Starting phenix.real_space_refine on Mon Aug 25 20:40:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8b4h_15848/08_2025/8b4h_15848.cif Found real_map, /net/cci-nas-00/data/ceres_data/8b4h_15848/08_2025/8b4h_15848.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8b4h_15848/08_2025/8b4h_15848.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8b4h_15848/08_2025/8b4h_15848.map" model { file = "/net/cci-nas-00/data/ceres_data/8b4h_15848/08_2025/8b4h_15848.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8b4h_15848/08_2025/8b4h_15848.cif" } resolution = 3.35 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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: 7 Type Number sf(0) Gaussians P 224 5.49 5 Mg 2 5.21 5 S 54 5.16 5 C 9898 2.51 5 N 2892 2.21 5 O 3498 1.98 5 H 14570 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 31138 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 5967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 358, 5967 Classifications: {'peptide': 358} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 14, 'TRANS': 343} Chain: "B" Number of atoms: 5967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 358, 5967 Classifications: {'peptide': 358} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 14, 'TRANS': 343} Chain: "C" Number of atoms: 6043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 6043 Classifications: {'peptide': 362} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 13, 'TRANS': 348} Chain breaks: 1 Chain: "D" Number of atoms: 6043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 6043 Classifications: {'peptide': 362} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 13, 'TRANS': 348} Chain breaks: 1 Chain: "E" Number of atoms: 1803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 1803 Classifications: {'DNA': 57} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 56} Chain: "F" Number of atoms: 1755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 1755 Classifications: {'DNA': 55} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 54} Chain: "G" Number of atoms: 1803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 1803 Classifications: {'DNA': 57} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 56} Chain: "H" Number of atoms: 1755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 1755 Classifications: {'DNA': 55} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 54} 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: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.02, per 1000 atoms: 0.19 Number of scatterers: 31138 At special positions: 0 Unit cell: (94.34, 102.82, 218.36, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 54 16.00 P 224 15.00 Mg 2 11.99 O 3498 8.00 N 2892 7.00 C 9898 6.00 H 14570 1.00 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: 2.83 Conformation dependent library (CDL) restraints added in 854.7 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2692 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 16 sheets defined 42.5% alpha, 14.3% beta 50 base pairs and 216 stacking pairs defined. Time for finding SS restraints: 5.69 Creating SS restraints... Processing helix chain 'A' and resid 3 through 17 Processing helix chain 'A' and resid 19 through 28 Processing helix chain 'A' and resid 30 through 39 removed outlier: 3.795A pdb=" N HIS A 39 " --> pdb=" O ARG A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 58 No H-bonds generated for 'chain 'A' and resid 56 through 58' Processing helix chain 'A' and resid 59 through 69 Processing helix chain 'A' and resid 74 through 84 removed outlier: 3.610A pdb=" N GLN A 84 " --> pdb=" O PHE A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 104 Proline residue: A 100 - end of helix Processing helix chain 'A' and resid 162 through 178 Processing helix chain 'A' and resid 204 through 215 Processing helix chain 'A' and resid 225 through 228 removed outlier: 3.699A pdb=" N THR A 228 " --> pdb=" O ARG A 225 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 225 through 228' Processing helix chain 'A' and resid 229 through 243 Processing helix chain 'A' and resid 251 through 266 Processing helix chain 'A' and resid 278 through 282 Processing helix chain 'A' and resid 322 through 326 Processing helix chain 'B' and resid 3 through 17 Processing helix chain 'B' and resid 19 through 28 Processing helix chain 'B' and resid 30 through 39 removed outlier: 3.795A pdb=" N HIS B 39 " --> pdb=" O ARG B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 58 No H-bonds generated for 'chain 'B' and resid 56 through 58' Processing helix chain 'B' and resid 59 through 69 Processing helix chain 'B' and resid 74 through 84 removed outlier: 3.610A pdb=" N GLN B 84 " --> pdb=" O PHE B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 104 Proline residue: B 100 - end of helix Processing helix chain 'B' and resid 162 through 178 Processing helix chain 'B' and resid 204 through 215 Processing helix chain 'B' and resid 225 through 228 removed outlier: 3.699A pdb=" N THR B 228 " --> pdb=" O ARG B 225 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 225 through 228' Processing helix chain 'B' and resid 229 through 243 Processing helix chain 'B' and resid 251 through 266 Processing helix chain 'B' and resid 278 through 282 Processing helix chain 'B' and resid 322 through 326 Processing helix chain 'C' and resid 3 through 17 Processing helix chain 'C' and resid 19 through 28 Processing helix chain 'C' and resid 30 through 39 removed outlier: 3.695A pdb=" N HIS C 39 " --> pdb=" O ARG C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 58 No H-bonds generated for 'chain 'C' and resid 56 through 58' Processing helix chain 'C' and resid 59 through 69 Processing helix chain 'C' and resid 76 through 85 Processing helix chain 'C' and resid 91 through 108 Proline residue: C 100 - end of helix removed outlier: 3.549A pdb=" N LYS C 108 " --> pdb=" O THR C 104 " (cutoff:3.500A) Processing helix chain 'C' and resid 162 through 178 Processing helix chain 'C' and resid 204 through 214 Processing helix chain 'C' and resid 235 through 243 Processing helix chain 'C' and resid 251 through 267 removed outlier: 3.565A pdb=" N ALA C 267 " --> pdb=" O LEU C 263 " (cutoff:3.500A) Processing helix chain 'C' and resid 278 through 285 removed outlier: 3.736A pdb=" N ARG C 282 " --> pdb=" O SER C 278 " (cutoff:3.500A) Processing helix chain 'C' and resid 322 through 326 Processing helix chain 'C' and resid 360 through 373 removed outlier: 3.507A pdb=" N LYS C 364 " --> pdb=" O SER C 360 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA C 373 " --> pdb=" O GLN C 369 " (cutoff:3.500A) Processing helix chain 'D' and resid 3 through 17 Processing helix chain 'D' and resid 19 through 28 Processing helix chain 'D' and resid 30 through 39 removed outlier: 3.695A pdb=" N HIS D 39 " --> pdb=" O ARG D 35 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 58 No H-bonds generated for 'chain 'D' and resid 56 through 58' Processing helix chain 'D' and resid 59 through 69 Processing helix chain 'D' and resid 76 through 85 Processing helix chain 'D' and resid 91 through 108 Proline residue: D 100 - end of helix removed outlier: 3.549A pdb=" N LYS D 108 " --> pdb=" O THR D 104 " (cutoff:3.500A) Processing helix chain 'D' and resid 162 through 178 Processing helix chain 'D' and resid 204 through 214 Processing helix chain 'D' and resid 235 through 243 Processing helix chain 'D' and resid 251 through 267 removed outlier: 3.565A pdb=" N ALA D 267 " --> pdb=" O LEU D 263 " (cutoff:3.500A) Processing helix chain 'D' and resid 278 through 285 removed outlier: 3.736A pdb=" N ARG D 282 " --> pdb=" O SER D 278 " (cutoff:3.500A) Processing helix chain 'D' and resid 322 through 326 Processing helix chain 'D' and resid 360 through 373 removed outlier: 3.507A pdb=" N LYS D 364 " --> pdb=" O SER D 360 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA D 373 " --> pdb=" O GLN D 369 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 153 through 158 removed outlier: 5.789A pdb=" N LYS A 136 " --> pdb=" O VAL A 132 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N VAL A 132 " --> pdb=" O LYS A 136 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N VAL A 138 " --> pdb=" O GLU A 130 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N GLU A 130 " --> pdb=" O VAL A 138 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N LEU A 140 " --> pdb=" O VAL A 128 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 303 through 305 removed outlier: 4.693A pdb=" N LEU A 342 " --> pdb=" O ILE A 349 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 311 through 314 removed outlier: 3.550A pdb=" N GLN A 318 " --> pdb=" O GLN A 355 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 153 through 158 removed outlier: 5.789A pdb=" N LYS B 136 " --> pdb=" O VAL B 132 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N VAL B 132 " --> pdb=" O LYS B 136 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N VAL B 138 " --> pdb=" O GLU B 130 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N GLU B 130 " --> pdb=" O VAL B 138 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N LEU B 140 " --> pdb=" O VAL B 128 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 303 through 305 removed outlier: 4.693A pdb=" N LEU B 342 " --> pdb=" O ILE B 349 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 311 through 314 removed outlier: 3.550A pdb=" N GLN B 318 " --> pdb=" O GLN B 355 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 153 through 158 Processing sheet with id=AA8, first strand: chain 'C' and resid 131 through 133 Processing sheet with id=AA9, first strand: chain 'C' and resid 193 through 196 removed outlier: 5.470A pdb=" N LYS C 202 " --> pdb=" O ASP C 194 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 303 through 305 Processing sheet with id=AB2, first strand: chain 'C' and resid 311 through 314 Processing sheet with id=AB3, first strand: chain 'D' and resid 153 through 158 Processing sheet with id=AB4, first strand: chain 'D' and resid 131 through 133 Processing sheet with id=AB5, first strand: chain 'D' and resid 193 through 196 removed outlier: 5.469A pdb=" N LYS D 202 " --> pdb=" O ASP D 194 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 303 through 305 Processing sheet with id=AB7, first strand: chain 'D' and resid 311 through 314 506 hydrogen bonds defined for protein. 1428 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 124 hydrogen bonds 248 hydrogen bond angles 0 basepair planarities 50 basepair parallelities 216 stacking parallelities Total time for adding SS restraints: 7.57 Time building geometry restraints manager: 3.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 14562 1.03 - 1.23: 82 1.23 - 1.42: 7616 1.42 - 1.62: 9616 1.62 - 1.81: 100 Bond restraints: 31976 Sorted by residual: bond pdb=" N PRO C 43 " pdb=" CA PRO C 43 " ideal model delta sigma weight residual 1.457 1.478 -0.021 1.31e-02 5.83e+03 2.50e+00 bond pdb=" N PRO D 43 " pdb=" CA PRO D 43 " ideal model delta sigma weight residual 1.457 1.477 -0.020 1.31e-02 5.83e+03 2.38e+00 bond pdb=" C3' DC F 49 " pdb=" O3' DC F 49 " ideal model delta sigma weight residual 1.422 1.386 0.036 3.00e-02 1.11e+03 1.47e+00 bond pdb=" C3' DC H 49 " pdb=" O3' DC H 49 " ideal model delta sigma weight residual 1.422 1.386 0.036 3.00e-02 1.11e+03 1.47e+00 bond pdb=" C3' DT H 50 " pdb=" O3' DT H 50 " ideal model delta sigma weight residual 1.422 1.389 0.033 3.00e-02 1.11e+03 1.20e+00 ... (remaining 31971 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.31: 53452 1.31 - 2.62: 3925 2.62 - 3.93: 445 3.93 - 5.24: 26 5.24 - 6.55: 10 Bond angle restraints: 57858 Sorted by residual: angle pdb=" CA LYS C 32 " pdb=" CB LYS C 32 " pdb=" CG LYS C 32 " ideal model delta sigma weight residual 114.10 108.47 5.63 2.00e+00 2.50e-01 7.93e+00 angle pdb=" CA LYS D 32 " pdb=" CB LYS D 32 " pdb=" CG LYS D 32 " ideal model delta sigma weight residual 114.10 108.52 5.58 2.00e+00 2.50e-01 7.77e+00 angle pdb=" O3' DT F 27 " pdb=" P DT F 28 " pdb=" O5' DT F 28 " ideal model delta sigma weight residual 104.00 99.94 4.06 1.50e+00 4.44e-01 7.34e+00 angle pdb=" O3' DT H 27 " pdb=" P DT H 28 " pdb=" O5' DT H 28 " ideal model delta sigma weight residual 104.00 99.94 4.06 1.50e+00 4.44e-01 7.34e+00 angle pdb=" C2' DG F 8 " pdb=" C1' DG F 8 " pdb=" N9 DG F 8 " ideal model delta sigma weight residual 113.50 117.56 -4.06 1.50e+00 4.44e-01 7.34e+00 ... (remaining 57853 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.02: 11111 16.02 - 32.04: 1399 32.04 - 48.07: 1065 48.07 - 64.09: 589 64.09 - 80.11: 8 Dihedral angle restraints: 14172 sinusoidal: 9010 harmonic: 5162 Sorted by residual: dihedral pdb=" CA LYS C 32 " pdb=" C LYS C 32 " pdb=" N THR C 33 " pdb=" CA THR C 33 " ideal model delta harmonic sigma weight residual 180.00 161.94 18.06 0 5.00e+00 4.00e-02 1.30e+01 dihedral pdb=" CA LYS D 32 " pdb=" C LYS D 32 " pdb=" N THR D 33 " pdb=" CA THR D 33 " ideal model delta harmonic sigma weight residual 180.00 161.99 18.01 0 5.00e+00 4.00e-02 1.30e+01 dihedral pdb=" CB GLU B 253 " pdb=" CG GLU B 253 " pdb=" CD GLU B 253 " pdb=" OE1 GLU B 253 " ideal model delta sinusoidal sigma weight residual 0.00 -80.11 80.11 1 3.00e+01 1.11e-03 8.83e+00 ... (remaining 14169 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1626 0.029 - 0.059: 678 0.059 - 0.088: 150 0.088 - 0.118: 100 0.118 - 0.147: 26 Chirality restraints: 2580 Sorted by residual: chirality pdb=" C1' DC H 5 " pdb=" O4' DC H 5 " pdb=" C2' DC H 5 " pdb=" N1 DC H 5 " both_signs ideal model delta sigma weight residual False 2.47 2.32 0.15 2.00e-01 2.50e+01 5.43e-01 chirality pdb=" C1' DC F 5 " pdb=" O4' DC F 5 " pdb=" C2' DC F 5 " pdb=" N1 DC F 5 " both_signs ideal model delta sigma weight residual False 2.47 2.32 0.15 2.00e-01 2.50e+01 5.43e-01 chirality pdb=" C1' DG H 8 " pdb=" O4' DG H 8 " pdb=" C2' DG H 8 " pdb=" N9 DG H 8 " both_signs ideal model delta sigma weight residual False 2.42 2.28 0.14 2.00e-01 2.50e+01 5.10e-01 ... (remaining 2577 not shown) Planarity restraints: 3846 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DC E 52 " -0.034 2.00e-02 2.50e+03 2.94e-02 2.37e+01 pdb=" N1 DC E 52 " 0.079 2.00e-02 2.50e+03 pdb=" C2 DC E 52 " -0.044 2.00e-02 2.50e+03 pdb=" O2 DC E 52 " 0.010 2.00e-02 2.50e+03 pdb=" N3 DC E 52 " 0.006 2.00e-02 2.50e+03 pdb=" C4 DC E 52 " -0.001 2.00e-02 2.50e+03 pdb=" N4 DC E 52 " -0.001 2.00e-02 2.50e+03 pdb=" C5 DC E 52 " -0.004 2.00e-02 2.50e+03 pdb=" C6 DC E 52 " -0.001 2.00e-02 2.50e+03 pdb=" H5 DC E 52 " -0.006 2.00e-02 2.50e+03 pdb=" H6 DC E 52 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC G 52 " 0.034 2.00e-02 2.50e+03 2.94e-02 2.37e+01 pdb=" N1 DC G 52 " -0.079 2.00e-02 2.50e+03 pdb=" C2 DC G 52 " 0.044 2.00e-02 2.50e+03 pdb=" O2 DC G 52 " -0.010 2.00e-02 2.50e+03 pdb=" N3 DC G 52 " -0.006 2.00e-02 2.50e+03 pdb=" C4 DC G 52 " 0.001 2.00e-02 2.50e+03 pdb=" N4 DC G 52 " 0.001 2.00e-02 2.50e+03 pdb=" C5 DC G 52 " 0.004 2.00e-02 2.50e+03 pdb=" C6 DC G 52 " 0.001 2.00e-02 2.50e+03 pdb=" H5 DC G 52 " 0.006 2.00e-02 2.50e+03 pdb=" H6 DC G 52 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC E 53 " -0.029 2.00e-02 2.50e+03 2.15e-02 1.27e+01 pdb=" N1 DC E 53 " 0.057 2.00e-02 2.50e+03 pdb=" C2 DC E 53 " -0.028 2.00e-02 2.50e+03 pdb=" O2 DC E 53 " 0.008 2.00e-02 2.50e+03 pdb=" N3 DC E 53 " 0.002 2.00e-02 2.50e+03 pdb=" C4 DC E 53 " -0.002 2.00e-02 2.50e+03 pdb=" N4 DC E 53 " -0.003 2.00e-02 2.50e+03 pdb=" C5 DC E 53 " 0.002 2.00e-02 2.50e+03 pdb=" C6 DC E 53 " 0.004 2.00e-02 2.50e+03 pdb=" H5 DC E 53 " -0.007 2.00e-02 2.50e+03 pdb=" H6 DC E 53 " -0.004 2.00e-02 2.50e+03 ... (remaining 3843 not shown) Histogram of nonbonded interaction distances: 1.50 - 2.12: 764 2.12 - 2.74: 53137 2.74 - 3.36: 83110 3.36 - 3.98: 111902 3.98 - 4.60: 173717 Nonbonded interactions: 422630 Sorted by model distance: nonbonded pdb=" H GLY B 90 " pdb=" OP2 DC F 45 " model vdw 1.502 2.450 nonbonded pdb=" H GLY A 90 " pdb=" OP2 DC H 45 " model vdw 1.502 2.450 nonbonded pdb="HH22 ARG C 52 " pdb=" O2 DT E 44 " model vdw 1.514 2.450 nonbonded pdb="HH22 ARG D 52 " pdb=" O2 DT G 44 " model vdw 1.515 2.450 nonbonded pdb=" HZ2 LYS D 32 " pdb=" O6 DG H 8 " model vdw 1.553 2.450 ... (remaining 422625 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'G' } ncs_group { reference = chain 'F' selection = chain 'H' } 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=1.00 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: 1.510 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: 0.160 Extract box with map and model: 0.390 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 34.920 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.060 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:1.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6376 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 : 0.004 0.036 17406 Z= 0.177 Angle : 0.709 6.553 24374 Z= 0.433 Chirality : 0.038 0.147 2580 Planarity : 0.006 0.093 2308 Dihedral : 22.551 80.111 7224 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % 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 aren not related in a simple way. whole: -0.27 (0.23), residues: 1428 helix: 1.34 (0.22), residues: 550 sheet: -1.97 (0.32), residues: 194 loop : -0.85 (0.24), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 4 TYR 0.013 0.001 TYR B 214 PHE 0.024 0.001 PHE B 257 TRP 0.007 0.001 TRP B 262 HIS 0.009 0.001 HIS A 242 Details of bonding type rmsd covalent geometry : bond 0.00408 (17406) covalent geometry : angle 0.70933 (24374) hydrogen bonds : bond 0.11138 ( 630) hydrogen bonds : angle 5.22142 ( 1676) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 167 time to evaluate : 0.829 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 291 LEU cc_start: 0.8239 (tt) cc_final: 0.7965 (tp) REVERT: D 291 LEU cc_start: 0.8241 (tt) cc_final: 0.7966 (tp) outliers start: 0 outliers final: 0 residues processed: 167 average time/residue: 0.3007 time to fit residues: 75.3769 Evaluate side-chains 146 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 146 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 20.0000 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 0.9980 chunk 149 optimal weight: 4.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 GLN C 265 GLN D 265 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4503 r_free = 0.4503 target = 0.216482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.174118 restraints weight = 57805.454| |-----------------------------------------------------------------------------| r_work (start): 0.4058 rms_B_bonded: 2.45 r_work: 0.3820 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3693 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7079 moved from start: 0.1470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 17406 Z= 0.237 Angle : 0.664 7.594 24374 Z= 0.390 Chirality : 0.045 0.174 2580 Planarity : 0.005 0.063 2308 Dihedral : 26.869 70.386 4094 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 0.62 % Allowed : 3.02 % Favored : 96.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.56 (0.22), residues: 1428 helix: 0.81 (0.21), residues: 554 sheet: -2.06 (0.32), residues: 194 loop : -0.76 (0.25), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 102 TYR 0.008 0.001 TYR C 87 PHE 0.017 0.002 PHE A 216 TRP 0.012 0.002 TRP B 125 HIS 0.004 0.001 HIS D 307 Details of bonding type rmsd covalent geometry : bond 0.00532 (17406) covalent geometry : angle 0.66429 (24374) hydrogen bonds : bond 0.05055 ( 630) hydrogen bonds : angle 4.57667 ( 1676) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 145 time to evaluate : 0.757 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 GLU cc_start: 0.7220 (OUTLIER) cc_final: 0.6989 (tm-30) REVERT: B 69 GLU cc_start: 0.7205 (OUTLIER) cc_final: 0.6973 (tm-30) REVERT: D 264 ASP cc_start: 0.7886 (t0) cc_final: 0.7576 (t0) outliers start: 8 outliers final: 4 residues processed: 151 average time/residue: 0.2903 time to fit residues: 66.0817 Evaluate side-chains 138 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 132 time to evaluate : 0.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ASN Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 69 GLU Chi-restraints excluded: chain B residue 42 ASN Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 69 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 159 optimal weight: 4.9990 chunk 22 optimal weight: 0.7980 chunk 134 optimal weight: 2.9990 chunk 59 optimal weight: 0.9980 chunk 4 optimal weight: 7.9990 chunk 71 optimal weight: 20.0000 chunk 76 optimal weight: 0.9990 chunk 138 optimal weight: 0.6980 chunk 6 optimal weight: 0.5980 chunk 150 optimal weight: 3.9990 chunk 38 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 227 GLN B 227 GLN D 265 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4506 r_free = 0.4506 target = 0.217227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.175502 restraints weight = 57730.939| |-----------------------------------------------------------------------------| r_work (start): 0.4083 rms_B_bonded: 2.32 r_work: 0.3849 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3733 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7033 moved from start: 0.1748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 17406 Z= 0.162 Angle : 0.573 5.052 24374 Z= 0.339 Chirality : 0.041 0.138 2580 Planarity : 0.004 0.057 2308 Dihedral : 26.974 62.449 4094 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 0.62 % Allowed : 4.64 % Favored : 94.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.27 (0.22), residues: 1428 helix: 1.16 (0.22), residues: 554 sheet: -1.84 (0.33), residues: 194 loop : -0.73 (0.24), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 261 TYR 0.007 0.001 TYR B 214 PHE 0.011 0.001 PHE A 216 TRP 0.008 0.001 TRP B 125 HIS 0.003 0.001 HIS A 39 Details of bonding type rmsd covalent geometry : bond 0.00366 (17406) covalent geometry : angle 0.57292 (24374) hydrogen bonds : bond 0.03757 ( 630) hydrogen bonds : angle 4.20065 ( 1676) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 137 time to evaluate : 0.876 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 GLU cc_start: 0.7031 (OUTLIER) cc_final: 0.6624 (tm-30) REVERT: A 114 GLU cc_start: 0.6845 (pp20) cc_final: 0.6590 (pp20) REVERT: A 219 LYS cc_start: 0.7038 (tptt) cc_final: 0.6814 (tptt) REVERT: B 69 GLU cc_start: 0.7047 (OUTLIER) cc_final: 0.6640 (tm-30) REVERT: B 219 LYS cc_start: 0.7029 (tptt) cc_final: 0.6807 (tptt) REVERT: C 291 LEU cc_start: 0.8533 (tt) cc_final: 0.8228 (tp) REVERT: C 317 GLU cc_start: 0.7580 (mt-10) cc_final: 0.7378 (mt-10) REVERT: D 264 ASP cc_start: 0.7965 (t0) cc_final: 0.7761 (t0) REVERT: D 291 LEU cc_start: 0.8539 (tt) cc_final: 0.8235 (tp) REVERT: D 317 GLU cc_start: 0.7571 (mt-10) cc_final: 0.7370 (mt-10) outliers start: 8 outliers final: 5 residues processed: 143 average time/residue: 0.2894 time to fit residues: 62.4368 Evaluate side-chains 135 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 128 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ASN Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 69 GLU Chi-restraints excluded: chain B residue 42 ASN Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain C residue 265 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 46 optimal weight: 0.9980 chunk 137 optimal weight: 2.9990 chunk 71 optimal weight: 20.0000 chunk 74 optimal weight: 2.9990 chunk 160 optimal weight: 3.9990 chunk 18 optimal weight: 0.6980 chunk 68 optimal weight: 8.9990 chunk 47 optimal weight: 2.9990 chunk 73 optimal weight: 5.9990 chunk 127 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 268 ASN B 268 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4462 r_free = 0.4462 target = 0.212584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.170525 restraints weight = 57440.019| |-----------------------------------------------------------------------------| r_work (start): 0.4023 rms_B_bonded: 2.30 r_work: 0.3773 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3657 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7149 moved from start: 0.2320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 17406 Z= 0.210 Angle : 0.593 6.039 24374 Z= 0.348 Chirality : 0.044 0.161 2580 Planarity : 0.005 0.066 2308 Dihedral : 26.757 69.359 4094 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 0.77 % Allowed : 5.88 % Favored : 93.34 % 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 aren not related in a simple way. whole: -0.47 (0.22), residues: 1428 helix: 0.94 (0.21), residues: 556 sheet: -2.00 (0.32), residues: 194 loop : -0.76 (0.25), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 102 TYR 0.015 0.001 TYR A 238 PHE 0.015 0.002 PHE B 216 TRP 0.010 0.001 TRP D 308 HIS 0.003 0.001 HIS D 307 Details of bonding type rmsd covalent geometry : bond 0.00475 (17406) covalent geometry : angle 0.59315 (24374) hydrogen bonds : bond 0.03968 ( 630) hydrogen bonds : angle 4.30577 ( 1676) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 132 time to evaluate : 0.756 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 GLU cc_start: 0.6983 (OUTLIER) cc_final: 0.6539 (tm-30) REVERT: A 96 ASP cc_start: 0.7649 (m-30) cc_final: 0.7384 (m-30) REVERT: B 69 GLU cc_start: 0.6984 (OUTLIER) cc_final: 0.6543 (tm-30) REVERT: B 96 ASP cc_start: 0.7655 (m-30) cc_final: 0.7391 (m-30) REVERT: C 189 MET cc_start: 0.7732 (ptm) cc_final: 0.7385 (ptp) REVERT: C 264 ASP cc_start: 0.8042 (t0) cc_final: 0.7811 (t0) REVERT: C 291 LEU cc_start: 0.8525 (tt) cc_final: 0.8208 (tp) REVERT: D 160 SER cc_start: 0.8132 (t) cc_final: 0.7690 (m) REVERT: D 189 MET cc_start: 0.7759 (ptm) cc_final: 0.7416 (ptp) REVERT: D 264 ASP cc_start: 0.8049 (t0) cc_final: 0.7822 (t0) REVERT: D 291 LEU cc_start: 0.8524 (tt) cc_final: 0.8211 (tp) outliers start: 10 outliers final: 7 residues processed: 140 average time/residue: 0.2905 time to fit residues: 61.5543 Evaluate side-chains 142 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 133 time to evaluate : 0.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ASN Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 69 GLU Chi-restraints excluded: chain B residue 42 ASN Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain C residue 302 SER Chi-restraints excluded: chain D residue 265 GLN Chi-restraints excluded: chain D residue 302 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 11 optimal weight: 0.9990 chunk 71 optimal weight: 9.9990 chunk 75 optimal weight: 4.9990 chunk 20 optimal weight: 3.9990 chunk 34 optimal weight: 5.9990 chunk 70 optimal weight: 10.0000 chunk 93 optimal weight: 3.9990 chunk 142 optimal weight: 1.9990 chunk 85 optimal weight: 3.9990 chunk 36 optimal weight: 0.5980 chunk 4 optimal weight: 0.0670 overall best weight: 1.5324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4458 r_free = 0.4458 target = 0.209782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.167093 restraints weight = 58748.740| |-----------------------------------------------------------------------------| r_work (start): 0.4000 rms_B_bonded: 2.51 r_work: 0.3739 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3616 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7157 moved from start: 0.2804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 17406 Z= 0.181 Angle : 0.572 4.572 24374 Z= 0.335 Chirality : 0.043 0.141 2580 Planarity : 0.005 0.074 2308 Dihedral : 26.595 69.356 4094 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 1.47 % Allowed : 7.20 % Favored : 91.33 % 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 aren not related in a simple way. whole: -0.43 (0.22), residues: 1428 helix: 1.06 (0.22), residues: 556 sheet: -2.04 (0.32), residues: 192 loop : -0.82 (0.24), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 102 TYR 0.019 0.001 TYR A 238 PHE 0.015 0.001 PHE A 216 TRP 0.010 0.001 TRP C 125 HIS 0.003 0.001 HIS A 39 Details of bonding type rmsd covalent geometry : bond 0.00402 (17406) covalent geometry : angle 0.57194 (24374) hydrogen bonds : bond 0.03532 ( 630) hydrogen bonds : angle 4.26955 ( 1676) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 132 time to evaluate : 0.550 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 ASP cc_start: 0.7720 (m-30) cc_final: 0.7463 (m-30) REVERT: B 96 ASP cc_start: 0.7739 (m-30) cc_final: 0.7479 (m-30) REVERT: C 264 ASP cc_start: 0.8052 (t0) cc_final: 0.7818 (t0) REVERT: C 291 LEU cc_start: 0.8589 (tt) cc_final: 0.8229 (tp) REVERT: D 264 ASP cc_start: 0.7997 (t0) cc_final: 0.7773 (t0) REVERT: D 291 LEU cc_start: 0.8586 (tt) cc_final: 0.8225 (tp) outliers start: 19 outliers final: 15 residues processed: 145 average time/residue: 0.2276 time to fit residues: 49.8299 Evaluate side-chains 141 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 126 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ASN Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 69 GLU Chi-restraints excluded: chain A residue 76 GLU Chi-restraints excluded: chain B residue 42 ASN Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 76 GLU Chi-restraints excluded: chain C residue 9 MET Chi-restraints excluded: chain C residue 265 GLN Chi-restraints excluded: chain C residue 302 SER Chi-restraints excluded: chain C residue 329 GLU Chi-restraints excluded: chain D residue 9 MET Chi-restraints excluded: chain D residue 302 SER Chi-restraints excluded: chain D residue 329 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 24 optimal weight: 3.9990 chunk 44 optimal weight: 0.7980 chunk 122 optimal weight: 3.9990 chunk 108 optimal weight: 6.9990 chunk 56 optimal weight: 5.9990 chunk 156 optimal weight: 8.9990 chunk 37 optimal weight: 0.8980 chunk 22 optimal weight: 3.9990 chunk 83 optimal weight: 5.9990 chunk 23 optimal weight: 0.7980 chunk 82 optimal weight: 0.6980 overall best weight: 1.4382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4440 r_free = 0.4440 target = 0.208202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.165390 restraints weight = 58647.903| |-----------------------------------------------------------------------------| r_work (start): 0.3991 rms_B_bonded: 2.56 r_work: 0.3693 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7138 moved from start: 0.3078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 17406 Z= 0.184 Angle : 0.573 5.587 24374 Z= 0.335 Chirality : 0.044 0.129 2580 Planarity : 0.004 0.064 2308 Dihedral : 26.463 73.987 4094 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 0.77 % Allowed : 8.05 % Favored : 91.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.51 (0.22), residues: 1428 helix: 1.05 (0.22), residues: 556 sheet: -2.21 (0.33), residues: 176 loop : -0.94 (0.24), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 16 TYR 0.017 0.001 TYR B 238 PHE 0.016 0.001 PHE D 157 TRP 0.011 0.001 TRP C 125 HIS 0.003 0.001 HIS D 307 Details of bonding type rmsd covalent geometry : bond 0.00415 (17406) covalent geometry : angle 0.57315 (24374) hydrogen bonds : bond 0.03542 ( 630) hydrogen bonds : angle 4.21626 ( 1676) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 135 time to evaluate : 0.672 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 ASP cc_start: 0.7633 (m-30) cc_final: 0.7361 (m-30) REVERT: B 96 ASP cc_start: 0.7634 (m-30) cc_final: 0.7359 (m-30) REVERT: C 212 SER cc_start: 0.7532 (m) cc_final: 0.7084 (p) REVERT: C 291 LEU cc_start: 0.8532 (tt) cc_final: 0.8158 (tp) REVERT: D 212 SER cc_start: 0.7531 (m) cc_final: 0.7083 (p) REVERT: D 291 LEU cc_start: 0.8529 (tt) cc_final: 0.8153 (tp) outliers start: 10 outliers final: 10 residues processed: 143 average time/residue: 0.2541 time to fit residues: 55.3178 Evaluate side-chains 140 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 130 time to evaluate : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ASN Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 69 GLU Chi-restraints excluded: chain B residue 42 ASN Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain C residue 265 GLN Chi-restraints excluded: chain C residue 302 SER Chi-restraints excluded: chain D residue 265 GLN Chi-restraints excluded: chain D residue 302 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 157 optimal weight: 20.0000 chunk 40 optimal weight: 1.9990 chunk 39 optimal weight: 4.9990 chunk 118 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 2 optimal weight: 0.8980 chunk 107 optimal weight: 8.9990 chunk 80 optimal weight: 0.9990 chunk 29 optimal weight: 5.9990 chunk 116 optimal weight: 0.8980 chunk 106 optimal weight: 9.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4433 r_free = 0.4433 target = 0.207498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.164625 restraints weight = 58915.315| |-----------------------------------------------------------------------------| r_work (start): 0.3983 rms_B_bonded: 2.53 r_work: 0.3697 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7140 moved from start: 0.3317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 17406 Z= 0.186 Angle : 0.570 5.218 24374 Z= 0.333 Chirality : 0.044 0.134 2580 Planarity : 0.005 0.066 2308 Dihedral : 26.446 76.866 4094 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 1.08 % Allowed : 8.36 % Favored : 90.56 % 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 aren not related in a simple way. whole: -0.52 (0.22), residues: 1428 helix: 1.08 (0.22), residues: 556 sheet: -2.19 (0.33), residues: 176 loop : -0.99 (0.24), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 261 TYR 0.016 0.001 TYR B 238 PHE 0.013 0.001 PHE A 216 TRP 0.011 0.001 TRP D 125 HIS 0.003 0.001 HIS C 307 Details of bonding type rmsd covalent geometry : bond 0.00418 (17406) covalent geometry : angle 0.56957 (24374) hydrogen bonds : bond 0.03456 ( 630) hydrogen bonds : angle 4.22953 ( 1676) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 142 time to evaluate : 0.634 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 212 SER cc_start: 0.7514 (m) cc_final: 0.7062 (p) REVERT: C 291 LEU cc_start: 0.8571 (tt) cc_final: 0.8199 (tp) REVERT: D 212 SER cc_start: 0.7513 (m) cc_final: 0.7064 (p) REVERT: D 291 LEU cc_start: 0.8563 (tt) cc_final: 0.8192 (tp) outliers start: 14 outliers final: 12 residues processed: 152 average time/residue: 0.2560 time to fit residues: 57.6388 Evaluate side-chains 148 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 136 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ASN Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 69 GLU Chi-restraints excluded: chain A residue 76 GLU Chi-restraints excluded: chain B residue 42 ASN Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 76 GLU Chi-restraints excluded: chain C residue 265 GLN Chi-restraints excluded: chain C residue 302 SER Chi-restraints excluded: chain D residue 265 GLN Chi-restraints excluded: chain D residue 302 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 21 optimal weight: 4.9990 chunk 161 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 chunk 57 optimal weight: 1.9990 chunk 127 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 121 optimal weight: 3.9990 chunk 110 optimal weight: 10.0000 chunk 122 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4421 r_free = 0.4421 target = 0.206398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.163649 restraints weight = 58835.348| |-----------------------------------------------------------------------------| r_work (start): 0.3971 rms_B_bonded: 2.59 r_work: 0.3679 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7162 moved from start: 0.3589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 17406 Z= 0.187 Angle : 0.574 6.348 24374 Z= 0.335 Chirality : 0.044 0.127 2580 Planarity : 0.005 0.060 2308 Dihedral : 26.301 79.927 4094 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 1.16 % Allowed : 9.06 % 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 aren not related in a simple way. whole: -0.54 (0.22), residues: 1428 helix: 1.07 (0.22), residues: 556 sheet: -2.16 (0.33), residues: 176 loop : -1.01 (0.24), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 261 TYR 0.017 0.001 TYR B 238 PHE 0.013 0.001 PHE A 79 TRP 0.011 0.001 TRP C 125 HIS 0.003 0.001 HIS A 242 Details of bonding type rmsd covalent geometry : bond 0.00421 (17406) covalent geometry : angle 0.57364 (24374) hydrogen bonds : bond 0.03488 ( 630) hydrogen bonds : angle 4.22985 ( 1676) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 143 time to evaluate : 0.767 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 212 SER cc_start: 0.7436 (m) cc_final: 0.7075 (p) REVERT: C 291 LEU cc_start: 0.8601 (tt) cc_final: 0.8231 (tp) REVERT: C 297 ASP cc_start: 0.7527 (t0) cc_final: 0.7276 (p0) REVERT: D 212 SER cc_start: 0.7503 (m) cc_final: 0.7071 (p) REVERT: D 291 LEU cc_start: 0.8597 (tt) cc_final: 0.8227 (tp) REVERT: D 297 ASP cc_start: 0.7540 (t0) cc_final: 0.7273 (p0) outliers start: 15 outliers final: 10 residues processed: 154 average time/residue: 0.2758 time to fit residues: 63.0917 Evaluate side-chains 153 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 143 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ASN Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 69 GLU Chi-restraints excluded: chain B residue 42 ASN Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain C residue 265 GLN Chi-restraints excluded: chain C residue 302 SER Chi-restraints excluded: chain D residue 265 GLN Chi-restraints excluded: chain D residue 302 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 107 optimal weight: 8.9990 chunk 67 optimal weight: 0.2980 chunk 145 optimal weight: 3.9990 chunk 147 optimal weight: 20.0000 chunk 70 optimal weight: 10.0000 chunk 79 optimal weight: 0.8980 chunk 128 optimal weight: 0.8980 chunk 14 optimal weight: 3.9990 chunk 159 optimal weight: 4.9990 chunk 32 optimal weight: 0.8980 chunk 21 optimal weight: 3.9990 overall best weight: 1.3982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4422 r_free = 0.4422 target = 0.206615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.163623 restraints weight = 58393.036| |-----------------------------------------------------------------------------| r_work (start): 0.3971 rms_B_bonded: 2.53 r_work: 0.3691 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7146 moved from start: 0.3734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 17406 Z= 0.174 Angle : 0.565 5.342 24374 Z= 0.331 Chirality : 0.043 0.126 2580 Planarity : 0.004 0.058 2308 Dihedral : 26.216 81.409 4094 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 0.85 % Allowed : 9.44 % Favored : 89.71 % 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 aren not related in a simple way. whole: -0.50 (0.22), residues: 1428 helix: 1.16 (0.22), residues: 552 sheet: -2.11 (0.33), residues: 176 loop : -1.03 (0.24), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 112 TYR 0.016 0.001 TYR B 238 PHE 0.011 0.001 PHE B 79 TRP 0.010 0.001 TRP D 125 HIS 0.003 0.001 HIS C 307 Details of bonding type rmsd covalent geometry : bond 0.00391 (17406) covalent geometry : angle 0.56489 (24374) hydrogen bonds : bond 0.03391 ( 630) hydrogen bonds : angle 4.20141 ( 1676) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 141 time to evaluate : 0.678 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 139 LYS cc_start: 0.7158 (pttt) cc_final: 0.6715 (ttmm) REVERT: C 212 SER cc_start: 0.7412 (m) cc_final: 0.7058 (p) REVERT: C 291 LEU cc_start: 0.8605 (tt) cc_final: 0.8230 (tp) REVERT: D 139 LYS cc_start: 0.7176 (pttt) cc_final: 0.6701 (ttmt) REVERT: D 212 SER cc_start: 0.7409 (m) cc_final: 0.7051 (p) outliers start: 11 outliers final: 11 residues processed: 149 average time/residue: 0.2675 time to fit residues: 58.8135 Evaluate side-chains 150 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 139 time to evaluate : 0.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ASN Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 69 GLU Chi-restraints excluded: chain A residue 96 ASP Chi-restraints excluded: chain B residue 42 ASN Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain C residue 265 GLN Chi-restraints excluded: chain C residue 302 SER Chi-restraints excluded: chain D residue 265 GLN Chi-restraints excluded: chain D residue 302 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 158 optimal weight: 8.9990 chunk 61 optimal weight: 0.6980 chunk 155 optimal weight: 3.9990 chunk 131 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 149 optimal weight: 4.9990 chunk 144 optimal weight: 2.9990 chunk 143 optimal weight: 3.9990 chunk 84 optimal weight: 1.9990 chunk 72 optimal weight: 7.9990 chunk 139 optimal weight: 1.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4410 r_free = 0.4410 target = 0.205375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.162513 restraints weight = 58396.668| |-----------------------------------------------------------------------------| r_work (start): 0.3952 rms_B_bonded: 2.53 r_work: 0.3679 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7173 moved from start: 0.3879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 17406 Z= 0.202 Angle : 0.582 5.972 24374 Z= 0.339 Chirality : 0.044 0.127 2580 Planarity : 0.005 0.058 2308 Dihedral : 26.178 83.792 4094 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 0.93 % Allowed : 9.37 % Favored : 89.71 % 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 aren not related in a simple way. whole: -0.59 (0.22), residues: 1428 helix: 1.01 (0.22), residues: 554 sheet: -2.18 (0.33), residues: 176 loop : -1.02 (0.24), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 261 TYR 0.019 0.001 TYR A 238 PHE 0.015 0.002 PHE B 79 TRP 0.011 0.001 TRP D 125 HIS 0.003 0.001 HIS B 39 Details of bonding type rmsd covalent geometry : bond 0.00458 (17406) covalent geometry : angle 0.58184 (24374) hydrogen bonds : bond 0.03665 ( 630) hydrogen bonds : angle 4.30744 ( 1676) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 142 time to evaluate : 0.682 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 212 SER cc_start: 0.7522 (m) cc_final: 0.7069 (p) REVERT: C 297 ASP cc_start: 0.7494 (t0) cc_final: 0.7271 (p0) REVERT: D 139 LYS cc_start: 0.7176 (pttt) cc_final: 0.6703 (ttmt) REVERT: D 212 SER cc_start: 0.7524 (m) cc_final: 0.7073 (p) outliers start: 12 outliers final: 12 residues processed: 150 average time/residue: 0.2644 time to fit residues: 59.2042 Evaluate side-chains 152 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 140 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ASN Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 69 GLU Chi-restraints excluded: chain A residue 96 ASP Chi-restraints excluded: chain B residue 42 ASN Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 96 ASP Chi-restraints excluded: chain C residue 265 GLN Chi-restraints excluded: chain C residue 302 SER Chi-restraints excluded: chain D residue 265 GLN Chi-restraints excluded: chain D residue 302 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 27 optimal weight: 0.9980 chunk 99 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 88 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 56 optimal weight: 4.9990 chunk 49 optimal weight: 0.5980 chunk 117 optimal weight: 0.9990 chunk 45 optimal weight: 0.7980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4434 r_free = 0.4434 target = 0.207653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.165059 restraints weight = 58801.185| |-----------------------------------------------------------------------------| r_work (start): 0.3980 rms_B_bonded: 2.49 r_work: 0.3712 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7119 moved from start: 0.3881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17406 Z= 0.148 Angle : 0.552 5.938 24374 Z= 0.324 Chirality : 0.041 0.129 2580 Planarity : 0.004 0.057 2308 Dihedral : 26.090 82.910 4094 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 0.93 % Allowed : 9.83 % Favored : 89.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.42 (0.23), residues: 1428 helix: 1.20 (0.22), residues: 556 sheet: -2.06 (0.34), residues: 176 loop : -0.98 (0.24), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 261 TYR 0.013 0.001 TYR A 238 PHE 0.010 0.001 PHE A 79 TRP 0.008 0.001 TRP D 308 HIS 0.003 0.001 HIS C 307 Details of bonding type rmsd covalent geometry : bond 0.00334 (17406) covalent geometry : angle 0.55184 (24374) hydrogen bonds : bond 0.03165 ( 630) hydrogen bonds : angle 4.10605 ( 1676) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6779.14 seconds wall clock time: 115 minutes 42.89 seconds (6942.89 seconds total)