Starting phenix.real_space_refine on Wed May 28 11:20:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8b4h_15848/05_2025/8b4h_15848.cif Found real_map, /net/cci-nas-00/data/ceres_data/8b4h_15848/05_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_15848/05_2025/8b4h_15848.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8b4h_15848/05_2025/8b4h_15848.map" model { file = "/net/cci-nas-00/data/ceres_data/8b4h_15848/05_2025/8b4h_15848.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8b4h_15848/05_2025/8b4h_15848.cif" } resolution = 3.35 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 13.36, per 1000 atoms: 0.43 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: 7.63 Conformation dependent library (CDL) restraints added in 1.9 seconds 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: 13.57 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: 11.59 Time building geometry restraints manager: 9.21 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: 0.08 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'E' selection = chain 'G' } ncs_group { reference = chain 'C' selection = chain 'D' } 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: 0.010 Normalize map: mean=0, sd=1: 2.130 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: 0.470 Extract box with map and model: 1.110 Check model and map are aligned: 0.200 Set scattering table: 0.270 Process input model: 70.320 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 77.470 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.007 0.001 TRP B 262 HIS 0.009 0.001 HIS A 242 PHE 0.024 0.001 PHE B 257 TYR 0.013 0.001 TYR B 214 ARG 0.010 0.001 ARG D 4 Details of bonding type rmsd hydrogen bonds : bond 0.11138 ( 630) hydrogen bonds : angle 5.22142 ( 1676) covalent geometry : bond 0.00408 (17406) covalent geometry : angle 0.70933 (24374) *********************** 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 : 2.249 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: 0.5929 time to fit residues: 147.1569 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 : 2.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 136 optimal weight: 2.9990 chunk 122 optimal weight: 0.9980 chunk 68 optimal weight: 9.9990 chunk 41 optimal weight: 0.5980 chunk 82 optimal weight: 0.9980 chunk 65 optimal weight: 9.9990 chunk 126 optimal weight: 0.7980 chunk 49 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 94 optimal weight: 3.9990 chunk 147 optimal weight: 20.0000 overall best weight: 1.2782 ------------------------------------------------------------------------------- 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 = 0.4531 r_free = 0.4531 target = 0.219481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.178109 restraints weight = 57815.461| |-----------------------------------------------------------------------------| r_work (start): 0.4105 rms_B_bonded: 2.19 r_work: 0.3876 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3768 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6973 moved from start: 0.1215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 17406 Z= 0.211 Angle : 0.640 7.182 24374 Z= 0.378 Chirality : 0.043 0.159 2580 Planarity : 0.005 0.061 2308 Dihedral : 26.830 68.459 4094 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 0.62 % Allowed : 2.71 % Favored : 96.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.22), residues: 1428 helix: 1.05 (0.22), residues: 548 sheet: -1.99 (0.32), residues: 194 loop : -0.74 (0.25), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 125 HIS 0.004 0.001 HIS D 307 PHE 0.016 0.002 PHE A 257 TYR 0.007 0.001 TYR D 214 ARG 0.005 0.001 ARG A 102 Details of bonding type rmsd hydrogen bonds : bond 0.04635 ( 630) hydrogen bonds : angle 4.46608 ( 1676) covalent geometry : bond 0.00473 (17406) covalent geometry : angle 0.63992 (24374) *********************** 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 154 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 146 time to evaluate : 2.123 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: C 264 ASP cc_start: 0.7879 (t0) cc_final: 0.7607 (t0) REVERT: C 317 GLU cc_start: 0.7582 (mt-10) cc_final: 0.7375 (mt-10) REVERT: D 264 ASP cc_start: 0.7793 (t0) cc_final: 0.7471 (t0) REVERT: D 317 GLU cc_start: 0.7651 (mt-10) cc_final: 0.7432 (mt-10) outliers start: 8 outliers final: 4 residues processed: 152 average time/residue: 0.6092 time to fit residues: 140.4178 Evaluate side-chains 136 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 132 time to evaluate : 2.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ASN Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain B residue 42 ASN Chi-restraints excluded: chain B residue 68 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 33 optimal weight: 9.9990 chunk 83 optimal weight: 0.9990 chunk 135 optimal weight: 3.9990 chunk 107 optimal weight: 20.0000 chunk 21 optimal weight: 4.9990 chunk 96 optimal weight: 2.9990 chunk 160 optimal weight: 3.9990 chunk 77 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 55 optimal weight: 0.9980 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 227 GLN A 268 ASN B 227 GLN B 268 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4462 r_free = 0.4462 target = 0.212412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.170792 restraints weight = 57469.101| |-----------------------------------------------------------------------------| r_work (start): 0.4024 rms_B_bonded: 2.39 r_work: 0.3764 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3641 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7158 moved from start: 0.2139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 17406 Z= 0.226 Angle : 0.625 5.880 24374 Z= 0.366 Chirality : 0.045 0.179 2580 Planarity : 0.005 0.071 2308 Dihedral : 26.978 67.254 4094 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 0.54 % Allowed : 5.57 % Favored : 93.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.22), residues: 1428 helix: 0.78 (0.21), residues: 556 sheet: -2.08 (0.32), residues: 194 loop : -0.86 (0.24), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 125 HIS 0.004 0.001 HIS A 39 PHE 0.019 0.002 PHE C 157 TYR 0.013 0.002 TYR B 238 ARG 0.007 0.001 ARG A 102 Details of bonding type rmsd hydrogen bonds : bond 0.04389 ( 630) hydrogen bonds : angle 4.47739 ( 1676) covalent geometry : bond 0.00519 (17406) covalent geometry : angle 0.62489 (24374) *********************** 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: 7 poor density : 138 time to evaluate : 2.009 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: 0.7064 (OUTLIER) cc_final: 0.6563 (tm-30) REVERT: A 96 ASP cc_start: 0.7598 (m-30) cc_final: 0.7382 (m-30) REVERT: A 152 MET cc_start: 0.8188 (tpt) cc_final: 0.7334 (tpt) REVERT: B 69 GLU cc_start: 0.7061 (OUTLIER) cc_final: 0.6568 (tm-30) REVERT: B 96 ASP cc_start: 0.7592 (m-30) cc_final: 0.7370 (m-30) REVERT: B 152 MET cc_start: 0.8178 (tpt) cc_final: 0.7323 (tpt) REVERT: C 189 MET cc_start: 0.7863 (ptm) cc_final: 0.7440 (ptp) REVERT: C 291 LEU cc_start: 0.8571 (tt) cc_final: 0.8353 (tp) REVERT: D 189 MET cc_start: 0.7908 (ptm) cc_final: 0.7497 (ptp) REVERT: D 264 ASP cc_start: 0.8052 (t0) cc_final: 0.7828 (t0) REVERT: D 291 LEU cc_start: 0.8565 (tt) cc_final: 0.8349 (tp) outliers start: 7 outliers final: 5 residues processed: 144 average time/residue: 0.5658 time to fit residues: 123.2502 Evaluate side-chains 136 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 129 time to evaluate : 2.321 ------------------------------------------------------------------------------- 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 146 optimal weight: 10.0000 chunk 131 optimal weight: 5.9990 chunk 113 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 10 optimal weight: 0.0980 chunk 121 optimal weight: 0.9980 chunk 70 optimal weight: 10.0000 chunk 23 optimal weight: 0.9990 chunk 29 optimal weight: 6.9990 chunk 147 optimal weight: 10.0000 chunk 17 optimal weight: 0.7980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 265 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4470 r_free = 0.4470 target = 0.213400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.171424 restraints weight = 57572.119| |-----------------------------------------------------------------------------| r_work (start): 0.4034 rms_B_bonded: 2.28 r_work: 0.3789 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3667 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7135 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 : 0.004 0.029 17406 Z= 0.166 Angle : 0.567 4.797 24374 Z= 0.334 Chirality : 0.042 0.132 2580 Planarity : 0.004 0.067 2308 Dihedral : 26.726 67.493 4094 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 1.08 % Allowed : 6.19 % Favored : 92.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.22), residues: 1428 helix: 1.13 (0.22), residues: 556 sheet: -2.08 (0.31), residues: 194 loop : -0.81 (0.25), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 125 HIS 0.003 0.001 HIS B 242 PHE 0.013 0.001 PHE B 216 TYR 0.014 0.001 TYR A 238 ARG 0.003 0.000 ARG A 234 Details of bonding type rmsd hydrogen bonds : bond 0.03596 ( 630) hydrogen bonds : angle 4.16110 ( 1676) covalent geometry : bond 0.00372 (17406) covalent geometry : angle 0.56654 (24374) *********************** 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 151 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 137 time to evaluate : 2.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 GLU cc_start: 0.7038 (OUTLIER) cc_final: 0.6669 (tm-30) REVERT: A 96 ASP cc_start: 0.7555 (m-30) cc_final: 0.7268 (m-30) REVERT: A 152 MET cc_start: 0.8176 (tpt) cc_final: 0.7284 (tpt) REVERT: B 69 GLU cc_start: 0.7044 (OUTLIER) cc_final: 0.6673 (tm-30) REVERT: B 96 ASP cc_start: 0.7549 (m-30) cc_final: 0.7253 (m-30) REVERT: B 152 MET cc_start: 0.8166 (tpt) cc_final: 0.7269 (tpt) REVERT: C 160 SER cc_start: 0.8160 (t) cc_final: 0.7725 (m) REVERT: C 189 MET cc_start: 0.7667 (ptm) cc_final: 0.7272 (ptp) REVERT: C 264 ASP cc_start: 0.8033 (t0) cc_final: 0.7793 (t0) REVERT: C 291 LEU cc_start: 0.8505 (tt) cc_final: 0.8210 (tp) REVERT: D 160 SER cc_start: 0.8162 (t) cc_final: 0.7712 (m) REVERT: D 189 MET cc_start: 0.7699 (ptm) cc_final: 0.7306 (ptp) REVERT: D 264 ASP cc_start: 0.8042 (t0) cc_final: 0.7807 (t0) REVERT: D 291 LEU cc_start: 0.8497 (tt) cc_final: 0.8201 (tp) outliers start: 14 outliers final: 8 residues processed: 149 average time/residue: 0.6150 time to fit residues: 139.8061 Evaluate side-chains 143 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 133 time to evaluate : 2.118 ------------------------------------------------------------------------------- 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 302 SER Chi-restraints excluded: chain D residue 329 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 36 optimal weight: 0.6980 chunk 47 optimal weight: 3.9990 chunk 154 optimal weight: 3.9990 chunk 138 optimal weight: 2.9990 chunk 156 optimal weight: 10.0000 chunk 37 optimal weight: 0.9980 chunk 132 optimal weight: 0.0270 chunk 21 optimal weight: 5.9990 chunk 111 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 overall best weight: 1.3442 ------------------------------------------------------------------------------- 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 = 0.4447 r_free = 0.4447 target = 0.208974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.165806 restraints weight = 58360.803| |-----------------------------------------------------------------------------| r_work (start): 0.3994 rms_B_bonded: 2.58 r_work: 0.3717 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7126 moved from start: 0.2872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 17406 Z= 0.181 Angle : 0.570 7.518 24374 Z= 0.334 Chirality : 0.043 0.131 2580 Planarity : 0.004 0.067 2308 Dihedral : 26.569 70.651 4094 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 1.32 % Allowed : 7.28 % Favored : 91.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.22), residues: 1428 helix: 1.12 (0.22), residues: 556 sheet: -2.18 (0.33), residues: 172 loop : -0.97 (0.23), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 125 HIS 0.006 0.001 HIS A 242 PHE 0.014 0.001 PHE B 79 TYR 0.012 0.001 TYR A 238 ARG 0.002 0.000 ARG A 261 Details of bonding type rmsd hydrogen bonds : bond 0.03470 ( 630) hydrogen bonds : angle 4.22806 ( 1676) covalent geometry : bond 0.00409 (17406) covalent geometry : angle 0.57032 (24374) *********************** 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 147 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 130 time to evaluate : 2.044 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 GLU cc_start: 0.6904 (OUTLIER) cc_final: 0.6427 (tt0) REVERT: A 96 ASP cc_start: 0.7586 (m-30) cc_final: 0.7284 (m-30) REVERT: A 152 MET cc_start: 0.8049 (tpt) cc_final: 0.7240 (tpt) REVERT: B 69 GLU cc_start: 0.6901 (OUTLIER) cc_final: 0.6423 (tt0) REVERT: B 96 ASP cc_start: 0.7593 (m-30) cc_final: 0.7293 (m-30) REVERT: B 152 MET cc_start: 0.8053 (tpt) cc_final: 0.7243 (tpt) REVERT: C 189 MET cc_start: 0.7190 (ptm) cc_final: 0.6858 (ptp) REVERT: C 291 LEU cc_start: 0.8510 (tt) cc_final: 0.8193 (tp) REVERT: D 189 MET cc_start: 0.7171 (ptm) cc_final: 0.6839 (ptp) REVERT: D 212 SER cc_start: 0.7545 (m) cc_final: 0.7094 (p) REVERT: D 291 LEU cc_start: 0.8514 (tt) cc_final: 0.8197 (tp) outliers start: 17 outliers final: 10 residues processed: 143 average time/residue: 0.6124 time to fit residues: 133.3709 Evaluate side-chains 143 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 131 time to evaluate : 2.014 ------------------------------------------------------------------------------- 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 9 MET Chi-restraints excluded: chain C residue 265 GLN Chi-restraints excluded: chain C residue 302 SER Chi-restraints excluded: chain D residue 9 MET Chi-restraints excluded: chain D residue 265 GLN Chi-restraints excluded: chain D residue 302 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 32 optimal weight: 0.9990 chunk 88 optimal weight: 1.9990 chunk 134 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 40 optimal weight: 0.9990 chunk 137 optimal weight: 0.7980 chunk 80 optimal weight: 0.0370 chunk 31 optimal weight: 0.7980 chunk 114 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 136 optimal weight: 0.6980 overall best weight: 0.6660 ------------------------------------------------------------------------------- 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 = 0.4472 r_free = 0.4472 target = 0.211607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.168729 restraints weight = 58651.988| |-----------------------------------------------------------------------------| r_work (start): 0.4023 rms_B_bonded: 2.40 r_work: 0.3770 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3653 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7114 moved from start: 0.2984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 17406 Z= 0.131 Angle : 0.534 4.252 24374 Z= 0.316 Chirality : 0.041 0.132 2580 Planarity : 0.004 0.063 2308 Dihedral : 26.402 72.329 4094 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 0.85 % Allowed : 7.74 % Favored : 91.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.22), residues: 1428 helix: 1.42 (0.22), residues: 556 sheet: -2.08 (0.33), residues: 178 loop : -0.87 (0.24), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 125 HIS 0.002 0.001 HIS D 307 PHE 0.010 0.001 PHE A 216 TYR 0.010 0.001 TYR A 238 ARG 0.002 0.000 ARG A 261 Details of bonding type rmsd hydrogen bonds : bond 0.03029 ( 630) hydrogen bonds : angle 3.97018 ( 1676) covalent geometry : bond 0.00294 (17406) covalent geometry : angle 0.53366 (24374) *********************** 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 143 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 132 time to evaluate : 2.296 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 MET cc_start: 0.7930 (mtt) cc_final: 0.7612 (mtt) REVERT: A 96 ASP cc_start: 0.7612 (m-30) cc_final: 0.7269 (m-30) REVERT: A 152 MET cc_start: 0.8235 (tpt) cc_final: 0.7351 (tpt) REVERT: B 9 MET cc_start: 0.7339 (mmm) cc_final: 0.6890 (mmm) REVERT: B 67 MET cc_start: 0.7930 (mtt) cc_final: 0.7611 (mtt) REVERT: B 96 ASP cc_start: 0.7616 (m-30) cc_final: 0.7258 (m-30) REVERT: B 152 MET cc_start: 0.8246 (tpt) cc_final: 0.7365 (tpt) REVERT: C 212 SER cc_start: 0.7906 (m) cc_final: 0.7616 (p) REVERT: C 264 ASP cc_start: 0.7962 (t0) cc_final: 0.7722 (t0) REVERT: C 291 LEU cc_start: 0.8581 (tt) cc_final: 0.8222 (tp) REVERT: D 212 SER cc_start: 0.7912 (m) cc_final: 0.7616 (p) REVERT: D 264 ASP cc_start: 0.7985 (t0) cc_final: 0.7751 (t0) outliers start: 11 outliers final: 8 residues processed: 139 average time/residue: 0.6168 time to fit residues: 131.3956 Evaluate side-chains 136 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 128 time to evaluate : 2.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ASN Chi-restraints excluded: chain B residue 42 ASN 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 D residue 9 MET 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 105 optimal weight: 1.9990 chunk 85 optimal weight: 3.9990 chunk 69 optimal weight: 9.9990 chunk 120 optimal weight: 3.9990 chunk 160 optimal weight: 3.9990 chunk 133 optimal weight: 0.9980 chunk 74 optimal weight: 0.0370 chunk 108 optimal weight: 10.0000 chunk 34 optimal weight: 9.9990 chunk 70 optimal weight: 0.9990 chunk 16 optimal weight: 7.9990 overall best weight: 1.6064 ------------------------------------------------------------------------------- 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 = 0.4432 r_free = 0.4432 target = 0.207653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.164457 restraints weight = 58444.117| |-----------------------------------------------------------------------------| r_work (start): 0.3981 rms_B_bonded: 2.59 r_work: 0.3710 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7133 moved from start: 0.3210 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= 0.188 Angle : 0.566 5.737 24374 Z= 0.331 Chirality : 0.044 0.126 2580 Planarity : 0.004 0.062 2308 Dihedral : 26.402 74.409 4094 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 1.08 % Allowed : 7.89 % Favored : 91.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.22), residues: 1428 helix: 1.22 (0.22), residues: 556 sheet: -2.13 (0.33), residues: 176 loop : -0.98 (0.24), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 125 HIS 0.005 0.001 HIS B 242 PHE 0.013 0.001 PHE A 79 TYR 0.015 0.001 TYR B 238 ARG 0.003 0.000 ARG B 261 Details of bonding type rmsd hydrogen bonds : bond 0.03465 ( 630) hydrogen bonds : angle 4.15671 ( 1676) covalent geometry : bond 0.00420 (17406) covalent geometry : angle 0.56580 (24374) *********************** 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 149 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 135 time to evaluate : 2.067 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: 0.7609 (m-30) cc_final: 0.7318 (m-30) REVERT: A 152 MET cc_start: 0.8052 (tpt) cc_final: 0.7234 (tpt) REVERT: B 9 MET cc_start: 0.7159 (mmm) cc_final: 0.6871 (mmm) REVERT: B 96 ASP cc_start: 0.7612 (m-30) cc_final: 0.7315 (m-30) REVERT: B 152 MET cc_start: 0.8053 (tpt) cc_final: 0.7237 (tpt) REVERT: C 212 SER cc_start: 0.7495 (m) cc_final: 0.7130 (p) REVERT: C 291 LEU cc_start: 0.8552 (tt) cc_final: 0.8201 (tp) REVERT: D 212 SER cc_start: 0.7412 (m) cc_final: 0.7059 (p) outliers start: 14 outliers final: 13 residues processed: 145 average time/residue: 0.6270 time to fit residues: 135.9578 Evaluate side-chains 146 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 133 time to evaluate : 2.161 ------------------------------------------------------------------------------- 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 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 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 83 optimal weight: 4.9990 chunk 59 optimal weight: 0.8980 chunk 86 optimal weight: 2.9990 chunk 94 optimal weight: 0.0270 chunk 102 optimal weight: 2.9990 chunk 104 optimal weight: 0.8980 chunk 139 optimal weight: 0.6980 chunk 65 optimal weight: 9.9990 chunk 148 optimal weight: 8.9990 chunk 126 optimal weight: 3.9990 chunk 153 optimal weight: 3.9990 overall best weight: 1.1040 ------------------------------------------------------------------------------- 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 = 0.4449 r_free = 0.4449 target = 0.209388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.166603 restraints weight = 58713.910| |-----------------------------------------------------------------------------| r_work (start): 0.3998 rms_B_bonded: 2.54 r_work: 0.3731 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7051 moved from start: 0.3378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 17406 Z= 0.148 Angle : 0.543 5.428 24374 Z= 0.319 Chirality : 0.042 0.128 2580 Planarity : 0.004 0.059 2308 Dihedral : 26.264 75.433 4094 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 1.01 % Allowed : 8.05 % Favored : 90.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.22), residues: 1428 helix: 1.35 (0.22), residues: 556 sheet: -2.07 (0.33), residues: 176 loop : -0.96 (0.24), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 125 HIS 0.004 0.001 HIS B 242 PHE 0.011 0.001 PHE B 216 TYR 0.012 0.001 TYR B 238 ARG 0.003 0.000 ARG A 261 Details of bonding type rmsd hydrogen bonds : bond 0.03065 ( 630) hydrogen bonds : angle 4.01906 ( 1676) covalent geometry : bond 0.00331 (17406) covalent geometry : angle 0.54323 (24374) *********************** 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 151 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 138 time to evaluate : 2.110 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 MET cc_start: 0.8148 (tpt) cc_final: 0.7335 (tpt) REVERT: B 9 MET cc_start: 0.7060 (mmm) cc_final: 0.6747 (mmm) REVERT: B 152 MET cc_start: 0.8136 (tpt) cc_final: 0.7327 (tpt) REVERT: C 112 ARG cc_start: 0.6515 (mmt-90) cc_final: 0.6217 (tpm170) REVERT: C 212 SER cc_start: 0.7740 (m) cc_final: 0.7434 (p) REVERT: C 291 LEU cc_start: 0.8550 (tt) cc_final: 0.8195 (tp) REVERT: D 212 SER cc_start: 0.7785 (m) cc_final: 0.7453 (p) outliers start: 13 outliers final: 10 residues processed: 147 average time/residue: 0.6563 time to fit residues: 143.0718 Evaluate side-chains 146 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 136 time to evaluate : 2.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ASN Chi-restraints excluded: chain A residue 69 GLU Chi-restraints excluded: chain B residue 42 ASN Chi-restraints excluded: chain B residue 69 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 D residue 9 MET 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 3 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 chunk 129 optimal weight: 5.9990 chunk 5 optimal weight: 0.9980 chunk 28 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 29 optimal weight: 0.6980 chunk 160 optimal weight: 3.9990 chunk 85 optimal weight: 2.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 = 0.4450 r_free = 0.4450 target = 0.209544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.166591 restraints weight = 58755.174| |-----------------------------------------------------------------------------| r_work (start): 0.4003 rms_B_bonded: 2.54 r_work: 0.3737 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7056 moved from start: 0.3507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 17406 Z= 0.142 Angle : 0.539 5.043 24374 Z= 0.317 Chirality : 0.042 0.127 2580 Planarity : 0.004 0.060 2308 Dihedral : 26.183 76.615 4094 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 0.77 % Allowed : 8.67 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.22), residues: 1428 helix: 1.45 (0.22), residues: 556 sheet: -1.93 (0.34), residues: 176 loop : -0.95 (0.24), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 125 HIS 0.004 0.001 HIS B 242 PHE 0.010 0.001 PHE A 216 TYR 0.012 0.001 TYR B 238 ARG 0.002 0.000 ARG A 261 Details of bonding type rmsd hydrogen bonds : bond 0.03069 ( 630) hydrogen bonds : angle 3.98898 ( 1676) covalent geometry : bond 0.00320 (17406) covalent geometry : angle 0.53900 (24374) *********************** 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 144 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 134 time to evaluate : 2.012 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: A 152 MET cc_start: 0.8127 (tpt) cc_final: 0.7317 (tpt) REVERT: B 9 MET cc_start: 0.6944 (mmm) cc_final: 0.6662 (mmm) REVERT: B 152 MET cc_start: 0.8139 (tpt) cc_final: 0.7331 (tpt) REVERT: C 112 ARG cc_start: 0.6602 (mmt-90) cc_final: 0.6327 (tpm170) REVERT: C 212 SER cc_start: 0.7819 (m) cc_final: 0.7512 (p) REVERT: C 291 LEU cc_start: 0.8559 (tt) cc_final: 0.8210 (tp) REVERT: D 112 ARG cc_start: 0.6583 (mmt-90) cc_final: 0.6316 (tpm170) REVERT: D 212 SER cc_start: 0.7724 (m) cc_final: 0.7411 (p) outliers start: 10 outliers final: 10 residues processed: 140 average time/residue: 0.6438 time to fit residues: 133.9152 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 : 2.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ASN Chi-restraints excluded: chain A residue 69 GLU Chi-restraints excluded: chain B residue 42 ASN Chi-restraints excluded: chain B residue 69 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 D residue 9 MET 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 50 optimal weight: 0.9990 chunk 30 optimal weight: 6.9990 chunk 94 optimal weight: 2.9990 chunk 106 optimal weight: 20.0000 chunk 143 optimal weight: 3.9990 chunk 101 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 70 optimal weight: 20.0000 chunk 68 optimal weight: 10.0000 chunk 161 optimal weight: 2.9990 chunk 134 optimal weight: 0.8980 overall best weight: 2.1788 ------------------------------------------------------------------------------- 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 = 0.4408 r_free = 0.4408 target = 0.205201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.162013 restraints weight = 58652.292| |-----------------------------------------------------------------------------| r_work (start): 0.3951 rms_B_bonded: 2.59 r_work: 0.3667 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7207 moved from start: 0.3774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 17406 Z= 0.240 Angle : 0.611 5.457 24374 Z= 0.353 Chirality : 0.046 0.136 2580 Planarity : 0.005 0.062 2308 Dihedral : 26.195 82.313 4094 Min Nonbonded Distance : 1.830 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 0.93 % Allowed : 8.98 % Favored : 90.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.22), residues: 1428 helix: 0.99 (0.22), residues: 554 sheet: -2.12 (0.33), residues: 176 loop : -1.08 (0.24), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 125 HIS 0.007 0.001 HIS B 242 PHE 0.018 0.002 PHE B 79 TYR 0.022 0.002 TYR B 238 ARG 0.004 0.001 ARG B 16 Details of bonding type rmsd hydrogen bonds : bond 0.03992 ( 630) hydrogen bonds : angle 4.37196 ( 1676) covalent geometry : bond 0.00547 (17406) covalent geometry : angle 0.61063 (24374) ********************** 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 157 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 145 time to evaluate : 2.194 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: A 152 MET cc_start: 0.8075 (tpt) cc_final: 0.7243 (tpt) REVERT: B 9 MET cc_start: 0.7041 (mmm) cc_final: 0.6740 (mmm) REVERT: B 152 MET cc_start: 0.8087 (tpt) cc_final: 0.7256 (tpt) REVERT: C 112 ARG cc_start: 0.6698 (mmt-90) cc_final: 0.6454 (tpm170) REVERT: C 212 SER cc_start: 0.7470 (m) cc_final: 0.7078 (p) REVERT: C 291 LEU cc_start: 0.8617 (tt) cc_final: 0.8280 (tp) REVERT: D 112 ARG cc_start: 0.6754 (mmt-90) cc_final: 0.6530 (tpm170) REVERT: D 212 SER cc_start: 0.7502 (m) cc_final: 0.7092 (p) outliers start: 12 outliers final: 12 residues processed: 152 average time/residue: 0.6560 time to fit residues: 145.4984 Evaluate side-chains 149 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 137 time to evaluate : 2.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ASN 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 69 GLU Chi-restraints excluded: chain B residue 96 ASP 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 D residue 9 MET 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 43 optimal weight: 1.9990 chunk 85 optimal weight: 0.5980 chunk 104 optimal weight: 3.9990 chunk 3 optimal weight: 0.9990 chunk 67 optimal weight: 5.9990 chunk 16 optimal weight: 5.9990 chunk 87 optimal weight: 0.3980 chunk 117 optimal weight: 0.7980 chunk 99 optimal weight: 1.9990 chunk 54 optimal weight: 0.7980 chunk 35 optimal weight: 3.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- 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 = 0.4443 r_free = 0.4443 target = 0.208608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.165717 restraints weight = 58486.746| |-----------------------------------------------------------------------------| r_work (start): 0.3992 rms_B_bonded: 2.49 r_work: 0.3717 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7119 moved from start: 0.3807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17406 Z= 0.137 Angle : 0.548 5.553 24374 Z= 0.322 Chirality : 0.041 0.130 2580 Planarity : 0.004 0.057 2308 Dihedral : 26.090 80.378 4094 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 0.77 % Allowed : 9.21 % Favored : 90.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.22), residues: 1428 helix: 1.31 (0.22), residues: 556 sheet: -1.97 (0.34), residues: 176 loop : -1.02 (0.24), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 308 HIS 0.004 0.001 HIS B 242 PHE 0.009 0.001 PHE A 216 TYR 0.010 0.001 TYR B 238 ARG 0.002 0.000 ARG A 282 Details of bonding type rmsd hydrogen bonds : bond 0.03049 ( 630) hydrogen bonds : angle 4.05301 ( 1676) covalent geometry : bond 0.00308 (17406) covalent geometry : angle 0.54845 (24374) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14657.48 seconds wall clock time: 251 minutes 51.74 seconds (15111.74 seconds total)