Starting phenix.real_space_refine on Thu Feb 15 05:20:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vqr_21355/02_2024/6vqr_21355_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vqr_21355/02_2024/6vqr_21355.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.78 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vqr_21355/02_2024/6vqr_21355.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vqr_21355/02_2024/6vqr_21355.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vqr_21355/02_2024/6vqr_21355_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vqr_21355/02_2024/6vqr_21355_updated.pdb" } resolution = 2.78 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.312 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 70 5.16 5 C 7482 2.51 5 N 1744 2.21 5 O 1933 1.98 5 F 25 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 283": "OE1" <-> "OE2" Residue "A GLU 289": "OE1" <-> "OE2" Residue "B GLU 22": "OE1" <-> "OE2" Residue "B GLU 30": "OE1" <-> "OE2" Residue "B GLU 162": "OE1" <-> "OE2" Residue "B GLU 175": "OE1" <-> "OE2" Residue "B GLU 289": "OE1" <-> "OE2" Residue "C PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 22": "OE1" <-> "OE2" Residue "D GLU 175": "OE1" <-> "OE2" Residue "D GLU 283": "OE1" <-> "OE2" Residue "D GLU 289": "OE1" <-> "OE2" Residue "E GLU 22": "OE1" <-> "OE2" Residue "E GLU 30": "OE1" <-> "OE2" Residue "E GLU 75": "OE1" <-> "OE2" Residue "E GLU 283": "OE1" <-> "OE2" Residue "E GLU 289": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 11254 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 2205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2205 Classifications: {'peptide': 281} Link IDs: {'PTRANS': 3, 'TRANS': 277} Chain: "B" Number of atoms: 2240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2240 Classifications: {'peptide': 285} Link IDs: {'PTRANS': 3, 'TRANS': 281} Chain: "C" Number of atoms: 2213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 2213 Classifications: {'peptide': 282} Link IDs: {'PTRANS': 4, 'TRANS': 277} Chain: "D" Number of atoms: 2228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2228 Classifications: {'peptide': 284} Link IDs: {'PTRANS': 4, 'TRANS': 279} Chain: "E" Number of atoms: 2263 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2263 Classifications: {'peptide': 288} Link IDs: {'PTRANS': 4, 'TRANS': 283} Chain: "A" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 21 Unusual residues: {'R7M': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 21 Unusual residues: {'R7M': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 21 Unusual residues: {'R7M': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 21 Unusual residues: {'R7M': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 21 Unusual residues: {'R7M': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.11, per 1000 atoms: 0.54 Number of scatterers: 11254 At special positions: 0 Unit cell: (90.72, 99.36, 97.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 70 16.00 F 25 9.00 O 1933 8.00 N 1744 7.00 C 7482 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.40 Conformation dependent library (CDL) restraints added in 2.2 seconds 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2620 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 68 helices and 0 sheets defined 72.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.04 Creating SS restraints... Processing helix chain 'A' and resid 22 through 37 removed outlier: 4.037A pdb=" N LYS A 35 " --> pdb=" O TYR A 31 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N ALA A 36 " --> pdb=" O GLY A 32 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N HIS A 37 " --> pdb=" O LYS A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 40 through 67 removed outlier: 3.726A pdb=" N LEU A 44 " --> pdb=" O ASN A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 77 removed outlier: 3.722A pdb=" N GLU A 75 " --> pdb=" O HIS A 71 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ILE A 76 " --> pdb=" O LYS A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 100 removed outlier: 3.777A pdb=" N PHE A 84 " --> pdb=" O SER A 80 " (cutoff:3.500A) Proline residue: A 91 - end of helix removed outlier: 5.221A pdb=" N PHE A 94 " --> pdb=" O PHE A 90 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N MET A 95 " --> pdb=" O PRO A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 118 removed outlier: 4.063A pdb=" N LEU A 110 " --> pdb=" O THR A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 147 removed outlier: 3.664A pdb=" N PHE A 146 " --> pdb=" O VAL A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 176 removed outlier: 3.910A pdb=" N LEU A 170 " --> pdb=" O PHE A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 205 removed outlier: 3.663A pdb=" N LEU A 204 " --> pdb=" O VAL A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 225 Processing helix chain 'A' and resid 231 through 243 Processing helix chain 'A' and resid 250 through 254 Processing helix chain 'A' and resid 258 through 270 Processing helix chain 'A' and resid 275 through 280 Processing helix chain 'A' and resid 282 through 290 removed outlier: 3.993A pdb=" N TYR A 286 " --> pdb=" O LYS A 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 22 through 36 removed outlier: 3.990A pdb=" N LYS B 35 " --> pdb=" O TYR B 31 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N ALA B 36 " --> pdb=" O GLY B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 67 Processing helix chain 'B' and resid 71 through 77 removed outlier: 3.775A pdb=" N GLU B 75 " --> pdb=" O HIS B 71 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N ILE B 76 " --> pdb=" O LYS B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 100 Proline residue: B 91 - end of helix removed outlier: 5.201A pdb=" N PHE B 94 " --> pdb=" O PHE B 90 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N MET B 95 " --> pdb=" O PRO B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 117 removed outlier: 4.526A pdb=" N LEU B 110 " --> pdb=" O THR B 106 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA B 111 " --> pdb=" O GLY B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 147 Processing helix chain 'B' and resid 165 through 177 removed outlier: 4.024A pdb=" N LEU B 170 " --> pdb=" O PHE B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 206 Processing helix chain 'B' and resid 209 through 225 Processing helix chain 'B' and resid 231 through 244 Processing helix chain 'B' and resid 250 through 254 Processing helix chain 'B' and resid 258 through 270 Processing helix chain 'B' and resid 276 through 295 removed outlier: 5.676A pdb=" N GLU B 283 " --> pdb=" O PHE B 279 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N HIS B 284 " --> pdb=" O ILE B 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 22 through 36 removed outlier: 4.569A pdb=" N ALA C 36 " --> pdb=" O GLY C 32 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 68 removed outlier: 3.648A pdb=" N PHE C 68 " --> pdb=" O ALA C 64 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 77 removed outlier: 4.057A pdb=" N ILE C 76 " --> pdb=" O LYS C 72 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 98 Proline residue: C 91 - end of helix removed outlier: 5.318A pdb=" N PHE C 94 " --> pdb=" O PHE C 90 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N MET C 95 " --> pdb=" O PRO C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 105 through 117 removed outlier: 4.809A pdb=" N LEU C 110 " --> pdb=" O THR C 106 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ALA C 111 " --> pdb=" O GLY C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 147 Processing helix chain 'C' and resid 164 through 176 removed outlier: 4.791A pdb=" N PHE C 169 " --> pdb=" O PHE C 166 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 205 Processing helix chain 'C' and resid 209 through 225 removed outlier: 4.065A pdb=" N VAL C 216 " --> pdb=" O TYR C 212 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 243 Processing helix chain 'C' and resid 250 through 254 Processing helix chain 'C' and resid 258 through 270 Processing helix chain 'C' and resid 275 through 280 Processing helix chain 'C' and resid 282 through 289 removed outlier: 3.894A pdb=" N TYR C 286 " --> pdb=" O LYS C 282 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N PHE C 288 " --> pdb=" O HIS C 284 " (cutoff:3.500A) Processing helix chain 'D' and resid 24 through 34 Processing helix chain 'D' and resid 40 through 67 Processing helix chain 'D' and resid 71 through 77 removed outlier: 3.833A pdb=" N GLU D 75 " --> pdb=" O HIS D 71 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N ILE D 76 " --> pdb=" O LYS D 72 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 89 Processing helix chain 'D' and resid 93 through 99 Processing helix chain 'D' and resid 105 through 117 removed outlier: 4.570A pdb=" N LEU D 110 " --> pdb=" O THR D 106 " (cutoff:3.500A) Processing helix chain 'D' and resid 123 through 147 Processing helix chain 'D' and resid 167 through 178 removed outlier: 3.787A pdb=" N ALA D 174 " --> pdb=" O LEU D 170 " (cutoff:3.500A) Processing helix chain 'D' and resid 182 through 206 removed outlier: 3.780A pdb=" N VAL D 203 " --> pdb=" O ALA D 199 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N LEU D 204 " --> pdb=" O VAL D 200 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N THR D 205 " --> pdb=" O TYR D 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 209 through 226 Processing helix chain 'D' and resid 231 through 243 Processing helix chain 'D' and resid 251 through 254 No H-bonds generated for 'chain 'D' and resid 251 through 254' Processing helix chain 'D' and resid 258 through 270 Processing helix chain 'D' and resid 274 through 280 Processing helix chain 'D' and resid 285 through 290 Processing helix chain 'E' and resid 24 through 37 removed outlier: 4.028A pdb=" N ALA E 36 " --> pdb=" O GLY E 32 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N HIS E 37 " --> pdb=" O LYS E 33 " (cutoff:3.500A) Processing helix chain 'E' and resid 40 through 69 removed outlier: 3.629A pdb=" N LEU E 44 " --> pdb=" O ASN E 40 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ALA E 45 " --> pdb=" O LEU E 41 " (cutoff:3.500A) Processing helix chain 'E' and resid 71 through 77 Processing helix chain 'E' and resid 81 through 100 Proline residue: E 91 - end of helix removed outlier: 5.391A pdb=" N PHE E 94 " --> pdb=" O PHE E 90 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N MET E 95 " --> pdb=" O PRO E 91 " (cutoff:3.500A) Processing helix chain 'E' and resid 105 through 117 removed outlier: 3.536A pdb=" N THR E 109 " --> pdb=" O PHE E 105 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N LEU E 110 " --> pdb=" O THR E 106 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N THR E 113 " --> pdb=" O THR E 109 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N MET E 114 " --> pdb=" O LEU E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 123 through 147 Processing helix chain 'E' and resid 165 through 178 removed outlier: 3.589A pdb=" N PHE E 169 " --> pdb=" O HIS E 165 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 205 Processing helix chain 'E' and resid 210 through 225 removed outlier: 4.024A pdb=" N SER E 215 " --> pdb=" O GLY E 211 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N VAL E 216 " --> pdb=" O TYR E 212 " (cutoff:3.500A) Processing helix chain 'E' and resid 231 through 243 Processing helix chain 'E' and resid 258 through 270 Processing helix chain 'E' and resid 275 through 289 removed outlier: 5.661A pdb=" N GLU E 283 " --> pdb=" O PHE E 279 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N HIS E 284 " --> pdb=" O ILE E 280 " (cutoff:3.500A) 692 hydrogen bonds defined for protein. 2049 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: 3.06 Time building geometry restraints manager: 4.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.12 - 1.25: 1683 1.25 - 1.39: 3321 1.39 - 1.53: 6117 1.53 - 1.67: 328 1.67 - 1.81: 100 Bond restraints: 11549 Sorted by residual: bond pdb=" C19 R7M C 401 " pdb=" C20 R7M C 401 " ideal model delta sigma weight residual 1.402 1.115 0.287 2.00e-02 2.50e+03 2.06e+02 bond pdb=" C19 R7M D 401 " pdb=" C20 R7M D 401 " ideal model delta sigma weight residual 1.402 1.117 0.285 2.00e-02 2.50e+03 2.03e+02 bond pdb=" C13 R7M D 401 " pdb=" C14 R7M D 401 " ideal model delta sigma weight residual 1.460 1.186 0.274 2.00e-02 2.50e+03 1.88e+02 bond pdb=" C13 R7M C 401 " pdb=" C14 R7M C 401 " ideal model delta sigma weight residual 1.460 1.190 0.270 2.00e-02 2.50e+03 1.82e+02 bond pdb=" C19 R7M B 401 " pdb=" C20 R7M B 401 " ideal model delta sigma weight residual 1.402 1.138 0.264 2.00e-02 2.50e+03 1.75e+02 ... (remaining 11544 not shown) Histogram of bond angle deviations from ideal: 99.46 - 106.40: 168 106.40 - 113.33: 6194 113.33 - 120.26: 4756 120.26 - 127.19: 4491 127.19 - 134.12: 75 Bond angle restraints: 15684 Sorted by residual: angle pdb=" N VAL E 77 " pdb=" CA VAL E 77 " pdb=" C VAL E 77 " ideal model delta sigma weight residual 110.72 121.64 -10.92 1.01e+00 9.80e-01 1.17e+02 angle pdb=" N LYS A 120 " pdb=" CA LYS A 120 " pdb=" C LYS A 120 " ideal model delta sigma weight residual 111.07 120.98 -9.91 1.07e+00 8.73e-01 8.58e+01 angle pdb=" N ALA B 270 " pdb=" CA ALA B 270 " pdb=" C ALA B 270 " ideal model delta sigma weight residual 111.36 118.40 -7.04 1.09e+00 8.42e-01 4.17e+01 angle pdb=" N ASN B 108 " pdb=" CA ASN B 108 " pdb=" C ASN B 108 " ideal model delta sigma weight residual 111.07 117.85 -6.78 1.07e+00 8.73e-01 4.01e+01 angle pdb=" N SER B 80 " pdb=" CA SER B 80 " pdb=" C SER B 80 " ideal model delta sigma weight residual 111.07 117.69 -6.62 1.07e+00 8.73e-01 3.82e+01 ... (remaining 15679 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.45: 5846 21.45 - 42.89: 657 42.89 - 64.34: 93 64.34 - 85.79: 8 85.79 - 107.23: 13 Dihedral angle restraints: 6617 sinusoidal: 2472 harmonic: 4145 Sorted by residual: dihedral pdb=" N LYS A 119 " pdb=" C LYS A 119 " pdb=" CA LYS A 119 " pdb=" CB LYS A 119 " ideal model delta harmonic sigma weight residual 122.80 137.16 -14.36 0 2.50e+00 1.60e-01 3.30e+01 dihedral pdb=" C LYS A 119 " pdb=" N LYS A 119 " pdb=" CA LYS A 119 " pdb=" CB LYS A 119 " ideal model delta harmonic sigma weight residual -122.60 -135.06 12.46 0 2.50e+00 1.60e-01 2.48e+01 dihedral pdb=" CA PHE C 90 " pdb=" C PHE C 90 " pdb=" N PRO C 91 " pdb=" CA PRO C 91 " ideal model delta harmonic sigma weight residual -180.00 -156.16 -23.84 0 5.00e+00 4.00e-02 2.27e+01 ... (remaining 6614 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.099: 1669 0.099 - 0.198: 86 0.198 - 0.297: 14 0.297 - 0.396: 5 0.396 - 0.495: 2 Chirality restraints: 1776 Sorted by residual: chirality pdb=" CA LYS A 119 " pdb=" N LYS A 119 " pdb=" C LYS A 119 " pdb=" CB LYS A 119 " both_signs ideal model delta sigma weight residual False 2.51 2.01 0.50 2.00e-01 2.50e+01 6.14e+00 chirality pdb=" CA ALA D 79 " pdb=" N ALA D 79 " pdb=" C ALA D 79 " pdb=" CB ALA D 79 " both_signs ideal model delta sigma weight residual False 2.48 2.03 0.45 2.00e-01 2.50e+01 5.17e+00 chirality pdb=" CA LYS C 256 " pdb=" N LYS C 256 " pdb=" C LYS C 256 " pdb=" CB LYS C 256 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.89e+00 ... (remaining 1773 not shown) Planarity restraints: 1904 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY B 269 " 0.019 2.00e-02 2.50e+03 3.77e-02 1.42e+01 pdb=" C GLY B 269 " -0.065 2.00e-02 2.50e+03 pdb=" O GLY B 269 " 0.025 2.00e-02 2.50e+03 pdb=" N ALA B 270 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR B 38 " 0.015 2.00e-02 2.50e+03 3.02e-02 9.15e+00 pdb=" C TYR B 38 " -0.052 2.00e-02 2.50e+03 pdb=" O TYR B 38 " 0.019 2.00e-02 2.50e+03 pdb=" N SER B 39 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 105 " 0.013 2.00e-02 2.50e+03 2.67e-02 7.13e+00 pdb=" C PHE A 105 " -0.046 2.00e-02 2.50e+03 pdb=" O PHE A 105 " 0.017 2.00e-02 2.50e+03 pdb=" N THR A 106 " 0.015 2.00e-02 2.50e+03 ... (remaining 1901 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 137 2.60 - 3.17: 10535 3.17 - 3.75: 17838 3.75 - 4.32: 26167 4.32 - 4.90: 42886 Nonbonded interactions: 97563 Sorted by model distance: nonbonded pdb=" F05 R7M C 401 " pdb=" O07 R7M C 401 " model vdw 2.021 2.390 nonbonded pdb=" F05 R7M E 401 " pdb=" O07 R7M E 401 " model vdw 2.129 2.390 nonbonded pdb=" F05 R7M A 401 " pdb=" O07 R7M A 401 " model vdw 2.134 2.390 nonbonded pdb=" F05 R7M B 401 " pdb=" O07 R7M B 401 " model vdw 2.137 2.390 nonbonded pdb=" O SER A 17 " pdb=" OG SER A 17 " model vdw 2.213 2.440 ... (remaining 97558 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 12 through 290 or resid 401)) selection = (chain 'B' and (resid 12 through 290 or resid 401)) selection = (chain 'C' and (resid 12 through 290 or resid 401)) selection = (chain 'D' and (resid 12 through 290 or resid 401)) selection = (chain 'E' and (resid 12 through 290 or resid 401)) } 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: 0.030 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: 0.010 Extract box with map and model: 0.900 Check model and map are aligned: 0.160 Set scattering table: 0.110 Process input model: 32.520 Find NCS groups from input model: 0.780 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7363 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 : 0.013 0.287 11549 Z= 0.874 Angle : 0.969 14.040 15684 Z= 0.538 Chirality : 0.058 0.495 1776 Planarity : 0.005 0.058 1904 Dihedral : 17.675 107.234 3997 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 15.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.30 % Favored : 91.70 % Rotamer: Outliers : 8.21 % Allowed : 25.21 % Favored : 66.58 % Cbeta Deviations : 0.15 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.79 (0.20), residues: 1410 helix: -1.20 (0.14), residues: 1086 sheet: None (None), residues: 0 loop : -3.68 (0.28), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS C 165 PHE 0.021 0.002 PHE B 223 TYR 0.018 0.002 TYR C 212 ARG 0.008 0.001 ARG B 293 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 301 time to evaluate : 1.054 Fit side-chains REVERT: A 33 LYS cc_start: 0.7169 (OUTLIER) cc_final: 0.6829 (pptt) REVERT: A 72 LYS cc_start: 0.8405 (mmtt) cc_final: 0.8033 (mmtp) REVERT: A 81 MET cc_start: 0.7225 (mmm) cc_final: 0.6968 (mmm) REVERT: A 95 MET cc_start: 0.7731 (mmm) cc_final: 0.7465 (tpp) REVERT: A 147 PHE cc_start: 0.7520 (m-80) cc_final: 0.7093 (m-80) REVERT: A 212 TYR cc_start: 0.7018 (OUTLIER) cc_final: 0.6214 (m-10) REVERT: A 273 LEU cc_start: 0.8927 (OUTLIER) cc_final: 0.8566 (tp) REVERT: A 282 LYS cc_start: 0.7476 (tttt) cc_final: 0.7244 (ttmt) REVERT: A 290 ARG cc_start: 0.7049 (mmm-85) cc_final: 0.6752 (mmm160) REVERT: B 164 ASN cc_start: 0.8514 (t0) cc_final: 0.8286 (t160) REVERT: B 202 PHE cc_start: 0.8149 (m-10) cc_final: 0.7889 (m-10) REVERT: B 247 LYS cc_start: 0.7025 (ttmm) cc_final: 0.6818 (ttmm) REVERT: B 251 TYR cc_start: 0.6228 (m-80) cc_final: 0.5973 (m-80) REVERT: C 81 MET cc_start: 0.7285 (OUTLIER) cc_final: 0.6585 (mtp) REVERT: C 201 TYR cc_start: 0.7855 (t80) cc_final: 0.7569 (t80) REVERT: D 33 LYS cc_start: 0.7015 (tmtm) cc_final: 0.6715 (tmtt) REVERT: D 35 LYS cc_start: 0.7907 (tptt) cc_final: 0.7698 (tptp) REVERT: D 106 THR cc_start: 0.8884 (m) cc_final: 0.8466 (p) REVERT: D 120 LYS cc_start: 0.7832 (mmmt) cc_final: 0.7430 (mptt) REVERT: D 271 ILE cc_start: 0.8563 (mm) cc_final: 0.8248 (mp) REVERT: E 33 LYS cc_start: 0.7845 (tttt) cc_final: 0.7532 (tttm) REVERT: E 35 LYS cc_start: 0.8432 (ttmm) cc_final: 0.8158 (mtpp) REVERT: E 52 MET cc_start: 0.7111 (tpp) cc_final: 0.6778 (tpp) REVERT: E 72 LYS cc_start: 0.7102 (mmtt) cc_final: 0.6822 (mmtm) REVERT: E 83 VAL cc_start: 0.8634 (t) cc_final: 0.8391 (t) REVERT: E 95 MET cc_start: 0.6499 (mpp) cc_final: 0.6194 (mpp) REVERT: E 162 GLU cc_start: 0.7478 (mm-30) cc_final: 0.5979 (mm-30) REVERT: E 185 CYS cc_start: 0.6969 (OUTLIER) cc_final: 0.6724 (t) outliers start: 96 outliers final: 58 residues processed: 377 average time/residue: 0.7403 time to fit residues: 315.6730 Evaluate side-chains 333 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 270 time to evaluate : 1.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 GLU Chi-restraints excluded: chain A residue 33 LYS Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 185 CYS Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 207 LYS Chi-restraints excluded: chain A residue 212 TYR Chi-restraints excluded: chain A residue 223 PHE Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 284 HIS Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 152 SER Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain C residue 17 SER Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 81 MET Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 148 VAL Chi-restraints excluded: chain C residue 165 HIS Chi-restraints excluded: chain C residue 185 CYS Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 212 TYR Chi-restraints excluded: chain C residue 223 PHE Chi-restraints excluded: chain C residue 271 ILE Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 40 ASN Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain D residue 96 CYS Chi-restraints excluded: chain D residue 104 LEU Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 143 SER Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 223 PHE Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain D residue 287 ASN Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 37 HIS Chi-restraints excluded: chain E residue 68 PHE Chi-restraints excluded: chain E residue 82 SER Chi-restraints excluded: chain E residue 113 THR Chi-restraints excluded: chain E residue 132 ILE Chi-restraints excluded: chain E residue 143 SER Chi-restraints excluded: chain E residue 185 CYS Chi-restraints excluded: chain E residue 203 VAL Chi-restraints excluded: chain E residue 223 PHE Chi-restraints excluded: chain E residue 255 ILE Chi-restraints excluded: chain E residue 263 LEU Chi-restraints excluded: chain E residue 273 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 118 optimal weight: 4.9990 chunk 106 optimal weight: 6.9990 chunk 58 optimal weight: 0.0070 chunk 36 optimal weight: 5.9990 chunk 71 optimal weight: 2.9990 chunk 56 optimal weight: 30.0000 chunk 109 optimal weight: 7.9990 chunk 42 optimal weight: 4.9990 chunk 66 optimal weight: 7.9990 chunk 81 optimal weight: 5.9990 chunk 127 optimal weight: 0.8980 overall best weight: 2.7804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 ASN A 284 HIS B 59 HIS B 165 HIS ** B 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 287 ASN C 137 ASN C 239 ASN D 59 HIS D 171 ASN E 59 HIS ** E 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 257 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7267 moved from start: 0.1373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11549 Z= 0.191 Angle : 0.586 9.484 15684 Z= 0.307 Chirality : 0.041 0.174 1776 Planarity : 0.003 0.036 1904 Dihedral : 12.475 94.878 1758 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 5.64 % Allowed : 28.46 % Favored : 65.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.22), residues: 1410 helix: 0.16 (0.16), residues: 1104 sheet: None (None), residues: 0 loop : -3.51 (0.28), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS C 71 PHE 0.023 0.001 PHE B 279 TYR 0.021 0.001 TYR E 31 ARG 0.005 0.000 ARG B 290 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 267 time to evaluate : 1.175 Fit side-chains revert: symmetry clash REVERT: A 72 LYS cc_start: 0.8402 (mmtt) cc_final: 0.8030 (mmtp) REVERT: A 81 MET cc_start: 0.7128 (mmm) cc_final: 0.6911 (mmm) REVERT: A 95 MET cc_start: 0.7478 (mmm) cc_final: 0.7200 (mpp) REVERT: A 116 LEU cc_start: 0.8499 (OUTLIER) cc_final: 0.7967 (tp) REVERT: A 273 LEU cc_start: 0.8780 (mt) cc_final: 0.8404 (tp) REVERT: A 282 LYS cc_start: 0.7449 (tttt) cc_final: 0.7192 (ttmt) REVERT: A 290 ARG cc_start: 0.6957 (mmm-85) cc_final: 0.6695 (mmm160) REVERT: B 16 LYS cc_start: 0.7722 (ptmm) cc_final: 0.7512 (ptmm) REVERT: B 30 GLU cc_start: 0.7888 (tp30) cc_final: 0.7618 (mm-30) REVERT: B 194 ILE cc_start: 0.7882 (mt) cc_final: 0.7582 (mm) REVERT: B 201 TYR cc_start: 0.7331 (OUTLIER) cc_final: 0.6660 (m-80) REVERT: B 202 PHE cc_start: 0.8043 (m-10) cc_final: 0.7798 (m-10) REVERT: B 279 PHE cc_start: 0.8153 (t80) cc_final: 0.7905 (t80) REVERT: C 122 LYS cc_start: 0.7378 (mmmt) cc_final: 0.7041 (tptt) REVERT: D 72 LYS cc_start: 0.8209 (OUTLIER) cc_final: 0.7238 (mttp) REVERT: D 163 LYS cc_start: 0.8135 (mptt) cc_final: 0.7914 (mptt) REVERT: D 232 ILE cc_start: 0.8059 (OUTLIER) cc_final: 0.7673 (mm) REVERT: D 271 ILE cc_start: 0.8560 (mm) cc_final: 0.8240 (mp) REVERT: E 33 LYS cc_start: 0.7847 (tttt) cc_final: 0.7597 (tttp) REVERT: E 37 HIS cc_start: 0.7557 (OUTLIER) cc_final: 0.7121 (t-90) REVERT: E 52 MET cc_start: 0.6918 (tpp) cc_final: 0.6435 (tpp) REVERT: E 72 LYS cc_start: 0.7022 (mmtt) cc_final: 0.6716 (mmtm) REVERT: E 162 GLU cc_start: 0.7296 (mm-30) cc_final: 0.5842 (mm-30) REVERT: E 212 TYR cc_start: 0.7840 (OUTLIER) cc_final: 0.7608 (m-80) REVERT: E 217 PHE cc_start: 0.7808 (t80) cc_final: 0.7421 (t80) outliers start: 66 outliers final: 36 residues processed: 316 average time/residue: 0.7055 time to fit residues: 252.8693 Evaluate side-chains 288 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 246 time to evaluate : 1.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 17 SER Chi-restraints excluded: chain A residue 22 GLU Chi-restraints excluded: chain A residue 52 MET Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 223 PHE Chi-restraints excluded: chain A residue 284 HIS Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain B residue 163 LYS Chi-restraints excluded: chain B residue 201 TYR Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain C residue 15 ILE Chi-restraints excluded: chain C residue 28 CYS Chi-restraints excluded: chain C residue 148 VAL Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 223 PHE Chi-restraints excluded: chain C residue 271 ILE Chi-restraints excluded: chain D residue 72 LYS Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain D residue 82 SER Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain D residue 96 CYS Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain D residue 200 VAL Chi-restraints excluded: chain D residue 232 ILE Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain D residue 291 SER Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 37 HIS Chi-restraints excluded: chain E residue 68 PHE Chi-restraints excluded: chain E residue 98 ILE Chi-restraints excluded: chain E residue 132 ILE Chi-restraints excluded: chain E residue 203 VAL Chi-restraints excluded: chain E residue 212 TYR Chi-restraints excluded: chain E residue 223 PHE Chi-restraints excluded: chain E residue 273 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 70 optimal weight: 20.0000 chunk 39 optimal weight: 6.9990 chunk 105 optimal weight: 20.0000 chunk 86 optimal weight: 30.0000 chunk 35 optimal weight: 6.9990 chunk 127 optimal weight: 5.9990 chunk 137 optimal weight: 8.9990 chunk 113 optimal weight: 7.9990 chunk 126 optimal weight: 9.9990 chunk 43 optimal weight: 0.0040 chunk 102 optimal weight: 5.9990 overall best weight: 5.2000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 ASN ** B 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 165 HIS B 230 HIS ** B 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 257 ASN ** E 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 257 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7307 moved from start: 0.1502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11549 Z= 0.258 Angle : 0.594 7.330 15684 Z= 0.315 Chirality : 0.041 0.166 1776 Planarity : 0.003 0.033 1904 Dihedral : 11.269 92.185 1686 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 7.01 % Allowed : 28.29 % Favored : 64.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.22), residues: 1410 helix: 0.44 (0.16), residues: 1118 sheet: None (None), residues: 0 loop : -3.28 (0.29), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS C 165 PHE 0.023 0.002 PHE A 288 TYR 0.020 0.002 TYR E 31 ARG 0.002 0.000 ARG B 290 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 248 time to evaluate : 1.123 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 33 LYS cc_start: 0.7123 (OUTLIER) cc_final: 0.6834 (tmtt) REVERT: A 72 LYS cc_start: 0.8419 (mmtt) cc_final: 0.8029 (mmtp) REVERT: A 81 MET cc_start: 0.7140 (mmm) cc_final: 0.6904 (mmm) REVERT: A 95 MET cc_start: 0.7400 (mmm) cc_final: 0.7113 (mpp) REVERT: A 116 LEU cc_start: 0.8540 (OUTLIER) cc_final: 0.8017 (tp) REVERT: A 263 LEU cc_start: 0.7601 (OUTLIER) cc_final: 0.7378 (tt) REVERT: A 273 LEU cc_start: 0.8755 (OUTLIER) cc_final: 0.8392 (tp) REVERT: A 282 LYS cc_start: 0.7431 (tttt) cc_final: 0.7191 (ttmm) REVERT: A 284 HIS cc_start: 0.6919 (OUTLIER) cc_final: 0.6129 (t-170) REVERT: A 290 ARG cc_start: 0.7028 (mmm-85) cc_final: 0.6773 (mmm160) REVERT: B 88 PHE cc_start: 0.7898 (t80) cc_final: 0.7560 (t80) REVERT: B 194 ILE cc_start: 0.7943 (mt) cc_final: 0.7625 (mm) REVERT: B 201 TYR cc_start: 0.7399 (OUTLIER) cc_final: 0.6680 (m-80) REVERT: B 279 PHE cc_start: 0.8217 (t80) cc_final: 0.7965 (t80) REVERT: C 16 LYS cc_start: 0.8060 (ttpm) cc_final: 0.7849 (ttpt) REVERT: C 195 PHE cc_start: 0.8036 (OUTLIER) cc_final: 0.5503 (m-80) REVERT: D 163 LYS cc_start: 0.8125 (mptt) cc_final: 0.7793 (mptt) REVERT: D 262 LEU cc_start: 0.8147 (pp) cc_final: 0.7860 (pp) REVERT: D 271 ILE cc_start: 0.8563 (mm) cc_final: 0.8246 (mp) REVERT: E 33 LYS cc_start: 0.7889 (tttt) cc_final: 0.7607 (tttp) REVERT: E 37 HIS cc_start: 0.7592 (OUTLIER) cc_final: 0.7115 (t-90) REVERT: E 52 MET cc_start: 0.6964 (tpp) cc_final: 0.6584 (tpp) REVERT: E 72 LYS cc_start: 0.7138 (mmtt) cc_final: 0.6836 (mmtm) REVERT: E 105 PHE cc_start: 0.8089 (t80) cc_final: 0.7871 (t80) REVERT: E 162 GLU cc_start: 0.7363 (mm-30) cc_final: 0.5935 (mm-30) REVERT: E 217 PHE cc_start: 0.7818 (t80) cc_final: 0.7512 (t80) outliers start: 82 outliers final: 48 residues processed: 306 average time/residue: 0.7150 time to fit residues: 248.7778 Evaluate side-chains 292 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 236 time to evaluate : 1.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 22 GLU Chi-restraints excluded: chain A residue 33 LYS Chi-restraints excluded: chain A residue 52 MET Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 223 PHE Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 284 HIS Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 128 ARG Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 201 TYR Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain C residue 15 ILE Chi-restraints excluded: chain C residue 28 CYS Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 114 MET Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 148 VAL Chi-restraints excluded: chain C residue 156 THR Chi-restraints excluded: chain C residue 195 PHE Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 223 PHE Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 271 ILE Chi-restraints excluded: chain D residue 40 ASN Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain D residue 80 SER Chi-restraints excluded: chain D residue 82 SER Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain D residue 96 CYS Chi-restraints excluded: chain D residue 133 SER Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain D residue 200 VAL Chi-restraints excluded: chain D residue 205 THR Chi-restraints excluded: chain D residue 223 PHE Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 37 HIS Chi-restraints excluded: chain E residue 68 PHE Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain E residue 203 VAL Chi-restraints excluded: chain E residue 223 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 125 optimal weight: 9.9990 chunk 95 optimal weight: 5.9990 chunk 66 optimal weight: 10.0000 chunk 14 optimal weight: 0.5980 chunk 60 optimal weight: 20.0000 chunk 85 optimal weight: 9.9990 chunk 127 optimal weight: 2.9990 chunk 135 optimal weight: 5.9990 chunk 121 optimal weight: 6.9990 chunk 36 optimal weight: 6.9990 chunk 112 optimal weight: 20.0000 overall best weight: 4.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 165 HIS ** B 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 234 ASN ** E 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 257 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7288 moved from start: 0.1710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 11549 Z= 0.233 Angle : 0.580 8.859 15684 Z= 0.303 Chirality : 0.040 0.165 1776 Planarity : 0.003 0.032 1904 Dihedral : 11.061 91.210 1680 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 7.52 % Allowed : 28.38 % Favored : 64.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.23), residues: 1410 helix: 0.65 (0.16), residues: 1117 sheet: None (None), residues: 0 loop : -3.13 (0.30), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS C 165 PHE 0.025 0.001 PHE A 279 TYR 0.019 0.001 TYR E 31 ARG 0.006 0.000 ARG D 290 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 238 time to evaluate : 1.120 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 33 LYS cc_start: 0.7151 (OUTLIER) cc_final: 0.6697 (tmtp) REVERT: A 72 LYS cc_start: 0.8436 (mmtt) cc_final: 0.8043 (mmtp) REVERT: A 81 MET cc_start: 0.7155 (mmm) cc_final: 0.6888 (mmm) REVERT: A 116 LEU cc_start: 0.8524 (OUTLIER) cc_final: 0.7996 (tp) REVERT: A 273 LEU cc_start: 0.8698 (OUTLIER) cc_final: 0.8354 (tp) REVERT: A 282 LYS cc_start: 0.7394 (tttt) cc_final: 0.7061 (ttmm) REVERT: A 284 HIS cc_start: 0.6938 (OUTLIER) cc_final: 0.6164 (t-170) REVERT: A 290 ARG cc_start: 0.7002 (mmm-85) cc_final: 0.6749 (mmm160) REVERT: B 88 PHE cc_start: 0.7871 (t80) cc_final: 0.7523 (t80) REVERT: B 165 HIS cc_start: 0.7736 (OUTLIER) cc_final: 0.7527 (m-70) REVERT: B 194 ILE cc_start: 0.7965 (mt) cc_final: 0.7671 (mm) REVERT: B 201 TYR cc_start: 0.7376 (OUTLIER) cc_final: 0.6763 (m-80) REVERT: B 279 PHE cc_start: 0.8017 (t80) cc_final: 0.7806 (t80) REVERT: C 28 CYS cc_start: 0.7582 (OUTLIER) cc_final: 0.7004 (m) REVERT: C 195 PHE cc_start: 0.8057 (OUTLIER) cc_final: 0.5450 (m-80) REVERT: D 72 LYS cc_start: 0.8302 (OUTLIER) cc_final: 0.7345 (mttp) REVERT: D 94 PHE cc_start: 0.7679 (t80) cc_final: 0.7269 (t80) REVERT: D 163 LYS cc_start: 0.8153 (mptt) cc_final: 0.7799 (mptt) REVERT: D 262 LEU cc_start: 0.8173 (pp) cc_final: 0.7905 (pp) REVERT: D 271 ILE cc_start: 0.8530 (mm) cc_final: 0.8227 (mp) REVERT: E 33 LYS cc_start: 0.7926 (tttt) cc_final: 0.7642 (tttp) REVERT: E 37 HIS cc_start: 0.7599 (OUTLIER) cc_final: 0.7172 (t-90) REVERT: E 52 MET cc_start: 0.6935 (tpp) cc_final: 0.6419 (tpp) REVERT: E 72 LYS cc_start: 0.7119 (mmtt) cc_final: 0.6808 (mmtm) REVERT: E 100 THR cc_start: 0.8251 (t) cc_final: 0.7977 (m) REVERT: E 105 PHE cc_start: 0.8061 (t80) cc_final: 0.7834 (t80) REVERT: E 114 MET cc_start: 0.8094 (OUTLIER) cc_final: 0.7821 (ttt) REVERT: E 162 GLU cc_start: 0.7319 (mm-30) cc_final: 0.5870 (mm-30) REVERT: E 217 PHE cc_start: 0.7707 (t80) cc_final: 0.7431 (t80) outliers start: 88 outliers final: 48 residues processed: 302 average time/residue: 0.7339 time to fit residues: 250.7341 Evaluate side-chains 289 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 230 time to evaluate : 1.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 22 GLU Chi-restraints excluded: chain A residue 33 LYS Chi-restraints excluded: chain A residue 52 MET Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 223 PHE Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 284 HIS Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 30 GLU Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 128 ARG Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain B residue 165 HIS Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 201 TYR Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain C residue 15 ILE Chi-restraints excluded: chain C residue 28 CYS Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 114 MET Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 148 VAL Chi-restraints excluded: chain C residue 156 THR Chi-restraints excluded: chain C residue 195 PHE Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 223 PHE Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 72 LYS Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain D residue 80 SER Chi-restraints excluded: chain D residue 82 SER Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain D residue 96 CYS Chi-restraints excluded: chain D residue 133 SER Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain D residue 200 VAL Chi-restraints excluded: chain D residue 291 SER Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 37 HIS Chi-restraints excluded: chain E residue 68 PHE Chi-restraints excluded: chain E residue 92 ILE Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain E residue 114 MET Chi-restraints excluded: chain E residue 203 VAL Chi-restraints excluded: chain E residue 223 PHE Chi-restraints excluded: chain E residue 273 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 76 optimal weight: 20.0000 chunk 1 optimal weight: 9.9990 chunk 100 optimal weight: 7.9990 chunk 55 optimal weight: 8.9990 chunk 115 optimal weight: 5.9990 chunk 93 optimal weight: 20.0000 chunk 0 optimal weight: 30.0000 chunk 69 optimal weight: 9.9990 chunk 121 optimal weight: 9.9990 chunk 34 optimal weight: 3.9990 chunk 45 optimal weight: 5.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 165 HIS ** B 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 257 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7324 moved from start: 0.1639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 11549 Z= 0.307 Angle : 0.617 8.632 15684 Z= 0.326 Chirality : 0.042 0.168 1776 Planarity : 0.003 0.033 1904 Dihedral : 10.939 89.801 1676 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 8.12 % Allowed : 27.86 % Favored : 64.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.23), residues: 1410 helix: 0.60 (0.16), residues: 1109 sheet: None (None), residues: 0 loop : -2.97 (0.31), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS C 165 PHE 0.026 0.002 PHE A 279 TYR 0.023 0.002 TYR C 70 ARG 0.008 0.000 ARG D 290 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 245 time to evaluate : 1.111 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 33 LYS cc_start: 0.7187 (OUTLIER) cc_final: 0.6707 (tmtp) REVERT: A 72 LYS cc_start: 0.8450 (mmtt) cc_final: 0.8052 (mmtp) REVERT: A 81 MET cc_start: 0.7139 (mmm) cc_final: 0.6920 (mmm) REVERT: A 116 LEU cc_start: 0.8527 (OUTLIER) cc_final: 0.7996 (tp) REVERT: A 147 PHE cc_start: 0.7448 (m-80) cc_final: 0.6947 (m-80) REVERT: A 263 LEU cc_start: 0.7633 (OUTLIER) cc_final: 0.7392 (tt) REVERT: A 273 LEU cc_start: 0.8807 (OUTLIER) cc_final: 0.8433 (tp) REVERT: A 282 LYS cc_start: 0.7426 (tttt) cc_final: 0.7083 (ttmm) REVERT: A 284 HIS cc_start: 0.7004 (OUTLIER) cc_final: 0.6223 (t-170) REVERT: A 290 ARG cc_start: 0.7048 (mmm-85) cc_final: 0.6770 (mmm160) REVERT: B 88 PHE cc_start: 0.7895 (t80) cc_final: 0.7535 (t80) REVERT: B 165 HIS cc_start: 0.7829 (OUTLIER) cc_final: 0.7609 (m-70) REVERT: B 194 ILE cc_start: 0.7954 (mt) cc_final: 0.7726 (mm) REVERT: B 201 TYR cc_start: 0.7404 (OUTLIER) cc_final: 0.6670 (m-80) REVERT: B 279 PHE cc_start: 0.8028 (t80) cc_final: 0.7813 (t80) REVERT: C 104 LEU cc_start: 0.7265 (OUTLIER) cc_final: 0.6998 (tm) REVERT: C 195 PHE cc_start: 0.8091 (OUTLIER) cc_final: 0.5528 (m-80) REVERT: D 33 LYS cc_start: 0.7110 (tmtm) cc_final: 0.6773 (tmtt) REVERT: D 120 LYS cc_start: 0.7789 (mmmt) cc_final: 0.7393 (mptt) REVERT: D 262 LEU cc_start: 0.8190 (pp) cc_final: 0.7953 (pp) REVERT: D 271 ILE cc_start: 0.8537 (mm) cc_final: 0.8210 (mp) REVERT: E 33 LYS cc_start: 0.7979 (tttt) cc_final: 0.7693 (tttp) REVERT: E 37 HIS cc_start: 0.7598 (OUTLIER) cc_final: 0.7110 (t-90) REVERT: E 52 MET cc_start: 0.6998 (tpp) cc_final: 0.6622 (tpp) REVERT: E 72 LYS cc_start: 0.7151 (mmtt) cc_final: 0.6846 (mmtm) REVERT: E 105 PHE cc_start: 0.8130 (t80) cc_final: 0.7900 (t80) REVERT: E 162 GLU cc_start: 0.7378 (mm-30) cc_final: 0.5941 (mm-30) REVERT: E 185 CYS cc_start: 0.6883 (OUTLIER) cc_final: 0.6585 (t) REVERT: E 217 PHE cc_start: 0.7769 (t80) cc_final: 0.7467 (t80) outliers start: 95 outliers final: 63 residues processed: 312 average time/residue: 0.7249 time to fit residues: 256.4155 Evaluate side-chains 309 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 235 time to evaluate : 1.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 22 GLU Chi-restraints excluded: chain A residue 33 LYS Chi-restraints excluded: chain A residue 52 MET Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 223 PHE Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 255 ILE Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 284 HIS Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 19 CYS Chi-restraints excluded: chain B residue 30 GLU Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 74 ARG Chi-restraints excluded: chain B residue 80 SER Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 128 ARG Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain B residue 165 HIS Chi-restraints excluded: chain B residue 176 LYS Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 201 TYR Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain C residue 15 ILE Chi-restraints excluded: chain C residue 28 CYS Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 114 MET Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 148 VAL Chi-restraints excluded: chain C residue 156 THR Chi-restraints excluded: chain C residue 195 PHE Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 223 PHE Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 271 ILE Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 40 ASN Chi-restraints excluded: chain D residue 61 SER Chi-restraints excluded: chain D residue 80 SER Chi-restraints excluded: chain D residue 82 SER Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain D residue 96 CYS Chi-restraints excluded: chain D residue 133 SER Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain D residue 192 CYS Chi-restraints excluded: chain D residue 200 VAL Chi-restraints excluded: chain D residue 223 PHE Chi-restraints excluded: chain D residue 291 SER Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 37 HIS Chi-restraints excluded: chain E residue 68 PHE Chi-restraints excluded: chain E residue 92 ILE Chi-restraints excluded: chain E residue 98 ILE Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain E residue 185 CYS Chi-restraints excluded: chain E residue 203 VAL Chi-restraints excluded: chain E residue 223 PHE Chi-restraints excluded: chain E residue 263 LEU Chi-restraints excluded: chain E residue 273 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 121 optimal weight: 9.9990 chunk 26 optimal weight: 7.9990 chunk 79 optimal weight: 6.9990 chunk 33 optimal weight: 10.0000 chunk 135 optimal weight: 7.9990 chunk 112 optimal weight: 6.9990 chunk 62 optimal weight: 0.5980 chunk 11 optimal weight: 9.9990 chunk 44 optimal weight: 10.0000 chunk 71 optimal weight: 5.9990 chunk 130 optimal weight: 7.9990 overall best weight: 5.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 165 HIS ** B 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 257 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7312 moved from start: 0.1744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 11549 Z= 0.276 Angle : 0.605 10.437 15684 Z= 0.317 Chirality : 0.041 0.169 1776 Planarity : 0.003 0.033 1904 Dihedral : 10.541 89.248 1675 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 7.78 % Allowed : 28.97 % Favored : 63.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.23), residues: 1410 helix: 0.70 (0.16), residues: 1101 sheet: None (None), residues: 0 loop : -2.82 (0.31), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS C 165 PHE 0.023 0.002 PHE A 288 TYR 0.019 0.002 TYR E 31 ARG 0.006 0.000 ARG D 290 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 235 time to evaluate : 1.161 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 33 LYS cc_start: 0.7163 (OUTLIER) cc_final: 0.6846 (tmtt) REVERT: A 72 LYS cc_start: 0.8445 (mmtt) cc_final: 0.8047 (mmtp) REVERT: A 81 MET cc_start: 0.7194 (mmm) cc_final: 0.6979 (mmm) REVERT: A 116 LEU cc_start: 0.8523 (OUTLIER) cc_final: 0.7982 (tp) REVERT: A 263 LEU cc_start: 0.7627 (OUTLIER) cc_final: 0.7386 (tt) REVERT: A 273 LEU cc_start: 0.8831 (OUTLIER) cc_final: 0.8417 (tp) REVERT: A 282 LYS cc_start: 0.7400 (tttt) cc_final: 0.7068 (ttmm) REVERT: A 284 HIS cc_start: 0.7057 (OUTLIER) cc_final: 0.6257 (t-170) REVERT: A 290 ARG cc_start: 0.7009 (mmm-85) cc_final: 0.6736 (mmm160) REVERT: B 194 ILE cc_start: 0.8026 (mt) cc_final: 0.7719 (mm) REVERT: B 201 TYR cc_start: 0.7385 (OUTLIER) cc_final: 0.6693 (m-80) REVERT: C 28 CYS cc_start: 0.7598 (OUTLIER) cc_final: 0.7019 (m) REVERT: C 104 LEU cc_start: 0.7274 (OUTLIER) cc_final: 0.7005 (tm) REVERT: C 204 LEU cc_start: 0.8317 (tp) cc_final: 0.8110 (tp) REVERT: D 33 LYS cc_start: 0.7100 (tmtm) cc_final: 0.6766 (tmtt) REVERT: D 120 LYS cc_start: 0.7783 (mmmt) cc_final: 0.7377 (mptt) REVERT: D 123 LEU cc_start: 0.5840 (OUTLIER) cc_final: 0.5558 (pt) REVERT: D 163 LYS cc_start: 0.8119 (mptp) cc_final: 0.7721 (mptt) REVERT: D 262 LEU cc_start: 0.8172 (pp) cc_final: 0.7947 (pp) REVERT: D 271 ILE cc_start: 0.8498 (mm) cc_final: 0.8188 (mp) REVERT: E 33 LYS cc_start: 0.7923 (tttt) cc_final: 0.7630 (tttp) REVERT: E 37 HIS cc_start: 0.7582 (OUTLIER) cc_final: 0.7112 (t-90) REVERT: E 52 MET cc_start: 0.6989 (tpp) cc_final: 0.6616 (tpp) REVERT: E 72 LYS cc_start: 0.7144 (mmtt) cc_final: 0.6837 (mmtm) REVERT: E 100 THR cc_start: 0.8267 (t) cc_final: 0.7967 (m) REVERT: E 105 PHE cc_start: 0.8114 (t80) cc_final: 0.7902 (t80) REVERT: E 162 GLU cc_start: 0.7357 (mm-30) cc_final: 0.5908 (mm-30) REVERT: E 217 PHE cc_start: 0.7768 (t80) cc_final: 0.7475 (t80) outliers start: 91 outliers final: 62 residues processed: 297 average time/residue: 0.7456 time to fit residues: 249.8797 Evaluate side-chains 302 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 230 time to evaluate : 1.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 22 GLU Chi-restraints excluded: chain A residue 33 LYS Chi-restraints excluded: chain A residue 52 MET Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 223 PHE Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 255 ILE Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 284 HIS Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 19 CYS Chi-restraints excluded: chain B residue 30 GLU Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 74 ARG Chi-restraints excluded: chain B residue 80 SER Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 128 ARG Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain B residue 176 LYS Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 201 TYR Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain C residue 15 ILE Chi-restraints excluded: chain C residue 28 CYS Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 52 MET Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 114 MET Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 148 VAL Chi-restraints excluded: chain C residue 156 THR Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 223 PHE Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 271 ILE Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 40 ASN Chi-restraints excluded: chain D residue 61 SER Chi-restraints excluded: chain D residue 80 SER Chi-restraints excluded: chain D residue 82 SER Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain D residue 133 SER Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain D residue 192 CYS Chi-restraints excluded: chain D residue 200 VAL Chi-restraints excluded: chain D residue 223 PHE Chi-restraints excluded: chain D residue 291 SER Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 37 HIS Chi-restraints excluded: chain E residue 68 PHE Chi-restraints excluded: chain E residue 92 ILE Chi-restraints excluded: chain E residue 98 ILE Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain E residue 203 VAL Chi-restraints excluded: chain E residue 223 PHE Chi-restraints excluded: chain E residue 273 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 15 optimal weight: 2.9990 chunk 77 optimal weight: 5.9990 chunk 98 optimal weight: 9.9990 chunk 76 optimal weight: 5.9990 chunk 114 optimal weight: 20.0000 chunk 75 optimal weight: 5.9990 chunk 134 optimal weight: 7.9990 chunk 84 optimal weight: 6.9990 chunk 82 optimal weight: 5.9990 chunk 62 optimal weight: 6.9990 chunk 83 optimal weight: 0.8980 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 165 HIS ** B 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 257 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7286 moved from start: 0.1870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 11549 Z= 0.231 Angle : 0.597 14.431 15684 Z= 0.307 Chirality : 0.040 0.171 1776 Planarity : 0.003 0.032 1904 Dihedral : 9.982 89.347 1674 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 7.26 % Allowed : 29.32 % Favored : 63.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.23), residues: 1410 helix: 0.77 (0.16), residues: 1114 sheet: None (None), residues: 0 loop : -2.85 (0.32), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS C 165 PHE 0.024 0.001 PHE A 288 TYR 0.018 0.001 TYR E 31 ARG 0.005 0.000 ARG D 290 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 240 time to evaluate : 1.222 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 33 LYS cc_start: 0.7145 (OUTLIER) cc_final: 0.6770 (tmtp) REVERT: A 72 LYS cc_start: 0.8442 (mmtt) cc_final: 0.8044 (mmtp) REVERT: A 81 MET cc_start: 0.7209 (mmm) cc_final: 0.6940 (mmm) REVERT: A 116 LEU cc_start: 0.8469 (OUTLIER) cc_final: 0.7911 (tp) REVERT: A 223 PHE cc_start: 0.7782 (OUTLIER) cc_final: 0.7397 (t80) REVERT: A 273 LEU cc_start: 0.8859 (mt) cc_final: 0.8419 (tp) REVERT: A 282 LYS cc_start: 0.7367 (tttt) cc_final: 0.7051 (ttmm) REVERT: A 284 HIS cc_start: 0.7068 (OUTLIER) cc_final: 0.6310 (t-170) REVERT: A 290 ARG cc_start: 0.6988 (mmm-85) cc_final: 0.6727 (mmm160) REVERT: B 88 PHE cc_start: 0.7872 (t80) cc_final: 0.7530 (t80) REVERT: B 194 ILE cc_start: 0.7966 (mt) cc_final: 0.7716 (mm) REVERT: B 201 TYR cc_start: 0.7327 (OUTLIER) cc_final: 0.6728 (m-80) REVERT: C 28 CYS cc_start: 0.7580 (OUTLIER) cc_final: 0.7026 (m) REVERT: C 104 LEU cc_start: 0.7299 (OUTLIER) cc_final: 0.7023 (tm) REVERT: C 195 PHE cc_start: 0.8068 (OUTLIER) cc_final: 0.5470 (m-80) REVERT: D 33 LYS cc_start: 0.7140 (tmtm) cc_final: 0.6833 (tmtt) REVERT: D 72 LYS cc_start: 0.8310 (OUTLIER) cc_final: 0.7344 (mttp) REVERT: D 94 PHE cc_start: 0.7759 (t80) cc_final: 0.7391 (t80) REVERT: D 120 LYS cc_start: 0.7794 (mmmt) cc_final: 0.7394 (mptt) REVERT: D 163 LYS cc_start: 0.8075 (mptp) cc_final: 0.7805 (mptt) REVERT: D 262 LEU cc_start: 0.8166 (pp) cc_final: 0.7907 (pp) REVERT: D 271 ILE cc_start: 0.8495 (mm) cc_final: 0.8198 (mp) REVERT: E 33 LYS cc_start: 0.7914 (tttt) cc_final: 0.7624 (tttp) REVERT: E 37 HIS cc_start: 0.7577 (OUTLIER) cc_final: 0.7155 (t-90) REVERT: E 52 MET cc_start: 0.6942 (tpp) cc_final: 0.6562 (tpp) REVERT: E 72 LYS cc_start: 0.7120 (mmtt) cc_final: 0.6808 (mmtm) REVERT: E 100 THR cc_start: 0.8274 (t) cc_final: 0.7965 (m) REVERT: E 105 PHE cc_start: 0.8097 (t80) cc_final: 0.7878 (t80) REVERT: E 162 GLU cc_start: 0.7306 (mm-30) cc_final: 0.5858 (mm-30) REVERT: E 185 CYS cc_start: 0.6750 (OUTLIER) cc_final: 0.6455 (t) REVERT: E 217 PHE cc_start: 0.7746 (t80) cc_final: 0.7496 (t80) outliers start: 85 outliers final: 57 residues processed: 299 average time/residue: 0.7595 time to fit residues: 255.9838 Evaluate side-chains 296 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 228 time to evaluate : 1.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 22 GLU Chi-restraints excluded: chain A residue 33 LYS Chi-restraints excluded: chain A residue 52 MET Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 223 PHE Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 284 HIS Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 19 CYS Chi-restraints excluded: chain B residue 30 GLU Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 74 ARG Chi-restraints excluded: chain B residue 80 SER Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 128 ARG Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain B residue 176 LYS Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 201 TYR Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain C residue 15 ILE Chi-restraints excluded: chain C residue 28 CYS Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 52 MET Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 114 MET Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 148 VAL Chi-restraints excluded: chain C residue 156 THR Chi-restraints excluded: chain C residue 195 PHE Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 223 PHE Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 40 ASN Chi-restraints excluded: chain D residue 61 SER Chi-restraints excluded: chain D residue 72 LYS Chi-restraints excluded: chain D residue 80 SER Chi-restraints excluded: chain D residue 82 SER Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain D residue 133 SER Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain D residue 291 SER Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 37 HIS Chi-restraints excluded: chain E residue 68 PHE Chi-restraints excluded: chain E residue 92 ILE Chi-restraints excluded: chain E residue 98 ILE Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain E residue 185 CYS Chi-restraints excluded: chain E residue 203 VAL Chi-restraints excluded: chain E residue 223 PHE Chi-restraints excluded: chain E residue 263 LEU Chi-restraints excluded: chain E residue 273 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 53 optimal weight: 20.0000 chunk 80 optimal weight: 6.9990 chunk 40 optimal weight: 3.9990 chunk 26 optimal weight: 9.9990 chunk 85 optimal weight: 20.0000 chunk 91 optimal weight: 10.0000 chunk 66 optimal weight: 5.9990 chunk 12 optimal weight: 20.0000 chunk 106 optimal weight: 4.9990 chunk 122 optimal weight: 6.9990 chunk 129 optimal weight: 10.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 165 HIS B 284 HIS E 168 GLN ** E 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 257 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7310 moved from start: 0.1858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 11549 Z= 0.281 Angle : 0.627 13.337 15684 Z= 0.325 Chirality : 0.042 0.169 1776 Planarity : 0.003 0.032 1904 Dihedral : 9.869 88.600 1674 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 7.18 % Allowed : 29.83 % Favored : 62.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.23), residues: 1410 helix: 0.71 (0.16), residues: 1104 sheet: None (None), residues: 0 loop : -2.79 (0.32), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS C 165 PHE 0.026 0.002 PHE A 279 TYR 0.018 0.002 TYR E 31 ARG 0.007 0.000 ARG D 290 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 224 time to evaluate : 1.208 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 33 LYS cc_start: 0.7182 (OUTLIER) cc_final: 0.6790 (tmtp) REVERT: A 72 LYS cc_start: 0.8442 (mmtt) cc_final: 0.8039 (mmtp) REVERT: A 81 MET cc_start: 0.7181 (mmm) cc_final: 0.6962 (mmm) REVERT: A 116 LEU cc_start: 0.8526 (OUTLIER) cc_final: 0.7983 (tp) REVERT: A 223 PHE cc_start: 0.7852 (OUTLIER) cc_final: 0.7496 (t80) REVERT: A 263 LEU cc_start: 0.7606 (OUTLIER) cc_final: 0.7359 (tt) REVERT: A 273 LEU cc_start: 0.8835 (mt) cc_final: 0.8470 (tp) REVERT: A 282 LYS cc_start: 0.7382 (tttt) cc_final: 0.7098 (ttmt) REVERT: A 284 HIS cc_start: 0.6929 (OUTLIER) cc_final: 0.6137 (t-170) REVERT: A 290 ARG cc_start: 0.6997 (mmm-85) cc_final: 0.6737 (mmm160) REVERT: B 88 PHE cc_start: 0.7857 (t80) cc_final: 0.7514 (t80) REVERT: B 194 ILE cc_start: 0.7920 (mt) cc_final: 0.7631 (mm) REVERT: B 201 TYR cc_start: 0.7335 (OUTLIER) cc_final: 0.6692 (m-80) REVERT: C 28 CYS cc_start: 0.7601 (OUTLIER) cc_final: 0.7065 (m) REVERT: C 104 LEU cc_start: 0.7273 (OUTLIER) cc_final: 0.6999 (tm) REVERT: C 195 PHE cc_start: 0.8074 (OUTLIER) cc_final: 0.5530 (m-80) REVERT: C 204 LEU cc_start: 0.8305 (tp) cc_final: 0.8093 (tp) REVERT: D 33 LYS cc_start: 0.7252 (tmtm) cc_final: 0.6861 (tmtt) REVERT: D 120 LYS cc_start: 0.7814 (mmmt) cc_final: 0.7391 (mptt) REVERT: D 123 LEU cc_start: 0.5832 (OUTLIER) cc_final: 0.5548 (pt) REVERT: D 163 LYS cc_start: 0.8112 (mptp) cc_final: 0.7840 (mptt) REVERT: D 271 ILE cc_start: 0.8535 (mm) cc_final: 0.8218 (mp) REVERT: E 33 LYS cc_start: 0.7966 (tttt) cc_final: 0.7693 (tttp) REVERT: E 37 HIS cc_start: 0.7575 (OUTLIER) cc_final: 0.7102 (t-90) REVERT: E 52 MET cc_start: 0.6988 (tpp) cc_final: 0.6611 (tpp) REVERT: E 72 LYS cc_start: 0.7144 (mmtt) cc_final: 0.6836 (mmtm) REVERT: E 100 THR cc_start: 0.8267 (t) cc_final: 0.7965 (m) REVERT: E 105 PHE cc_start: 0.8123 (t80) cc_final: 0.7895 (t80) REVERT: E 162 GLU cc_start: 0.7338 (mm-30) cc_final: 0.5881 (mm-30) REVERT: E 185 CYS cc_start: 0.6812 (OUTLIER) cc_final: 0.6595 (t) REVERT: E 217 PHE cc_start: 0.7768 (t80) cc_final: 0.7462 (t80) outliers start: 84 outliers final: 64 residues processed: 285 average time/residue: 0.7534 time to fit residues: 243.3814 Evaluate side-chains 298 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 222 time to evaluate : 1.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 17 SER Chi-restraints excluded: chain A residue 22 GLU Chi-restraints excluded: chain A residue 33 LYS Chi-restraints excluded: chain A residue 52 MET Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 223 PHE Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 284 HIS Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 19 CYS Chi-restraints excluded: chain B residue 30 GLU Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 74 ARG Chi-restraints excluded: chain B residue 80 SER Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 128 ARG Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain B residue 176 LYS Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 201 TYR Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain C residue 15 ILE Chi-restraints excluded: chain C residue 28 CYS Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 52 MET Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 114 MET Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 148 VAL Chi-restraints excluded: chain C residue 156 THR Chi-restraints excluded: chain C residue 185 CYS Chi-restraints excluded: chain C residue 195 PHE Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 223 PHE Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 271 ILE Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 40 ASN Chi-restraints excluded: chain D residue 61 SER Chi-restraints excluded: chain D residue 80 SER Chi-restraints excluded: chain D residue 82 SER Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain D residue 133 SER Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain D residue 289 GLU Chi-restraints excluded: chain D residue 291 SER Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 37 HIS Chi-restraints excluded: chain E residue 68 PHE Chi-restraints excluded: chain E residue 92 ILE Chi-restraints excluded: chain E residue 98 ILE Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain E residue 185 CYS Chi-restraints excluded: chain E residue 203 VAL Chi-restraints excluded: chain E residue 223 PHE Chi-restraints excluded: chain E residue 263 LEU Chi-restraints excluded: chain E residue 273 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 117 optimal weight: 20.0000 chunk 125 optimal weight: 3.9990 chunk 129 optimal weight: 10.0000 chunk 75 optimal weight: 8.9990 chunk 54 optimal weight: 3.9990 chunk 98 optimal weight: 8.9990 chunk 38 optimal weight: 6.9990 chunk 113 optimal weight: 8.9990 chunk 118 optimal weight: 0.9990 chunk 82 optimal weight: 0.9990 chunk 132 optimal weight: 6.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 165 HIS ** E 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 257 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7258 moved from start: 0.2091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11549 Z= 0.201 Angle : 0.580 12.727 15684 Z= 0.298 Chirality : 0.039 0.166 1776 Planarity : 0.003 0.031 1904 Dihedral : 9.494 89.552 1674 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 6.41 % Allowed : 30.77 % Favored : 62.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.23), residues: 1410 helix: 0.94 (0.16), residues: 1103 sheet: None (None), residues: 0 loop : -2.66 (0.32), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS C 165 PHE 0.025 0.001 PHE A 279 TYR 0.016 0.001 TYR E 31 ARG 0.007 0.000 ARG D 290 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 224 time to evaluate : 1.162 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 33 LYS cc_start: 0.7168 (OUTLIER) cc_final: 0.6824 (tmtp) REVERT: A 72 LYS cc_start: 0.8418 (mmtt) cc_final: 0.8010 (mmtp) REVERT: A 81 MET cc_start: 0.7139 (mmm) cc_final: 0.6873 (mmm) REVERT: A 116 LEU cc_start: 0.8472 (OUTLIER) cc_final: 0.7901 (tp) REVERT: A 223 PHE cc_start: 0.7802 (OUTLIER) cc_final: 0.7429 (t80) REVERT: A 263 LEU cc_start: 0.7556 (OUTLIER) cc_final: 0.7328 (tt) REVERT: A 273 LEU cc_start: 0.8812 (mt) cc_final: 0.8447 (tp) REVERT: A 282 LYS cc_start: 0.7341 (tttt) cc_final: 0.7041 (ttmt) REVERT: A 284 HIS cc_start: 0.7021 (OUTLIER) cc_final: 0.6270 (t-170) REVERT: A 290 ARG cc_start: 0.6928 (mmm-85) cc_final: 0.6669 (mmm160) REVERT: B 88 PHE cc_start: 0.7829 (t80) cc_final: 0.7495 (t80) REVERT: B 194 ILE cc_start: 0.7792 (mt) cc_final: 0.7565 (mm) REVERT: B 201 TYR cc_start: 0.7301 (OUTLIER) cc_final: 0.6647 (m-80) REVERT: C 28 CYS cc_start: 0.7569 (OUTLIER) cc_final: 0.7029 (m) REVERT: C 48 ILE cc_start: 0.7450 (mm) cc_final: 0.7235 (mm) REVERT: C 104 LEU cc_start: 0.7288 (OUTLIER) cc_final: 0.6990 (tm) REVERT: C 195 PHE cc_start: 0.8091 (OUTLIER) cc_final: 0.5510 (m-80) REVERT: D 16 LYS cc_start: 0.7149 (pttm) cc_final: 0.6771 (pttp) REVERT: D 33 LYS cc_start: 0.7252 (tmtm) cc_final: 0.6912 (tmtt) REVERT: D 94 PHE cc_start: 0.7713 (t80) cc_final: 0.7375 (t80) REVERT: D 120 LYS cc_start: 0.7782 (mmmt) cc_final: 0.7415 (mptt) REVERT: D 163 LYS cc_start: 0.8097 (mptp) cc_final: 0.7829 (mptt) REVERT: D 271 ILE cc_start: 0.8539 (mm) cc_final: 0.8215 (mp) REVERT: E 33 LYS cc_start: 0.7844 (tttt) cc_final: 0.7585 (tttp) REVERT: E 37 HIS cc_start: 0.7530 (OUTLIER) cc_final: 0.7150 (t-90) REVERT: E 52 MET cc_start: 0.6876 (tpp) cc_final: 0.6555 (tpp) REVERT: E 72 LYS cc_start: 0.7080 (mmtt) cc_final: 0.6765 (mmtm) REVERT: E 100 THR cc_start: 0.8199 (t) cc_final: 0.7908 (m) REVERT: E 105 PHE cc_start: 0.8042 (t80) cc_final: 0.7816 (t80) REVERT: E 162 GLU cc_start: 0.7293 (mm-30) cc_final: 0.6044 (mm-30) REVERT: E 185 CYS cc_start: 0.6676 (OUTLIER) cc_final: 0.6393 (t) REVERT: E 217 PHE cc_start: 0.7723 (t80) cc_final: 0.7479 (t80) outliers start: 75 outliers final: 57 residues processed: 278 average time/residue: 0.7418 time to fit residues: 234.1104 Evaluate side-chains 286 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 218 time to evaluate : 1.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 22 GLU Chi-restraints excluded: chain A residue 33 LYS Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 223 PHE Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 284 HIS Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 19 CYS Chi-restraints excluded: chain B residue 30 GLU Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 80 SER Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 128 ARG Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain B residue 176 LYS Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 201 TYR Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain C residue 15 ILE Chi-restraints excluded: chain C residue 28 CYS Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 52 MET Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 114 MET Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 148 VAL Chi-restraints excluded: chain C residue 156 THR Chi-restraints excluded: chain C residue 185 CYS Chi-restraints excluded: chain C residue 195 PHE Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 223 PHE Chi-restraints excluded: chain C residue 271 ILE Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 40 ASN Chi-restraints excluded: chain D residue 61 SER Chi-restraints excluded: chain D residue 80 SER Chi-restraints excluded: chain D residue 82 SER Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain D residue 133 SER Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 37 HIS Chi-restraints excluded: chain E residue 68 PHE Chi-restraints excluded: chain E residue 92 ILE Chi-restraints excluded: chain E residue 98 ILE Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain E residue 185 CYS Chi-restraints excluded: chain E residue 203 VAL Chi-restraints excluded: chain E residue 223 PHE Chi-restraints excluded: chain E residue 263 LEU Chi-restraints excluded: chain E residue 273 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 81 optimal weight: 2.9990 chunk 63 optimal weight: 5.9990 chunk 92 optimal weight: 5.9990 chunk 139 optimal weight: 1.9990 chunk 128 optimal weight: 6.9990 chunk 111 optimal weight: 6.9990 chunk 11 optimal weight: 7.9990 chunk 85 optimal weight: 20.0000 chunk 68 optimal weight: 4.9990 chunk 88 optimal weight: 6.9990 chunk 118 optimal weight: 1.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 165 HIS ** B 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 257 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7260 moved from start: 0.2133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11549 Z= 0.209 Angle : 0.591 13.285 15684 Z= 0.304 Chirality : 0.040 0.170 1776 Planarity : 0.003 0.033 1904 Dihedral : 9.457 89.132 1674 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 6.32 % Allowed : 31.11 % Favored : 62.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.23), residues: 1410 helix: 0.96 (0.16), residues: 1102 sheet: None (None), residues: 0 loop : -2.65 (0.32), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS C 165 PHE 0.025 0.001 PHE A 144 TYR 0.016 0.001 TYR E 31 ARG 0.008 0.000 ARG D 290 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 222 time to evaluate : 1.114 Fit side-chains revert: symmetry clash REVERT: A 33 LYS cc_start: 0.7173 (OUTLIER) cc_final: 0.6955 (tmtt) REVERT: A 72 LYS cc_start: 0.8403 (mmtt) cc_final: 0.8002 (mmtp) REVERT: A 81 MET cc_start: 0.7041 (mmm) cc_final: 0.6807 (mmm) REVERT: A 116 LEU cc_start: 0.8502 (OUTLIER) cc_final: 0.7932 (tp) REVERT: A 223 PHE cc_start: 0.7828 (OUTLIER) cc_final: 0.7449 (t80) REVERT: A 263 LEU cc_start: 0.7568 (OUTLIER) cc_final: 0.7349 (tt) REVERT: A 273 LEU cc_start: 0.8828 (mt) cc_final: 0.8446 (tp) REVERT: A 282 LYS cc_start: 0.7334 (tttt) cc_final: 0.7033 (ttmt) REVERT: A 284 HIS cc_start: 0.7068 (OUTLIER) cc_final: 0.6310 (t-170) REVERT: A 290 ARG cc_start: 0.6947 (mmm-85) cc_final: 0.6697 (mmm160) REVERT: B 88 PHE cc_start: 0.7820 (t80) cc_final: 0.7446 (t80) REVERT: B 194 ILE cc_start: 0.7960 (mt) cc_final: 0.7719 (mm) REVERT: B 201 TYR cc_start: 0.7239 (OUTLIER) cc_final: 0.6617 (m-80) REVERT: C 28 CYS cc_start: 0.7565 (OUTLIER) cc_final: 0.7033 (m) REVERT: C 75 GLU cc_start: 0.7655 (mt-10) cc_final: 0.7110 (mt-10) REVERT: C 95 MET cc_start: 0.7212 (tpp) cc_final: 0.7004 (mmp) REVERT: C 104 LEU cc_start: 0.7291 (OUTLIER) cc_final: 0.6996 (tm) REVERT: C 195 PHE cc_start: 0.8032 (OUTLIER) cc_final: 0.5499 (m-80) REVERT: C 204 LEU cc_start: 0.8122 (tp) cc_final: 0.7920 (tp) REVERT: D 16 LYS cc_start: 0.7232 (pttm) cc_final: 0.6850 (pttp) REVERT: D 33 LYS cc_start: 0.7285 (tmtm) cc_final: 0.6936 (tmtt) REVERT: D 94 PHE cc_start: 0.7698 (t80) cc_final: 0.7375 (t80) REVERT: D 120 LYS cc_start: 0.7771 (mmmt) cc_final: 0.7418 (mptt) REVERT: D 163 LYS cc_start: 0.8091 (mptp) cc_final: 0.7820 (mptt) REVERT: D 267 ILE cc_start: 0.8109 (mt) cc_final: 0.7846 (mt) REVERT: D 271 ILE cc_start: 0.8528 (mm) cc_final: 0.8215 (mp) REVERT: E 33 LYS cc_start: 0.7849 (tttt) cc_final: 0.7575 (tttp) REVERT: E 35 LYS cc_start: 0.8304 (ttmm) cc_final: 0.8063 (mtpp) REVERT: E 37 HIS cc_start: 0.7517 (OUTLIER) cc_final: 0.7142 (t-90) REVERT: E 52 MET cc_start: 0.6862 (tpp) cc_final: 0.6538 (tpp) REVERT: E 72 LYS cc_start: 0.7087 (mmtt) cc_final: 0.6759 (mmtm) REVERT: E 95 MET cc_start: 0.6341 (mpp) cc_final: 0.5980 (mpp) REVERT: E 100 THR cc_start: 0.8227 (t) cc_final: 0.7920 (m) REVERT: E 105 PHE cc_start: 0.8053 (t80) cc_final: 0.7839 (t80) REVERT: E 162 GLU cc_start: 0.7292 (mm-30) cc_final: 0.6002 (mm-30) REVERT: E 185 CYS cc_start: 0.6684 (OUTLIER) cc_final: 0.6451 (t) REVERT: E 217 PHE cc_start: 0.7739 (t80) cc_final: 0.7496 (t80) outliers start: 74 outliers final: 52 residues processed: 275 average time/residue: 0.7758 time to fit residues: 240.1221 Evaluate side-chains 282 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 219 time to evaluate : 1.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 22 GLU Chi-restraints excluded: chain A residue 33 LYS Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 223 PHE Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 284 HIS Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 19 CYS Chi-restraints excluded: chain B residue 30 GLU Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 74 ARG Chi-restraints excluded: chain B residue 80 SER Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 128 ARG Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain B residue 176 LYS Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 201 TYR Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain C residue 15 ILE Chi-restraints excluded: chain C residue 28 CYS Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 52 MET Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 114 MET Chi-restraints excluded: chain C residue 148 VAL Chi-restraints excluded: chain C residue 156 THR Chi-restraints excluded: chain C residue 185 CYS Chi-restraints excluded: chain C residue 195 PHE Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 223 PHE Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 40 ASN Chi-restraints excluded: chain D residue 61 SER Chi-restraints excluded: chain D residue 80 SER Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain D residue 133 SER Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 37 HIS Chi-restraints excluded: chain E residue 68 PHE Chi-restraints excluded: chain E residue 92 ILE Chi-restraints excluded: chain E residue 98 ILE Chi-restraints excluded: chain E residue 185 CYS Chi-restraints excluded: chain E residue 203 VAL Chi-restraints excluded: chain E residue 223 PHE Chi-restraints excluded: chain E residue 263 LEU Chi-restraints excluded: chain E residue 273 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 34 optimal weight: 8.9990 chunk 102 optimal weight: 5.9990 chunk 16 optimal weight: 9.9990 chunk 30 optimal weight: 20.0000 chunk 111 optimal weight: 4.9990 chunk 46 optimal weight: 5.9990 chunk 114 optimal weight: 20.0000 chunk 14 optimal weight: 20.0000 chunk 20 optimal weight: 20.0000 chunk 97 optimal weight: 3.9990 chunk 6 optimal weight: 6.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 165 HIS ** E 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 257 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.167446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.152170 restraints weight = 13980.192| |-----------------------------------------------------------------------------| r_work (start): 0.3794 rms_B_bonded: 1.79 r_work: 0.3705 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3587 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7365 moved from start: 0.1996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 11549 Z= 0.275 Angle : 0.634 13.290 15684 Z= 0.328 Chirality : 0.041 0.171 1776 Planarity : 0.003 0.035 1904 Dihedral : 9.668 88.480 1674 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 6.58 % Allowed : 30.68 % Favored : 62.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.22), residues: 1410 helix: 0.84 (0.16), residues: 1093 sheet: None (None), residues: 0 loop : -2.57 (0.31), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS C 165 PHE 0.025 0.002 PHE A 288 TYR 0.018 0.001 TYR E 31 ARG 0.008 0.000 ARG D 290 =============================================================================== Job complete usr+sys time: 4061.76 seconds wall clock time: 73 minutes 26.65 seconds (4406.65 seconds total)