Starting phenix.real_space_refine on Sat Sep 12 10:00:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9why_65979/09_2026/9why_65979.cif Found real_map, /net/cci-nas-00/data/ceres_data/9why_65979/09_2026/9why_65979.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9why_65979/09_2026/9why_65979.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9why_65979/09_2026/9why_65979.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9why_65979/09_2026/9why_65979.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9why_65979/09_2026/9why_65979.map" } resolution = 2.6 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.012 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 239 5.49 5 Mg 2 5.21 5 S 48 5.16 5 C 8492 2.51 5 N 2748 2.21 5 O 3331 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-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14860 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 2420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2420 Classifications: {'peptide': 306} Link IDs: {'PTRANS': 12, 'TRANS': 293} Chain breaks: 1 Chain: "B" Number of atoms: 2511 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 318, 2503 Classifications: {'peptide': 318} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 305} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Conformer: "B" Number of residues, atoms: 318, 2503 Classifications: {'peptide': 318} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 305} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 bond proxies already assigned to first conformer: 2543 Chain: "C" Number of atoms: 2445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2445 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 12, 'TRANS': 296} Chain breaks: 1 Chain: "D" Number of atoms: 2494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2494 Classifications: {'peptide': 317} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 304} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "E" Number of atoms: 1250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 1250 Classifications: {'RNA': 59} Modifications used: {'rna2p_pur': 5, 'rna2p_pyr': 10, 'rna3p_pur': 21, 'rna3p_pyr': 23} Link IDs: {'rna2p': 15, 'rna3p': 43} Chain: "F" Number of atoms: 1399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 1399 Classifications: {'RNA': 66} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 6, 'rna3p_pur': 26, 'rna3p_pyr': 28} Link IDs: {'rna2p': 12, 'rna3p': 53} Chain: "G" Number of atoms: 567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 567 Classifications: {'DNA': 28} Link IDs: {'rna3p': 27} Chain breaks: 1 Chain: "H" Number of atoms: 607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 607 Classifications: {'DNA': 29} Link IDs: {'rna3p': 28} Chain: "I" Number of atoms: 587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 587 Classifications: {'DNA': 29} Link IDs: {'rna3p': 28} Chain breaks: 1 Chain: "J" Number of atoms: 574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 574 Classifications: {'DNA': 28} Link IDs: {'rna3p': 27} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 4.14, per 1000 atoms: 0.28 Number of scatterers: 14860 At special positions: 0 Unit cell: (115.37, 120.35, 115.37, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 48 16.00 P 239 15.00 Mg 2 11.99 O 3331 8.00 N 2748 7.00 C 8492 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: 1.29 Conformation dependent library (CDL) restraints added in 683.8 milliseconds 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2342 Finding SS restraints... Secondary structure from input PDB file: 59 helices and 9 sheets defined 68.0% alpha, 9.4% beta 89 base pairs and 139 stacking pairs defined. Time for finding SS restraints: 2.21 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: 3.806A pdb=" N GLY A 88 " --> pdb=" O ASN A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 117 Processing helix chain 'A' and resid 125 through 155 removed outlier: 3.999A pdb=" N GLU A 153 " --> pdb=" O LEU A 149 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N THR A 154 " --> pdb=" O ASN A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 187 Processing helix chain 'A' and resid 188 through 200 Processing helix chain 'A' and resid 205 through 217 Processing helix chain 'A' and resid 224 through 232 Processing helix chain 'A' and resid 256 through 262 Processing helix chain 'A' and resid 263 through 274 Processing helix chain 'A' and resid 274 through 286 Processing helix chain 'A' and resid 290 through 313 Processing helix chain 'A' and resid 317 through 321 removed outlier: 3.504A pdb=" N ARG A 320 " --> pdb=" O ASP A 317 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 50 Processing helix chain 'B' and resid 63 through 65 No H-bonds generated for 'chain 'B' and resid 63 through 65' Processing helix chain 'B' and resid 66 through 76 Processing helix chain 'B' and resid 84 through 94 removed outlier: 3.765A pdb=" N GLY B 88 " --> pdb=" O ASN B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 117 Processing helix chain 'B' and resid 125 through 155 removed outlier: 3.843A pdb=" N GLU B 153 " --> pdb=" O LEU B 149 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N THR B 154 " --> pdb=" O ASN B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 158 No H-bonds generated for 'chain 'B' and resid 156 through 158' Processing helix chain 'B' and resid 159 through 187 Processing helix chain 'B' and resid 188 through 200 Processing helix chain 'B' and resid 205 through 217 removed outlier: 3.503A pdb=" N VAL B 211 " --> pdb=" O LYS B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 232 removed outlier: 3.639A pdb=" N PHE B 228 " --> pdb=" O HIS B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 256 through 263 removed outlier: 3.507A pdb=" N ARG B 260 " --> pdb=" O HIS B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 274 Processing helix chain 'B' and resid 274 through 287 Processing helix chain 'B' and resid 290 through 313 Processing helix chain 'B' and resid 317 through 321 Processing helix chain 'C' and resid 36 through 50 Processing helix chain 'C' and resid 66 through 76 Processing helix chain 'C' and resid 84 through 95 removed outlier: 3.672A pdb=" N GLY C 88 " --> pdb=" O ASN C 84 " (cutoff:3.500A) Processing helix chain 'C' and resid 101 through 117 Processing helix chain 'C' and resid 125 through 153 removed outlier: 3.872A pdb=" N GLU C 153 " --> pdb=" O LEU C 149 " (cutoff:3.500A) Processing helix chain 'C' and resid 156 through 158 No H-bonds generated for 'chain 'C' and resid 156 through 158' Processing helix chain 'C' and resid 159 through 188 removed outlier: 3.556A pdb=" N ASP C 188 " --> pdb=" O LEU C 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 188 through 201 removed outlier: 3.940A pdb=" N ILE C 201 " --> pdb=" O LEU C 197 " (cutoff:3.500A) Processing helix chain 'C' and resid 205 through 217 Processing helix chain 'C' and resid 224 through 232 removed outlier: 3.644A pdb=" N PHE C 228 " --> pdb=" O HIS C 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 256 through 262 removed outlier: 3.543A pdb=" N ALA C 262 " --> pdb=" O SER C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 263 through 274 Processing helix chain 'C' and resid 274 through 287 removed outlier: 3.664A pdb=" N ASN C 287 " --> pdb=" O ARG C 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 290 through 313 Processing helix chain 'C' and resid 317 through 321 Processing helix chain 'D' and resid 36 through 50 removed outlier: 3.634A pdb=" N HIS D 50 " --> pdb=" O TRP D 46 " (cutoff:3.500A) Processing helix chain 'D' and resid 63 through 65 No H-bonds generated for 'chain 'D' and resid 63 through 65' Processing helix chain 'D' and resid 66 through 76 Processing helix chain 'D' and resid 84 through 96 removed outlier: 3.749A pdb=" N GLY D 88 " --> pdb=" O ASN D 84 " (cutoff:3.500A) removed outlier: 3.642A 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 155 removed outlier: 3.961A pdb=" N GLU D 153 " --> pdb=" O LEU D 149 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N THR D 154 " --> pdb=" O ASN D 150 " (cutoff:3.500A) Processing helix chain 'D' and resid 159 through 187 Processing helix chain 'D' and resid 188 through 200 Processing helix chain 'D' and resid 205 through 217 Processing helix chain 'D' and resid 224 through 232 removed outlier: 3.576A pdb=" N PHE D 228 " --> pdb=" O HIS D 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 256 through 271 removed outlier: 3.537A pdb=" N ALA D 262 " --> pdb=" O SER D 258 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N TYR D 264 " --> pdb=" O ARG D 260 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N MET D 265 " --> pdb=" O ARG D 261 " (cutoff:3.500A) Proline residue: D 266 - end of helix Processing helix chain 'D' and resid 274 through 287 Processing helix chain 'D' and resid 290 through 313 Processing helix chain 'D' and resid 317 through 321 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 34 removed outlier: 6.589A pdb=" N HIS A 6 " --> pdb=" O HIS A 56 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N CYS A 58 " --> pdb=" O HIS A 6 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ILE A 8 " --> pdb=" O CYS A 58 " (cutoff:3.500A) removed outlier: 8.385A pdb=" N GLU A 60 " --> pdb=" O ILE A 8 " (cutoff:3.500A) removed outlier: 8.238A 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: 6.612A pdb=" N HIS B 6 " --> pdb=" O HIS B 56 " (cutoff:3.500A) removed outlier: 7.965A pdb=" N CYS B 58 " --> pdb=" O HIS B 6 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N ILE B 8 " --> pdb=" O CYS B 58 " (cutoff:3.500A) removed outlier: 8.548A pdb=" N GLU B 60 " --> pdb=" O ILE B 8 " (cutoff:3.500A) removed outlier: 8.475A pdb=" N ILE B 10 " --> pdb=" O GLU B 60 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 236 through 237 removed outlier: 3.814A 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: 6.451A pdb=" N HIS C 6 " --> pdb=" O HIS C 56 " (cutoff:3.500A) removed outlier: 7.948A pdb=" N CYS C 58 " --> pdb=" O HIS C 6 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ILE C 8 " --> pdb=" O CYS C 58 " (cutoff:3.500A) removed outlier: 8.497A pdb=" N GLU C 60 " --> pdb=" O ILE C 8 " (cutoff:3.500A) removed outlier: 8.419A pdb=" N ILE C 10 " --> pdb=" O GLU C 60 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 236 through 237 Processing sheet with id=AA7, first strand: chain 'D' and resid 28 through 34 removed outlier: 6.526A pdb=" N HIS D 6 " --> pdb=" O HIS D 56 " (cutoff:3.500A) removed outlier: 7.948A pdb=" N CYS D 58 " --> pdb=" O HIS D 6 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ILE D 8 " --> pdb=" O CYS D 58 " (cutoff:3.500A) removed outlier: 8.453A pdb=" N GLU D 60 " --> pdb=" O ILE D 8 " (cutoff:3.500A) removed outlier: 8.254A pdb=" N ILE D 10 " --> pdb=" O GLU D 60 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 236 through 237 removed outlier: 3.750A pdb=" N ARG D 250 " --> pdb=" O ARG D 237 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 240 through 241 669 hydrogen bonds defined for protein. 1964 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 229 hydrogen bonds 454 hydrogen bond angles 0 basepair planarities 89 basepair parallelities 139 stacking parallelities Total time for adding SS restraints: 2.87 Time building geometry restraints manager: 1.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2681 1.33 - 1.45: 5142 1.45 - 1.57: 7256 1.57 - 1.69: 470 1.69 - 1.82: 84 Bond restraints: 15633 Sorted by residual: bond pdb=" N1 DC H 17 " pdb=" C6 DC H 17 " ideal model delta sigma weight residual 1.367 1.333 0.034 6.00e-03 2.78e+04 3.27e+01 bond pdb=" C8 G E 80 " pdb=" N7 G E 80 " ideal model delta sigma weight residual 1.305 1.336 -0.031 6.00e-03 2.78e+04 2.68e+01 bond pdb=" N1 DC H 19 " pdb=" C6 DC H 19 " ideal model delta sigma weight residual 1.367 1.336 0.031 6.00e-03 2.78e+04 2.59e+01 bond pdb=" N1 C F 130 " pdb=" C6 C F 130 " ideal model delta sigma weight residual 1.367 1.337 0.030 6.00e-03 2.78e+04 2.49e+01 bond pdb=" N1 DC I 19 " pdb=" C6 DC I 19 " ideal model delta sigma weight residual 1.367 1.338 0.029 6.00e-03 2.78e+04 2.38e+01 ... (remaining 15628 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.06: 20406 3.06 - 6.12: 1573 6.12 - 9.18: 181 9.18 - 12.24: 8 12.24 - 15.29: 5 Bond angle restraints: 22173 Sorted by residual: angle pdb=" O4' DT I 26 " pdb=" C1' DT I 26 " pdb=" N1 DT I 26 " ideal model delta sigma weight residual 108.00 102.65 5.35 7.00e-01 2.04e+00 5.84e+01 angle pdb=" O4' DG H 15 " pdb=" C4' DG H 15 " pdb=" C3' DG H 15 " ideal model delta sigma weight residual 106.00 101.50 4.50 6.00e-01 2.78e+00 5.63e+01 angle pdb=" O4' DC H 19 " pdb=" C4' DC H 19 " pdb=" C3' DC H 19 " ideal model delta sigma weight residual 106.00 101.52 4.48 6.00e-01 2.78e+00 5.57e+01 angle pdb=" O3' DA H 21 " pdb=" P DT H 22 " pdb=" O5' DT H 22 " ideal model delta sigma weight residual 104.00 90.32 13.68 1.90e+00 2.77e-01 5.18e+01 angle pdb=" O4' DT G 31 " pdb=" C1' DT G 31 " pdb=" N1 DT G 31 " ideal model delta sigma weight residual 108.00 103.00 5.00 7.00e-01 2.04e+00 5.10e+01 ... (remaining 22168 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.91: 8560 35.91 - 71.83: 756 71.83 - 107.74: 50 107.74 - 143.66: 0 143.66 - 179.57: 2 Dihedral angle restraints: 9368 sinusoidal: 5749 harmonic: 3619 Sorted by residual: dihedral pdb=" CD BARG B 261 " pdb=" NE BARG B 261 " pdb=" CZ BARG B 261 " pdb=" NH1BARG B 261 " ideal model delta sinusoidal sigma weight residual 0.00 -178.05 178.05 1 1.00e+01 1.00e-02 1.92e+02 dihedral pdb=" O4' U F 159 " pdb=" C1' U F 159 " pdb=" N1 U F 159 " pdb=" C2 U F 159 " ideal model delta sinusoidal sigma weight residual -128.00 51.57 -179.57 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" C4' A E 85 " pdb=" O4' A E 85 " pdb=" C1' A E 85 " pdb=" C2' A E 85 " ideal model delta sinusoidal sigma weight residual -21.00 14.28 -35.28 1 8.00e+00 1.56e-02 2.76e+01 ... (remaining 9365 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.132: 2140 0.132 - 0.264: 389 0.264 - 0.396: 34 0.396 - 0.528: 1 0.528 - 0.660: 6 Chirality restraints: 2570 Sorted by residual: chirality pdb=" P DG J 13 " pdb=" OP1 DG J 13 " pdb=" OP2 DG J 13 " pdb=" O5' DG J 13 " both_signs ideal model delta sigma weight residual True 2.34 -3.00 -0.66 2.00e-01 2.50e+01 1.09e+01 chirality pdb=" P DG I 5 " pdb=" OP1 DG I 5 " pdb=" OP2 DG I 5 " pdb=" O5' DG I 5 " both_signs ideal model delta sigma weight residual True 2.34 -2.99 -0.66 2.00e-01 2.50e+01 1.08e+01 chirality pdb=" P DG H 1 " pdb=" OP1 DG H 1 " pdb=" OP2 DG H 1 " pdb=" O5' DG H 1 " 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 2567 not shown) Planarity restraints: 1985 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A F 157 " -0.120 2.00e-02 2.50e+03 4.88e-02 6.54e+01 pdb=" N9 A F 157 " 0.052 2.00e-02 2.50e+03 pdb=" C8 A F 157 " 0.036 2.00e-02 2.50e+03 pdb=" N7 A F 157 " 0.013 2.00e-02 2.50e+03 pdb=" C5 A F 157 " 0.031 2.00e-02 2.50e+03 pdb=" C6 A F 157 " -0.016 2.00e-02 2.50e+03 pdb=" N6 A F 157 " -0.058 2.00e-02 2.50e+03 pdb=" N1 A F 157 " -0.020 2.00e-02 2.50e+03 pdb=" C2 A F 157 " 0.023 2.00e-02 2.50e+03 pdb=" N3 A F 157 " 0.039 2.00e-02 2.50e+03 pdb=" C4 A F 157 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U E 74 " -0.113 2.00e-02 2.50e+03 5.25e-02 6.20e+01 pdb=" N1 U E 74 " 0.072 2.00e-02 2.50e+03 pdb=" C2 U E 74 " 0.043 2.00e-02 2.50e+03 pdb=" O2 U E 74 " 0.015 2.00e-02 2.50e+03 pdb=" N3 U E 74 " -0.004 2.00e-02 2.50e+03 pdb=" C4 U E 74 " -0.025 2.00e-02 2.50e+03 pdb=" O4 U E 74 " -0.048 2.00e-02 2.50e+03 pdb=" C5 U E 74 " 0.023 2.00e-02 2.50e+03 pdb=" C6 U E 74 " 0.037 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C F 130 " 0.079 2.00e-02 2.50e+03 4.11e-02 3.80e+01 pdb=" N1 C F 130 " -0.007 2.00e-02 2.50e+03 pdb=" C2 C F 130 " -0.014 2.00e-02 2.50e+03 pdb=" O2 C F 130 " -0.026 2.00e-02 2.50e+03 pdb=" N3 C F 130 " -0.010 2.00e-02 2.50e+03 pdb=" C4 C F 130 " 0.014 2.00e-02 2.50e+03 pdb=" N4 C F 130 " 0.037 2.00e-02 2.50e+03 pdb=" C5 C F 130 " 0.008 2.00e-02 2.50e+03 pdb=" C6 C F 130 " -0.079 2.00e-02 2.50e+03 ... (remaining 1982 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.27: 15 2.27 - 2.93: 5526 2.93 - 3.58: 21777 3.58 - 4.24: 40870 4.24 - 4.90: 60704 Nonbonded interactions: 128892 Sorted by model distance: nonbonded pdb=" OG SER D 241 " pdb=" P DA G 26 " model vdw 1.609 3.400 nonbonded pdb=" OG SER B 241 " pdb=" P DT I 21 " model vdw 1.611 3.400 nonbonded pdb="MG MG C 401 " pdb=" O HOH C 502 " model vdw 1.971 2.170 nonbonded pdb=" O3' DT G 25 " pdb="MG MG A 401 " model vdw 2.042 2.170 nonbonded pdb="MG MG A 401 " pdb=" O HOH A 501 " model vdw 2.052 2.170 ... (remaining 128887 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 5 through 99 or (resid 100 and (name N or name CA or name \ C or name O or name CB )) or resid 101 through 260 or resid 262 through 321)) selection = (chain 'B' and (resid 5 through 238 or resid 251 through 260 or resid 262 throug \ h 321)) selection = (chain 'C' and (resid 5 through 99 or (resid 100 and (name N or name CA or name \ C or name O or name CB )) or resid 101 through 238 or resid 251 through 260 or r \ esid 262 through 321)) selection = (chain 'D' and (resid 5 through 238 or resid 251 through 260 or resid 262 throug \ h 321)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 17.780 Find NCS groups from input model: 0.280 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:8.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9184 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 : 0.010 0.067 15633 Z= 0.720 Angle : 1.736 15.295 22173 Z= 1.167 Chirality : 0.100 0.660 2570 Planarity : 0.011 0.135 1985 Dihedral : 21.925 179.574 7026 Min Nonbonded Distance : 1.609 Molprobity Statistics. All-atom Clashscore : 2.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 2.86 % Allowed : 5.42 % Favored : 91.72 % Cbeta Deviations : 0.34 % 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: -2.02 (0.20), residues: 1239 helix: -1.41 (0.14), residues: 782 sheet: -0.85 (0.36), residues: 178 loop : -0.63 (0.33), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.065 0.005 ARG D 238 TYR 0.034 0.007 TYR C 264 PHE 0.059 0.010 PHE C 231 TRP 0.053 0.017 TRP B 169 HIS 0.026 0.004 HIS D 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00997 / 0.72 (15633) covalent geometry : angle 1.73553 / 1.17 (22173) hydrogen bonds : bond 0.20443 / 13.86 ( 898) hydrogen bonds : angle 7.04403 / 5.13 ( 2418) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 102 time to evaluate : 0.477 Fit side-chains REVERT: B 129 ARG cc_start: 0.8875 (ttm170) cc_final: 0.8648 (ttp80) REVERT: B 206 GLU cc_start: 0.9011 (mt-10) cc_final: 0.8770 (mp0) REVERT: D 18 ASP cc_start: 0.8673 (t0) cc_final: 0.8468 (t0) REVERT: D 129 ARG cc_start: 0.8885 (mtp-110) cc_final: 0.8491 (mtt-85) REVERT: D 206 GLU cc_start: 0.8956 (mt-10) cc_final: 0.8655 (mm-30) REVERT: D 250 ARG cc_start: 0.8829 (OUTLIER) cc_final: 0.8377 (ptt90) REVERT: D 287 ASN cc_start: 0.8905 (t0) cc_final: 0.8563 (t0) outliers start: 27 outliers final: 8 residues processed: 120 average time/residue: 0.8727 time to fit residues: 112.5027 Evaluate side-chains 88 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 79 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 MET Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain C residue 154 THR Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain D residue 250 ARG Chi-restraints excluded: chain D residue 273 LYS Chi-restraints excluded: chain D residue 274 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 40.0000 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 50.0000 chunk 91 optimal weight: 7.9990 chunk 55 optimal weight: 3.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 139 GLN B 93 GLN D 99 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.092539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2791 r_free = 0.2791 target = 0.060181 restraints weight = 35313.053| |-----------------------------------------------------------------------------| r_work (start): 0.2758 rms_B_bonded: 2.03 r_work: 0.2550 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work: 0.2399 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2399 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2408 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2408 r_free = 0.2408 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2408 r_free = 0.2408 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.2408 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9177 moved from start: 0.1637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 15633 Z= 0.191 Angle : 0.672 7.766 22173 Z= 0.389 Chirality : 0.046 0.305 2570 Planarity : 0.005 0.045 1985 Dihedral : 23.298 179.272 4611 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Rotamer: Outliers : 1.28 % Allowed : 9.86 % Favored : 88.86 % 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: 1.22 (0.23), residues: 1239 helix: 1.53 (0.17), residues: 793 sheet: -0.49 (0.36), residues: 176 loop : -0.23 (0.36), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 246 TYR 0.016 0.002 TYR B 215 PHE 0.011 0.002 PHE B 316 TRP 0.023 0.003 TRP B 46 HIS 0.008 0.001 HIS A 224 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.19 (15633) covalent geometry : angle 0.67188 / 0.39 (22173) hydrogen bonds : bond 0.06770 / 4.52 ( 898) hydrogen bonds : angle 4.09659 / 2.94 ( 2418) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 81 time to evaluate : 0.464 Fit side-chains REVERT: A 66 MET cc_start: 0.9193 (OUTLIER) cc_final: 0.7995 (pmt) REVERT: A 219 LYS cc_start: 0.8853 (OUTLIER) cc_final: 0.8510 (pptt) REVERT: A 261 ARG cc_start: 0.8904 (OUTLIER) cc_final: 0.8645 (ptt180) REVERT: D 129 ARG cc_start: 0.8924 (mtp-110) cc_final: 0.8519 (mtt-85) REVERT: D 206 GLU cc_start: 0.8182 (mt-10) cc_final: 0.7823 (mm-30) REVERT: D 250 ARG cc_start: 0.8899 (OUTLIER) cc_final: 0.8478 (ptt90) REVERT: D 273 LYS cc_start: 0.9269 (OUTLIER) cc_final: 0.9023 (ptpp) REVERT: D 287 ASN cc_start: 0.8874 (t0) cc_final: 0.8631 (t160) outliers start: 11 outliers final: 4 residues processed: 88 average time/residue: 0.8441 time to fit residues: 80.1541 Evaluate side-chains 80 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 71 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 MET Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 219 LYS Chi-restraints excluded: chain A residue 261 ARG Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain D residue 32 LYS Chi-restraints excluded: chain D residue 250 ARG Chi-restraints excluded: chain D residue 273 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 59 optimal weight: 0.9980 chunk 15 optimal weight: 0.8980 chunk 10 optimal weight: 9.9990 chunk 101 optimal weight: 0.7980 chunk 23 optimal weight: 20.0000 chunk 126 optimal weight: 20.0000 chunk 129 optimal weight: 20.0000 chunk 86 optimal weight: 6.9990 chunk 118 optimal weight: 9.9990 chunk 95 optimal weight: 10.0000 chunk 81 optimal weight: 4.9990 overall best weight: 2.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 139 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.092378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2779 r_free = 0.2779 target = 0.059338 restraints weight = 43282.624| |-----------------------------------------------------------------------------| r_work (start): 0.2743 rms_B_bonded: 2.25 r_work: 0.2535 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2535 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2546 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2546 r_free = 0.2546 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2546 r_free = 0.2546 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.2546 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9125 moved from start: 0.2138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 15633 Z= 0.165 Angle : 0.556 7.003 22173 Z= 0.328 Chirality : 0.040 0.223 2570 Planarity : 0.005 0.044 1985 Dihedral : 23.081 179.866 4608 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Rotamer: Outliers : 1.78 % Allowed : 8.97 % Favored : 89.25 % 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: 2.10 (0.24), residues: 1239 helix: 2.26 (0.18), residues: 796 sheet: -0.07 (0.37), residues: 164 loop : -0.16 (0.36), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 129 TYR 0.022 0.002 TYR D 74 PHE 0.013 0.002 PHE B 231 TRP 0.016 0.002 TRP B 46 HIS 0.005 0.001 HIS D 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.17 (15633) covalent geometry : angle 0.55625 / 0.33 (22173) hydrogen bonds : bond 0.05633 / 3.79 ( 898) hydrogen bonds : angle 3.78186 / 2.70 ( 2418) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 76 time to evaluate : 0.475 Fit side-chains REVERT: A 32 LYS cc_start: 0.9198 (mtmt) cc_final: 0.8992 (mtpm) REVERT: A 66 MET cc_start: 0.9015 (OUTLIER) cc_final: 0.7868 (pmt) REVERT: A 219 LYS cc_start: 0.8925 (OUTLIER) cc_final: 0.8661 (pptt) REVERT: D 129 ARG cc_start: 0.8685 (mtp-110) cc_final: 0.8362 (mtt-85) REVERT: D 153 GLU cc_start: 0.8779 (OUTLIER) cc_final: 0.8467 (tt0) REVERT: D 250 ARG cc_start: 0.8718 (OUTLIER) cc_final: 0.8264 (ptt90) REVERT: D 287 ASN cc_start: 0.8850 (t0) cc_final: 0.8640 (t160) outliers start: 16 outliers final: 5 residues processed: 87 average time/residue: 0.7123 time to fit residues: 67.5556 Evaluate side-chains 77 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 68 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 MET Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 219 LYS Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain D residue 32 LYS Chi-restraints excluded: chain D residue 153 GLU Chi-restraints excluded: chain D residue 250 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 101 optimal weight: 9.9990 chunk 95 optimal weight: 9.9990 chunk 56 optimal weight: 3.9990 chunk 118 optimal weight: 4.9990 chunk 93 optimal weight: 10.0000 chunk 79 optimal weight: 5.9990 chunk 37 optimal weight: 0.2980 chunk 13 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 chunk 126 optimal weight: 20.0000 chunk 46 optimal weight: 10.0000 overall best weight: 3.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 139 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.092164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2807 r_free = 0.2807 target = 0.060530 restraints weight = 28710.105| |-----------------------------------------------------------------------------| r_work (start): 0.2775 rms_B_bonded: 1.80 r_work: 0.2577 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2431 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2431 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2435 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2435 r_free = 0.2435 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2435 r_free = 0.2435 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2435 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9179 moved from start: 0.2327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 15633 Z= 0.163 Angle : 0.531 8.956 22173 Z= 0.313 Chirality : 0.039 0.191 2570 Planarity : 0.004 0.046 1985 Dihedral : 23.034 179.318 4603 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % Rotamer: Outliers : 1.78 % Allowed : 9.57 % Favored : 88.66 % 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: 2.41 (0.24), residues: 1239 helix: 2.52 (0.18), residues: 797 sheet: 0.08 (0.38), residues: 164 loop : -0.17 (0.36), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 250 TYR 0.017 0.002 TYR A 74 PHE 0.012 0.002 PHE B 112 TRP 0.013 0.002 TRP B 46 HIS 0.005 0.001 HIS D 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.16 (15633) covalent geometry : angle 0.53075 / 0.31 (22173) hydrogen bonds : bond 0.05134 / 3.43 ( 898) hydrogen bonds : angle 3.66517 / 2.62 ( 2418) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 71 time to evaluate : 0.462 Fit side-chains REVERT: A 219 LYS cc_start: 0.9003 (OUTLIER) cc_final: 0.8708 (pptt) REVERT: D 51 LYS cc_start: 0.9401 (mmmm) cc_final: 0.9200 (mmmm) REVERT: D 129 ARG cc_start: 0.8838 (mtp-110) cc_final: 0.8434 (mtt-85) REVERT: D 250 ARG cc_start: 0.8853 (ppt170) cc_final: 0.8439 (ptt90) outliers start: 16 outliers final: 6 residues processed: 81 average time/residue: 0.7443 time to fit residues: 65.5832 Evaluate side-chains 74 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 67 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain A residue 219 LYS Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain B residue 108 MET Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 251 MET Chi-restraints excluded: chain D residue 32 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 137 optimal weight: 40.0000 chunk 38 optimal weight: 2.9990 chunk 16 optimal weight: 7.9990 chunk 107 optimal weight: 1.9990 chunk 2 optimal weight: 9.9990 chunk 81 optimal weight: 4.9990 chunk 117 optimal weight: 6.9990 chunk 94 optimal weight: 20.0000 chunk 133 optimal weight: 50.0000 chunk 6 optimal weight: 9.9990 chunk 31 optimal weight: 8.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 139 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.090824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2775 r_free = 0.2775 target = 0.059052 restraints weight = 28715.062| |-----------------------------------------------------------------------------| r_work (start): 0.2744 rms_B_bonded: 1.79 r_work: 0.2541 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2391 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2391 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2397 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2397 r_free = 0.2397 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2397 r_free = 0.2397 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2397 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9208 moved from start: 0.2339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 15633 Z= 0.221 Angle : 0.552 7.165 22173 Z= 0.320 Chirality : 0.041 0.206 2570 Planarity : 0.004 0.047 1985 Dihedral : 23.008 179.547 4594 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % Rotamer: Outliers : 1.68 % Allowed : 9.66 % Favored : 88.66 % 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: 2.43 (0.24), residues: 1239 helix: 2.52 (0.18), residues: 797 sheet: 0.17 (0.39), residues: 164 loop : -0.20 (0.36), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 137 TYR 0.015 0.002 TYR C 307 PHE 0.014 0.002 PHE B 112 TRP 0.014 0.002 TRP B 46 HIS 0.006 0.001 HIS D 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00479 / 0.22 (15633) covalent geometry : angle 0.55158 / 0.32 (22173) hydrogen bonds : bond 0.05573 / 3.74 ( 898) hydrogen bonds : angle 3.70858 / 2.65 ( 2418) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 66 time to evaluate : 0.504 Fit side-chains REVERT: A 219 LYS cc_start: 0.9024 (OUTLIER) cc_final: 0.8712 (pptt) REVERT: D 51 LYS cc_start: 0.9414 (mmmm) cc_final: 0.9206 (mmmm) REVERT: D 129 ARG cc_start: 0.8870 (mtp-110) cc_final: 0.8453 (mtt-85) REVERT: D 250 ARG cc_start: 0.8889 (ppt170) cc_final: 0.8565 (ptt90) outliers start: 15 outliers final: 9 residues processed: 77 average time/residue: 0.7380 time to fit residues: 62.0884 Evaluate side-chains 74 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 64 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 219 LYS Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain B residue 108 MET Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 251 MET Chi-restraints excluded: chain D residue 32 LYS Chi-restraints excluded: chain D residue 256 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 33 optimal weight: 10.0000 chunk 44 optimal weight: 2.9990 chunk 99 optimal weight: 0.9990 chunk 121 optimal weight: 6.9990 chunk 46 optimal weight: 0.9990 chunk 69 optimal weight: 6.9990 chunk 65 optimal weight: 9.9990 chunk 109 optimal weight: 6.9990 chunk 58 optimal weight: 10.0000 chunk 114 optimal weight: 5.9990 chunk 10 optimal weight: 4.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 139 GLN D 287 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.091874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2802 r_free = 0.2802 target = 0.060165 restraints weight = 28695.503| |-----------------------------------------------------------------------------| r_work (start): 0.2771 rms_B_bonded: 1.80 r_work: 0.2574 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2434 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2434 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2440 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2440 r_free = 0.2440 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2440 r_free = 0.2440 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2440 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9182 moved from start: 0.2493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 15633 Z= 0.159 Angle : 0.509 7.062 22173 Z= 0.301 Chirality : 0.038 0.196 2570 Planarity : 0.004 0.047 1985 Dihedral : 22.928 179.367 4594 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % Rotamer: Outliers : 1.48 % Allowed : 9.86 % Favored : 88.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.56 (0.24), residues: 1239 helix: 2.63 (0.18), residues: 797 sheet: 0.27 (0.39), residues: 164 loop : -0.18 (0.37), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 250 TYR 0.013 0.001 TYR C 215 PHE 0.012 0.002 PHE B 112 TRP 0.013 0.002 TRP B 46 HIS 0.006 0.001 HIS A 224 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.16 (15633) covalent geometry : angle 0.50880 / 0.30 (22173) hydrogen bonds : bond 0.04966 / 3.32 ( 898) hydrogen bonds : angle 3.61709 / 2.59 ( 2418) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 70 time to evaluate : 0.466 Fit side-chains REVERT: A 219 LYS cc_start: 0.9025 (OUTLIER) cc_final: 0.8729 (pptt) REVERT: C 153 GLU cc_start: 0.8948 (OUTLIER) cc_final: 0.8304 (tm-30) REVERT: D 51 LYS cc_start: 0.9409 (mmmm) cc_final: 0.9207 (mmmm) REVERT: D 129 ARG cc_start: 0.8841 (mtp-110) cc_final: 0.8435 (mtt-85) REVERT: D 250 ARG cc_start: 0.8845 (ppt170) cc_final: 0.8457 (ptt90) outliers start: 13 outliers final: 8 residues processed: 79 average time/residue: 0.7255 time to fit residues: 62.6255 Evaluate side-chains 76 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 66 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 219 LYS Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain C residue 153 GLU Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 251 MET Chi-restraints excluded: chain D residue 32 LYS Chi-restraints excluded: chain D residue 256 HIS Chi-restraints excluded: chain D residue 287 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 95 optimal weight: 10.0000 chunk 20 optimal weight: 10.0000 chunk 122 optimal weight: 50.0000 chunk 126 optimal weight: 20.0000 chunk 89 optimal weight: 10.0000 chunk 100 optimal weight: 8.9990 chunk 120 optimal weight: 1.9990 chunk 11 optimal weight: 4.9990 chunk 37 optimal weight: 10.0000 chunk 51 optimal weight: 10.0000 chunk 114 optimal weight: 5.9990 overall best weight: 6.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 139 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.090009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2761 r_free = 0.2761 target = 0.058292 restraints weight = 28531.660| |-----------------------------------------------------------------------------| r_work (start): 0.2731 rms_B_bonded: 1.78 r_work: 0.2527 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2385 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2385 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2389 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2389 r_free = 0.2389 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2389 r_free = 0.2389 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2389 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9217 moved from start: 0.2423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.097 15633 Z= 0.267 Angle : 0.568 7.116 22173 Z= 0.325 Chirality : 0.043 0.208 2570 Planarity : 0.005 0.047 1985 Dihedral : 22.936 179.420 4594 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % Rotamer: Outliers : 1.68 % Allowed : 10.36 % Favored : 87.97 % 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: 2.45 (0.24), residues: 1239 helix: 2.54 (0.18), residues: 797 sheet: 0.22 (0.39), residues: 164 loop : -0.21 (0.37), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 260 TYR 0.015 0.002 TYR C 307 PHE 0.015 0.002 PHE B 112 TRP 0.015 0.002 TRP B 46 HIS 0.007 0.001 HIS D 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00588 / 0.27 (15633) covalent geometry : angle 0.56845 / 0.33 (22173) hydrogen bonds : bond 0.05818 / 3.90 ( 898) hydrogen bonds : angle 3.70230 / 2.65 ( 2418) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 65 time to evaluate : 0.463 Fit side-chains REVERT: A 219 LYS cc_start: 0.9062 (OUTLIER) cc_final: 0.8737 (pptt) REVERT: C 153 GLU cc_start: 0.8970 (OUTLIER) cc_final: 0.8334 (tm-30) REVERT: D 51 LYS cc_start: 0.9410 (mmmm) cc_final: 0.9209 (mmmm) REVERT: D 129 ARG cc_start: 0.8898 (mtp-110) cc_final: 0.8469 (mtt-85) REVERT: D 250 ARG cc_start: 0.8882 (OUTLIER) cc_final: 0.8606 (ptt90) outliers start: 15 outliers final: 9 residues processed: 75 average time/residue: 0.7622 time to fit residues: 62.2736 Evaluate side-chains 76 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 64 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 219 LYS Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain B residue 108 MET Chi-restraints excluded: chain C residue 153 GLU Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 251 MET Chi-restraints excluded: chain D residue 32 LYS Chi-restraints excluded: chain D residue 250 ARG Chi-restraints excluded: chain D residue 256 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 60 optimal weight: 8.9990 chunk 45 optimal weight: 5.9990 chunk 50 optimal weight: 0.6980 chunk 20 optimal weight: 5.9990 chunk 37 optimal weight: 0.6980 chunk 7 optimal weight: 5.9990 chunk 53 optimal weight: 9.9990 chunk 85 optimal weight: 5.9990 chunk 77 optimal weight: 4.9990 chunk 24 optimal weight: 8.9990 chunk 5 optimal weight: 0.9980 overall best weight: 2.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 139 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.091647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2794 r_free = 0.2794 target = 0.059710 restraints weight = 31374.316| |-----------------------------------------------------------------------------| r_work (start): 0.2761 rms_B_bonded: 1.88 r_work: 0.2558 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2411 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2411 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2418 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2418 r_free = 0.2418 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2418 r_free = 0.2418 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2418 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9197 moved from start: 0.2587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 15633 Z= 0.159 Angle : 0.506 7.022 22173 Z= 0.298 Chirality : 0.038 0.195 2570 Planarity : 0.004 0.047 1985 Dihedral : 22.869 179.350 4594 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % Rotamer: Outliers : 1.68 % Allowed : 10.45 % Favored : 87.87 % 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: 1239 helix: 2.66 (0.18), residues: 798 sheet: 0.31 (0.40), residues: 164 loop : -0.13 (0.37), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 151 TYR 0.014 0.001 TYR D 74 PHE 0.011 0.002 PHE B 112 TRP 0.014 0.002 TRP B 46 HIS 0.005 0.001 HIS A 224 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.16 (15633) covalent geometry : angle 0.50617 / 0.30 (22173) hydrogen bonds : bond 0.04959 / 3.32 ( 898) hydrogen bonds : angle 3.60839 / 2.59 ( 2418) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 68 time to evaluate : 0.478 Fit side-chains REVERT: A 219 LYS cc_start: 0.9077 (OUTLIER) cc_final: 0.8777 (pptt) REVERT: C 153 GLU cc_start: 0.8973 (OUTLIER) cc_final: 0.8335 (tm-30) REVERT: D 129 ARG cc_start: 0.8862 (mtp-110) cc_final: 0.8444 (mtt-85) REVERT: D 250 ARG cc_start: 0.8879 (OUTLIER) cc_final: 0.8388 (ptt90) outliers start: 15 outliers final: 10 residues processed: 77 average time/residue: 0.7599 time to fit residues: 63.6149 Evaluate side-chains 78 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 65 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 219 LYS Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain B residue 108 MET Chi-restraints excluded: chain C residue 153 GLU Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 251 MET Chi-restraints excluded: chain C residue 268 MET Chi-restraints excluded: chain D residue 32 LYS Chi-restraints excluded: chain D residue 250 ARG Chi-restraints excluded: chain D residue 256 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 40 optimal weight: 9.9990 chunk 15 optimal weight: 0.8980 chunk 104 optimal weight: 10.0000 chunk 23 optimal weight: 5.9990 chunk 33 optimal weight: 10.0000 chunk 58 optimal weight: 10.0000 chunk 47 optimal weight: 4.9990 chunk 120 optimal weight: 4.9990 chunk 117 optimal weight: 8.9990 chunk 116 optimal weight: 4.9990 chunk 77 optimal weight: 7.9990 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 139 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.090802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2775 r_free = 0.2775 target = 0.058918 restraints weight = 28632.352| |-----------------------------------------------------------------------------| r_work (start): 0.2746 rms_B_bonded: 1.78 r_work: 0.2545 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2399 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2399 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2407 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2407 r_free = 0.2407 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2406 r_free = 0.2406 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2406 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9197 moved from start: 0.2580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 15633 Z= 0.202 Angle : 0.532 8.471 22173 Z= 0.307 Chirality : 0.040 0.201 2570 Planarity : 0.004 0.049 1985 Dihedral : 22.851 179.391 4594 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % Rotamer: Outliers : 1.58 % Allowed : 10.95 % Favored : 87.48 % 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: 1239 helix: 2.66 (0.18), residues: 799 sheet: 0.31 (0.40), residues: 164 loop : -0.13 (0.37), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 261 TYR 0.017 0.002 TYR D 74 PHE 0.013 0.002 PHE B 112 TRP 0.013 0.002 TRP B 46 HIS 0.005 0.001 HIS D 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00437 / 0.20 (15633) covalent geometry : angle 0.53226 / 0.31 (22173) hydrogen bonds : bond 0.05304 / 3.55 ( 898) hydrogen bonds : angle 3.61358 / 2.59 ( 2418) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 64 time to evaluate : 0.470 Fit side-chains REVERT: A 219 LYS cc_start: 0.9079 (OUTLIER) cc_final: 0.8764 (pptt) REVERT: C 153 GLU cc_start: 0.8974 (OUTLIER) cc_final: 0.8335 (tm-30) REVERT: C 238 ARG cc_start: 0.8465 (tmt170) cc_final: 0.8247 (tmm160) REVERT: D 129 ARG cc_start: 0.8851 (mtp-110) cc_final: 0.8435 (mtt-85) REVERT: D 250 ARG cc_start: 0.8833 (OUTLIER) cc_final: 0.8453 (ptt90) outliers start: 14 outliers final: 9 residues processed: 73 average time/residue: 0.7623 time to fit residues: 60.4749 Evaluate side-chains 73 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 61 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 219 LYS Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain B residue 108 MET Chi-restraints excluded: chain C residue 153 GLU Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 251 MET Chi-restraints excluded: chain D residue 32 LYS Chi-restraints excluded: chain D residue 250 ARG Chi-restraints excluded: chain D residue 256 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 52 optimal weight: 4.9990 chunk 72 optimal weight: 1.9990 chunk 32 optimal weight: 8.9990 chunk 99 optimal weight: 0.8980 chunk 67 optimal weight: 6.9990 chunk 87 optimal weight: 7.9990 chunk 98 optimal weight: 7.9990 chunk 48 optimal weight: 6.9990 chunk 39 optimal weight: 0.0980 chunk 51 optimal weight: 4.9990 chunk 138 optimal weight: 20.0000 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 139 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.092215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2813 r_free = 0.2813 target = 0.060484 restraints weight = 30479.290| |-----------------------------------------------------------------------------| r_work (start): 0.2778 rms_B_bonded: 1.85 r_work: 0.2577 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2431 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2431 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2436 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2436 r_free = 0.2436 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2436 r_free = 0.2436 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2436 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9188 moved from start: 0.2710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 15633 Z= 0.145 Angle : 0.496 8.117 22173 Z= 0.291 Chirality : 0.037 0.198 2570 Planarity : 0.004 0.048 1985 Dihedral : 22.809 179.361 4594 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Rotamer: Outliers : 1.28 % Allowed : 11.44 % Favored : 87.28 % 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: 2.74 (0.24), residues: 1239 helix: 2.75 (0.18), residues: 799 sheet: 0.35 (0.40), residues: 164 loop : -0.10 (0.37), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 261 TYR 0.016 0.001 TYR D 74 PHE 0.011 0.001 PHE B 112 TRP 0.013 0.002 TRP B 46 HIS 0.005 0.001 HIS A 224 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.15 (15633) covalent geometry : angle 0.49642 / 0.29 (22173) hydrogen bonds : bond 0.04735 / 3.16 ( 898) hydrogen bonds : angle 3.54198 / 2.54 ( 2418) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 67 time to evaluate : 0.459 Fit side-chains REVERT: A 219 LYS cc_start: 0.9090 (OUTLIER) cc_final: 0.8774 (pptt) REVERT: C 153 GLU cc_start: 0.8979 (OUTLIER) cc_final: 0.8342 (tm-30) REVERT: C 238 ARG cc_start: 0.8494 (tmt170) cc_final: 0.8268 (tmm160) REVERT: D 129 ARG cc_start: 0.8824 (mtp-110) cc_final: 0.8414 (mtt-85) REVERT: D 250 ARG cc_start: 0.8841 (OUTLIER) cc_final: 0.8484 (ptt90) outliers start: 11 outliers final: 8 residues processed: 74 average time/residue: 0.6948 time to fit residues: 56.2796 Evaluate side-chains 76 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 65 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 219 LYS Chi-restraints excluded: chain B residue 108 MET Chi-restraints excluded: chain C residue 153 GLU Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 251 MET Chi-restraints excluded: chain D residue 32 LYS Chi-restraints excluded: chain D residue 250 ARG Chi-restraints excluded: chain D residue 256 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 121 optimal weight: 8.9990 chunk 133 optimal weight: 50.0000 chunk 32 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 chunk 55 optimal weight: 9.9990 chunk 34 optimal weight: 1.9990 chunk 109 optimal weight: 3.9990 chunk 61 optimal weight: 9.9990 chunk 5 optimal weight: 3.9990 chunk 135 optimal weight: 40.0000 chunk 112 optimal weight: 8.9990 overall best weight: 3.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 139 GLN ** C 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 99 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.091312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2786 r_free = 0.2786 target = 0.059243 restraints weight = 31421.404| |-----------------------------------------------------------------------------| r_work (start): 0.2755 rms_B_bonded: 1.88 r_work: 0.2551 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2404 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2404 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2408 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2408 r_free = 0.2408 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2408 r_free = 0.2408 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2408 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9206 moved from start: 0.2697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 15633 Z= 0.186 Angle : 0.516 7.963 22173 Z= 0.298 Chirality : 0.039 0.192 2570 Planarity : 0.004 0.049 1985 Dihedral : 22.788 179.250 4594 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % Rotamer: Outliers : 1.38 % Allowed : 11.54 % Favored : 87.08 % 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: 2.70 (0.24), residues: 1239 helix: 2.73 (0.18), residues: 799 sheet: 0.33 (0.40), residues: 164 loop : -0.11 (0.37), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 250 TYR 0.016 0.002 TYR D 74 PHE 0.013 0.002 PHE B 112 TRP 0.013 0.002 TRP B 46 HIS 0.005 0.001 HIS D 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.19 (15633) covalent geometry : angle 0.51605 / 0.30 (22173) hydrogen bonds : bond 0.05069 / 3.39 ( 898) hydrogen bonds : angle 3.55765 / 2.55 ( 2418) =============================================================================== Job complete usr+sys time: 5823.06 seconds wall clock time: 99 minutes 48.65 seconds (5988.65 seconds total)