Starting phenix.real_space_refine on Thu Feb 22 09:05:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wub_21909/02_2024/6wub_21909.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wub_21909/02_2024/6wub_21909.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wub_21909/02_2024/6wub_21909.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wub_21909/02_2024/6wub_21909.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wub_21909/02_2024/6wub_21909.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wub_21909/02_2024/6wub_21909.pdb" } resolution = 3.2 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= -0.001 sd= 0.005 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: 5 Type Number sf(0) Gaussians P 1121 5.49 5 S 26 5.16 5 C 16918 2.51 5 N 6288 2.21 5 O 9596 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "d GLU 25": "OE1" <-> "OE2" Residue "d ASP 169": "OD1" <-> "OD2" Residue "d GLU 182": "OE1" <-> "OE2" Residue "f GLU 8": "OE1" <-> "OE2" Residue "h GLU 23": "OE1" <-> "OE2" Residue "k GLU 94": "OE1" <-> "OE2" Residue "l ASP 122": "OD1" <-> "OD2" Residue "o ARG 89": "NH1" <-> "NH2" Residue "p PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p GLU 53": "OE1" <-> "OE2" Residue "q GLU 4": "OE1" <-> "OE2" Residue "q GLU 66": "OE1" <-> "OE2" Residue "r TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 33949 Number of models: 1 Model: "" Number of chains: 12 Chain: "a" Number of atoms: 24077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1121, 24077 Classifications: {'RNA': 1121} Modifications used: {'rna2p_pur': 85, 'rna2p_pyr': 50, 'rna3p_pur': 562, 'rna3p_pyr': 424} Link IDs: {'rna2p': 135, 'rna3p': 985} Chain breaks: 3 Chain: "d" Number of atoms: 1620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1620 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 8, 'TRANS': 192} Chain: "e" Number of atoms: 1204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1204 Classifications: {'peptide': 163} Link IDs: {'PTRANS': 7, 'TRANS': 155} Chain: "f" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 795 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 2, 'TRANS': 94} Chain: "h" Number of atoms: 1041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1041 Classifications: {'peptide': 131} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 4, 'TRANS': 125} Chain: "k" Number of atoms: 863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 863 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 110} Chain: "l" Number of atoms: 1065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1065 Classifications: {'peptide': 136} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 127} Chain: "o" Number of atoms: 741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 741 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 86} Chain: "p" Number of atoms: 708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 708 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 5, 'TRANS': 83} Chain: "q" Number of atoms: 681 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 681 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 2, 'TRANS': 80} Chain: "r" Number of atoms: 537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 537 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 2, 'TRANS': 63} Chain: "t" Number of atoms: 617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 617 Classifications: {'peptide': 82} Link IDs: {'TRANS': 81} Time building chain proxies: 18.92, per 1000 atoms: 0.56 Number of scatterers: 33949 At special positions: 0 Unit cell: (161.259, 189.781, 173.326, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 26 16.00 P 1121 15.00 O 9596 8.00 N 6288 7.00 C 16918 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 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: 15.38 Conformation dependent library (CDL) restraints added in 2.4 seconds 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2322 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 12 sheets defined 36.5% alpha, 21.3% beta 375 base pairs and 632 stacking pairs defined. Time for finding SS restraints: 17.16 Creating SS restraints... Processing helix chain 'd' and resid 9 through 16 Processing helix chain 'd' and resid 45 through 61 removed outlier: 3.510A pdb=" N MET d 49 " --> pdb=" O SER d 45 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N GLN d 50 " --> pdb=" O GLU d 46 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N TYR d 61 " --> pdb=" O LEU d 57 " (cutoff:3.500A) Processing helix chain 'd' and resid 64 through 76 Processing helix chain 'd' and resid 83 through 91 removed outlier: 3.589A pdb=" N PHE d 87 " --> pdb=" O HIS d 83 " (cutoff:3.500A) Processing helix chain 'd' and resid 94 through 103 Processing helix chain 'd' and resid 107 through 117 removed outlier: 3.806A pdb=" N ALA d 111 " --> pdb=" O THR d 107 " (cutoff:3.500A) Processing helix chain 'd' and resid 149 through 158 removed outlier: 3.586A pdb=" N GLU d 157 " --> pdb=" O LYS d 153 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA d 158 " --> pdb=" O GLU d 154 " (cutoff:3.500A) Processing helix chain 'd' and resid 182 through 186 Processing helix chain 'd' and resid 193 through 199 removed outlier: 3.540A pdb=" N TYR d 199 " --> pdb=" O VAL d 195 " (cutoff:3.500A) Processing helix chain 'e' and resid 55 through 69 removed outlier: 3.838A pdb=" N LYS e 69 " --> pdb=" O GLU e 65 " (cutoff:3.500A) Processing helix chain 'e' and resid 108 through 117 removed outlier: 3.643A pdb=" N ALA e 113 " --> pdb=" O GLY e 109 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL e 114 " --> pdb=" O PRO e 110 " (cutoff:3.500A) Processing helix chain 'e' and resid 132 through 145 Processing helix chain 'e' and resid 149 through 157 removed outlier: 3.666A pdb=" N VAL e 153 " --> pdb=" O ARG e 149 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA e 154 " --> pdb=" O ALA e 150 " (cutoff:3.500A) Processing helix chain 'f' and resid 20 through 35 Processing helix chain 'f' and resid 76 through 85 removed outlier: 3.738A pdb=" N ASP f 81 " --> pdb=" O ILE f 77 " (cutoff:3.500A) Processing helix chain 'h' and resid 5 through 20 Processing helix chain 'h' and resid 30 through 43 Processing helix chain 'h' and resid 115 through 122 Processing helix chain 'k' and resid 48 through 51 Processing helix chain 'k' and resid 53 through 58 Processing helix chain 'k' and resid 59 through 75 removed outlier: 3.747A pdb=" N ALA k 63 " --> pdb=" O THR k 59 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N VAL k 73 " --> pdb=" O ALA k 69 " (cutoff:3.500A) Processing helix chain 'k' and resid 92 through 102 removed outlier: 3.667A pdb=" N ILE k 97 " --> pdb=" O ARG k 93 " (cutoff:3.500A) Processing helix chain 'l' and resid 3 through 10 Processing helix chain 'l' and resid 21 through 25 Processing helix chain 'o' and resid 4 through 13 removed outlier: 3.901A pdb=" N ASN o 9 " --> pdb=" O GLN o 5 " (cutoff:3.500A) Processing helix chain 'o' and resid 24 through 46 removed outlier: 3.938A pdb=" N GLN o 28 " --> pdb=" O SER o 24 " (cutoff:3.500A) Processing helix chain 'o' and resid 49 through 74 removed outlier: 3.667A pdb=" N ARG o 54 " --> pdb=" O HIS o 50 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N GLY o 55 " --> pdb=" O HIS o 51 " (cutoff:3.500A) Processing helix chain 'o' and resid 74 through 86 removed outlier: 3.713A pdb=" N GLY o 86 " --> pdb=" O ILE o 82 " (cutoff:3.500A) Processing helix chain 'p' and resid 55 through 61 removed outlier: 3.551A pdb=" N SER p 61 " --> pdb=" O LEU p 57 " (cutoff:3.500A) Processing helix chain 'p' and resid 67 through 76 Processing helix chain 'p' and resid 78 through 88 removed outlier: 3.937A pdb=" N LYS p 82 " --> pdb=" O GLY p 78 " (cutoff:3.500A) Processing helix chain 'r' and resid 15 through 20 removed outlier: 3.722A pdb=" N ASN r 20 " --> pdb=" O TYR r 16 " (cutoff:3.500A) Processing helix chain 'r' and resid 29 through 34 Processing helix chain 'r' and resid 45 through 50 removed outlier: 3.643A pdb=" N THR r 49 " --> pdb=" O PRO r 45 " (cutoff:3.500A) Processing helix chain 'r' and resid 52 through 69 removed outlier: 3.565A pdb=" N ARG r 57 " --> pdb=" O ALA r 53 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE r 68 " --> pdb=" O LYS r 64 " (cutoff:3.500A) Processing helix chain 't' and resid 4 through 40 removed outlier: 3.524A pdb=" N ILE t 8 " --> pdb=" O ILE t 4 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LYS t 9 " --> pdb=" O GLU t 5 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ARG t 10 " --> pdb=" O SER t 6 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL t 11 " --> pdb=" O ALA t 7 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ARG t 12 " --> pdb=" O ILE t 8 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA t 38 " --> pdb=" O LYS t 34 " (cutoff:3.500A) Processing helix chain 't' and resid 46 through 63 removed outlier: 3.648A pdb=" N TYR t 50 " --> pdb=" O VAL t 46 " (cutoff:3.500A) Processing helix chain 't' and resid 68 through 80 Processing sheet with id=AA1, first strand: chain 'd' and resid 125 through 126 Processing sheet with id=AA2, first strand: chain 'd' and resid 166 through 169 Processing sheet with id=AA3, first strand: chain 'e' and resid 14 through 24 removed outlier: 5.688A pdb=" N VAL e 15 " --> pdb=" O VAL e 38 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N VAL e 38 " --> pdb=" O VAL e 15 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ALA e 17 " --> pdb=" O LEU e 36 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'e' and resid 85 through 88 Processing sheet with id=AA5, first strand: chain 'f' and resid 39 through 50 removed outlier: 6.062A pdb=" N ASN f 67 " --> pdb=" O ILE f 41 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N SER f 43 " --> pdb=" O ILE f 65 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N ILE f 65 " --> pdb=" O SER f 43 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N ASP f 45 " --> pdb=" O TYR f 63 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N TYR f 63 " --> pdb=" O ASP f 45 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N GLU f 47 " --> pdb=" O GLY f 61 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N GLY f 61 " --> pdb=" O GLU f 47 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL f 68 " --> pdb=" O TYR f 7 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N MET f 10 " --> pdb=" O HIS f 93 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N HIS f 93 " --> pdb=" O MET f 10 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ILE f 12 " --> pdb=" O ILE f 91 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'f' and resid 39 through 50 removed outlier: 6.062A pdb=" N ASN f 67 " --> pdb=" O ILE f 41 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N SER f 43 " --> pdb=" O ILE f 65 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N ILE f 65 " --> pdb=" O SER f 43 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N ASP f 45 " --> pdb=" O TYR f 63 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N TYR f 63 " --> pdb=" O ASP f 45 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N GLU f 47 " --> pdb=" O GLY f 61 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N GLY f 61 " --> pdb=" O GLU f 47 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL f 68 " --> pdb=" O TYR f 7 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N LYS f 6 " --> pdb=" O VAL f 98 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'h' and resid 25 through 27 removed outlier: 3.650A pdb=" N ASP h 48 " --> pdb=" O PHE h 63 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'h' and resid 77 through 79 removed outlier: 6.805A pdb=" N ILE h 105 " --> pdb=" O ILE h 128 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N TYR h 130 " --> pdb=" O ILE h 103 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N ILE h 103 " --> pdb=" O TYR h 130 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLY h 111 " --> pdb=" O THR h 108 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'k' and resid 41 through 46 removed outlier: 6.344A pdb=" N VAL k 82 " --> pdb=" O VAL k 107 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ALA k 109 " --> pdb=" O VAL k 82 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'l' and resid 43 through 53 removed outlier: 5.875A pdb=" N CYS l 47 " --> pdb=" O ARG l 69 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ARG l 69 " --> pdb=" O CYS l 47 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ARG l 49 " --> pdb=" O ARG l 67 " (cutoff:3.500A) removed outlier: 13.538A pdb=" N GLU l 75 " --> pdb=" O VAL l 106 " (cutoff:3.500A) removed outlier: 10.192A pdb=" N TYR l 108 " --> pdb=" O GLU l 75 " (cutoff:3.500A) removed outlier: 7.646A pdb=" N THR l 77 " --> pdb=" O TYR l 108 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N ILE l 110 " --> pdb=" O THR l 77 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N TYR l 79 " --> pdb=" O ILE l 110 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'p' and resid 48 through 50 removed outlier: 3.595A pdb=" N GLU p 48 " --> pdb=" O ASN p 41 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLU p 35 " --> pdb=" O VAL p 22 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N ILE p 20 " --> pdb=" O VAL p 37 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N THR p 39 " --> pdb=" O TYR p 18 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N TYR p 18 " --> pdb=" O THR p 39 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'q' and resid 10 through 17 removed outlier: 17.366A pdb=" N VAL q 10 " --> pdb=" O LYS q 31 " (cutoff:3.500A) removed outlier: 14.270A pdb=" N LYS q 31 " --> pdb=" O VAL q 10 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N GLN q 12 " --> pdb=" O GLU q 29 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N GLU q 29 " --> pdb=" O GLN q 12 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N THR q 25 " --> pdb=" O VAL q 16 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N LEU q 78 " --> pdb=" O MET q 65 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N MET q 65 " --> pdb=" O LEU q 78 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLU q 80 " --> pdb=" O LYS q 63 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ILE q 61 " --> pdb=" O VAL q 82 " (cutoff:3.500A) 414 hydrogen bonds defined for protein. 1167 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 946 hydrogen bonds 1510 hydrogen bond angles 0 basepair planarities 375 basepair parallelities 632 stacking parallelities Total time for adding SS restraints: 26.44 Time building geometry restraints manager: 16.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 3684 1.32 - 1.44: 16134 1.44 - 1.56: 14868 1.56 - 1.68: 2238 1.68 - 1.81: 50 Bond restraints: 36974 Sorted by residual: bond pdb=" C ARG q 68 " pdb=" N PRO q 69 " ideal model delta sigma weight residual 1.332 1.307 0.025 1.12e-02 7.97e+03 5.04e+00 bond pdb=" N9 G a 183 " pdb=" C4 G a 183 " ideal model delta sigma weight residual 1.375 1.333 0.042 2.00e-02 2.50e+03 4.41e+00 bond pdb=" P G a 35 " pdb=" O5' G a 35 " ideal model delta sigma weight residual 1.593 1.564 0.029 1.50e-02 4.44e+03 3.73e+00 bond pdb=" CB VAL p 37 " pdb=" CG1 VAL p 37 " ideal model delta sigma weight residual 1.521 1.461 0.060 3.30e-02 9.18e+02 3.27e+00 bond pdb=" C2 G a 183 " pdb=" N3 G a 183 " ideal model delta sigma weight residual 1.323 1.287 0.036 2.00e-02 2.50e+03 3.21e+00 ... (remaining 36969 not shown) Histogram of bond angle deviations from ideal: 94.45 - 102.60: 1884 102.60 - 110.74: 18982 110.74 - 118.88: 16417 118.88 - 127.02: 15436 127.02 - 135.17: 2790 Bond angle restraints: 55509 Sorted by residual: angle pdb=" O3' U a 34 " pdb=" P G a 35 " pdb=" O5' G a 35 " ideal model delta sigma weight residual 104.00 112.98 -8.98 1.50e+00 4.44e-01 3.59e+01 angle pdb=" C3' U a 34 " pdb=" O3' U a 34 " pdb=" P G a 35 " ideal model delta sigma weight residual 120.20 111.59 8.61 1.50e+00 4.44e-01 3.29e+01 angle pdb=" C2' C a 31 " pdb=" C1' C a 31 " pdb=" N1 C a 31 " ideal model delta sigma weight residual 114.00 106.92 7.08 1.50e+00 4.44e-01 2.23e+01 angle pdb=" OP1 G a 35 " pdb=" P G a 35 " pdb=" O5' G a 35 " ideal model delta sigma weight residual 108.00 94.45 13.55 3.00e+00 1.11e-01 2.04e+01 angle pdb=" C2' C a 201 " pdb=" C1' C a 201 " pdb=" N1 C a 201 " ideal model delta sigma weight residual 112.00 118.53 -6.53 1.50e+00 4.44e-01 1.89e+01 ... (remaining 55504 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.08: 20647 34.08 - 68.15: 2758 68.15 - 102.23: 323 102.23 - 136.30: 5 136.30 - 170.38: 11 Dihedral angle restraints: 23744 sinusoidal: 20143 harmonic: 3601 Sorted by residual: dihedral pdb=" O4' U a 586 " pdb=" C1' U a 586 " pdb=" N1 U a 586 " pdb=" C2 U a 586 " ideal model delta sinusoidal sigma weight residual 200.00 29.62 170.38 1 1.50e+01 4.44e-03 8.47e+01 dihedral pdb=" O4' U a 579 " pdb=" C1' U a 579 " pdb=" N1 U a 579 " pdb=" C2 U a 579 " ideal model delta sinusoidal sigma weight residual -160.00 9.15 -169.15 1 1.50e+01 4.44e-03 8.46e+01 dihedral pdb=" C4' G a1447 " pdb=" C3' G a1447 " pdb=" C2' G a1447 " pdb=" C1' G a1447 " ideal model delta sinusoidal sigma weight residual 36.00 -24.66 60.66 1 8.00e+00 1.56e-02 7.65e+01 ... (remaining 23741 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 6312 0.082 - 0.165: 739 0.165 - 0.247: 63 0.247 - 0.329: 8 0.329 - 0.411: 2 Chirality restraints: 7124 Sorted by residual: chirality pdb=" C1' C a 201 " pdb=" O4' C a 201 " pdb=" C2' C a 201 " pdb=" N1 C a 201 " both_signs ideal model delta sigma weight residual False 2.47 2.05 0.41 2.00e-01 2.50e+01 4.23e+00 chirality pdb=" C3' U a 214 " pdb=" C4' U a 214 " pdb=" O3' U a 214 " pdb=" C2' U a 214 " both_signs ideal model delta sigma weight residual False -2.48 -2.11 -0.37 2.00e-01 2.50e+01 3.41e+00 chirality pdb=" C3' C a 37 " pdb=" C4' C a 37 " pdb=" O3' C a 37 " pdb=" C2' C a 37 " both_signs ideal model delta sigma weight residual False -2.48 -2.15 -0.32 2.00e-01 2.50e+01 2.60e+00 ... (remaining 7121 not shown) Planarity restraints: 2853 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' C a 31 " -0.068 2.00e-02 2.50e+03 3.64e-02 2.99e+01 pdb=" N1 C a 31 " 0.081 2.00e-02 2.50e+03 pdb=" C2 C a 31 " 0.005 2.00e-02 2.50e+03 pdb=" O2 C a 31 " 0.004 2.00e-02 2.50e+03 pdb=" N3 C a 31 " -0.005 2.00e-02 2.50e+03 pdb=" C4 C a 31 " -0.016 2.00e-02 2.50e+03 pdb=" N4 C a 31 " -0.013 2.00e-02 2.50e+03 pdb=" C5 C a 31 " -0.004 2.00e-02 2.50e+03 pdb=" C6 C a 31 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U a 255 " 0.064 2.00e-02 2.50e+03 3.51e-02 2.77e+01 pdb=" N1 U a 255 " -0.080 2.00e-02 2.50e+03 pdb=" C2 U a 255 " -0.005 2.00e-02 2.50e+03 pdb=" O2 U a 255 " -0.005 2.00e-02 2.50e+03 pdb=" N3 U a 255 " 0.008 2.00e-02 2.50e+03 pdb=" C4 U a 255 " 0.017 2.00e-02 2.50e+03 pdb=" O4 U a 255 " 0.011 2.00e-02 2.50e+03 pdb=" C5 U a 255 " -0.001 2.00e-02 2.50e+03 pdb=" C6 U a 255 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G a1447 " 0.061 2.00e-02 2.50e+03 2.77e-02 2.30e+01 pdb=" N9 G a1447 " -0.070 2.00e-02 2.50e+03 pdb=" C8 G a1447 " -0.008 2.00e-02 2.50e+03 pdb=" N7 G a1447 " 0.008 2.00e-02 2.50e+03 pdb=" C5 G a1447 " 0.011 2.00e-02 2.50e+03 pdb=" C6 G a1447 " 0.004 2.00e-02 2.50e+03 pdb=" O6 G a1447 " 0.008 2.00e-02 2.50e+03 pdb=" N1 G a1447 " 0.011 2.00e-02 2.50e+03 pdb=" C2 G a1447 " -0.001 2.00e-02 2.50e+03 pdb=" N2 G a1447 " -0.003 2.00e-02 2.50e+03 pdb=" N3 G a1447 " -0.007 2.00e-02 2.50e+03 pdb=" C4 G a1447 " -0.013 2.00e-02 2.50e+03 ... (remaining 2850 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 631 2.60 - 3.18: 24582 3.18 - 3.75: 61162 3.75 - 4.33: 89739 4.33 - 4.90: 118572 Nonbonded interactions: 294686 Sorted by model distance: nonbonded pdb=" O2 U a 858 " pdb=" N4 C a 860 " model vdw 2.029 2.520 nonbonded pdb=" O2' A a 26 " pdb=" O2 C a 27 " model vdw 2.108 2.440 nonbonded pdb=" NH1 ARG e 61 " pdb=" OE2 GLU e 65 " model vdw 2.125 2.520 nonbonded pdb=" O2' C a 483 " pdb=" O4' U a 484 " model vdw 2.137 2.440 nonbonded pdb=" O2' A a1508 " pdb=" O5' A a1509 " model vdw 2.142 2.440 ... (remaining 294681 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 5.020 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: 0.040 Extract box with map and model: 19.620 Check model and map are aligned: 0.540 Set scattering table: 0.320 Process input model: 112.630 Find NCS groups from input model: 0.630 Set up NCS constraints: 0.100 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:3.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 142.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 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 : 0.009 0.072 36974 Z= 0.546 Angle : 0.966 13.545 55509 Z= 0.486 Chirality : 0.054 0.411 7124 Planarity : 0.007 0.060 2853 Dihedral : 23.658 170.377 21422 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.41 % Allowed : 13.40 % Favored : 86.19 % Rotamer: Outliers : 18.19 % Allowed : 15.65 % Favored : 66.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -4.06 (0.20), residues: 1231 helix: -2.07 (0.21), residues: 419 sheet: -1.85 (0.29), residues: 250 loop : -3.62 (0.22), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.004 TRP d 9 HIS 0.010 0.002 HIS h 22 PHE 0.020 0.003 PHE d 72 TYR 0.029 0.004 TYR l 28 ARG 0.008 0.001 ARG l 12 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 461 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 193 poor density : 268 time to evaluate : 1.941 Fit side-chains revert: symmetry clash REVERT: d 9 TRP cc_start: 0.7149 (OUTLIER) cc_final: 0.6912 (t60) REVERT: d 28 ARG cc_start: 0.6992 (OUTLIER) cc_final: 0.6178 (mpt90) REVERT: d 29 ARG cc_start: 0.8189 (OUTLIER) cc_final: 0.7769 (ptt180) REVERT: d 65 GLU cc_start: 0.7953 (OUTLIER) cc_final: 0.7464 (mm-30) REVERT: d 114 LEU cc_start: 0.8941 (OUTLIER) cc_final: 0.8705 (mt) REVERT: d 143 ARG cc_start: 0.7867 (OUTLIER) cc_final: 0.7280 (ttt-90) REVERT: d 159 THR cc_start: 0.6294 (OUTLIER) cc_final: 0.6022 (p) REVERT: e 41 ASP cc_start: 0.8209 (p0) cc_final: 0.8006 (p0) REVERT: e 101 GLU cc_start: 0.6005 (OUTLIER) cc_final: 0.5531 (mm-30) REVERT: e 112 ARG cc_start: 0.8193 (OUTLIER) cc_final: 0.7952 (ttm-80) REVERT: h 49 VAL cc_start: 0.8799 (OUTLIER) cc_final: 0.8570 (t) REVERT: h 74 ILE cc_start: 0.8207 (OUTLIER) cc_final: 0.7978 (mt) REVERT: k 40 ASN cc_start: 0.7599 (OUTLIER) cc_final: 0.7393 (m110) REVERT: k 112 ASP cc_start: 0.7267 (t0) cc_final: 0.7048 (t70) REVERT: k 113 VAL cc_start: 0.8463 (OUTLIER) cc_final: 0.8238 (m) REVERT: l 32 LYS cc_start: 0.6799 (OUTLIER) cc_final: 0.6456 (mtmt) REVERT: l 35 GLN cc_start: 0.7523 (OUTLIER) cc_final: 0.6575 (pp30) REVERT: l 63 ARG cc_start: 0.8374 (OUTLIER) cc_final: 0.7715 (mtt90) REVERT: o 7 ARG cc_start: 0.7359 (OUTLIER) cc_final: 0.7068 (tmt170) REVERT: o 12 ILE cc_start: 0.7903 (OUTLIER) cc_final: 0.7558 (pt) REVERT: o 89 ARG cc_start: 0.3224 (OUTLIER) cc_final: 0.0814 (ptt180) REVERT: t 36 GLU cc_start: 0.6487 (OUTLIER) cc_final: 0.6257 (mm-30) outliers start: 193 outliers final: 108 residues processed: 401 average time/residue: 0.5111 time to fit residues: 316.2847 Evaluate side-chains 329 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 201 time to evaluate : 1.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain d residue 9 TRP Chi-restraints excluded: chain d residue 14 ARG Chi-restraints excluded: chain d residue 25 GLU Chi-restraints excluded: chain d residue 28 ARG Chi-restraints excluded: chain d residue 29 ARG Chi-restraints excluded: chain d residue 53 GLU Chi-restraints excluded: chain d residue 58 ARG Chi-restraints excluded: chain d residue 63 MET Chi-restraints excluded: chain d residue 65 GLU Chi-restraints excluded: chain d residue 71 LEU Chi-restraints excluded: chain d residue 114 LEU Chi-restraints excluded: chain d residue 139 VAL Chi-restraints excluded: chain d residue 140 ILE Chi-restraints excluded: chain d residue 143 ARG Chi-restraints excluded: chain d residue 159 THR Chi-restraints excluded: chain d residue 186 LEU Chi-restraints excluded: chain d residue 189 GLU Chi-restraints excluded: chain d residue 192 GLU Chi-restraints excluded: chain d residue 202 LYS Chi-restraints excluded: chain e residue 22 THR Chi-restraints excluded: chain e residue 24 VAL Chi-restraints excluded: chain e residue 39 VAL Chi-restraints excluded: chain e residue 76 MET Chi-restraints excluded: chain e residue 95 LEU Chi-restraints excluded: chain e residue 100 VAL Chi-restraints excluded: chain e residue 101 GLU Chi-restraints excluded: chain e residue 105 VAL Chi-restraints excluded: chain e residue 111 VAL Chi-restraints excluded: chain e residue 112 ARG Chi-restraints excluded: chain e residue 117 LEU Chi-restraints excluded: chain e residue 123 ILE Chi-restraints excluded: chain e residue 128 LEU Chi-restraints excluded: chain e residue 144 LEU Chi-restraints excluded: chain e residue 147 LEU Chi-restraints excluded: chain e residue 160 SER Chi-restraints excluded: chain e residue 165 ILE Chi-restraints excluded: chain f residue 3 GLN Chi-restraints excluded: chain f residue 4 ASP Chi-restraints excluded: chain f residue 5 THR Chi-restraints excluded: chain f residue 33 LEU Chi-restraints excluded: chain f residue 36 ASN Chi-restraints excluded: chain f residue 41 ILE Chi-restraints excluded: chain f residue 45 ASP Chi-restraints excluded: chain f residue 65 ILE Chi-restraints excluded: chain f residue 66 VAL Chi-restraints excluded: chain f residue 68 VAL Chi-restraints excluded: chain f residue 77 ILE Chi-restraints excluded: chain f residue 96 VAL Chi-restraints excluded: chain h residue 2 VAL Chi-restraints excluded: chain h residue 11 LEU Chi-restraints excluded: chain h residue 25 LEU Chi-restraints excluded: chain h residue 27 VAL Chi-restraints excluded: chain h residue 49 VAL Chi-restraints excluded: chain h residue 52 ILE Chi-restraints excluded: chain h residue 54 ASP Chi-restraints excluded: chain h residue 57 GLN Chi-restraints excluded: chain h residue 69 ASN Chi-restraints excluded: chain h residue 73 VAL Chi-restraints excluded: chain h residue 74 ILE Chi-restraints excluded: chain h residue 75 THR Chi-restraints excluded: chain h residue 89 VAL Chi-restraints excluded: chain h residue 97 VAL Chi-restraints excluded: chain h residue 113 ILE Chi-restraints excluded: chain h residue 114 THR Chi-restraints excluded: chain h residue 131 VAL Chi-restraints excluded: chain k residue 30 THR Chi-restraints excluded: chain k residue 35 THR Chi-restraints excluded: chain k residue 37 THR Chi-restraints excluded: chain k residue 40 ASN Chi-restraints excluded: chain k residue 45 SER Chi-restraints excluded: chain k residue 55 SER Chi-restraints excluded: chain k residue 82 VAL Chi-restraints excluded: chain k residue 85 THR Chi-restraints excluded: chain k residue 86 VAL Chi-restraints excluded: chain k residue 113 VAL Chi-restraints excluded: chain l residue 8 VAL Chi-restraints excluded: chain l residue 24 LEU Chi-restraints excluded: chain l residue 25 ASN Chi-restraints excluded: chain l residue 32 LYS Chi-restraints excluded: chain l residue 35 GLN Chi-restraints excluded: chain l residue 37 ASN Chi-restraints excluded: chain l residue 42 GLN Chi-restraints excluded: chain l residue 54 THR Chi-restraints excluded: chain l residue 63 ARG Chi-restraints excluded: chain l residue 64 LYS Chi-restraints excluded: chain l residue 72 ASN Chi-restraints excluded: chain l residue 77 THR Chi-restraints excluded: chain l residue 80 ILE Chi-restraints excluded: chain l residue 92 VAL Chi-restraints excluded: chain l residue 106 VAL Chi-restraints excluded: chain l residue 110 ILE Chi-restraints excluded: chain l residue 111 VAL Chi-restraints excluded: chain l residue 117 THR Chi-restraints excluded: chain l residue 120 VAL Chi-restraints excluded: chain l residue 122 ASP Chi-restraints excluded: chain o residue 7 ARG Chi-restraints excluded: chain o residue 12 ILE Chi-restraints excluded: chain o residue 29 ILE Chi-restraints excluded: chain o residue 54 ARG Chi-restraints excluded: chain o residue 56 LEU Chi-restraints excluded: chain o residue 75 ILE Chi-restraints excluded: chain o residue 87 LEU Chi-restraints excluded: chain o residue 89 ARG Chi-restraints excluded: chain p residue 32 ARG Chi-restraints excluded: chain p residue 36 THR Chi-restraints excluded: chain p residue 39 THR Chi-restraints excluded: chain p residue 44 LYS Chi-restraints excluded: chain p residue 56 VAL Chi-restraints excluded: chain p residue 73 ILE Chi-restraints excluded: chain q residue 10 VAL Chi-restraints excluded: chain q residue 14 ARG Chi-restraints excluded: chain q residue 16 VAL Chi-restraints excluded: chain q residue 21 ASP Chi-restraints excluded: chain q residue 30 THR Chi-restraints excluded: chain q residue 42 LYS Chi-restraints excluded: chain q residue 55 THR Chi-restraints excluded: chain q residue 79 LEU Chi-restraints excluded: chain q residue 81 VAL Chi-restraints excluded: chain r residue 20 ASN Chi-restraints excluded: chain r residue 22 ILE Chi-restraints excluded: chain r residue 63 ILE Chi-restraints excluded: chain t residue 13 THR Chi-restraints excluded: chain t residue 20 LYS Chi-restraints excluded: chain t residue 36 GLU Chi-restraints excluded: chain t residue 39 VAL Chi-restraints excluded: chain t residue 44 ASP Chi-restraints excluded: chain t residue 62 THR Chi-restraints excluded: chain t residue 81 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 195 optimal weight: 0.9980 chunk 175 optimal weight: 0.6980 chunk 97 optimal weight: 10.0000 chunk 60 optimal weight: 7.9990 chunk 118 optimal weight: 2.9990 chunk 93 optimal weight: 8.9990 chunk 181 optimal weight: 0.8980 chunk 70 optimal weight: 6.9990 chunk 110 optimal weight: 8.9990 chunk 135 optimal weight: 0.9990 chunk 210 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 55 GLN d 147 GLN e 8 HIS e 43 ASN h 22 HIS l 5 ASN l 109 HIS l 125 GLN o 38 GLN o 42 HIS o 46 HIS p 41 ASN p 65 GLN q 50 HIS t 45 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.1800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 36974 Z= 0.130 Angle : 0.553 8.355 55509 Z= 0.292 Chirality : 0.035 0.214 7124 Planarity : 0.005 0.058 2853 Dihedral : 23.148 167.409 19157 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.39 % Favored : 92.45 % Rotamer: Outliers : 11.31 % Allowed : 20.26 % Favored : 68.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.08 % 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: -2.56 (0.22), residues: 1231 helix: -0.30 (0.24), residues: 429 sheet: -1.20 (0.32), residues: 231 loop : -3.11 (0.23), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP d 9 HIS 0.005 0.001 HIS p 84 PHE 0.013 0.001 PHE f 58 TYR 0.016 0.001 TYR r 27 ARG 0.006 0.000 ARG o 71 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 213 time to evaluate : 1.724 Fit side-chains revert: symmetry clash REVERT: d 17 ILE cc_start: 0.7656 (OUTLIER) cc_final: 0.7427 (mp) REVERT: d 53 GLU cc_start: 0.7617 (OUTLIER) cc_final: 0.7077 (mm-30) REVERT: d 114 LEU cc_start: 0.8841 (OUTLIER) cc_final: 0.8579 (mt) REVERT: d 143 ARG cc_start: 0.7916 (OUTLIER) cc_final: 0.6663 (ttm-80) REVERT: d 192 GLU cc_start: 0.5509 (OUTLIER) cc_final: 0.5081 (pm20) REVERT: e 117 LEU cc_start: 0.8705 (OUTLIER) cc_final: 0.8317 (mt) REVERT: h 36 ILE cc_start: 0.8114 (pt) cc_final: 0.7609 (mt) REVERT: l 35 GLN cc_start: 0.7233 (OUTLIER) cc_final: 0.6838 (pp30) REVERT: l 53 MET cc_start: 0.7886 (ptp) cc_final: 0.7478 (ptp) REVERT: o 29 ILE cc_start: 0.8150 (pt) cc_final: 0.7866 (mt) REVERT: o 56 LEU cc_start: 0.8757 (OUTLIER) cc_final: 0.8534 (tp) REVERT: o 89 ARG cc_start: 0.2763 (OUTLIER) cc_final: 0.0666 (ptp-170) REVERT: q 42 LYS cc_start: 0.8724 (OUTLIER) cc_final: 0.8400 (mttt) outliers start: 120 outliers final: 69 residues processed: 298 average time/residue: 0.4943 time to fit residues: 230.4752 Evaluate side-chains 261 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 182 time to evaluate : 2.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain d residue 17 ILE Chi-restraints excluded: chain d residue 53 GLU Chi-restraints excluded: chain d residue 71 LEU Chi-restraints excluded: chain d residue 114 LEU Chi-restraints excluded: chain d residue 139 VAL Chi-restraints excluded: chain d residue 140 ILE Chi-restraints excluded: chain d residue 143 ARG Chi-restraints excluded: chain d residue 192 GLU Chi-restraints excluded: chain d residue 202 LYS Chi-restraints excluded: chain e residue 22 THR Chi-restraints excluded: chain e residue 24 VAL Chi-restraints excluded: chain e residue 39 VAL Chi-restraints excluded: chain e residue 50 THR Chi-restraints excluded: chain e residue 100 VAL Chi-restraints excluded: chain e residue 111 VAL Chi-restraints excluded: chain e residue 117 LEU Chi-restraints excluded: chain e residue 128 LEU Chi-restraints excluded: chain e residue 144 LEU Chi-restraints excluded: chain e residue 147 LEU Chi-restraints excluded: chain e residue 160 SER Chi-restraints excluded: chain e residue 164 ILE Chi-restraints excluded: chain e residue 165 ILE Chi-restraints excluded: chain f residue 3 GLN Chi-restraints excluded: chain f residue 5 THR Chi-restraints excluded: chain f residue 36 ASN Chi-restraints excluded: chain f residue 40 VAL Chi-restraints excluded: chain f residue 45 ASP Chi-restraints excluded: chain f residue 60 GLU Chi-restraints excluded: chain f residue 65 ILE Chi-restraints excluded: chain f residue 66 VAL Chi-restraints excluded: chain f residue 68 VAL Chi-restraints excluded: chain f residue 77 ILE Chi-restraints excluded: chain f residue 88 ASP Chi-restraints excluded: chain h residue 27 VAL Chi-restraints excluded: chain h residue 49 VAL Chi-restraints excluded: chain h residue 52 ILE Chi-restraints excluded: chain h residue 54 ASP Chi-restraints excluded: chain h residue 62 VAL Chi-restraints excluded: chain h residue 69 ASN Chi-restraints excluded: chain h residue 75 THR Chi-restraints excluded: chain h residue 89 VAL Chi-restraints excluded: chain h residue 97 VAL Chi-restraints excluded: chain h residue 126 GLU Chi-restraints excluded: chain h residue 131 VAL Chi-restraints excluded: chain k residue 30 THR Chi-restraints excluded: chain k residue 35 THR Chi-restraints excluded: chain k residue 37 THR Chi-restraints excluded: chain k residue 46 SER Chi-restraints excluded: chain k residue 65 MET Chi-restraints excluded: chain k residue 85 THR Chi-restraints excluded: chain k residue 86 VAL Chi-restraints excluded: chain l residue 4 ILE Chi-restraints excluded: chain l residue 8 VAL Chi-restraints excluded: chain l residue 20 ASP Chi-restraints excluded: chain l residue 25 ASN Chi-restraints excluded: chain l residue 35 GLN Chi-restraints excluded: chain l residue 72 ASN Chi-restraints excluded: chain l residue 77 THR Chi-restraints excluded: chain l residue 92 VAL Chi-restraints excluded: chain l residue 111 VAL Chi-restraints excluded: chain l residue 120 VAL Chi-restraints excluded: chain l residue 121 ASN Chi-restraints excluded: chain l residue 122 ASP Chi-restraints excluded: chain o residue 38 GLN Chi-restraints excluded: chain o residue 56 LEU Chi-restraints excluded: chain o residue 75 ILE Chi-restraints excluded: chain o residue 89 ARG Chi-restraints excluded: chain p residue 32 ARG Chi-restraints excluded: chain p residue 36 THR Chi-restraints excluded: chain q residue 10 VAL Chi-restraints excluded: chain q residue 21 ASP Chi-restraints excluded: chain q residue 42 LYS Chi-restraints excluded: chain q residue 55 THR Chi-restraints excluded: chain q residue 81 VAL Chi-restraints excluded: chain r residue 20 ASN Chi-restraints excluded: chain r residue 48 VAL Chi-restraints excluded: chain r residue 63 ILE Chi-restraints excluded: chain t residue 39 VAL Chi-restraints excluded: chain t residue 62 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 117 optimal weight: 9.9990 chunk 65 optimal weight: 10.0000 chunk 175 optimal weight: 0.9980 chunk 143 optimal weight: 0.0370 chunk 58 optimal weight: 10.0000 chunk 211 optimal weight: 0.0670 chunk 228 optimal weight: 10.0000 chunk 187 optimal weight: 9.9990 chunk 209 optimal weight: 5.9990 chunk 71 optimal weight: 7.9990 chunk 169 optimal weight: 10.0000 overall best weight: 3.0200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 59 HIS d 113 GLN l 37 ASN o 38 GLN p 41 ASN p 72 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.1648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 36974 Z= 0.227 Angle : 0.629 9.041 55509 Z= 0.327 Chirality : 0.038 0.245 7124 Planarity : 0.005 0.053 2853 Dihedral : 23.080 170.361 19012 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.16 % Allowed : 8.85 % Favored : 90.98 % Rotamer: Outliers : 10.27 % Allowed : 20.64 % Favored : 69.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.08 % 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: -2.01 (0.23), residues: 1231 helix: 0.23 (0.25), residues: 429 sheet: -0.82 (0.32), residues: 232 loop : -2.88 (0.23), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP d 9 HIS 0.005 0.001 HIS p 84 PHE 0.014 0.002 PHE d 72 TYR 0.020 0.002 TYR r 27 ARG 0.005 0.000 ARG l 12 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 179 time to evaluate : 1.842 Fit side-chains revert: symmetry clash REVERT: d 17 ILE cc_start: 0.7660 (OUTLIER) cc_final: 0.7435 (mp) REVERT: d 94 ARG cc_start: 0.8555 (OUTLIER) cc_final: 0.6681 (ptm-80) REVERT: d 114 LEU cc_start: 0.8929 (OUTLIER) cc_final: 0.8653 (mt) REVERT: d 143 ARG cc_start: 0.7968 (OUTLIER) cc_final: 0.7122 (ttt-90) REVERT: d 179 ARG cc_start: 0.6706 (ppt170) cc_final: 0.6317 (ptt90) REVERT: e 117 LEU cc_start: 0.8783 (OUTLIER) cc_final: 0.8362 (mt) REVERT: f 3 GLN cc_start: 0.6177 (OUTLIER) cc_final: 0.5639 (pp30) REVERT: h 36 ILE cc_start: 0.8133 (pt) cc_final: 0.7767 (mt) REVERT: l 35 GLN cc_start: 0.7304 (OUTLIER) cc_final: 0.7034 (pp30) REVERT: l 53 MET cc_start: 0.8053 (ptp) cc_final: 0.7705 (ptp) REVERT: o 22 THR cc_start: 0.8224 (p) cc_final: 0.8007 (p) REVERT: o 29 ILE cc_start: 0.8379 (OUTLIER) cc_final: 0.8022 (mt) outliers start: 109 outliers final: 82 residues processed: 256 average time/residue: 0.4788 time to fit residues: 194.4861 Evaluate side-chains 267 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 177 time to evaluate : 1.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain d residue 17 ILE Chi-restraints excluded: chain d residue 53 GLU Chi-restraints excluded: chain d residue 63 MET Chi-restraints excluded: chain d residue 71 LEU Chi-restraints excluded: chain d residue 94 ARG Chi-restraints excluded: chain d residue 114 LEU Chi-restraints excluded: chain d residue 139 VAL Chi-restraints excluded: chain d residue 140 ILE Chi-restraints excluded: chain d residue 143 ARG Chi-restraints excluded: chain d residue 159 THR Chi-restraints excluded: chain d residue 190 ILE Chi-restraints excluded: chain d residue 202 LYS Chi-restraints excluded: chain e residue 4 ILE Chi-restraints excluded: chain e residue 9 LEU Chi-restraints excluded: chain e residue 22 THR Chi-restraints excluded: chain e residue 24 VAL Chi-restraints excluded: chain e residue 39 VAL Chi-restraints excluded: chain e residue 76 MET Chi-restraints excluded: chain e residue 84 GLU Chi-restraints excluded: chain e residue 100 VAL Chi-restraints excluded: chain e residue 111 VAL Chi-restraints excluded: chain e residue 117 LEU Chi-restraints excluded: chain e residue 125 SER Chi-restraints excluded: chain e residue 128 LEU Chi-restraints excluded: chain e residue 144 LEU Chi-restraints excluded: chain e residue 147 LEU Chi-restraints excluded: chain e residue 160 SER Chi-restraints excluded: chain e residue 164 ILE Chi-restraints excluded: chain f residue 3 GLN Chi-restraints excluded: chain f residue 5 THR Chi-restraints excluded: chain f residue 13 ILE Chi-restraints excluded: chain f residue 36 ASN Chi-restraints excluded: chain f residue 40 VAL Chi-restraints excluded: chain f residue 45 ASP Chi-restraints excluded: chain f residue 60 GLU Chi-restraints excluded: chain f residue 65 ILE Chi-restraints excluded: chain f residue 66 VAL Chi-restraints excluded: chain f residue 68 VAL Chi-restraints excluded: chain h residue 20 VAL Chi-restraints excluded: chain h residue 24 THR Chi-restraints excluded: chain h residue 27 VAL Chi-restraints excluded: chain h residue 49 VAL Chi-restraints excluded: chain h residue 54 ASP Chi-restraints excluded: chain h residue 62 VAL Chi-restraints excluded: chain h residue 69 ASN Chi-restraints excluded: chain h residue 75 THR Chi-restraints excluded: chain h residue 89 VAL Chi-restraints excluded: chain h residue 97 VAL Chi-restraints excluded: chain h residue 131 VAL Chi-restraints excluded: chain k residue 20 VAL Chi-restraints excluded: chain k residue 30 THR Chi-restraints excluded: chain k residue 35 THR Chi-restraints excluded: chain k residue 37 THR Chi-restraints excluded: chain k residue 46 SER Chi-restraints excluded: chain k residue 65 MET Chi-restraints excluded: chain k residue 82 VAL Chi-restraints excluded: chain k residue 85 THR Chi-restraints excluded: chain k residue 86 VAL Chi-restraints excluded: chain k residue 107 VAL Chi-restraints excluded: chain l residue 4 ILE Chi-restraints excluded: chain l residue 8 VAL Chi-restraints excluded: chain l residue 20 ASP Chi-restraints excluded: chain l residue 21 SER Chi-restraints excluded: chain l residue 25 ASN Chi-restraints excluded: chain l residue 35 GLN Chi-restraints excluded: chain l residue 40 SER Chi-restraints excluded: chain l residue 72 ASN Chi-restraints excluded: chain l residue 77 THR Chi-restraints excluded: chain l residue 92 VAL Chi-restraints excluded: chain l residue 111 VAL Chi-restraints excluded: chain l residue 120 VAL Chi-restraints excluded: chain l residue 122 ASP Chi-restraints excluded: chain o residue 5 GLN Chi-restraints excluded: chain o residue 29 ILE Chi-restraints excluded: chain o residue 73 THR Chi-restraints excluded: chain o residue 75 ILE Chi-restraints excluded: chain o residue 89 ARG Chi-restraints excluded: chain p residue 32 ARG Chi-restraints excluded: chain p residue 36 THR Chi-restraints excluded: chain q residue 10 VAL Chi-restraints excluded: chain q residue 21 ASP Chi-restraints excluded: chain q residue 42 LYS Chi-restraints excluded: chain q residue 55 THR Chi-restraints excluded: chain q residue 81 VAL Chi-restraints excluded: chain r residue 20 ASN Chi-restraints excluded: chain r residue 32 LEU Chi-restraints excluded: chain r residue 48 VAL Chi-restraints excluded: chain r residue 63 ILE Chi-restraints excluded: chain r residue 76 SER Chi-restraints excluded: chain t residue 39 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 208 optimal weight: 6.9990 chunk 158 optimal weight: 3.9990 chunk 109 optimal weight: 10.0000 chunk 23 optimal weight: 10.0000 chunk 100 optimal weight: 10.0000 chunk 141 optimal weight: 6.9990 chunk 211 optimal weight: 0.0670 chunk 224 optimal weight: 0.0020 chunk 110 optimal weight: 10.0000 chunk 200 optimal weight: 5.9990 chunk 60 optimal weight: 10.0000 overall best weight: 3.4132 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 50 GLN l 37 ASN o 38 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.1753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 36974 Z= 0.245 Angle : 0.644 9.078 55509 Z= 0.334 Chirality : 0.039 0.251 7124 Planarity : 0.005 0.049 2853 Dihedral : 23.043 171.581 19000 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.16 % Allowed : 8.53 % Favored : 91.31 % Rotamer: Outliers : 11.40 % Allowed : 20.36 % Favored : 68.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.08 % 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: -1.72 (0.23), residues: 1231 helix: 0.39 (0.25), residues: 435 sheet: -0.55 (0.33), residues: 231 loop : -2.73 (0.24), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP d 9 HIS 0.006 0.001 HIS h 22 PHE 0.018 0.002 PHE f 29 TYR 0.020 0.002 TYR r 27 ARG 0.006 0.001 ARG l 12 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 172 time to evaluate : 1.861 Fit side-chains revert: symmetry clash REVERT: d 17 ILE cc_start: 0.7697 (OUTLIER) cc_final: 0.7390 (mp) REVERT: d 114 LEU cc_start: 0.8927 (OUTLIER) cc_final: 0.8657 (mt) REVERT: d 143 ARG cc_start: 0.7860 (OUTLIER) cc_final: 0.6534 (ttt-90) REVERT: d 179 ARG cc_start: 0.7036 (ppt170) cc_final: 0.6742 (ptt-90) REVERT: d 192 GLU cc_start: 0.5761 (OUTLIER) cc_final: 0.5070 (pm20) REVERT: e 101 GLU cc_start: 0.6181 (OUTLIER) cc_final: 0.5425 (mm-30) REVERT: e 117 LEU cc_start: 0.8877 (OUTLIER) cc_final: 0.8479 (mt) REVERT: h 36 ILE cc_start: 0.8129 (pt) cc_final: 0.7827 (mt) REVERT: l 53 MET cc_start: 0.8058 (ptp) cc_final: 0.7790 (ptp) REVERT: o 29 ILE cc_start: 0.8443 (OUTLIER) cc_final: 0.8126 (mt) outliers start: 121 outliers final: 94 residues processed: 260 average time/residue: 0.4824 time to fit residues: 202.6668 Evaluate side-chains 270 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 169 time to evaluate : 1.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain d residue 17 ILE Chi-restraints excluded: chain d residue 53 GLU Chi-restraints excluded: chain d residue 63 MET Chi-restraints excluded: chain d residue 71 LEU Chi-restraints excluded: chain d residue 114 LEU Chi-restraints excluded: chain d residue 139 VAL Chi-restraints excluded: chain d residue 140 ILE Chi-restraints excluded: chain d residue 143 ARG Chi-restraints excluded: chain d residue 150 SER Chi-restraints excluded: chain d residue 159 THR Chi-restraints excluded: chain d residue 189 GLU Chi-restraints excluded: chain d residue 192 GLU Chi-restraints excluded: chain e residue 4 ILE Chi-restraints excluded: chain e residue 9 LEU Chi-restraints excluded: chain e residue 22 THR Chi-restraints excluded: chain e residue 24 VAL Chi-restraints excluded: chain e residue 39 VAL Chi-restraints excluded: chain e residue 50 THR Chi-restraints excluded: chain e residue 76 MET Chi-restraints excluded: chain e residue 84 GLU Chi-restraints excluded: chain e residue 95 LEU Chi-restraints excluded: chain e residue 100 VAL Chi-restraints excluded: chain e residue 101 GLU Chi-restraints excluded: chain e residue 111 VAL Chi-restraints excluded: chain e residue 117 LEU Chi-restraints excluded: chain e residue 125 SER Chi-restraints excluded: chain e residue 128 LEU Chi-restraints excluded: chain e residue 144 LEU Chi-restraints excluded: chain e residue 147 LEU Chi-restraints excluded: chain e residue 160 SER Chi-restraints excluded: chain e residue 164 ILE Chi-restraints excluded: chain e residue 165 ILE Chi-restraints excluded: chain f residue 5 THR Chi-restraints excluded: chain f residue 13 ILE Chi-restraints excluded: chain f residue 33 LEU Chi-restraints excluded: chain f residue 36 ASN Chi-restraints excluded: chain f residue 40 VAL Chi-restraints excluded: chain f residue 45 ASP Chi-restraints excluded: chain f residue 60 GLU Chi-restraints excluded: chain f residue 65 ILE Chi-restraints excluded: chain f residue 66 VAL Chi-restraints excluded: chain f residue 68 VAL Chi-restraints excluded: chain h residue 20 VAL Chi-restraints excluded: chain h residue 24 THR Chi-restraints excluded: chain h residue 27 VAL Chi-restraints excluded: chain h residue 49 VAL Chi-restraints excluded: chain h residue 52 ILE Chi-restraints excluded: chain h residue 54 ASP Chi-restraints excluded: chain h residue 62 VAL Chi-restraints excluded: chain h residue 69 ASN Chi-restraints excluded: chain h residue 75 THR Chi-restraints excluded: chain h residue 89 VAL Chi-restraints excluded: chain h residue 97 VAL Chi-restraints excluded: chain h residue 98 LEU Chi-restraints excluded: chain h residue 131 VAL Chi-restraints excluded: chain k residue 30 THR Chi-restraints excluded: chain k residue 35 THR Chi-restraints excluded: chain k residue 37 THR Chi-restraints excluded: chain k residue 46 SER Chi-restraints excluded: chain k residue 65 MET Chi-restraints excluded: chain k residue 81 THR Chi-restraints excluded: chain k residue 82 VAL Chi-restraints excluded: chain k residue 85 THR Chi-restraints excluded: chain k residue 86 VAL Chi-restraints excluded: chain k residue 107 VAL Chi-restraints excluded: chain l residue 4 ILE Chi-restraints excluded: chain l residue 8 VAL Chi-restraints excluded: chain l residue 20 ASP Chi-restraints excluded: chain l residue 21 SER Chi-restraints excluded: chain l residue 25 ASN Chi-restraints excluded: chain l residue 35 GLN Chi-restraints excluded: chain l residue 40 SER Chi-restraints excluded: chain l residue 54 THR Chi-restraints excluded: chain l residue 72 ASN Chi-restraints excluded: chain l residue 77 THR Chi-restraints excluded: chain l residue 92 VAL Chi-restraints excluded: chain l residue 111 VAL Chi-restraints excluded: chain l residue 120 VAL Chi-restraints excluded: chain l residue 121 ASN Chi-restraints excluded: chain l residue 122 ASP Chi-restraints excluded: chain o residue 5 GLN Chi-restraints excluded: chain o residue 29 ILE Chi-restraints excluded: chain o residue 73 THR Chi-restraints excluded: chain o residue 75 ILE Chi-restraints excluded: chain o residue 89 ARG Chi-restraints excluded: chain p residue 32 ARG Chi-restraints excluded: chain p residue 36 THR Chi-restraints excluded: chain p residue 56 VAL Chi-restraints excluded: chain q residue 10 VAL Chi-restraints excluded: chain q residue 21 ASP Chi-restraints excluded: chain q residue 30 THR Chi-restraints excluded: chain q residue 55 THR Chi-restraints excluded: chain q residue 81 VAL Chi-restraints excluded: chain r residue 20 ASN Chi-restraints excluded: chain r residue 32 LEU Chi-restraints excluded: chain r residue 48 VAL Chi-restraints excluded: chain r residue 63 ILE Chi-restraints excluded: chain r residue 76 SER Chi-restraints excluded: chain t residue 13 THR Chi-restraints excluded: chain t residue 39 VAL Chi-restraints excluded: chain t residue 81 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 186 optimal weight: 0.4980 chunk 127 optimal weight: 0.9980 chunk 3 optimal weight: 8.9990 chunk 166 optimal weight: 0.0060 chunk 92 optimal weight: 20.0000 chunk 191 optimal weight: 2.9990 chunk 155 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 114 optimal weight: 9.9990 chunk 201 optimal weight: 9.9990 chunk 56 optimal weight: 8.9990 overall best weight: 1.0998 ------------------------------------------------------------------------------- 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: 0.8158 moved from start: 0.1944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.062 36974 Z= 0.138 Angle : 0.578 8.934 55509 Z= 0.302 Chirality : 0.035 0.225 7124 Planarity : 0.004 0.043 2853 Dihedral : 23.028 170.831 18989 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.16 % Allowed : 8.04 % Favored : 91.80 % Rotamer: Outliers : 9.80 % Allowed : 21.87 % Favored : 68.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.08 % 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: -1.37 (0.24), residues: 1231 helix: 0.78 (0.26), residues: 429 sheet: -0.37 (0.33), residues: 232 loop : -2.59 (0.24), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP d 9 HIS 0.004 0.001 HIS p 84 PHE 0.015 0.002 PHE f 29 TYR 0.019 0.001 TYR r 27 ARG 0.008 0.001 ARG r 40 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 173 time to evaluate : 2.067 Fit side-chains revert: symmetry clash REVERT: d 17 ILE cc_start: 0.7689 (OUTLIER) cc_final: 0.7346 (mp) REVERT: d 53 GLU cc_start: 0.7712 (OUTLIER) cc_final: 0.6335 (mp0) REVERT: d 94 ARG cc_start: 0.8491 (OUTLIER) cc_final: 0.6847 (ptm-80) REVERT: d 114 LEU cc_start: 0.8954 (OUTLIER) cc_final: 0.8666 (mt) REVERT: e 101 GLU cc_start: 0.6126 (OUTLIER) cc_final: 0.5344 (mm-30) REVERT: e 117 LEU cc_start: 0.8863 (OUTLIER) cc_final: 0.8478 (mt) REVERT: h 36 ILE cc_start: 0.8062 (pt) cc_final: 0.7796 (mt) REVERT: l 53 MET cc_start: 0.8064 (ptp) cc_final: 0.7797 (ptp) REVERT: o 29 ILE cc_start: 0.8330 (OUTLIER) cc_final: 0.7982 (mt) REVERT: o 84 ARG cc_start: 0.8407 (OUTLIER) cc_final: 0.8203 (ttp-170) outliers start: 104 outliers final: 86 residues processed: 250 average time/residue: 0.4662 time to fit residues: 186.9452 Evaluate side-chains 264 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 170 time to evaluate : 1.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain d residue 17 ILE Chi-restraints excluded: chain d residue 53 GLU Chi-restraints excluded: chain d residue 63 MET Chi-restraints excluded: chain d residue 71 LEU Chi-restraints excluded: chain d residue 94 ARG Chi-restraints excluded: chain d residue 114 LEU Chi-restraints excluded: chain d residue 139 VAL Chi-restraints excluded: chain d residue 140 ILE Chi-restraints excluded: chain d residue 150 SER Chi-restraints excluded: chain e residue 4 ILE Chi-restraints excluded: chain e residue 9 LEU Chi-restraints excluded: chain e residue 22 THR Chi-restraints excluded: chain e residue 24 VAL Chi-restraints excluded: chain e residue 39 VAL Chi-restraints excluded: chain e residue 50 THR Chi-restraints excluded: chain e residue 84 GLU Chi-restraints excluded: chain e residue 95 LEU Chi-restraints excluded: chain e residue 100 VAL Chi-restraints excluded: chain e residue 101 GLU Chi-restraints excluded: chain e residue 111 VAL Chi-restraints excluded: chain e residue 117 LEU Chi-restraints excluded: chain e residue 125 SER Chi-restraints excluded: chain e residue 128 LEU Chi-restraints excluded: chain e residue 144 LEU Chi-restraints excluded: chain e residue 147 LEU Chi-restraints excluded: chain e residue 160 SER Chi-restraints excluded: chain e residue 164 ILE Chi-restraints excluded: chain e residue 165 ILE Chi-restraints excluded: chain f residue 4 ASP Chi-restraints excluded: chain f residue 5 THR Chi-restraints excluded: chain f residue 13 ILE Chi-restraints excluded: chain f residue 36 ASN Chi-restraints excluded: chain f residue 40 VAL Chi-restraints excluded: chain f residue 45 ASP Chi-restraints excluded: chain f residue 60 GLU Chi-restraints excluded: chain f residue 65 ILE Chi-restraints excluded: chain f residue 66 VAL Chi-restraints excluded: chain f residue 68 VAL Chi-restraints excluded: chain h residue 20 VAL Chi-restraints excluded: chain h residue 24 THR Chi-restraints excluded: chain h residue 27 VAL Chi-restraints excluded: chain h residue 46 ILE Chi-restraints excluded: chain h residue 49 VAL Chi-restraints excluded: chain h residue 54 ASP Chi-restraints excluded: chain h residue 62 VAL Chi-restraints excluded: chain h residue 69 ASN Chi-restraints excluded: chain h residue 75 THR Chi-restraints excluded: chain h residue 89 VAL Chi-restraints excluded: chain h residue 97 VAL Chi-restraints excluded: chain h residue 98 LEU Chi-restraints excluded: chain h residue 126 GLU Chi-restraints excluded: chain h residue 131 VAL Chi-restraints excluded: chain k residue 30 THR Chi-restraints excluded: chain k residue 37 THR Chi-restraints excluded: chain k residue 46 SER Chi-restraints excluded: chain k residue 65 MET Chi-restraints excluded: chain k residue 81 THR Chi-restraints excluded: chain k residue 82 VAL Chi-restraints excluded: chain k residue 85 THR Chi-restraints excluded: chain k residue 86 VAL Chi-restraints excluded: chain k residue 107 VAL Chi-restraints excluded: chain l residue 4 ILE Chi-restraints excluded: chain l residue 8 VAL Chi-restraints excluded: chain l residue 21 SER Chi-restraints excluded: chain l residue 25 ASN Chi-restraints excluded: chain l residue 35 GLN Chi-restraints excluded: chain l residue 54 THR Chi-restraints excluded: chain l residue 72 ASN Chi-restraints excluded: chain l residue 77 THR Chi-restraints excluded: chain l residue 92 VAL Chi-restraints excluded: chain l residue 111 VAL Chi-restraints excluded: chain l residue 120 VAL Chi-restraints excluded: chain l residue 121 ASN Chi-restraints excluded: chain l residue 122 ASP Chi-restraints excluded: chain o residue 5 GLN Chi-restraints excluded: chain o residue 10 GLU Chi-restraints excluded: chain o residue 29 ILE Chi-restraints excluded: chain o residue 75 ILE Chi-restraints excluded: chain o residue 84 ARG Chi-restraints excluded: chain o residue 89 ARG Chi-restraints excluded: chain p residue 32 ARG Chi-restraints excluded: chain p residue 36 THR Chi-restraints excluded: chain p residue 56 VAL Chi-restraints excluded: chain q residue 10 VAL Chi-restraints excluded: chain q residue 21 ASP Chi-restraints excluded: chain q residue 53 ASN Chi-restraints excluded: chain q residue 55 THR Chi-restraints excluded: chain q residue 81 VAL Chi-restraints excluded: chain r residue 20 ASN Chi-restraints excluded: chain r residue 34 LYS Chi-restraints excluded: chain r residue 48 VAL Chi-restraints excluded: chain r residue 63 ILE Chi-restraints excluded: chain t residue 39 VAL Chi-restraints excluded: chain t residue 81 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 75 optimal weight: 10.0000 chunk 201 optimal weight: 8.9990 chunk 44 optimal weight: 10.0000 chunk 131 optimal weight: 2.9990 chunk 55 optimal weight: 8.9990 chunk 224 optimal weight: 0.0670 chunk 186 optimal weight: 0.8980 chunk 103 optimal weight: 10.0000 chunk 18 optimal weight: 10.0000 chunk 74 optimal weight: 10.0000 chunk 117 optimal weight: 6.9990 overall best weight: 3.9924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 147 GLN l 37 ASN o 38 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.1748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 36974 Z= 0.280 Angle : 0.674 9.431 55509 Z= 0.346 Chirality : 0.040 0.257 7124 Planarity : 0.005 0.052 2853 Dihedral : 23.043 172.049 18984 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.16 % Allowed : 8.94 % Favored : 90.90 % Rotamer: Outliers : 10.46 % Allowed : 21.77 % Favored : 67.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.08 % 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: -1.47 (0.24), residues: 1231 helix: 0.58 (0.26), residues: 436 sheet: -0.33 (0.33), residues: 232 loop : -2.62 (0.24), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP d 9 HIS 0.007 0.001 HIS h 22 PHE 0.016 0.002 PHE f 29 TYR 0.021 0.002 TYR r 27 ARG 0.007 0.001 ARG l 12 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 172 time to evaluate : 2.031 Fit side-chains revert: symmetry clash REVERT: d 17 ILE cc_start: 0.7708 (OUTLIER) cc_final: 0.7366 (mp) REVERT: d 114 LEU cc_start: 0.8962 (OUTLIER) cc_final: 0.8675 (mt) REVERT: d 143 ARG cc_start: 0.7994 (OUTLIER) cc_final: 0.6789 (ttm-80) REVERT: d 192 GLU cc_start: 0.5845 (OUTLIER) cc_final: 0.5150 (pm20) REVERT: e 101 GLU cc_start: 0.6181 (OUTLIER) cc_final: 0.5424 (mm-30) REVERT: e 117 LEU cc_start: 0.8898 (OUTLIER) cc_final: 0.8499 (mt) REVERT: h 36 ILE cc_start: 0.8131 (pt) cc_final: 0.7835 (mt) REVERT: l 53 MET cc_start: 0.8050 (ptp) cc_final: 0.7777 (ptp) REVERT: o 29 ILE cc_start: 0.8460 (OUTLIER) cc_final: 0.8114 (mt) outliers start: 111 outliers final: 92 residues processed: 254 average time/residue: 0.5024 time to fit residues: 205.8025 Evaluate side-chains 268 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 169 time to evaluate : 1.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain d residue 17 ILE Chi-restraints excluded: chain d residue 53 GLU Chi-restraints excluded: chain d residue 63 MET Chi-restraints excluded: chain d residue 71 LEU Chi-restraints excluded: chain d residue 114 LEU Chi-restraints excluded: chain d residue 139 VAL Chi-restraints excluded: chain d residue 140 ILE Chi-restraints excluded: chain d residue 143 ARG Chi-restraints excluded: chain d residue 150 SER Chi-restraints excluded: chain d residue 159 THR Chi-restraints excluded: chain d residue 192 GLU Chi-restraints excluded: chain e residue 4 ILE Chi-restraints excluded: chain e residue 9 LEU Chi-restraints excluded: chain e residue 22 THR Chi-restraints excluded: chain e residue 24 VAL Chi-restraints excluded: chain e residue 39 VAL Chi-restraints excluded: chain e residue 50 THR Chi-restraints excluded: chain e residue 84 GLU Chi-restraints excluded: chain e residue 95 LEU Chi-restraints excluded: chain e residue 100 VAL Chi-restraints excluded: chain e residue 101 GLU Chi-restraints excluded: chain e residue 111 VAL Chi-restraints excluded: chain e residue 117 LEU Chi-restraints excluded: chain e residue 125 SER Chi-restraints excluded: chain e residue 128 LEU Chi-restraints excluded: chain e residue 144 LEU Chi-restraints excluded: chain e residue 147 LEU Chi-restraints excluded: chain e residue 160 SER Chi-restraints excluded: chain e residue 164 ILE Chi-restraints excluded: chain e residue 165 ILE Chi-restraints excluded: chain f residue 4 ASP Chi-restraints excluded: chain f residue 5 THR Chi-restraints excluded: chain f residue 13 ILE Chi-restraints excluded: chain f residue 36 ASN Chi-restraints excluded: chain f residue 40 VAL Chi-restraints excluded: chain f residue 45 ASP Chi-restraints excluded: chain f residue 60 GLU Chi-restraints excluded: chain f residue 65 ILE Chi-restraints excluded: chain f residue 66 VAL Chi-restraints excluded: chain f residue 68 VAL Chi-restraints excluded: chain h residue 20 VAL Chi-restraints excluded: chain h residue 24 THR Chi-restraints excluded: chain h residue 27 VAL Chi-restraints excluded: chain h residue 46 ILE Chi-restraints excluded: chain h residue 49 VAL Chi-restraints excluded: chain h residue 52 ILE Chi-restraints excluded: chain h residue 54 ASP Chi-restraints excluded: chain h residue 62 VAL Chi-restraints excluded: chain h residue 69 ASN Chi-restraints excluded: chain h residue 75 THR Chi-restraints excluded: chain h residue 89 VAL Chi-restraints excluded: chain h residue 97 VAL Chi-restraints excluded: chain h residue 98 LEU Chi-restraints excluded: chain h residue 131 VAL Chi-restraints excluded: chain k residue 30 THR Chi-restraints excluded: chain k residue 35 THR Chi-restraints excluded: chain k residue 37 THR Chi-restraints excluded: chain k residue 46 SER Chi-restraints excluded: chain k residue 65 MET Chi-restraints excluded: chain k residue 81 THR Chi-restraints excluded: chain k residue 82 VAL Chi-restraints excluded: chain k residue 85 THR Chi-restraints excluded: chain k residue 86 VAL Chi-restraints excluded: chain k residue 107 VAL Chi-restraints excluded: chain l residue 4 ILE Chi-restraints excluded: chain l residue 8 VAL Chi-restraints excluded: chain l residue 21 SER Chi-restraints excluded: chain l residue 25 ASN Chi-restraints excluded: chain l residue 35 GLN Chi-restraints excluded: chain l residue 40 SER Chi-restraints excluded: chain l residue 54 THR Chi-restraints excluded: chain l residue 72 ASN Chi-restraints excluded: chain l residue 77 THR Chi-restraints excluded: chain l residue 92 VAL Chi-restraints excluded: chain l residue 111 VAL Chi-restraints excluded: chain l residue 120 VAL Chi-restraints excluded: chain l residue 121 ASN Chi-restraints excluded: chain l residue 122 ASP Chi-restraints excluded: chain o residue 11 ILE Chi-restraints excluded: chain o residue 29 ILE Chi-restraints excluded: chain o residue 38 GLN Chi-restraints excluded: chain o residue 75 ILE Chi-restraints excluded: chain o residue 89 ARG Chi-restraints excluded: chain p residue 32 ARG Chi-restraints excluded: chain p residue 36 THR Chi-restraints excluded: chain p residue 56 VAL Chi-restraints excluded: chain q residue 10 VAL Chi-restraints excluded: chain q residue 21 ASP Chi-restraints excluded: chain q residue 55 THR Chi-restraints excluded: chain q residue 81 VAL Chi-restraints excluded: chain r residue 20 ASN Chi-restraints excluded: chain r residue 32 LEU Chi-restraints excluded: chain r residue 34 LYS Chi-restraints excluded: chain r residue 48 VAL Chi-restraints excluded: chain r residue 63 ILE Chi-restraints excluded: chain r residue 76 SER Chi-restraints excluded: chain t residue 13 THR Chi-restraints excluded: chain t residue 39 VAL Chi-restraints excluded: chain t residue 81 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 216 optimal weight: 3.9990 chunk 25 optimal weight: 7.9990 chunk 127 optimal weight: 0.5980 chunk 163 optimal weight: 10.0000 chunk 188 optimal weight: 3.9990 chunk 125 optimal weight: 3.9990 chunk 223 optimal weight: 3.9990 chunk 139 optimal weight: 8.9990 chunk 136 optimal weight: 10.0000 chunk 103 optimal weight: 10.0000 chunk 138 optimal weight: 0.9980 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 147 GLN l 37 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.1851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 36974 Z= 0.206 Angle : 0.617 9.148 55509 Z= 0.322 Chirality : 0.037 0.241 7124 Planarity : 0.005 0.059 2853 Dihedral : 23.014 171.682 18984 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.16 % Allowed : 8.45 % Favored : 91.39 % Rotamer: Outliers : 9.80 % Allowed : 22.81 % Favored : 67.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.08 % 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: -1.33 (0.24), residues: 1231 helix: 0.76 (0.26), residues: 429 sheet: -0.31 (0.33), residues: 232 loop : -2.52 (0.24), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP d 9 HIS 0.006 0.001 HIS h 22 PHE 0.014 0.002 PHE f 29 TYR 0.019 0.002 TYR r 27 ARG 0.005 0.000 ARG r 40 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 168 time to evaluate : 2.050 Fit side-chains revert: symmetry clash REVERT: d 17 ILE cc_start: 0.7752 (OUTLIER) cc_final: 0.7415 (mp) REVERT: d 94 ARG cc_start: 0.8538 (OUTLIER) cc_final: 0.6809 (ptm-80) REVERT: d 114 LEU cc_start: 0.8958 (OUTLIER) cc_final: 0.8666 (mt) REVERT: d 143 ARG cc_start: 0.8065 (OUTLIER) cc_final: 0.6796 (ttm-80) REVERT: d 192 GLU cc_start: 0.5698 (OUTLIER) cc_final: 0.5004 (pm20) REVERT: e 4 ILE cc_start: 0.7051 (OUTLIER) cc_final: 0.6797 (pt) REVERT: e 101 GLU cc_start: 0.6176 (OUTLIER) cc_final: 0.5410 (mm-30) REVERT: e 117 LEU cc_start: 0.8880 (OUTLIER) cc_final: 0.8482 (mt) REVERT: h 36 ILE cc_start: 0.8112 (pt) cc_final: 0.7822 (mt) REVERT: l 20 ASP cc_start: 0.7171 (m-30) cc_final: 0.6948 (m-30) REVERT: l 53 MET cc_start: 0.8069 (ptp) cc_final: 0.7771 (ptp) REVERT: o 22 THR cc_start: 0.8257 (p) cc_final: 0.8023 (p) REVERT: o 29 ILE cc_start: 0.8421 (OUTLIER) cc_final: 0.8084 (mt) outliers start: 104 outliers final: 90 residues processed: 250 average time/residue: 0.4619 time to fit residues: 186.6418 Evaluate side-chains 264 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 165 time to evaluate : 1.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain d residue 17 ILE Chi-restraints excluded: chain d residue 53 GLU Chi-restraints excluded: chain d residue 63 MET Chi-restraints excluded: chain d residue 71 LEU Chi-restraints excluded: chain d residue 94 ARG Chi-restraints excluded: chain d residue 114 LEU Chi-restraints excluded: chain d residue 139 VAL Chi-restraints excluded: chain d residue 140 ILE Chi-restraints excluded: chain d residue 143 ARG Chi-restraints excluded: chain d residue 150 SER Chi-restraints excluded: chain d residue 159 THR Chi-restraints excluded: chain d residue 192 GLU Chi-restraints excluded: chain e residue 4 ILE Chi-restraints excluded: chain e residue 9 LEU Chi-restraints excluded: chain e residue 22 THR Chi-restraints excluded: chain e residue 24 VAL Chi-restraints excluded: chain e residue 39 VAL Chi-restraints excluded: chain e residue 50 THR Chi-restraints excluded: chain e residue 84 GLU Chi-restraints excluded: chain e residue 95 LEU Chi-restraints excluded: chain e residue 100 VAL Chi-restraints excluded: chain e residue 101 GLU Chi-restraints excluded: chain e residue 111 VAL Chi-restraints excluded: chain e residue 117 LEU Chi-restraints excluded: chain e residue 125 SER Chi-restraints excluded: chain e residue 128 LEU Chi-restraints excluded: chain e residue 144 LEU Chi-restraints excluded: chain e residue 147 LEU Chi-restraints excluded: chain e residue 160 SER Chi-restraints excluded: chain e residue 164 ILE Chi-restraints excluded: chain e residue 165 ILE Chi-restraints excluded: chain f residue 4 ASP Chi-restraints excluded: chain f residue 5 THR Chi-restraints excluded: chain f residue 13 ILE Chi-restraints excluded: chain f residue 36 ASN Chi-restraints excluded: chain f residue 40 VAL Chi-restraints excluded: chain f residue 45 ASP Chi-restraints excluded: chain f residue 60 GLU Chi-restraints excluded: chain f residue 65 ILE Chi-restraints excluded: chain f residue 66 VAL Chi-restraints excluded: chain f residue 68 VAL Chi-restraints excluded: chain h residue 20 VAL Chi-restraints excluded: chain h residue 24 THR Chi-restraints excluded: chain h residue 27 VAL Chi-restraints excluded: chain h residue 46 ILE Chi-restraints excluded: chain h residue 49 VAL Chi-restraints excluded: chain h residue 52 ILE Chi-restraints excluded: chain h residue 54 ASP Chi-restraints excluded: chain h residue 62 VAL Chi-restraints excluded: chain h residue 69 ASN Chi-restraints excluded: chain h residue 75 THR Chi-restraints excluded: chain h residue 89 VAL Chi-restraints excluded: chain h residue 97 VAL Chi-restraints excluded: chain h residue 98 LEU Chi-restraints excluded: chain h residue 126 GLU Chi-restraints excluded: chain h residue 131 VAL Chi-restraints excluded: chain k residue 30 THR Chi-restraints excluded: chain k residue 35 THR Chi-restraints excluded: chain k residue 37 THR Chi-restraints excluded: chain k residue 46 SER Chi-restraints excluded: chain k residue 65 MET Chi-restraints excluded: chain k residue 81 THR Chi-restraints excluded: chain k residue 82 VAL Chi-restraints excluded: chain k residue 85 THR Chi-restraints excluded: chain k residue 86 VAL Chi-restraints excluded: chain k residue 107 VAL Chi-restraints excluded: chain l residue 4 ILE Chi-restraints excluded: chain l residue 8 VAL Chi-restraints excluded: chain l residue 21 SER Chi-restraints excluded: chain l residue 25 ASN Chi-restraints excluded: chain l residue 35 GLN Chi-restraints excluded: chain l residue 54 THR Chi-restraints excluded: chain l residue 72 ASN Chi-restraints excluded: chain l residue 77 THR Chi-restraints excluded: chain l residue 92 VAL Chi-restraints excluded: chain l residue 111 VAL Chi-restraints excluded: chain l residue 120 VAL Chi-restraints excluded: chain l residue 121 ASN Chi-restraints excluded: chain l residue 122 ASP Chi-restraints excluded: chain o residue 10 GLU Chi-restraints excluded: chain o residue 29 ILE Chi-restraints excluded: chain o residue 75 ILE Chi-restraints excluded: chain o residue 89 ARG Chi-restraints excluded: chain p residue 32 ARG Chi-restraints excluded: chain p residue 36 THR Chi-restraints excluded: chain p residue 56 VAL Chi-restraints excluded: chain q residue 10 VAL Chi-restraints excluded: chain q residue 21 ASP Chi-restraints excluded: chain q residue 53 ASN Chi-restraints excluded: chain q residue 55 THR Chi-restraints excluded: chain q residue 81 VAL Chi-restraints excluded: chain r residue 20 ASN Chi-restraints excluded: chain r residue 32 LEU Chi-restraints excluded: chain r residue 34 LYS Chi-restraints excluded: chain r residue 48 VAL Chi-restraints excluded: chain r residue 63 ILE Chi-restraints excluded: chain r residue 76 SER Chi-restraints excluded: chain t residue 39 VAL Chi-restraints excluded: chain t residue 81 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 89 optimal weight: 10.0000 chunk 133 optimal weight: 9.9990 chunk 67 optimal weight: 10.0000 chunk 43 optimal weight: 10.0000 chunk 142 optimal weight: 9.9990 chunk 152 optimal weight: 2.9990 chunk 110 optimal weight: 10.0000 chunk 20 optimal weight: 10.0000 chunk 175 optimal weight: 1.9990 chunk 203 optimal weight: 5.9990 chunk 214 optimal weight: 5.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** d 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 87 ASN h 18 ASN l 37 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.1607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.092 36974 Z= 0.371 Angle : 0.773 10.507 55509 Z= 0.392 Chirality : 0.045 0.298 7124 Planarity : 0.006 0.073 2853 Dihedral : 23.176 173.070 18984 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.24 % Allowed : 9.99 % Favored : 89.76 % Rotamer: Outliers : 10.93 % Allowed : 21.96 % Favored : 67.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.08 % 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: -1.64 (0.23), residues: 1231 helix: 0.39 (0.25), residues: 436 sheet: -0.51 (0.33), residues: 243 loop : -2.66 (0.24), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP d 9 HIS 0.008 0.002 HIS h 22 PHE 0.020 0.003 PHE d 72 TYR 0.022 0.003 TYR r 27 ARG 0.008 0.001 ARG l 12 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 162 time to evaluate : 1.744 Fit side-chains revert: symmetry clash REVERT: d 17 ILE cc_start: 0.7880 (OUTLIER) cc_final: 0.7589 (mp) REVERT: d 114 LEU cc_start: 0.9006 (OUTLIER) cc_final: 0.8688 (mt) REVERT: d 143 ARG cc_start: 0.8227 (OUTLIER) cc_final: 0.7052 (ttt-90) REVERT: e 101 GLU cc_start: 0.6177 (OUTLIER) cc_final: 0.5418 (mm-30) REVERT: e 117 LEU cc_start: 0.8901 (OUTLIER) cc_final: 0.8482 (mt) REVERT: l 20 ASP cc_start: 0.7271 (m-30) cc_final: 0.6941 (m-30) REVERT: l 35 GLN cc_start: 0.7544 (OUTLIER) cc_final: 0.7107 (pp30) REVERT: l 53 MET cc_start: 0.8064 (ptp) cc_final: 0.7757 (ptp) REVERT: o 29 ILE cc_start: 0.8521 (OUTLIER) cc_final: 0.8189 (mt) outliers start: 116 outliers final: 96 residues processed: 249 average time/residue: 0.4782 time to fit residues: 190.7454 Evaluate side-chains 266 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 163 time to evaluate : 2.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain d residue 17 ILE Chi-restraints excluded: chain d residue 53 GLU Chi-restraints excluded: chain d residue 63 MET Chi-restraints excluded: chain d residue 71 LEU Chi-restraints excluded: chain d residue 114 LEU Chi-restraints excluded: chain d residue 139 VAL Chi-restraints excluded: chain d residue 140 ILE Chi-restraints excluded: chain d residue 143 ARG Chi-restraints excluded: chain d residue 150 SER Chi-restraints excluded: chain d residue 159 THR Chi-restraints excluded: chain d residue 189 GLU Chi-restraints excluded: chain d residue 190 ILE Chi-restraints excluded: chain e residue 9 LEU Chi-restraints excluded: chain e residue 22 THR Chi-restraints excluded: chain e residue 24 VAL Chi-restraints excluded: chain e residue 39 VAL Chi-restraints excluded: chain e residue 50 THR Chi-restraints excluded: chain e residue 76 MET Chi-restraints excluded: chain e residue 84 GLU Chi-restraints excluded: chain e residue 95 LEU Chi-restraints excluded: chain e residue 100 VAL Chi-restraints excluded: chain e residue 101 GLU Chi-restraints excluded: chain e residue 111 VAL Chi-restraints excluded: chain e residue 117 LEU Chi-restraints excluded: chain e residue 125 SER Chi-restraints excluded: chain e residue 128 LEU Chi-restraints excluded: chain e residue 144 LEU Chi-restraints excluded: chain e residue 147 LEU Chi-restraints excluded: chain e residue 160 SER Chi-restraints excluded: chain e residue 164 ILE Chi-restraints excluded: chain f residue 4 ASP Chi-restraints excluded: chain f residue 5 THR Chi-restraints excluded: chain f residue 13 ILE Chi-restraints excluded: chain f residue 33 LEU Chi-restraints excluded: chain f residue 36 ASN Chi-restraints excluded: chain f residue 40 VAL Chi-restraints excluded: chain f residue 45 ASP Chi-restraints excluded: chain f residue 60 GLU Chi-restraints excluded: chain f residue 65 ILE Chi-restraints excluded: chain f residue 66 VAL Chi-restraints excluded: chain f residue 68 VAL Chi-restraints excluded: chain f residue 87 ASN Chi-restraints excluded: chain f residue 98 VAL Chi-restraints excluded: chain h residue 20 VAL Chi-restraints excluded: chain h residue 27 VAL Chi-restraints excluded: chain h residue 46 ILE Chi-restraints excluded: chain h residue 49 VAL Chi-restraints excluded: chain h residue 52 ILE Chi-restraints excluded: chain h residue 54 ASP Chi-restraints excluded: chain h residue 62 VAL Chi-restraints excluded: chain h residue 69 ASN Chi-restraints excluded: chain h residue 75 THR Chi-restraints excluded: chain h residue 89 VAL Chi-restraints excluded: chain h residue 97 VAL Chi-restraints excluded: chain h residue 98 LEU Chi-restraints excluded: chain h residue 131 VAL Chi-restraints excluded: chain k residue 20 VAL Chi-restraints excluded: chain k residue 30 THR Chi-restraints excluded: chain k residue 35 THR Chi-restraints excluded: chain k residue 37 THR Chi-restraints excluded: chain k residue 46 SER Chi-restraints excluded: chain k residue 65 MET Chi-restraints excluded: chain k residue 82 VAL Chi-restraints excluded: chain k residue 85 THR Chi-restraints excluded: chain k residue 86 VAL Chi-restraints excluded: chain k residue 107 VAL Chi-restraints excluded: chain l residue 4 ILE Chi-restraints excluded: chain l residue 8 VAL Chi-restraints excluded: chain l residue 21 SER Chi-restraints excluded: chain l residue 25 ASN Chi-restraints excluded: chain l residue 35 GLN Chi-restraints excluded: chain l residue 36 THR Chi-restraints excluded: chain l residue 54 THR Chi-restraints excluded: chain l residue 72 ASN Chi-restraints excluded: chain l residue 77 THR Chi-restraints excluded: chain l residue 92 VAL Chi-restraints excluded: chain l residue 111 VAL Chi-restraints excluded: chain l residue 120 VAL Chi-restraints excluded: chain l residue 121 ASN Chi-restraints excluded: chain l residue 122 ASP Chi-restraints excluded: chain o residue 11 ILE Chi-restraints excluded: chain o residue 29 ILE Chi-restraints excluded: chain o residue 75 ILE Chi-restraints excluded: chain o residue 89 ARG Chi-restraints excluded: chain p residue 32 ARG Chi-restraints excluded: chain p residue 36 THR Chi-restraints excluded: chain p residue 56 VAL Chi-restraints excluded: chain q residue 10 VAL Chi-restraints excluded: chain q residue 16 VAL Chi-restraints excluded: chain q residue 21 ASP Chi-restraints excluded: chain q residue 30 THR Chi-restraints excluded: chain q residue 32 LYS Chi-restraints excluded: chain q residue 55 THR Chi-restraints excluded: chain q residue 81 VAL Chi-restraints excluded: chain r residue 20 ASN Chi-restraints excluded: chain r residue 32 LEU Chi-restraints excluded: chain r residue 34 LYS Chi-restraints excluded: chain r residue 48 VAL Chi-restraints excluded: chain r residue 63 ILE Chi-restraints excluded: chain r residue 76 SER Chi-restraints excluded: chain t residue 13 THR Chi-restraints excluded: chain t residue 39 VAL Chi-restraints excluded: chain t residue 81 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 195 optimal weight: 3.9990 chunk 208 optimal weight: 4.9990 chunk 214 optimal weight: 5.9990 chunk 125 optimal weight: 0.9990 chunk 90 optimal weight: 8.9990 chunk 163 optimal weight: 4.9990 chunk 63 optimal weight: 10.0000 chunk 188 optimal weight: 3.9990 chunk 197 optimal weight: 2.9990 chunk 207 optimal weight: 4.9990 chunk 136 optimal weight: 9.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** d 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 87 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.1739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 36974 Z= 0.250 Angle : 0.671 9.898 55509 Z= 0.348 Chirality : 0.040 0.259 7124 Planarity : 0.005 0.055 2853 Dihedral : 23.109 172.782 18984 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.16 % Allowed : 8.53 % Favored : 91.31 % Rotamer: Outliers : 9.80 % Allowed : 23.28 % Favored : 66.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.08 % 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: -1.51 (0.24), residues: 1231 helix: 0.49 (0.25), residues: 436 sheet: -0.37 (0.33), residues: 237 loop : -2.60 (0.24), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP d 9 HIS 0.007 0.001 HIS h 22 PHE 0.015 0.002 PHE d 72 TYR 0.019 0.002 TYR r 27 ARG 0.006 0.001 ARG l 12 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 172 time to evaluate : 1.911 Fit side-chains revert: symmetry clash REVERT: d 17 ILE cc_start: 0.7810 (OUTLIER) cc_final: 0.7507 (mp) REVERT: d 114 LEU cc_start: 0.8991 (OUTLIER) cc_final: 0.8677 (mt) REVERT: d 143 ARG cc_start: 0.8258 (OUTLIER) cc_final: 0.6931 (ttm-80) REVERT: d 192 GLU cc_start: 0.6080 (OUTLIER) cc_final: 0.5379 (pm20) REVERT: e 101 GLU cc_start: 0.6173 (OUTLIER) cc_final: 0.5426 (mm-30) REVERT: e 117 LEU cc_start: 0.8901 (OUTLIER) cc_final: 0.8492 (mt) REVERT: h 36 ILE cc_start: 0.8157 (pt) cc_final: 0.7785 (mt) REVERT: l 20 ASP cc_start: 0.7204 (m-30) cc_final: 0.6883 (m-30) REVERT: l 53 MET cc_start: 0.8072 (ptp) cc_final: 0.7761 (ptp) REVERT: o 29 ILE cc_start: 0.8450 (OUTLIER) cc_final: 0.8114 (mt) outliers start: 104 outliers final: 94 residues processed: 252 average time/residue: 0.4887 time to fit residues: 197.4322 Evaluate side-chains 270 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 169 time to evaluate : 1.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain d residue 17 ILE Chi-restraints excluded: chain d residue 53 GLU Chi-restraints excluded: chain d residue 63 MET Chi-restraints excluded: chain d residue 71 LEU Chi-restraints excluded: chain d residue 114 LEU Chi-restraints excluded: chain d residue 139 VAL Chi-restraints excluded: chain d residue 140 ILE Chi-restraints excluded: chain d residue 143 ARG Chi-restraints excluded: chain d residue 150 SER Chi-restraints excluded: chain d residue 152 ILE Chi-restraints excluded: chain d residue 159 THR Chi-restraints excluded: chain d residue 192 GLU Chi-restraints excluded: chain e residue 9 LEU Chi-restraints excluded: chain e residue 22 THR Chi-restraints excluded: chain e residue 24 VAL Chi-restraints excluded: chain e residue 39 VAL Chi-restraints excluded: chain e residue 50 THR Chi-restraints excluded: chain e residue 76 MET Chi-restraints excluded: chain e residue 84 GLU Chi-restraints excluded: chain e residue 95 LEU Chi-restraints excluded: chain e residue 96 MET Chi-restraints excluded: chain e residue 100 VAL Chi-restraints excluded: chain e residue 101 GLU Chi-restraints excluded: chain e residue 111 VAL Chi-restraints excluded: chain e residue 117 LEU Chi-restraints excluded: chain e residue 125 SER Chi-restraints excluded: chain e residue 128 LEU Chi-restraints excluded: chain e residue 144 LEU Chi-restraints excluded: chain e residue 147 LEU Chi-restraints excluded: chain e residue 160 SER Chi-restraints excluded: chain e residue 164 ILE Chi-restraints excluded: chain e residue 165 ILE Chi-restraints excluded: chain f residue 4 ASP Chi-restraints excluded: chain f residue 5 THR Chi-restraints excluded: chain f residue 13 ILE Chi-restraints excluded: chain f residue 33 LEU Chi-restraints excluded: chain f residue 36 ASN Chi-restraints excluded: chain f residue 40 VAL Chi-restraints excluded: chain f residue 45 ASP Chi-restraints excluded: chain f residue 60 GLU Chi-restraints excluded: chain f residue 65 ILE Chi-restraints excluded: chain f residue 66 VAL Chi-restraints excluded: chain f residue 68 VAL Chi-restraints excluded: chain h residue 20 VAL Chi-restraints excluded: chain h residue 27 VAL Chi-restraints excluded: chain h residue 46 ILE Chi-restraints excluded: chain h residue 49 VAL Chi-restraints excluded: chain h residue 52 ILE Chi-restraints excluded: chain h residue 54 ASP Chi-restraints excluded: chain h residue 62 VAL Chi-restraints excluded: chain h residue 69 ASN Chi-restraints excluded: chain h residue 75 THR Chi-restraints excluded: chain h residue 89 VAL Chi-restraints excluded: chain h residue 97 VAL Chi-restraints excluded: chain h residue 98 LEU Chi-restraints excluded: chain h residue 131 VAL Chi-restraints excluded: chain k residue 30 THR Chi-restraints excluded: chain k residue 35 THR Chi-restraints excluded: chain k residue 37 THR Chi-restraints excluded: chain k residue 46 SER Chi-restraints excluded: chain k residue 65 MET Chi-restraints excluded: chain k residue 82 VAL Chi-restraints excluded: chain k residue 85 THR Chi-restraints excluded: chain k residue 86 VAL Chi-restraints excluded: chain k residue 107 VAL Chi-restraints excluded: chain l residue 4 ILE Chi-restraints excluded: chain l residue 8 VAL Chi-restraints excluded: chain l residue 21 SER Chi-restraints excluded: chain l residue 25 ASN Chi-restraints excluded: chain l residue 34 THR Chi-restraints excluded: chain l residue 35 GLN Chi-restraints excluded: chain l residue 40 SER Chi-restraints excluded: chain l residue 54 THR Chi-restraints excluded: chain l residue 72 ASN Chi-restraints excluded: chain l residue 77 THR Chi-restraints excluded: chain l residue 92 VAL Chi-restraints excluded: chain l residue 111 VAL Chi-restraints excluded: chain l residue 120 VAL Chi-restraints excluded: chain l residue 121 ASN Chi-restraints excluded: chain l residue 122 ASP Chi-restraints excluded: chain o residue 10 GLU Chi-restraints excluded: chain o residue 29 ILE Chi-restraints excluded: chain o residue 75 ILE Chi-restraints excluded: chain o residue 89 ARG Chi-restraints excluded: chain p residue 32 ARG Chi-restraints excluded: chain p residue 36 THR Chi-restraints excluded: chain q residue 10 VAL Chi-restraints excluded: chain q residue 16 VAL Chi-restraints excluded: chain q residue 21 ASP Chi-restraints excluded: chain q residue 32 LYS Chi-restraints excluded: chain q residue 53 ASN Chi-restraints excluded: chain q residue 55 THR Chi-restraints excluded: chain q residue 81 VAL Chi-restraints excluded: chain r residue 20 ASN Chi-restraints excluded: chain r residue 32 LEU Chi-restraints excluded: chain r residue 34 LYS Chi-restraints excluded: chain r residue 48 VAL Chi-restraints excluded: chain r residue 63 ILE Chi-restraints excluded: chain r residue 76 SER Chi-restraints excluded: chain t residue 39 VAL Chi-restraints excluded: chain t residue 81 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 220 optimal weight: 0.9980 chunk 134 optimal weight: 5.9990 chunk 104 optimal weight: 10.0000 chunk 153 optimal weight: 9.9990 chunk 231 optimal weight: 6.9990 chunk 212 optimal weight: 4.9990 chunk 184 optimal weight: 8.9990 chunk 19 optimal weight: 10.0000 chunk 142 optimal weight: 5.9990 chunk 112 optimal weight: 2.9990 chunk 146 optimal weight: 1.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** d 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 87 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.1825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 36974 Z= 0.249 Angle : 0.654 9.465 55509 Z= 0.340 Chirality : 0.039 0.251 7124 Planarity : 0.005 0.056 2853 Dihedral : 23.043 171.992 18984 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.16 % Allowed : 9.26 % Favored : 90.58 % Rotamer: Outliers : 9.71 % Allowed : 23.47 % Favored : 66.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.08 % 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: -1.41 (0.24), residues: 1231 helix: 0.59 (0.26), residues: 430 sheet: -0.32 (0.33), residues: 232 loop : -2.50 (0.24), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP d 9 HIS 0.007 0.001 HIS h 22 PHE 0.014 0.002 PHE d 72 TYR 0.020 0.002 TYR r 27 ARG 0.006 0.001 ARG l 12 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 173 time to evaluate : 1.971 Fit side-chains revert: symmetry clash REVERT: d 17 ILE cc_start: 0.7724 (OUTLIER) cc_final: 0.7388 (mp) REVERT: d 114 LEU cc_start: 0.8952 (OUTLIER) cc_final: 0.8650 (mt) REVERT: d 143 ARG cc_start: 0.8251 (OUTLIER) cc_final: 0.6945 (ttm-80) REVERT: d 192 GLU cc_start: 0.5939 (OUTLIER) cc_final: 0.5237 (pm20) REVERT: e 101 GLU cc_start: 0.6175 (OUTLIER) cc_final: 0.5416 (mm-30) REVERT: e 117 LEU cc_start: 0.8896 (OUTLIER) cc_final: 0.8489 (mt) REVERT: h 36 ILE cc_start: 0.8139 (pt) cc_final: 0.7809 (mt) REVERT: l 20 ASP cc_start: 0.7203 (m-30) cc_final: 0.6900 (m-30) REVERT: l 53 MET cc_start: 0.8043 (ptp) cc_final: 0.7743 (ptp) REVERT: o 29 ILE cc_start: 0.8420 (OUTLIER) cc_final: 0.8085 (mt) REVERT: p 73 ILE cc_start: 0.7982 (pt) cc_final: 0.7708 (pt) outliers start: 103 outliers final: 95 residues processed: 251 average time/residue: 0.4708 time to fit residues: 189.5126 Evaluate side-chains 274 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 172 time to evaluate : 1.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain d residue 17 ILE Chi-restraints excluded: chain d residue 53 GLU Chi-restraints excluded: chain d residue 63 MET Chi-restraints excluded: chain d residue 71 LEU Chi-restraints excluded: chain d residue 114 LEU Chi-restraints excluded: chain d residue 139 VAL Chi-restraints excluded: chain d residue 140 ILE Chi-restraints excluded: chain d residue 143 ARG Chi-restraints excluded: chain d residue 150 SER Chi-restraints excluded: chain d residue 152 ILE Chi-restraints excluded: chain d residue 159 THR Chi-restraints excluded: chain d residue 190 ILE Chi-restraints excluded: chain d residue 192 GLU Chi-restraints excluded: chain e residue 9 LEU Chi-restraints excluded: chain e residue 22 THR Chi-restraints excluded: chain e residue 24 VAL Chi-restraints excluded: chain e residue 39 VAL Chi-restraints excluded: chain e residue 50 THR Chi-restraints excluded: chain e residue 84 GLU Chi-restraints excluded: chain e residue 95 LEU Chi-restraints excluded: chain e residue 96 MET Chi-restraints excluded: chain e residue 100 VAL Chi-restraints excluded: chain e residue 101 GLU Chi-restraints excluded: chain e residue 111 VAL Chi-restraints excluded: chain e residue 117 LEU Chi-restraints excluded: chain e residue 125 SER Chi-restraints excluded: chain e residue 128 LEU Chi-restraints excluded: chain e residue 144 LEU Chi-restraints excluded: chain e residue 147 LEU Chi-restraints excluded: chain e residue 160 SER Chi-restraints excluded: chain e residue 164 ILE Chi-restraints excluded: chain e residue 165 ILE Chi-restraints excluded: chain f residue 4 ASP Chi-restraints excluded: chain f residue 5 THR Chi-restraints excluded: chain f residue 13 ILE Chi-restraints excluded: chain f residue 33 LEU Chi-restraints excluded: chain f residue 36 ASN Chi-restraints excluded: chain f residue 40 VAL Chi-restraints excluded: chain f residue 45 ASP Chi-restraints excluded: chain f residue 60 GLU Chi-restraints excluded: chain f residue 65 ILE Chi-restraints excluded: chain f residue 66 VAL Chi-restraints excluded: chain f residue 68 VAL Chi-restraints excluded: chain h residue 20 VAL Chi-restraints excluded: chain h residue 27 VAL Chi-restraints excluded: chain h residue 46 ILE Chi-restraints excluded: chain h residue 49 VAL Chi-restraints excluded: chain h residue 52 ILE Chi-restraints excluded: chain h residue 54 ASP Chi-restraints excluded: chain h residue 62 VAL Chi-restraints excluded: chain h residue 69 ASN Chi-restraints excluded: chain h residue 75 THR Chi-restraints excluded: chain h residue 89 VAL Chi-restraints excluded: chain h residue 97 VAL Chi-restraints excluded: chain h residue 98 LEU Chi-restraints excluded: chain h residue 131 VAL Chi-restraints excluded: chain k residue 20 VAL Chi-restraints excluded: chain k residue 30 THR Chi-restraints excluded: chain k residue 35 THR Chi-restraints excluded: chain k residue 37 THR Chi-restraints excluded: chain k residue 46 SER Chi-restraints excluded: chain k residue 65 MET Chi-restraints excluded: chain k residue 82 VAL Chi-restraints excluded: chain k residue 85 THR Chi-restraints excluded: chain k residue 86 VAL Chi-restraints excluded: chain k residue 107 VAL Chi-restraints excluded: chain l residue 4 ILE Chi-restraints excluded: chain l residue 8 VAL Chi-restraints excluded: chain l residue 21 SER Chi-restraints excluded: chain l residue 25 ASN Chi-restraints excluded: chain l residue 34 THR Chi-restraints excluded: chain l residue 35 GLN Chi-restraints excluded: chain l residue 40 SER Chi-restraints excluded: chain l residue 54 THR Chi-restraints excluded: chain l residue 72 ASN Chi-restraints excluded: chain l residue 77 THR Chi-restraints excluded: chain l residue 92 VAL Chi-restraints excluded: chain l residue 111 VAL Chi-restraints excluded: chain l residue 120 VAL Chi-restraints excluded: chain l residue 121 ASN Chi-restraints excluded: chain l residue 122 ASP Chi-restraints excluded: chain o residue 10 GLU Chi-restraints excluded: chain o residue 29 ILE Chi-restraints excluded: chain o residue 75 ILE Chi-restraints excluded: chain o residue 89 ARG Chi-restraints excluded: chain p residue 32 ARG Chi-restraints excluded: chain p residue 36 THR Chi-restraints excluded: chain q residue 10 VAL Chi-restraints excluded: chain q residue 16 VAL Chi-restraints excluded: chain q residue 21 ASP Chi-restraints excluded: chain q residue 32 LYS Chi-restraints excluded: chain q residue 53 ASN Chi-restraints excluded: chain q residue 55 THR Chi-restraints excluded: chain q residue 81 VAL Chi-restraints excluded: chain r residue 20 ASN Chi-restraints excluded: chain r residue 32 LEU Chi-restraints excluded: chain r residue 34 LYS Chi-restraints excluded: chain r residue 48 VAL Chi-restraints excluded: chain r residue 63 ILE Chi-restraints excluded: chain r residue 76 SER Chi-restraints excluded: chain t residue 39 VAL Chi-restraints excluded: chain t residue 81 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 196 optimal weight: 6.9990 chunk 56 optimal weight: 8.9990 chunk 169 optimal weight: 3.9990 chunk 27 optimal weight: 10.0000 chunk 51 optimal weight: 10.0000 chunk 184 optimal weight: 4.9990 chunk 77 optimal weight: 10.0000 chunk 189 optimal weight: 2.9990 chunk 23 optimal weight: 10.0000 chunk 33 optimal weight: 10.0000 chunk 161 optimal weight: 0.8980 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** d 147 GLN ** 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 = 0.3119 r_free = 0.3119 target = 0.079681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 107)---------------| | r_work = 0.2787 r_free = 0.2787 target = 0.063421 restraints weight = 70465.570| |-----------------------------------------------------------------------------| r_work (start): 0.2778 rms_B_bonded: 0.57 r_work: 0.2619 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2530 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.1792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 36974 Z= 0.282 Angle : 0.679 9.576 55509 Z= 0.351 Chirality : 0.041 0.264 7124 Planarity : 0.005 0.057 2853 Dihedral : 23.055 172.199 18984 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.16 % Allowed : 8.61 % Favored : 91.23 % Rotamer: Outliers : 10.08 % Allowed : 23.28 % Favored : 66.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.08 % 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: -1.50 (0.24), residues: 1231 helix: 0.48 (0.25), residues: 436 sheet: -0.34 (0.33), residues: 236 loop : -2.59 (0.24), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP d 9 HIS 0.008 0.001 HIS h 22 PHE 0.016 0.002 PHE d 72 TYR 0.020 0.002 TYR r 27 ARG 0.006 0.001 ARG l 12 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5940.58 seconds wall clock time: 109 minutes 45.35 seconds (6585.35 seconds total)