Starting phenix.real_space_refine on Thu Mar 21 19:28:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b4h_15848/03_2024/8b4h_15848.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b4h_15848/03_2024/8b4h_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b4h_15848/03_2024/8b4h_15848.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b4h_15848/03_2024/8b4h_15848.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b4h_15848/03_2024/8b4h_15848.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b4h_15848/03_2024/8b4h_15848.pdb" } 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 Residue "A ASP 30": "OD1" <-> "OD2" Residue "A ASP 70": "OD1" <-> "OD2" Residue "A TYR 214": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 216": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 253": "OE1" <-> "OE2" Residue "B ASP 30": "OD1" <-> "OD2" Residue "B ASP 70": "OD1" <-> "OD2" Residue "B TYR 214": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 216": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 253": "OE1" <-> "OE2" Residue "C TYR 213": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 264": "OD1" <-> "OD2" Residue "C TYR 300": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 213": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 264": "OD1" <-> "OD2" Residue "D TYR 300": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 13.84, 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 - 3.50 Amino acid : False - 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: 25.84 Conformation dependent library (CDL) restraints added in 2.4 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: 13.79 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: 11.97 Time building geometry restraints manager: 26.64 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: 98.66 - 105.74: 1495 105.74 - 112.82: 35298 112.82 - 119.90: 9009 119.90 - 126.98: 11387 126.98 - 134.06: 669 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 1.850 nonbonded pdb=" H GLY A 90 " pdb=" OP2 DC H 45 " model vdw 1.502 1.850 nonbonded pdb="HH22 ARG C 52 " pdb=" O2 DT E 44 " model vdw 1.514 1.850 nonbonded pdb="HH22 ARG D 52 " pdb=" O2 DT G 44 " model vdw 1.515 1.850 nonbonded pdb=" HZ2 LYS D 32 " pdb=" O6 DG H 8 " model vdw 1.553 1.850 ... (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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 222 or resid 234 through 358)) selection = (chain 'B' and (resid 1 through 222 or resid 234 through 358)) selection = (chain 'C' and (resid 1 through 300 or (resid 301 and (name N or name CA or name \ C or name O or name CB or name CG or name CD1 or name CD2 or name HA or name HB \ 2 or name HB3 or name HG or name HD11 or name HD12 or name HD13 or name HD21 or \ name HD22 or name HD23)) or resid 302 through 334 or (resid 335 and (name N or n \ ame CA or name C or name O or name CB or name CG or name CD or name NE or name C \ Z or name NH1 or name NH2 or name H or name HA or name HB2 or name HB3 or name H \ G2 or name HG3 or name HD2 or name HD3 or name HE or name HH11 or name HH12)) or \ resid 336 through 358)) selection = (chain 'D' and (resid 1 through 300 or (resid 301 and (name N or name CA or name \ C or name O or name CB or name CG or name CD1 or name CD2 or name HA or name HB \ 2 or name HB3 or name HG or name HD11 or name HD12 or name HD13 or name HD21 or \ name HD22 or name HD23)) or resid 302 through 334 or (resid 335 and (name N or n \ ame CA or name C or name O or name CB or name CG or name CD or name NE or name C \ Z or name NH1 or name NH2 or name H or name HA or name HB2 or name HB3 or name H \ G2 or name HG3 or name HD2 or name HD3 or name HE or name HH11 or name HH12)) or \ resid 336 through 358)) } ncs_group { reference = chain 'E' selection = chain 'G' } ncs_group { reference = chain 'F' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.380 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: 0.380 Extract box with map and model: 6.870 Check model and map are aligned: 0.430 Set scattering table: 0.260 Process input model: 103.500 Find NCS groups from input model: 1.280 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 116.780 ------------------------------------------------------------------------------- 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= 0.222 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 *********************** 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 fitting. rotamer outliers: 0 poor density : 167 time to evaluate : 1.963 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: 0.5914 time to fit residues: 147.1245 Evaluate side-chains 146 residues out of total 1292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 146 time to evaluate : 2.055 ------------------------------------------------------------------------------- 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: 1.9990 chunk 68 optimal weight: 8.9990 chunk 41 optimal weight: 0.8980 chunk 82 optimal weight: 0.5980 chunk 65 optimal weight: 9.9990 chunk 126 optimal weight: 0.9980 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: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6577 moved from start: 0.1291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 17406 Z= 0.295 Angle : 0.643 5.863 24374 Z= 0.378 Chirality : 0.044 0.156 2580 Planarity : 0.004 0.035 2308 Dihedral : 26.808 71.363 4094 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 13.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 0.46 % Allowed : 2.71 % Favored : 96.83 % 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: 0.97 (0.22), residues: 552 sheet: -2.10 (0.32), residues: 194 loop : -0.77 (0.24), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 125 HIS 0.004 0.001 HIS D 165 PHE 0.017 0.002 PHE B 216 TYR 0.010 0.001 TYR D 213 ARG 0.004 0.000 ARG B 234 *********************** 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 159 residues out of total 1292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 153 time to evaluate : 1.990 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: 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 317 GLU cc_start: 0.7017 (mt-10) cc_final: 0.6797 (mt-10) outliers start: 6 outliers final: 6 residues processed: 159 average time/residue: 0.5905 time to fit residues: 142.7422 Evaluate side-chains 144 residues out of total 1292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 138 time to evaluate : 1.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ASN Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 69 GLU Chi-restraints excluded: chain B residue 42 ASN Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 69 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 81 optimal weight: 0.6980 chunk 45 optimal weight: 0.9990 chunk 122 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 147 optimal weight: 20.0000 chunk 159 optimal weight: 3.9990 chunk 131 optimal weight: 0.8980 chunk 146 optimal weight: 10.0000 chunk 50 optimal weight: 2.9990 chunk 118 optimal weight: 0.3980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 227 GLN B 227 GLN C 265 GLN D 265 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6591 moved from start: 0.1664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 17406 Z= 0.222 Angle : 0.562 4.865 24374 Z= 0.333 Chirality : 0.041 0.135 2580 Planarity : 0.003 0.033 2308 Dihedral : 26.929 62.536 4094 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 0.62 % Allowed : 4.57 % Favored : 94.81 % 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: -0.23 (0.22), residues: 1428 helix: 1.28 (0.22), residues: 560 sheet: -1.96 (0.32), residues: 194 loop : -0.76 (0.25), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 125 HIS 0.002 0.001 HIS C 307 PHE 0.010 0.001 PHE A 216 TYR 0.008 0.001 TYR D 214 ARG 0.005 0.000 ARG B 234 *********************** 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 147 residues out of total 1292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 139 time to evaluate : 2.068 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 GLU cc_start: 0.6545 (OUTLIER) cc_final: 0.6331 (tm-30) REVERT: A 219 LYS cc_start: 0.6839 (tptt) cc_final: 0.6636 (tptt) REVERT: B 69 GLU cc_start: 0.6546 (OUTLIER) cc_final: 0.6329 (tm-30) REVERT: B 219 LYS cc_start: 0.6834 (tptt) cc_final: 0.6634 (tptt) REVERT: C 291 LEU cc_start: 0.8337 (tt) cc_final: 0.8070 (tp) REVERT: C 317 GLU cc_start: 0.7034 (mt-10) cc_final: 0.6824 (mt-10) REVERT: D 291 LEU cc_start: 0.8307 (tt) cc_final: 0.8043 (tp) REVERT: D 317 GLU cc_start: 0.7017 (mt-10) cc_final: 0.6812 (mt-10) outliers start: 8 outliers final: 4 residues processed: 145 average time/residue: 0.5804 time to fit residues: 127.0166 Evaluate side-chains 136 residues out of total 1292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 130 time to evaluate : 2.058 ------------------------------------------------------------------------------- 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 145 optimal weight: 3.9990 chunk 110 optimal weight: 0.0770 chunk 76 optimal weight: 3.9990 chunk 16 optimal weight: 6.9990 chunk 70 optimal weight: 20.0000 chunk 98 optimal weight: 1.9990 chunk 147 optimal weight: 10.0000 chunk 156 optimal weight: 9.9990 chunk 77 optimal weight: 0.9990 chunk 140 optimal weight: 7.9990 chunk 42 optimal weight: 1.9990 overall best weight: 1.8146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6735 moved from start: 0.2448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 17406 Z= 0.300 Angle : 0.603 7.313 24374 Z= 0.353 Chirality : 0.045 0.159 2580 Planarity : 0.005 0.034 2308 Dihedral : 26.733 71.087 4094 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 0.85 % Allowed : 6.11 % Favored : 93.03 % 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: 0.91 (0.22), residues: 552 sheet: -2.12 (0.32), residues: 192 loop : -0.93 (0.24), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 125 HIS 0.004 0.001 HIS D 165 PHE 0.017 0.002 PHE D 207 TYR 0.016 0.001 TYR A 238 ARG 0.004 0.001 ARG B 234 *********************** 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 153 residues out of total 1292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 142 time to evaluate : 2.092 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 ASP cc_start: 0.7228 (m-30) cc_final: 0.6835 (m-30) REVERT: B 96 ASP cc_start: 0.7227 (m-30) cc_final: 0.6835 (m-30) REVERT: C 160 SER cc_start: 0.8031 (t) cc_final: 0.7781 (m) REVERT: C 291 LEU cc_start: 0.8296 (tt) cc_final: 0.8021 (tp) REVERT: D 160 SER cc_start: 0.8109 (t) cc_final: 0.7865 (m) REVERT: D 291 LEU cc_start: 0.8302 (tt) cc_final: 0.8032 (tp) outliers start: 11 outliers final: 10 residues processed: 151 average time/residue: 0.6214 time to fit residues: 143.2227 Evaluate side-chains 143 residues out of total 1292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 133 time to evaluate : 2.089 ------------------------------------------------------------------------------- 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 299 SER Chi-restraints excluded: chain D residue 265 GLN Chi-restraints excluded: chain D residue 299 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 130 optimal weight: 3.9990 chunk 88 optimal weight: 2.9990 chunk 2 optimal weight: 0.8980 chunk 116 optimal weight: 1.9990 chunk 64 optimal weight: 5.9990 chunk 133 optimal weight: 0.9980 chunk 108 optimal weight: 8.9990 chunk 0 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 140 optimal weight: 5.9990 chunk 39 optimal weight: 2.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6732 moved from start: 0.2797 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= 0.242 Angle : 0.560 4.590 24374 Z= 0.330 Chirality : 0.043 0.132 2580 Planarity : 0.004 0.034 2308 Dihedral : 26.585 69.165 4094 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 1.39 % Allowed : 6.81 % Favored : 91.80 % 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: -0.61 (0.22), residues: 1428 helix: 1.03 (0.22), residues: 552 sheet: -2.24 (0.34), residues: 172 loop : -1.06 (0.23), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 125 HIS 0.004 0.001 HIS C 307 PHE 0.011 0.001 PHE C 207 TYR 0.014 0.001 TYR A 238 ARG 0.003 0.000 ARG B 102 *********************** 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 159 residues out of total 1292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 141 time to evaluate : 2.099 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 160 SER cc_start: 0.8061 (t) cc_final: 0.7827 (m) REVERT: C 291 LEU cc_start: 0.8352 (tt) cc_final: 0.8041 (tp) REVERT: D 291 LEU cc_start: 0.8354 (tt) cc_final: 0.8045 (tp) REVERT: D 317 GLU cc_start: 0.6941 (mt-10) cc_final: 0.6729 (mt-10) outliers start: 18 outliers final: 14 residues processed: 153 average time/residue: 0.5700 time to fit residues: 133.0079 Evaluate side-chains 150 residues out of total 1292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 136 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 A residue 69 GLU Chi-restraints excluded: chain A residue 76 GLU Chi-restraints excluded: chain B residue 42 ASN Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 76 GLU Chi-restraints excluded: chain C residue 9 MET Chi-restraints excluded: chain C residue 265 GLN Chi-restraints excluded: chain C residue 302 SER Chi-restraints excluded: chain 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 52 optimal weight: 0.5980 chunk 141 optimal weight: 1.9990 chunk 30 optimal weight: 20.0000 chunk 91 optimal weight: 0.6980 chunk 38 optimal weight: 0.9980 chunk 156 optimal weight: 10.0000 chunk 130 optimal weight: 3.9990 chunk 72 optimal weight: 5.9990 chunk 13 optimal weight: 3.9990 chunk 51 optimal weight: 0.9980 chunk 82 optimal weight: 1.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6721 moved from start: 0.3013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 17406 Z= 0.202 Angle : 0.544 5.126 24374 Z= 0.321 Chirality : 0.042 0.128 2580 Planarity : 0.004 0.036 2308 Dihedral : 26.384 73.046 4094 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 1.16 % Allowed : 7.43 % 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: -0.45 (0.22), residues: 1428 helix: 1.17 (0.22), residues: 554 sheet: -2.21 (0.33), residues: 176 loop : -0.94 (0.24), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 125 HIS 0.002 0.000 HIS C 307 PHE 0.011 0.001 PHE C 207 TYR 0.014 0.001 TYR A 214 ARG 0.002 0.000 ARG A 234 *********************** 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 156 residues out of total 1292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 141 time to evaluate : 2.136 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 67 MET cc_start: 0.7642 (mtt) cc_final: 0.7393 (mtt) REVERT: A 96 ASP cc_start: 0.7200 (m-30) cc_final: 0.6745 (m-30) REVERT: B 96 ASP cc_start: 0.7198 (m-30) cc_final: 0.6751 (m-30) REVERT: C 212 SER cc_start: 0.7476 (m) cc_final: 0.7131 (p) REVERT: C 291 LEU cc_start: 0.8343 (tt) cc_final: 0.8016 (tp) REVERT: D 212 SER cc_start: 0.7487 (m) cc_final: 0.7138 (p) REVERT: D 291 LEU cc_start: 0.8321 (tt) cc_final: 0.7981 (tp) REVERT: D 317 GLU cc_start: 0.6932 (mt-10) cc_final: 0.6714 (mt-10) outliers start: 15 outliers final: 12 residues processed: 152 average time/residue: 0.5730 time to fit residues: 132.6677 Evaluate side-chains 149 residues out of total 1292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 137 time to evaluate : 2.250 ------------------------------------------------------------------------------- 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 299 SER Chi-restraints excluded: chain C residue 302 SER Chi-restraints excluded: chain C residue 329 GLU 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 151 optimal weight: 2.9990 chunk 17 optimal weight: 0.5980 chunk 89 optimal weight: 3.9990 chunk 114 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 chunk 131 optimal weight: 2.9990 chunk 87 optimal weight: 0.9990 chunk 156 optimal weight: 10.0000 chunk 97 optimal weight: 0.9990 chunk 95 optimal weight: 4.9990 chunk 72 optimal weight: 9.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6756 moved from start: 0.3197 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= 0.241 Angle : 0.553 4.334 24374 Z= 0.326 Chirality : 0.043 0.131 2580 Planarity : 0.004 0.034 2308 Dihedral : 26.364 73.989 4094 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 1.47 % Allowed : 7.59 % 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: -0.53 (0.22), residues: 1428 helix: 1.13 (0.22), residues: 552 sheet: -2.27 (0.33), residues: 176 loop : -1.00 (0.24), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 125 HIS 0.003 0.001 HIS C 307 PHE 0.013 0.001 PHE B 79 TYR 0.013 0.001 TYR B 238 ARG 0.002 0.000 ARG B 234 *********************** 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 159 residues out of total 1292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 140 time to evaluate : 2.095 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: A 96 ASP cc_start: 0.7229 (m-30) cc_final: 0.6797 (m-30) REVERT: B 96 ASP cc_start: 0.7228 (m-30) cc_final: 0.6798 (m-30) REVERT: C 212 SER cc_start: 0.7462 (m) cc_final: 0.7111 (p) REVERT: C 291 LEU cc_start: 0.8355 (tt) cc_final: 0.8008 (tp) REVERT: C 299 SER cc_start: 0.7918 (OUTLIER) cc_final: 0.7525 (t) REVERT: D 212 SER cc_start: 0.7467 (m) cc_final: 0.7116 (p) REVERT: D 291 LEU cc_start: 0.8357 (tt) cc_final: 0.8015 (tp) REVERT: D 317 GLU cc_start: 0.6958 (mt-10) cc_final: 0.6739 (mt-10) outliers start: 19 outliers final: 14 residues processed: 153 average time/residue: 0.5826 time to fit residues: 136.8892 Evaluate side-chains 153 residues out of total 1292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 138 time to evaluate : 2.089 ------------------------------------------------------------------------------- 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 115 THR 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 115 THR Chi-restraints excluded: chain C residue 265 GLN Chi-restraints excluded: chain C residue 299 SER Chi-restraints excluded: chain C residue 302 SER Chi-restraints excluded: chain C residue 329 GLU 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 96 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 93 optimal weight: 6.9990 chunk 47 optimal weight: 2.9990 chunk 30 optimal weight: 20.0000 chunk 99 optimal weight: 0.8980 chunk 106 optimal weight: 20.0000 chunk 77 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 chunk 142 optimal weight: 2.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6823 moved from start: 0.3548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 17406 Z= 0.317 Angle : 0.596 5.350 24374 Z= 0.348 Chirality : 0.046 0.138 2580 Planarity : 0.005 0.037 2308 Dihedral : 26.346 79.309 4094 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 1.16 % Allowed : 8.51 % Favored : 90.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.78 (0.22), residues: 1428 helix: 0.86 (0.22), residues: 550 sheet: -2.33 (0.33), residues: 176 loop : -1.11 (0.24), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 125 HIS 0.004 0.001 HIS C 307 PHE 0.017 0.002 PHE B 79 TYR 0.021 0.002 TYR A 238 ARG 0.004 0.001 ARG B 234 *********************** 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 159 residues out of total 1292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 144 time to evaluate : 2.122 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 ASP cc_start: 0.7287 (m-30) cc_final: 0.6926 (m-30) REVERT: B 96 ASP cc_start: 0.7284 (m-30) cc_final: 0.6924 (m-30) REVERT: C 291 LEU cc_start: 0.8423 (tt) cc_final: 0.8081 (tp) REVERT: C 299 SER cc_start: 0.7960 (OUTLIER) cc_final: 0.7567 (t) REVERT: D 291 LEU cc_start: 0.8425 (tt) cc_final: 0.8087 (tp) REVERT: D 317 GLU cc_start: 0.6946 (mt-10) cc_final: 0.6728 (mt-10) outliers start: 15 outliers final: 14 residues processed: 155 average time/residue: 0.6433 time to fit residues: 145.2509 Evaluate side-chains 155 residues out of total 1292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 140 time to evaluate : 2.138 ------------------------------------------------------------------------------- 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 115 THR 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 115 THR Chi-restraints excluded: chain C residue 265 GLN Chi-restraints excluded: chain C residue 299 SER Chi-restraints excluded: chain C residue 302 SER Chi-restraints excluded: chain C residue 329 GLU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 149 optimal weight: 4.9990 chunk 136 optimal weight: 0.9990 chunk 145 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 chunk 114 optimal weight: 1.9990 chunk 44 optimal weight: 0.5980 chunk 131 optimal weight: 3.9990 chunk 137 optimal weight: 0.6980 chunk 144 optimal weight: 2.9990 chunk 95 optimal weight: 3.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6777 moved from start: 0.3647 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= 0.211 Angle : 0.552 5.162 24374 Z= 0.325 Chirality : 0.042 0.134 2580 Planarity : 0.004 0.038 2308 Dihedral : 26.213 78.747 4094 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 1.08 % Allowed : 9.06 % 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: -0.69 (0.22), residues: 1428 helix: 1.02 (0.22), residues: 564 sheet: -2.25 (0.33), residues: 176 loop : -1.20 (0.23), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 308 HIS 0.003 0.001 HIS C 307 PHE 0.011 0.001 PHE D 207 TYR 0.015 0.001 TYR A 238 ARG 0.002 0.000 ARG B 261 *********************** 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 157 residues out of total 1292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 143 time to evaluate : 2.056 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 ASP cc_start: 0.7167 (m-30) cc_final: 0.6774 (m-30) REVERT: B 96 ASP cc_start: 0.7165 (m-30) cc_final: 0.6777 (m-30) REVERT: C 212 SER cc_start: 0.7429 (m) cc_final: 0.7053 (p) REVERT: C 291 LEU cc_start: 0.8416 (tt) cc_final: 0.8071 (tp) REVERT: C 299 SER cc_start: 0.7955 (OUTLIER) cc_final: 0.7550 (t) REVERT: D 212 SER cc_start: 0.7429 (m) cc_final: 0.7044 (p) REVERT: D 291 LEU cc_start: 0.8418 (tt) cc_final: 0.8079 (tp) REVERT: D 317 GLU cc_start: 0.6926 (mt-10) cc_final: 0.6719 (mt-10) outliers start: 14 outliers final: 13 residues processed: 153 average time/residue: 0.6389 time to fit residues: 146.1175 Evaluate side-chains 156 residues out of total 1292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 142 time to evaluate : 2.082 ------------------------------------------------------------------------------- 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 115 THR 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 115 THR Chi-restraints excluded: chain C residue 265 GLN Chi-restraints excluded: chain C residue 299 SER Chi-restraints excluded: chain C residue 302 SER Chi-restraints excluded: chain C residue 329 GLU 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 153 optimal weight: 3.9990 chunk 93 optimal weight: 7.9990 chunk 72 optimal weight: 10.0000 chunk 106 optimal weight: 20.0000 chunk 161 optimal weight: 2.9990 chunk 148 optimal weight: 8.9990 chunk 128 optimal weight: 0.9980 chunk 13 optimal weight: 5.9990 chunk 99 optimal weight: 3.9990 chunk 78 optimal weight: 1.9990 chunk 102 optimal weight: 0.9980 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6852 moved from start: 0.3947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 17406 Z= 0.323 Angle : 0.610 5.517 24374 Z= 0.356 Chirality : 0.046 0.158 2580 Planarity : 0.005 0.038 2308 Dihedral : 26.220 83.817 4094 Min Nonbonded Distance : 1.817 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.35 % Favored : 92.65 % Rotamer: Outliers : 1.16 % Allowed : 9.29 % Favored : 89.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.90 (0.22), residues: 1428 helix: 0.74 (0.22), residues: 550 sheet: -2.32 (0.34), residues: 176 loop : -1.18 (0.24), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 125 HIS 0.007 0.001 HIS A 242 PHE 0.018 0.002 PHE D 207 TYR 0.024 0.002 TYR B 238 ARG 0.004 0.000 ARG A 234 ********************** 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 fitting. rotamer outliers: 15 poor density : 142 time to evaluate : 2.097 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: symmetry clash REVERT: A 96 ASP cc_start: 0.7281 (m-30) cc_final: 0.6920 (m-30) REVERT: B 96 ASP cc_start: 0.7281 (m-30) cc_final: 0.6923 (m-30) REVERT: C 299 SER cc_start: 0.8100 (OUTLIER) cc_final: 0.7709 (t) REVERT: D 317 GLU cc_start: 0.6974 (mt-10) cc_final: 0.6755 (mt-10) outliers start: 15 outliers final: 14 residues processed: 153 average time/residue: 0.6317 time to fit residues: 141.3644 Evaluate side-chains 154 residues out of total 1292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 139 time to evaluate : 2.130 ------------------------------------------------------------------------------- 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 115 THR 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 115 THR Chi-restraints excluded: chain C residue 265 GLN Chi-restraints excluded: chain C residue 299 SER Chi-restraints excluded: chain C residue 302 SER Chi-restraints excluded: chain C residue 329 GLU 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 136 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 118 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 128 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 132 optimal weight: 2.9990 chunk 16 optimal weight: 6.9990 chunk 23 optimal weight: 0.9980 chunk 113 optimal weight: 1.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- 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 = 0.4407 r_free = 0.4407 target = 0.205010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.162857 restraints weight = 57917.312| |-----------------------------------------------------------------------------| r_work (start): 0.3955 rms_B_bonded: 2.45 r_work: 0.3679 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7162 moved from start: 0.3997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 17406 Z= 0.248 Angle : 0.570 5.813 24374 Z= 0.335 Chirality : 0.043 0.132 2580 Planarity : 0.004 0.039 2308 Dihedral : 26.138 84.114 4094 Min Nonbonded Distance : 1.831 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 1.08 % Allowed : 9.75 % Favored : 89.16 % 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: -0.76 (0.22), residues: 1428 helix: 0.93 (0.22), residues: 550 sheet: -2.29 (0.34), residues: 176 loop : -1.15 (0.24), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 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 0.002 0.000 ARG C 102 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6455.64 seconds wall clock time: 114 minutes 36.89 seconds (6876.89 seconds total)