Starting phenix.real_space_refine on Sat Apr 6 22:44:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jlq_36404/04_2024/8jlq_36404_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jlq_36404/04_2024/8jlq_36404.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jlq_36404/04_2024/8jlq_36404.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jlq_36404/04_2024/8jlq_36404.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jlq_36404/04_2024/8jlq_36404_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jlq_36404/04_2024/8jlq_36404_updated.pdb" } resolution = 2.84 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.006 sd= 0.121 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 67 5.16 5 Cl 1 4.86 5 C 5767 2.51 5 N 1541 2.21 5 O 1657 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 389": "NH1" <-> "NH2" Residue "B PHE 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 9033 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1902 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 6, 'TRANS': 221} Chain breaks: 3 Chain: "B" Number of atoms: 2587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2587 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "R" Number of atoms: 2294 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2294 Classifications: {'peptide': 283} Link IDs: {'PTRANS': 11, 'TRANS': 271} Chain breaks: 1 Chain: "S" Number of atoms: 1784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1784 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 10, 'TRANS': 222} Chain breaks: 1 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Chain: "Y" Number of atoms: 445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 445 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 4, 'TRANS': 53} Chain: "R" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 21 Unusual residues: {'G3C': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.39, per 1000 atoms: 0.60 Number of scatterers: 9033 At special positions: 0 Unit cell: (107.12, 128.96, 101.92, 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) Cl 1 17.00 S 67 16.00 O 1657 8.00 N 1541 7.00 C 5767 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS B 121 " - pdb=" SG CYS B 149 " distance=2.04 Simple disulfide: pdb=" SG CYS R 96 " - pdb=" SG CYS R 182 " distance=2.03 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.03 Simple disulfide: pdb=" SG CYS S 159 " - pdb=" SG CYS S 229 " distance=2.04 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: 3.30 Conformation dependent library (CDL) restraints added in 1.7 seconds 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2140 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 25 helices and 13 sheets defined 34.9% alpha, 19.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.67 Creating SS restraints... Processing helix chain 'A' and resid 14 through 38 Processing helix chain 'A' and resid 53 through 61 Processing helix chain 'A' and resid 234 through 237 Processing helix chain 'A' and resid 265 through 277 Processing helix chain 'A' and resid 280 through 282 No H-bonds generated for 'chain 'A' and resid 280 through 282' Processing helix chain 'A' and resid 294 through 301 removed outlier: 3.525A pdb=" N LYS A 300 " --> pdb=" O LEU A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 350 removed outlier: 4.572A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N SER A 349 " --> pdb=" O PHE A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 390 removed outlier: 4.031A pdb=" N GLN A 384 " --> pdb=" O ARG A 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 25 Processing helix chain 'B' and resid 30 through 33 No H-bonds generated for 'chain 'B' and resid 30 through 33' Processing helix chain 'R' and resid 23 through 50 Processing helix chain 'R' and resid 52 through 54 No H-bonds generated for 'chain 'R' and resid 52 through 54' Processing helix chain 'R' and resid 57 through 86 removed outlier: 4.269A pdb=" N MET R 77 " --> pdb=" O GLY R 73 " (cutoff:3.500A) Proline residue: R 78 - end of helix Processing helix chain 'R' and resid 93 through 123 Processing helix chain 'R' and resid 128 through 134 removed outlier: 3.571A pdb=" N TYR R 131 " --> pdb=" O PRO R 128 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N LYS R 132 " --> pdb=" O LEU R 129 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ALA R 133 " --> pdb=" O ARG R 130 " (cutoff:3.500A) Processing helix chain 'R' and resid 137 through 159 Proline residue: R 151 - end of helix Processing helix chain 'R' and resid 169 through 179 removed outlier: 4.201A pdb=" N ARG R 179 " --> pdb=" O HIS R 175 " (cutoff:3.500A) Processing helix chain 'R' and resid 188 through 198 Processing helix chain 'R' and resid 200 through 231 removed outlier: 3.871A pdb=" N ILE R 224 " --> pdb=" O GLN R 220 " (cutoff:3.500A) Processing helix chain 'R' and resid 249 through 276 Proline residue: R 266 - end of helix Proline residue: R 275 - end of helix Processing helix chain 'R' and resid 283 through 304 Proline residue: R 301 - end of helix Processing helix chain 'R' and resid 309 through 318 Processing helix chain 'S' and resid 221 through 223 No H-bonds generated for 'chain 'S' and resid 221 through 223' Processing helix chain 'Y' and resid 7 through 23 Processing helix chain 'Y' and resid 30 through 43 Processing sheet with id= A, first strand: chain 'A' and resid 359 through 363 removed outlier: 7.368A pdb=" N VAL A 287 " --> pdb=" O TYR A 360 " (cutoff:3.500A) removed outlier: 8.067A pdb=" N HIS A 362 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N LEU A 289 " --> pdb=" O HIS A 362 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ASN A 218 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N LEU A 43 " --> pdb=" O ASN A 218 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N HIS A 220 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N LEU A 45 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N PHE A 222 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 8.121A pdb=" N GLY A 47 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N VAL A 224 " --> pdb=" O GLY A 47 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 48 through 52 removed outlier: 3.809A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.893A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 137 through 139 Processing sheet with id= E, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.752A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.750A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N SER B 161 " --> pdb=" O THR B 165 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N CYS B 166 " --> pdb=" O PHE B 180 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N PHE B 180 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N LEU B 168 " --> pdb=" O THR B 178 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.839A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N ALA B 203 " --> pdb=" O SER B 207 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.658A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 5.230A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 296 through 298 removed outlier: 3.744A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'S' and resid 3 through 7 Processing sheet with id= J, first strand: chain 'S' and resid 97 through 99 removed outlier: 3.978A pdb=" N ALA S 49 " --> pdb=" O TRP S 36 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'S' and resid 140 through 142 Processing sheet with id= L, first strand: chain 'S' and resid 146 through 148 removed outlier: 6.303A pdb=" N LYS S 244 " --> pdb=" O VAL S 147 " (cutoff:3.500A) No H-bonds generated for sheet with id= L Processing sheet with id= M, first strand: chain 'S' and resid 174 through 176 400 hydrogen bonds defined for protein. 1161 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.73 Time building geometry restraints manager: 3.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1446 1.30 - 1.44: 2616 1.44 - 1.57: 5074 1.57 - 1.71: 0 1.71 - 1.84: 101 Bond restraints: 9237 Sorted by residual: bond pdb=" CA HIS R 99 " pdb=" CB HIS R 99 " ideal model delta sigma weight residual 1.530 1.447 0.083 1.57e-02 4.06e+03 2.79e+01 bond pdb=" C ARG B 134 " pdb=" O ARG B 134 " ideal model delta sigma weight residual 1.234 1.170 0.063 1.26e-02 6.30e+03 2.52e+01 bond pdb=" N ARG A 347 " pdb=" CA ARG A 347 " ideal model delta sigma weight residual 1.457 1.393 0.064 1.29e-02 6.01e+03 2.48e+01 bond pdb=" C ARG A 283 " pdb=" O ARG A 283 " ideal model delta sigma weight residual 1.236 1.180 0.057 1.16e-02 7.43e+03 2.39e+01 bond pdb=" CA PHE R 154 " pdb=" C PHE R 154 " ideal model delta sigma weight residual 1.524 1.461 0.063 1.32e-02 5.74e+03 2.28e+01 ... (remaining 9232 not shown) Histogram of bond angle deviations from ideal: 98.15 - 105.37: 149 105.37 - 112.60: 4750 112.60 - 119.83: 3149 119.83 - 127.05: 4348 127.05 - 134.28: 109 Bond angle restraints: 12505 Sorted by residual: angle pdb=" C ARG A 283 " pdb=" N ASP A 284 " pdb=" CA ASP A 284 " ideal model delta sigma weight residual 122.21 110.02 12.19 1.48e+00 4.57e-01 6.78e+01 angle pdb=" C GLU S 234 " pdb=" N TYR S 235 " pdb=" CA TYR S 235 " ideal model delta sigma weight residual 122.89 115.22 7.67 1.12e+00 7.97e-01 4.69e+01 angle pdb=" N VAL R 184 " pdb=" CA VAL R 184 " pdb=" C VAL R 184 " ideal model delta sigma weight residual 109.37 116.64 -7.27 1.35e+00 5.49e-01 2.90e+01 angle pdb=" N TYR A 358 " pdb=" CA TYR A 358 " pdb=" CB TYR A 358 " ideal model delta sigma weight residual 111.43 103.57 7.86 1.59e+00 3.96e-01 2.44e+01 angle pdb=" N THR B 223 " pdb=" CA THR B 223 " pdb=" C THR B 223 " ideal model delta sigma weight residual 110.17 102.80 7.37 1.51e+00 4.39e-01 2.38e+01 ... (remaining 12500 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.77: 4954 16.77 - 33.53: 412 33.53 - 50.30: 101 50.30 - 67.07: 9 67.07 - 83.84: 6 Dihedral angle restraints: 5482 sinusoidal: 2165 harmonic: 3317 Sorted by residual: dihedral pdb=" CB CYS R 96 " pdb=" SG CYS R 96 " pdb=" SG CYS R 182 " pdb=" CB CYS R 182 " ideal model delta sinusoidal sigma weight residual -86.00 -148.00 62.00 1 1.00e+01 1.00e-02 5.09e+01 dihedral pdb=" C ARG B 134 " pdb=" N ARG B 134 " pdb=" CA ARG B 134 " pdb=" CB ARG B 134 " ideal model delta harmonic sigma weight residual -122.60 -110.44 -12.16 0 2.50e+00 1.60e-01 2.37e+01 dihedral pdb=" CA TYR S 235 " pdb=" C TYR S 235 " pdb=" N PRO S 236 " pdb=" CA PRO S 236 " ideal model delta harmonic sigma weight residual 180.00 158.91 21.09 0 5.00e+00 4.00e-02 1.78e+01 ... (remaining 5479 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1085 0.054 - 0.108: 265 0.108 - 0.162: 35 0.162 - 0.216: 7 0.216 - 0.270: 1 Chirality restraints: 1393 Sorted by residual: chirality pdb=" CA ARG B 134 " pdb=" N ARG B 134 " pdb=" C ARG B 134 " pdb=" CB ARG B 134 " both_signs ideal model delta sigma weight residual False 2.51 2.78 -0.27 2.00e-01 2.50e+01 1.82e+00 chirality pdb=" CA ILE B 338 " pdb=" N ILE B 338 " pdb=" C ILE B 338 " pdb=" CB ILE B 338 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.19 2.00e-01 2.50e+01 9.30e-01 chirality pdb=" CA ILE B 229 " pdb=" N ILE B 229 " pdb=" C ILE B 229 " pdb=" CB ILE B 229 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 8.74e-01 ... (remaining 1390 not shown) Planarity restraints: 1577 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN R 220 " 0.019 2.00e-02 2.50e+03 3.84e-02 1.48e+01 pdb=" C GLN R 220 " -0.066 2.00e-02 2.50e+03 pdb=" O GLN R 220 " 0.024 2.00e-02 2.50e+03 pdb=" N ALA R 221 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS R 99 " -0.028 2.00e-02 2.50e+03 2.33e-02 8.16e+00 pdb=" CG HIS R 99 " 0.048 2.00e-02 2.50e+03 pdb=" ND1 HIS R 99 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 HIS R 99 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 HIS R 99 " -0.008 2.00e-02 2.50e+03 pdb=" NE2 HIS R 99 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE R 292 " 0.014 2.00e-02 2.50e+03 2.84e-02 8.06e+00 pdb=" C PHE R 292 " -0.049 2.00e-02 2.50e+03 pdb=" O PHE R 292 " 0.019 2.00e-02 2.50e+03 pdb=" N GLY R 293 " 0.016 2.00e-02 2.50e+03 ... (remaining 1574 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 840 2.74 - 3.28: 9521 3.28 - 3.82: 16213 3.82 - 4.36: 19166 4.36 - 4.90: 32359 Nonbonded interactions: 78099 Sorted by model distance: nonbonded pdb=" OE2 GLU A 15 " pdb=" OH TYR S 175 " model vdw 2.203 2.440 nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.210 2.440 nonbonded pdb=" ND1 HIS A 387 " pdb=" O ALA R 124 " model vdw 2.230 2.520 nonbonded pdb=" OD2 ASP B 83 " pdb=" OG1 THR B 86 " model vdw 2.241 2.440 nonbonded pdb=" OG SER B 108 " pdb=" OD1 ASP B 154 " model vdw 2.261 2.440 ... (remaining 78094 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.390 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: 2.480 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 27.940 Find NCS groups from input model: 0.260 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:11.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6613 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 : 0.005 0.083 9237 Z= 0.308 Angle : 0.782 12.189 12505 Z= 0.475 Chirality : 0.047 0.270 1393 Planarity : 0.005 0.044 1577 Dihedral : 13.144 83.836 3330 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 18.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 0.41 % Allowed : 1.02 % Favored : 98.57 % Cbeta Deviations : 0.09 % 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: -0.45 (0.25), residues: 1120 helix: 0.90 (0.26), residues: 403 sheet: -0.51 (0.32), residues: 270 loop : -1.19 (0.29), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 82 HIS 0.016 0.001 HIS R 99 PHE 0.018 0.001 PHE R 154 TYR 0.029 0.002 TYR A 358 ARG 0.006 0.000 ARG A 20 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 170 time to evaluate : 0.995 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 65 MET cc_start: 0.7214 (ttp) cc_final: 0.7003 (mtp) REVERT: Y 32 LYS cc_start: 0.8155 (tttm) cc_final: 0.7781 (tppt) outliers start: 4 outliers final: 3 residues processed: 173 average time/residue: 1.1086 time to fit residues: 206.2282 Evaluate side-chains 140 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 137 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 229 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 0.6980 chunk 84 optimal weight: 10.0000 chunk 46 optimal weight: 0.9990 chunk 28 optimal weight: 0.7980 chunk 56 optimal weight: 5.9990 chunk 44 optimal weight: 4.9990 chunk 87 optimal weight: 0.8980 chunk 33 optimal weight: 0.6980 chunk 52 optimal weight: 4.9990 chunk 64 optimal weight: 1.9990 chunk 100 optimal weight: 7.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS ** B 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 156 GLN B 183 HIS B 220 GLN ** B 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 164 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6773 moved from start: 0.1382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9237 Z= 0.214 Angle : 0.592 7.775 12505 Z= 0.308 Chirality : 0.043 0.202 1393 Planarity : 0.004 0.045 1577 Dihedral : 4.748 51.206 1261 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 16.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 2.14 % Allowed : 11.30 % Favored : 86.56 % 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: -0.21 (0.25), residues: 1120 helix: 1.25 (0.25), residues: 409 sheet: -0.51 (0.32), residues: 275 loop : -1.17 (0.29), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 211 HIS 0.005 0.001 HIS R 55 PHE 0.016 0.002 PHE R 299 TYR 0.018 0.001 TYR A 37 ARG 0.007 0.000 ARG A 38 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 144 time to evaluate : 1.084 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 338 LYS cc_start: 0.6973 (OUTLIER) cc_final: 0.6615 (ptmt) REVERT: A 356 ARG cc_start: 0.6903 (mtp180) cc_final: 0.6456 (pmm150) REVERT: B 132 ASN cc_start: 0.6384 (m-40) cc_final: 0.6173 (p0) REVERT: Y 32 LYS cc_start: 0.8130 (tttm) cc_final: 0.7745 (tppt) outliers start: 21 outliers final: 6 residues processed: 152 average time/residue: 1.0833 time to fit residues: 177.8415 Evaluate side-chains 134 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 127 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 338 LYS Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain R residue 126 CYS Chi-restraints excluded: chain R residue 138 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 56 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 chunk 83 optimal weight: 2.9990 chunk 68 optimal weight: 6.9990 chunk 27 optimal weight: 4.9990 chunk 100 optimal weight: 8.9990 chunk 109 optimal weight: 4.9990 chunk 89 optimal weight: 0.0670 chunk 34 optimal weight: 0.7980 chunk 81 optimal weight: 0.8980 chunk 99 optimal weight: 0.9980 overall best weight: 0.7518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS A 357 HIS ** B 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 ASN ** B 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6801 moved from start: 0.1755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9237 Z= 0.200 Angle : 0.571 12.095 12505 Z= 0.295 Chirality : 0.043 0.191 1393 Planarity : 0.004 0.047 1577 Dihedral : 4.653 53.170 1258 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 16.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 2.85 % Allowed : 13.14 % Favored : 84.01 % 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 (0.25), residues: 1120 helix: 1.48 (0.26), residues: 405 sheet: -0.42 (0.32), residues: 273 loop : -1.23 (0.29), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 211 HIS 0.006 0.001 HIS A 357 PHE 0.014 0.001 PHE B 253 TYR 0.016 0.001 TYR R 200 ARG 0.005 0.000 ARG A 38 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 132 time to evaluate : 0.955 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 338 LYS cc_start: 0.6860 (OUTLIER) cc_final: 0.6495 (ptmt) REVERT: B 134 ARG cc_start: 0.6884 (ptp-170) cc_final: 0.6518 (ptt-90) REVERT: R 65 MET cc_start: 0.7437 (ttp) cc_final: 0.7105 (ttp) REVERT: Y 32 LYS cc_start: 0.8144 (tttm) cc_final: 0.7740 (tppt) outliers start: 28 outliers final: 12 residues processed: 145 average time/residue: 1.0749 time to fit residues: 168.4859 Evaluate side-chains 135 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 122 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 338 LYS Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain R residue 32 LEU Chi-restraints excluded: chain R residue 76 VAL Chi-restraints excluded: chain R residue 126 CYS Chi-restraints excluded: chain R residue 138 LEU Chi-restraints excluded: chain R residue 209 VAL Chi-restraints excluded: chain S residue 23 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 75 optimal weight: 0.0770 chunk 52 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 chunk 67 optimal weight: 0.4980 chunk 101 optimal weight: 6.9990 chunk 107 optimal weight: 7.9990 chunk 96 optimal weight: 10.0000 chunk 28 optimal weight: 0.6980 chunk 89 optimal weight: 20.0000 chunk 60 optimal weight: 2.9990 overall best weight: 0.8140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS A 357 HIS B 32 GLN ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 175 GLN B 230 ASN B 268 ASN ** B 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 164 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6826 moved from start: 0.2056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9237 Z= 0.206 Angle : 0.577 9.786 12505 Z= 0.296 Chirality : 0.043 0.179 1393 Planarity : 0.004 0.047 1577 Dihedral : 4.583 50.361 1258 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 15.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 3.26 % Allowed : 16.09 % Favored : 80.65 % 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: -0.04 (0.25), residues: 1120 helix: 1.48 (0.25), residues: 405 sheet: -0.41 (0.32), residues: 275 loop : -1.16 (0.29), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 82 HIS 0.006 0.001 HIS A 357 PHE 0.014 0.001 PHE A 212 TYR 0.014 0.001 TYR R 200 ARG 0.004 0.000 ARG S 38 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 136 time to evaluate : 1.073 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 338 LYS cc_start: 0.6828 (OUTLIER) cc_final: 0.6479 (ptmt) REVERT: A 356 ARG cc_start: 0.6873 (mtp180) cc_final: 0.6536 (mtm-85) REVERT: B 134 ARG cc_start: 0.6960 (ptp-170) cc_final: 0.6508 (ptt-90) REVERT: B 159 THR cc_start: 0.7778 (p) cc_final: 0.7232 (m) REVERT: R 65 MET cc_start: 0.7468 (ttp) cc_final: 0.7254 (ttp) REVERT: R 123 TYR cc_start: 0.8162 (m-80) cc_final: 0.7646 (m-80) REVERT: Y 32 LYS cc_start: 0.8134 (tttm) cc_final: 0.7727 (tppt) outliers start: 32 outliers final: 10 residues processed: 157 average time/residue: 1.0411 time to fit residues: 176.9050 Evaluate side-chains 134 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 123 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 338 LYS Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 76 VAL Chi-restraints excluded: chain R residue 126 CYS Chi-restraints excluded: chain R residue 138 LEU Chi-restraints excluded: chain S residue 23 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 1 optimal weight: 1.9990 chunk 79 optimal weight: 3.9990 chunk 44 optimal weight: 8.9990 chunk 91 optimal weight: 7.9990 chunk 74 optimal weight: 0.8980 chunk 0 optimal weight: 8.9990 chunk 54 optimal weight: 0.9980 chunk 96 optimal weight: 10.0000 chunk 27 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS ** B 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 175 GLN B 230 ASN B 268 ASN ** B 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6931 moved from start: 0.2543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 9237 Z= 0.310 Angle : 0.647 11.676 12505 Z= 0.328 Chirality : 0.046 0.349 1393 Planarity : 0.004 0.048 1577 Dihedral : 4.532 25.295 1256 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 18.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 4.68 % Allowed : 16.29 % Favored : 79.02 % 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: -0.13 (0.25), residues: 1120 helix: 1.37 (0.25), residues: 405 sheet: -0.46 (0.32), residues: 275 loop : -1.17 (0.29), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 82 HIS 0.008 0.001 HIS A 357 PHE 0.016 0.002 PHE A 212 TYR 0.019 0.002 TYR B 105 ARG 0.006 0.001 ARG S 38 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 136 time to evaluate : 1.067 Fit side-chains revert: symmetry clash REVERT: A 338 LYS cc_start: 0.6815 (OUTLIER) cc_final: 0.6281 (ptmt) REVERT: B 134 ARG cc_start: 0.7054 (ptp-170) cc_final: 0.6752 (ptp90) REVERT: R 59 ASN cc_start: 0.7539 (m-40) cc_final: 0.7337 (m-40) REVERT: R 123 TYR cc_start: 0.8175 (m-80) cc_final: 0.7649 (m-80) REVERT: Y 32 LYS cc_start: 0.8168 (tttm) cc_final: 0.7771 (tppt) outliers start: 46 outliers final: 18 residues processed: 164 average time/residue: 1.0376 time to fit residues: 184.3840 Evaluate side-chains 145 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 126 time to evaluate : 1.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 338 LYS Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain R residue 32 LEU Chi-restraints excluded: chain R residue 76 VAL Chi-restraints excluded: chain R residue 126 CYS Chi-restraints excluded: chain R residue 138 LEU Chi-restraints excluded: chain R residue 154 PHE Chi-restraints excluded: chain R residue 209 VAL Chi-restraints excluded: chain R residue 253 LEU Chi-restraints excluded: chain S residue 23 SER Chi-restraints excluded: chain S residue 189 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 62 optimal weight: 6.9990 chunk 26 optimal weight: 4.9990 chunk 107 optimal weight: 9.9990 chunk 89 optimal weight: 10.0000 chunk 49 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 chunk 56 optimal weight: 9.9990 chunk 103 optimal weight: 30.0000 chunk 12 optimal weight: 0.5980 chunk 61 optimal weight: 0.8980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS ** B 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 ASN B 268 ASN ** B 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6924 moved from start: 0.2677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 9237 Z= 0.268 Angle : 0.648 10.320 12505 Z= 0.327 Chirality : 0.046 0.290 1393 Planarity : 0.004 0.048 1577 Dihedral : 4.544 25.677 1256 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 18.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 3.97 % Allowed : 17.52 % Favored : 78.51 % 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: -0.19 (0.25), residues: 1120 helix: 1.29 (0.25), residues: 405 sheet: -0.47 (0.32), residues: 273 loop : -1.17 (0.29), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 82 HIS 0.006 0.001 HIS A 357 PHE 0.014 0.002 PHE A 212 TYR 0.015 0.002 TYR B 105 ARG 0.006 0.000 ARG A 283 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 129 time to evaluate : 1.007 Fit side-chains revert: symmetry clash REVERT: A 338 LYS cc_start: 0.6790 (OUTLIER) cc_final: 0.6376 (ptmt) REVERT: B 134 ARG cc_start: 0.7073 (ptp-170) cc_final: 0.6773 (ptp90) REVERT: B 180 PHE cc_start: 0.6696 (OUTLIER) cc_final: 0.4814 (p90) REVERT: B 262 MET cc_start: 0.7210 (OUTLIER) cc_final: 0.6899 (ttt) REVERT: R 65 MET cc_start: 0.7475 (ttp) cc_final: 0.7154 (mtp) REVERT: R 123 TYR cc_start: 0.8169 (m-80) cc_final: 0.7653 (m-80) REVERT: R 220 GLN cc_start: 0.6710 (OUTLIER) cc_final: 0.6507 (mp10) REVERT: Y 32 LYS cc_start: 0.8191 (tttm) cc_final: 0.7811 (tppt) outliers start: 39 outliers final: 19 residues processed: 153 average time/residue: 1.0988 time to fit residues: 181.3977 Evaluate side-chains 142 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 119 time to evaluate : 1.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 338 LYS Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 180 PHE Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain R residue 76 VAL Chi-restraints excluded: chain R residue 126 CYS Chi-restraints excluded: chain R residue 138 LEU Chi-restraints excluded: chain R residue 154 PHE Chi-restraints excluded: chain R residue 209 VAL Chi-restraints excluded: chain R residue 220 GLN Chi-restraints excluded: chain R residue 253 LEU Chi-restraints excluded: chain S residue 23 SER Chi-restraints excluded: chain S residue 189 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 78 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 90 optimal weight: 4.9990 chunk 59 optimal weight: 0.6980 chunk 106 optimal weight: 5.9990 chunk 66 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 42 optimal weight: 10.0000 chunk 63 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS ** B 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 ASN B 268 ASN ** B 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6988 moved from start: 0.3000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 9237 Z= 0.359 Angle : 0.689 10.523 12505 Z= 0.351 Chirality : 0.047 0.276 1393 Planarity : 0.005 0.048 1577 Dihedral : 4.761 26.748 1256 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 19.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 3.36 % Allowed : 18.74 % Favored : 77.90 % 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: -0.30 (0.25), residues: 1120 helix: 1.19 (0.25), residues: 403 sheet: -0.48 (0.32), residues: 264 loop : -1.25 (0.29), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 82 HIS 0.007 0.001 HIS A 357 PHE 0.016 0.002 PHE A 212 TYR 0.017 0.002 TYR B 105 ARG 0.007 0.000 ARG A 283 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 129 time to evaluate : 0.986 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 338 LYS cc_start: 0.6780 (OUTLIER) cc_final: 0.6219 (ptmt) REVERT: A 381 ASP cc_start: 0.7675 (t0) cc_final: 0.7414 (m-30) REVERT: B 134 ARG cc_start: 0.7092 (ptp-170) cc_final: 0.6784 (ptp90) REVERT: B 180 PHE cc_start: 0.7236 (OUTLIER) cc_final: 0.5091 (p90) REVERT: R 65 MET cc_start: 0.7667 (ttp) cc_final: 0.7357 (ttp) REVERT: R 250 VAL cc_start: 0.8028 (t) cc_final: 0.7770 (t) REVERT: Y 32 LYS cc_start: 0.8230 (tttm) cc_final: 0.7866 (tppt) outliers start: 33 outliers final: 18 residues processed: 151 average time/residue: 1.0286 time to fit residues: 168.1213 Evaluate side-chains 141 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 121 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 338 LYS Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 180 PHE Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain R residue 32 LEU Chi-restraints excluded: chain R residue 76 VAL Chi-restraints excluded: chain R residue 126 CYS Chi-restraints excluded: chain R residue 138 LEU Chi-restraints excluded: chain R residue 209 VAL Chi-restraints excluded: chain R residue 253 LEU Chi-restraints excluded: chain R residue 318 MET Chi-restraints excluded: chain S residue 23 SER Chi-restraints excluded: chain S residue 189 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 21 optimal weight: 0.6980 chunk 20 optimal weight: 0.9990 chunk 68 optimal weight: 0.9990 chunk 72 optimal weight: 1.9990 chunk 52 optimal weight: 5.9990 chunk 9 optimal weight: 0.9980 chunk 84 optimal weight: 0.0770 chunk 97 optimal weight: 9.9990 chunk 102 optimal weight: 3.9990 chunk 93 optimal weight: 2.9990 chunk 99 optimal weight: 5.9990 overall best weight: 0.7542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS ** B 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 ASN B 268 ASN ** B 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6905 moved from start: 0.2874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 9237 Z= 0.213 Angle : 0.642 12.009 12505 Z= 0.324 Chirality : 0.044 0.209 1393 Planarity : 0.004 0.048 1577 Dihedral : 4.539 26.169 1256 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 18.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 3.05 % Allowed : 19.86 % Favored : 77.09 % 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: -0.22 (0.25), residues: 1120 helix: 1.26 (0.25), residues: 405 sheet: -0.46 (0.32), residues: 263 loop : -1.19 (0.29), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 82 HIS 0.004 0.001 HIS A 357 PHE 0.014 0.001 PHE R 154 TYR 0.014 0.001 TYR S 102 ARG 0.008 0.000 ARG A 283 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 127 time to evaluate : 0.994 Fit side-chains revert: symmetry clash REVERT: A 338 LYS cc_start: 0.6698 (OUTLIER) cc_final: 0.6290 (ptmt) REVERT: B 134 ARG cc_start: 0.7047 (ptp-170) cc_final: 0.6767 (ptp90) REVERT: B 180 PHE cc_start: 0.6805 (OUTLIER) cc_final: 0.4872 (p90) REVERT: R 192 VAL cc_start: 0.7884 (OUTLIER) cc_final: 0.7606 (t) REVERT: R 196 MET cc_start: 0.7579 (mpp) cc_final: 0.6678 (mpp) REVERT: S 140 MET cc_start: 0.5532 (mmm) cc_final: 0.5036 (mmm) REVERT: Y 32 LYS cc_start: 0.8219 (tttm) cc_final: 0.7829 (tppt) outliers start: 30 outliers final: 17 residues processed: 146 average time/residue: 1.0929 time to fit residues: 172.5159 Evaluate side-chains 142 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 122 time to evaluate : 1.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 338 LYS Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 180 PHE Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain R residue 76 VAL Chi-restraints excluded: chain R residue 126 CYS Chi-restraints excluded: chain R residue 138 LEU Chi-restraints excluded: chain R residue 147 SER Chi-restraints excluded: chain R residue 192 VAL Chi-restraints excluded: chain R residue 209 VAL Chi-restraints excluded: chain R residue 253 LEU Chi-restraints excluded: chain S residue 23 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 102 optimal weight: 8.9990 chunk 60 optimal weight: 0.9990 chunk 43 optimal weight: 5.9990 chunk 78 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 90 optimal weight: 0.0870 chunk 94 optimal weight: 20.0000 chunk 99 optimal weight: 3.9990 chunk 65 optimal weight: 0.4980 chunk 105 optimal weight: 1.9990 chunk 64 optimal weight: 0.9980 overall best weight: 0.6760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS ** B 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 ASN B 268 ASN ** B 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6887 moved from start: 0.2902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9237 Z= 0.200 Angle : 0.624 9.934 12505 Z= 0.317 Chirality : 0.044 0.185 1393 Planarity : 0.004 0.048 1577 Dihedral : 4.461 25.789 1256 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 17.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 2.75 % Allowed : 20.77 % Favored : 76.48 % 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: -0.13 (0.25), residues: 1120 helix: 1.34 (0.25), residues: 404 sheet: -0.38 (0.32), residues: 262 loop : -1.17 (0.29), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 82 HIS 0.004 0.001 HIS A 357 PHE 0.013 0.001 PHE A 212 TYR 0.013 0.001 TYR S 102 ARG 0.007 0.000 ARG R 23 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 124 time to evaluate : 1.022 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 338 LYS cc_start: 0.6651 (OUTLIER) cc_final: 0.6167 (ptmt) REVERT: B 134 ARG cc_start: 0.7067 (ptp-170) cc_final: 0.6802 (ptp90) REVERT: B 180 PHE cc_start: 0.6534 (OUTLIER) cc_final: 0.4830 (p90) REVERT: B 197 ARG cc_start: 0.7039 (mtp85) cc_final: 0.6777 (tpp-160) REVERT: R 23 ARG cc_start: 0.6600 (tpp-160) cc_final: 0.6357 (tpp-160) REVERT: R 123 TYR cc_start: 0.8067 (m-80) cc_final: 0.7441 (m-80) REVERT: S 93 MET cc_start: 0.5310 (mmm) cc_final: 0.4524 (mmm) REVERT: Y 32 LYS cc_start: 0.8216 (tttm) cc_final: 0.7817 (tppt) outliers start: 27 outliers final: 18 residues processed: 143 average time/residue: 1.1486 time to fit residues: 177.1081 Evaluate side-chains 139 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 119 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 338 LYS Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 180 PHE Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain R residue 32 LEU Chi-restraints excluded: chain R residue 76 VAL Chi-restraints excluded: chain R residue 126 CYS Chi-restraints excluded: chain R residue 138 LEU Chi-restraints excluded: chain R residue 147 SER Chi-restraints excluded: chain R residue 209 VAL Chi-restraints excluded: chain R residue 253 LEU Chi-restraints excluded: chain S residue 23 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 50 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 chunk 110 optimal weight: 0.0020 chunk 101 optimal weight: 0.0040 chunk 88 optimal weight: 4.9990 chunk 9 optimal weight: 0.6980 chunk 68 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 chunk 69 optimal weight: 4.9990 chunk 93 optimal weight: 2.9990 chunk 26 optimal weight: 6.9990 overall best weight: 0.7402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS ** B 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 ASN ** B 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6884 moved from start: 0.2955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 9237 Z= 0.209 Angle : 0.640 11.135 12505 Z= 0.324 Chirality : 0.044 0.202 1393 Planarity : 0.004 0.051 1577 Dihedral : 4.481 26.054 1256 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 18.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 2.65 % Allowed : 21.38 % Favored : 75.97 % 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: -0.14 (0.25), residues: 1120 helix: 1.29 (0.26), residues: 409 sheet: -0.38 (0.32), residues: 262 loop : -1.16 (0.29), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.004 0.001 HIS R 55 PHE 0.015 0.001 PHE R 299 TYR 0.016 0.001 TYR R 123 ARG 0.009 0.001 ARG A 283 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 119 time to evaluate : 0.979 Fit side-chains revert: symmetry clash REVERT: A 338 LYS cc_start: 0.6636 (OUTLIER) cc_final: 0.6102 (ptmt) REVERT: B 134 ARG cc_start: 0.7039 (ptp-170) cc_final: 0.6740 (ptp90) REVERT: B 180 PHE cc_start: 0.6577 (OUTLIER) cc_final: 0.4761 (p90) REVERT: B 197 ARG cc_start: 0.7039 (mtp85) cc_final: 0.6837 (tpp-160) REVERT: B 262 MET cc_start: 0.7152 (OUTLIER) cc_final: 0.6889 (ttm) REVERT: R 23 ARG cc_start: 0.6574 (tpp-160) cc_final: 0.6359 (tpp-160) REVERT: Y 32 LYS cc_start: 0.8204 (tttm) cc_final: 0.7801 (tppt) outliers start: 26 outliers final: 16 residues processed: 135 average time/residue: 1.1515 time to fit residues: 167.0000 Evaluate side-chains 137 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 118 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 338 LYS Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 180 PHE Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain R residue 76 VAL Chi-restraints excluded: chain R residue 96 CYS Chi-restraints excluded: chain R residue 126 CYS Chi-restraints excluded: chain R residue 138 LEU Chi-restraints excluded: chain R residue 147 SER Chi-restraints excluded: chain R residue 253 LEU Chi-restraints excluded: chain S residue 23 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 81 optimal weight: 0.5980 chunk 13 optimal weight: 3.9990 chunk 24 optimal weight: 0.9980 chunk 88 optimal weight: 10.0000 chunk 36 optimal weight: 0.7980 chunk 90 optimal weight: 7.9990 chunk 11 optimal weight: 0.0040 chunk 16 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 63 optimal weight: 3.9990 overall best weight: 0.6592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS ** B 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 ASN B 268 ASN ** B 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 164 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4585 r_free = 0.4585 target = 0.238475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.177129 restraints weight = 10014.021| |-----------------------------------------------------------------------------| r_work (start): 0.4003 rms_B_bonded: 2.23 r_work: 0.3874 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3735 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7141 moved from start: 0.2964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 9237 Z= 0.198 Angle : 0.631 11.315 12505 Z= 0.319 Chirality : 0.044 0.217 1393 Planarity : 0.004 0.053 1577 Dihedral : 4.405 25.933 1256 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 17.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 2.65 % Allowed : 21.28 % Favored : 76.07 % 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 (0.25), residues: 1120 helix: 1.30 (0.26), residues: 409 sheet: -0.39 (0.32), residues: 262 loop : -1.12 (0.29), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.004 0.001 HIS R 55 PHE 0.020 0.001 PHE R 299 TYR 0.014 0.001 TYR R 123 ARG 0.009 0.001 ARG A 283 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3690.32 seconds wall clock time: 67 minutes 2.76 seconds (4022.76 seconds total)