8_37829.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wt8_37829/08_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8wt8_37829/08_2026/8wt8_37829.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wt8_37829/08_2026/8wt8_37829.map" model { file = "/net/cci-nas-00/data/ceres_data/8wt8_37829/08_2026/8wt8_37829.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wt8_37829/08_2026/8wt8_37829.cif" } 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-2.2rc3-6140/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: 5.04, per 1000 atoms: 0.34 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: 1.45 Conformation dependent library (CDL) restraints added in 709.0 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: 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: 3.668A 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: 2.94 Time building geometry restraints manager: 1.87 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=" P DT G 10 " pdb=" OP1 DT G 10 " ideal model delta sigma weight residual 1.480 1.527 -0.047 2.00e-02 2.50e+03 5.57e+00 bond pdb=" C ILE A 201 " pdb=" N PRO A 202 " ideal model delta sigma weight residual 1.333 1.357 -0.024 1.01e-02 9.80e+03 5.44e+00 bond pdb=" P DA H 3 " pdb=" O5' DA H 3 " ideal model delta sigma weight residual 1.593 1.616 -0.023 1.00e-02 1.00e+04 5.38e+00 ... (remaining 15700 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.47: 17349 1.47 - 2.94: 4087 2.94 - 4.42: 723 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=" 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 angle pdb=" CA ASP C 25 " pdb=" CB ASP C 25 " pdb=" CG ASP C 25 " ideal model delta sigma weight residual 112.60 117.06 -4.46 1.00e+00 1.00e+00 1.99e+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: 2366 0.137 - 0.275: 208 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: 1.270 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: 0.050 Set scattering table: 0.040 Process input model: 18.390 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.130 ------------------------------------------------------------------------------- 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= 0.545 Angle : 1.301 7.360 22290 Z= 0.893 Chirality : 0.076 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 0.00815 / 0.55 (15705) covalent geometry : angle 1.30098 / 0.89 (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 : 0.449 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: 0.8689 time to fit residues: 111.4177 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 : 0.408 ------------------------------------------------------------------------------- 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: 20.0000 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: 0.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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 = 0.091384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.059791 restraints weight = 88784.578| |-----------------------------------------------------------------------------| r_work (start): 0.2806 rms_B_bonded: 3.37 r_work: 0.2591 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.2591 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2592 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2592 r_free = 0.2592 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 = 0.2591 r_free = 0.2591 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (7 function evaluations) r_final: 0.2591 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8669 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 : 0.004 0.039 15705 Z= 0.182 Angle : 0.652 9.042 22290 Z= 0.382 Chirality : 0.046 0.482 2581 Planarity : 0.005 0.039 1996 Dihedral : 22.600 170.943 4635 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 1.08 % Allowed : 7.07 % Favored : 91.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.20 (0.23), residues: 1252 helix: 1.74 (0.17), residues: 812 sheet: -0.93 (0.37), residues: 138 loop : -0.87 (0.35), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 261 TYR 0.018 0.002 TYR D 215 PHE 0.012 0.002 PHE B 112 TRP 0.021 0.003 TRP A 46 HIS 0.006 0.001 HIS C 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.18 (15705) covalent geometry : angle 0.65246 / 0.38 (22290) hydrogen bonds : bond 0.06688 / 4.45 ( 901) hydrogen bonds : angle 4.31898 / 3.09 ( 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: 10 poor density : 76 time to evaluate : 0.449 Fit side-chains REVERT: A 265 MET cc_start: 0.9246 (mmm) cc_final: 0.8910 (mmm) REVERT: B 51 LYS cc_start: 0.9132 (mmtm) cc_final: 0.8817 (mmmm) REVERT: D 265 MET cc_start: 0.9199 (mmm) cc_final: 0.8169 (mmm) outliers start: 10 outliers final: 1 residues processed: 81 average time/residue: 0.7141 time to fit residues: 62.9470 Evaluate side-chains 75 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 74 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 97 LEU 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: 5.9990 chunk 60 optimal weight: 0.8980 chunk 75 optimal weight: 0.0980 chunk 52 optimal weight: 0.7980 chunk 30 optimal weight: 6.9990 chunk 2 optimal weight: 6.9990 chunk 121 optimal weight: 2.9990 chunk 118 optimal weight: 1.9990 chunk 67 optimal weight: 3.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- 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 = 0.3406 r_free = 0.3406 target = 0.091479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.060059 restraints weight = 97270.960| |-----------------------------------------------------------------------------| r_work (start): 0.2813 rms_B_bonded: 3.53 r_work: 0.2598 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.2598 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2589 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2589 r_free = 0.2589 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2589 r_free = 0.2589 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.2589 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8666 moved from start: 0.2117 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= 0.155 Angle : 0.557 8.005 22290 Z= 0.329 Chirality : 0.040 0.310 2581 Planarity : 0.004 0.042 1996 Dihedral : 22.634 175.596 4635 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 0.79 % Allowed : 7.66 % Favored : 91.55 % 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: 1.78 (0.24), residues: 1252 helix: 2.21 (0.18), residues: 816 sheet: -0.75 (0.36), residues: 141 loop : -0.76 (0.36), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.024 0.001 ARG C 27 TYR 0.019 0.002 TYR B 264 PHE 0.052 0.002 PHE C 33 TRP 0.015 0.002 TRP D 46 HIS 0.005 0.001 HIS B 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.16 (15705) covalent geometry : angle 0.55714 / 0.33 (22290) hydrogen bonds : bond 0.05261 / 3.51 ( 901) hydrogen bonds : angle 3.91307 / 2.80 ( 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: 7 poor density : 76 time to evaluate : 0.354 Fit side-chains REVERT: D 265 MET cc_start: 0.9199 (mmm) cc_final: 0.8853 (mmt) outliers start: 7 outliers final: 0 residues processed: 79 average time/residue: 0.7234 time to fit residues: 62.1894 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 : 0.521 ------------------------------------------------------------------------------- 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: 0.9990 chunk 74 optimal weight: 0.8980 chunk 67 optimal weight: 0.2980 chunk 89 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 chunk 108 optimal weight: 0.6980 chunk 77 optimal weight: 4.9990 chunk 9 optimal weight: 7.9990 chunk 88 optimal weight: 5.9990 chunk 91 optimal weight: 1.9990 chunk 59 optimal weight: 5.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- 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 = 0.3436 r_free = 0.3436 target = 0.092854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.061788 restraints weight = 79388.336| |-----------------------------------------------------------------------------| r_work (start): 0.2855 rms_B_bonded: 3.27 r_work: 0.2650 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.2650 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2652 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2652 r_free = 0.2652 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2652 r_free = 0.2652 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2652 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8644 moved from start: 0.2510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15705 Z= 0.132 Angle : 0.513 8.063 22290 Z= 0.301 Chirality : 0.037 0.284 2581 Planarity : 0.004 0.040 1996 Dihedral : 22.665 177.000 4635 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 0.59 % Allowed : 8.35 % Favored : 91.06 % 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: -0.40 (0.36), residues: 140 loop : -0.63 (0.37), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 27 TYR 0.020 0.001 TYR C 307 PHE 0.020 0.002 PHE C 33 TRP 0.012 0.002 TRP D 276 HIS 0.004 0.001 HIS C 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.13 (15705) covalent geometry : angle 0.51275 / 0.30 (22290) hydrogen bonds : bond 0.04392 / 2.92 ( 901) hydrogen bonds : angle 3.68471 / 2.63 ( 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 86 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 81 time to evaluate : 0.445 Fit side-chains REVERT: C 107 ARG cc_start: 0.8544 (ttm-80) cc_final: 0.8273 (ttp80) outliers start: 5 outliers final: 1 residues processed: 81 average time/residue: 0.7081 time to fit residues: 62.6038 Evaluate side-chains 72 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 71 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 97 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 113 optimal weight: 5.9990 chunk 104 optimal weight: 0.8980 chunk 103 optimal weight: 1.9990 chunk 126 optimal weight: 10.0000 chunk 116 optimal weight: 0.8980 chunk 129 optimal weight: 9.9990 chunk 55 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 chunk 6 optimal weight: 5.9990 chunk 44 optimal weight: 0.9980 chunk 117 optimal weight: 0.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 93 GLN A 99 ASN 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 = 0.3429 r_free = 0.3429 target = 0.092483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.061292 restraints weight = 90883.070| |-----------------------------------------------------------------------------| r_work (start): 0.2847 rms_B_bonded: 3.42 r_work: 0.2635 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.2635 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2637 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2637 r_free = 0.2637 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2637 r_free = 0.2637 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2637 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8657 moved from start: 0.2667 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= 0.139 Angle : 0.505 8.017 22290 Z= 0.294 Chirality : 0.037 0.279 2581 Planarity : 0.004 0.049 1996 Dihedral : 22.680 177.844 4635 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 0.69 % Allowed : 9.53 % 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: 2.34 (0.24), residues: 1252 helix: 2.62 (0.18), residues: 819 sheet: -0.37 (0.35), residues: 140 loop : -0.60 (0.37), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 27 TYR 0.016 0.001 TYR C 307 PHE 0.026 0.002 PHE C 33 TRP 0.012 0.002 TRP D 46 HIS 0.003 0.001 HIS C 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.14 (15705) covalent geometry : angle 0.50515 / 0.29 (22290) hydrogen bonds : bond 0.04349 / 2.90 ( 901) hydrogen bonds : angle 3.62018 / 2.58 ( 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 83 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 77 time to evaluate : 0.485 Fit side-chains REVERT: B 238 ARG cc_start: 0.7504 (mtp180) cc_final: 0.6139 (tpt90) REVERT: C 54 HIS cc_start: 0.8094 (t70) cc_final: 0.7844 (t70) REVERT: C 107 ARG cc_start: 0.8555 (ttm-80) cc_final: 0.8278 (ttp80) REVERT: C 307 TYR cc_start: 0.8862 (t80) cc_final: 0.8638 (t80) outliers start: 6 outliers final: 1 residues processed: 79 average time/residue: 0.7377 time to fit residues: 63.5884 Evaluate side-chains 75 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 74 time to evaluate : 0.437 ------------------------------------------------------------------------------- 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: 0.7980 chunk 58 optimal weight: 0.1980 chunk 85 optimal weight: 3.9990 chunk 11 optimal weight: 0.3980 chunk 27 optimal weight: 0.7980 chunk 14 optimal weight: 0.9980 chunk 8 optimal weight: 4.9990 chunk 129 optimal weight: 10.0000 chunk 125 optimal weight: 10.0000 chunk 56 optimal weight: 2.9990 chunk 123 optimal weight: 9.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 93 GLN A 99 ASN D 93 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.093882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.062763 restraints weight = 92816.189| |-----------------------------------------------------------------------------| r_work (start): 0.2876 rms_B_bonded: 3.45 r_work: 0.2667 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.2667 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2659 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2659 r_free = 0.2659 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2659 r_free = 0.2659 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2659 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.2876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 15705 Z= 0.116 Angle : 0.481 8.470 22290 Z= 0.282 Chirality : 0.035 0.256 2581 Planarity : 0.004 0.037 1996 Dihedral : 22.652 178.656 4635 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 1.08 % Allowed : 8.94 % Favored : 89.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.49 (0.24), residues: 1252 helix: 2.71 (0.18), residues: 819 sheet: -0.22 (0.35), residues: 138 loop : -0.53 (0.37), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 27 TYR 0.016 0.001 TYR C 307 PHE 0.020 0.001 PHE C 33 TRP 0.011 0.001 TRP D 46 HIS 0.003 0.001 HIS B 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00214 / 0.12 (15705) covalent geometry : angle 0.48076 / 0.28 (22290) hydrogen bonds : bond 0.03959 / 2.63 ( 901) hydrogen bonds : angle 3.52839 / 2.52 ( 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 87 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 77 time to evaluate : 0.502 Fit side-chains REVERT: A 153 GLU cc_start: 0.9121 (tp30) cc_final: 0.8867 (tp30) REVERT: B 191 MET cc_start: 0.8956 (mtt) cc_final: 0.8714 (mtm) REVERT: B 238 ARG cc_start: 0.7488 (mtp180) cc_final: 0.6110 (tpt90) REVERT: C 54 HIS cc_start: 0.8087 (t70) cc_final: 0.7830 (t70) outliers start: 10 outliers final: 1 residues processed: 79 average time/residue: 0.6889 time to fit residues: 59.5965 Evaluate side-chains 72 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 71 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 268 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 69 optimal weight: 0.7980 chunk 84 optimal weight: 4.9990 chunk 48 optimal weight: 4.9990 chunk 129 optimal weight: 10.0000 chunk 60 optimal weight: 5.9990 chunk 4 optimal weight: 5.9990 chunk 22 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 59 optimal weight: 0.9980 overall best weight: 2.1586 ------------------------------------------------------------------------------- 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 = 0.3408 r_free = 0.3408 target = 0.091084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.059407 restraints weight = 100113.155| |-----------------------------------------------------------------------------| r_work (start): 0.2817 rms_B_bonded: 3.57 r_work: 0.2600 rms_B_bonded: 4.52 restraints_weight: 0.5000 r_work (final): 0.2600 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2597 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2597 r_free = 0.2597 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2597 r_free = 0.2597 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2597 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8687 moved from start: 0.2791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 15705 Z= 0.190 Angle : 0.535 9.349 22290 Z= 0.301 Chirality : 0.039 0.307 2581 Planarity : 0.004 0.043 1996 Dihedral : 22.664 177.245 4635 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 0.59 % Allowed : 9.92 % Favored : 89.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.49 (0.24), residues: 1252 helix: 2.74 (0.18), residues: 819 sheet: -0.19 (0.35), residues: 140 loop : -0.63 (0.37), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 27 TYR 0.017 0.002 TYR C 307 PHE 0.017 0.002 PHE C 33 TRP 0.013 0.002 TRP A 46 HIS 0.003 0.001 HIS A 145 Details of bonding type rmsd/Z covalent geometry : bond 0.00406 / 0.19 (15705) covalent geometry : angle 0.53543 / 0.30 (22290) hydrogen bonds : bond 0.04656 / 3.11 ( 901) hydrogen bonds : angle 3.62582 / 2.59 ( 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 77 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 72 time to evaluate : 0.394 Fit side-chains REVERT: A 153 GLU cc_start: 0.9155 (tp30) cc_final: 0.8894 (tp30) REVERT: B 191 MET cc_start: 0.8943 (mtt) cc_final: 0.8621 (mtm) REVERT: B 226 ARG cc_start: 0.8699 (mtp85) cc_final: 0.8496 (tpt-90) REVERT: B 238 ARG cc_start: 0.7632 (mtp180) cc_final: 0.6229 (tpt90) REVERT: C 307 TYR cc_start: 0.8889 (t80) cc_final: 0.8676 (t80) outliers start: 5 outliers final: 0 residues processed: 74 average time/residue: 0.7381 time to fit residues: 59.4821 Evaluate side-chains 70 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 70 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 117 optimal weight: 0.6980 chunk 136 optimal weight: 10.0000 chunk 1 optimal weight: 0.9990 chunk 82 optimal weight: 0.7980 chunk 29 optimal weight: 0.8980 chunk 8 optimal weight: 4.9990 chunk 74 optimal weight: 0.7980 chunk 137 optimal weight: 20.0000 chunk 79 optimal weight: 5.9990 chunk 16 optimal weight: 0.9990 chunk 65 optimal weight: 4.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 93 GLN A 99 ASN D 93 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.092845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.061509 restraints weight = 96257.142| |-----------------------------------------------------------------------------| r_work (start): 0.2850 rms_B_bonded: 3.51 r_work: 0.2635 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.2635 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2640 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2640 r_free = 0.2640 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2640 r_free = 0.2640 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2640 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8657 moved from start: 0.2925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 15705 Z= 0.122 Angle : 0.490 8.399 22290 Z= 0.282 Chirality : 0.035 0.266 2581 Planarity : 0.004 0.046 1996 Dihedral : 22.632 178.177 4635 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 0.39 % Allowed : 10.51 % Favored : 89.10 % 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: 2.79 (0.18), residues: 819 sheet: -0.04 (0.35), residues: 139 loop : -0.59 (0.37), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG C 27 TYR 0.016 0.001 TYR C 307 PHE 0.019 0.001 PHE C 33 TRP 0.012 0.001 TRP D 46 HIS 0.008 0.001 HIS C 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.12 (15705) covalent geometry : angle 0.48969 / 0.28 (22290) hydrogen bonds : bond 0.04105 / 2.73 ( 901) hydrogen bonds : angle 3.53593 / 2.52 ( 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 75 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 72 time to evaluate : 0.437 Fit side-chains REVERT: A 153 GLU cc_start: 0.9150 (tp30) cc_final: 0.8889 (tp30) REVERT: B 191 MET cc_start: 0.8920 (mtt) cc_final: 0.8608 (mtm) REVERT: B 226 ARG cc_start: 0.8655 (mtp85) cc_final: 0.8454 (tpt-90) REVERT: B 238 ARG cc_start: 0.7626 (mtp180) cc_final: 0.6265 (tpt90) outliers start: 3 outliers final: 0 residues processed: 73 average time/residue: 0.7341 time to fit residues: 58.3144 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 : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 16 optimal weight: 0.7980 chunk 59 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 131 optimal weight: 10.0000 chunk 53 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 4 optimal weight: 4.9990 chunk 87 optimal weight: 5.9990 chunk 1 optimal weight: 2.9990 chunk 58 optimal weight: 4.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- 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 = 0.3414 r_free = 0.3414 target = 0.091258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.059899 restraints weight = 98660.269| |-----------------------------------------------------------------------------| r_work (start): 0.2823 rms_B_bonded: 3.52 r_work: 0.2607 rms_B_bonded: 4.49 restraints_weight: 0.5000 r_work (final): 0.2607 ------------------------------------------------------------------------------- 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 = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2605 r_free = 0.2605 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2605 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 moved from start: 0.2888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 15705 Z= 0.178 Angle : 0.522 8.607 22290 Z= 0.294 Chirality : 0.038 0.297 2581 Planarity : 0.004 0.048 1996 Dihedral : 22.617 177.311 4635 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 0.49 % Allowed : 10.61 % 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: 2.57 (0.24), residues: 1252 helix: 2.77 (0.18), residues: 819 sheet: 0.07 (0.35), residues: 139 loop : -0.64 (0.37), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 27 TYR 0.011 0.001 TYR D 307 PHE 0.016 0.002 PHE C 33 TRP 0.012 0.002 TRP D 46 HIS 0.007 0.001 HIS C 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.18 (15705) covalent geometry : angle 0.52224 / 0.29 (22290) hydrogen bonds : bond 0.04520 / 3.02 ( 901) hydrogen bonds : angle 3.57552 / 2.53 ( 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 76 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 72 time to evaluate : 0.483 Fit side-chains REVERT: A 153 GLU cc_start: 0.9149 (tp30) cc_final: 0.8889 (tp30) REVERT: B 226 ARG cc_start: 0.8685 (mtp85) cc_final: 0.8485 (tpt-90) REVERT: B 238 ARG cc_start: 0.7692 (mtp180) cc_final: 0.6280 (tpt90) outliers start: 4 outliers final: 0 residues processed: 73 average time/residue: 0.7640 time to fit residues: 60.8097 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 : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9980 chunk 124 optimal weight: 10.0000 chunk 12 optimal weight: 3.9990 chunk 119 optimal weight: 2.9990 chunk 69 optimal weight: 0.7980 chunk 16 optimal weight: 0.6980 chunk 65 optimal weight: 0.5980 chunk 121 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 93 GLN A 99 ASN D 93 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.093135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.061789 restraints weight = 101773.554| |-----------------------------------------------------------------------------| r_work (start): 0.2858 rms_B_bonded: 3.58 r_work: 0.2641 rms_B_bonded: 4.55 restraints_weight: 0.5000 r_work (final): 0.2641 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2632 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2632 r_free = 0.2632 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2632 r_free = 0.2632 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2632 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8657 moved from start: 0.3039 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= 0.122 Angle : 0.485 8.741 22290 Z= 0.280 Chirality : 0.035 0.260 2581 Planarity : 0.004 0.051 1996 Dihedral : 22.580 178.407 4635 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.08 % Allowed : 1.13 % Favored : 98.78 % Rotamer: Outliers : 0.29 % Allowed : 10.61 % Favored : 89.10 % 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: 2.63 (0.24), residues: 1252 helix: 2.79 (0.18), residues: 819 sheet: 0.23 (0.35), residues: 138 loop : -0.60 (0.37), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 27 TYR 0.012 0.001 TYR D 307 PHE 0.019 0.001 PHE C 33 TRP 0.011 0.001 TRP D 46 HIS 0.006 0.001 HIS C 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.12 (15705) covalent geometry : angle 0.48509 / 0.28 (22290) hydrogen bonds : bond 0.04054 / 2.70 ( 901) hydrogen bonds : angle 3.47740 / 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 77 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 75 time to evaluate : 0.403 Fit side-chains REVERT: A 153 GLU cc_start: 0.9156 (tp30) cc_final: 0.8895 (tp30) REVERT: B 238 ARG cc_start: 0.7632 (mtp180) cc_final: 0.6252 (tpt90) outliers start: 2 outliers final: 0 residues processed: 75 average time/residue: 0.6959 time to fit residues: 56.8233 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 : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 96 optimal weight: 0.0070 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: 0.1980 chunk 85 optimal weight: 3.9990 chunk 135 optimal weight: 20.0000 chunk 95 optimal weight: 4.9990 chunk 40 optimal weight: 2.9990 overall best weight: 1.6404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 93 GLN A 99 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.092020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.060646 restraints weight = 99048.242| |-----------------------------------------------------------------------------| r_work (start): 0.2834 rms_B_bonded: 3.54 r_work: 0.2616 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.2616 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2621 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2621 r_free = 0.2621 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2621 r_free = 0.2621 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2621 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8675 moved from start: 0.3012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15705 Z= 0.160 Angle : 0.507 8.574 22290 Z= 0.287 Chirality : 0.037 0.282 2581 Planarity : 0.004 0.052 1996 Dihedral : 22.557 177.734 4635 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.08 % Allowed : 1.05 % Favored : 98.87 % Rotamer: Outliers : 0.29 % Allowed : 10.61 % Favored : 89.10 % 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: 2.64 (0.24), residues: 1252 helix: 2.81 (0.18), residues: 819 sheet: 0.24 (0.35), residues: 138 loop : -0.63 (0.37), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG C 27 TYR 0.011 0.001 TYR D 307 PHE 0.016 0.002 PHE C 33 TRP 0.012 0.002 TRP D 46 HIS 0.006 0.001 HIS C 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.16 (15705) covalent geometry : angle 0.50729 / 0.29 (22290) hydrogen bonds : bond 0.04312 / 2.87 ( 901) hydrogen bonds : angle 3.50687 / 2.47 ( 2450) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4030.54 seconds wall clock time: 69 minutes 37.06 seconds (4177.06 seconds total)