Starting phenix.real_space_refine on Thu Jun 26 14:50:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8b4h_15848/06_2025/8b4h_15848.cif Found real_map, /net/cci-nas-00/data/ceres_data/8b4h_15848/06_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_15848/06_2025/8b4h_15848.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8b4h_15848/06_2025/8b4h_15848.map" model { file = "/net/cci-nas-00/data/ceres_data/8b4h_15848/06_2025/8b4h_15848.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8b4h_15848/06_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-5710/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: 13.71, per 1000 atoms: 0.44 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: 8.97 Conformation dependent library (CDL) restraints added in 1.8 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: 14.57 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: 12.88 Time building geometry restraints manager: 10.62 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: 0.000 Normalize map: mean=0, sd=1: 2.150 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: 1.040 Check model and map are aligned: 0.190 Set scattering table: 0.250 Process input model: 76.250 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.130 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: 0.020 Load rotamer database and sin/cos tables:3.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 83.980 ------------------------------------------------------------------------------- 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 : 2.046 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: 0.6106 time to fit residues: 151.9577 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 : 1.965 ------------------------------------------------------------------------------- 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 = 0.219442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.178777 restraints weight = 57811.951| |-----------------------------------------------------------------------------| r_work (start): 0.4110 rms_B_bonded: 2.23 r_work: 0.3880 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3762 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6991 moved from start: 0.1219 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= 0.210 Angle : 0.640 7.193 24374 Z= 0.378 Chirality : 0.043 0.154 2580 Planarity : 0.005 0.060 2308 Dihedral : 26.830 68.441 4094 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 10.05 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 0.015 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 0.04638 ( 630) hydrogen bonds : angle 4.46625 ( 1676) covalent geometry : bond 0.00473 (17406) covalent geometry : angle 0.63956 (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 : 2.108 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: 0.7881 (t0) cc_final: 0.7614 (t0) REVERT: D 264 ASP cc_start: 0.7816 (t0) cc_final: 0.7502 (t0) REVERT: D 317 GLU cc_start: 0.7644 (mt-10) cc_final: 0.7433 (mt-10) outliers start: 8 outliers final: 4 residues processed: 152 average time/residue: 0.6316 time to fit residues: 145.7805 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 : 2.021 ------------------------------------------------------------------------------- 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: 0.8980 chunk 135 optimal weight: 3.9990 chunk 107 optimal weight: 20.0000 chunk 21 optimal weight: 3.9990 chunk 96 optimal weight: 0.0770 chunk 160 optimal weight: 3.9990 chunk 77 optimal weight: 0.6980 chunk 24 optimal weight: 2.9990 chunk 54 optimal weight: 5.9990 chunk 55 optimal weight: 0.8980 overall best weight: 1.1140 ------------------------------------------------------------------------------- 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 = 0.4502 r_free = 0.4502 target = 0.216753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.175165 restraints weight = 57498.488| |-----------------------------------------------------------------------------| r_work (start): 0.4075 rms_B_bonded: 2.29 r_work: 0.3839 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3729 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7052 moved from start: 0.1848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 17406 Z= 0.177 Angle : 0.583 5.553 24374 Z= 0.344 Chirality : 0.042 0.158 2580 Planarity : 0.004 0.063 2308 Dihedral : 26.911 62.464 4094 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 0.54 % Allowed : 4.88 % Favored : 94.58 % 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: -0.30 (0.22), residues: 1428 helix: 1.08 (0.22), residues: 556 sheet: -1.85 (0.33), residues: 194 loop : -0.69 (0.25), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 125 HIS 0.005 0.001 HIS A 39 PHE 0.021 0.002 PHE C 157 TYR 0.013 0.001 TYR D 87 ARG 0.006 0.001 ARG A 102 Details of bonding type rmsd hydrogen bonds : bond 0.03806 ( 630) hydrogen bonds : angle 4.21999 ( 1676) covalent geometry : bond 0.00403 (17406) covalent geometry : angle 0.58279 (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 : 2.335 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: 0.7008 (OUTLIER) cc_final: 0.6630 (tm-30) REVERT: A 152 MET cc_start: 0.8107 (tpt) cc_final: 0.7320 (tpt) REVERT: A 219 LYS cc_start: 0.7010 (tptt) cc_final: 0.6785 (tptt) REVERT: B 69 GLU cc_start: 0.7004 (OUTLIER) cc_final: 0.6620 (tm-30) REVERT: B 152 MET cc_start: 0.8113 (tpt) cc_final: 0.7327 (tpt) REVERT: B 219 LYS cc_start: 0.7010 (tptt) cc_final: 0.6785 (tptt) REVERT: C 291 LEU cc_start: 0.8510 (tt) cc_final: 0.8252 (tp) REVERT: D 264 ASP cc_start: 0.7976 (t0) cc_final: 0.7732 (t0) REVERT: D 291 LEU cc_start: 0.8508 (tt) cc_final: 0.8252 (tp) REVERT: D 317 GLU cc_start: 0.7596 (mt-10) cc_final: 0.7395 (mt-10) outliers start: 7 outliers final: 4 residues processed: 144 average time/residue: 0.6057 time to fit residues: 132.3990 Evaluate side-chains 130 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 124 time to evaluate : 2.155 ------------------------------------------------------------------------------- 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 146 optimal weight: 10.0000 chunk 131 optimal weight: 4.9990 chunk 113 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 121 optimal weight: 2.9990 chunk 70 optimal weight: 10.0000 chunk 23 optimal weight: 1.9990 chunk 29 optimal weight: 5.9990 chunk 147 optimal weight: 10.0000 chunk 17 optimal weight: 0.6980 overall best weight: 2.3388 ------------------------------------------------------------------------------- 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 = 0.4429 r_free = 0.4429 target = 0.209160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.166351 restraints weight = 57784.502| |-----------------------------------------------------------------------------| r_work (start): 0.3974 rms_B_bonded: 2.49 r_work: 0.3705 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7145 moved from start: 0.2685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 17406 Z= 0.261 Angle : 0.647 5.154 24374 Z= 0.375 Chirality : 0.048 0.169 2580 Planarity : 0.005 0.080 2308 Dihedral : 26.791 73.565 4094 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 1.08 % Allowed : 6.50 % Favored : 92.41 % 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: -0.81 (0.22), residues: 1428 helix: 0.62 (0.21), residues: 556 sheet: -2.19 (0.32), residues: 192 loop : -0.93 (0.24), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 125 HIS 0.004 0.001 HIS B 242 PHE 0.019 0.002 PHE B 79 TYR 0.023 0.002 TYR B 238 ARG 0.006 0.001 ARG A 16 Details of bonding type rmsd hydrogen bonds : bond 0.04469 ( 630) hydrogen bonds : angle 4.58762 ( 1676) covalent geometry : bond 0.00592 (17406) covalent geometry : angle 0.64719 (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 147 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 133 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: A 69 GLU cc_start: 0.6958 (OUTLIER) cc_final: 0.6569 (tm-30) REVERT: A 96 ASP cc_start: 0.7630 (m-30) cc_final: 0.7414 (m-30) REVERT: A 152 MET cc_start: 0.8190 (tpt) cc_final: 0.7321 (tpt) REVERT: B 69 GLU cc_start: 0.6945 (OUTLIER) cc_final: 0.6557 (tm-30) REVERT: B 96 ASP cc_start: 0.7607 (m-30) cc_final: 0.7397 (m-30) REVERT: B 152 MET cc_start: 0.8193 (tpt) cc_final: 0.7326 (tpt) REVERT: C 160 SER cc_start: 0.8164 (t) cc_final: 0.7788 (m) REVERT: C 291 LEU cc_start: 0.8495 (tt) cc_final: 0.8208 (tp) REVERT: D 160 SER cc_start: 0.8205 (t) cc_final: 0.7816 (m) REVERT: D 291 LEU cc_start: 0.8496 (tt) cc_final: 0.8211 (tp) outliers start: 14 outliers final: 9 residues processed: 143 average time/residue: 0.6629 time to fit residues: 144.2179 Evaluate side-chains 136 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 125 time to evaluate : 2.002 ------------------------------------------------------------------------------- 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 189 MET Chi-restraints excluded: chain C residue 265 GLN Chi-restraints excluded: chain C residue 302 SER Chi-restraints excluded: chain D residue 189 MET 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 36 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 154 optimal weight: 2.9990 chunk 138 optimal weight: 3.9990 chunk 156 optimal weight: 10.0000 chunk 37 optimal weight: 0.9980 chunk 132 optimal weight: 0.8980 chunk 21 optimal weight: 5.9990 chunk 111 optimal weight: 3.9990 chunk 22 optimal weight: 0.6980 chunk 122 optimal weight: 1.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- 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 = 0.4427 r_free = 0.4427 target = 0.207953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.164251 restraints weight = 58174.211| |-----------------------------------------------------------------------------| r_work (start): 0.3969 rms_B_bonded: 2.57 r_work: 0.3710 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7061 moved from start: 0.2890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 17406 Z= 0.185 Angle : 0.573 4.641 24374 Z= 0.336 Chirality : 0.043 0.136 2580 Planarity : 0.005 0.073 2308 Dihedral : 26.665 71.636 4094 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 1.63 % Allowed : 7.28 % Favored : 91.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.70 (0.22), residues: 1428 helix: 0.88 (0.22), residues: 556 sheet: -2.33 (0.33), residues: 172 loop : -1.04 (0.23), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 125 HIS 0.004 0.001 HIS C 307 PHE 0.011 0.001 PHE B 216 TYR 0.014 0.001 TYR A 238 ARG 0.002 0.000 ARG B 261 Details of bonding type rmsd hydrogen bonds : bond 0.03560 ( 630) hydrogen bonds : angle 4.33447 ( 1676) covalent geometry : bond 0.00414 (17406) covalent geometry : angle 0.57273 (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 152 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 131 time to evaluate : 2.086 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 GLU cc_start: 0.6933 (OUTLIER) cc_final: 0.6571 (tm-30) REVERT: A 96 ASP cc_start: 0.7563 (m-30) cc_final: 0.7297 (m-30) REVERT: A 152 MET cc_start: 0.8126 (tpt) cc_final: 0.7289 (tpt) REVERT: B 69 GLU cc_start: 0.6943 (OUTLIER) cc_final: 0.6585 (tm-30) REVERT: B 96 ASP cc_start: 0.7565 (m-30) cc_final: 0.7297 (m-30) REVERT: B 152 MET cc_start: 0.8133 (tpt) cc_final: 0.7294 (tpt) REVERT: C 291 LEU cc_start: 0.8507 (tt) cc_final: 0.8201 (tp) REVERT: D 291 LEU cc_start: 0.8509 (tt) cc_final: 0.8202 (tp) outliers start: 21 outliers final: 14 residues processed: 144 average time/residue: 0.5992 time to fit residues: 131.2190 Evaluate side-chains 145 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 129 time to evaluate : 2.027 ------------------------------------------------------------------------------- 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 189 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 189 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: 2.9990 chunk 134 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 chunk 40 optimal weight: 0.9990 chunk 137 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 31 optimal weight: 6.9990 chunk 114 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 chunk 136 optimal weight: 1.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- 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 = 0.4437 r_free = 0.4437 target = 0.207840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.164797 restraints weight = 58624.484| |-----------------------------------------------------------------------------| r_work (start): 0.3982 rms_B_bonded: 2.56 r_work: 0.3714 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7084 moved from start: 0.3125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 17406 Z= 0.178 Angle : 0.566 5.276 24374 Z= 0.332 Chirality : 0.043 0.128 2580 Planarity : 0.005 0.066 2308 Dihedral : 26.538 74.086 4094 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 1.32 % Allowed : 7.59 % Favored : 91.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.62 (0.22), residues: 1428 helix: 0.99 (0.22), residues: 556 sheet: -2.30 (0.32), residues: 176 loop : -1.01 (0.24), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 125 HIS 0.003 0.001 HIS D 307 PHE 0.013 0.001 PHE B 216 TYR 0.015 0.001 TYR B 238 ARG 0.003 0.000 ARG B 261 Details of bonding type rmsd hydrogen bonds : bond 0.03484 ( 630) hydrogen bonds : angle 4.25540 ( 1676) covalent geometry : bond 0.00403 (17406) covalent geometry : angle 0.56626 (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 148 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 131 time to evaluate : 2.031 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 GLU cc_start: 0.6827 (OUTLIER) cc_final: 0.6519 (tm-30) REVERT: A 96 ASP cc_start: 0.7610 (m-30) cc_final: 0.7313 (m-30) REVERT: A 152 MET cc_start: 0.8122 (tpt) cc_final: 0.7296 (tpt) REVERT: B 69 GLU cc_start: 0.6831 (OUTLIER) cc_final: 0.6525 (tm-30) REVERT: B 96 ASP cc_start: 0.7608 (m-30) cc_final: 0.7312 (m-30) REVERT: B 152 MET cc_start: 0.8123 (tpt) cc_final: 0.7297 (tpt) REVERT: C 291 LEU cc_start: 0.8535 (tt) cc_final: 0.8187 (tp) REVERT: D 291 LEU cc_start: 0.8533 (tt) cc_final: 0.8185 (tp) outliers start: 17 outliers final: 11 residues processed: 143 average time/residue: 0.6352 time to fit residues: 138.6772 Evaluate side-chains 141 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 128 time to evaluate : 2.041 ------------------------------------------------------------------------------- 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 189 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 189 MET Chi-restraints excluded: chain D residue 302 SER Chi-restraints excluded: chain D residue 329 GLU 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: 2.9990 chunk 69 optimal weight: 10.0000 chunk 120 optimal weight: 2.9990 chunk 160 optimal weight: 3.9990 chunk 133 optimal weight: 0.7980 chunk 74 optimal weight: 7.9990 chunk 108 optimal weight: 6.9990 chunk 34 optimal weight: 9.9990 chunk 70 optimal weight: 0.9990 chunk 16 optimal weight: 7.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- 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 = 0.4401 r_free = 0.4401 target = 0.204353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.161351 restraints weight = 58684.610| |-----------------------------------------------------------------------------| r_work (start): 0.3939 rms_B_bonded: 2.57 r_work: 0.3665 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7163 moved from start: 0.3596 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= 0.228 Angle : 0.612 6.215 24374 Z= 0.355 Chirality : 0.046 0.143 2580 Planarity : 0.005 0.070 2308 Dihedral : 26.493 81.779 4094 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 1.47 % Allowed : 8.67 % Favored : 89.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.96 (0.22), residues: 1428 helix: 0.70 (0.22), residues: 562 sheet: -2.39 (0.33), residues: 176 loop : -1.25 (0.23), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 125 HIS 0.005 0.001 HIS B 242 PHE 0.017 0.002 PHE B 79 TYR 0.028 0.002 TYR D 87 ARG 0.004 0.000 ARG A 16 Details of bonding type rmsd hydrogen bonds : bond 0.03926 ( 630) hydrogen bonds : angle 4.50598 ( 1676) covalent geometry : bond 0.00512 (17406) covalent geometry : angle 0.61190 (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 161 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 142 time to evaluate : 1.754 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 152 MET cc_start: 0.8163 (tpt) cc_final: 0.7308 (tpt) REVERT: B 152 MET cc_start: 0.8174 (tpt) cc_final: 0.7317 (tpt) REVERT: C 291 LEU cc_start: 0.8619 (tt) cc_final: 0.8278 (tp) REVERT: D 291 LEU cc_start: 0.8617 (tt) cc_final: 0.8278 (tp) REVERT: D 297 ASP cc_start: 0.7521 (t0) cc_final: 0.7249 (p0) outliers start: 19 outliers final: 18 residues processed: 153 average time/residue: 0.7589 time to fit residues: 173.6642 Evaluate side-chains 157 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 139 time to evaluate : 2.171 ------------------------------------------------------------------------------- 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 189 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 189 MET Chi-restraints excluded: chain D residue 265 GLN Chi-restraints excluded: chain D residue 302 SER Chi-restraints excluded: chain D residue 329 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 83 optimal weight: 7.9990 chunk 59 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 102 optimal weight: 0.9980 chunk 104 optimal weight: 0.6980 chunk 139 optimal weight: 0.8980 chunk 65 optimal weight: 6.9990 chunk 148 optimal weight: 8.9990 chunk 126 optimal weight: 2.9990 chunk 153 optimal weight: 3.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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 = 0.4418 r_free = 0.4418 target = 0.206129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.163229 restraints weight = 58684.314| |-----------------------------------------------------------------------------| r_work (start): 0.3966 rms_B_bonded: 2.59 r_work: 0.3688 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7149 moved from start: 0.3735 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= 0.169 Angle : 0.565 5.200 24374 Z= 0.332 Chirality : 0.043 0.130 2580 Planarity : 0.005 0.061 2308 Dihedral : 26.340 81.418 4094 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 1.32 % Allowed : 9.98 % Favored : 88.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.81 (0.22), residues: 1428 helix: 0.90 (0.22), residues: 568 sheet: -2.34 (0.33), residues: 176 loop : -1.23 (0.23), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 125 HIS 0.004 0.001 HIS D 307 PHE 0.012 0.001 PHE A 216 TYR 0.022 0.001 TYR D 87 ARG 0.002 0.000 ARG B 261 Details of bonding type rmsd hydrogen bonds : bond 0.03369 ( 630) hydrogen bonds : angle 4.25890 ( 1676) covalent geometry : bond 0.00378 (17406) covalent geometry : angle 0.56513 (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 163 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 146 time to evaluate : 2.288 Fit side-chains revert: symmetry clash REVERT: A 69 GLU cc_start: 0.6832 (OUTLIER) cc_final: 0.6597 (tm-30) REVERT: A 152 MET cc_start: 0.8129 (tpt) cc_final: 0.7326 (tpt) REVERT: B 69 GLU cc_start: 0.6826 (OUTLIER) cc_final: 0.6578 (tm-30) REVERT: B 152 MET cc_start: 0.8134 (tpt) cc_final: 0.7337 (tpt) REVERT: C 212 SER cc_start: 0.7644 (m) cc_final: 0.7188 (p) REVERT: C 291 LEU cc_start: 0.8591 (tt) cc_final: 0.8240 (tp) REVERT: C 297 ASP cc_start: 0.7451 (t0) cc_final: 0.7214 (p0) REVERT: D 112 ARG cc_start: 0.6737 (mmt-90) cc_final: 0.6514 (tpm170) REVERT: D 291 LEU cc_start: 0.8581 (tt) cc_final: 0.8230 (tp) outliers start: 17 outliers final: 12 residues processed: 157 average time/residue: 0.6591 time to fit residues: 154.1229 Evaluate side-chains 154 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 140 time to evaluate : 2.292 ------------------------------------------------------------------------------- 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 189 MET Chi-restraints excluded: chain C residue 265 GLN Chi-restraints excluded: chain C residue 302 SER Chi-restraints excluded: chain D residue 189 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: 0.5980 chunk 36 optimal weight: 0.9990 chunk 129 optimal weight: 4.9990 chunk 5 optimal weight: 0.5980 chunk 28 optimal weight: 0.1980 chunk 58 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 24 optimal weight: 0.4980 chunk 29 optimal weight: 3.9990 chunk 160 optimal weight: 3.9990 chunk 85 optimal weight: 3.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.4441 r_free = 0.4441 target = 0.208409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.166045 restraints weight = 59006.104| |-----------------------------------------------------------------------------| r_work (start): 0.3998 rms_B_bonded: 2.61 r_work: 0.3718 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7106 moved from start: 0.3776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 17406 Z= 0.131 Angle : 0.544 5.469 24374 Z= 0.321 Chirality : 0.041 0.134 2580 Planarity : 0.004 0.063 2308 Dihedral : 26.203 80.541 4094 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 1.01 % Allowed : 10.45 % Favored : 88.54 % 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: -0.50 (0.22), residues: 1428 helix: 1.22 (0.22), residues: 566 sheet: -2.11 (0.33), residues: 176 loop : -1.15 (0.23), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 125 HIS 0.004 0.001 HIS B 39 PHE 0.008 0.001 PHE D 207 TYR 0.019 0.001 TYR D 87 ARG 0.002 0.000 ARG B 25 Details of bonding type rmsd hydrogen bonds : bond 0.03043 ( 630) hydrogen bonds : angle 4.06254 ( 1676) covalent geometry : bond 0.00294 (17406) covalent geometry : angle 0.54445 (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 150 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 137 time to evaluate : 2.779 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 MET cc_start: 0.8113 (tpt) cc_final: 0.7378 (tpt) REVERT: B 152 MET cc_start: 0.8112 (tpt) cc_final: 0.7376 (tpt) REVERT: C 212 SER cc_start: 0.7730 (m) cc_final: 0.7437 (p) REVERT: C 291 LEU cc_start: 0.8582 (tt) cc_final: 0.8211 (tp) REVERT: C 297 ASP cc_start: 0.7476 (t0) cc_final: 0.7218 (p0) REVERT: D 212 SER cc_start: 0.7506 (m) cc_final: 0.7217 (p) REVERT: D 291 LEU cc_start: 0.8569 (tt) cc_final: 0.8200 (tp) REVERT: D 297 ASP cc_start: 0.7492 (t0) cc_final: 0.7235 (p0) outliers start: 13 outliers final: 10 residues processed: 146 average time/residue: 0.7096 time to fit residues: 157.5769 Evaluate side-chains 147 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 137 time to evaluate : 2.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ASN Chi-restraints excluded: chain A residue 76 GLU Chi-restraints excluded: chain B residue 42 ASN 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 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: 1.9990 chunk 30 optimal weight: 6.9990 chunk 94 optimal weight: 3.9990 chunk 106 optimal weight: 10.0000 chunk 143 optimal weight: 3.9990 chunk 101 optimal weight: 0.8980 chunk 84 optimal weight: 1.9990 chunk 70 optimal weight: 10.0000 chunk 68 optimal weight: 10.0000 chunk 161 optimal weight: 2.9990 chunk 134 optimal weight: 3.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- 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 = 0.4394 r_free = 0.4394 target = 0.203680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.161938 restraints weight = 58855.916| |-----------------------------------------------------------------------------| r_work (start): 0.3959 rms_B_bonded: 2.42 r_work: 0.3646 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7229 moved from start: 0.3996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 17406 Z= 0.249 Angle : 0.616 5.585 24374 Z= 0.356 Chirality : 0.047 0.139 2580 Planarity : 0.005 0.066 2308 Dihedral : 26.231 85.535 4094 Min Nonbonded Distance : 1.791 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 1.01 % Allowed : 10.29 % Favored : 88.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.85 (0.22), residues: 1428 helix: 0.79 (0.22), residues: 566 sheet: -2.32 (0.33), residues: 176 loop : -1.20 (0.24), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 125 HIS 0.006 0.001 HIS A 242 PHE 0.018 0.002 PHE B 79 TYR 0.020 0.002 TYR B 238 ARG 0.004 0.001 ARG A 102 Details of bonding type rmsd hydrogen bonds : bond 0.04066 ( 630) hydrogen bonds : angle 4.43505 ( 1676) covalent geometry : bond 0.00562 (17406) covalent geometry : angle 0.61554 (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 153 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 140 time to evaluate : 2.089 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 MET cc_start: 0.8081 (tpt) cc_final: 0.7249 (tpt) REVERT: B 152 MET cc_start: 0.8084 (tpt) cc_final: 0.7251 (tpt) outliers start: 13 outliers final: 11 residues processed: 146 average time/residue: 0.6697 time to fit residues: 143.5941 Evaluate side-chains 149 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 138 time to evaluate : 2.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ASN Chi-restraints excluded: chain A residue 96 ASP Chi-restraints excluded: chain B residue 42 ASN 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 Chi-restraints excluded: chain D residue 329 GLU 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: 2.9990 chunk 104 optimal weight: 4.9990 chunk 3 optimal weight: 0.9980 chunk 67 optimal weight: 9.9990 chunk 16 optimal weight: 5.9990 chunk 87 optimal weight: 0.5980 chunk 117 optimal weight: 0.0060 chunk 99 optimal weight: 2.9990 chunk 54 optimal weight: 6.9990 chunk 35 optimal weight: 2.9990 overall best weight: 1.3200 ------------------------------------------------------------------------------- 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 = 0.4414 r_free = 0.4414 target = 0.205681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.162818 restraints weight = 58570.240| |-----------------------------------------------------------------------------| r_work (start): 0.3963 rms_B_bonded: 2.57 r_work: 0.3669 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7191 moved from start: 0.4040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 17406 Z= 0.172 Angle : 0.569 5.434 24374 Z= 0.333 Chirality : 0.043 0.126 2580 Planarity : 0.005 0.059 2308 Dihedral : 26.167 84.846 4094 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 0.93 % Allowed : 10.22 % Favored : 88.85 % 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: -0.72 (0.22), residues: 1428 helix: 1.04 (0.22), residues: 558 sheet: -2.27 (0.33), residues: 176 loop : -1.23 (0.23), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 125 HIS 0.003 0.001 HIS C 307 PHE 0.012 0.001 PHE B 79 TYR 0.015 0.001 TYR C 87 ARG 0.002 0.000 ARG B 261 Details of bonding type rmsd hydrogen bonds : bond 0.03433 ( 630) hydrogen bonds : angle 4.25812 ( 1676) covalent geometry : bond 0.00386 (17406) covalent geometry : angle 0.56895 (24374) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14483.21 seconds wall clock time: 248 minutes 9.82 seconds (14889.82 seconds total)