Starting phenix.real_space_refine on Fri Jan 24 07:55:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9g6v_51105/01_2025/9g6v_51105.cif Found real_map, /net/cci-nas-00/data/ceres_data/9g6v_51105/01_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_51105/01_2025/9g6v_51105.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9g6v_51105/01_2025/9g6v_51105.map" model { file = "/net/cci-nas-00/data/ceres_data/9g6v_51105/01_2025/9g6v_51105.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9g6v_51105/01_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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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: 12.21, per 1000 atoms: 0.56 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: 4.87 Conformation dependent library (CDL) restraints added in 3.0 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: 1.69 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: 4.44 Time building geometry restraints manager: 5.72 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: 1.710 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: 0.800 Check model and map are aligned: 0.150 Set scattering table: 0.180 Process input model: 43.260 Find NCS groups from input model: 0.830 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.010 ------------------------------------------------------------------------------- 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 22445 Z= 0.175 Angle : 0.442 5.218 30585 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 *********************** 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 : 2.329 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: 1.2916 time to fit residues: 780.1885 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 : 2.346 ------------------------------------------------------------------------------- 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 = 43)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.108966 restraints weight = 29121.676| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 3.31 r_work: 0.3174 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 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 22445 Z= 0.499 Angle : 0.588 6.290 30585 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 *********************** 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 : 2.378 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: 0.8265 (mp0) cc_final: 0.7764 (mp0) REVERT: 2 101 MET cc_start: 0.5107 (ptp) cc_final: 0.4605 (ptp) REVERT: 2 137 GLU cc_start: 0.7909 (pm20) cc_final: 0.7633 (pm20) REVERT: 2 199 GLU cc_start: 0.7730 (mp0) cc_final: 0.7292 (mp0) REVERT: 3 42 SER cc_start: 0.8949 (p) cc_final: 0.8425 (t) REVERT: 3 109 MET cc_start: 0.8722 (ttp) cc_final: 0.8132 (ttp) REVERT: 3 119 LYS cc_start: 0.8324 (mttt) cc_final: 0.8020 (mptt) REVERT: 3 179 MET cc_start: 0.7445 (tpt) cc_final: 0.6426 (mpt) REVERT: 3 190 GLN cc_start: 0.8204 (pt0) cc_final: 0.6608 (pp30) REVERT: 3 221 ARG cc_start: 0.5836 (OUTLIER) cc_final: 0.5513 (mtp180) REVERT: B 45 ASN cc_start: 0.8679 (t0) cc_final: 0.8345 (t0) REVERT: D 42 SER cc_start: 0.8963 (p) cc_final: 0.8455 (t) REVERT: D 119 LYS cc_start: 0.8353 (mttt) cc_final: 0.8066 (mptt) REVERT: D 149 TRP cc_start: 0.6363 (p-90) cc_final: 0.6131 (p-90) REVERT: D 189 PHE cc_start: 0.7996 (m-80) cc_final: 0.7692 (m-80) REVERT: D 190 GLN cc_start: 0.8146 (pt0) cc_final: 0.6853 (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: 0.8454 (t) REVERT: H 190 GLN cc_start: 0.8082 (pt0) cc_final: 0.6659 (pp30) REVERT: J 124 ARG cc_start: 0.7778 (ttp-170) cc_final: 0.7516 (ttp-170) REVERT: L 42 SER cc_start: 0.8797 (p) cc_final: 0.8332 (t) REVERT: L 121 MET cc_start: 0.7785 (pmm) cc_final: 0.7455 (pmm) REVERT: L 179 MET cc_start: 0.7496 (tpt) cc_final: 0.6260 (mpt) REVERT: L 204 SER cc_start: 0.8751 (p) cc_final: 0.8277 (t) REVERT: N 111 ASN cc_start: 0.8948 (m-40) cc_final: 0.8691 (m110) REVERT: P 119 LYS cc_start: 0.8549 (mttt) cc_final: 0.8302 (mptt) REVERT: P 179 MET cc_start: 0.7741 (tpt) cc_final: 0.7293 (tpp) REVERT: E 141 ILE cc_start: 0.8408 (mt) cc_final: 0.8067 (mm) REVERT: I 141 ILE cc_start: 0.8403 (mt) cc_final: 0.8088 (mm) REVERT: Q 141 ILE cc_start: 0.8455 (mt) cc_final: 0.8165 (mm) REVERT: C 79 TYR cc_start: 0.7419 (m-80) cc_final: 0.7198 (m-80) REVERT: C 101 MET cc_start: 0.4042 (ptp) cc_final: 0.3650 (ptp) REVERT: C 108 GLN cc_start: 0.8054 (mt0) cc_final: 0.7537 (mt0) REVERT: C 128 GLU cc_start: 0.8643 (mt-10) cc_final: 0.8430 (mt-10) REVERT: C 137 GLU cc_start: 0.8480 (OUTLIER) cc_final: 0.8028 (pm20) REVERT: C 199 GLU cc_start: 0.7526 (mp0) cc_final: 0.7068 (mp0) REVERT: G 108 GLN cc_start: 0.8143 (mt0) cc_final: 0.7863 (mt0) REVERT: G 137 GLU cc_start: 0.8309 (OUTLIER) cc_final: 0.7813 (pm20) REVERT: G 158 ILE cc_start: 0.8591 (OUTLIER) cc_final: 0.8253 (mp) REVERT: G 162 TYR cc_start: 0.8139 (t80) cc_final: 0.7927 (t80) REVERT: G 199 GLU cc_start: 0.7459 (mp0) cc_final: 0.6980 (mp0) REVERT: K 102 ARG cc_start: 0.6406 (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: 0.7613 (mp0) cc_final: 0.7189 (mp0) REVERT: O 137 GLU cc_start: 0.8186 (OUTLIER) cc_final: 0.7713 (pm20) REVERT: O 199 GLU cc_start: 0.7564 (mp0) cc_final: 0.7051 (mp0) outliers start: 82 outliers final: 45 residues processed: 421 average time/residue: 1.3103 time to fit residues: 630.8124 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 : 2.403 ------------------------------------------------------------------------------- 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: 2.9990 chunk 141 optimal weight: 0.4980 chunk 215 optimal weight: 0.7980 chunk 195 optimal weight: 5.9990 chunk 6 optimal weight: 0.6980 chunk 190 optimal weight: 6.9990 chunk 77 optimal weight: 3.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- 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 = 0.4048 r_free = 0.4048 target = 0.161171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.111210 restraints weight = 28661.587| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 3.27 r_work: 0.3206 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.1918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 22445 Z= 0.275 Angle : 0.498 6.221 30585 Z= 0.259 Chirality : 0.042 0.164 3290 Planarity : 0.004 0.032 3970 Dihedral : 4.130 18.635 3005 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 3.31 % Allowed : 12.36 % Favored : 84.33 % 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: -1.92 (0.30), residues: 240 sheet: -0.78 (0.18), residues: 865 loop : -0.83 (0.17), residues: 1555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP 3 149 HIS 0.007 0.001 HIS 3 146 PHE 0.014 0.001 PHE 1 115 TYR 0.018 0.001 TYR G 34 ARG 0.006 0.000 ARG G 102 *********************** 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 461 residues out of total 2355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 383 time to evaluate : 2.273 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: 0.8904 (OUTLIER) cc_final: 0.8397 (ttp) REVERT: 1 111 ASN cc_start: 0.8924 (m-40) cc_final: 0.8679 (m-40) REVERT: 2 82 GLU cc_start: 0.8262 (mp0) cc_final: 0.7870 (mp0) REVERT: 2 101 MET cc_start: 0.4756 (ptp) cc_final: 0.4305 (ptp) REVERT: 2 137 GLU cc_start: 0.8048 (pm20) cc_final: 0.7704 (pm20) REVERT: 2 199 GLU cc_start: 0.7800 (mp0) cc_final: 0.7341 (mp0) REVERT: 3 42 SER cc_start: 0.8895 (p) cc_final: 0.8354 (t) REVERT: 3 109 MET cc_start: 0.8652 (ttp) cc_final: 0.8165 (ttp) REVERT: 3 119 LYS cc_start: 0.8390 (mttt) cc_final: 0.8082 (mppt) REVERT: 3 190 GLN cc_start: 0.8233 (pt0) cc_final: 0.6611 (pp30) REVERT: 3 221 ARG cc_start: 0.5851 (OUTLIER) cc_final: 0.5591 (mtp180) REVERT: B 45 ASN cc_start: 0.8701 (t0) cc_final: 0.8327 (t0) REVERT: D 21 THR cc_start: 0.8373 (p) cc_final: 0.7938 (t) REVERT: D 42 SER cc_start: 0.8917 (p) cc_final: 0.8386 (t) REVERT: D 119 LYS cc_start: 0.8379 (mttt) cc_final: 0.8130 (mppt) REVERT: D 121 MET cc_start: 0.7131 (ttt) cc_final: 0.6686 (mmm) REVERT: D 149 TRP cc_start: 0.6365 (p-90) cc_final: 0.6084 (p-90) REVERT: D 179 MET cc_start: 0.7358 (tpt) cc_final: 0.6093 (mpt) REVERT: D 189 PHE cc_start: 0.7932 (m-80) cc_final: 0.7602 (m-80) REVERT: D 190 GLN cc_start: 0.8232 (pt0) cc_final: 0.6926 (pp30) REVERT: F 43 LEU cc_start: 0.9195 (OUTLIER) cc_final: 0.8961 (pp) REVERT: F 102 ASP cc_start: 0.8136 (p0) cc_final: 0.7866 (p0) REVERT: F 124 ARG cc_start: 0.7701 (ttp-170) cc_final: 0.7479 (ttp-170) REVERT: H 42 SER cc_start: 0.8796 (p) cc_final: 0.8322 (t) REVERT: H 119 LYS cc_start: 0.8546 (mttt) cc_final: 0.8330 (mppt) REVERT: H 190 GLN cc_start: 0.8105 (pt0) cc_final: 0.6657 (pp30) REVERT: J 124 ARG cc_start: 0.7799 (ttp-170) cc_final: 0.7530 (ttp-170) REVERT: L 42 SER cc_start: 0.8694 (p) cc_final: 0.8193 (t) REVERT: L 119 LYS cc_start: 0.8427 (mttt) cc_final: 0.8089 (mppt) REVERT: L 121 MET cc_start: 0.7791 (OUTLIER) cc_final: 0.7451 (pmm) REVERT: L 179 MET cc_start: 0.7378 (tpt) cc_final: 0.7088 (tpp) REVERT: L 190 GLN cc_start: 0.7697 (pt0) cc_final: 0.6279 (pp30) REVERT: L 204 SER cc_start: 0.8776 (p) cc_final: 0.8282 (t) REVERT: N 45 ASN cc_start: 0.8420 (OUTLIER) cc_final: 0.8216 (t0) REVERT: N 105 MET cc_start: 0.8953 (OUTLIER) cc_final: 0.8444 (ttp) REVERT: N 111 ASN cc_start: 0.8914 (m-40) cc_final: 0.8659 (m110) REVERT: P 86 LYS cc_start: 0.8105 (ttpt) cc_final: 0.7623 (ptmm) REVERT: P 119 LYS cc_start: 0.8528 (mttt) cc_final: 0.8297 (mppt) REVERT: P 179 MET cc_start: 0.7647 (tpt) cc_final: 0.7249 (tpp) REVERT: E 141 ILE cc_start: 0.8338 (mt) cc_final: 0.7995 (mm) REVERT: Q 141 ILE cc_start: 0.8371 (mt) cc_final: 0.8084 (mm) REVERT: C 79 TYR cc_start: 0.7426 (m-80) cc_final: 0.7138 (m-80) REVERT: C 101 MET cc_start: 0.4033 (ptp) cc_final: 0.3674 (ptp) REVERT: C 108 GLN cc_start: 0.8026 (mt0) cc_final: 0.7515 (mt0) REVERT: C 137 GLU cc_start: 0.8464 (OUTLIER) cc_final: 0.7901 (pm20) REVERT: C 182 MET cc_start: 0.7995 (ttp) cc_final: 0.7575 (ptm) REVERT: C 199 GLU cc_start: 0.7584 (mp0) cc_final: 0.7125 (mp0) REVERT: G 101 MET cc_start: 0.4174 (ptt) cc_final: 0.3603 (ptp) REVERT: G 108 GLN cc_start: 0.8102 (mt0) cc_final: 0.7850 (mt0) REVERT: G 137 GLU cc_start: 0.8360 (OUTLIER) cc_final: 0.7774 (pm20) REVERT: G 158 ILE cc_start: 0.8565 (OUTLIER) cc_final: 0.8277 (mp) REVERT: G 199 GLU cc_start: 0.7437 (mp0) cc_final: 0.6949 (mp0) REVERT: K 137 GLU cc_start: 0.8327 (OUTLIER) cc_final: 0.7846 (pm20) REVERT: K 199 GLU cc_start: 0.7657 (mp0) cc_final: 0.7258 (mp0) REVERT: O 108 GLN cc_start: 0.8044 (mt0) cc_final: 0.7821 (mt0) REVERT: O 137 GLU cc_start: 0.8237 (OUTLIER) cc_final: 0.7824 (pm20) REVERT: O 199 GLU cc_start: 0.7618 (mp0) cc_final: 0.7038 (mp0) outliers start: 78 outliers final: 41 residues processed: 417 average time/residue: 1.3712 time to fit residues: 651.1160 Evaluate side-chains 419 residues out of total 2355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 367 time to evaluate : 2.493 ------------------------------------------------------------------------------- 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 2 residue 141 SER Chi-restraints excluded: chain 2 residue 178 SER Chi-restraints excluded: chain 2 residue 188 THR Chi-restraints excluded: chain 3 residue 204 SER Chi-restraints excluded: chain 3 residue 217 VAL Chi-restraints excluded: chain 3 residue 221 ARG Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 108 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 204 SER 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 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 N residue 105 MET 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 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 K residue 110 SER Chi-restraints excluded: chain K residue 137 GLU Chi-restraints excluded: chain K residue 158 ILE Chi-restraints excluded: chain K residue 188 THR Chi-restraints excluded: chain O residue 110 SER Chi-restraints excluded: chain O residue 137 GLU Chi-restraints excluded: chain O residue 188 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 107 optimal weight: 0.8980 chunk 158 optimal weight: 0.7980 chunk 21 optimal weight: 0.0970 chunk 146 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 48 optimal weight: 0.9980 chunk 229 optimal weight: 5.9990 chunk 182 optimal weight: 8.9990 chunk 72 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 142 optimal weight: 0.6980 overall best weight: 0.6978 ------------------------------------------------------------------------------- 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 B 92 ASN B 110 ASN D 15 GLN ** F 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4065 r_free = 0.4065 target = 0.162827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.113149 restraints weight = 28999.308| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 3.27 r_work: 0.3236 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.2017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 22445 Z= 0.175 Angle : 0.471 5.988 30585 Z= 0.245 Chirality : 0.041 0.162 3290 Planarity : 0.004 0.037 3970 Dihedral : 3.913 16.982 3005 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 2.89 % Allowed : 14.18 % Favored : 82.93 % 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: -1.88 (0.30), residues: 240 sheet: -0.77 (0.18), residues: 870 loop : -0.76 (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 0.011 0.001 PHE G 116 TYR 0.011 0.001 TYR O 79 ARG 0.005 0.000 ARG G 102 *********************** 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 456 residues out of total 2355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 388 time to evaluate : 2.573 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: 0.8930 (m-40) cc_final: 0.8678 (m-40) REVERT: 1 129 ARG cc_start: 0.8086 (mtp-110) cc_final: 0.7862 (mtp-110) REVERT: 2 82 GLU cc_start: 0.8252 (mp0) cc_final: 0.7946 (mp0) REVERT: 2 101 MET cc_start: 0.5130 (ptp) cc_final: 0.4697 (ptp) REVERT: 2 137 GLU cc_start: 0.8079 (pm20) cc_final: 0.7749 (pm20) REVERT: 2 199 GLU cc_start: 0.7894 (mp0) cc_final: 0.7432 (mp0) REVERT: 3 42 SER cc_start: 0.8892 (p) cc_final: 0.8379 (t) REVERT: 3 109 MET cc_start: 0.8685 (ttp) cc_final: 0.8107 (ttp) REVERT: 3 119 LYS cc_start: 0.8308 (mttt) cc_final: 0.8007 (mppt) REVERT: 3 179 MET cc_start: 0.7364 (tpt) cc_final: 0.6406 (mpt) REVERT: 3 190 GLN cc_start: 0.8082 (pt0) cc_final: 0.6410 (pp30) REVERT: B 45 ASN cc_start: 0.8712 (t0) cc_final: 0.8317 (t0) REVERT: D 21 THR cc_start: 0.8364 (p) cc_final: 0.7946 (t) REVERT: D 42 SER cc_start: 0.8931 (p) cc_final: 0.8425 (t) REVERT: D 121 MET cc_start: 0.7129 (ttt) cc_final: 0.6702 (mmm) REVERT: D 179 MET cc_start: 0.7352 (tpt) cc_final: 0.6133 (mmt) REVERT: D 189 PHE cc_start: 0.7878 (m-80) cc_final: 0.7598 (m-80) REVERT: D 190 GLN cc_start: 0.8183 (pt0) cc_final: 0.6799 (pp30) REVERT: F 43 LEU cc_start: 0.9182 (OUTLIER) cc_final: 0.8948 (pp) REVERT: F 102 ASP cc_start: 0.8179 (p0) cc_final: 0.7868 (p0) REVERT: H 42 SER cc_start: 0.8809 (p) cc_final: 0.8345 (t) REVERT: H 119 LYS cc_start: 0.8545 (mttt) cc_final: 0.8334 (mppt) REVERT: H 121 MET cc_start: 0.7215 (ttt) cc_final: 0.6960 (mmm) REVERT: H 179 MET cc_start: 0.7519 (tpt) cc_final: 0.6394 (mmt) REVERT: H 190 GLN cc_start: 0.8212 (pt0) cc_final: 0.6701 (pp30) REVERT: J 36 MET cc_start: 0.8964 (mmm) cc_final: 0.8503 (mmt) REVERT: J 124 ARG cc_start: 0.7806 (ttp-170) cc_final: 0.7535 (ttp-170) REVERT: L 42 SER cc_start: 0.8684 (p) cc_final: 0.8200 (t) REVERT: L 121 MET cc_start: 0.7765 (pmm) cc_final: 0.7450 (pmm) REVERT: L 179 MET cc_start: 0.7343 (tpt) cc_final: 0.6187 (mpt) REVERT: L 190 GLN cc_start: 0.7690 (pt0) cc_final: 0.6319 (pp30) REVERT: L 204 SER cc_start: 0.8986 (p) cc_final: 0.8596 (t) REVERT: N 92 ASN cc_start: 0.8279 (t0) cc_final: 0.7969 (t0) REVERT: N 111 ASN cc_start: 0.8925 (m-40) cc_final: 0.8682 (m110) REVERT: N 129 ARG cc_start: 0.7832 (mtp-110) cc_final: 0.7548 (mtp-110) REVERT: P 86 LYS cc_start: 0.8085 (ttpt) cc_final: 0.7656 (ptmm) REVERT: P 119 LYS cc_start: 0.8523 (mttt) cc_final: 0.8265 (mppt) REVERT: P 179 MET cc_start: 0.7621 (tpt) cc_final: 0.7266 (tpp) REVERT: E 141 ILE cc_start: 0.8333 (mt) cc_final: 0.7981 (mm) REVERT: C 79 TYR cc_start: 0.7466 (m-80) cc_final: 0.7171 (m-80) REVERT: C 101 MET cc_start: 0.4572 (ptp) cc_final: 0.4283 (ptp) REVERT: C 108 GLN cc_start: 0.8057 (mt0) cc_final: 0.7610 (mt0) REVERT: C 137 GLU cc_start: 0.8500 (OUTLIER) cc_final: 0.7963 (pm20) REVERT: C 182 MET cc_start: 0.7972 (ttp) cc_final: 0.7674 (ptm) REVERT: C 199 GLU cc_start: 0.7600 (mp0) cc_final: 0.7153 (mp0) REVERT: G 101 MET cc_start: 0.4681 (ptt) cc_final: 0.4048 (ptp) REVERT: G 108 GLN cc_start: 0.8114 (mt0) cc_final: 0.7869 (mt0) REVERT: G 135 ARG cc_start: 0.8199 (mtm180) cc_final: 0.7881 (mtm-85) REVERT: G 137 GLU cc_start: 0.8344 (OUTLIER) cc_final: 0.7873 (pm20) REVERT: G 158 ILE cc_start: 0.8592 (OUTLIER) cc_final: 0.8320 (mp) REVERT: G 162 TYR cc_start: 0.8180 (t80) cc_final: 0.7962 (t80) REVERT: G 199 GLU cc_start: 0.7443 (mp0) cc_final: 0.6931 (mp0) REVERT: K 128 GLU cc_start: 0.8686 (mt-10) cc_final: 0.7967 (mt-10) REVERT: K 137 GLU cc_start: 0.8453 (OUTLIER) cc_final: 0.7994 (pm20) REVERT: K 199 GLU cc_start: 0.7800 (mp0) cc_final: 0.7444 (mp0) REVERT: O 73 LYS cc_start: 0.8390 (mttp) cc_final: 0.8188 (mttp) REVERT: O 108 GLN cc_start: 0.8095 (mt0) cc_final: 0.7843 (mt0) REVERT: O 117 ASN cc_start: 0.8691 (OUTLIER) cc_final: 0.8460 (t0) REVERT: O 137 GLU cc_start: 0.8267 (OUTLIER) cc_final: 0.7844 (pm20) REVERT: O 199 GLU cc_start: 0.7619 (mp0) cc_final: 0.7043 (mp0) outliers start: 68 outliers final: 38 residues processed: 422 average time/residue: 1.3514 time to fit residues: 650.4336 Evaluate side-chains 419 residues out of total 2355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 374 time to evaluate : 2.634 ------------------------------------------------------------------------------- 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 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 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 N residue 28 VAL Chi-restraints excluded: chain N residue 87 VAL 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 Q residue 120 ARG Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 137 GLU Chi-restraints excluded: chain C residue 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 158 ILE 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 176 optimal weight: 2.9990 chunk 173 optimal weight: 0.6980 chunk 8 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 184 optimal weight: 0.5980 chunk 201 optimal weight: 5.9990 chunk 163 optimal weight: 0.7980 chunk 25 optimal weight: 10.0000 chunk 47 optimal weight: 3.9990 chunk 213 optimal weight: 8.9990 chunk 45 optimal weight: 2.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- 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 F 110 ASN J 45 ASN J 110 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 ** G 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 157 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.160394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.110094 restraints weight = 28921.016| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 3.31 r_work: 0.3193 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.2250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 22445 Z= 0.319 Angle : 0.519 6.249 30585 Z= 0.268 Chirality : 0.043 0.185 3290 Planarity : 0.004 0.034 3970 Dihedral : 4.132 18.686 3005 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 3.78 % Allowed : 14.56 % Favored : 81.66 % 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: -1.94 (0.30), residues: 240 sheet: -0.95 (0.18), residues: 875 loop : -0.83 (0.17), residues: 1545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP 3 149 HIS 0.007 0.001 HIS H 143 PHE 0.013 0.001 PHE P 8 TYR 0.011 0.001 TYR H 11 ARG 0.005 0.000 ARG E 120 *********************** 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 470 residues out of total 2355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 381 time to evaluate : 2.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 45 ASN cc_start: 0.8838 (t0) cc_final: 0.8497 (t0) REVERT: 1 111 ASN cc_start: 0.8920 (m-40) cc_final: 0.8670 (m-40) REVERT: 1 129 ARG cc_start: 0.8101 (OUTLIER) cc_final: 0.7761 (mtp-110) REVERT: 2 82 GLU cc_start: 0.8269 (mp0) cc_final: 0.7933 (mp0) REVERT: 2 101 MET cc_start: 0.5209 (ptp) cc_final: 0.4725 (ptp) REVERT: 2 137 GLU cc_start: 0.8188 (pm20) cc_final: 0.7835 (pm20) REVERT: 2 199 GLU cc_start: 0.7914 (mp0) cc_final: 0.7448 (mp0) REVERT: 3 42 SER cc_start: 0.8933 (p) cc_final: 0.8386 (t) REVERT: 3 109 MET cc_start: 0.8673 (ttp) cc_final: 0.8131 (ttp) REVERT: 3 119 LYS cc_start: 0.8364 (mttt) cc_final: 0.8048 (mtmm) REVERT: 3 179 MET cc_start: 0.7329 (tpt) cc_final: 0.6359 (mpt) REVERT: 3 190 GLN cc_start: 0.8141 (pt0) cc_final: 0.6485 (pp30) REVERT: 3 221 ARG cc_start: 0.5930 (OUTLIER) cc_final: 0.5714 (mtp180) REVERT: B 43 LEU cc_start: 0.9127 (OUTLIER) cc_final: 0.8709 (pp) REVERT: B 45 ASN cc_start: 0.8774 (t0) cc_final: 0.8367 (t0) REVERT: B 92 ASN cc_start: 0.8516 (t0) cc_final: 0.8282 (t0) REVERT: B 120 THR cc_start: 0.8964 (m) cc_final: 0.8730 (m) REVERT: B 124 ARG cc_start: 0.7758 (ttp-170) cc_final: 0.7442 (ttt-90) REVERT: D 21 THR cc_start: 0.8369 (p) cc_final: 0.7931 (t) REVERT: D 42 SER cc_start: 0.8952 (p) cc_final: 0.8431 (t) REVERT: D 119 LYS cc_start: 0.8393 (mttt) cc_final: 0.8154 (mppt) REVERT: D 121 MET cc_start: 0.7251 (ttt) cc_final: 0.6689 (mmm) REVERT: D 179 MET cc_start: 0.7390 (tpt) cc_final: 0.7013 (tpp) REVERT: D 190 GLN cc_start: 0.8175 (pt0) cc_final: 0.6826 (pp30) REVERT: F 43 LEU cc_start: 0.9222 (OUTLIER) cc_final: 0.9009 (pp) REVERT: F 102 ASP cc_start: 0.8265 (p0) cc_final: 0.8003 (p0) REVERT: H 42 SER cc_start: 0.8824 (p) cc_final: 0.8347 (t) REVERT: H 119 LYS cc_start: 0.8552 (mttt) cc_final: 0.8351 (mppt) REVERT: H 190 GLN cc_start: 0.8294 (pt0) cc_final: 0.6721 (pp30) REVERT: J 36 MET cc_start: 0.8975 (mmm) cc_final: 0.8530 (mmt) REVERT: J 108 SER cc_start: 0.9343 (OUTLIER) cc_final: 0.8999 (p) REVERT: L 42 SER cc_start: 0.8724 (p) cc_final: 0.8222 (t) REVERT: L 119 LYS cc_start: 0.8369 (mttt) cc_final: 0.8107 (mppt) REVERT: L 121 MET cc_start: 0.7791 (OUTLIER) cc_final: 0.7444 (pmm) REVERT: L 179 MET cc_start: 0.7402 (tpt) cc_final: 0.7111 (tpp) REVERT: L 190 GLN cc_start: 0.7870 (pt0) cc_final: 0.6566 (pp30) REVERT: L 204 SER cc_start: 0.8779 (p) cc_final: 0.8386 (t) REVERT: N 45 ASN cc_start: 0.8370 (t0) cc_final: 0.8162 (t0) REVERT: N 105 MET cc_start: 0.8914 (OUTLIER) cc_final: 0.8452 (ttp) REVERT: N 111 ASN cc_start: 0.8926 (m-40) cc_final: 0.8683 (m110) REVERT: N 129 ARG cc_start: 0.7933 (OUTLIER) cc_final: 0.7580 (mtp-110) REVERT: P 86 LYS cc_start: 0.8068 (ttpt) cc_final: 0.7715 (ptmt) REVERT: P 179 MET cc_start: 0.7661 (tpt) cc_final: 0.7277 (tpp) REVERT: P 190 GLN cc_start: 0.7511 (pt0) cc_final: 0.6119 (pp30) REVERT: E 141 ILE cc_start: 0.8340 (mt) cc_final: 0.7961 (mm) REVERT: Q 141 ILE cc_start: 0.8393 (mt) cc_final: 0.8090 (mm) REVERT: C 79 TYR cc_start: 0.7540 (m-80) cc_final: 0.7241 (m-80) REVERT: C 101 MET cc_start: 0.4899 (ptp) cc_final: 0.4562 (ptp) REVERT: C 108 GLN cc_start: 0.8008 (mt0) cc_final: 0.7534 (mt0) REVERT: C 137 GLU cc_start: 0.8564 (OUTLIER) cc_final: 0.7953 (pm20) REVERT: C 182 MET cc_start: 0.8028 (ttp) cc_final: 0.7638 (ptm) REVERT: C 199 GLU cc_start: 0.7628 (mp0) cc_final: 0.7177 (mp0) REVERT: G 101 MET cc_start: 0.4835 (ptt) cc_final: 0.4169 (ptp) REVERT: G 135 ARG cc_start: 0.8239 (mtm180) cc_final: 0.7937 (mtm-85) REVERT: G 137 GLU cc_start: 0.8324 (OUTLIER) cc_final: 0.7844 (pm20) REVERT: G 158 ILE cc_start: 0.8604 (OUTLIER) cc_final: 0.8335 (mp) REVERT: G 199 GLU cc_start: 0.7413 (mp0) cc_final: 0.6926 (mp0) REVERT: K 137 GLU cc_start: 0.8526 (OUTLIER) cc_final: 0.8040 (pm20) REVERT: K 199 GLU cc_start: 0.7806 (mp0) cc_final: 0.7437 (mp0) REVERT: O 73 LYS cc_start: 0.8408 (mttp) cc_final: 0.8208 (mttp) REVERT: O 108 GLN cc_start: 0.8131 (mt0) cc_final: 0.7831 (mt0) REVERT: O 137 GLU cc_start: 0.8336 (OUTLIER) cc_final: 0.7906 (pm20) REVERT: O 199 GLU cc_start: 0.7666 (mp0) cc_final: 0.7045 (mp0) outliers start: 89 outliers final: 52 residues processed: 426 average time/residue: 1.3021 time to fit residues: 634.7696 Evaluate side-chains 435 residues out of total 2355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 370 time to evaluate : 2.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 28 VAL Chi-restraints excluded: chain 1 residue 30 THR Chi-restraints excluded: chain 1 residue 44 THR Chi-restraints excluded: chain 1 residue 47 THR Chi-restraints excluded: chain 1 residue 99 THR Chi-restraints excluded: chain 1 residue 108 SER Chi-restraints excluded: chain 1 residue 129 ARG Chi-restraints excluded: chain 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 3 residue 204 SER Chi-restraints excluded: chain 3 residue 217 VAL Chi-restraints excluded: chain 3 residue 221 ARG Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 108 SER Chi-restraints excluded: chain D residue 204 SER Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 43 LEU 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 108 SER Chi-restraints excluded: chain L residue 121 MET Chi-restraints excluded: chain L residue 206 SER Chi-restraints excluded: chain L residue 217 VAL Chi-restraints excluded: chain N residue 28 VAL Chi-restraints excluded: chain N residue 87 VAL Chi-restraints excluded: chain N residue 99 THR Chi-restraints excluded: chain N residue 105 MET Chi-restraints excluded: chain N residue 129 ARG Chi-restraints excluded: chain P residue 42 SER Chi-restraints excluded: chain P residue 204 SER Chi-restraints excluded: chain P residue 211 LEU Chi-restraints excluded: chain P residue 217 VAL Chi-restraints excluded: chain 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 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 137 GLU Chi-restraints excluded: chain K residue 158 ILE Chi-restraints excluded: chain K residue 188 THR 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: 4.9990 chunk 263 optimal weight: 0.8980 chunk 159 optimal weight: 0.8980 chunk 217 optimal weight: 1.9990 chunk 177 optimal weight: 0.9980 chunk 173 optimal weight: 0.9980 chunk 33 optimal weight: 0.6980 chunk 232 optimal weight: 0.9980 chunk 75 optimal weight: 2.9990 chunk 195 optimal weight: 5.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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 F 110 ASN J 110 ASN 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.162101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.112089 restraints weight = 28809.660| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 3.31 r_work: 0.3223 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.2322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 22445 Z= 0.204 Angle : 0.487 6.283 30585 Z= 0.252 Chirality : 0.042 0.182 3290 Planarity : 0.003 0.040 3970 Dihedral : 3.949 17.736 3005 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 3.06 % Allowed : 16.09 % Favored : 80.85 % 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: -1.88 (0.31), residues: 240 sheet: -0.74 (0.18), residues: 825 loop : -0.85 (0.16), residues: 1595 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP 3 149 HIS 0.004 0.001 HIS O 145 PHE 0.010 0.001 PHE 1 115 TYR 0.012 0.001 TYR K 79 ARG 0.005 0.000 ARG E 120 *********************** 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 463 residues out of total 2355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 391 time to evaluate : 2.417 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 45 ASN cc_start: 0.8824 (t0) cc_final: 0.8578 (t0) REVERT: 1 111 ASN cc_start: 0.8917 (m-40) cc_final: 0.8668 (m-40) REVERT: 1 129 ARG cc_start: 0.8002 (OUTLIER) cc_final: 0.7740 (mtp-110) REVERT: 2 82 GLU cc_start: 0.8255 (mp0) cc_final: 0.7875 (mp0) REVERT: 2 101 MET cc_start: 0.5218 (ptp) cc_final: 0.4762 (ptp) REVERT: 2 137 GLU cc_start: 0.8097 (pm20) cc_final: 0.7806 (pm20) REVERT: 2 199 GLU cc_start: 0.7933 (mp0) cc_final: 0.7453 (mp0) REVERT: 3 42 SER cc_start: 0.8895 (p) cc_final: 0.8372 (t) REVERT: 3 109 MET cc_start: 0.8695 (ttp) cc_final: 0.8124 (ttp) REVERT: 3 119 LYS cc_start: 0.8396 (mttt) cc_final: 0.8098 (mtmm) REVERT: 3 121 MET cc_start: 0.8222 (mtm) cc_final: 0.7562 (mtm) REVERT: 3 179 MET cc_start: 0.7341 (tpt) cc_final: 0.6375 (mpt) REVERT: 3 190 GLN cc_start: 0.8300 (pt0) cc_final: 0.6536 (pp30) REVERT: 3 221 ARG cc_start: 0.5850 (OUTLIER) cc_final: 0.5634 (mtp180) REVERT: B 43 LEU cc_start: 0.9088 (OUTLIER) cc_final: 0.8646 (pp) REVERT: B 45 ASN cc_start: 0.8761 (t0) cc_final: 0.8356 (t0) REVERT: B 92 ASN cc_start: 0.8407 (t0) cc_final: 0.8179 (t0) REVERT: B 124 ARG cc_start: 0.7739 (ttp-170) cc_final: 0.7433 (ttt-90) REVERT: D 11 TYR cc_start: 0.9283 (OUTLIER) cc_final: 0.8862 (m-80) REVERT: D 21 THR cc_start: 0.8363 (p) cc_final: 0.7922 (t) REVERT: D 42 SER cc_start: 0.8935 (p) cc_final: 0.8416 (t) REVERT: D 119 LYS cc_start: 0.8420 (mttt) cc_final: 0.8157 (mppt) REVERT: D 121 MET cc_start: 0.7292 (ttt) cc_final: 0.6744 (mmm) REVERT: D 179 MET cc_start: 0.7348 (tpt) cc_final: 0.6098 (mmt) REVERT: D 190 GLN cc_start: 0.8232 (pt0) cc_final: 0.6892 (pp30) REVERT: F 83 GLU cc_start: 0.6670 (pm20) cc_final: 0.6428 (pm20) REVERT: F 102 ASP cc_start: 0.8230 (p0) cc_final: 0.7988 (p0) REVERT: F 124 ARG cc_start: 0.7765 (ttp-170) cc_final: 0.7542 (ttp-170) REVERT: F 176 ASP cc_start: 0.7937 (t0) cc_final: 0.7638 (t0) REVERT: H 42 SER cc_start: 0.8770 (p) cc_final: 0.8283 (t) REVERT: H 119 LYS cc_start: 0.8564 (mttt) cc_final: 0.8360 (mppt) REVERT: H 121 MET cc_start: 0.7292 (ttt) cc_final: 0.6940 (mmm) REVERT: H 190 GLN cc_start: 0.8333 (pt0) cc_final: 0.6818 (pp30) REVERT: J 45 ASN cc_start: 0.8784 (t0) cc_final: 0.8276 (t0) REVERT: L 42 SER cc_start: 0.8704 (p) cc_final: 0.8208 (t) REVERT: L 119 LYS cc_start: 0.8351 (mttt) cc_final: 0.8107 (mppt) REVERT: L 121 MET cc_start: 0.7755 (OUTLIER) cc_final: 0.7427 (pmm) REVERT: L 179 MET cc_start: 0.7350 (tpt) cc_final: 0.6222 (mpt) REVERT: L 204 SER cc_start: 0.8991 (p) cc_final: 0.8607 (t) REVERT: N 45 ASN cc_start: 0.8349 (t0) cc_final: 0.8090 (t0) REVERT: N 92 ASN cc_start: 0.8267 (t0) cc_final: 0.7979 (t0) REVERT: N 105 MET cc_start: 0.8948 (OUTLIER) cc_final: 0.8436 (ttp) REVERT: N 111 ASN cc_start: 0.8922 (m-40) cc_final: 0.8681 (m110) REVERT: N 129 ARG cc_start: 0.7750 (OUTLIER) cc_final: 0.7236 (mtp-110) REVERT: P 15 GLN cc_start: 0.8145 (mt0) cc_final: 0.7806 (mt0) REVERT: P 86 LYS cc_start: 0.8074 (ttpt) cc_final: 0.7777 (ptmm) REVERT: P 179 MET cc_start: 0.7620 (tpt) cc_final: 0.7254 (tpp) REVERT: E 141 ILE cc_start: 0.8324 (mt) cc_final: 0.7945 (mm) REVERT: Q 141 ILE cc_start: 0.8361 (mt) cc_final: 0.8052 (mm) REVERT: C 79 TYR cc_start: 0.7522 (m-80) cc_final: 0.7186 (m-80) REVERT: C 101 MET cc_start: 0.5211 (ptp) cc_final: 0.4864 (ptp) REVERT: C 108 GLN cc_start: 0.8053 (mt0) cc_final: 0.7604 (mt0) REVERT: C 137 GLU cc_start: 0.8590 (OUTLIER) cc_final: 0.7995 (pm20) REVERT: C 182 MET cc_start: 0.7966 (ttp) cc_final: 0.7701 (ptm) REVERT: C 199 GLU cc_start: 0.7633 (mp0) cc_final: 0.7178 (mp0) REVERT: G 101 MET cc_start: 0.4844 (ptt) cc_final: 0.4027 (ptp) REVERT: G 102 ARG cc_start: 0.6099 (ttt180) cc_final: 0.5720 (tpp-160) REVERT: G 135 ARG cc_start: 0.8225 (mtm180) cc_final: 0.7923 (mtm-85) REVERT: G 137 GLU cc_start: 0.8322 (OUTLIER) cc_final: 0.7838 (pm20) REVERT: G 199 GLU cc_start: 0.7437 (mp0) cc_final: 0.6921 (mp0) REVERT: K 101 MET cc_start: 0.4659 (ptt) cc_final: 0.4022 (ptp) REVERT: K 128 GLU cc_start: 0.8775 (mt-10) cc_final: 0.7969 (mt-10) REVERT: K 137 GLU cc_start: 0.8567 (OUTLIER) cc_final: 0.8066 (pm20) REVERT: K 199 GLU cc_start: 0.7827 (mp0) cc_final: 0.7445 (mp0) REVERT: O 73 LYS cc_start: 0.8423 (mttp) cc_final: 0.8200 (mttp) REVERT: O 108 GLN cc_start: 0.8121 (mt0) cc_final: 0.7878 (mt0) REVERT: O 117 ASN cc_start: 0.8673 (OUTLIER) cc_final: 0.8420 (t0) REVERT: O 128 GLU cc_start: 0.8615 (mt-10) cc_final: 0.8410 (mt-10) REVERT: O 137 GLU cc_start: 0.8304 (OUTLIER) cc_final: 0.7865 (pm20) REVERT: O 199 GLU cc_start: 0.7642 (mp0) cc_final: 0.7022 (mp0) outliers start: 72 outliers final: 46 residues processed: 426 average time/residue: 1.3264 time to fit residues: 645.0311 Evaluate side-chains 431 residues out of total 2355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 373 time to evaluate : 2.457 ------------------------------------------------------------------------------- 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 108 SER Chi-restraints excluded: chain 1 residue 129 ARG Chi-restraints excluded: chain 1 residue 185 MET Chi-restraints excluded: chain 2 residue 106 ASP Chi-restraints excluded: chain 2 residue 136 GLU Chi-restraints excluded: chain 2 residue 141 SER Chi-restraints excluded: chain 2 residue 178 SER Chi-restraints excluded: chain 2 residue 188 THR Chi-restraints excluded: chain 3 residue 221 ARG Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 29 HIS 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 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 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 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 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 107 VAL Chi-restraints excluded: chain K residue 110 SER Chi-restraints excluded: chain K residue 137 GLU Chi-restraints excluded: chain K residue 188 THR Chi-restraints excluded: chain O residue 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 102 optimal weight: 2.9990 chunk 244 optimal weight: 0.3980 chunk 137 optimal weight: 2.9990 chunk 39 optimal weight: 6.9990 chunk 217 optimal weight: 4.9990 chunk 223 optimal weight: 4.9990 chunk 231 optimal weight: 1.9990 chunk 81 optimal weight: 6.9990 chunk 101 optimal weight: 0.1980 chunk 24 optimal weight: 4.9990 chunk 55 optimal weight: 0.8980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 110 ASN B 29 HIS B 110 ASN D 15 GLN F 110 ASN J 110 ASN ** L 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 92 ASN N 110 ASN ** 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.161201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.110967 restraints weight = 28902.269| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 3.32 r_work: 0.3209 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.2434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 22445 Z= 0.264 Angle : 0.511 6.158 30585 Z= 0.264 Chirality : 0.042 0.193 3290 Planarity : 0.004 0.044 3970 Dihedral : 4.028 18.013 3005 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 3.01 % Allowed : 16.94 % Favored : 80.04 % 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: -1.46 (0.17), residues: 2660 helix: -1.90 (0.31), residues: 240 sheet: -0.79 (0.18), residues: 825 loop : -0.86 (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 F 84 PHE 0.012 0.001 PHE 1 115 TYR 0.011 0.001 TYR H 11 ARG 0.006 0.000 ARG E 120 *********************** 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 456 residues out of total 2355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 385 time to evaluate : 2.302 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 45 ASN cc_start: 0.8878 (t0) cc_final: 0.8555 (t0) REVERT: 1 111 ASN cc_start: 0.8917 (m-40) cc_final: 0.8672 (m-40) REVERT: 2 82 GLU cc_start: 0.8269 (mp0) cc_final: 0.7881 (mp0) REVERT: 2 101 MET cc_start: 0.5397 (ptp) cc_final: 0.4984 (ptp) REVERT: 2 137 GLU cc_start: 0.8127 (pm20) cc_final: 0.7830 (pm20) REVERT: 2 199 GLU cc_start: 0.7941 (mp0) cc_final: 0.7454 (mp0) REVERT: 3 42 SER cc_start: 0.8928 (p) cc_final: 0.8381 (t) REVERT: 3 109 MET cc_start: 0.8681 (ttp) cc_final: 0.8110 (ttp) REVERT: 3 119 LYS cc_start: 0.8410 (mttt) cc_final: 0.8093 (mtmm) REVERT: 3 121 MET cc_start: 0.8330 (mtm) cc_final: 0.7547 (mpp) REVERT: 3 179 MET cc_start: 0.7327 (tpt) cc_final: 0.6241 (mmt) REVERT: 3 190 GLN cc_start: 0.8317 (pt0) cc_final: 0.6552 (pp30) REVERT: 3 221 ARG cc_start: 0.5906 (OUTLIER) cc_final: 0.5678 (mtp180) REVERT: B 43 LEU cc_start: 0.9089 (OUTLIER) cc_final: 0.8701 (pp) REVERT: B 45 ASN cc_start: 0.8778 (t0) cc_final: 0.8356 (t0) REVERT: D 21 THR cc_start: 0.8356 (p) cc_final: 0.7929 (t) REVERT: D 42 SER cc_start: 0.8948 (p) cc_final: 0.8430 (t) REVERT: D 119 LYS cc_start: 0.8436 (mttt) cc_final: 0.8161 (mppt) REVERT: D 121 MET cc_start: 0.7361 (ttt) cc_final: 0.6802 (mmm) REVERT: D 179 MET cc_start: 0.7357 (tpt) cc_final: 0.6985 (tpp) REVERT: D 190 GLN cc_start: 0.8273 (pt0) cc_final: 0.6895 (pp30) REVERT: F 83 GLU cc_start: 0.6754 (pm20) cc_final: 0.6512 (pm20) REVERT: F 102 ASP cc_start: 0.8282 (p0) cc_final: 0.8003 (p0) REVERT: F 176 ASP cc_start: 0.7968 (t0) cc_final: 0.7668 (t0) REVERT: H 42 SER cc_start: 0.8823 (p) cc_final: 0.8337 (t) REVERT: H 119 LYS cc_start: 0.8639 (mttt) cc_final: 0.8438 (mppt) REVERT: H 121 MET cc_start: 0.7351 (ttt) cc_final: 0.6999 (mmm) REVERT: H 190 GLN cc_start: 0.8385 (pt0) cc_final: 0.6913 (pp30) REVERT: J 43 LEU cc_start: 0.9126 (OUTLIER) cc_final: 0.8383 (pp) REVERT: J 45 ASN cc_start: 0.8821 (t0) cc_final: 0.8331 (t0) REVERT: L 42 SER cc_start: 0.8722 (p) cc_final: 0.8227 (t) REVERT: L 119 LYS cc_start: 0.8360 (mttt) cc_final: 0.8127 (mppt) REVERT: L 121 MET cc_start: 0.7833 (OUTLIER) cc_final: 0.7439 (pmm) REVERT: L 179 MET cc_start: 0.7417 (tpt) cc_final: 0.7156 (tpp) REVERT: L 204 SER cc_start: 0.8999 (p) cc_final: 0.8621 (t) REVERT: N 45 ASN cc_start: 0.8455 (t0) cc_final: 0.8168 (t0) REVERT: N 83 GLU cc_start: 0.6555 (pm20) cc_final: 0.6327 (pm20) REVERT: N 92 ASN cc_start: 0.8461 (t0) cc_final: 0.8163 (t0) REVERT: N 105 MET cc_start: 0.8958 (OUTLIER) cc_final: 0.8442 (ttp) REVERT: N 111 ASN cc_start: 0.8934 (m-40) cc_final: 0.8703 (m110) REVERT: N 129 ARG cc_start: 0.7782 (OUTLIER) cc_final: 0.7282 (mtp-110) REVERT: P 86 LYS cc_start: 0.8059 (ttpt) cc_final: 0.7823 (ptmt) REVERT: P 179 MET cc_start: 0.7644 (tpt) cc_final: 0.7285 (tpp) REVERT: M 141 ILE cc_start: 0.8443 (mt) cc_final: 0.8186 (mm) REVERT: Q 141 ILE cc_start: 0.8371 (mt) cc_final: 0.8064 (mm) REVERT: C 79 TYR cc_start: 0.7568 (m-80) cc_final: 0.7270 (m-80) REVERT: C 101 MET cc_start: 0.5313 (ptp) cc_final: 0.4970 (ptp) REVERT: C 108 GLN cc_start: 0.8061 (mt0) cc_final: 0.7600 (mt0) REVERT: C 137 GLU cc_start: 0.8606 (OUTLIER) cc_final: 0.8004 (pm20) REVERT: C 182 MET cc_start: 0.7993 (ttp) cc_final: 0.7664 (ptm) REVERT: C 199 GLU cc_start: 0.7627 (mp0) cc_final: 0.7161 (mp0) REVERT: G 101 MET cc_start: 0.4896 (ptt) cc_final: 0.4111 (ptp) REVERT: G 102 ARG cc_start: 0.6153 (ttt180) cc_final: 0.5701 (tpp-160) REVERT: G 135 ARG cc_start: 0.8248 (mtm180) cc_final: 0.7939 (mtm-85) REVERT: G 137 GLU cc_start: 0.8359 (OUTLIER) cc_final: 0.7892 (pm20) REVERT: G 199 GLU cc_start: 0.7461 (mp0) cc_final: 0.6934 (mp0) REVERT: K 101 MET cc_start: 0.4696 (ptt) cc_final: 0.4098 (ptp) REVERT: K 128 GLU cc_start: 0.8785 (mt-10) cc_final: 0.7941 (mt-10) REVERT: K 137 GLU cc_start: 0.8628 (OUTLIER) cc_final: 0.8156 (pm20) REVERT: K 199 GLU cc_start: 0.7825 (mp0) cc_final: 0.7423 (mp0) REVERT: O 108 GLN cc_start: 0.8135 (mt0) cc_final: 0.7818 (mt0) REVERT: O 137 GLU cc_start: 0.8308 (OUTLIER) cc_final: 0.7871 (pm20) REVERT: O 199 GLU cc_start: 0.7651 (mp0) cc_final: 0.7114 (mp0) outliers start: 71 outliers final: 50 residues processed: 418 average time/residue: 1.3409 time to fit residues: 638.3155 Evaluate side-chains 432 residues out of total 2355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 372 time to evaluate : 2.236 ------------------------------------------------------------------------------- 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 2 residue 204 ILE Chi-restraints excluded: chain 3 residue 204 SER Chi-restraints excluded: chain 3 residue 217 VAL Chi-restraints excluded: chain 3 residue 221 ARG Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 108 SER Chi-restraints excluded: chain D residue 204 SER Chi-restraints excluded: chain D residue 217 VAL Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 105 MET Chi-restraints excluded: chain F residue 108 SER Chi-restraints excluded: chain H residue 182 THR Chi-restraints excluded: chain H residue 204 SER Chi-restraints excluded: chain H residue 206 SER Chi-restraints excluded: chain J residue 28 VAL Chi-restraints excluded: chain J residue 43 LEU Chi-restraints excluded: chain J residue 108 SER Chi-restraints excluded: chain L residue 121 MET Chi-restraints excluded: chain L residue 206 SER Chi-restraints excluded: chain L residue 217 VAL Chi-restraints excluded: chain N residue 28 VAL Chi-restraints excluded: chain N residue 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 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 122 optimal weight: 0.0980 chunk 256 optimal weight: 0.0670 chunk 258 optimal weight: 0.8980 chunk 73 optimal weight: 0.9990 chunk 72 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 209 optimal weight: 4.9990 chunk 153 optimal weight: 0.8980 chunk 66 optimal weight: 0.4980 chunk 103 optimal weight: 2.9990 chunk 109 optimal weight: 4.9990 overall best weight: 0.4918 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** N 92 ASN 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** ** 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: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.163654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.113767 restraints weight = 28900.848| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 3.34 r_work: 0.3244 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.2494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 22445 Z= 0.155 Angle : 0.489 7.151 30585 Z= 0.253 Chirality : 0.041 0.189 3290 Planarity : 0.003 0.049 3970 Dihedral : 3.821 16.421 3005 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 2.59 % Allowed : 17.58 % Favored : 79.83 % 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: -1.82 (0.31), residues: 240 sheet: -0.67 (0.19), residues: 825 loop : -0.80 (0.16), residues: 1595 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP 3 149 HIS 0.007 0.001 HIS D 116 PHE 0.007 0.001 PHE 2 116 TYR 0.011 0.001 TYR H 11 ARG 0.006 0.000 ARG E 120 *********************** 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 445 residues out of total 2355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 384 time to evaluate : 2.957 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 45 ASN cc_start: 0.8851 (t0) cc_final: 0.8631 (t0) REVERT: 1 111 ASN cc_start: 0.8898 (m-40) cc_final: 0.8648 (m-40) REVERT: 2 82 GLU cc_start: 0.8280 (mp0) cc_final: 0.7885 (mp0) REVERT: 2 101 MET cc_start: 0.5505 (ptp) cc_final: 0.5074 (ptp) REVERT: 2 199 GLU cc_start: 0.7912 (mp0) cc_final: 0.7416 (mp0) REVERT: 3 42 SER cc_start: 0.8892 (p) cc_final: 0.8372 (t) REVERT: 3 109 MET cc_start: 0.8681 (ttp) cc_final: 0.8100 (ttp) REVERT: 3 119 LYS cc_start: 0.8423 (mttt) cc_final: 0.8104 (mtmm) REVERT: 3 121 MET cc_start: 0.8331 (mtm) cc_final: 0.7538 (mpp) REVERT: 3 179 MET cc_start: 0.7269 (tpt) cc_final: 0.6294 (mpt) REVERT: B 43 LEU cc_start: 0.9008 (OUTLIER) cc_final: 0.8585 (pp) REVERT: B 45 ASN cc_start: 0.8751 (t0) cc_final: 0.8341 (t0) REVERT: B 124 ARG cc_start: 0.7735 (ttp-170) cc_final: 0.7468 (ttt-90) REVERT: D 11 TYR cc_start: 0.9272 (OUTLIER) cc_final: 0.8835 (m-80) REVERT: D 15 GLN cc_start: 0.7932 (mt0) cc_final: 0.7429 (mt0) REVERT: D 21 THR cc_start: 0.8350 (p) cc_final: 0.7922 (t) REVERT: D 42 SER cc_start: 0.8937 (p) cc_final: 0.8429 (t) REVERT: D 115 HIS cc_start: 0.8538 (p90) cc_final: 0.8157 (p90) REVERT: D 119 LYS cc_start: 0.8432 (mttt) cc_final: 0.8151 (mppt) REVERT: D 121 MET cc_start: 0.7319 (ttt) cc_final: 0.6772 (mmm) REVERT: D 179 MET cc_start: 0.7302 (tpt) cc_final: 0.6115 (mpt) REVERT: D 190 GLN cc_start: 0.8275 (pt0) cc_final: 0.6847 (pp30) REVERT: F 83 GLU cc_start: 0.6759 (pm20) cc_final: 0.6456 (pm20) REVERT: F 102 ASP cc_start: 0.8204 (p0) cc_final: 0.7892 (p0) REVERT: F 124 ARG cc_start: 0.7786 (ttp-170) cc_final: 0.7585 (ttp-170) REVERT: F 176 ASP cc_start: 0.7958 (t0) cc_final: 0.7659 (t0) REVERT: H 42 SER cc_start: 0.8766 (p) cc_final: 0.8274 (t) REVERT: H 121 MET cc_start: 0.7327 (ttt) cc_final: 0.6981 (mmm) REVERT: H 149 TRP cc_start: 0.6003 (p-90) cc_final: 0.5753 (p-90) REVERT: H 190 GLN cc_start: 0.8439 (pt0) cc_final: 0.6872 (pp30) REVERT: J 43 LEU cc_start: 0.9068 (OUTLIER) cc_final: 0.8264 (pp) REVERT: J 45 ASN cc_start: 0.8807 (t0) cc_final: 0.8312 (t0) REVERT: J 101 ARG cc_start: 0.7873 (OUTLIER) cc_final: 0.7267 (ptt90) REVERT: L 42 SER cc_start: 0.8679 (p) cc_final: 0.8176 (t) REVERT: L 119 LYS cc_start: 0.8375 (mttt) cc_final: 0.8131 (mppt) REVERT: L 121 MET cc_start: 0.7816 (OUTLIER) cc_final: 0.7408 (pmm) REVERT: L 179 MET cc_start: 0.7318 (tpt) cc_final: 0.6097 (mpt) REVERT: L 204 SER cc_start: 0.8975 (p) cc_final: 0.8609 (t) REVERT: N 28 VAL cc_start: 0.8573 (OUTLIER) cc_final: 0.8326 (p) REVERT: N 45 ASN cc_start: 0.8378 (t0) cc_final: 0.8070 (t0) REVERT: N 105 MET cc_start: 0.8909 (OUTLIER) cc_final: 0.8390 (ttp) REVERT: N 111 ASN cc_start: 0.8910 (m-40) cc_final: 0.8651 (m110) REVERT: N 129 ARG cc_start: 0.7698 (OUTLIER) cc_final: 0.7234 (mtp-110) REVERT: P 15 GLN cc_start: 0.8074 (mt0) cc_final: 0.7765 (mt0) REVERT: P 86 LYS cc_start: 0.8055 (ttpt) cc_final: 0.7790 (ptmm) REVERT: P 179 MET cc_start: 0.7523 (tpt) cc_final: 0.7186 (tpp) REVERT: Q 120 ARG cc_start: 0.7780 (OUTLIER) cc_final: 0.7260 (ttm-80) REVERT: C 79 TYR cc_start: 0.7577 (m-80) cc_final: 0.7243 (m-80) REVERT: C 101 MET cc_start: 0.5095 (ptp) cc_final: 0.4782 (ptp) REVERT: C 108 GLN cc_start: 0.8052 (mt0) cc_final: 0.7589 (mt0) REVERT: C 137 GLU cc_start: 0.8599 (OUTLIER) cc_final: 0.7997 (pm20) REVERT: C 182 MET cc_start: 0.7939 (ttp) cc_final: 0.7715 (ptm) REVERT: C 199 GLU cc_start: 0.7656 (mp0) cc_final: 0.7154 (mp0) REVERT: G 101 MET cc_start: 0.4855 (ptt) cc_final: 0.4202 (ptp) REVERT: G 102 ARG cc_start: 0.6094 (ttt180) cc_final: 0.5633 (tpp-160) REVERT: G 108 GLN cc_start: 0.8022 (mt0) cc_final: 0.7610 (tp40) REVERT: G 135 ARG cc_start: 0.8225 (mtm180) cc_final: 0.7911 (mtm-85) REVERT: G 137 GLU cc_start: 0.8344 (OUTLIER) cc_final: 0.7867 (pm20) REVERT: G 199 GLU cc_start: 0.7453 (mp0) cc_final: 0.6933 (mp0) REVERT: K 79 TYR cc_start: 0.7204 (m-80) cc_final: 0.6957 (m-10) REVERT: K 101 MET cc_start: 0.4873 (ptt) cc_final: 0.4287 (ptp) REVERT: K 102 ARG cc_start: 0.5880 (ttt180) cc_final: 0.5376 (tpp-160) REVERT: K 128 GLU cc_start: 0.8770 (mt-10) cc_final: 0.7940 (mt-10) REVERT: K 137 GLU cc_start: 0.8567 (OUTLIER) cc_final: 0.8078 (pm20) REVERT: K 199 GLU cc_start: 0.7798 (mp0) cc_final: 0.7391 (mp0) REVERT: O 108 GLN cc_start: 0.8102 (mt0) cc_final: 0.7850 (mt0) REVERT: O 137 GLU cc_start: 0.8292 (OUTLIER) cc_final: 0.7834 (pm20) REVERT: O 199 GLU cc_start: 0.7783 (mp0) cc_final: 0.7335 (mp0) outliers start: 61 outliers final: 41 residues processed: 413 average time/residue: 1.3645 time to fit residues: 643.2715 Evaluate side-chains 422 residues out of total 2355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 368 time to evaluate : 2.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 101 ARG Chi-restraints excluded: chain J residue 108 SER Chi-restraints excluded: chain L residue 121 MET Chi-restraints excluded: chain L residue 206 SER Chi-restraints excluded: chain L residue 217 VAL Chi-restraints excluded: chain N residue 28 VAL Chi-restraints excluded: chain N residue 43 LEU 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 A residue 120 ARG Chi-restraints excluded: chain I residue 120 ARG Chi-restraints excluded: chain Q residue 120 ARG Chi-restraints excluded: chain C residue 137 GLU 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 107 VAL Chi-restraints excluded: chain K residue 110 SER Chi-restraints excluded: chain K residue 137 GLU Chi-restraints excluded: chain K residue 188 THR Chi-restraints excluded: chain O residue 110 SER Chi-restraints excluded: chain O residue 137 GLU Chi-restraints excluded: chain O residue 188 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 78 optimal weight: 2.9990 chunk 228 optimal weight: 4.9990 chunk 51 optimal weight: 0.9990 chunk 135 optimal weight: 2.9990 chunk 143 optimal weight: 3.9990 chunk 3 optimal weight: 4.9990 chunk 224 optimal weight: 10.0000 chunk 136 optimal weight: 7.9990 chunk 187 optimal weight: 2.9990 chunk 239 optimal weight: 10.0000 chunk 41 optimal weight: 0.0070 overall best weight: 2.0006 ------------------------------------------------------------------------------- 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 29 HIS B 110 ASN ** D 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 110 ASN J 110 ASN L 56 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** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.159957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.109194 restraints weight = 28935.768| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 3.32 r_work: 0.3184 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.2626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 22445 Z= 0.383 Angle : 0.563 6.800 30585 Z= 0.292 Chirality : 0.044 0.182 3290 Planarity : 0.004 0.034 3970 Dihedral : 4.194 19.003 3005 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 2.93 % Allowed : 17.54 % Favored : 79.53 % 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: -1.89 (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 0.034 0.002 TRP 3 149 HIS 0.005 0.001 HIS C 145 PHE 0.016 0.002 PHE N 115 TYR 0.011 0.002 TYR K 79 ARG 0.004 0.000 ARG B 101 *********************** 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 441 residues out of total 2355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 372 time to evaluate : 2.519 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 43 LEU cc_start: 0.9238 (OUTLIER) cc_final: 0.8969 (pt) REVERT: 1 45 ASN cc_start: 0.8918 (t0) cc_final: 0.8643 (t0) REVERT: 1 111 ASN cc_start: 0.8936 (m-40) cc_final: 0.8691 (m-40) REVERT: 2 82 GLU cc_start: 0.8300 (mp0) cc_final: 0.7956 (mp0) REVERT: 2 101 MET cc_start: 0.5720 (ptp) cc_final: 0.5320 (ptp) REVERT: 2 137 GLU cc_start: 0.8179 (pm20) cc_final: 0.7875 (pm20) REVERT: 2 199 GLU cc_start: 0.7958 (mp0) cc_final: 0.7454 (mp0) REVERT: 3 42 SER cc_start: 0.8955 (p) cc_final: 0.8414 (t) REVERT: 3 109 MET cc_start: 0.8693 (ttp) cc_final: 0.8122 (ttp) REVERT: 3 119 LYS cc_start: 0.8426 (mttt) cc_final: 0.8146 (mtmm) REVERT: 3 121 MET cc_start: 0.8448 (mtm) cc_final: 0.7806 (mtm) REVERT: 3 179 MET cc_start: 0.7381 (tpt) cc_final: 0.6437 (mpt) REVERT: B 43 LEU cc_start: 0.9118 (OUTLIER) cc_final: 0.8761 (pp) REVERT: B 45 ASN cc_start: 0.8819 (t0) cc_final: 0.8404 (t0) REVERT: B 124 ARG cc_start: 0.7765 (ttp-170) cc_final: 0.7563 (ttp-110) REVERT: B 176 ASP cc_start: 0.8146 (t0) cc_final: 0.7907 (t0) REVERT: D 11 TYR cc_start: 0.9323 (OUTLIER) cc_final: 0.8973 (m-80) REVERT: D 21 THR cc_start: 0.8362 (p) cc_final: 0.7911 (t) REVERT: D 42 SER cc_start: 0.8969 (p) cc_final: 0.8452 (t) REVERT: D 115 HIS cc_start: 0.8584 (p90) cc_final: 0.8347 (p90) REVERT: D 119 LYS cc_start: 0.8436 (mttt) cc_final: 0.8176 (mppt) REVERT: D 121 MET cc_start: 0.7442 (ttt) cc_final: 0.6854 (mmm) REVERT: D 179 MET cc_start: 0.7380 (tpt) cc_final: 0.7019 (tpp) REVERT: D 190 GLN cc_start: 0.8320 (pt0) cc_final: 0.6992 (pp30) REVERT: F 83 GLU cc_start: 0.6860 (pm20) cc_final: 0.6637 (pm20) REVERT: F 102 ASP cc_start: 0.8340 (p0) cc_final: 0.8080 (p0) REVERT: F 124 ARG cc_start: 0.7785 (ttp-170) cc_final: 0.7574 (ttp-170) REVERT: F 176 ASP cc_start: 0.7986 (t0) cc_final: 0.7682 (t0) REVERT: H 42 SER cc_start: 0.8862 (p) cc_final: 0.8378 (t) REVERT: H 121 MET cc_start: 0.7451 (ttt) cc_final: 0.7038 (mmm) REVERT: H 190 GLN cc_start: 0.8474 (pt0) cc_final: 0.6925 (pp30) REVERT: J 45 ASN cc_start: 0.8876 (t0) cc_final: 0.8381 (t0) REVERT: J 101 ARG cc_start: 0.7817 (OUTLIER) cc_final: 0.7376 (ptt-90) REVERT: J 108 SER cc_start: 0.9331 (OUTLIER) cc_final: 0.8958 (p) REVERT: J 124 ARG cc_start: 0.7740 (ttp-170) cc_final: 0.7395 (ttt-90) REVERT: L 15 GLN cc_start: 0.8260 (mt0) cc_final: 0.7932 (mt0) REVERT: L 42 SER cc_start: 0.8765 (p) cc_final: 0.8272 (t) REVERT: L 119 LYS cc_start: 0.8378 (mttt) cc_final: 0.8157 (mppt) REVERT: L 121 MET cc_start: 0.7914 (OUTLIER) cc_final: 0.7514 (pmm) REVERT: L 179 MET cc_start: 0.7463 (tpt) cc_final: 0.7197 (tpp) REVERT: L 204 SER cc_start: 0.8799 (p) cc_final: 0.8429 (t) REVERT: N 45 ASN cc_start: 0.8619 (t0) cc_final: 0.8317 (t0) REVERT: N 105 MET cc_start: 0.8950 (OUTLIER) cc_final: 0.8495 (ttp) REVERT: N 111 ASN cc_start: 0.8948 (m-40) cc_final: 0.8720 (m110) REVERT: N 129 ARG cc_start: 0.7757 (OUTLIER) cc_final: 0.7305 (mtp-110) REVERT: P 86 LYS cc_start: 0.8104 (ttpt) cc_final: 0.7729 (ptmt) REVERT: P 179 MET cc_start: 0.7656 (tpt) cc_final: 0.7310 (tpp) REVERT: A 131 CYS cc_start: 0.5889 (m) cc_final: 0.5448 (m) REVERT: M 117 TYR cc_start: 0.7990 (m-80) cc_final: 0.7526 (m-80) REVERT: M 141 ILE cc_start: 0.8479 (mt) cc_final: 0.8243 (mm) REVERT: Q 120 ARG cc_start: 0.7853 (OUTLIER) cc_final: 0.7257 (ttm-80) REVERT: Q 141 ILE cc_start: 0.8416 (mt) cc_final: 0.8098 (mm) REVERT: C 79 TYR cc_start: 0.7649 (m-80) cc_final: 0.7293 (m-80) REVERT: C 101 MET cc_start: 0.5452 (ptp) cc_final: 0.5155 (ptp) REVERT: C 108 GLN cc_start: 0.8101 (mt0) cc_final: 0.7833 (mt0) REVERT: C 137 GLU cc_start: 0.8632 (OUTLIER) cc_final: 0.8055 (pm20) REVERT: C 182 MET cc_start: 0.8049 (ttp) cc_final: 0.7775 (ptm) REVERT: C 199 GLU cc_start: 0.7679 (mp0) cc_final: 0.7167 (mp0) REVERT: G 101 MET cc_start: 0.5180 (ptt) cc_final: 0.4560 (ptp) REVERT: G 108 GLN cc_start: 0.8072 (mt0) cc_final: 0.7596 (tp40) REVERT: G 135 ARG cc_start: 0.8270 (mtm180) cc_final: 0.7957 (mtm-85) REVERT: G 137 GLU cc_start: 0.8384 (OUTLIER) cc_final: 0.7923 (pm20) REVERT: G 199 GLU cc_start: 0.7467 (mp0) cc_final: 0.6940 (mp0) REVERT: K 79 TYR cc_start: 0.7260 (m-80) cc_final: 0.6996 (m-80) REVERT: K 101 MET cc_start: 0.4985 (ptt) cc_final: 0.4475 (ptp) REVERT: K 137 GLU cc_start: 0.8630 (OUTLIER) cc_final: 0.8158 (pm20) REVERT: K 199 GLU cc_start: 0.7798 (mp0) cc_final: 0.7401 (mp0) REVERT: O 101 MET cc_start: 0.4918 (ptt) cc_final: 0.4422 (ptp) REVERT: O 108 GLN cc_start: 0.8158 (mt0) cc_final: 0.7947 (mt0) REVERT: O 137 GLU cc_start: 0.8367 (OUTLIER) cc_final: 0.7940 (pm20) REVERT: O 199 GLU cc_start: 0.7844 (mp0) cc_final: 0.7390 (mp0) outliers start: 69 outliers final: 42 residues processed: 405 average time/residue: 1.4051 time to fit residues: 646.3807 Evaluate side-chains 418 residues out of total 2355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 363 time to evaluate : 2.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 30 THR Chi-restraints excluded: chain 1 residue 43 LEU Chi-restraints excluded: chain 1 residue 44 THR Chi-restraints excluded: chain 1 residue 47 THR Chi-restraints excluded: chain 1 residue 108 SER Chi-restraints excluded: chain 1 residue 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 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 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 J residue 108 SER 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 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 204 SER Chi-restraints excluded: chain A residue 120 ARG Chi-restraints excluded: chain I residue 120 ARG 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 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 107 VAL Chi-restraints excluded: chain K residue 110 SER Chi-restraints excluded: chain K residue 137 GLU Chi-restraints excluded: chain K residue 188 THR Chi-restraints excluded: chain O residue 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 245 optimal weight: 0.7980 chunk 62 optimal weight: 0.8980 chunk 180 optimal weight: 0.9980 chunk 249 optimal weight: 0.7980 chunk 86 optimal weight: 0.7980 chunk 182 optimal weight: 3.9990 chunk 151 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 69 optimal weight: 0.3980 chunk 33 optimal weight: 1.9990 chunk 75 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 ** 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** ** O 149 ASN ** 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 = 0.4060 r_free = 0.4060 target = 0.162512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.112330 restraints weight = 28979.303| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 3.32 r_work: 0.3229 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.2645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 22445 Z= 0.188 Angle : 0.509 7.483 30585 Z= 0.263 Chirality : 0.042 0.176 3290 Planarity : 0.003 0.034 3970 Dihedral : 3.967 17.452 3005 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 2.42 % Allowed : 18.47 % 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: -1.42 (0.17), residues: 2660 helix: -1.86 (0.31), residues: 240 sheet: -0.78 (0.19), residues: 825 loop : -0.83 (0.16), residues: 1595 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP D 149 HIS 0.004 0.001 HIS O 145 PHE 0.009 0.001 PHE 3 213 TYR 0.011 0.001 TYR H 11 ARG 0.008 0.000 ARG E 120 ********************** 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 433 residues out of total 2355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 376 time to evaluate : 2.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 45 ASN cc_start: 0.8899 (t0) cc_final: 0.8637 (t0) REVERT: 1 111 ASN cc_start: 0.8919 (m-40) cc_final: 0.8675 (m-40) REVERT: 2 82 GLU cc_start: 0.8297 (mp0) cc_final: 0.7904 (mp0) REVERT: 2 101 MET cc_start: 0.6023 (ptp) cc_final: 0.5696 (ptp) REVERT: 2 108 GLN cc_start: 0.7530 (mm110) cc_final: 0.7002 (mm-40) REVERT: 2 199 GLU cc_start: 0.7962 (mp0) cc_final: 0.7473 (mp0) REVERT: 3 42 SER cc_start: 0.8901 (p) cc_final: 0.8378 (t) REVERT: 3 109 MET cc_start: 0.8700 (ttp) cc_final: 0.8122 (ttp) REVERT: 3 119 LYS cc_start: 0.8424 (mttt) cc_final: 0.8112 (mtmm) REVERT: 3 121 MET cc_start: 0.8367 (mtm) cc_final: 0.7643 (mpp) REVERT: 3 179 MET cc_start: 0.7324 (tpt) cc_final: 0.6359 (mpt) REVERT: B 43 LEU cc_start: 0.9048 (OUTLIER) cc_final: 0.8642 (pp) REVERT: B 45 ASN cc_start: 0.8792 (t0) cc_final: 0.8380 (t0) REVERT: D 11 TYR cc_start: 0.9280 (OUTLIER) cc_final: 0.8845 (m-80) REVERT: D 15 GLN cc_start: 0.7934 (mt0) cc_final: 0.7424 (mt0) REVERT: D 21 THR cc_start: 0.8357 (p) cc_final: 0.7944 (t) REVERT: D 42 SER cc_start: 0.8938 (p) cc_final: 0.8420 (t) REVERT: D 115 HIS cc_start: 0.8587 (p90) cc_final: 0.8353 (p90) REVERT: D 119 LYS cc_start: 0.8428 (mttt) cc_final: 0.8168 (mppt) REVERT: D 121 MET cc_start: 0.7456 (ttt) cc_final: 0.6849 (mmm) REVERT: D 179 MET cc_start: 0.7326 (tpt) cc_final: 0.7003 (tpp) REVERT: D 190 GLN cc_start: 0.8315 (pt0) cc_final: 0.6965 (pp30) REVERT: F 83 GLU cc_start: 0.6829 (pm20) cc_final: 0.6612 (pm20) REVERT: F 102 ASP cc_start: 0.8257 (p0) cc_final: 0.7975 (p0) REVERT: F 124 ARG cc_start: 0.7778 (ttp-170) cc_final: 0.7558 (ttp-170) REVERT: F 176 ASP cc_start: 0.7977 (t0) cc_final: 0.7672 (t0) REVERT: H 42 SER cc_start: 0.8775 (p) cc_final: 0.8282 (t) REVERT: H 190 GLN cc_start: 0.8536 (pt0) cc_final: 0.6873 (pp30) REVERT: J 45 ASN cc_start: 0.8860 (t0) cc_final: 0.8389 (t0) REVERT: J 101 ARG cc_start: 0.7862 (OUTLIER) cc_final: 0.7242 (ptt90) REVERT: J 124 ARG cc_start: 0.7734 (ttp-170) cc_final: 0.7408 (ttt-90) REVERT: L 42 SER cc_start: 0.8693 (p) cc_final: 0.8194 (t) REVERT: L 119 LYS cc_start: 0.8381 (mttt) cc_final: 0.8150 (mppt) REVERT: L 121 MET cc_start: 0.7881 (OUTLIER) cc_final: 0.7461 (pmm) REVERT: L 179 MET cc_start: 0.7437 (tpt) cc_final: 0.6163 (mpt) REVERT: L 204 SER cc_start: 0.8983 (p) cc_final: 0.8617 (t) REVERT: N 28 VAL cc_start: 0.8613 (OUTLIER) cc_final: 0.8360 (p) REVERT: N 45 ASN cc_start: 0.8566 (t0) cc_final: 0.8263 (t0) REVERT: N 105 MET cc_start: 0.8940 (OUTLIER) cc_final: 0.8427 (ttp) REVERT: N 111 ASN cc_start: 0.8922 (m-40) cc_final: 0.8686 (m110) REVERT: N 129 ARG cc_start: 0.7712 (OUTLIER) cc_final: 0.7226 (mtp-110) REVERT: P 15 GLN cc_start: 0.8088 (mt0) cc_final: 0.7743 (mt0) REVERT: P 86 LYS cc_start: 0.8097 (ttpt) cc_final: 0.7754 (ptmm) REVERT: P 179 MET cc_start: 0.7588 (tpt) cc_final: 0.7253 (tpp) REVERT: E 120 ARG cc_start: 0.8535 (ttm110) cc_final: 0.8032 (ttm-80) REVERT: M 117 TYR cc_start: 0.8012 (m-80) cc_final: 0.7632 (m-80) REVERT: C 79 TYR cc_start: 0.7628 (m-80) cc_final: 0.7337 (m-80) REVERT: C 101 MET cc_start: 0.5540 (ptp) cc_final: 0.5165 (ptp) REVERT: C 102 ARG cc_start: 0.6257 (ttt180) cc_final: 0.5638 (tpp-160) REVERT: C 137 GLU cc_start: 0.8603 (OUTLIER) cc_final: 0.8003 (pm20) REVERT: C 182 MET cc_start: 0.7960 (ttp) cc_final: 0.7669 (ptm) REVERT: C 199 GLU cc_start: 0.7688 (mp0) cc_final: 0.7101 (mp0) REVERT: G 101 MET cc_start: 0.5393 (ptt) cc_final: 0.4727 (ptp) REVERT: G 108 GLN cc_start: 0.8009 (mt0) cc_final: 0.7601 (tp40) REVERT: G 135 ARG cc_start: 0.8252 (mtm180) cc_final: 0.7930 (mtm-85) REVERT: G 137 GLU cc_start: 0.8362 (OUTLIER) cc_final: 0.7897 (pm20) REVERT: G 199 GLU cc_start: 0.7484 (mp0) cc_final: 0.7035 (mp0) REVERT: K 79 TYR cc_start: 0.7328 (m-80) cc_final: 0.7089 (m-80) REVERT: K 101 MET cc_start: 0.5234 (ptt) cc_final: 0.4767 (ptp) REVERT: K 108 GLN cc_start: 0.7420 (mm110) cc_final: 0.6914 (mm-40) REVERT: K 128 GLU cc_start: 0.8734 (mt-10) cc_final: 0.7990 (mt-10) REVERT: K 137 GLU cc_start: 0.8594 (OUTLIER) cc_final: 0.8108 (pm20) REVERT: O 79 TYR cc_start: 0.7403 (m-80) cc_final: 0.6918 (m-80) REVERT: O 101 MET cc_start: 0.5184 (ptt) cc_final: 0.4639 (ptp) REVERT: O 108 GLN cc_start: 0.8094 (mt0) cc_final: 0.7853 (mt0) REVERT: O 137 GLU cc_start: 0.8341 (OUTLIER) cc_final: 0.7885 (pm20) REVERT: O 199 GLU cc_start: 0.7876 (mp0) cc_final: 0.7409 (mp0) outliers start: 57 outliers final: 37 residues processed: 405 average time/residue: 1.3514 time to fit residues: 626.2637 Evaluate side-chains 415 residues out of total 2355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 367 time to evaluate : 2.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 D residue 217 VAL Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 105 MET Chi-restraints excluded: chain F residue 108 SER Chi-restraints excluded: chain H residue 182 THR Chi-restraints excluded: chain H residue 204 SER Chi-restraints excluded: chain H residue 206 SER Chi-restraints excluded: chain J residue 28 VAL Chi-restraints excluded: chain J residue 101 ARG Chi-restraints excluded: chain J residue 108 SER Chi-restraints excluded: chain L residue 121 MET Chi-restraints excluded: chain L residue 206 SER Chi-restraints excluded: chain L residue 217 VAL Chi-restraints excluded: chain N residue 28 VAL Chi-restraints excluded: chain N residue 87 VAL Chi-restraints excluded: chain N residue 99 THR Chi-restraints excluded: chain N residue 105 MET Chi-restraints excluded: chain N residue 129 ARG Chi-restraints excluded: chain P residue 42 SER Chi-restraints excluded: chain P residue 204 SER Chi-restraints excluded: chain A residue 120 ARG 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 137 GLU Chi-restraints excluded: chain G residue 178 SER Chi-restraints excluded: chain K residue 110 SER Chi-restraints excluded: chain K residue 137 GLU Chi-restraints excluded: chain K residue 188 THR Chi-restraints excluded: chain O residue 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 4 optimal weight: 2.9990 chunk 191 optimal weight: 6.9990 chunk 21 optimal weight: 0.0040 chunk 157 optimal weight: 5.9990 chunk 237 optimal weight: 6.9990 chunk 177 optimal weight: 0.8980 chunk 122 optimal weight: 2.9990 chunk 216 optimal weight: 0.0370 chunk 101 optimal weight: 2.9990 chunk 165 optimal weight: 3.9990 chunk 233 optimal weight: 0.8980 overall best weight: 0.9672 ------------------------------------------------------------------------------- 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 116 HIS F 45 ASN F 110 ASN J 110 ASN L 115 HIS N 110 ASN P 173 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.162389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.112099 restraints weight = 28856.481| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 3.33 r_work: 0.3220 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.2718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 22445 Z= 0.219 Angle : 0.515 7.250 30585 Z= 0.265 Chirality : 0.042 0.180 3290 Planarity : 0.004 0.032 3970 Dihedral : 3.960 17.290 3005 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 2.42 % Allowed : 18.64 % Favored : 78.94 % 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: -1.40 (0.17), residues: 2660 helix: -1.84 (0.31), residues: 240 sheet: -0.68 (0.19), residues: 800 loop : -0.87 (0.16), residues: 1620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP D 149 HIS 0.004 0.001 HIS O 145 PHE 0.011 0.001 PHE 1 115 TYR 0.012 0.001 TYR N 183 ARG 0.006 0.000 ARG E 120 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14623.75 seconds wall clock time: 263 minutes 2.23 seconds (15782.23 seconds total)