Starting phenix.real_space_refine on Wed Jun 18 18:40:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9g6v_51105/06_2025/9g6v_51105.cif Found real_map, /net/cci-nas-00/data/ceres_data/9g6v_51105/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9g6v_51105/06_2025/9g6v_51105.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9g6v_51105/06_2025/9g6v_51105.map" model { file = "/net/cci-nas-00/data/ceres_data/9g6v_51105/06_2025/9g6v_51105.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9g6v_51105/06_2025/9g6v_51105.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 12.60, per 1000 atoms: 0.58 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: 4.72 Conformation dependent library (CDL) restraints added in 2.8 seconds 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: 1.56 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: 4.62 Time building geometry restraints manager: 5.71 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: 0.08 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: 2.000 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: 0.820 Check model and map are aligned: 0.140 Set scattering table: 0.180 Process input model: 43.390 Find NCS groups from input model: 0.890 Set up NCS constraints: 0.150 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:15.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.820 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (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 TRP 0.010 0.001 TRP Q 138 HIS 0.002 0.000 HIS G 145 PHE 0.010 0.001 PHE 1 115 TYR 0.008 0.001 TYR P 41 ARG 0.003 0.000 ARG H 214 Details of bonding type rmsd hydrogen bonds : bond 0.02783 ( 89) hydrogen bonds : angle 4.30819 ( 318) SS BOND : bond 0.00078 ( 20) SS BOND : angle 0.54538 ( 40) covalent geometry : bond 0.00265 (22445) covalent geometry : angle 0.44179 (30585) *********************** 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 : 2.222 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: 2 199 GLU cc_start: 0.7421 (mp0) cc_final: 0.7078 (mp0) REVERT: 2 207 THR cc_start: 0.8096 (p) cc_final: 0.7721 (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: 0.7797 (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: 0.3823 (ptp) REVERT: C 108 GLN cc_start: 0.8275 (mt0) cc_final: 0.8030 (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: 0.7021 (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: 0.7708 (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: 1.2406 time to fit residues: 748.2681 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 : 1.880 ------------------------------------------------------------------------------- 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 223 optimal weight: 4.9990 chunk 200 optimal weight: 4.9990 chunk 111 optimal weight: 9.9990 chunk 68 optimal weight: 3.9990 chunk 135 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 207 optimal weight: 0.7980 chunk 80 optimal weight: 5.9990 chunk 126 optimal weight: 2.9990 chunk 154 optimal weight: 3.9990 chunk 240 optimal weight: 4.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- 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 2 117 ASN 2 145 HIS 2 149 ASN 2 174 HIS ** B 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 110 ASN B 111 ASN D 173 HIS ** F 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 110 ASN F 111 ASN ** J 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 110 ASN J 111 ASN L 173 HIS N 45 ASN ** N 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 110 ASN P 143 HIS P 146 HIS P 173 HIS ** C 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 145 HIS ** C 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 174 HIS ** G 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 174 HIS K 145 HIS O 139 GLN O 145 HIS ** O 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 174 HIS Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.160032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.108965 restraints weight = 29121.675| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 3.31 r_work: 0.3174 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.1724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.077 22465 Z= 0.313 Angle : 0.588 6.290 30625 Z= 0.307 Chirality : 0.045 0.165 3290 Planarity : 0.005 0.042 3970 Dihedral : 4.378 27.136 3010 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer: Outliers : 3.48 % Allowed : 10.11 % Favored : 86.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.17), residues: 2660 helix: -1.97 (0.30), residues: 240 sheet: -0.68 (0.18), residues: 865 loop : -0.82 (0.17), residues: 1555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP Q 138 HIS 0.011 0.001 HIS P 143 PHE 0.018 0.002 PHE N 115 TYR 0.013 0.002 TYR 3 124 ARG 0.008 0.001 ARG G 102 Details of bonding type rmsd hydrogen bonds : bond 0.03560 ( 89) hydrogen bonds : angle 4.74391 ( 318) SS BOND : bond 0.00137 ( 20) SS BOND : angle 0.55881 ( 40) covalent geometry : bond 0.00749 (22445) covalent geometry : angle 0.58813 (30585) *********************** 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 461 residues out of total 2355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 379 time to evaluate : 2.243 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 111 ASN cc_start: 0.8951 (m-40) cc_final: 0.8672 (m-40) REVERT: 2 82 GLU cc_start: 0.8266 (mp0) cc_final: 0.7763 (mp0) REVERT: 2 101 MET cc_start: 0.5112 (ptp) cc_final: 0.4610 (ptp) REVERT: 2 137 GLU cc_start: 0.7908 (pm20) cc_final: 0.7631 (pm20) REVERT: 2 199 GLU cc_start: 0.7725 (mp0) cc_final: 0.7287 (mp0) REVERT: 3 42 SER cc_start: 0.8950 (p) cc_final: 0.8426 (t) REVERT: 3 109 MET cc_start: 0.8722 (ttp) cc_final: 0.8131 (ttp) REVERT: 3 119 LYS cc_start: 0.8322 (mttt) cc_final: 0.8019 (mptt) REVERT: 3 179 MET cc_start: 0.7446 (tpt) cc_final: 0.6426 (mpt) REVERT: 3 190 GLN cc_start: 0.8205 (pt0) cc_final: 0.6609 (pp30) REVERT: 3 221 ARG cc_start: 0.5837 (OUTLIER) cc_final: 0.5515 (mtp180) REVERT: B 45 ASN cc_start: 0.8680 (t0) cc_final: 0.8345 (t0) REVERT: D 42 SER cc_start: 0.8964 (p) cc_final: 0.8455 (t) REVERT: D 119 LYS cc_start: 0.8351 (mttt) cc_final: 0.8065 (mptt) REVERT: D 149 TRP cc_start: 0.6361 (p-90) cc_final: 0.6129 (p-90) REVERT: D 189 PHE cc_start: 0.7994 (m-80) cc_final: 0.7689 (m-80) REVERT: D 190 GLN cc_start: 0.8146 (pt0) cc_final: 0.6852 (pp30) REVERT: F 83 GLU cc_start: 0.7006 (pm20) cc_final: 0.6796 (pm20) REVERT: H 42 SER cc_start: 0.8875 (p) cc_final: 0.8453 (t) REVERT: H 190 GLN cc_start: 0.8082 (pt0) cc_final: 0.6659 (pp30) REVERT: J 124 ARG cc_start: 0.7776 (ttp-170) cc_final: 0.7512 (ttp-170) REVERT: L 42 SER cc_start: 0.8797 (p) cc_final: 0.8332 (t) REVERT: L 121 MET cc_start: 0.7781 (pmm) cc_final: 0.7452 (pmm) REVERT: L 179 MET cc_start: 0.7499 (tpt) cc_final: 0.6261 (mpt) REVERT: L 204 SER cc_start: 0.8750 (p) cc_final: 0.8275 (t) REVERT: N 111 ASN cc_start: 0.8948 (m-40) cc_final: 0.8691 (m110) REVERT: P 119 LYS cc_start: 0.8547 (mttt) cc_final: 0.8301 (mptt) REVERT: P 179 MET cc_start: 0.7743 (tpt) cc_final: 0.7295 (tpp) REVERT: E 141 ILE cc_start: 0.8410 (mt) cc_final: 0.8067 (mm) REVERT: I 141 ILE cc_start: 0.8407 (mt) cc_final: 0.8092 (mm) REVERT: Q 141 ILE cc_start: 0.8457 (mt) cc_final: 0.8165 (mm) REVERT: C 79 TYR cc_start: 0.7417 (m-80) cc_final: 0.7195 (m-80) REVERT: C 101 MET cc_start: 0.4046 (ptp) cc_final: 0.3653 (ptp) REVERT: C 108 GLN cc_start: 0.8052 (mt0) cc_final: 0.7535 (mt0) REVERT: C 128 GLU cc_start: 0.8646 (mt-10) cc_final: 0.8432 (mt-10) REVERT: C 137 GLU cc_start: 0.8478 (OUTLIER) cc_final: 0.8026 (pm20) REVERT: C 199 GLU cc_start: 0.7523 (mp0) cc_final: 0.7067 (mp0) REVERT: G 108 GLN cc_start: 0.8140 (mt0) cc_final: 0.7860 (mt0) REVERT: G 137 GLU cc_start: 0.8307 (OUTLIER) cc_final: 0.7812 (pm20) REVERT: G 158 ILE cc_start: 0.8589 (OUTLIER) cc_final: 0.8252 (mp) REVERT: G 162 TYR cc_start: 0.8137 (t80) cc_final: 0.7924 (t80) REVERT: G 199 GLU cc_start: 0.7458 (mp0) cc_final: 0.6978 (mp0) REVERT: K 102 ARG cc_start: 0.6405 (ttt180) cc_final: 0.6143 (ttm110) REVERT: K 137 GLU cc_start: 0.8329 (OUTLIER) cc_final: 0.7799 (pm20) REVERT: K 199 GLU cc_start: 0.7611 (mp0) cc_final: 0.7187 (mp0) REVERT: O 137 GLU cc_start: 0.8185 (OUTLIER) cc_final: 0.7713 (pm20) REVERT: O 199 GLU cc_start: 0.7560 (mp0) cc_final: 0.7048 (mp0) outliers start: 82 outliers final: 45 residues processed: 421 average time/residue: 1.2490 time to fit residues: 602.1448 Evaluate side-chains 418 residues out of total 2355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 367 time to evaluate : 2.193 ------------------------------------------------------------------------------- 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 99 THR Chi-restraints excluded: chain 1 residue 108 SER 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 204 SER 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 99 THR 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 175 ASP Chi-restraints excluded: chain L residue 206 SER Chi-restraints excluded: chain L residue 221 ARG Chi-restraints excluded: chain N residue 28 VAL Chi-restraints excluded: chain N residue 45 ASN Chi-restraints excluded: chain N residue 87 VAL Chi-restraints excluded: chain P residue 204 SER 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 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 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 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 237 optimal weight: 4.9990 chunk 206 optimal weight: 9.9990 chunk 235 optimal weight: 1.9990 chunk 162 optimal weight: 2.9990 chunk 101 optimal weight: 0.9990 chunk 141 optimal weight: 0.9980 chunk 215 optimal weight: 0.8980 chunk 195 optimal weight: 6.9990 chunk 6 optimal weight: 0.6980 chunk 190 optimal weight: 6.9990 chunk 77 optimal weight: 3.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 110 ASN ** B 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 110 ASN F 45 ASN ** F 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 110 ASN H 146 HIS J 45 ASN ** J 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 110 ASN N 45 ASN ** N 92 ASN ** 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** ** G 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 149 ASN ** O 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.161883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.112030 restraints weight = 28617.579| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 3.26 r_work: 0.3216 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.1878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 22465 Z= 0.147 Angle : 0.485 6.097 30625 Z= 0.252 Chirality : 0.042 0.165 3290 Planarity : 0.004 0.035 3970 Dihedral : 4.057 18.130 3005 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 3.01 % Allowed : 12.70 % Favored : 84.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.39 (0.17), residues: 2660 helix: -1.90 (0.30), residues: 240 sheet: -0.73 (0.18), residues: 865 loop : -0.80 (0.17), residues: 1555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP 3 149 HIS 0.007 0.001 HIS 3 146 PHE 0.015 0.001 PHE O 116 TYR 0.019 0.001 TYR G 34 ARG 0.005 0.000 ARG G 102 Details of bonding type rmsd hydrogen bonds : bond 0.03046 ( 89) hydrogen bonds : angle 4.59467 ( 318) SS BOND : bond 0.00094 ( 20) SS BOND : angle 0.46786 ( 40) covalent geometry : bond 0.00347 (22445) covalent geometry : angle 0.48544 (30585) *********************** 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 456 residues out of total 2355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 385 time to evaluate : 2.264 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: 1 105 MET cc_start: 0.8906 (OUTLIER) cc_final: 0.8447 (ttp) REVERT: 1 111 ASN cc_start: 0.8940 (m-40) cc_final: 0.8687 (m-40) REVERT: 2 82 GLU cc_start: 0.8265 (mp0) cc_final: 0.7882 (mp0) REVERT: 2 101 MET cc_start: 0.4785 (ptp) cc_final: 0.4341 (ptp) REVERT: 2 137 GLU cc_start: 0.8048 (pm20) cc_final: 0.7710 (pm20) REVERT: 2 199 GLU cc_start: 0.7796 (mp0) cc_final: 0.7333 (mp0) REVERT: 3 42 SER cc_start: 0.8892 (p) cc_final: 0.8379 (t) REVERT: 3 109 MET cc_start: 0.8636 (ttp) cc_final: 0.8154 (ttp) REVERT: 3 119 LYS cc_start: 0.8331 (mttt) cc_final: 0.8006 (mppt) REVERT: 3 179 MET cc_start: 0.7275 (tpt) cc_final: 0.6312 (mpt) REVERT: 3 190 GLN cc_start: 0.8177 (pt0) cc_final: 0.6527 (pp30) REVERT: 3 221 ARG cc_start: 0.5846 (OUTLIER) cc_final: 0.5576 (mtp180) REVERT: B 45 ASN cc_start: 0.8673 (t0) cc_final: 0.8317 (t0) REVERT: D 21 THR cc_start: 0.8385 (p) cc_final: 0.7968 (t) REVERT: D 42 SER cc_start: 0.8920 (p) cc_final: 0.8400 (t) REVERT: D 121 MET cc_start: 0.7120 (ttt) cc_final: 0.6689 (mmm) REVERT: D 149 TRP cc_start: 0.6365 (p-90) cc_final: 0.6090 (p-90) REVERT: D 179 MET cc_start: 0.7302 (tpt) cc_final: 0.6055 (mpt) REVERT: D 189 PHE cc_start: 0.7974 (m-80) cc_final: 0.7589 (m-80) REVERT: D 190 GLN cc_start: 0.8190 (pt0) cc_final: 0.6835 (pp30) REVERT: F 43 LEU cc_start: 0.9169 (OUTLIER) cc_final: 0.8945 (pp) REVERT: F 102 ASP cc_start: 0.8131 (p0) cc_final: 0.7861 (p0) REVERT: F 124 ARG cc_start: 0.7714 (ttp-170) cc_final: 0.7501 (ttp-170) REVERT: H 42 SER cc_start: 0.8807 (p) cc_final: 0.8340 (t) REVERT: H 119 LYS cc_start: 0.8533 (mttt) cc_final: 0.8323 (mppt) REVERT: H 190 GLN cc_start: 0.8115 (pt0) cc_final: 0.6691 (pp30) REVERT: J 124 ARG cc_start: 0.7809 (ttp-170) cc_final: 0.7550 (ttp-170) REVERT: L 42 SER cc_start: 0.8697 (p) cc_final: 0.8205 (t) REVERT: L 119 LYS cc_start: 0.8419 (mttt) cc_final: 0.8097 (mppt) REVERT: L 121 MET cc_start: 0.7792 (OUTLIER) cc_final: 0.7460 (pmm) REVERT: L 179 MET cc_start: 0.7365 (tpt) cc_final: 0.7080 (tpp) REVERT: L 190 GLN cc_start: 0.7669 (pt0) cc_final: 0.6264 (pp30) REVERT: L 204 SER cc_start: 0.8786 (p) cc_final: 0.8346 (t) REVERT: N 45 ASN cc_start: 0.8407 (OUTLIER) cc_final: 0.8203 (t0) REVERT: N 111 ASN cc_start: 0.8926 (m-40) cc_final: 0.8671 (m110) REVERT: P 119 LYS cc_start: 0.8517 (mttt) cc_final: 0.8260 (mppt) REVERT: P 179 MET cc_start: 0.7646 (tpt) cc_final: 0.7262 (tpp) REVERT: E 141 ILE cc_start: 0.8358 (mt) cc_final: 0.8021 (mm) REVERT: Q 143 LEU cc_start: 0.8242 (mt) cc_final: 0.8007 (mt) REVERT: C 79 TYR cc_start: 0.7421 (m-80) cc_final: 0.7200 (m-80) REVERT: C 101 MET cc_start: 0.4062 (ptp) cc_final: 0.3695 (ptp) REVERT: C 108 GLN cc_start: 0.8039 (mt0) cc_final: 0.7534 (mt0) REVERT: C 137 GLU cc_start: 0.8475 (OUTLIER) cc_final: 0.7917 (pm20) REVERT: C 182 MET cc_start: 0.7995 (ttp) cc_final: 0.7586 (ptm) REVERT: C 199 GLU cc_start: 0.7537 (mp0) cc_final: 0.7051 (mp0) REVERT: G 101 MET cc_start: 0.4192 (ptt) cc_final: 0.3632 (ptp) REVERT: G 108 GLN cc_start: 0.8110 (mt0) cc_final: 0.7862 (mt0) REVERT: G 137 GLU cc_start: 0.8365 (OUTLIER) cc_final: 0.7783 (pm20) REVERT: G 158 ILE cc_start: 0.8590 (OUTLIER) cc_final: 0.8300 (mp) REVERT: G 162 TYR cc_start: 0.8155 (t80) cc_final: 0.7902 (t80) REVERT: G 199 GLU cc_start: 0.7434 (mp0) cc_final: 0.6947 (mp0) REVERT: K 102 ARG cc_start: 0.6446 (ttt180) cc_final: 0.6100 (ttm110) REVERT: K 137 GLU cc_start: 0.8306 (OUTLIER) cc_final: 0.7828 (pm20) REVERT: K 199 GLU cc_start: 0.7666 (mp0) cc_final: 0.7268 (mp0) REVERT: O 108 GLN cc_start: 0.8063 (mt0) cc_final: 0.7777 (mt0) REVERT: O 137 GLU cc_start: 0.8199 (OUTLIER) cc_final: 0.7794 (pm20) REVERT: O 199 GLU cc_start: 0.7620 (mp0) cc_final: 0.7047 (mp0) outliers start: 71 outliers final: 35 residues processed: 416 average time/residue: 1.3882 time to fit residues: 657.1405 Evaluate side-chains 411 residues out of total 2355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 366 time to evaluate : 2.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 28 VAL Chi-restraints excluded: chain 1 residue 44 THR Chi-restraints excluded: chain 1 residue 47 THR Chi-restraints excluded: chain 1 residue 105 MET Chi-restraints excluded: chain 1 residue 108 SER 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 221 ARG 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 105 MET 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 L residue 217 VAL Chi-restraints excluded: chain N residue 28 VAL Chi-restraints excluded: chain N residue 45 ASN Chi-restraints excluded: chain N residue 87 VAL Chi-restraints excluded: chain N residue 99 THR 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 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 158 ILE 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 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 107 optimal weight: 1.9990 chunk 158 optimal weight: 0.6980 chunk 21 optimal weight: 1.9990 chunk 146 optimal weight: 0.0030 chunk 77 optimal weight: 6.9990 chunk 48 optimal weight: 1.9990 chunk 229 optimal weight: 4.9990 chunk 182 optimal weight: 6.9990 chunk 72 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 chunk 142 optimal weight: 2.9990 overall best weight: 1.0994 ------------------------------------------------------------------------------- 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 2 166 ASN B 92 ASN B 110 ASN F 110 ASN J 45 ASN ** J 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.161949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.112006 restraints weight = 29075.079| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 3.30 r_work: 0.3217 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.2016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 22465 Z= 0.147 Angle : 0.486 6.081 30625 Z= 0.253 Chirality : 0.042 0.165 3290 Planarity : 0.004 0.036 3970 Dihedral : 3.989 17.719 3005 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 3.23 % Allowed : 13.76 % Favored : 83.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.17), residues: 2660 helix: -1.91 (0.30), residues: 240 sheet: -0.82 (0.18), residues: 870 loop : -0.81 (0.17), residues: 1550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP 3 149 HIS 0.005 0.001 HIS 3 146 PHE 0.012 0.001 PHE 1 115 TYR 0.010 0.001 TYR O 79 ARG 0.005 0.000 ARG G 102 Details of bonding type rmsd hydrogen bonds : bond 0.03037 ( 89) hydrogen bonds : angle 4.52289 ( 318) SS BOND : bond 0.00079 ( 20) SS BOND : angle 0.42175 ( 40) covalent geometry : bond 0.00350 (22445) covalent geometry : angle 0.48607 (30585) *********************** 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 457 residues out of total 2355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 381 time to evaluate : 2.511 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 105 MET cc_start: 0.8894 (OUTLIER) cc_final: 0.8419 (ttp) REVERT: 1 111 ASN cc_start: 0.8935 (m-40) cc_final: 0.8682 (m-40) REVERT: 2 82 GLU cc_start: 0.8257 (mp0) cc_final: 0.7943 (mp0) REVERT: 2 101 MET cc_start: 0.5152 (ptp) cc_final: 0.4717 (ptp) REVERT: 2 137 GLU cc_start: 0.8083 (pm20) cc_final: 0.7740 (pm20) REVERT: 2 199 GLU cc_start: 0.7889 (mp0) cc_final: 0.7428 (mp0) REVERT: 3 42 SER cc_start: 0.8910 (p) cc_final: 0.8383 (t) REVERT: 3 109 MET cc_start: 0.8686 (ttp) cc_final: 0.8106 (ttp) REVERT: 3 119 LYS cc_start: 0.8287 (mttt) cc_final: 0.8004 (mppt) REVERT: 3 179 MET cc_start: 0.7372 (tpt) cc_final: 0.6387 (mpt) REVERT: 3 190 GLN cc_start: 0.8096 (pt0) cc_final: 0.6425 (pp30) REVERT: B 45 ASN cc_start: 0.8706 (t0) cc_final: 0.8315 (t0) REVERT: D 21 THR cc_start: 0.8373 (p) cc_final: 0.7932 (t) REVERT: D 42 SER cc_start: 0.8930 (p) cc_final: 0.8415 (t) REVERT: D 121 MET cc_start: 0.7139 (ttt) cc_final: 0.6706 (mmm) REVERT: D 179 MET cc_start: 0.7317 (tpt) cc_final: 0.5982 (mpt) REVERT: D 189 PHE cc_start: 0.7912 (m-80) cc_final: 0.7640 (m-80) REVERT: D 190 GLN cc_start: 0.8177 (pt0) cc_final: 0.6848 (pp30) REVERT: F 43 LEU cc_start: 0.9197 (OUTLIER) cc_final: 0.8940 (pp) REVERT: F 102 ASP cc_start: 0.8192 (p0) cc_final: 0.7896 (p0) REVERT: F 124 ARG cc_start: 0.7748 (ttp-170) cc_final: 0.7510 (ttp-170) REVERT: H 42 SER cc_start: 0.8781 (p) cc_final: 0.8310 (t) REVERT: H 119 LYS cc_start: 0.8554 (mttt) cc_final: 0.8344 (mppt) REVERT: H 121 MET cc_start: 0.7208 (ttt) cc_final: 0.6931 (mmm) REVERT: H 190 GLN cc_start: 0.8231 (pt0) cc_final: 0.6730 (pp30) REVERT: J 36 MET cc_start: 0.8981 (mmm) cc_final: 0.8505 (mmt) REVERT: J 124 ARG cc_start: 0.7819 (ttp-170) cc_final: 0.7536 (ttp-170) REVERT: L 42 SER cc_start: 0.8704 (p) cc_final: 0.8224 (t) REVERT: L 121 MET cc_start: 0.7819 (pmm) cc_final: 0.7495 (pmm) REVERT: L 190 GLN cc_start: 0.7705 (pt0) cc_final: 0.6327 (pp30) REVERT: L 204 SER cc_start: 0.8822 (p) cc_final: 0.8417 (t) REVERT: N 92 ASN cc_start: 0.8496 (t0) cc_final: 0.8292 (t0) REVERT: N 105 MET cc_start: 0.8954 (OUTLIER) cc_final: 0.8451 (ttp) REVERT: N 111 ASN cc_start: 0.8927 (m-40) cc_final: 0.8685 (m110) REVERT: N 129 ARG cc_start: 0.7851 (mtp-110) cc_final: 0.7625 (mtp-110) REVERT: P 119 LYS cc_start: 0.8521 (mttt) cc_final: 0.8298 (mppt) REVERT: P 171 TYR cc_start: 0.8421 (m-10) cc_final: 0.8129 (m-80) REVERT: P 179 MET cc_start: 0.7644 (tpt) cc_final: 0.7281 (tpp) REVERT: E 141 ILE cc_start: 0.8345 (mt) cc_final: 0.7987 (mm) REVERT: Q 143 LEU cc_start: 0.8281 (mt) cc_final: 0.8066 (mt) REVERT: C 79 TYR cc_start: 0.7470 (m-80) cc_final: 0.7178 (m-80) REVERT: C 101 MET cc_start: 0.4596 (ptp) cc_final: 0.4321 (ptp) REVERT: C 108 GLN cc_start: 0.8047 (mt0) cc_final: 0.7544 (mt0) REVERT: C 137 GLU cc_start: 0.8495 (OUTLIER) cc_final: 0.7919 (pm20) REVERT: C 182 MET cc_start: 0.8011 (ttp) cc_final: 0.7618 (ptm) REVERT: C 199 GLU cc_start: 0.7621 (mp0) cc_final: 0.7156 (mp0) REVERT: G 101 MET cc_start: 0.4685 (ptt) cc_final: 0.4072 (ptp) REVERT: G 102 ARG cc_start: 0.5992 (ttt180) cc_final: 0.5784 (ttm-80) REVERT: G 128 GLU cc_start: 0.8789 (mt-10) cc_final: 0.8408 (mt-10) REVERT: G 137 GLU cc_start: 0.8333 (OUTLIER) cc_final: 0.7852 (pm20) REVERT: G 158 ILE cc_start: 0.8598 (OUTLIER) cc_final: 0.8323 (mp) REVERT: G 162 TYR cc_start: 0.8180 (t80) cc_final: 0.7955 (t80) REVERT: G 199 GLU cc_start: 0.7440 (mp0) cc_final: 0.6932 (mp0) REVERT: K 102 ARG cc_start: 0.6400 (ttt180) cc_final: 0.6085 (ttm110) REVERT: K 137 GLU cc_start: 0.8432 (OUTLIER) cc_final: 0.7973 (pm20) REVERT: K 199 GLU cc_start: 0.7792 (mp0) cc_final: 0.7431 (mp0) REVERT: O 108 GLN cc_start: 0.8134 (mt0) cc_final: 0.7876 (mt0) REVERT: O 137 GLU cc_start: 0.8299 (OUTLIER) cc_final: 0.7886 (pm20) REVERT: O 199 GLU cc_start: 0.7602 (mp0) cc_final: 0.7029 (mp0) outliers start: 76 outliers final: 45 residues processed: 417 average time/residue: 1.3127 time to fit residues: 625.3662 Evaluate side-chains 425 residues out of total 2355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 372 time to evaluate : 2.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 28 VAL 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 105 MET Chi-restraints excluded: chain 1 residue 108 SER 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 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 204 SER Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 43 LEU Chi-restraints excluded: chain F residue 108 SER 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 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 42 SER Chi-restraints excluded: chain P residue 204 SER Chi-restraints excluded: chain P residue 211 LEU Chi-restraints excluded: chain Q residue 120 ARG 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 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 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 176 optimal weight: 0.6980 chunk 173 optimal weight: 0.7980 chunk 8 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 184 optimal weight: 4.9990 chunk 201 optimal weight: 5.9990 chunk 163 optimal weight: 0.7980 chunk 25 optimal weight: 6.9990 chunk 47 optimal weight: 5.9990 chunk 213 optimal weight: 7.9990 chunk 45 optimal weight: 1.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 110 ASN 3 173 HIS B 110 ASN D 15 GLN F 110 ASN J 45 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 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.161434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.111310 restraints weight = 28849.593| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 3.31 r_work: 0.3211 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.2179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 22465 Z= 0.159 Angle : 0.491 6.077 30625 Z= 0.254 Chirality : 0.042 0.180 3290 Planarity : 0.004 0.035 3970 Dihedral : 4.006 18.078 3005 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 3.57 % Allowed : 14.44 % Favored : 82.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.17), residues: 2660 helix: -1.92 (0.30), residues: 240 sheet: -0.89 (0.18), residues: 875 loop : -0.80 (0.17), residues: 1545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP 3 149 HIS 0.006 0.001 HIS H 143 PHE 0.012 0.001 PHE 1 115 TYR 0.012 0.001 TYR O 79 ARG 0.005 0.000 ARG E 120 Details of bonding type rmsd hydrogen bonds : bond 0.02944 ( 89) hydrogen bonds : angle 4.51427 ( 318) SS BOND : bond 0.00077 ( 20) SS BOND : angle 0.41198 ( 40) covalent geometry : bond 0.00381 (22445) covalent geometry : angle 0.49125 (30585) *********************** 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 463 residues out of total 2355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 379 time to evaluate : 5.688 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 45 ASN cc_start: 0.8831 (t0) cc_final: 0.8501 (t0) REVERT: 1 105 MET cc_start: 0.8931 (OUTLIER) cc_final: 0.8456 (ttp) REVERT: 1 111 ASN cc_start: 0.8922 (m-40) cc_final: 0.8674 (m-40) REVERT: 2 82 GLU cc_start: 0.8263 (mp0) cc_final: 0.7879 (mp0) REVERT: 2 101 MET cc_start: 0.5129 (ptp) cc_final: 0.4679 (ptp) REVERT: 2 137 GLU cc_start: 0.8167 (pm20) cc_final: 0.7816 (pm20) REVERT: 2 199 GLU cc_start: 0.7906 (mp0) cc_final: 0.7444 (mp0) REVERT: 3 42 SER cc_start: 0.8922 (p) cc_final: 0.8377 (t) REVERT: 3 109 MET cc_start: 0.8653 (ttp) cc_final: 0.8071 (ttp) REVERT: 3 119 LYS cc_start: 0.8357 (mttt) cc_final: 0.8043 (mtmm) REVERT: 3 179 MET cc_start: 0.7311 (tpt) cc_final: 0.6342 (mpt) REVERT: 3 190 GLN cc_start: 0.8121 (pt0) cc_final: 0.6474 (pp30) REVERT: B 43 LEU cc_start: 0.9098 (OUTLIER) cc_final: 0.8760 (pp) REVERT: B 45 ASN cc_start: 0.8717 (t0) cc_final: 0.8327 (t0) REVERT: B 124 ARG cc_start: 0.7774 (ttp-170) cc_final: 0.7484 (ttt-90) REVERT: D 21 THR cc_start: 0.8356 (p) cc_final: 0.7917 (t) REVERT: D 42 SER cc_start: 0.8940 (p) cc_final: 0.8424 (t) REVERT: D 119 LYS cc_start: 0.8386 (mttt) cc_final: 0.8140 (mppt) REVERT: D 121 MET cc_start: 0.7201 (ttt) cc_final: 0.6666 (mmm) REVERT: D 179 MET cc_start: 0.7357 (tpt) cc_final: 0.6994 (tpp) REVERT: D 190 GLN cc_start: 0.8188 (pt0) cc_final: 0.6836 (pp30) REVERT: F 102 ASP cc_start: 0.8231 (p0) cc_final: 0.7950 (p0) REVERT: F 176 ASP cc_start: 0.7902 (t0) cc_final: 0.7610 (t0) REVERT: H 42 SER cc_start: 0.8778 (p) cc_final: 0.8295 (t) REVERT: H 119 LYS cc_start: 0.8543 (mttt) cc_final: 0.8332 (mppt) REVERT: H 190 GLN cc_start: 0.8238 (pt0) cc_final: 0.6719 (pp30) REVERT: J 124 ARG cc_start: 0.7818 (ttp-170) cc_final: 0.7519 (ttp-170) REVERT: L 42 SER cc_start: 0.8714 (p) cc_final: 0.8227 (t) REVERT: L 119 LYS cc_start: 0.8363 (mttt) cc_final: 0.8110 (mppt) REVERT: L 121 MET cc_start: 0.7747 (OUTLIER) cc_final: 0.7402 (pmm) REVERT: L 179 MET cc_start: 0.7360 (tpt) cc_final: 0.7105 (tpp) REVERT: L 190 GLN cc_start: 0.7833 (pt0) cc_final: 0.6442 (pp30) REVERT: L 204 SER cc_start: 0.8957 (p) cc_final: 0.8550 (t) REVERT: N 45 ASN cc_start: 0.8369 (t0) cc_final: 0.8128 (t0) REVERT: N 105 MET cc_start: 0.8900 (OUTLIER) cc_final: 0.8436 (ttp) REVERT: N 111 ASN cc_start: 0.8928 (m-40) cc_final: 0.8688 (m110) REVERT: N 129 ARG cc_start: 0.7727 (OUTLIER) cc_final: 0.7309 (mtp-110) REVERT: P 119 LYS cc_start: 0.8549 (mttt) cc_final: 0.8349 (mppt) REVERT: P 179 MET cc_start: 0.7626 (tpt) cc_final: 0.7259 (tpp) REVERT: E 141 ILE cc_start: 0.8346 (mt) cc_final: 0.7962 (mm) REVERT: Q 141 ILE cc_start: 0.8378 (mt) cc_final: 0.8066 (mm) REVERT: C 79 TYR cc_start: 0.7519 (m-80) cc_final: 0.7224 (m-80) REVERT: C 101 MET cc_start: 0.4885 (ptp) cc_final: 0.4540 (ptp) REVERT: C 108 GLN cc_start: 0.8001 (mt0) cc_final: 0.7530 (mt0) REVERT: C 137 GLU cc_start: 0.8580 (OUTLIER) cc_final: 0.7978 (pm20) REVERT: C 182 MET cc_start: 0.7985 (ttp) cc_final: 0.7627 (ptm) REVERT: C 199 GLU cc_start: 0.7631 (mp0) cc_final: 0.7182 (mp0) REVERT: G 101 MET cc_start: 0.4726 (ptt) cc_final: 0.4078 (ptp) REVERT: G 102 ARG cc_start: 0.6071 (ttt180) cc_final: 0.5622 (tpp-160) REVERT: G 128 GLU cc_start: 0.8819 (mt-10) cc_final: 0.8423 (mt-10) REVERT: G 135 ARG cc_start: 0.8239 (mtm180) cc_final: 0.7921 (mtm-85) REVERT: G 137 GLU cc_start: 0.8316 (OUTLIER) cc_final: 0.7830 (pm20) REVERT: G 158 ILE cc_start: 0.8601 (OUTLIER) cc_final: 0.8324 (mp) REVERT: G 162 TYR cc_start: 0.8174 (t80) cc_final: 0.7910 (t80) REVERT: G 199 GLU cc_start: 0.7412 (mp0) cc_final: 0.6909 (mp0) REVERT: K 102 ARG cc_start: 0.6521 (ttt180) cc_final: 0.6218 (ttm110) REVERT: K 137 GLU cc_start: 0.8512 (OUTLIER) cc_final: 0.8050 (pm20) REVERT: K 199 GLU cc_start: 0.7803 (mp0) cc_final: 0.7434 (mp0) REVERT: O 108 GLN cc_start: 0.8129 (mt0) cc_final: 0.7894 (mt0) REVERT: O 117 ASN cc_start: 0.8706 (OUTLIER) cc_final: 0.8458 (t0) REVERT: O 137 GLU cc_start: 0.8290 (OUTLIER) cc_final: 0.7859 (pm20) REVERT: O 199 GLU cc_start: 0.7620 (mp0) cc_final: 0.7003 (mp0) outliers start: 84 outliers final: 51 residues processed: 419 average time/residue: 1.3385 time to fit residues: 643.0742 Evaluate side-chains 432 residues out of total 2355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 370 time to evaluate : 2.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 28 VAL 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 105 MET Chi-restraints excluded: chain 1 residue 108 SER 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 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 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 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 A residue 120 ARG Chi-restraints excluded: chain M residue 120 ARG Chi-restraints excluded: chain Q 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 C residue 188 THR 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 G residue 204 ILE Chi-restraints excluded: chain K residue 107 VAL 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 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 38 optimal weight: 2.9990 chunk 221 optimal weight: 0.8980 chunk 263 optimal weight: 2.9990 chunk 159 optimal weight: 1.9990 chunk 217 optimal weight: 1.9990 chunk 177 optimal weight: 1.9990 chunk 173 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 232 optimal weight: 0.9990 chunk 75 optimal weight: 1.9990 chunk 195 optimal weight: 6.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 110 ASN B 110 ASN D 15 GLN F 110 ASN ** J 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 110 ASN L 116 HIS N 110 ASN ** C 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 145 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.160511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.109796 restraints weight = 28945.623| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 3.30 r_work: 0.3194 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.2340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 22465 Z= 0.193 Angle : 0.519 6.209 30625 Z= 0.268 Chirality : 0.043 0.200 3290 Planarity : 0.004 0.041 3970 Dihedral : 4.149 18.805 3005 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 3.65 % Allowed : 14.99 % Favored : 81.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.17), residues: 2660 helix: -1.92 (0.31), residues: 240 sheet: -0.84 (0.18), residues: 825 loop : -0.92 (0.16), residues: 1595 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP 3 149 HIS 0.005 0.001 HIS H 143 PHE 0.013 0.001 PHE P 8 TYR 0.013 0.001 TYR K 79 ARG 0.006 0.000 ARG E 120 Details of bonding type rmsd hydrogen bonds : bond 0.03142 ( 89) hydrogen bonds : angle 4.60949 ( 318) SS BOND : bond 0.00081 ( 20) SS BOND : angle 0.41313 ( 40) covalent geometry : bond 0.00461 (22445) covalent geometry : angle 0.51905 (30585) *********************** 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 470 residues out of total 2355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 384 time to evaluate : 2.228 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 45 ASN cc_start: 0.8850 (t0) cc_final: 0.8564 (t0) REVERT: 1 105 MET cc_start: 0.8921 (OUTLIER) cc_final: 0.8457 (ttp) REVERT: 1 111 ASN cc_start: 0.8939 (m-40) cc_final: 0.8694 (m-40) REVERT: 2 82 GLU cc_start: 0.8283 (mp0) cc_final: 0.7966 (mp0) REVERT: 2 101 MET cc_start: 0.5458 (ptp) cc_final: 0.5033 (ptp) REVERT: 2 137 GLU cc_start: 0.8152 (pm20) cc_final: 0.7864 (pm20) REVERT: 2 199 GLU cc_start: 0.7941 (mp0) cc_final: 0.7449 (mp0) REVERT: 3 42 SER cc_start: 0.8923 (p) cc_final: 0.8390 (t) REVERT: 3 109 MET cc_start: 0.8668 (ttp) cc_final: 0.8139 (ttp) REVERT: 3 119 LYS cc_start: 0.8412 (mttt) cc_final: 0.8108 (mtmm) REVERT: 3 121 MET cc_start: 0.8181 (mtm) cc_final: 0.7565 (mpp) REVERT: 3 179 MET cc_start: 0.7353 (tpt) cc_final: 0.6256 (mmt) REVERT: 3 190 GLN cc_start: 0.8289 (pt0) cc_final: 0.6507 (pp30) REVERT: B 43 LEU cc_start: 0.9103 (OUTLIER) cc_final: 0.8715 (pp) REVERT: B 45 ASN cc_start: 0.8800 (t0) cc_final: 0.8390 (t0) REVERT: B 120 THR cc_start: 0.8933 (m) cc_final: 0.8699 (m) REVERT: B 124 ARG cc_start: 0.7765 (ttp-170) cc_final: 0.7542 (ttp-110) REVERT: D 11 TYR cc_start: 0.9306 (OUTLIER) cc_final: 0.8890 (m-80) REVERT: D 21 THR cc_start: 0.8379 (p) cc_final: 0.7943 (t) REVERT: D 42 SER cc_start: 0.8961 (p) cc_final: 0.8445 (t) REVERT: D 121 MET cc_start: 0.7327 (ttt) cc_final: 0.6761 (mmm) REVERT: D 179 MET cc_start: 0.7391 (tpt) cc_final: 0.6089 (mmt) REVERT: D 190 GLN cc_start: 0.8252 (pt0) cc_final: 0.6917 (pp30) REVERT: F 102 ASP cc_start: 0.8297 (p0) cc_final: 0.8046 (p0) REVERT: F 124 ARG cc_start: 0.7800 (ttp-170) cc_final: 0.7570 (ttp-170) REVERT: H 42 SER cc_start: 0.8816 (p) cc_final: 0.8332 (t) REVERT: H 119 LYS cc_start: 0.8574 (mttt) cc_final: 0.8372 (mppt) REVERT: H 121 MET cc_start: 0.7288 (ttt) cc_final: 0.6918 (mmm) REVERT: H 190 GLN cc_start: 0.8334 (pt0) cc_final: 0.6860 (pp30) REVERT: J 45 ASN cc_start: 0.8846 (t0) cc_final: 0.8329 (t0) REVERT: L 42 SER cc_start: 0.8752 (p) cc_final: 0.8259 (t) REVERT: L 119 LYS cc_start: 0.8344 (mttt) cc_final: 0.8115 (mppt) REVERT: L 121 MET cc_start: 0.7804 (OUTLIER) cc_final: 0.7424 (pmm) REVERT: L 179 MET cc_start: 0.7444 (tpt) cc_final: 0.6301 (mpt) REVERT: L 204 SER cc_start: 0.8775 (p) cc_final: 0.8373 (t) REVERT: N 45 ASN cc_start: 0.8458 (t0) cc_final: 0.8194 (t0) REVERT: N 105 MET cc_start: 0.8940 (OUTLIER) cc_final: 0.8481 (ttp) REVERT: N 111 ASN cc_start: 0.8942 (m-40) cc_final: 0.8713 (m110) REVERT: N 129 ARG cc_start: 0.7816 (OUTLIER) cc_final: 0.7368 (mtp-110) REVERT: P 56 ASN cc_start: 0.8846 (t0) cc_final: 0.8618 (t0) REVERT: P 179 MET cc_start: 0.7695 (tpt) cc_final: 0.7324 (tpp) REVERT: E 141 ILE cc_start: 0.8373 (mt) cc_final: 0.7989 (mm) REVERT: M 141 ILE cc_start: 0.8481 (mt) cc_final: 0.8231 (mm) REVERT: Q 141 ILE cc_start: 0.8397 (mt) cc_final: 0.8103 (mm) REVERT: C 79 TYR cc_start: 0.7571 (m-80) cc_final: 0.7224 (m-80) REVERT: C 101 MET cc_start: 0.5287 (ptp) cc_final: 0.4938 (ptp) REVERT: C 108 GLN cc_start: 0.8043 (mt0) cc_final: 0.7612 (mt0) REVERT: C 137 GLU cc_start: 0.8590 (OUTLIER) cc_final: 0.7970 (pm20) REVERT: C 182 MET cc_start: 0.8021 (ttp) cc_final: 0.7659 (ptm) REVERT: C 199 GLU cc_start: 0.7632 (mp0) cc_final: 0.7185 (mp0) REVERT: G 101 MET cc_start: 0.4902 (ptt) cc_final: 0.4071 (ptp) REVERT: G 128 GLU cc_start: 0.8819 (mt-10) cc_final: 0.8427 (mt-10) REVERT: G 135 ARG cc_start: 0.8247 (mtm180) cc_final: 0.7934 (mtm-85) REVERT: G 137 GLU cc_start: 0.8351 (OUTLIER) cc_final: 0.7883 (pm20) REVERT: G 158 ILE cc_start: 0.8641 (OUTLIER) cc_final: 0.8387 (mp) REVERT: G 162 TYR cc_start: 0.8195 (t80) cc_final: 0.7964 (t80) REVERT: G 199 GLU cc_start: 0.7406 (mp0) cc_final: 0.6908 (mp0) REVERT: K 102 ARG cc_start: 0.6558 (ttt180) cc_final: 0.6139 (ttm110) REVERT: K 128 GLU cc_start: 0.8718 (mt-10) cc_final: 0.7929 (mt-10) REVERT: K 137 GLU cc_start: 0.8594 (OUTLIER) cc_final: 0.8127 (pm20) REVERT: K 199 GLU cc_start: 0.7849 (mp0) cc_final: 0.7466 (mp0) REVERT: O 108 GLN cc_start: 0.8151 (mt0) cc_final: 0.7830 (mt0) REVERT: O 137 GLU cc_start: 0.8361 (OUTLIER) cc_final: 0.7933 (pm20) REVERT: O 199 GLU cc_start: 0.7641 (mp0) cc_final: 0.7025 (mp0) outliers start: 86 outliers final: 54 residues processed: 427 average time/residue: 1.2669 time to fit residues: 617.7556 Evaluate side-chains 428 residues out of total 2355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 363 time to evaluate : 2.385 ------------------------------------------------------------------------------- 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 105 MET Chi-restraints excluded: chain 1 residue 108 SER Chi-restraints excluded: chain 1 residue 185 MET Chi-restraints excluded: chain 2 residue 106 ASP 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 204 SER Chi-restraints excluded: chain D residue 217 VAL Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 99 THR 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 L residue 121 MET Chi-restraints excluded: chain L residue 153 LEU 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 A residue 120 ARG Chi-restraints excluded: chain M residue 120 ARG Chi-restraints excluded: chain Q 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 107 VAL Chi-restraints excluded: chain G residue 137 GLU 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 102 optimal weight: 0.8980 chunk 244 optimal weight: 0.6980 chunk 137 optimal weight: 0.6980 chunk 39 optimal weight: 5.9990 chunk 217 optimal weight: 4.9990 chunk 223 optimal weight: 5.9990 chunk 231 optimal weight: 2.9990 chunk 81 optimal weight: 7.9990 chunk 101 optimal weight: 0.8980 chunk 24 optimal weight: 4.9990 chunk 55 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 110 ASN 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 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 149 ASN ** 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 = 0.4059 r_free = 0.4059 target = 0.162444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.112254 restraints weight = 28832.233| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 3.32 r_work: 0.3225 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.2427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 22465 Z= 0.120 Angle : 0.490 6.875 30625 Z= 0.253 Chirality : 0.042 0.183 3290 Planarity : 0.004 0.045 3970 Dihedral : 3.937 17.415 3005 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 2.76 % Allowed : 16.82 % Favored : 80.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.42 (0.17), residues: 2660 helix: -1.90 (0.30), residues: 240 sheet: -0.74 (0.18), residues: 825 loop : -0.84 (0.16), residues: 1595 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP 3 149 HIS 0.004 0.001 HIS O 145 PHE 0.009 0.001 PHE 1 115 TYR 0.011 0.001 TYR K 79 ARG 0.005 0.000 ARG F 38 Details of bonding type rmsd hydrogen bonds : bond 0.02769 ( 89) hydrogen bonds : angle 4.46272 ( 318) SS BOND : bond 0.00062 ( 20) SS BOND : angle 0.46321 ( 40) covalent geometry : bond 0.00284 (22445) covalent geometry : angle 0.48993 (30585) *********************** 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 452 residues out of total 2355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 387 time to evaluate : 3.130 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 45 ASN cc_start: 0.8849 (t0) cc_final: 0.8577 (t0) REVERT: 1 111 ASN cc_start: 0.8927 (m-40) cc_final: 0.8683 (m-40) REVERT: 2 82 GLU cc_start: 0.8278 (mp0) cc_final: 0.7900 (mp0) REVERT: 2 101 MET cc_start: 0.5409 (ptp) cc_final: 0.4993 (ptp) REVERT: 2 137 GLU cc_start: 0.8118 (pm20) cc_final: 0.7834 (pm20) REVERT: 2 199 GLU cc_start: 0.7937 (mp0) cc_final: 0.7447 (mp0) REVERT: 3 42 SER cc_start: 0.8914 (p) cc_final: 0.8371 (t) REVERT: 3 109 MET cc_start: 0.8701 (ttp) cc_final: 0.8140 (ttp) REVERT: 3 119 LYS cc_start: 0.8431 (mttt) cc_final: 0.8152 (mtmm) REVERT: 3 121 MET cc_start: 0.8353 (mtm) cc_final: 0.7793 (mtm) REVERT: 3 179 MET cc_start: 0.7304 (tpt) cc_final: 0.6334 (mpt) REVERT: 3 190 GLN cc_start: 0.8330 (pt0) cc_final: 0.6616 (pp30) REVERT: B 43 LEU cc_start: 0.9063 (OUTLIER) cc_final: 0.8661 (pp) REVERT: B 45 ASN cc_start: 0.8796 (t0) cc_final: 0.8375 (t0) REVERT: D 11 TYR cc_start: 0.9279 (OUTLIER) cc_final: 0.8859 (m-80) REVERT: D 21 THR cc_start: 0.8375 (p) cc_final: 0.7938 (t) REVERT: D 42 SER cc_start: 0.8949 (p) cc_final: 0.8443 (t) REVERT: D 119 LYS cc_start: 0.8429 (mttt) cc_final: 0.8157 (mppt) REVERT: D 121 MET cc_start: 0.7337 (ttt) cc_final: 0.6782 (mmm) REVERT: D 179 MET cc_start: 0.7351 (tpt) cc_final: 0.7001 (tpp) REVERT: D 190 GLN cc_start: 0.8265 (pt0) cc_final: 0.6904 (pp30) REVERT: F 83 GLU cc_start: 0.6680 (pm20) cc_final: 0.6464 (pm20) REVERT: F 102 ASP cc_start: 0.8233 (p0) cc_final: 0.7999 (p0) REVERT: F 176 ASP cc_start: 0.7937 (t0) cc_final: 0.7645 (t0) REVERT: H 42 SER cc_start: 0.8764 (p) cc_final: 0.8280 (t) REVERT: H 119 LYS cc_start: 0.8570 (mttt) cc_final: 0.8369 (mppt) REVERT: H 121 MET cc_start: 0.7316 (ttt) cc_final: 0.6940 (mmm) REVERT: H 190 GLN cc_start: 0.8370 (pt0) cc_final: 0.6865 (pp30) REVERT: H 212 GLU cc_start: 0.8263 (tt0) cc_final: 0.8002 (tt0) REVERT: J 43 LEU cc_start: 0.9108 (OUTLIER) cc_final: 0.8310 (pp) REVERT: J 45 ASN cc_start: 0.8827 (t0) cc_final: 0.8331 (t0) REVERT: L 42 SER cc_start: 0.8700 (p) cc_final: 0.8210 (t) REVERT: L 119 LYS cc_start: 0.8339 (mttt) cc_final: 0.8116 (mppt) REVERT: L 121 MET cc_start: 0.7760 (OUTLIER) cc_final: 0.7382 (pmm) REVERT: L 179 MET cc_start: 0.7446 (tpt) cc_final: 0.7164 (tpp) REVERT: L 204 SER cc_start: 0.8993 (p) cc_final: 0.8617 (t) REVERT: N 28 VAL cc_start: 0.8580 (OUTLIER) cc_final: 0.8329 (p) REVERT: N 45 ASN cc_start: 0.8424 (t0) cc_final: 0.8144 (t0) REVERT: N 105 MET cc_start: 0.8939 (OUTLIER) cc_final: 0.8432 (ttp) REVERT: N 111 ASN cc_start: 0.8941 (m-40) cc_final: 0.8694 (m110) REVERT: N 129 ARG cc_start: 0.7758 (OUTLIER) cc_final: 0.7325 (mtp-110) REVERT: P 15 GLN cc_start: 0.8203 (OUTLIER) cc_final: 0.7887 (mt0) REVERT: P 171 TYR cc_start: 0.8440 (m-10) cc_final: 0.8148 (m-80) REVERT: P 179 MET cc_start: 0.7605 (tpt) cc_final: 0.7265 (tpp) REVERT: E 141 ILE cc_start: 0.8337 (mt) cc_final: 0.7965 (mm) REVERT: M 120 ARG cc_start: 0.8243 (OUTLIER) cc_final: 0.6127 (ttm-80) REVERT: Q 143 LEU cc_start: 0.8296 (mt) cc_final: 0.8075 (mt) REVERT: C 79 TYR cc_start: 0.7575 (m-80) cc_final: 0.7210 (m-80) REVERT: C 101 MET cc_start: 0.5374 (ptp) cc_final: 0.5036 (ptp) REVERT: C 108 GLN cc_start: 0.8087 (mt0) cc_final: 0.7654 (mt0) REVERT: C 137 GLU cc_start: 0.8603 (OUTLIER) cc_final: 0.7992 (pm20) REVERT: C 182 MET cc_start: 0.7963 (ttp) cc_final: 0.7667 (ptm) REVERT: C 199 GLU cc_start: 0.7657 (mp0) cc_final: 0.7169 (mp0) REVERT: G 101 MET cc_start: 0.4844 (ptt) cc_final: 0.4106 (ptp) REVERT: G 102 ARG cc_start: 0.6204 (ttt180) cc_final: 0.5779 (tpp-160) REVERT: G 128 GLU cc_start: 0.8841 (mt-10) cc_final: 0.8455 (mt-10) REVERT: G 135 ARG cc_start: 0.8234 (mtm180) cc_final: 0.7927 (mtm-85) REVERT: G 137 GLU cc_start: 0.8359 (OUTLIER) cc_final: 0.7887 (pm20) REVERT: G 162 TYR cc_start: 0.8207 (t80) cc_final: 0.7865 (t80) REVERT: G 199 GLU cc_start: 0.7442 (mp0) cc_final: 0.6914 (mp0) REVERT: K 79 TYR cc_start: 0.7231 (m-80) cc_final: 0.6968 (m-80) REVERT: K 101 MET cc_start: 0.5168 (ptt) cc_final: 0.4535 (ptp) REVERT: K 102 ARG cc_start: 0.6588 (ttt180) cc_final: 0.6175 (ttm110) REVERT: K 128 GLU cc_start: 0.8699 (mt-10) cc_final: 0.7891 (mt-10) REVERT: K 137 GLU cc_start: 0.8595 (OUTLIER) cc_final: 0.8111 (pm20) REVERT: K 199 GLU cc_start: 0.7831 (mp0) cc_final: 0.7430 (mp0) REVERT: O 108 GLN cc_start: 0.8125 (mt0) cc_final: 0.7868 (mt0) REVERT: O 137 GLU cc_start: 0.8322 (OUTLIER) cc_final: 0.7885 (pm20) REVERT: O 199 GLU cc_start: 0.7635 (mp0) cc_final: 0.7079 (mp0) outliers start: 65 outliers final: 42 residues processed: 416 average time/residue: 1.5186 time to fit residues: 721.1270 Evaluate side-chains 425 residues out of total 2355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 370 time to evaluate : 7.298 ------------------------------------------------------------------------------- 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 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 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 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 43 LEU 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 43 LEU 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 15 GLN 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 A residue 120 ARG Chi-restraints excluded: chain I residue 120 ARG Chi-restraints excluded: chain M 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 110 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 122 optimal weight: 1.9990 chunk 256 optimal weight: 0.0060 chunk 258 optimal weight: 0.9980 chunk 73 optimal weight: 0.8980 chunk 72 optimal weight: 0.5980 chunk 1 optimal weight: 3.9990 chunk 209 optimal weight: 4.9990 chunk 153 optimal weight: 0.9980 chunk 66 optimal weight: 0.0000 chunk 103 optimal weight: 0.8980 chunk 109 optimal weight: 4.9990 overall best weight: 0.4800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 110 ASN 2 108 GLN B 29 HIS B 110 ASN D 15 GLN F 110 ASN ** J 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 110 ASN L 115 HIS N 110 ASN P 190 GLN ** C 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 146 GLN ** C 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 149 ASN ** 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 = 0.4077 r_free = 0.4077 target = 0.163932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.114089 restraints weight = 28892.879| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 3.32 r_work: 0.3254 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.2505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 22465 Z= 0.097 Angle : 0.485 7.293 30625 Z= 0.251 Chirality : 0.041 0.180 3290 Planarity : 0.003 0.044 3970 Dihedral : 3.770 15.897 3005 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 2.68 % Allowed : 17.71 % Favored : 79.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.17), residues: 2660 helix: -1.80 (0.31), residues: 240 sheet: -0.65 (0.19), residues: 825 loop : -0.78 (0.16), residues: 1595 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP 3 149 HIS 0.004 0.001 HIS O 145 PHE 0.009 0.001 PHE G 116 TYR 0.011 0.001 TYR H 11 ARG 0.006 0.000 ARG E 120 Details of bonding type rmsd hydrogen bonds : bond 0.02663 ( 89) hydrogen bonds : angle 4.43820 ( 318) SS BOND : bond 0.00100 ( 20) SS BOND : angle 0.46039 ( 40) covalent geometry : bond 0.00227 (22445) covalent geometry : angle 0.48545 (30585) *********************** 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 454 residues out of total 2355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 391 time to evaluate : 2.453 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 45 ASN cc_start: 0.8844 (t0) cc_final: 0.8643 (t0) REVERT: 1 111 ASN cc_start: 0.8914 (m-40) cc_final: 0.8698 (m110) REVERT: 2 82 GLU cc_start: 0.8303 (mp0) cc_final: 0.7853 (mp0) REVERT: 2 101 MET cc_start: 0.5514 (ptp) cc_final: 0.5076 (ptp) REVERT: 2 199 GLU cc_start: 0.7920 (mp0) cc_final: 0.7419 (mp0) REVERT: 3 42 SER cc_start: 0.8902 (p) cc_final: 0.8378 (t) REVERT: 3 109 MET cc_start: 0.8689 (ttp) cc_final: 0.8133 (ttp) REVERT: 3 119 LYS cc_start: 0.8425 (mttt) cc_final: 0.8078 (mtmm) REVERT: 3 121 MET cc_start: 0.8320 (mtm) cc_final: 0.7548 (mpp) REVERT: 3 179 MET cc_start: 0.7234 (tpt) cc_final: 0.6280 (mpt) REVERT: B 43 LEU cc_start: 0.8990 (OUTLIER) cc_final: 0.8530 (pp) REVERT: B 45 ASN cc_start: 0.8753 (t0) cc_final: 0.8345 (t0) REVERT: B 124 ARG cc_start: 0.7771 (ttp-170) cc_final: 0.7481 (ttt-90) REVERT: D 21 THR cc_start: 0.8342 (p) cc_final: 0.7912 (t) REVERT: D 42 SER cc_start: 0.8947 (p) cc_final: 0.8455 (t) REVERT: D 115 HIS cc_start: 0.8273 (p90) cc_final: 0.7932 (p90) REVERT: D 119 LYS cc_start: 0.8441 (mttt) cc_final: 0.8159 (mppt) REVERT: D 121 MET cc_start: 0.7313 (ttt) cc_final: 0.6769 (mmm) REVERT: D 179 MET cc_start: 0.7278 (tpt) cc_final: 0.6105 (mpt) REVERT: D 190 GLN cc_start: 0.8262 (pt0) cc_final: 0.6846 (pp30) REVERT: F 83 GLU cc_start: 0.6718 (pm20) cc_final: 0.6437 (pm20) REVERT: F 102 ASP cc_start: 0.8185 (p0) cc_final: 0.7868 (p0) REVERT: F 124 ARG cc_start: 0.7798 (ttp-170) cc_final: 0.7465 (ttp80) REVERT: F 176 ASP cc_start: 0.7932 (t0) cc_final: 0.7628 (t0) REVERT: H 42 SER cc_start: 0.8759 (p) cc_final: 0.8282 (t) REVERT: H 119 LYS cc_start: 0.8580 (mttt) cc_final: 0.8374 (mppt) REVERT: H 121 MET cc_start: 0.7313 (ttt) cc_final: 0.6957 (mmm) REVERT: H 190 GLN cc_start: 0.8382 (pt0) cc_final: 0.6820 (pp30) REVERT: H 212 GLU cc_start: 0.8240 (tt0) cc_final: 0.7974 (tt0) REVERT: J 43 LEU cc_start: 0.9058 (OUTLIER) cc_final: 0.8295 (pp) REVERT: J 45 ASN cc_start: 0.8824 (t0) cc_final: 0.8342 (t0) REVERT: J 59 LYS cc_start: 0.8840 (OUTLIER) cc_final: 0.8368 (mmpt) REVERT: J 101 ARG cc_start: 0.7899 (OUTLIER) cc_final: 0.7313 (ptt90) REVERT: L 42 SER cc_start: 0.8677 (p) cc_final: 0.8188 (t) REVERT: L 119 LYS cc_start: 0.8345 (mttt) cc_final: 0.8121 (mppt) REVERT: L 121 MET cc_start: 0.7755 (OUTLIER) cc_final: 0.7362 (pmm) REVERT: L 157 PHE cc_start: 0.8340 (t80) cc_final: 0.8007 (t80) REVERT: L 204 SER cc_start: 0.8972 (p) cc_final: 0.8627 (t) REVERT: N 28 VAL cc_start: 0.8539 (OUTLIER) cc_final: 0.8318 (p) REVERT: N 45 ASN cc_start: 0.8482 (t0) cc_final: 0.8169 (t0) REVERT: N 105 MET cc_start: 0.8912 (OUTLIER) cc_final: 0.8399 (ttp) REVERT: N 111 ASN cc_start: 0.8917 (m-40) cc_final: 0.8668 (m110) REVERT: N 129 ARG cc_start: 0.7691 (OUTLIER) cc_final: 0.7230 (mtp-110) REVERT: P 15 GLN cc_start: 0.8155 (OUTLIER) cc_final: 0.7833 (mt0) REVERT: P 86 LYS cc_start: 0.8110 (ttpt) cc_final: 0.7730 (ptmt) REVERT: P 179 MET cc_start: 0.7554 (tpt) cc_final: 0.7250 (tpp) REVERT: M 120 ARG cc_start: 0.8245 (OUTLIER) cc_final: 0.6445 (ttm-80) REVERT: M 141 ILE cc_start: 0.8446 (mt) cc_final: 0.8069 (mm) REVERT: C 79 TYR cc_start: 0.7570 (m-80) cc_final: 0.7253 (m-80) REVERT: C 101 MET cc_start: 0.5311 (ptp) cc_final: 0.5057 (ptp) REVERT: C 108 GLN cc_start: 0.8076 (mt0) cc_final: 0.7608 (mt0) REVERT: C 137 GLU cc_start: 0.8603 (OUTLIER) cc_final: 0.8014 (pm20) REVERT: C 182 MET cc_start: 0.7934 (ttp) cc_final: 0.7726 (ptm) REVERT: C 199 GLU cc_start: 0.7665 (mp0) cc_final: 0.7161 (mp0) REVERT: G 101 MET cc_start: 0.5057 (ptt) cc_final: 0.4461 (ptp) REVERT: G 108 GLN cc_start: 0.7835 (mt0) cc_final: 0.7502 (tp40) REVERT: G 128 GLU cc_start: 0.8821 (mt-10) cc_final: 0.8425 (mt-10) REVERT: G 135 ARG cc_start: 0.8218 (mtm180) cc_final: 0.8002 (mtp-110) REVERT: G 137 GLU cc_start: 0.8358 (OUTLIER) cc_final: 0.7894 (pm20) REVERT: G 162 TYR cc_start: 0.8137 (t80) cc_final: 0.7890 (t80) REVERT: G 199 GLU cc_start: 0.7439 (mp0) cc_final: 0.6945 (mp0) REVERT: K 79 TYR cc_start: 0.7268 (m-80) cc_final: 0.7006 (m-80) REVERT: K 101 MET cc_start: 0.5162 (ptt) cc_final: 0.4582 (ptp) REVERT: K 102 ARG cc_start: 0.6453 (ttt180) cc_final: 0.5533 (ttm110) REVERT: K 137 GLU cc_start: 0.8582 (OUTLIER) cc_final: 0.8101 (pm20) REVERT: K 199 GLU cc_start: 0.7799 (mp0) cc_final: 0.7395 (mp0) REVERT: O 101 MET cc_start: 0.4547 (ptt) cc_final: 0.4030 (ptp) REVERT: O 102 ARG cc_start: 0.6349 (ttt180) cc_final: 0.6041 (ttm-80) REVERT: O 108 GLN cc_start: 0.8135 (mt0) cc_final: 0.7924 (mt0) REVERT: O 137 GLU cc_start: 0.8319 (OUTLIER) cc_final: 0.7871 (pm20) REVERT: O 199 GLU cc_start: 0.7794 (mp0) cc_final: 0.7350 (mp0) outliers start: 63 outliers final: 39 residues processed: 420 average time/residue: 1.3283 time to fit residues: 637.3326 Evaluate side-chains 431 residues out of total 2355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 378 time to evaluate : 2.403 ------------------------------------------------------------------------------- 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 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 43 LEU Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 108 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 43 LEU Chi-restraints excluded: chain J residue 59 LYS Chi-restraints excluded: chain J residue 87 VAL Chi-restraints excluded: chain J residue 101 ARG 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 99 THR Chi-restraints excluded: chain N residue 105 MET Chi-restraints excluded: chain N residue 129 ARG Chi-restraints excluded: chain P residue 15 GLN 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 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 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 G residue 188 THR Chi-restraints excluded: chain G residue 204 ILE 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 78 optimal weight: 2.9990 chunk 228 optimal weight: 6.9990 chunk 51 optimal weight: 2.9990 chunk 135 optimal weight: 4.9990 chunk 143 optimal weight: 2.9990 chunk 3 optimal weight: 4.9990 chunk 224 optimal weight: 10.0000 chunk 136 optimal weight: 0.9980 chunk 187 optimal weight: 0.4980 chunk 239 optimal weight: 8.9990 chunk 41 optimal weight: 8.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 110 ASN B 29 HIS B 110 ASN D 15 GLN D 116 HIS F 110 ASN J 110 ASN L 115 HIS N 110 ASN P 190 GLN ** C 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.159898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.109133 restraints weight = 28957.288| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 3.32 r_work: 0.3182 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.2642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 22465 Z= 0.248 Angle : 0.569 7.310 30625 Z= 0.295 Chirality : 0.044 0.185 3290 Planarity : 0.004 0.037 3970 Dihedral : 4.218 18.866 3005 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 2.76 % Allowed : 18.13 % Favored : 79.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.52 (0.17), residues: 2660 helix: -1.91 (0.31), residues: 240 sheet: -0.86 (0.18), residues: 825 loop : -0.90 (0.16), residues: 1595 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP D 149 HIS 0.005 0.001 HIS D 116 PHE 0.016 0.002 PHE N 115 TYR 0.012 0.002 TYR H 11 ARG 0.007 0.000 ARG 1 124 Details of bonding type rmsd hydrogen bonds : bond 0.03137 ( 89) hydrogen bonds : angle 4.63012 ( 318) SS BOND : bond 0.00118 ( 20) SS BOND : angle 0.63781 ( 40) covalent geometry : bond 0.00593 (22445) covalent geometry : angle 0.56935 (30585) *********************** 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 437 residues out of total 2355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 372 time to evaluate : 2.512 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 45 ASN cc_start: 0.8917 (t0) cc_final: 0.8602 (t0) REVERT: 1 111 ASN cc_start: 0.8938 (m-40) cc_final: 0.8694 (m-40) REVERT: 2 82 GLU cc_start: 0.8297 (mp0) cc_final: 0.7894 (mp0) REVERT: 2 101 MET cc_start: 0.5940 (ptp) cc_final: 0.5534 (ptp) REVERT: 2 108 GLN cc_start: 0.7745 (mm110) cc_final: 0.7106 (mm-40) REVERT: 2 137 GLU cc_start: 0.8167 (pm20) cc_final: 0.7858 (pm20) REVERT: 2 199 GLU cc_start: 0.7957 (mp0) cc_final: 0.7451 (mp0) REVERT: 3 42 SER cc_start: 0.8951 (p) cc_final: 0.8407 (t) REVERT: 3 109 MET cc_start: 0.8715 (ttp) cc_final: 0.8150 (ttp) REVERT: 3 119 LYS cc_start: 0.8422 (mttt) cc_final: 0.8118 (mtmm) REVERT: 3 121 MET cc_start: 0.8317 (mtm) cc_final: 0.7623 (mpp) REVERT: 3 179 MET cc_start: 0.7370 (tpt) cc_final: 0.6388 (mpt) REVERT: B 43 LEU cc_start: 0.9102 (OUTLIER) cc_final: 0.8733 (pp) REVERT: B 45 ASN cc_start: 0.8822 (t0) cc_final: 0.8409 (t0) REVERT: B 124 ARG cc_start: 0.7760 (ttp-170) cc_final: 0.7550 (ttp-110) REVERT: B 176 ASP cc_start: 0.8149 (t0) cc_final: 0.7911 (t0) REVERT: D 21 THR cc_start: 0.8365 (p) cc_final: 0.7914 (t) REVERT: D 42 SER cc_start: 0.8975 (p) cc_final: 0.8462 (t) REVERT: D 115 HIS cc_start: 0.8588 (p90) cc_final: 0.8323 (p90) REVERT: D 119 LYS cc_start: 0.8439 (mttt) cc_final: 0.8178 (mppt) REVERT: D 121 MET cc_start: 0.7465 (ttt) cc_final: 0.6900 (mmm) REVERT: D 179 MET cc_start: 0.7403 (tpt) cc_final: 0.7052 (tpp) REVERT: D 190 GLN cc_start: 0.8320 (pt0) cc_final: 0.6990 (pp30) REVERT: D 221 ARG cc_start: 0.5485 (mtp180) cc_final: 0.5170 (mtt180) REVERT: F 102 ASP cc_start: 0.8343 (p0) cc_final: 0.8083 (p0) REVERT: F 124 ARG cc_start: 0.7784 (ttp-170) cc_final: 0.7574 (ttp-170) REVERT: F 176 ASP cc_start: 0.7991 (t0) cc_final: 0.7687 (t0) REVERT: H 42 SER cc_start: 0.8861 (p) cc_final: 0.8380 (t) REVERT: H 119 LYS cc_start: 0.8629 (mttt) cc_final: 0.8423 (mppt) REVERT: H 121 MET cc_start: 0.7423 (ttt) cc_final: 0.6966 (mmm) REVERT: H 190 GLN cc_start: 0.8594 (pt0) cc_final: 0.7047 (pp30) REVERT: J 45 ASN cc_start: 0.8885 (t0) cc_final: 0.8408 (t0) REVERT: J 101 ARG cc_start: 0.7829 (OUTLIER) cc_final: 0.7408 (ptt-90) REVERT: L 15 GLN cc_start: 0.8224 (mt0) cc_final: 0.7891 (mt0) REVERT: L 42 SER cc_start: 0.8766 (p) cc_final: 0.8274 (t) REVERT: L 119 LYS cc_start: 0.8342 (mttt) cc_final: 0.8138 (mppt) REVERT: L 121 MET cc_start: 0.7858 (OUTLIER) cc_final: 0.7458 (pmm) REVERT: L 179 MET cc_start: 0.7507 (tpt) cc_final: 0.7221 (tpp) REVERT: L 204 SER cc_start: 0.8761 (p) cc_final: 0.8380 (t) REVERT: N 45 ASN cc_start: 0.8621 (t0) cc_final: 0.8298 (t0) REVERT: N 105 MET cc_start: 0.8960 (OUTLIER) cc_final: 0.8500 (ttp) REVERT: N 111 ASN cc_start: 0.8945 (m-40) cc_final: 0.8715 (m110) REVERT: N 129 ARG cc_start: 0.7792 (OUTLIER) cc_final: 0.7329 (mtp-110) REVERT: P 86 LYS cc_start: 0.8083 (ttpt) cc_final: 0.7631 (ptmm) REVERT: P 179 MET cc_start: 0.7645 (tpt) cc_final: 0.7305 (tpp) REVERT: A 117 TYR cc_start: 0.7876 (m-80) cc_final: 0.7666 (m-80) REVERT: A 131 CYS cc_start: 0.5860 (m) cc_final: 0.5333 (m) REVERT: M 117 TYR cc_start: 0.8010 (m-80) cc_final: 0.7653 (m-80) REVERT: M 120 ARG cc_start: 0.8282 (OUTLIER) cc_final: 0.6157 (ttm-80) REVERT: M 141 ILE cc_start: 0.8468 (mt) cc_final: 0.8238 (mm) REVERT: Q 141 ILE cc_start: 0.8441 (mt) cc_final: 0.8115 (mm) REVERT: C 79 TYR cc_start: 0.7655 (m-80) cc_final: 0.7294 (m-80) REVERT: C 101 MET cc_start: 0.5637 (ptp) cc_final: 0.5337 (ptp) REVERT: C 108 GLN cc_start: 0.8112 (mt0) cc_final: 0.7650 (mt0) REVERT: C 137 GLU cc_start: 0.8601 (OUTLIER) cc_final: 0.8010 (pm20) REVERT: C 182 MET cc_start: 0.8011 (ttp) cc_final: 0.7729 (ptm) REVERT: C 199 GLU cc_start: 0.7694 (mp0) cc_final: 0.7174 (mp0) REVERT: G 101 MET cc_start: 0.5336 (ptt) cc_final: 0.4665 (ptp) REVERT: G 108 GLN cc_start: 0.8027 (mt0) cc_final: 0.7582 (tp40) REVERT: G 128 GLU cc_start: 0.8846 (mt-10) cc_final: 0.8423 (mt-10) REVERT: G 135 ARG cc_start: 0.8259 (mtm180) cc_final: 0.7945 (mtm-85) REVERT: G 137 GLU cc_start: 0.8384 (OUTLIER) cc_final: 0.7924 (pm20) REVERT: G 162 TYR cc_start: 0.8250 (t80) cc_final: 0.8007 (t80) REVERT: G 199 GLU cc_start: 0.7466 (mp0) cc_final: 0.6935 (mp0) REVERT: K 79 TYR cc_start: 0.7316 (m-80) cc_final: 0.6972 (m-80) REVERT: K 101 MET cc_start: 0.5201 (ptt) cc_final: 0.4617 (ptp) REVERT: K 102 ARG cc_start: 0.6595 (ttt180) cc_final: 0.5619 (ttm110) REVERT: K 108 GLN cc_start: 0.7585 (mm110) cc_final: 0.6975 (mm-40) REVERT: K 137 GLU cc_start: 0.8630 (OUTLIER) cc_final: 0.8155 (pm20) REVERT: K 199 GLU cc_start: 0.7800 (mp0) cc_final: 0.7399 (mp0) REVERT: O 101 MET cc_start: 0.5081 (ptt) cc_final: 0.4577 (ptp) REVERT: O 137 GLU cc_start: 0.8367 (OUTLIER) cc_final: 0.7923 (pm20) REVERT: O 199 GLU cc_start: 0.7876 (mp0) cc_final: 0.7412 (mp0) outliers start: 65 outliers final: 44 residues processed: 403 average time/residue: 1.3377 time to fit residues: 612.4975 Evaluate side-chains 419 residues out of total 2355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 365 time to evaluate : 2.114 ------------------------------------------------------------------------------- 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 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 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 204 SER Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 99 THR 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 101 ARG Chi-restraints excluded: chain L residue 116 HIS 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 43 LEU 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 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 178 SER Chi-restraints excluded: chain G residue 137 GLU 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 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 245 optimal weight: 0.5980 chunk 62 optimal weight: 0.7980 chunk 180 optimal weight: 0.0040 chunk 249 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 182 optimal weight: 6.9990 chunk 151 optimal weight: 6.9990 chunk 9 optimal weight: 1.9990 chunk 69 optimal weight: 0.5980 chunk 33 optimal weight: 0.8980 chunk 75 optimal weight: 0.0670 overall best weight: 0.4130 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 110 ASN 3 146 HIS B 29 HIS B 110 ASN D 15 GLN F 110 ASN ** J 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 110 ASN L 115 HIS N 110 ASN P 87 ASN ** C 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.160230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.112376 restraints weight = 28844.458| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 3.16 r_work: 0.3263 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 moved from start: 0.2664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 22465 Z= 0.095 Angle : 0.506 7.864 30625 Z= 0.262 Chirality : 0.042 0.181 3290 Planarity : 0.003 0.034 3970 Dihedral : 3.865 16.370 3005 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 1.87 % Allowed : 19.11 % Favored : 79.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.17), residues: 2660 helix: -1.85 (0.30), residues: 240 sheet: -0.61 (0.19), residues: 800 loop : -0.84 (0.16), residues: 1620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP 3 149 HIS 0.004 0.001 HIS O 145 PHE 0.010 0.001 PHE G 116 TYR 0.011 0.001 TYR O 79 ARG 0.003 0.000 ARG E 120 Details of bonding type rmsd hydrogen bonds : bond 0.02627 ( 89) hydrogen bonds : angle 4.44411 ( 318) SS BOND : bond 0.00215 ( 20) SS BOND : angle 0.66688 ( 40) covalent geometry : bond 0.00222 (22445) covalent geometry : angle 0.50619 (30585) ********************** 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 430 residues out of total 2355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 386 time to evaluate : 2.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 45 ASN cc_start: 0.8842 (t0) cc_final: 0.8632 (t0) REVERT: 1 111 ASN cc_start: 0.8900 (m-40) cc_final: 0.8661 (m-40) REVERT: 2 82 GLU cc_start: 0.8293 (mp0) cc_final: 0.7916 (mp0) REVERT: 2 101 MET cc_start: 0.6238 (ptp) cc_final: 0.5881 (ptp) REVERT: 2 108 GLN cc_start: 0.7493 (mm110) cc_final: 0.6860 (mm-40) REVERT: 2 199 GLU cc_start: 0.7939 (mp0) cc_final: 0.7436 (mp0) REVERT: 3 42 SER cc_start: 0.8892 (p) cc_final: 0.8357 (t) REVERT: 3 109 MET cc_start: 0.8696 (ttp) cc_final: 0.8147 (ttp) REVERT: 3 119 LYS cc_start: 0.8448 (mttt) cc_final: 0.8148 (mtmm) REVERT: 3 121 MET cc_start: 0.8181 (mtm) cc_final: 0.7597 (mpp) REVERT: 3 179 MET cc_start: 0.7253 (tpt) cc_final: 0.6307 (mpt) REVERT: B 43 LEU cc_start: 0.8972 (OUTLIER) cc_final: 0.8577 (pp) REVERT: B 45 ASN cc_start: 0.8781 (t0) cc_final: 0.8372 (t0) REVERT: D 21 THR cc_start: 0.8319 (p) cc_final: 0.7923 (t) REVERT: D 42 SER cc_start: 0.8945 (p) cc_final: 0.8447 (t) REVERT: D 115 HIS cc_start: 0.8641 (p90) cc_final: 0.8375 (p90) REVERT: D 119 LYS cc_start: 0.8450 (mttt) cc_final: 0.8148 (mppt) REVERT: D 121 MET cc_start: 0.7285 (ttt) cc_final: 0.6814 (mmm) REVERT: D 179 MET cc_start: 0.7275 (tpt) cc_final: 0.6137 (mpt) REVERT: D 190 GLN cc_start: 0.8294 (pt0) cc_final: 0.6929 (pp30) REVERT: D 221 ARG cc_start: 0.5546 (mtp180) cc_final: 0.5194 (mtt180) REVERT: F 102 ASP cc_start: 0.8207 (p0) cc_final: 0.7888 (p0) REVERT: F 124 ARG cc_start: 0.7768 (ttp-170) cc_final: 0.7477 (ttp-170) REVERT: F 176 ASP cc_start: 0.7953 (t0) cc_final: 0.7658 (t0) REVERT: H 42 SER cc_start: 0.8744 (p) cc_final: 0.8261 (t) REVERT: H 121 MET cc_start: 0.7297 (ttt) cc_final: 0.6837 (mmm) REVERT: H 190 GLN cc_start: 0.8539 (pt0) cc_final: 0.6966 (pp30) REVERT: J 45 ASN cc_start: 0.8812 (t0) cc_final: 0.8357 (t0) REVERT: J 101 ARG cc_start: 0.7880 (OUTLIER) cc_final: 0.7321 (ptt90) REVERT: J 124 ARG cc_start: 0.7810 (ttp-170) cc_final: 0.7532 (ttp-170) REVERT: L 42 SER cc_start: 0.8673 (p) cc_final: 0.8180 (t) REVERT: L 119 LYS cc_start: 0.8376 (mttt) cc_final: 0.8148 (mppt) REVERT: L 121 MET cc_start: 0.7830 (OUTLIER) cc_final: 0.7435 (pmm) REVERT: L 179 MET cc_start: 0.7364 (tpt) cc_final: 0.6022 (mpm) REVERT: L 204 SER cc_start: 0.8976 (p) cc_final: 0.8611 (t) REVERT: N 28 VAL cc_start: 0.8556 (t) cc_final: 0.8343 (p) REVERT: N 45 ASN cc_start: 0.8522 (t0) cc_final: 0.8185 (t0) REVERT: N 105 MET cc_start: 0.8920 (OUTLIER) cc_final: 0.8411 (ttp) REVERT: N 111 ASN cc_start: 0.8918 (m-40) cc_final: 0.8690 (m110) REVERT: N 129 ARG cc_start: 0.7661 (OUTLIER) cc_final: 0.7188 (mtp-110) REVERT: P 15 GLN cc_start: 0.8129 (mt0) cc_final: 0.7822 (mt0) REVERT: P 86 LYS cc_start: 0.8057 (ttpt) cc_final: 0.7660 (ptmm) REVERT: P 179 MET cc_start: 0.7534 (tpt) cc_final: 0.7237 (tpp) REVERT: A 131 CYS cc_start: 0.5654 (m) cc_final: 0.5137 (m) REVERT: M 117 TYR cc_start: 0.8017 (m-80) cc_final: 0.7669 (m-80) REVERT: C 79 TYR cc_start: 0.7634 (m-80) cc_final: 0.7279 (m-80) REVERT: C 101 MET cc_start: 0.5512 (ptp) cc_final: 0.5168 (ptp) REVERT: C 102 ARG cc_start: 0.6459 (ttt180) cc_final: 0.6056 (ttm-80) REVERT: C 108 GLN cc_start: 0.8090 (mt0) cc_final: 0.7689 (mt0) REVERT: C 137 GLU cc_start: 0.8581 (OUTLIER) cc_final: 0.8016 (pm20) REVERT: C 199 GLU cc_start: 0.7667 (mp0) cc_final: 0.7133 (mp0) REVERT: G 101 MET cc_start: 0.5312 (ptt) cc_final: 0.4701 (ptp) REVERT: G 102 ARG cc_start: 0.6195 (ttt180) cc_final: 0.5758 (mtt90) REVERT: G 108 GLN cc_start: 0.7899 (mt0) cc_final: 0.7630 (tp40) REVERT: G 128 GLU cc_start: 0.8805 (mt-10) cc_final: 0.8417 (mt-10) REVERT: G 135 ARG cc_start: 0.8205 (mtm180) cc_final: 0.7994 (mtp-110) REVERT: G 137 GLU cc_start: 0.8368 (OUTLIER) cc_final: 0.7903 (pm20) REVERT: G 162 TYR cc_start: 0.8236 (t80) cc_final: 0.7952 (t80) REVERT: G 199 GLU cc_start: 0.7452 (mp0) cc_final: 0.6998 (mp0) REVERT: K 79 TYR cc_start: 0.7331 (m-80) cc_final: 0.7035 (m-80) REVERT: K 101 MET cc_start: 0.5262 (ptt) cc_final: 0.4704 (ptp) REVERT: K 108 GLN cc_start: 0.7404 (mm110) cc_final: 0.6840 (mm-40) REVERT: K 137 GLU cc_start: 0.8589 (OUTLIER) cc_final: 0.8104 (pm20) REVERT: O 101 MET cc_start: 0.5288 (ptt) cc_final: 0.4777 (ptp) REVERT: O 137 GLU cc_start: 0.8337 (OUTLIER) cc_final: 0.7875 (pm20) REVERT: O 199 GLU cc_start: 0.7867 (mp0) cc_final: 0.7403 (mp0) outliers start: 44 outliers final: 21 residues processed: 403 average time/residue: 1.3753 time to fit residues: 637.7670 Evaluate side-chains 398 residues out of total 2355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 368 time to evaluate : 2.290 ------------------------------------------------------------------------------- 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 2 residue 188 THR 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 D residue 204 SER Chi-restraints excluded: chain H residue 182 THR Chi-restraints excluded: chain H residue 206 SER Chi-restraints excluded: chain J residue 101 ARG Chi-restraints excluded: chain L residue 116 HIS 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 42 SER Chi-restraints excluded: chain I 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 110 SER Chi-restraints excluded: chain G residue 137 GLU Chi-restraints excluded: chain G residue 178 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 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 4 optimal weight: 0.3980 chunk 191 optimal weight: 0.9990 chunk 21 optimal weight: 3.9990 chunk 157 optimal weight: 6.9990 chunk 237 optimal weight: 6.9990 chunk 177 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 chunk 216 optimal weight: 0.0000 chunk 101 optimal weight: 5.9990 chunk 165 optimal weight: 3.9990 chunk 233 optimal weight: 0.9990 overall best weight: 0.8790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 110 ASN 3 146 HIS B 29 HIS B 110 ASN F 45 ASN F 110 ASN ** J 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 110 ASN L 115 HIS N 110 ASN P 190 GLN ** C 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.159241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.111162 restraints weight = 28734.180| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 3.15 r_work: 0.3244 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.2743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 22465 Z= 0.128 Angle : 0.509 7.731 30625 Z= 0.263 Chirality : 0.042 0.176 3290 Planarity : 0.004 0.047 3970 Dihedral : 3.872 16.430 3005 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 1.70 % Allowed : 19.62 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.17), residues: 2660 helix: -1.79 (0.31), residues: 240 sheet: -0.77 (0.19), residues: 825 loop : -0.78 (0.16), residues: 1595 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP P 149 HIS 0.007 0.001 HIS 3 146 PHE 0.010 0.001 PHE G 116 TYR 0.011 0.001 TYR F 183 ARG 0.007 0.000 ARG E 120 Details of bonding type rmsd hydrogen bonds : bond 0.02711 ( 89) hydrogen bonds : angle 4.38113 ( 318) SS BOND : bond 0.00064 ( 20) SS BOND : angle 0.60172 ( 40) covalent geometry : bond 0.00305 (22445) covalent geometry : angle 0.50850 (30585) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15508.60 seconds wall clock time: 270 minutes 32.86 seconds (16232.86 seconds total)