Starting phenix.real_space_refine on Sun Aug 24 17:08:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9g6v_51105/08_2025/9g6v_51105.cif Found real_map, /net/cci-nas-00/data/ceres_data/9g6v_51105/08_2025/9g6v_51105.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9g6v_51105/08_2025/9g6v_51105.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9g6v_51105/08_2025/9g6v_51105.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9g6v_51105/08_2025/9g6v_51105.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9g6v_51105/08_2025/9g6v_51105.map" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 sd= 0.140 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: 4 Type Number sf(0) Gaussians S 140 5.16 5 C 13905 2.51 5 N 3705 2.21 5 O 4065 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 21815 Number of models: 1 Model: "" Number of chains: 20 Chain: "1" Number of atoms: 1190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1190 Classifications: {'peptide': 146} Link IDs: {'PTRANS': 10, 'TRANS': 135} Chain breaks: 1 Chain: "2" Number of atoms: 1176 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1176 Classifications: {'peptide': 147} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 137} Chain breaks: 4 Chain: "3" Number of atoms: 1682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1682 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 16, 'TRANS': 198} Chain breaks: 1 Chain: "B" Number of atoms: 1190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1190 Classifications: {'peptide': 146} Link IDs: {'PTRANS': 10, 'TRANS': 135} Chain breaks: 1 Chain: "D" Number of atoms: 1682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1682 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 16, 'TRANS': 198} Chain breaks: 1 Chain: "F" Number of atoms: 1190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1190 Classifications: {'peptide': 146} Link IDs: {'PTRANS': 10, 'TRANS': 135} Chain breaks: 1 Chain: "H" Number of atoms: 1682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1682 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 16, 'TRANS': 198} Chain breaks: 1 Chain: "J" Number of atoms: 1190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1190 Classifications: {'peptide': 146} Link IDs: {'PTRANS': 10, 'TRANS': 135} Chain breaks: 1 Chain: "L" Number of atoms: 1682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1682 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 16, 'TRANS': 198} Chain breaks: 1 Chain: "N" Number of atoms: 1190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1190 Classifications: {'peptide': 146} Link IDs: {'PTRANS': 10, 'TRANS': 135} Chain breaks: 1 Chain: "P" Number of atoms: 1682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1682 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 16, 'TRANS': 198} Chain breaks: 1 Chain: "A" Number of atoms: 315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 315 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "E" Number of atoms: 315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 315 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "I" Number of atoms: 315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 315 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "M" Number of atoms: 315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 315 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "Q" Number of atoms: 315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 315 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "C" Number of atoms: 1176 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1176 Classifications: {'peptide': 147} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 137} Chain breaks: 4 Chain: "G" Number of atoms: 1176 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1176 Classifications: {'peptide': 147} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 137} Chain breaks: 4 Chain: "K" Number of atoms: 1176 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1176 Classifications: {'peptide': 147} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 137} Chain breaks: 4 Chain: "O" Number of atoms: 1176 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1176 Classifications: {'peptide': 147} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 137} Chain breaks: 4 Time building chain proxies: 4.85, per 1000 atoms: 0.22 Number of scatterers: 21815 At special positions: 0 Unit cell: (177.072, 172.856, 79.05, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 140 16.00 O 4065 8.00 N 3705 7.00 C 13905 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=20, symmetry=0 Simple disulfide: pdb=" SG CYS A 109 " - pdb=" SG CYS A 131 " distance=2.03 Simple disulfide: pdb=" SG CYS A 115 " - pdb=" SG CYS A 147 " distance=2.03 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 130 " distance=2.03 Simple disulfide: pdb=" SG CYS A 125 " - pdb=" SG CYS A 146 " distance=2.03 Simple disulfide: pdb=" SG CYS E 109 " - pdb=" SG CYS E 131 " distance=2.03 Simple disulfide: pdb=" SG CYS E 115 " - pdb=" SG CYS E 147 " distance=2.03 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 130 " distance=2.03 Simple disulfide: pdb=" SG CYS E 125 " - pdb=" SG CYS E 146 " distance=2.03 Simple disulfide: pdb=" SG CYS I 109 " - pdb=" SG CYS I 131 " distance=2.03 Simple disulfide: pdb=" SG CYS I 115 " - pdb=" SG CYS I 147 " distance=2.03 Simple disulfide: pdb=" SG CYS I 119 " - pdb=" SG CYS I 130 " distance=2.03 Simple disulfide: pdb=" SG CYS I 125 " - pdb=" SG CYS I 146 " distance=2.03 Simple disulfide: pdb=" SG CYS M 109 " - pdb=" SG CYS M 131 " distance=2.03 Simple disulfide: pdb=" SG CYS M 115 " - pdb=" SG CYS M 147 " distance=2.03 Simple disulfide: pdb=" SG CYS M 119 " - pdb=" SG CYS M 130 " distance=2.03 Simple disulfide: pdb=" SG CYS M 125 " - pdb=" SG CYS M 146 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 109 " - pdb=" SG CYS Q 131 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 115 " - pdb=" SG CYS Q 147 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 119 " - pdb=" SG CYS Q 130 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 125 " - pdb=" SG CYS Q 146 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.51 Conformation dependent library (CDL) restraints added in 846.5 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 5320 Ramachandran restraints generated. 2660 Oldfield, 0 Emsley, 2660 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5140 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 14 sheets defined 2.0% alpha, 9.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain '1' and resid 31 through 36 Processing helix chain '1' and resid 52 through 56 removed outlier: 3.630A pdb=" N THR 1 56 " --> pdb=" O LEU 1 53 " (cutoff:3.500A) Processing helix chain '1' and resid 60 through 67 Processing helix chain '2' and resid 135 through 143 removed outlier: 3.770A pdb=" N PHE 2 138 " --> pdb=" O ARG 2 135 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N SER 2 141 " --> pdb=" O PHE 2 138 " (cutoff:3.500A) Processing helix chain '3' and resid 43 through 51 removed outlier: 3.518A pdb=" N VAL 3 47 " --> pdb=" O ASN 3 43 " (cutoff:3.500A) Processing helix chain '3' and resid 82 through 86 Processing helix chain '3' and resid 88 through 94 Processing helix chain '3' and resid 137 through 142 Processing sheet with id=1A, first strand: chain '1' and resid 39 through 46 removed outlier: 9.264A pdb=" N THR 1 40 " --> pdb=" O MET 1 185 " (cutoff:3.500A) removed outlier: 8.329A pdb=" N MET 1 185 " --> pdb=" O THR 1 40 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N VAL 1 42 " --> pdb=" O TYR 1 183 " (cutoff:3.500A) removed outlier: 8.181A pdb=" N TYR 1 183 " --> pdb=" O VAL 1 42 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N THR 1 44 " --> pdb=" O VAL 1 181 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N VAL 1 181 " --> pdb=" O THR 1 44 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N TYR 1 182 " --> pdb=" O CYS 1 80 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N CYS 1 80 " --> pdb=" O TYR 1 182 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N ARG 1 184 " --> pdb=" O ILE 1 78 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N ILE 1 78 " --> pdb=" O ARG 1 184 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N LYS 1 186 " --> pdb=" O LEU 1 76 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N LEU 1 76 " --> pdb=" O LYS 1 186 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N ALA 1 188 " --> pdb=" O CYS 1 74 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N CYS 1 74 " --> pdb=" O ALA 1 188 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N LEU 1 190 " --> pdb=" O TYR 1 72 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N TYR 1 72 " --> pdb=" O LEU 1 190 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N CYS 1 192 " --> pdb=" O THR 1 70 " (cutoff:3.500A) Processing sheet with id=1B, first strand: chain '1' and resid 39 through 46 removed outlier: 9.264A pdb=" N THR 1 40 " --> pdb=" O MET 1 185 " (cutoff:3.500A) removed outlier: 8.329A pdb=" N MET 1 185 " --> pdb=" O THR 1 40 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N VAL 1 42 " --> pdb=" O TYR 1 183 " (cutoff:3.500A) removed outlier: 8.181A pdb=" N TYR 1 183 " --> pdb=" O VAL 1 42 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N THR 1 44 " --> pdb=" O VAL 1 181 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N VAL 1 181 " --> pdb=" O THR 1 44 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N TYR 1 182 " --> pdb=" O CYS 1 80 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N CYS 1 80 " --> pdb=" O TYR 1 182 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N ARG 1 184 " --> pdb=" O ILE 1 78 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N ILE 1 78 " --> pdb=" O ARG 1 184 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N LYS 1 186 " --> pdb=" O LEU 1 76 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N LEU 1 76 " --> pdb=" O LYS 1 186 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N ALA 1 188 " --> pdb=" O CYS 1 74 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N CYS 1 74 " --> pdb=" O ALA 1 188 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N LEU 1 190 " --> pdb=" O TYR 1 72 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N TYR 1 72 " --> pdb=" O LEU 1 190 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N CYS 1 192 " --> pdb=" O THR 1 70 " (cutoff:3.500A) Processing sheet with id=1C, first strand: chain '1' and resid 112 through 117 Processing sheet with id=1D, first strand: chain '1' and resid 49 through 50 Processing sheet with id=2E, first strand: chain '2' and resid 78 through 79 Processing sheet with id=2F, first strand: chain '2' and resid 82 through 83 removed outlier: 7.446A pdb=" N LEU 2 179 " --> pdb=" O LEU 2 83 " (cutoff:3.500A) Processing sheet with id=2G, first strand: chain '2' and resid 145 through 148 removed outlier: 6.625A pdb=" N GLY 2 118 " --> pdb=" O PRO 2 186 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N SER 2 120 " --> pdb=" O LEU 2 184 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N TRP 2 177 " --> pdb=" O LEU 2 83 " (cutoff:3.500A) Processing sheet with id=2H, first strand: chain '2' and resid 145 through 148 removed outlier: 6.625A pdb=" N GLY 2 118 " --> pdb=" O PRO 2 186 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N SER 2 120 " --> pdb=" O LEU 2 184 " (cutoff:3.500A) Processing sheet with id=3A, first strand: chain '3' and resid 53 through 54 Processing sheet with id=3B, first strand: chain '3' and resid 62 through 64 removed outlier: 7.648A pdb=" N VAL 3 203 " --> pdb=" O VAL 3 63 " (cutoff:3.500A) Processing sheet with id=3C, first strand: chain '3' and resid 156 through 161 Processing sheet with id=3D, first strand: chain '3' and resid 156 through 161 Processing sheet with id=3E, first strand: chain '3' and resid 72 through 77 removed outlier: 6.292A pdb=" N VAL 3 72 " --> pdb=" O GLN 3 190 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N GLN 3 190 " --> pdb=" O VAL 3 72 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N THR 3 74 " --> pdb=" O VAL 3 188 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N TRP 3 185 " --> pdb=" O ILE 3 125 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ILE 3 125 " --> pdb=" O TRP 3 185 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N TYR 3 145 " --> pdb=" O TYR 3 124 " (cutoff:3.500A) Processing sheet with id=3F, first strand: chain '3' and resid 170 through 171 125 hydrogen bonds defined for protein. 318 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.54 Time building geometry restraints manager: 2.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 7041 1.34 - 1.46: 5645 1.46 - 1.58: 9564 1.58 - 1.69: 0 1.69 - 1.81: 195 Bond restraints: 22445 Sorted by residual: bond pdb=" N THR C 154 " pdb=" CA THR C 154 " ideal model delta sigma weight residual 1.462 1.474 -0.012 1.48e-02 4.57e+03 6.37e-01 bond pdb=" N THR G 154 " pdb=" CA THR G 154 " ideal model delta sigma weight residual 1.462 1.473 -0.012 1.48e-02 4.57e+03 6.34e-01 bond pdb=" N THR K 154 " pdb=" CA THR K 154 " ideal model delta sigma weight residual 1.462 1.473 -0.011 1.48e-02 4.57e+03 5.52e-01 bond pdb=" N THR O 154 " pdb=" CA THR O 154 " ideal model delta sigma weight residual 1.462 1.472 -0.011 1.48e-02 4.57e+03 5.20e-01 bond pdb=" CA THR K 154 " pdb=" CB THR K 154 " ideal model delta sigma weight residual 1.532 1.543 -0.011 1.51e-02 4.39e+03 5.02e-01 ... (remaining 22440 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.04: 29641 1.04 - 2.09: 673 2.09 - 3.13: 251 3.13 - 4.17: 14 4.17 - 5.22: 6 Bond angle restraints: 30585 Sorted by residual: angle pdb=" CA ASN 2 153 " pdb=" C ASN 2 153 " pdb=" N THR 2 154 " ideal model delta sigma weight residual 119.71 116.92 2.79 1.17e+00 7.31e-01 5.69e+00 angle pdb=" CA ASN G 153 " pdb=" C ASN G 153 " pdb=" N THR G 154 " ideal model delta sigma weight residual 119.71 116.96 2.75 1.17e+00 7.31e-01 5.52e+00 angle pdb=" CA ASN C 153 " pdb=" C ASN C 153 " pdb=" N THR C 154 " ideal model delta sigma weight residual 119.71 117.00 2.71 1.17e+00 7.31e-01 5.38e+00 angle pdb=" CA ASN O 153 " pdb=" C ASN O 153 " pdb=" N THR O 154 " ideal model delta sigma weight residual 119.71 117.00 2.71 1.17e+00 7.31e-01 5.38e+00 angle pdb=" CA ASN K 153 " pdb=" C ASN K 153 " pdb=" N THR K 154 " ideal model delta sigma weight residual 119.71 117.03 2.68 1.17e+00 7.31e-01 5.27e+00 ... (remaining 30580 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.35: 12083 12.35 - 24.70: 811 24.70 - 37.04: 169 37.04 - 49.39: 22 49.39 - 61.74: 5 Dihedral angle restraints: 13090 sinusoidal: 5080 harmonic: 8010 Sorted by residual: dihedral pdb=" CA GLN N 90 " pdb=" CB GLN N 90 " pdb=" CG GLN N 90 " pdb=" CD GLN N 90 " ideal model delta sinusoidal sigma weight residual 60.00 118.66 -58.66 3 1.50e+01 4.44e-03 9.47e+00 dihedral pdb=" CA ASN D 31 " pdb=" C ASN D 31 " pdb=" N PRO D 32 " pdb=" CA PRO D 32 " ideal model delta harmonic sigma weight residual -180.00 -164.67 -15.33 0 5.00e+00 4.00e-02 9.41e+00 dihedral pdb=" CA ASN L 31 " pdb=" C ASN L 31 " pdb=" N PRO L 32 " pdb=" CA PRO L 32 " ideal model delta harmonic sigma weight residual -180.00 -164.78 -15.22 0 5.00e+00 4.00e-02 9.27e+00 ... (remaining 13087 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 1904 0.027 - 0.053: 890 0.053 - 0.080: 236 0.080 - 0.106: 190 0.106 - 0.133: 70 Chirality restraints: 3290 Sorted by residual: chirality pdb=" CA VAL 1 117 " pdb=" N VAL 1 117 " pdb=" C VAL 1 117 " pdb=" CB VAL 1 117 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.40e-01 chirality pdb=" CA VAL 3 161 " pdb=" N VAL 3 161 " pdb=" C VAL 3 161 " pdb=" CB VAL 3 161 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.36e-01 chirality pdb=" CA ILE I 141 " pdb=" N ILE I 141 " pdb=" C ILE I 141 " pdb=" CB ILE I 141 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.98e-01 ... (remaining 3287 not shown) Planarity restraints: 3970 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG 1 194 " -0.019 5.00e-02 4.00e+02 2.89e-02 1.34e+00 pdb=" N PRO 1 195 " 0.050 5.00e-02 4.00e+02 pdb=" CA PRO 1 195 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO 1 195 " -0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG J 194 " -0.019 5.00e-02 4.00e+02 2.87e-02 1.31e+00 pdb=" N PRO J 195 " 0.050 5.00e-02 4.00e+02 pdb=" CA PRO J 195 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO J 195 " -0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG B 194 " -0.019 5.00e-02 4.00e+02 2.79e-02 1.25e+00 pdb=" N PRO B 195 " 0.048 5.00e-02 4.00e+02 pdb=" CA PRO B 195 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO B 195 " -0.016 5.00e-02 4.00e+02 ... (remaining 3967 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 4831 2.78 - 3.31: 19057 3.31 - 3.84: 35575 3.84 - 4.37: 43805 4.37 - 4.90: 76224 Nonbonded interactions: 179492 Sorted by model distance: nonbonded pdb=" OH TYR 3 163 " pdb=" OG SER 3 170 " model vdw 2.254 3.040 nonbonded pdb=" O PRO 3 52 " pdb=" OG SER O 141 " model vdw 2.268 3.040 nonbonded pdb=" O PRO H 52 " pdb=" OG SER C 141 " model vdw 2.271 3.040 nonbonded pdb=" O PRO P 52 " pdb=" OG SER K 141 " model vdw 2.275 3.040 nonbonded pdb=" OH TYR P 124 " pdb=" O ASN P 183 " model vdw 2.278 3.040 ... (remaining 179487 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain '1' selection = chain 'B' selection = chain 'F' selection = chain 'J' selection = chain 'N' } ncs_group { reference = chain '2' selection = chain 'C' selection = chain 'G' selection = chain 'K' selection = chain 'O' } ncs_group { reference = chain '3' selection = chain 'D' selection = chain 'H' selection = chain 'L' selection = chain 'P' } ncs_group { reference = chain 'A' selection = chain 'E' selection = chain 'I' selection = chain 'M' selection = chain 'Q' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.490 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: 0.020 Extract box with map and model: 0.370 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 17.240 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.050 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:7.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 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 : 0.003 0.030 22465 Z= 0.115 Angle : 0.442 5.218 30625 Z= 0.237 Chirality : 0.040 0.133 3290 Planarity : 0.003 0.029 3970 Dihedral : 8.594 61.740 7890 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 0.68 % Allowed : 2.89 % Favored : 96.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.91 (0.17), residues: 2660 helix: -1.69 (0.30), residues: 240 sheet: -0.26 (0.19), residues: 845 loop : -0.55 (0.17), residues: 1575 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 214 TYR 0.008 0.001 TYR P 41 PHE 0.010 0.001 PHE 1 115 TRP 0.010 0.001 TRP Q 138 HIS 0.002 0.000 HIS G 145 Details of bonding type rmsd covalent geometry : bond 0.00265 (22445) covalent geometry : angle 0.44179 (30585) SS BOND : bond 0.00078 ( 20) SS BOND : angle 0.54538 ( 40) hydrogen bonds : bond 0.02783 ( 89) hydrogen bonds : angle 4.30819 ( 318) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5320 Ramachandran restraints generated. 2660 Oldfield, 0 Emsley, 2660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5320 Ramachandran restraints generated. 2660 Oldfield, 0 Emsley, 2660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 537 residues out of total 2355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 521 time to evaluate : 0.670 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 111 ASN cc_start: 0.9009 (m-40) cc_final: 0.8749 (m-40) REVERT: 2 101 MET cc_start: 0.4859 (ptp) cc_final: 0.4292 (ptp) REVERT: 2 108 GLN cc_start: 0.8112 (mt0) cc_final: 0.7851 (mt0) REVERT: 2 199 GLU cc_start: 0.7421 (mp0) cc_final: 0.7078 (mp0) REVERT: 2 207 THR cc_start: 0.8096 (p) cc_final: 0.7722 (p) REVERT: 3 42 SER cc_start: 0.8842 (p) cc_final: 0.8549 (t) REVERT: 3 179 MET cc_start: 0.7046 (tpt) cc_final: 0.6554 (mpt) REVERT: 3 190 GLN cc_start: 0.7747 (pt0) cc_final: 0.6609 (pp30) REVERT: D 42 SER cc_start: 0.8919 (p) cc_final: 0.8590 (t) REVERT: D 179 MET cc_start: 0.7116 (tpt) cc_final: 0.6304 (mpt) REVERT: D 189 PHE cc_start: 0.7508 (m-80) cc_final: 0.7269 (m-80) REVERT: D 190 GLN cc_start: 0.7792 (pt0) cc_final: 0.6860 (pp30) REVERT: F 102 ASP cc_start: 0.7446 (m-30) cc_final: 0.7235 (m-30) REVERT: H 42 SER cc_start: 0.8796 (p) cc_final: 0.8526 (t) REVERT: H 179 MET cc_start: 0.7497 (tpt) cc_final: 0.6812 (mmt) REVERT: H 190 GLN cc_start: 0.7739 (pt0) cc_final: 0.6827 (pp30) REVERT: J 36 MET cc_start: 0.8950 (mmm) cc_final: 0.8642 (mmt) REVERT: L 42 SER cc_start: 0.8705 (p) cc_final: 0.8404 (t) REVERT: L 179 MET cc_start: 0.7073 (tpt) cc_final: 0.6307 (mpt) REVERT: L 190 GLN cc_start: 0.7708 (pt0) cc_final: 0.6719 (pp30) REVERT: L 220 VAL cc_start: 0.8497 (OUTLIER) cc_final: 0.8292 (t) REVERT: N 111 ASN cc_start: 0.9012 (m-40) cc_final: 0.8795 (m110) REVERT: P 42 SER cc_start: 0.8679 (p) cc_final: 0.8372 (t) REVERT: P 86 LYS cc_start: 0.8107 (ttpt) cc_final: 0.7798 (ptmt) REVERT: P 179 MET cc_start: 0.7418 (tpt) cc_final: 0.6710 (mpt) REVERT: P 190 GLN cc_start: 0.7691 (pt0) cc_final: 0.6764 (pp30) REVERT: Q 143 LEU cc_start: 0.8943 (mt) cc_final: 0.8743 (mt) REVERT: C 101 MET cc_start: 0.4463 (ptp) cc_final: 0.3824 (ptp) REVERT: C 108 GLN cc_start: 0.8275 (mt0) cc_final: 0.8011 (mt0) REVERT: C 182 MET cc_start: 0.8088 (ttp) cc_final: 0.7858 (ptm) REVERT: C 199 GLU cc_start: 0.7326 (mp0) cc_final: 0.7070 (mp0) REVERT: C 207 THR cc_start: 0.8152 (p) cc_final: 0.7870 (p) REVERT: G 108 GLN cc_start: 0.8256 (mt0) cc_final: 0.7945 (mm110) REVERT: G 128 GLU cc_start: 0.8616 (mt-10) cc_final: 0.8338 (mt-10) REVERT: G 175 GLN cc_start: 0.7075 (mp10) cc_final: 0.6745 (mm-40) REVERT: G 199 GLU cc_start: 0.7325 (mp0) cc_final: 0.7022 (mp0) REVERT: G 204 ILE cc_start: 0.8913 (mt) cc_final: 0.8675 (mt) REVERT: G 207 THR cc_start: 0.8083 (p) cc_final: 0.7753 (p) REVERT: K 199 GLU cc_start: 0.7375 (mp0) cc_final: 0.7112 (mp0) REVERT: K 207 THR cc_start: 0.8205 (p) cc_final: 0.7707 (p) REVERT: O 128 GLU cc_start: 0.8721 (mt-10) cc_final: 0.8492 (mt-10) REVERT: O 175 GLN cc_start: 0.7044 (mp10) cc_final: 0.6533 (mm-40) REVERT: O 199 GLU cc_start: 0.7204 (mp0) cc_final: 0.6978 (mp0) outliers start: 16 outliers final: 2 residues processed: 527 average time/residue: 0.5844 time to fit residues: 351.8142 Evaluate side-chains 407 residues out of total 2355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 404 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 45 ASN Chi-restraints excluded: chain F residue 45 ASN Chi-restraints excluded: chain L residue 220 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 8.9990 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 8.9990 chunk 207 optimal weight: 0.7980 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 0.9980 chunk 183 optimal weight: 4.9990 chunk 111 optimal weight: 9.9990 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 45 ASN ** 1 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 110 ASN ** 2 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 117 ASN 2 145 HIS 2 149 ASN ** 2 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 174 HIS B 92 ASN B 110 ASN B 111 ASN ** F 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 110 ASN F 111 ASN H 146 HIS J 92 ASN J 110 ASN J 111 ASN N 45 ASN N 92 ASN N 110 ASN P 143 HIS P 146 HIS ** C 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 145 HIS ** C 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 145 HIS ** G 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 174 HIS K 145 HIS O 139 GLN O 145 HIS O 149 ASN O 174 HIS Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.163208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.112925 restraints weight = 28888.013| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 3.32 r_work: 0.3230 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.1507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 22465 Z= 0.171 Angle : 0.497 6.507 30625 Z= 0.259 Chirality : 0.042 0.143 3290 Planarity : 0.004 0.038 3970 Dihedral : 3.957 27.004 3010 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 3.14 % Allowed : 9.60 % Favored : 87.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.11 (0.17), residues: 2660 helix: -1.84 (0.30), residues: 240 sheet: -0.46 (0.18), residues: 865 loop : -0.65 (0.17), residues: 1555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 102 TYR 0.011 0.001 TYR P 11 PHE 0.015 0.001 PHE O 116 TRP 0.010 0.001 TRP Q 138 HIS 0.011 0.001 HIS P 143 Details of bonding type rmsd covalent geometry : bond 0.00410 (22445) covalent geometry : angle 0.49719 (30585) SS BOND : bond 0.00103 ( 20) SS BOND : angle 0.49677 ( 40) hydrogen bonds : bond 0.03040 ( 89) hydrogen bonds : angle 4.46637 ( 318) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5320 Ramachandran restraints generated. 2660 Oldfield, 0 Emsley, 2660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5320 Ramachandran restraints generated. 2660 Oldfield, 0 Emsley, 2660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 469 residues out of total 2355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 395 time to evaluate : 0.764 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 43 LEU cc_start: 0.9013 (OUTLIER) cc_final: 0.8495 (pp) REVERT: 1 111 ASN cc_start: 0.8908 (m-40) cc_final: 0.8635 (m-40) REVERT: 2 82 GLU cc_start: 0.8198 (mp0) cc_final: 0.7711 (mp0) REVERT: 2 101 MET cc_start: 0.4972 (ptp) cc_final: 0.4508 (ptp) REVERT: 2 137 GLU cc_start: 0.7867 (pm20) cc_final: 0.7613 (pm20) REVERT: 2 199 GLU cc_start: 0.7709 (mp0) cc_final: 0.7170 (mp0) REVERT: 3 42 SER cc_start: 0.8892 (p) cc_final: 0.8378 (t) REVERT: 3 109 MET cc_start: 0.8693 (ttp) cc_final: 0.8141 (ttp) REVERT: 3 119 LYS cc_start: 0.8298 (mttt) cc_final: 0.7979 (mptt) REVERT: 3 179 MET cc_start: 0.7337 (tpt) cc_final: 0.6315 (mpt) REVERT: 3 190 GLN cc_start: 0.8005 (pt0) cc_final: 0.6406 (pp30) REVERT: 3 214 ARG cc_start: 0.8730 (ptm160) cc_final: 0.8473 (ptm-80) REVERT: 3 221 ARG cc_start: 0.5560 (OUTLIER) cc_final: 0.5179 (mtp180) REVERT: B 45 ASN cc_start: 0.8569 (t0) cc_final: 0.8248 (t0) REVERT: B 86 ARG cc_start: 0.8408 (ptt180) cc_final: 0.8183 (ptp90) REVERT: D 21 THR cc_start: 0.8418 (p) cc_final: 0.8021 (t) REVERT: D 42 SER cc_start: 0.8933 (p) cc_final: 0.8433 (t) REVERT: D 179 MET cc_start: 0.7426 (tpt) cc_final: 0.6148 (mpt) REVERT: D 189 PHE cc_start: 0.7778 (m-80) cc_final: 0.7496 (m-80) REVERT: D 190 GLN cc_start: 0.8057 (pt0) cc_final: 0.6779 (pp30) REVERT: F 83 GLU cc_start: 0.6921 (pm20) cc_final: 0.6716 (pm20) REVERT: H 42 SER cc_start: 0.8864 (p) cc_final: 0.8422 (t) REVERT: H 119 LYS cc_start: 0.8414 (mttt) cc_final: 0.8192 (mppt) REVERT: H 179 MET cc_start: 0.7488 (tpt) cc_final: 0.6492 (mmt) REVERT: H 190 GLN cc_start: 0.7945 (pt0) cc_final: 0.6521 (pp30) REVERT: J 36 MET cc_start: 0.8934 (mmm) cc_final: 0.8536 (mmt) REVERT: L 42 SER cc_start: 0.8749 (p) cc_final: 0.8274 (t) REVERT: L 119 LYS cc_start: 0.8407 (mttt) cc_final: 0.8069 (mppt) REVERT: L 121 MET cc_start: 0.7779 (pmm) cc_final: 0.7476 (pmm) REVERT: L 179 MET cc_start: 0.7369 (tpt) cc_final: 0.6117 (mpt) REVERT: L 204 SER cc_start: 0.8751 (p) cc_final: 0.8383 (t) REVERT: N 92 ASN cc_start: 0.8476 (t0) cc_final: 0.8270 (t0) REVERT: N 111 ASN cc_start: 0.8922 (m-40) cc_final: 0.8664 (m110) REVERT: P 42 SER cc_start: 0.8765 (p) cc_final: 0.8297 (t) REVERT: P 119 LYS cc_start: 0.8555 (mttt) cc_final: 0.8210 (mppt) REVERT: P 179 MET cc_start: 0.7649 (tpt) cc_final: 0.7286 (tpp) REVERT: E 141 ILE cc_start: 0.8336 (mt) cc_final: 0.8035 (mm) REVERT: C 101 MET cc_start: 0.3902 (ptp) cc_final: 0.3501 (ptp) REVERT: C 108 GLN cc_start: 0.8062 (mt0) cc_final: 0.7590 (mt0) REVERT: C 128 GLU cc_start: 0.8632 (mt-10) cc_final: 0.8410 (mt-10) REVERT: C 137 GLU cc_start: 0.8367 (OUTLIER) cc_final: 0.7869 (pm20) REVERT: C 182 MET cc_start: 0.8149 (ttp) cc_final: 0.7726 (ptm) REVERT: C 199 GLU cc_start: 0.7511 (mp0) cc_final: 0.7050 (mp0) REVERT: G 101 MET cc_start: 0.3994 (OUTLIER) cc_final: 0.3329 (ptp) REVERT: G 108 GLN cc_start: 0.8094 (mt0) cc_final: 0.7830 (mt0) REVERT: G 137 GLU cc_start: 0.8260 (OUTLIER) cc_final: 0.7762 (pm20) REVERT: G 158 ILE cc_start: 0.8527 (OUTLIER) cc_final: 0.8191 (mp) REVERT: G 162 TYR cc_start: 0.8053 (t80) cc_final: 0.7826 (t80) REVERT: G 199 GLU cc_start: 0.7471 (mp0) cc_final: 0.6992 (mp0) REVERT: G 204 ILE cc_start: 0.8754 (mt) cc_final: 0.8553 (mt) REVERT: K 137 GLU cc_start: 0.8282 (OUTLIER) cc_final: 0.7768 (pm20) REVERT: K 199 GLU cc_start: 0.7593 (mp0) cc_final: 0.7163 (mp0) REVERT: O 128 GLU cc_start: 0.8757 (mt-10) cc_final: 0.8548 (mt-10) REVERT: O 137 GLU cc_start: 0.8043 (OUTLIER) cc_final: 0.7646 (pm20) REVERT: O 199 GLU cc_start: 0.7546 (mp0) cc_final: 0.7051 (mp0) outliers start: 74 outliers final: 35 residues processed: 428 average time/residue: 0.5898 time to fit residues: 287.0647 Evaluate side-chains 420 residues out of total 2355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 377 time to evaluate : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 28 VAL Chi-restraints excluded: chain 1 residue 43 LEU Chi-restraints excluded: chain 1 residue 44 THR Chi-restraints excluded: chain 1 residue 108 SER Chi-restraints excluded: chain 1 residue 185 MET Chi-restraints excluded: chain 2 residue 141 SER Chi-restraints excluded: chain 2 residue 178 SER Chi-restraints excluded: chain 2 residue 188 THR Chi-restraints excluded: chain 3 residue 221 ARG Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 108 SER Chi-restraints excluded: chain D residue 175 ASP Chi-restraints excluded: chain D residue 206 SER Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 108 SER Chi-restraints excluded: chain H residue 2 ILE Chi-restraints excluded: chain H residue 206 SER Chi-restraints excluded: chain J residue 28 VAL Chi-restraints excluded: chain J residue 185 MET Chi-restraints excluded: chain L residue 206 SER Chi-restraints excluded: chain N residue 28 VAL Chi-restraints excluded: chain N residue 87 VAL Chi-restraints excluded: chain P residue 204 SER Chi-restraints excluded: chain C residue 137 GLU Chi-restraints excluded: chain C residue 178 SER Chi-restraints excluded: chain C residue 188 THR Chi-restraints excluded: chain G residue 101 MET Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain G residue 137 GLU Chi-restraints excluded: chain G residue 141 SER Chi-restraints excluded: chain G residue 158 ILE Chi-restraints excluded: chain G residue 178 SER Chi-restraints excluded: chain G residue 188 THR Chi-restraints excluded: chain K residue 101 MET Chi-restraints excluded: chain K residue 110 SER Chi-restraints excluded: chain K residue 137 GLU Chi-restraints excluded: chain K residue 188 THR Chi-restraints excluded: chain O residue 101 MET Chi-restraints excluded: chain O residue 107 VAL Chi-restraints excluded: chain O residue 110 SER Chi-restraints excluded: chain O residue 137 GLU Chi-restraints excluded: chain O residue 178 SER Chi-restraints excluded: chain O residue 188 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 119 optimal weight: 3.9990 chunk 248 optimal weight: 20.0000 chunk 120 optimal weight: 0.8980 chunk 261 optimal weight: 9.9990 chunk 255 optimal weight: 0.0370 chunk 87 optimal weight: 0.9990 chunk 106 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 12 optimal weight: 0.6980 chunk 126 optimal weight: 0.6980 overall best weight: 0.6660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 92 ASN 1 110 ASN 3 146 HIS B 110 ASN B 111 ASN D 173 HIS F 45 ASN F 92 ASN F 110 ASN J 45 ASN J 110 ASN N 45 ASN N 110 ASN ** C 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.164531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.114842 restraints weight = 28815.862| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 3.29 r_work: 0.3258 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.1743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 22465 Z= 0.107 Angle : 0.456 5.608 30625 Z= 0.236 Chirality : 0.041 0.168 3290 Planarity : 0.004 0.032 3970 Dihedral : 3.726 15.770 3005 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 2.63 % Allowed : 12.06 % Favored : 85.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.08 (0.17), residues: 2660 helix: -1.82 (0.30), residues: 240 sheet: -0.35 (0.18), residues: 840 loop : -0.68 (0.17), residues: 1580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 102 TYR 0.011 0.001 TYR C 79 PHE 0.011 0.001 PHE 2 116 TRP 0.010 0.001 TRP 3 149 HIS 0.008 0.001 HIS 3 146 Details of bonding type rmsd covalent geometry : bond 0.00251 (22445) covalent geometry : angle 0.45595 (30585) SS BOND : bond 0.00092 ( 20) SS BOND : angle 0.44057 ( 40) hydrogen bonds : bond 0.02886 ( 89) hydrogen bonds : angle 4.36683 ( 318) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5320 Ramachandran restraints generated. 2660 Oldfield, 0 Emsley, 2660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5320 Ramachandran restraints generated. 2660 Oldfield, 0 Emsley, 2660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 457 residues out of total 2355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 395 time to evaluate : 0.629 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 43 LEU cc_start: 0.9033 (OUTLIER) cc_final: 0.8529 (pp) REVERT: 1 111 ASN cc_start: 0.8923 (m-40) cc_final: 0.8665 (m-40) REVERT: 2 82 GLU cc_start: 0.8216 (mp0) cc_final: 0.7778 (mp0) REVERT: 2 101 MET cc_start: 0.4695 (ptp) cc_final: 0.4284 (ptp) REVERT: 2 108 GLN cc_start: 0.7922 (mt0) cc_final: 0.7681 (mt0) REVERT: 2 137 GLU cc_start: 0.7902 (pm20) cc_final: 0.7599 (pm20) REVERT: 2 199 GLU cc_start: 0.7815 (mp0) cc_final: 0.7314 (mp0) REVERT: 3 42 SER cc_start: 0.8854 (p) cc_final: 0.8352 (t) REVERT: 3 109 MET cc_start: 0.8630 (ttp) cc_final: 0.8103 (ttp) REVERT: 3 119 LYS cc_start: 0.8343 (mttt) cc_final: 0.8023 (mppt) REVERT: 3 121 MET cc_start: 0.8001 (mtm) cc_final: 0.7524 (mtm) REVERT: 3 179 MET cc_start: 0.7229 (tpt) cc_final: 0.6317 (mpt) REVERT: 3 190 GLN cc_start: 0.8023 (pt0) cc_final: 0.6313 (pp30) REVERT: B 45 ASN cc_start: 0.8584 (t0) cc_final: 0.8238 (t0) REVERT: B 46 ARG cc_start: 0.8233 (mtp180) cc_final: 0.7975 (mtp180) REVERT: B 92 ASN cc_start: 0.8415 (t0) cc_final: 0.8207 (t0) REVERT: B 124 ARG cc_start: 0.7771 (ttp-170) cc_final: 0.7518 (ttp-170) REVERT: D 21 THR cc_start: 0.8414 (p) cc_final: 0.8003 (t) REVERT: D 42 SER cc_start: 0.8932 (p) cc_final: 0.8439 (t) REVERT: D 121 MET cc_start: 0.6975 (ttt) cc_final: 0.6540 (mmm) REVERT: D 179 MET cc_start: 0.7244 (tpt) cc_final: 0.6085 (mpt) REVERT: D 189 PHE cc_start: 0.7781 (m-80) cc_final: 0.7429 (m-80) REVERT: D 190 GLN cc_start: 0.8066 (pt0) cc_final: 0.6724 (pp30) REVERT: F 43 LEU cc_start: 0.9126 (OUTLIER) cc_final: 0.8504 (pp) REVERT: F 83 GLU cc_start: 0.6908 (pm20) cc_final: 0.6706 (pm20) REVERT: F 124 ARG cc_start: 0.7737 (ttp-170) cc_final: 0.7523 (ttp-170) REVERT: H 42 SER cc_start: 0.8812 (p) cc_final: 0.8364 (t) REVERT: H 179 MET cc_start: 0.7455 (tpt) cc_final: 0.6237 (mmt) REVERT: H 190 GLN cc_start: 0.8027 (pt0) cc_final: 0.6646 (pp30) REVERT: J 36 MET cc_start: 0.8964 (mmm) cc_final: 0.8556 (mmt) REVERT: L 42 SER cc_start: 0.8742 (p) cc_final: 0.8282 (t) REVERT: L 119 LYS cc_start: 0.8398 (mttt) cc_final: 0.8112 (mppt) REVERT: L 121 MET cc_start: 0.7750 (OUTLIER) cc_final: 0.7393 (pmm) REVERT: L 204 SER cc_start: 0.8818 (p) cc_final: 0.8452 (t) REVERT: N 92 ASN cc_start: 0.8330 (t0) cc_final: 0.7941 (t0) REVERT: N 111 ASN cc_start: 0.8927 (m-40) cc_final: 0.8663 (m110) REVERT: P 42 SER cc_start: 0.8753 (p) cc_final: 0.8261 (t) REVERT: P 119 LYS cc_start: 0.8558 (mttt) cc_final: 0.8304 (mppt) REVERT: P 179 MET cc_start: 0.7537 (tpt) cc_final: 0.7181 (tpp) REVERT: Q 141 ILE cc_start: 0.8383 (mt) cc_final: 0.8086 (mm) REVERT: C 101 MET cc_start: 0.4031 (ptp) cc_final: 0.3700 (ptp) REVERT: C 108 GLN cc_start: 0.8063 (mt0) cc_final: 0.7586 (mt0) REVERT: C 128 GLU cc_start: 0.8578 (mt-10) cc_final: 0.8375 (mt-10) REVERT: C 137 GLU cc_start: 0.8452 (OUTLIER) cc_final: 0.7923 (pm20) REVERT: C 182 MET cc_start: 0.8121 (ttp) cc_final: 0.7725 (ptm) REVERT: C 199 GLU cc_start: 0.7558 (mp0) cc_final: 0.7069 (mp0) REVERT: G 101 MET cc_start: 0.4172 (ptt) cc_final: 0.3612 (ptp) REVERT: G 108 GLN cc_start: 0.8075 (mt0) cc_final: 0.7777 (mt0) REVERT: G 137 GLU cc_start: 0.8334 (OUTLIER) cc_final: 0.7762 (pm20) REVERT: G 158 ILE cc_start: 0.8591 (OUTLIER) cc_final: 0.8282 (mp) REVERT: G 162 TYR cc_start: 0.8104 (t80) cc_final: 0.7839 (t80) REVERT: G 199 GLU cc_start: 0.7473 (mp0) cc_final: 0.6975 (mp0) REVERT: G 204 ILE cc_start: 0.8764 (mt) cc_final: 0.8540 (mt) REVERT: K 128 GLU cc_start: 0.8500 (mt-10) cc_final: 0.8098 (mt-10) REVERT: K 137 GLU cc_start: 0.8248 (OUTLIER) cc_final: 0.7771 (pm20) REVERT: K 199 GLU cc_start: 0.7634 (mp0) cc_final: 0.7209 (mp0) REVERT: O 108 GLN cc_start: 0.8126 (mt0) cc_final: 0.7911 (mt0) REVERT: O 128 GLU cc_start: 0.8694 (mt-10) cc_final: 0.8449 (mt-10) REVERT: O 137 GLU cc_start: 0.8116 (OUTLIER) cc_final: 0.7699 (pm20) REVERT: O 199 GLU cc_start: 0.7580 (mp0) cc_final: 0.7045 (mp0) outliers start: 62 outliers final: 35 residues processed: 423 average time/residue: 0.5499 time to fit residues: 264.6782 Evaluate side-chains 415 residues out of total 2355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 372 time to evaluate : 0.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 28 VAL Chi-restraints excluded: chain 1 residue 43 LEU Chi-restraints excluded: chain 1 residue 44 THR Chi-restraints excluded: chain 1 residue 47 THR Chi-restraints excluded: chain 1 residue 99 THR Chi-restraints excluded: chain 1 residue 108 SER Chi-restraints excluded: chain 1 residue 185 MET Chi-restraints excluded: chain 2 residue 136 GLU Chi-restraints excluded: chain 2 residue 141 SER Chi-restraints excluded: chain 2 residue 178 SER Chi-restraints excluded: chain 2 residue 188 THR Chi-restraints excluded: chain 3 residue 204 SER Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 108 SER Chi-restraints excluded: chain D residue 206 SER Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 43 LEU Chi-restraints excluded: chain F residue 99 THR Chi-restraints excluded: chain F residue 108 SER Chi-restraints excluded: chain H residue 2 ILE Chi-restraints excluded: chain H residue 204 SER Chi-restraints excluded: chain H residue 206 SER Chi-restraints excluded: chain J residue 28 VAL Chi-restraints excluded: chain L residue 121 MET Chi-restraints excluded: chain L residue 206 SER Chi-restraints excluded: chain N residue 28 VAL Chi-restraints excluded: chain N residue 87 VAL Chi-restraints excluded: chain P residue 204 SER Chi-restraints excluded: chain E residue 120 ARG Chi-restraints excluded: chain M residue 120 ARG Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 137 GLU Chi-restraints excluded: chain C residue 188 THR Chi-restraints excluded: chain G residue 110 SER Chi-restraints excluded: chain G residue 137 GLU Chi-restraints excluded: chain G residue 141 SER Chi-restraints excluded: chain G residue 158 ILE Chi-restraints excluded: chain G residue 188 THR Chi-restraints excluded: chain K residue 137 GLU Chi-restraints excluded: chain K residue 188 THR Chi-restraints excluded: chain O residue 110 SER Chi-restraints excluded: chain O residue 137 GLU Chi-restraints excluded: chain O residue 188 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 234 optimal weight: 9.9990 chunk 210 optimal weight: 10.0000 chunk 203 optimal weight: 1.9990 chunk 190 optimal weight: 7.9990 chunk 97 optimal weight: 0.8980 chunk 135 optimal weight: 5.9990 chunk 100 optimal weight: 4.9990 chunk 205 optimal weight: 8.9990 chunk 96 optimal weight: 3.9990 chunk 30 optimal weight: 0.6980 chunk 216 optimal weight: 3.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 45 ASN 1 110 ASN 3 146 HIS B 29 HIS B 110 ASN B 111 ASN F 45 ASN F 110 ASN J 45 ASN J 110 ASN N 45 ASN N 110 ASN P 173 HIS ** C 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 174 HIS ** G 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.159521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.108538 restraints weight = 29132.337| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 3.33 r_work: 0.3167 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.2125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.040 22465 Z= 0.272 Angle : 0.567 6.534 30625 Z= 0.295 Chirality : 0.044 0.154 3290 Planarity : 0.004 0.038 3970 Dihedral : 4.345 19.707 3005 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer: Outliers : 3.69 % Allowed : 13.25 % Favored : 83.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.53 (0.17), residues: 2660 helix: -1.98 (0.30), residues: 240 sheet: -0.90 (0.17), residues: 875 loop : -0.85 (0.17), residues: 1545 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 67 TYR 0.013 0.002 TYR 1 172 PHE 0.019 0.002 PHE P 8 TRP 0.018 0.001 TRP 3 149 HIS 0.008 0.001 HIS D 143 Details of bonding type rmsd covalent geometry : bond 0.00652 (22445) covalent geometry : angle 0.56714 (30585) SS BOND : bond 0.00106 ( 20) SS BOND : angle 0.45288 ( 40) hydrogen bonds : bond 0.03535 ( 89) hydrogen bonds : angle 4.71640 ( 318) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5320 Ramachandran restraints generated. 2660 Oldfield, 0 Emsley, 2660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5320 Ramachandran restraints generated. 2660 Oldfield, 0 Emsley, 2660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 467 residues out of total 2355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 380 time to evaluate : 0.767 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 111 ASN cc_start: 0.8933 (m-40) cc_final: 0.8671 (m-40) REVERT: 1 129 ARG cc_start: 0.8056 (OUTLIER) cc_final: 0.7690 (mtp-110) REVERT: 2 82 GLU cc_start: 0.8276 (mp0) cc_final: 0.7922 (mp0) REVERT: 2 101 MET cc_start: 0.5164 (ptp) cc_final: 0.4739 (ptp) REVERT: 2 108 GLN cc_start: 0.7952 (mt0) cc_final: 0.7716 (mt0) REVERT: 2 137 GLU cc_start: 0.8191 (pm20) cc_final: 0.7834 (pm20) REVERT: 2 199 GLU cc_start: 0.7898 (mp0) cc_final: 0.7429 (mp0) REVERT: 3 42 SER cc_start: 0.8939 (p) cc_final: 0.8402 (t) REVERT: 3 109 MET cc_start: 0.8743 (ttp) cc_final: 0.8174 (ttp) REVERT: 3 119 LYS cc_start: 0.8421 (mttt) cc_final: 0.8131 (mppt) REVERT: 3 121 MET cc_start: 0.8003 (mtm) cc_final: 0.7482 (mtm) REVERT: 3 179 MET cc_start: 0.7397 (tpt) cc_final: 0.6389 (mpt) REVERT: 3 189 PHE cc_start: 0.7910 (m-80) cc_final: 0.7609 (m-80) REVERT: 3 190 GLN cc_start: 0.8183 (pt0) cc_final: 0.6418 (pp30) REVERT: 3 221 ARG cc_start: 0.5932 (OUTLIER) cc_final: 0.5701 (mtp180) REVERT: B 45 ASN cc_start: 0.8785 (t0) cc_final: 0.8384 (t0) REVERT: D 11 TYR cc_start: 0.9331 (OUTLIER) cc_final: 0.8915 (m-80) REVERT: D 21 THR cc_start: 0.8418 (p) cc_final: 0.8007 (t) REVERT: D 121 MET cc_start: 0.7156 (ttt) cc_final: 0.6620 (mmm) REVERT: D 179 MET cc_start: 0.7451 (tpt) cc_final: 0.6157 (mpt) REVERT: D 190 GLN cc_start: 0.8245 (pt0) cc_final: 0.6906 (pp30) REVERT: F 102 ASP cc_start: 0.8280 (p0) cc_final: 0.8056 (p0) REVERT: F 124 ARG cc_start: 0.7758 (ttp-170) cc_final: 0.7554 (ttp-170) REVERT: H 42 SER cc_start: 0.8825 (p) cc_final: 0.8379 (t) REVERT: H 119 LYS cc_start: 0.8381 (mppt) cc_final: 0.8166 (mppt) REVERT: H 121 MET cc_start: 0.8205 (mtp) cc_final: 0.7552 (mmm) REVERT: H 190 GLN cc_start: 0.8210 (pt0) cc_final: 0.6616 (pp30) REVERT: J 36 MET cc_start: 0.9002 (mmm) cc_final: 0.8613 (mmt) REVERT: J 108 SER cc_start: 0.9380 (OUTLIER) cc_final: 0.9053 (p) REVERT: J 124 ARG cc_start: 0.7726 (ttp-170) cc_final: 0.7388 (ttt-90) REVERT: L 15 GLN cc_start: 0.8180 (mt0) cc_final: 0.7832 (mt0) REVERT: L 42 SER cc_start: 0.8775 (p) cc_final: 0.8291 (t) REVERT: L 121 MET cc_start: 0.7835 (OUTLIER) cc_final: 0.7439 (pmm) REVERT: L 190 GLN cc_start: 0.7852 (pt0) cc_final: 0.6444 (pp30) REVERT: L 204 SER cc_start: 0.8773 (p) cc_final: 0.8335 (t) REVERT: N 105 MET cc_start: 0.8951 (OUTLIER) cc_final: 0.8500 (ttp) REVERT: P 56 ASN cc_start: 0.8888 (t0) cc_final: 0.8680 (t0) REVERT: P 119 LYS cc_start: 0.8503 (mttt) cc_final: 0.8287 (mppt) REVERT: P 179 MET cc_start: 0.7706 (tpt) cc_final: 0.7312 (tpp) REVERT: P 190 GLN cc_start: 0.7572 (pt0) cc_final: 0.6189 (pp30) REVERT: E 141 ILE cc_start: 0.8375 (mt) cc_final: 0.8032 (mm) REVERT: I 141 ILE cc_start: 0.8369 (mt) cc_final: 0.8028 (mm) REVERT: Q 141 ILE cc_start: 0.8407 (mt) cc_final: 0.8106 (mm) REVERT: C 101 MET cc_start: 0.4846 (ptp) cc_final: 0.4507 (ptp) REVERT: C 108 GLN cc_start: 0.7994 (mt0) cc_final: 0.7459 (mt0) REVERT: C 128 GLU cc_start: 0.8704 (mt-10) cc_final: 0.8478 (mt-10) REVERT: C 137 GLU cc_start: 0.8580 (OUTLIER) cc_final: 0.8066 (pm20) REVERT: C 199 GLU cc_start: 0.7620 (mp0) cc_final: 0.7141 (mp0) REVERT: G 101 MET cc_start: 0.4677 (ptt) cc_final: 0.4056 (ptp) REVERT: G 108 GLN cc_start: 0.8124 (mt0) cc_final: 0.7866 (mt0) REVERT: G 128 GLU cc_start: 0.8825 (mt-10) cc_final: 0.8454 (mt-10) REVERT: G 135 ARG cc_start: 0.8301 (mtp180) cc_final: 0.7995 (mtm-85) REVERT: G 137 GLU cc_start: 0.8381 (OUTLIER) cc_final: 0.7903 (pm20) REVERT: G 199 GLU cc_start: 0.7481 (mp0) cc_final: 0.6975 (mp0) REVERT: K 137 GLU cc_start: 0.8441 (OUTLIER) cc_final: 0.8003 (pm20) REVERT: K 199 GLU cc_start: 0.7762 (mp0) cc_final: 0.7409 (mp0) REVERT: O 137 GLU cc_start: 0.8331 (OUTLIER) cc_final: 0.7919 (pm20) REVERT: O 199 GLU cc_start: 0.7613 (mp0) cc_final: 0.7037 (mp0) outliers start: 87 outliers final: 46 residues processed: 424 average time/residue: 0.5601 time to fit residues: 270.8345 Evaluate side-chains 420 residues out of total 2355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 364 time to evaluate : 0.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 28 VAL Chi-restraints excluded: chain 1 residue 30 THR Chi-restraints excluded: chain 1 residue 44 THR Chi-restraints excluded: chain 1 residue 47 THR Chi-restraints excluded: chain 1 residue 99 THR Chi-restraints excluded: chain 1 residue 108 SER Chi-restraints excluded: chain 1 residue 129 ARG Chi-restraints excluded: chain 2 residue 106 ASP Chi-restraints excluded: chain 2 residue 107 VAL Chi-restraints excluded: chain 2 residue 141 SER Chi-restraints excluded: chain 2 residue 178 SER Chi-restraints excluded: chain 2 residue 188 THR Chi-restraints excluded: chain 3 residue 146 HIS Chi-restraints excluded: chain 3 residue 204 SER Chi-restraints excluded: chain 3 residue 221 ARG Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 108 SER Chi-restraints excluded: chain D residue 11 TYR Chi-restraints excluded: chain D residue 175 ASP Chi-restraints excluded: chain D residue 204 SER Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 99 THR Chi-restraints excluded: chain F residue 108 SER Chi-restraints excluded: chain H residue 182 THR Chi-restraints excluded: chain H residue 204 SER Chi-restraints excluded: chain H residue 206 SER Chi-restraints excluded: chain J residue 28 VAL Chi-restraints excluded: chain J residue 108 SER Chi-restraints excluded: chain L residue 121 MET Chi-restraints excluded: chain L residue 206 SER Chi-restraints excluded: chain L residue 217 VAL Chi-restraints excluded: chain N residue 28 VAL Chi-restraints excluded: chain N residue 87 VAL Chi-restraints excluded: chain N residue 105 MET Chi-restraints excluded: chain P residue 204 SER Chi-restraints excluded: chain P residue 211 LEU Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 137 GLU Chi-restraints excluded: chain C residue 178 SER Chi-restraints excluded: chain C residue 188 THR Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain G residue 110 SER Chi-restraints excluded: chain G residue 137 GLU Chi-restraints excluded: chain G residue 141 SER Chi-restraints excluded: chain G residue 178 SER Chi-restraints excluded: chain G residue 188 THR Chi-restraints excluded: chain K residue 107 VAL Chi-restraints excluded: chain K residue 110 SER Chi-restraints excluded: chain K residue 137 GLU Chi-restraints excluded: chain K residue 158 ILE Chi-restraints excluded: chain K residue 188 THR Chi-restraints excluded: chain O residue 107 VAL Chi-restraints excluded: chain O residue 137 GLU Chi-restraints excluded: chain O residue 178 SER Chi-restraints excluded: chain O residue 188 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 260 optimal weight: 3.9990 chunk 248 optimal weight: 10.0000 chunk 210 optimal weight: 5.9990 chunk 56 optimal weight: 0.9990 chunk 120 optimal weight: 0.7980 chunk 84 optimal weight: 2.9990 chunk 252 optimal weight: 0.7980 chunk 226 optimal weight: 5.9990 chunk 39 optimal weight: 0.8980 chunk 262 optimal weight: 4.9990 chunk 233 optimal weight: 3.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 45 ASN 1 110 ASN 3 101 GLN B 110 ASN D 15 GLN F 110 ASN J 45 ASN J 110 ASN L 101 GLN L 173 HIS N 110 ASN ** C 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.162143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.111278 restraints weight = 29010.447| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 3.31 r_work: 0.3208 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.2213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 22465 Z= 0.164 Angle : 0.505 6.397 30625 Z= 0.262 Chirality : 0.042 0.158 3290 Planarity : 0.004 0.037 3970 Dihedral : 4.134 18.774 3005 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 3.69 % Allowed : 14.82 % Favored : 81.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.51 (0.17), residues: 2660 helix: -1.98 (0.30), residues: 240 sheet: -0.88 (0.18), residues: 865 loop : -0.84 (0.17), residues: 1555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 67 TYR 0.014 0.001 TYR C 79 PHE 0.013 0.001 PHE 1 115 TRP 0.015 0.001 TRP D 149 HIS 0.014 0.001 HIS 3 146 Details of bonding type rmsd covalent geometry : bond 0.00390 (22445) covalent geometry : angle 0.50521 (30585) SS BOND : bond 0.00081 ( 20) SS BOND : angle 0.41144 ( 40) hydrogen bonds : bond 0.03085 ( 89) hydrogen bonds : angle 4.63106 ( 318) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5320 Ramachandran restraints generated. 2660 Oldfield, 0 Emsley, 2660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5320 Ramachandran restraints generated. 2660 Oldfield, 0 Emsley, 2660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 461 residues out of total 2355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 374 time to evaluate : 0.746 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 111 ASN cc_start: 0.8923 (m-40) cc_final: 0.8675 (m-40) REVERT: 1 129 ARG cc_start: 0.8053 (OUTLIER) cc_final: 0.7702 (mtp-110) REVERT: 2 82 GLU cc_start: 0.8308 (mp0) cc_final: 0.7903 (mp0) REVERT: 2 101 MET cc_start: 0.5293 (ptp) cc_final: 0.4802 (ptp) REVERT: 2 137 GLU cc_start: 0.8213 (pm20) cc_final: 0.7864 (pm20) REVERT: 2 199 GLU cc_start: 0.7915 (mp0) cc_final: 0.7446 (mp0) REVERT: 3 42 SER cc_start: 0.8910 (p) cc_final: 0.8366 (t) REVERT: 3 109 MET cc_start: 0.8697 (ttp) cc_final: 0.8114 (ttp) REVERT: 3 119 LYS cc_start: 0.8399 (mttt) cc_final: 0.8098 (mppt) REVERT: 3 121 MET cc_start: 0.8130 (mtm) cc_final: 0.7445 (mpp) REVERT: 3 179 MET cc_start: 0.7374 (tpt) cc_final: 0.6443 (mpt) REVERT: 3 190 GLN cc_start: 0.8191 (pt0) cc_final: 0.6383 (pp30) REVERT: 3 221 ARG cc_start: 0.5902 (OUTLIER) cc_final: 0.5659 (mtp180) REVERT: B 43 LEU cc_start: 0.9151 (OUTLIER) cc_final: 0.8718 (pp) REVERT: B 45 ASN cc_start: 0.8789 (t0) cc_final: 0.8380 (t0) REVERT: D 11 TYR cc_start: 0.9310 (OUTLIER) cc_final: 0.8884 (m-80) REVERT: D 21 THR cc_start: 0.8385 (p) cc_final: 0.7998 (t) REVERT: D 119 LYS cc_start: 0.8409 (mttt) cc_final: 0.8174 (mppt) REVERT: D 121 MET cc_start: 0.7342 (ttt) cc_final: 0.6759 (mmm) REVERT: D 179 MET cc_start: 0.7331 (tpt) cc_final: 0.6925 (tpp) REVERT: D 190 GLN cc_start: 0.8259 (pt0) cc_final: 0.6850 (pp30) REVERT: F 83 GLU cc_start: 0.6764 (pm20) cc_final: 0.6516 (pm20) REVERT: F 102 ASP cc_start: 0.8295 (p0) cc_final: 0.8038 (p0) REVERT: F 124 ARG cc_start: 0.7750 (ttp-170) cc_final: 0.7535 (ttp-170) REVERT: H 42 SER cc_start: 0.8815 (p) cc_final: 0.8353 (t) REVERT: H 121 MET cc_start: 0.8208 (mtp) cc_final: 0.7496 (mmm) REVERT: H 190 GLN cc_start: 0.8175 (pt0) cc_final: 0.6683 (pp30) REVERT: H 212 GLU cc_start: 0.8280 (tt0) cc_final: 0.8062 (tt0) REVERT: J 124 ARG cc_start: 0.7704 (ttp-170) cc_final: 0.7358 (ttt-90) REVERT: L 42 SER cc_start: 0.8710 (p) cc_final: 0.8208 (t) REVERT: L 121 MET cc_start: 0.7827 (OUTLIER) cc_final: 0.7434 (pmm) REVERT: L 179 MET cc_start: 0.7425 (tpt) cc_final: 0.7132 (tpp) REVERT: L 190 GLN cc_start: 0.7870 (pt0) cc_final: 0.6470 (pp30) REVERT: L 204 SER cc_start: 0.8784 (p) cc_final: 0.8372 (t) REVERT: N 101 ARG cc_start: 0.7775 (OUTLIER) cc_final: 0.7538 (ptt-90) REVERT: N 105 MET cc_start: 0.8953 (OUTLIER) cc_final: 0.8497 (ttp) REVERT: N 111 ASN cc_start: 0.8939 (m-40) cc_final: 0.8680 (m110) REVERT: N 129 ARG cc_start: 0.7845 (OUTLIER) cc_final: 0.7428 (mtp-110) REVERT: P 119 LYS cc_start: 0.8502 (mttt) cc_final: 0.8291 (mppt) REVERT: P 179 MET cc_start: 0.7669 (tpt) cc_final: 0.7302 (tpp) REVERT: P 190 GLN cc_start: 0.7549 (pt0) cc_final: 0.6198 (pp30) REVERT: E 141 ILE cc_start: 0.8364 (mt) cc_final: 0.8033 (mm) REVERT: Q 141 ILE cc_start: 0.8411 (mt) cc_final: 0.8110 (mm) REVERT: C 101 MET cc_start: 0.4971 (ptp) cc_final: 0.4606 (ptp) REVERT: C 108 GLN cc_start: 0.8007 (mt0) cc_final: 0.7536 (mt0) REVERT: C 128 GLU cc_start: 0.8679 (mt-10) cc_final: 0.8451 (mt-10) REVERT: C 137 GLU cc_start: 0.8619 (OUTLIER) cc_final: 0.8115 (pm20) REVERT: C 199 GLU cc_start: 0.7602 (mp0) cc_final: 0.7167 (mp0) REVERT: G 101 MET cc_start: 0.4880 (ptt) cc_final: 0.4180 (ptp) REVERT: G 108 GLN cc_start: 0.8126 (mt0) cc_final: 0.7870 (mt0) REVERT: G 128 GLU cc_start: 0.8854 (mt-10) cc_final: 0.8451 (mt-10) REVERT: G 135 ARG cc_start: 0.8291 (mtp180) cc_final: 0.7980 (mtm-85) REVERT: G 137 GLU cc_start: 0.8363 (OUTLIER) cc_final: 0.7872 (pm20) REVERT: G 158 ILE cc_start: 0.8630 (OUTLIER) cc_final: 0.8366 (mp) REVERT: G 199 GLU cc_start: 0.7461 (mp0) cc_final: 0.6956 (mp0) REVERT: K 137 GLU cc_start: 0.8486 (OUTLIER) cc_final: 0.8031 (pm20) REVERT: K 199 GLU cc_start: 0.7821 (mp0) cc_final: 0.7458 (mp0) REVERT: O 117 ASN cc_start: 0.8686 (OUTLIER) cc_final: 0.8454 (t0) REVERT: O 137 GLU cc_start: 0.8350 (OUTLIER) cc_final: 0.7912 (pm20) REVERT: O 199 GLU cc_start: 0.7665 (mp0) cc_final: 0.7045 (mp0) outliers start: 87 outliers final: 50 residues processed: 418 average time/residue: 0.5946 time to fit residues: 282.5747 Evaluate side-chains 430 residues out of total 2355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 366 time to evaluate : 0.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 28 VAL Chi-restraints excluded: chain 1 residue 30 THR Chi-restraints excluded: chain 1 residue 44 THR Chi-restraints excluded: chain 1 residue 47 THR Chi-restraints excluded: chain 1 residue 108 SER Chi-restraints excluded: chain 1 residue 129 ARG Chi-restraints excluded: chain 1 residue 185 MET Chi-restraints excluded: chain 2 residue 106 ASP Chi-restraints excluded: chain 2 residue 136 GLU Chi-restraints excluded: chain 2 residue 141 SER Chi-restraints excluded: chain 2 residue 178 SER Chi-restraints excluded: chain 2 residue 188 THR Chi-restraints excluded: chain 3 residue 204 SER Chi-restraints excluded: chain 3 residue 217 VAL Chi-restraints excluded: chain 3 residue 221 ARG Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 108 SER Chi-restraints excluded: chain D residue 11 TYR Chi-restraints excluded: chain D residue 42 SER Chi-restraints excluded: chain D residue 204 SER Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 105 MET Chi-restraints excluded: chain F residue 108 SER Chi-restraints excluded: chain H residue 2 ILE Chi-restraints excluded: chain H residue 182 THR Chi-restraints excluded: chain H residue 204 SER Chi-restraints excluded: chain H residue 206 SER Chi-restraints excluded: chain J residue 28 VAL Chi-restraints excluded: chain J residue 108 SER Chi-restraints excluded: chain L residue 121 MET Chi-restraints excluded: chain L residue 206 SER Chi-restraints excluded: chain N residue 28 VAL Chi-restraints excluded: chain N residue 87 VAL Chi-restraints excluded: chain N residue 101 ARG Chi-restraints excluded: chain N residue 105 MET Chi-restraints excluded: chain N residue 129 ARG Chi-restraints excluded: chain P residue 42 SER Chi-restraints excluded: chain P residue 204 SER Chi-restraints excluded: chain M residue 120 ARG Chi-restraints excluded: chain Q residue 120 ARG Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 137 GLU Chi-restraints excluded: chain C residue 178 SER Chi-restraints excluded: chain C residue 188 THR Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain G residue 110 SER Chi-restraints excluded: chain G residue 137 GLU Chi-restraints excluded: chain G residue 141 SER Chi-restraints excluded: chain G residue 158 ILE Chi-restraints excluded: chain G residue 178 SER Chi-restraints excluded: chain G residue 188 THR Chi-restraints excluded: chain G residue 204 ILE Chi-restraints excluded: chain K residue 107 VAL Chi-restraints excluded: chain K residue 110 SER Chi-restraints excluded: chain K residue 137 GLU Chi-restraints excluded: chain K residue 188 THR Chi-restraints excluded: chain O residue 107 VAL Chi-restraints excluded: chain O residue 110 SER Chi-restraints excluded: chain O residue 117 ASN Chi-restraints excluded: chain O residue 137 GLU Chi-restraints excluded: chain O residue 178 SER Chi-restraints excluded: chain O residue 188 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 29 optimal weight: 0.0770 chunk 96 optimal weight: 1.9990 chunk 69 optimal weight: 4.9990 chunk 27 optimal weight: 6.9990 chunk 212 optimal weight: 0.6980 chunk 207 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 195 optimal weight: 6.9990 overall best weight: 1.3544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 110 ASN 3 146 HIS B 110 ASN D 15 GLN F 110 ASN J 110 ASN N 110 ASN ** C 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.157669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.109077 restraints weight = 29000.327| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 3.13 r_work: 0.3223 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.2334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 22465 Z= 0.171 Angle : 0.504 6.300 30625 Z= 0.260 Chirality : 0.042 0.164 3290 Planarity : 0.004 0.039 3970 Dihedral : 4.099 18.348 3005 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 3.52 % Allowed : 15.46 % Favored : 81.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.51 (0.17), residues: 2660 helix: -1.95 (0.30), residues: 240 sheet: -0.83 (0.18), residues: 840 loop : -0.88 (0.16), residues: 1580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 120 TYR 0.021 0.001 TYR C 79 PHE 0.013 0.001 PHE 1 115 TRP 0.023 0.001 TRP 3 149 HIS 0.007 0.001 HIS 3 146 Details of bonding type rmsd covalent geometry : bond 0.00408 (22445) covalent geometry : angle 0.50401 (30585) SS BOND : bond 0.00078 ( 20) SS BOND : angle 0.40121 ( 40) hydrogen bonds : bond 0.02986 ( 89) hydrogen bonds : angle 4.53606 ( 318) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5320 Ramachandran restraints generated. 2660 Oldfield, 0 Emsley, 2660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5320 Ramachandran restraints generated. 2660 Oldfield, 0 Emsley, 2660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 456 residues out of total 2355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 373 time to evaluate : 0.829 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 45 ASN cc_start: 0.8838 (t0) cc_final: 0.8511 (t0) REVERT: 1 111 ASN cc_start: 0.8936 (m-40) cc_final: 0.8699 (m-40) REVERT: 1 129 ARG cc_start: 0.7985 (OUTLIER) cc_final: 0.7546 (mtp-110) REVERT: 2 82 GLU cc_start: 0.8314 (mp0) cc_final: 0.7906 (mp0) REVERT: 2 101 MET cc_start: 0.5454 (ptp) cc_final: 0.5041 (ptp) REVERT: 2 137 GLU cc_start: 0.8235 (pm20) cc_final: 0.7896 (pm20) REVERT: 2 199 GLU cc_start: 0.7932 (mp0) cc_final: 0.7475 (mp0) REVERT: 3 42 SER cc_start: 0.8908 (p) cc_final: 0.8363 (t) REVERT: 3 109 MET cc_start: 0.8726 (ttp) cc_final: 0.8140 (ttp) REVERT: 3 119 LYS cc_start: 0.8388 (mttt) cc_final: 0.8132 (mppt) REVERT: 3 121 MET cc_start: 0.8059 (mtm) cc_final: 0.7522 (mtm) REVERT: 3 179 MET cc_start: 0.7397 (tpt) cc_final: 0.6448 (mpt) REVERT: 3 190 GLN cc_start: 0.8312 (pt0) cc_final: 0.6552 (pp30) REVERT: 3 221 ARG cc_start: 0.5901 (OUTLIER) cc_final: 0.5661 (mtp180) REVERT: B 43 LEU cc_start: 0.9138 (OUTLIER) cc_final: 0.8745 (pp) REVERT: B 45 ASN cc_start: 0.8785 (t0) cc_final: 0.8372 (t0) REVERT: D 11 TYR cc_start: 0.9319 (OUTLIER) cc_final: 0.8889 (m-80) REVERT: D 21 THR cc_start: 0.8431 (p) cc_final: 0.8011 (t) REVERT: D 42 SER cc_start: 0.8945 (OUTLIER) cc_final: 0.8386 (t) REVERT: D 119 LYS cc_start: 0.8414 (mttt) cc_final: 0.8180 (mppt) REVERT: D 121 MET cc_start: 0.7360 (ttt) cc_final: 0.6792 (mmm) REVERT: D 179 MET cc_start: 0.7387 (tpt) cc_final: 0.6064 (mmt) REVERT: D 190 GLN cc_start: 0.8240 (pt0) cc_final: 0.6927 (pp30) REVERT: F 83 GLU cc_start: 0.6780 (pm20) cc_final: 0.6487 (pm20) REVERT: F 102 ASP cc_start: 0.8350 (p0) cc_final: 0.8106 (p0) REVERT: F 124 ARG cc_start: 0.7719 (ttp-170) cc_final: 0.7483 (ttp-170) REVERT: F 176 ASP cc_start: 0.7941 (t0) cc_final: 0.7650 (t0) REVERT: H 42 SER cc_start: 0.8804 (p) cc_final: 0.8337 (t) REVERT: H 121 MET cc_start: 0.8186 (mtp) cc_final: 0.7495 (mmm) REVERT: H 190 GLN cc_start: 0.8245 (pt0) cc_final: 0.6779 (pp30) REVERT: J 36 MET cc_start: 0.8982 (mmm) cc_final: 0.8523 (mmt) REVERT: J 43 LEU cc_start: 0.9159 (OUTLIER) cc_final: 0.8399 (pp) REVERT: J 45 ASN cc_start: 0.8793 (t0) cc_final: 0.8297 (t0) REVERT: J 124 ARG cc_start: 0.7700 (ttp-170) cc_final: 0.7339 (ttt-90) REVERT: L 42 SER cc_start: 0.8711 (p) cc_final: 0.8216 (t) REVERT: L 119 LYS cc_start: 0.8314 (mttt) cc_final: 0.8112 (mppt) REVERT: L 121 MET cc_start: 0.7911 (OUTLIER) cc_final: 0.7505 (pmm) REVERT: L 179 MET cc_start: 0.7447 (tpt) cc_final: 0.6349 (mpt) REVERT: L 204 SER cc_start: 0.8808 (p) cc_final: 0.8426 (t) REVERT: N 105 MET cc_start: 0.8957 (OUTLIER) cc_final: 0.8502 (ttp) REVERT: N 111 ASN cc_start: 0.8953 (m-40) cc_final: 0.8707 (m110) REVERT: N 129 ARG cc_start: 0.7863 (OUTLIER) cc_final: 0.7366 (mtp-110) REVERT: P 56 ASN cc_start: 0.8834 (t0) cc_final: 0.8616 (t0) REVERT: P 179 MET cc_start: 0.7692 (tpt) cc_final: 0.7334 (tpp) REVERT: E 141 ILE cc_start: 0.8350 (mt) cc_final: 0.7997 (mm) REVERT: Q 141 ILE cc_start: 0.8416 (mt) cc_final: 0.8104 (mm) REVERT: C 101 MET cc_start: 0.5407 (ptp) cc_final: 0.5053 (ptp) REVERT: C 108 GLN cc_start: 0.8035 (mt0) cc_final: 0.7524 (mt0) REVERT: C 128 GLU cc_start: 0.8658 (mt-10) cc_final: 0.8422 (mt-10) REVERT: C 137 GLU cc_start: 0.8608 (OUTLIER) cc_final: 0.8110 (pm20) REVERT: C 199 GLU cc_start: 0.7648 (mp0) cc_final: 0.7199 (mp0) REVERT: G 101 MET cc_start: 0.4973 (ptt) cc_final: 0.4202 (ptp) REVERT: G 102 ARG cc_start: 0.6199 (ttt180) cc_final: 0.5953 (ttm-80) REVERT: G 108 GLN cc_start: 0.8151 (mt0) cc_final: 0.7922 (mt0) REVERT: G 128 GLU cc_start: 0.8869 (mt-10) cc_final: 0.8489 (mt-10) REVERT: G 135 ARG cc_start: 0.8271 (mtp180) cc_final: 0.7966 (mtm-85) REVERT: G 137 GLU cc_start: 0.8392 (OUTLIER) cc_final: 0.7920 (pm20) REVERT: G 158 ILE cc_start: 0.8674 (OUTLIER) cc_final: 0.8422 (mp) REVERT: G 199 GLU cc_start: 0.7462 (mp0) cc_final: 0.6962 (mp0) REVERT: K 79 TYR cc_start: 0.7116 (m-80) cc_final: 0.6759 (m-80) REVERT: K 101 MET cc_start: 0.4710 (ptt) cc_final: 0.4069 (ptp) REVERT: K 137 GLU cc_start: 0.8529 (OUTLIER) cc_final: 0.8040 (pm20) REVERT: K 199 GLU cc_start: 0.7862 (mp0) cc_final: 0.7489 (mp0) REVERT: O 108 GLN cc_start: 0.8108 (mt0) cc_final: 0.7903 (mm110) REVERT: O 117 ASN cc_start: 0.8680 (OUTLIER) cc_final: 0.8434 (t0) REVERT: O 137 GLU cc_start: 0.8340 (OUTLIER) cc_final: 0.7909 (pm20) REVERT: O 199 GLU cc_start: 0.7665 (mp0) cc_final: 0.7045 (mp0) outliers start: 83 outliers final: 51 residues processed: 418 average time/residue: 0.5501 time to fit residues: 262.9101 Evaluate side-chains 430 residues out of total 2355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 364 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 28 VAL Chi-restraints excluded: chain 1 residue 30 THR Chi-restraints excluded: chain 1 residue 44 THR Chi-restraints excluded: chain 1 residue 47 THR Chi-restraints excluded: chain 1 residue 108 SER Chi-restraints excluded: chain 1 residue 129 ARG Chi-restraints excluded: chain 1 residue 185 MET Chi-restraints excluded: chain 2 residue 106 ASP Chi-restraints excluded: chain 2 residue 136 GLU Chi-restraints excluded: chain 2 residue 141 SER Chi-restraints excluded: chain 2 residue 178 SER Chi-restraints excluded: chain 2 residue 188 THR Chi-restraints excluded: chain 2 residue 204 ILE Chi-restraints excluded: chain 3 residue 204 SER Chi-restraints excluded: chain 3 residue 217 VAL Chi-restraints excluded: chain 3 residue 221 ARG Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 108 SER Chi-restraints excluded: chain D residue 11 TYR Chi-restraints excluded: chain D residue 42 SER Chi-restraints excluded: chain D residue 204 SER Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 105 MET Chi-restraints excluded: chain F residue 108 SER Chi-restraints excluded: chain H residue 182 THR Chi-restraints excluded: chain H residue 204 SER Chi-restraints excluded: chain H residue 206 SER Chi-restraints excluded: chain J residue 28 VAL Chi-restraints excluded: chain J residue 43 LEU Chi-restraints excluded: chain J residue 108 SER Chi-restraints excluded: chain L residue 121 MET Chi-restraints excluded: chain L residue 206 SER Chi-restraints excluded: chain L residue 217 VAL Chi-restraints excluded: chain N residue 28 VAL Chi-restraints excluded: chain N residue 87 VAL Chi-restraints excluded: chain N residue 99 THR Chi-restraints excluded: chain N residue 105 MET Chi-restraints excluded: chain N residue 129 ARG Chi-restraints excluded: chain P residue 42 SER Chi-restraints excluded: chain P residue 204 SER Chi-restraints excluded: chain P residue 211 LEU Chi-restraints excluded: chain P residue 217 VAL Chi-restraints excluded: chain M residue 120 ARG Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 137 GLU Chi-restraints excluded: chain C residue 178 SER Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain G residue 110 SER Chi-restraints excluded: chain G residue 137 GLU Chi-restraints excluded: chain G residue 141 SER Chi-restraints excluded: chain G residue 158 ILE Chi-restraints excluded: chain G residue 178 SER Chi-restraints excluded: chain G residue 188 THR Chi-restraints excluded: chain G residue 204 ILE Chi-restraints excluded: chain K residue 107 VAL Chi-restraints excluded: chain K residue 110 SER Chi-restraints excluded: chain K residue 137 GLU Chi-restraints excluded: chain K residue 158 ILE Chi-restraints excluded: chain K residue 188 THR Chi-restraints excluded: chain O residue 117 ASN Chi-restraints excluded: chain O residue 137 GLU Chi-restraints excluded: chain O residue 178 SER Chi-restraints excluded: chain O residue 188 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 84 optimal weight: 3.9990 chunk 81 optimal weight: 8.9990 chunk 181 optimal weight: 0.2980 chunk 126 optimal weight: 0.7980 chunk 174 optimal weight: 0.0570 chunk 104 optimal weight: 0.1980 chunk 166 optimal weight: 0.8980 chunk 253 optimal weight: 7.9990 chunk 195 optimal weight: 0.8980 chunk 7 optimal weight: 3.9990 chunk 178 optimal weight: 1.9990 overall best weight: 0.4498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 110 ASN 3 146 HIS B 110 ASN D 15 GLN F 110 ASN ** J 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 110 ASN N 110 ASN ** C 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 146 GLN ** C 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 108 GLN G 157 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.162683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.114172 restraints weight = 28770.721| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 3.23 r_work: 0.3249 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.2413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 22465 Z= 0.095 Angle : 0.474 6.425 30625 Z= 0.244 Chirality : 0.041 0.156 3290 Planarity : 0.003 0.039 3970 Dihedral : 3.803 16.231 3005 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 2.38 % Allowed : 17.37 % Favored : 80.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.30 (0.17), residues: 2660 helix: -1.87 (0.31), residues: 240 sheet: -0.63 (0.19), residues: 820 loop : -0.77 (0.16), residues: 1600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 120 TYR 0.012 0.001 TYR C 79 PHE 0.007 0.001 PHE 3 213 TRP 0.028 0.001 TRP 3 149 HIS 0.006 0.001 HIS 3 146 Details of bonding type rmsd covalent geometry : bond 0.00221 (22445) covalent geometry : angle 0.47429 (30585) SS BOND : bond 0.00258 ( 20) SS BOND : angle 0.45539 ( 40) hydrogen bonds : bond 0.02715 ( 89) hydrogen bonds : angle 4.39382 ( 318) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5320 Ramachandran restraints generated. 2660 Oldfield, 0 Emsley, 2660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5320 Ramachandran restraints generated. 2660 Oldfield, 0 Emsley, 2660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 458 residues out of total 2355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 402 time to evaluate : 0.811 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 45 ASN cc_start: 0.8823 (t0) cc_final: 0.8555 (t0) REVERT: 1 111 ASN cc_start: 0.8882 (m-40) cc_final: 0.8677 (m110) REVERT: 1 129 ARG cc_start: 0.7783 (OUTLIER) cc_final: 0.7079 (mtp-110) REVERT: 2 82 GLU cc_start: 0.8296 (mp0) cc_final: 0.7932 (mp0) REVERT: 2 101 MET cc_start: 0.5351 (ptp) cc_final: 0.4918 (ptp) REVERT: 2 137 GLU cc_start: 0.8144 (pm20) cc_final: 0.7825 (pm20) REVERT: 2 199 GLU cc_start: 0.7942 (mp0) cc_final: 0.7463 (mp0) REVERT: 3 42 SER cc_start: 0.8849 (p) cc_final: 0.8286 (t) REVERT: 3 109 MET cc_start: 0.8685 (ttp) cc_final: 0.8110 (ttp) REVERT: 3 119 LYS cc_start: 0.8407 (mttt) cc_final: 0.8086 (mtmm) REVERT: 3 121 MET cc_start: 0.8138 (mtm) cc_final: 0.7543 (mtm) REVERT: 3 179 MET cc_start: 0.7208 (tpt) cc_final: 0.6362 (mpt) REVERT: B 43 LEU cc_start: 0.9034 (OUTLIER) cc_final: 0.8612 (pp) REVERT: B 45 ASN cc_start: 0.8747 (t0) cc_final: 0.8331 (t0) REVERT: D 11 TYR cc_start: 0.9316 (OUTLIER) cc_final: 0.8866 (m-80) REVERT: D 15 GLN cc_start: 0.7868 (mt0) cc_final: 0.7360 (mt0) REVERT: D 21 THR cc_start: 0.8382 (p) cc_final: 0.7956 (t) REVERT: D 42 SER cc_start: 0.8948 (p) cc_final: 0.8388 (t) REVERT: D 119 LYS cc_start: 0.8400 (mttt) cc_final: 0.8123 (mppt) REVERT: D 121 MET cc_start: 0.7366 (ttt) cc_final: 0.6763 (mmm) REVERT: D 179 MET cc_start: 0.7249 (tpt) cc_final: 0.6917 (tpp) REVERT: D 190 GLN cc_start: 0.8243 (pt0) cc_final: 0.6888 (pp30) REVERT: F 83 GLU cc_start: 0.6755 (pm20) cc_final: 0.6452 (pm20) REVERT: F 102 ASP cc_start: 0.8188 (p0) cc_final: 0.7976 (p0) REVERT: F 124 ARG cc_start: 0.7741 (ttp-170) cc_final: 0.7496 (ttp-170) REVERT: F 176 ASP cc_start: 0.7930 (t0) cc_final: 0.7634 (t0) REVERT: H 42 SER cc_start: 0.8742 (p) cc_final: 0.8266 (t) REVERT: H 121 MET cc_start: 0.8238 (mtp) cc_final: 0.7520 (mmm) REVERT: H 190 GLN cc_start: 0.8219 (pt0) cc_final: 0.6623 (pp30) REVERT: H 212 GLU cc_start: 0.8281 (tt0) cc_final: 0.8076 (tt0) REVERT: J 45 ASN cc_start: 0.8798 (t0) cc_final: 0.8338 (t0) REVERT: J 124 ARG cc_start: 0.7682 (ttp-170) cc_final: 0.7340 (ttt-90) REVERT: L 42 SER cc_start: 0.8674 (p) cc_final: 0.8176 (t) REVERT: L 119 LYS cc_start: 0.8352 (mttt) cc_final: 0.8120 (mppt) REVERT: L 121 MET cc_start: 0.7863 (OUTLIER) cc_final: 0.7440 (pmm) REVERT: L 179 MET cc_start: 0.7310 (tpt) cc_final: 0.6051 (mpt) REVERT: L 204 SER cc_start: 0.8964 (p) cc_final: 0.8584 (t) REVERT: N 28 VAL cc_start: 0.8570 (t) cc_final: 0.8319 (p) REVERT: N 105 MET cc_start: 0.8872 (OUTLIER) cc_final: 0.8389 (ttp) REVERT: N 111 ASN cc_start: 0.8904 (m-40) cc_final: 0.8659 (m110) REVERT: N 129 ARG cc_start: 0.7779 (OUTLIER) cc_final: 0.7029 (mtp-110) REVERT: P 179 MET cc_start: 0.7451 (tpt) cc_final: 0.7145 (tpp) REVERT: E 141 ILE cc_start: 0.8248 (mt) cc_final: 0.7891 (mm) REVERT: C 79 TYR cc_start: 0.7191 (m-10) cc_final: 0.6844 (m-10) REVERT: C 101 MET cc_start: 0.5139 (ptp) cc_final: 0.4835 (ptp) REVERT: C 108 GLN cc_start: 0.8010 (mt0) cc_final: 0.7542 (mt0) REVERT: C 137 GLU cc_start: 0.8596 (OUTLIER) cc_final: 0.7989 (pm20) REVERT: C 199 GLU cc_start: 0.7671 (mp0) cc_final: 0.7173 (mp0) REVERT: G 101 MET cc_start: 0.5113 (ptt) cc_final: 0.4332 (ptp) REVERT: G 102 ARG cc_start: 0.6139 (ttt180) cc_final: 0.5693 (tpp-160) REVERT: G 128 GLU cc_start: 0.8807 (mt-10) cc_final: 0.8356 (mt-10) REVERT: G 135 ARG cc_start: 0.8215 (mtp180) cc_final: 0.7909 (mtm-85) REVERT: G 137 GLU cc_start: 0.8361 (OUTLIER) cc_final: 0.7876 (pm20) REVERT: G 199 GLU cc_start: 0.7535 (mp0) cc_final: 0.7031 (mp0) REVERT: K 79 TYR cc_start: 0.7146 (m-80) cc_final: 0.6856 (m-80) REVERT: K 101 MET cc_start: 0.4589 (ptt) cc_final: 0.4091 (ptp) REVERT: K 128 GLU cc_start: 0.8661 (mt-10) cc_final: 0.7905 (mt-10) REVERT: K 137 GLU cc_start: 0.8535 (OUTLIER) cc_final: 0.8029 (pm20) REVERT: K 199 GLU cc_start: 0.7787 (mp0) cc_final: 0.7384 (mp0) REVERT: O 79 TYR cc_start: 0.7289 (m-80) cc_final: 0.6821 (m-80) REVERT: O 117 ASN cc_start: 0.8614 (OUTLIER) cc_final: 0.8352 (t0) REVERT: O 137 GLU cc_start: 0.8282 (OUTLIER) cc_final: 0.7832 (pm20) REVERT: O 199 GLU cc_start: 0.7641 (mp0) cc_final: 0.7091 (mp0) outliers start: 56 outliers final: 30 residues processed: 431 average time/residue: 0.5959 time to fit residues: 292.2888 Evaluate side-chains 420 residues out of total 2355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 379 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 30 THR Chi-restraints excluded: chain 1 residue 44 THR Chi-restraints excluded: chain 1 residue 47 THR Chi-restraints excluded: chain 1 residue 129 ARG Chi-restraints excluded: chain 1 residue 185 MET Chi-restraints excluded: chain 2 residue 136 GLU Chi-restraints excluded: chain 2 residue 141 SER Chi-restraints excluded: chain 2 residue 178 SER Chi-restraints excluded: chain 2 residue 188 THR Chi-restraints excluded: chain 3 residue 146 HIS Chi-restraints excluded: chain 3 residue 204 SER Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 108 SER Chi-restraints excluded: chain D residue 11 TYR Chi-restraints excluded: chain F residue 105 MET Chi-restraints excluded: chain H residue 2 ILE Chi-restraints excluded: chain H residue 182 THR Chi-restraints excluded: chain H residue 204 SER Chi-restraints excluded: chain H residue 206 SER Chi-restraints excluded: chain J residue 28 VAL Chi-restraints excluded: chain L residue 121 MET Chi-restraints excluded: chain L residue 206 SER Chi-restraints excluded: chain N residue 43 LEU Chi-restraints excluded: chain N residue 105 MET Chi-restraints excluded: chain N residue 129 ARG Chi-restraints excluded: chain P residue 204 SER Chi-restraints excluded: chain P residue 211 LEU Chi-restraints excluded: chain I residue 120 ARG Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 137 GLU Chi-restraints excluded: chain C residue 178 SER Chi-restraints excluded: chain G residue 137 GLU Chi-restraints excluded: chain G residue 188 THR Chi-restraints excluded: chain K residue 110 SER Chi-restraints excluded: chain K residue 137 GLU Chi-restraints excluded: chain K residue 188 THR Chi-restraints excluded: chain O residue 110 SER Chi-restraints excluded: chain O residue 117 ASN Chi-restraints excluded: chain O residue 137 GLU Chi-restraints excluded: chain O residue 188 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 43 optimal weight: 5.9990 chunk 212 optimal weight: 4.9990 chunk 18 optimal weight: 0.9990 chunk 96 optimal weight: 3.9990 chunk 15 optimal weight: 10.0000 chunk 6 optimal weight: 0.9980 chunk 168 optimal weight: 0.6980 chunk 191 optimal weight: 5.9990 chunk 227 optimal weight: 7.9990 chunk 255 optimal weight: 4.9990 chunk 175 optimal weight: 4.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 110 ASN 3 146 HIS 3 173 HIS B 29 HIS B 110 ASN F 110 ASN J 110 ASN ** L 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 110 ASN P 190 GLN ** C 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.160516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.109567 restraints weight = 29125.746| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 3.32 r_work: 0.3185 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.2585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 22465 Z= 0.260 Angle : 0.568 6.895 30625 Z= 0.295 Chirality : 0.044 0.176 3290 Planarity : 0.004 0.046 3970 Dihedral : 4.283 19.395 3005 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 2.89 % Allowed : 17.71 % Favored : 79.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.55 (0.17), residues: 2660 helix: -1.97 (0.30), residues: 240 sheet: -0.87 (0.18), residues: 825 loop : -0.91 (0.16), residues: 1595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG P 214 TYR 0.023 0.002 TYR 3 145 PHE 0.016 0.002 PHE N 115 TRP 0.029 0.002 TRP D 149 HIS 0.006 0.001 HIS F 84 Details of bonding type rmsd covalent geometry : bond 0.00621 (22445) covalent geometry : angle 0.56752 (30585) SS BOND : bond 0.00552 ( 20) SS BOND : angle 0.68059 ( 40) hydrogen bonds : bond 0.03326 ( 89) hydrogen bonds : angle 4.69235 ( 318) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5320 Ramachandran restraints generated. 2660 Oldfield, 0 Emsley, 2660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5320 Ramachandran restraints generated. 2660 Oldfield, 0 Emsley, 2660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 444 residues out of total 2355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 376 time to evaluate : 0.767 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 43 LEU cc_start: 0.9280 (OUTLIER) cc_final: 0.9029 (pt) REVERT: 1 45 ASN cc_start: 0.8867 (t0) cc_final: 0.8569 (t0) REVERT: 1 111 ASN cc_start: 0.8935 (m-40) cc_final: 0.8681 (m-40) REVERT: 1 129 ARG cc_start: 0.8082 (OUTLIER) cc_final: 0.7614 (mtp-110) REVERT: 2 82 GLU cc_start: 0.8301 (mp0) cc_final: 0.7952 (mp0) REVERT: 2 101 MET cc_start: 0.5809 (ptp) cc_final: 0.5373 (ptp) REVERT: 2 137 GLU cc_start: 0.8246 (pm20) cc_final: 0.7910 (pm20) REVERT: 2 199 GLU cc_start: 0.7941 (mp0) cc_final: 0.7466 (mp0) REVERT: 3 42 SER cc_start: 0.8925 (p) cc_final: 0.8370 (t) REVERT: 3 109 MET cc_start: 0.8714 (ttp) cc_final: 0.8165 (ttp) REVERT: 3 119 LYS cc_start: 0.8375 (mttt) cc_final: 0.8082 (mtmm) REVERT: 3 121 MET cc_start: 0.8181 (mtm) cc_final: 0.7639 (mtm) REVERT: 3 179 MET cc_start: 0.7394 (tpt) cc_final: 0.6425 (mpt) REVERT: B 43 LEU cc_start: 0.9149 (OUTLIER) cc_final: 0.8769 (pp) REVERT: B 45 ASN cc_start: 0.8759 (t0) cc_final: 0.8353 (t0) REVERT: D 11 TYR cc_start: 0.9341 (OUTLIER) cc_final: 0.8918 (m-80) REVERT: D 21 THR cc_start: 0.8392 (p) cc_final: 0.7995 (t) REVERT: D 42 SER cc_start: 0.8962 (OUTLIER) cc_final: 0.8400 (t) REVERT: D 119 LYS cc_start: 0.8427 (mttt) cc_final: 0.8114 (mppt) REVERT: D 121 MET cc_start: 0.7465 (ttt) cc_final: 0.6859 (mmm) REVERT: D 179 MET cc_start: 0.7409 (tpt) cc_final: 0.6066 (mmt) REVERT: D 190 GLN cc_start: 0.8300 (pt0) cc_final: 0.6960 (pp30) REVERT: D 221 ARG cc_start: 0.5448 (mtp180) cc_final: 0.5115 (mtt180) REVERT: F 83 GLU cc_start: 0.6864 (pm20) cc_final: 0.6625 (pm20) REVERT: F 102 ASP cc_start: 0.8388 (p0) cc_final: 0.8179 (p0) REVERT: F 124 ARG cc_start: 0.7800 (ttp-170) cc_final: 0.7557 (ttp-170) REVERT: F 176 ASP cc_start: 0.7947 (t0) cc_final: 0.7653 (t0) REVERT: H 42 SER cc_start: 0.8852 (p) cc_final: 0.8378 (t) REVERT: H 121 MET cc_start: 0.8262 (mtp) cc_final: 0.7556 (mmm) REVERT: H 190 GLN cc_start: 0.8425 (pt0) cc_final: 0.6736 (pp30) REVERT: J 43 LEU cc_start: 0.9212 (OUTLIER) cc_final: 0.8426 (pp) REVERT: J 45 ASN cc_start: 0.8870 (t0) cc_final: 0.8402 (t0) REVERT: J 108 SER cc_start: 0.9330 (OUTLIER) cc_final: 0.8968 (p) REVERT: L 15 GLN cc_start: 0.8214 (mt0) cc_final: 0.7873 (mt0) REVERT: L 42 SER cc_start: 0.8770 (p) cc_final: 0.8281 (t) REVERT: L 121 MET cc_start: 0.7918 (OUTLIER) cc_final: 0.7509 (pmm) REVERT: L 179 MET cc_start: 0.7536 (tpt) cc_final: 0.7227 (tpp) REVERT: L 204 SER cc_start: 0.8767 (p) cc_final: 0.8388 (t) REVERT: N 105 MET cc_start: 0.8979 (OUTLIER) cc_final: 0.8527 (ttp) REVERT: N 129 ARG cc_start: 0.7928 (OUTLIER) cc_final: 0.7430 (mtp-110) REVERT: P 179 MET cc_start: 0.7738 (tpt) cc_final: 0.7411 (tpp) REVERT: E 141 ILE cc_start: 0.8446 (mt) cc_final: 0.8060 (mm) REVERT: I 141 ILE cc_start: 0.8377 (mt) cc_final: 0.8081 (mm) REVERT: M 117 TYR cc_start: 0.7955 (m-80) cc_final: 0.7600 (m-80) REVERT: Q 141 ILE cc_start: 0.8423 (mt) cc_final: 0.8092 (mm) REVERT: C 79 TYR cc_start: 0.7269 (m-10) cc_final: 0.7019 (m-10) REVERT: C 101 MET cc_start: 0.5328 (ptp) cc_final: 0.5015 (ptp) REVERT: C 102 ARG cc_start: 0.6415 (ttt180) cc_final: 0.6009 (tpp-160) REVERT: C 108 GLN cc_start: 0.8059 (mt0) cc_final: 0.7542 (mt0) REVERT: C 137 GLU cc_start: 0.8524 (OUTLIER) cc_final: 0.8044 (pm20) REVERT: C 199 GLU cc_start: 0.7646 (mp0) cc_final: 0.7152 (mp0) REVERT: G 101 MET cc_start: 0.5220 (ptt) cc_final: 0.4481 (ptp) REVERT: G 128 GLU cc_start: 0.8870 (mt-10) cc_final: 0.8479 (mt-10) REVERT: G 135 ARG cc_start: 0.8302 (mtp180) cc_final: 0.7997 (mtm-85) REVERT: G 137 GLU cc_start: 0.8403 (OUTLIER) cc_final: 0.7943 (pm20) REVERT: G 199 GLU cc_start: 0.7473 (mp0) cc_final: 0.6947 (mp0) REVERT: K 101 MET cc_start: 0.4805 (ptt) cc_final: 0.4307 (ptp) REVERT: K 128 GLU cc_start: 0.8754 (mt-10) cc_final: 0.7967 (mt-10) REVERT: K 137 GLU cc_start: 0.8625 (OUTLIER) cc_final: 0.8159 (pm20) REVERT: K 199 GLU cc_start: 0.7812 (mp0) cc_final: 0.7418 (mp0) REVERT: O 137 GLU cc_start: 0.8384 (OUTLIER) cc_final: 0.7955 (pm20) REVERT: O 199 GLU cc_start: 0.7845 (mp0) cc_final: 0.7395 (mp0) outliers start: 68 outliers final: 42 residues processed: 411 average time/residue: 0.6240 time to fit residues: 290.7959 Evaluate side-chains 423 residues out of total 2355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 367 time to evaluate : 0.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 30 THR Chi-restraints excluded: chain 1 residue 43 LEU Chi-restraints excluded: chain 1 residue 44 THR Chi-restraints excluded: chain 1 residue 47 THR Chi-restraints excluded: chain 1 residue 108 SER Chi-restraints excluded: chain 1 residue 129 ARG Chi-restraints excluded: chain 2 residue 107 VAL Chi-restraints excluded: chain 2 residue 136 GLU Chi-restraints excluded: chain 2 residue 141 SER Chi-restraints excluded: chain 2 residue 178 SER Chi-restraints excluded: chain 2 residue 188 THR Chi-restraints excluded: chain 2 residue 204 ILE Chi-restraints excluded: chain 3 residue 204 SER Chi-restraints excluded: chain 3 residue 217 VAL Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 108 SER Chi-restraints excluded: chain D residue 11 TYR Chi-restraints excluded: chain D residue 42 SER Chi-restraints excluded: chain D residue 204 SER Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 105 MET Chi-restraints excluded: chain F residue 108 SER Chi-restraints excluded: chain H residue 182 THR Chi-restraints excluded: chain H residue 204 SER Chi-restraints excluded: chain H residue 206 SER Chi-restraints excluded: chain J residue 28 VAL Chi-restraints excluded: chain J residue 43 LEU Chi-restraints excluded: chain J residue 108 SER Chi-restraints excluded: chain L residue 121 MET Chi-restraints excluded: chain L residue 206 SER Chi-restraints excluded: chain N residue 28 VAL Chi-restraints excluded: chain N residue 87 VAL Chi-restraints excluded: chain N residue 99 THR Chi-restraints excluded: chain N residue 105 MET Chi-restraints excluded: chain N residue 129 ARG Chi-restraints excluded: chain P residue 42 SER Chi-restraints excluded: chain P residue 190 GLN Chi-restraints excluded: chain P residue 204 SER Chi-restraints excluded: chain P residue 217 VAL Chi-restraints excluded: chain A residue 120 ARG Chi-restraints excluded: chain I residue 120 ARG Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 137 GLU Chi-restraints excluded: chain C residue 178 SER Chi-restraints excluded: chain G residue 137 GLU Chi-restraints excluded: chain G residue 188 THR Chi-restraints excluded: chain G residue 204 ILE Chi-restraints excluded: chain K residue 110 SER Chi-restraints excluded: chain K residue 137 GLU Chi-restraints excluded: chain K residue 158 ILE Chi-restraints excluded: chain K residue 188 THR Chi-restraints excluded: chain O residue 110 SER Chi-restraints excluded: chain O residue 137 GLU Chi-restraints excluded: chain O residue 188 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 142 optimal weight: 0.7980 chunk 13 optimal weight: 0.9990 chunk 253 optimal weight: 6.9990 chunk 27 optimal weight: 9.9990 chunk 107 optimal weight: 0.7980 chunk 129 optimal weight: 0.0970 chunk 215 optimal weight: 1.9990 chunk 201 optimal weight: 0.0000 chunk 109 optimal weight: 0.0270 chunk 32 optimal weight: 0.7980 chunk 39 optimal weight: 3.9990 overall best weight: 0.3440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 110 ASN 3 146 HIS B 29 HIS B 110 ASN D 15 GLN F 110 ASN J 92 ASN J 110 ASN ** L 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 110 ASN ** C 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.159100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.109983 restraints weight = 28422.516| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 3.27 r_work: 0.3264 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.2632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 22465 Z= 0.095 Angle : 0.503 7.346 30625 Z= 0.261 Chirality : 0.042 0.177 3290 Planarity : 0.004 0.047 3970 Dihedral : 3.885 16.490 3005 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 2.04 % Allowed : 18.98 % Favored : 78.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.35 (0.17), residues: 2660 helix: -1.89 (0.30), residues: 240 sheet: -0.68 (0.19), residues: 825 loop : -0.80 (0.16), residues: 1595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 120 TYR 0.011 0.001 TYR 3 124 PHE 0.012 0.001 PHE P 189 TRP 0.032 0.001 TRP D 149 HIS 0.004 0.001 HIS G 145 Details of bonding type rmsd covalent geometry : bond 0.00221 (22445) covalent geometry : angle 0.50278 (30585) SS BOND : bond 0.00101 ( 20) SS BOND : angle 0.62224 ( 40) hydrogen bonds : bond 0.02653 ( 89) hydrogen bonds : angle 4.47691 ( 318) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5320 Ramachandran restraints generated. 2660 Oldfield, 0 Emsley, 2660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5320 Ramachandran restraints generated. 2660 Oldfield, 0 Emsley, 2660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 436 residues out of total 2355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 388 time to evaluate : 0.931 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 45 ASN cc_start: 0.8877 (t0) cc_final: 0.8648 (t0) REVERT: 1 111 ASN cc_start: 0.8897 (m-40) cc_final: 0.8658 (m-40) REVERT: 1 129 ARG cc_start: 0.7900 (OUTLIER) cc_final: 0.7200 (mtp-110) REVERT: 2 82 GLU cc_start: 0.8312 (mp0) cc_final: 0.7926 (mp0) REVERT: 2 101 MET cc_start: 0.5920 (ptp) cc_final: 0.5523 (ptp) REVERT: 2 137 GLU cc_start: 0.8196 (pm20) cc_final: 0.7907 (pm20) REVERT: 2 199 GLU cc_start: 0.7962 (mp0) cc_final: 0.7480 (mp0) REVERT: 3 42 SER cc_start: 0.8871 (p) cc_final: 0.8332 (t) REVERT: 3 109 MET cc_start: 0.8735 (ttp) cc_final: 0.8168 (ttp) REVERT: 3 119 LYS cc_start: 0.8412 (mttt) cc_final: 0.8086 (mtmm) REVERT: 3 121 MET cc_start: 0.8117 (mtm) cc_final: 0.7592 (mtm) REVERT: 3 179 MET cc_start: 0.7225 (tpt) cc_final: 0.6368 (mpt) REVERT: B 43 LEU cc_start: 0.9013 (OUTLIER) cc_final: 0.8591 (pp) REVERT: B 45 ASN cc_start: 0.8760 (t0) cc_final: 0.8363 (t0) REVERT: B 124 ARG cc_start: 0.7789 (ttp-170) cc_final: 0.7494 (ttt-90) REVERT: D 11 TYR cc_start: 0.9297 (OUTLIER) cc_final: 0.8822 (m-80) REVERT: D 15 GLN cc_start: 0.7892 (mt0) cc_final: 0.7395 (mt0) REVERT: D 21 THR cc_start: 0.8335 (p) cc_final: 0.7941 (t) REVERT: D 42 SER cc_start: 0.8947 (p) cc_final: 0.8399 (t) REVERT: D 119 LYS cc_start: 0.8415 (mttt) cc_final: 0.8146 (mppt) REVERT: D 121 MET cc_start: 0.7408 (ttt) cc_final: 0.6834 (mmm) REVERT: D 179 MET cc_start: 0.7268 (tpt) cc_final: 0.6967 (tpp) REVERT: D 190 GLN cc_start: 0.8258 (pt0) cc_final: 0.6884 (pp30) REVERT: D 221 ARG cc_start: 0.5485 (mtp180) cc_final: 0.5178 (mtt180) REVERT: F 83 GLU cc_start: 0.6833 (pm20) cc_final: 0.6615 (pm20) REVERT: F 102 ASP cc_start: 0.8205 (p0) cc_final: 0.7974 (p0) REVERT: F 124 ARG cc_start: 0.7736 (ttp-170) cc_final: 0.7508 (ttp-170) REVERT: F 176 ASP cc_start: 0.7944 (t0) cc_final: 0.7669 (t0) REVERT: H 42 SER cc_start: 0.8742 (p) cc_final: 0.8272 (t) REVERT: H 121 MET cc_start: 0.8270 (mtp) cc_final: 0.7597 (mmm) REVERT: H 190 GLN cc_start: 0.8405 (pt0) cc_final: 0.6646 (pp30) REVERT: H 212 GLU cc_start: 0.8238 (tt0) cc_final: 0.7965 (tt0) REVERT: J 45 ASN cc_start: 0.8842 (t0) cc_final: 0.8386 (t0) REVERT: L 42 SER cc_start: 0.8663 (p) cc_final: 0.8173 (t) REVERT: L 121 MET cc_start: 0.7873 (OUTLIER) cc_final: 0.7451 (pmm) REVERT: L 179 MET cc_start: 0.7346 (tpt) cc_final: 0.6110 (mpt) REVERT: L 204 SER cc_start: 0.8944 (p) cc_final: 0.8607 (t) REVERT: N 28 VAL cc_start: 0.8571 (t) cc_final: 0.8348 (p) REVERT: N 105 MET cc_start: 0.8898 (OUTLIER) cc_final: 0.8433 (ttp) REVERT: N 111 ASN cc_start: 0.8927 (m-40) cc_final: 0.8689 (m110) REVERT: N 129 ARG cc_start: 0.7840 (OUTLIER) cc_final: 0.7128 (mtp-110) REVERT: P 15 GLN cc_start: 0.8040 (mt0) cc_final: 0.7752 (mt0) REVERT: P 86 LYS cc_start: 0.8072 (ttpt) cc_final: 0.7645 (ptmm) REVERT: P 179 MET cc_start: 0.7483 (tpt) cc_final: 0.7205 (tpp) REVERT: E 141 ILE cc_start: 0.8336 (mt) cc_final: 0.7951 (mm) REVERT: M 117 TYR cc_start: 0.7908 (m-80) cc_final: 0.7606 (m-80) REVERT: C 79 TYR cc_start: 0.7365 (m-10) cc_final: 0.7016 (m-10) REVERT: C 101 MET cc_start: 0.5404 (ptp) cc_final: 0.5108 (ptp) REVERT: C 102 ARG cc_start: 0.6456 (ttt180) cc_final: 0.6051 (tpp-160) REVERT: C 108 GLN cc_start: 0.8104 (mt0) cc_final: 0.7664 (mt0) REVERT: C 137 GLU cc_start: 0.8499 (OUTLIER) cc_final: 0.8050 (pm20) REVERT: C 199 GLU cc_start: 0.7648 (mp0) cc_final: 0.7120 (mp0) REVERT: G 101 MET cc_start: 0.5441 (ptt) cc_final: 0.4741 (ptp) REVERT: G 108 GLN cc_start: 0.8060 (mt0) cc_final: 0.7381 (mm-40) REVERT: G 128 GLU cc_start: 0.8808 (mt-10) cc_final: 0.8389 (mt-10) REVERT: G 135 ARG cc_start: 0.8245 (mtp180) cc_final: 0.7944 (mtm-85) REVERT: G 137 GLU cc_start: 0.8377 (OUTLIER) cc_final: 0.7907 (pm20) REVERT: G 199 GLU cc_start: 0.7502 (mp0) cc_final: 0.7012 (mp0) REVERT: K 79 TYR cc_start: 0.7191 (m-80) cc_final: 0.6928 (m-10) REVERT: K 101 MET cc_start: 0.5412 (ptt) cc_final: 0.4921 (ptp) REVERT: K 108 GLN cc_start: 0.7371 (OUTLIER) cc_final: 0.6891 (mm-40) REVERT: K 137 GLU cc_start: 0.8583 (OUTLIER) cc_final: 0.8110 (pm20) REVERT: K 199 GLU cc_start: 0.7795 (mp0) cc_final: 0.7397 (mp0) REVERT: O 79 TYR cc_start: 0.7294 (m-80) cc_final: 0.6799 (m-80) REVERT: O 101 MET cc_start: 0.5170 (ptt) cc_final: 0.4667 (ptp) REVERT: O 102 ARG cc_start: 0.6372 (ttt180) cc_final: 0.6146 (ttt180) REVERT: O 137 GLU cc_start: 0.8322 (OUTLIER) cc_final: 0.7873 (pm20) REVERT: O 199 GLU cc_start: 0.7850 (mp0) cc_final: 0.7399 (mp0) outliers start: 48 outliers final: 22 residues processed: 414 average time/residue: 0.6627 time to fit residues: 311.7954 Evaluate side-chains 403 residues out of total 2355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 370 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 30 THR Chi-restraints excluded: chain 1 residue 44 THR Chi-restraints excluded: chain 1 residue 47 THR Chi-restraints excluded: chain 1 residue 108 SER Chi-restraints excluded: chain 1 residue 129 ARG Chi-restraints excluded: chain 2 residue 141 SER Chi-restraints excluded: chain 2 residue 188 THR Chi-restraints excluded: chain 3 residue 204 SER Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain D residue 11 TYR Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 108 SER Chi-restraints excluded: chain H residue 182 THR Chi-restraints excluded: chain H residue 206 SER Chi-restraints excluded: chain L residue 121 MET Chi-restraints excluded: chain L residue 206 SER Chi-restraints excluded: chain N residue 99 THR Chi-restraints excluded: chain N residue 105 MET Chi-restraints excluded: chain N residue 129 ARG Chi-restraints excluded: chain P residue 217 VAL Chi-restraints excluded: chain A residue 120 ARG Chi-restraints excluded: chain C residue 137 GLU Chi-restraints excluded: chain C residue 178 SER Chi-restraints excluded: chain G residue 137 GLU Chi-restraints excluded: chain G residue 178 SER Chi-restraints excluded: chain K residue 108 GLN Chi-restraints excluded: chain K residue 110 SER Chi-restraints excluded: chain K residue 137 GLU Chi-restraints excluded: chain K residue 188 THR Chi-restraints excluded: chain O residue 137 GLU Chi-restraints excluded: chain O residue 188 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 238 optimal weight: 9.9990 chunk 72 optimal weight: 0.9990 chunk 113 optimal weight: 4.9990 chunk 30 optimal weight: 0.5980 chunk 191 optimal weight: 10.0000 chunk 102 optimal weight: 0.0670 chunk 12 optimal weight: 0.6980 chunk 205 optimal weight: 6.9990 chunk 25 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 213 optimal weight: 5.9990 overall best weight: 1.0722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 110 ASN 3 146 HIS B 29 HIS B 110 ASN F 45 ASN F 110 ASN J 110 ASN ** L 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 110 ASN P 87 ASN P 190 GLN C 108 GLN C 157 HIS ** K 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.155817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.109265 restraints weight = 28453.201| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 3.09 r_work: 0.3246 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.2679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 22465 Z= 0.147 Angle : 0.523 7.625 30625 Z= 0.271 Chirality : 0.042 0.177 3290 Planarity : 0.004 0.032 3970 Dihedral : 3.930 16.783 3005 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 1.87 % Allowed : 19.41 % Favored : 78.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.35 (0.17), residues: 2660 helix: -1.82 (0.31), residues: 240 sheet: -0.72 (0.19), residues: 825 loop : -0.78 (0.16), residues: 1595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 67 TYR 0.013 0.001 TYR H 145 PHE 0.012 0.001 PHE 1 115 TRP 0.038 0.002 TRP H 149 HIS 0.005 0.001 HIS 3 146 Details of bonding type rmsd covalent geometry : bond 0.00352 (22445) covalent geometry : angle 0.52305 (30585) SS BOND : bond 0.00191 ( 20) SS BOND : angle 0.68079 ( 40) hydrogen bonds : bond 0.02799 ( 89) hydrogen bonds : angle 4.41880 ( 318) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5320 Ramachandran restraints generated. 2660 Oldfield, 0 Emsley, 2660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5320 Ramachandran restraints generated. 2660 Oldfield, 0 Emsley, 2660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 2355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 371 time to evaluate : 0.880 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 45 ASN cc_start: 0.8922 (t0) cc_final: 0.8637 (t0) REVERT: 1 111 ASN cc_start: 0.8910 (m-40) cc_final: 0.8660 (m-40) REVERT: 2 82 GLU cc_start: 0.8308 (mp0) cc_final: 0.7854 (mp0) REVERT: 2 101 MET cc_start: 0.6275 (ptp) cc_final: 0.5907 (ptp) REVERT: 2 102 ARG cc_start: 0.6460 (ttt180) cc_final: 0.5810 (tpp-160) REVERT: 2 137 GLU cc_start: 0.8204 (pm20) cc_final: 0.7901 (pm20) REVERT: 2 199 GLU cc_start: 0.7954 (mp0) cc_final: 0.7469 (mp0) REVERT: 3 42 SER cc_start: 0.8895 (p) cc_final: 0.8363 (t) REVERT: 3 109 MET cc_start: 0.8742 (ttp) cc_final: 0.8175 (ttp) REVERT: 3 119 LYS cc_start: 0.8406 (mttt) cc_final: 0.8107 (mtmm) REVERT: 3 121 MET cc_start: 0.8304 (mtm) cc_final: 0.7753 (mtm) REVERT: 3 179 MET cc_start: 0.7252 (tpt) cc_final: 0.6361 (mpt) REVERT: B 43 LEU cc_start: 0.9071 (OUTLIER) cc_final: 0.8641 (pp) REVERT: B 45 ASN cc_start: 0.8769 (t0) cc_final: 0.8371 (t0) REVERT: D 11 TYR cc_start: 0.9307 (OUTLIER) cc_final: 0.8825 (m-80) REVERT: D 21 THR cc_start: 0.8353 (p) cc_final: 0.7971 (t) REVERT: D 42 SER cc_start: 0.8952 (OUTLIER) cc_final: 0.8406 (t) REVERT: D 119 LYS cc_start: 0.8420 (mttt) cc_final: 0.8093 (mppt) REVERT: D 121 MET cc_start: 0.7428 (ttt) cc_final: 0.6856 (mmm) REVERT: D 179 MET cc_start: 0.7305 (tpt) cc_final: 0.6190 (mpt) REVERT: D 190 GLN cc_start: 0.8294 (pt0) cc_final: 0.6954 (pp30) REVERT: D 221 ARG cc_start: 0.5494 (mtp180) cc_final: 0.5196 (mtt180) REVERT: F 102 ASP cc_start: 0.8262 (p0) cc_final: 0.8042 (p0) REVERT: F 124 ARG cc_start: 0.7764 (ttp-170) cc_final: 0.7513 (ttp-170) REVERT: F 176 ASP cc_start: 0.7899 (t0) cc_final: 0.7607 (t0) REVERT: H 42 SER cc_start: 0.8770 (p) cc_final: 0.8297 (t) REVERT: H 121 MET cc_start: 0.8239 (mtp) cc_final: 0.7697 (mmm) REVERT: H 190 GLN cc_start: 0.8326 (pt0) cc_final: 0.6716 (pp30) REVERT: H 212 GLU cc_start: 0.8247 (tt0) cc_final: 0.7972 (tt0) REVERT: J 45 ASN cc_start: 0.8844 (t0) cc_final: 0.8398 (t0) REVERT: L 42 SER cc_start: 0.8704 (p) cc_final: 0.8218 (t) REVERT: L 121 MET cc_start: 0.7937 (OUTLIER) cc_final: 0.7513 (pmm) REVERT: L 179 MET cc_start: 0.7406 (tpt) cc_final: 0.6076 (mpm) REVERT: L 204 SER cc_start: 0.8957 (p) cc_final: 0.8618 (t) REVERT: N 28 VAL cc_start: 0.8590 (t) cc_final: 0.8355 (p) REVERT: N 105 MET cc_start: 0.8918 (OUTLIER) cc_final: 0.8441 (ttp) REVERT: N 111 ASN cc_start: 0.8941 (m-40) cc_final: 0.8697 (m110) REVERT: N 129 ARG cc_start: 0.7867 (OUTLIER) cc_final: 0.7321 (mtp-110) REVERT: P 15 GLN cc_start: 0.8121 (mt0) cc_final: 0.7807 (mt0) REVERT: P 86 LYS cc_start: 0.8079 (ttpt) cc_final: 0.7652 (ptmm) REVERT: P 179 MET cc_start: 0.7629 (tpt) cc_final: 0.7328 (tpp) REVERT: P 221 ARG cc_start: 0.6163 (mtt180) cc_final: 0.5918 (mtt-85) REVERT: C 79 TYR cc_start: 0.7359 (m-10) cc_final: 0.6998 (m-10) REVERT: C 101 MET cc_start: 0.5661 (ptp) cc_final: 0.5295 (ptp) REVERT: C 102 ARG cc_start: 0.6540 (ttt180) cc_final: 0.6106 (tpp-160) REVERT: C 108 GLN cc_start: 0.8140 (mt0) cc_final: 0.7684 (mt0) REVERT: C 137 GLU cc_start: 0.8520 (OUTLIER) cc_final: 0.8059 (pm20) REVERT: C 178 SER cc_start: 0.9021 (OUTLIER) cc_final: 0.8807 (p) REVERT: C 199 GLU cc_start: 0.7678 (mp0) cc_final: 0.7135 (mp0) REVERT: G 101 MET cc_start: 0.5336 (ptt) cc_final: 0.4711 (ptp) REVERT: G 102 ARG cc_start: 0.6152 (ttt180) cc_final: 0.5648 (tpp-160) REVERT: G 108 GLN cc_start: 0.8126 (mt0) cc_final: 0.7428 (mm-40) REVERT: G 128 GLU cc_start: 0.8876 (mt-10) cc_final: 0.8459 (mt-10) REVERT: G 135 ARG cc_start: 0.8257 (mtp180) cc_final: 0.7962 (mtm-85) REVERT: G 137 GLU cc_start: 0.8381 (OUTLIER) cc_final: 0.7926 (pm20) REVERT: G 199 GLU cc_start: 0.7504 (mp0) cc_final: 0.7012 (mp0) REVERT: K 79 TYR cc_start: 0.7301 (m-80) cc_final: 0.7055 (m-10) REVERT: K 101 MET cc_start: 0.5479 (ptt) cc_final: 0.5039 (ptp) REVERT: K 102 ARG cc_start: 0.6240 (ttt180) cc_final: 0.5861 (mtt90) REVERT: K 108 GLN cc_start: 0.7571 (mm110) cc_final: 0.7098 (mm-40) REVERT: K 128 GLU cc_start: 0.8748 (mt-10) cc_final: 0.8014 (mt-10) REVERT: K 137 GLU cc_start: 0.8622 (OUTLIER) cc_final: 0.8149 (pm20) REVERT: O 79 TYR cc_start: 0.7336 (m-80) cc_final: 0.6853 (m-80) REVERT: O 101 MET cc_start: 0.5389 (ptt) cc_final: 0.4827 (ptp) REVERT: O 102 ARG cc_start: 0.6387 (ttt180) cc_final: 0.6177 (ttt180) REVERT: O 108 GLN cc_start: 0.7868 (mm110) cc_final: 0.7384 (mm-40) REVERT: O 137 GLU cc_start: 0.8331 (OUTLIER) cc_final: 0.7880 (pm20) REVERT: O 199 GLU cc_start: 0.7856 (mp0) cc_final: 0.7399 (mp0) outliers start: 44 outliers final: 24 residues processed: 392 average time/residue: 0.6835 time to fit residues: 303.3979 Evaluate side-chains 401 residues out of total 2355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 366 time to evaluate : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 28 VAL Chi-restraints excluded: chain 1 residue 30 THR Chi-restraints excluded: chain 1 residue 44 THR Chi-restraints excluded: chain 1 residue 47 THR Chi-restraints excluded: chain 1 residue 108 SER Chi-restraints excluded: chain 2 residue 141 SER Chi-restraints excluded: chain 2 residue 188 THR Chi-restraints excluded: chain 3 residue 204 SER Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain D residue 11 TYR Chi-restraints excluded: chain D residue 42 SER Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 108 SER Chi-restraints excluded: chain H residue 182 THR Chi-restraints excluded: chain H residue 204 SER Chi-restraints excluded: chain H residue 206 SER Chi-restraints excluded: chain L residue 121 MET Chi-restraints excluded: chain L residue 206 SER Chi-restraints excluded: chain L residue 217 VAL Chi-restraints excluded: chain N residue 99 THR Chi-restraints excluded: chain N residue 105 MET Chi-restraints excluded: chain N residue 129 ARG Chi-restraints excluded: chain P residue 217 VAL Chi-restraints excluded: chain C residue 137 GLU Chi-restraints excluded: chain C residue 178 SER Chi-restraints excluded: chain G residue 110 SER Chi-restraints excluded: chain G residue 137 GLU Chi-restraints excluded: chain G residue 178 SER Chi-restraints excluded: chain K residue 110 SER Chi-restraints excluded: chain K residue 137 GLU Chi-restraints excluded: chain K residue 188 THR Chi-restraints excluded: chain O residue 137 GLU Chi-restraints excluded: chain O residue 188 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 139 optimal weight: 0.0770 chunk 217 optimal weight: 0.0050 chunk 192 optimal weight: 0.9980 chunk 212 optimal weight: 0.9980 chunk 233 optimal weight: 4.9990 chunk 20 optimal weight: 5.9990 chunk 180 optimal weight: 0.8980 chunk 252 optimal weight: 0.0970 chunk 234 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 chunk 200 optimal weight: 6.9990 overall best weight: 0.4150 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 110 ASN 3 146 HIS B 29 HIS B 110 ASN D 15 GLN F 110 ASN J 110 ASN N 45 ASN N 110 ASN P 190 GLN ** G 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 149 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.164480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.115456 restraints weight = 28758.313| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 3.29 r_work: 0.3270 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.2772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 22465 Z= 0.096 Angle : 0.500 7.565 30625 Z= 0.258 Chirality : 0.042 0.186 3290 Planarity : 0.004 0.047 3970 Dihedral : 3.729 15.043 3005 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 1.66 % Allowed : 19.66 % Favored : 78.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.25 (0.17), residues: 2660 helix: -1.77 (0.31), residues: 240 sheet: -0.57 (0.19), residues: 800 loop : -0.76 (0.16), residues: 1620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG E 120 TYR 0.012 0.001 TYR J 183 PHE 0.010 0.001 PHE D 157 TRP 0.035 0.001 TRP 3 149 HIS 0.006 0.001 HIS 3 146 Details of bonding type rmsd covalent geometry : bond 0.00228 (22445) covalent geometry : angle 0.49974 (30585) SS BOND : bond 0.00109 ( 20) SS BOND : angle 0.63872 ( 40) hydrogen bonds : bond 0.02667 ( 89) hydrogen bonds : angle 4.33055 ( 318) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6913.50 seconds wall clock time: 118 minutes 39.20 seconds (7119.20 seconds total)