Starting phenix.real_space_refine on Wed Feb 14 08:36:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wig_32529/02_2024/7wig_32529_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wig_32529/02_2024/7wig_32529.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wig_32529/02_2024/7wig_32529.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wig_32529/02_2024/7wig_32529.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wig_32529/02_2024/7wig_32529_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wig_32529/02_2024/7wig_32529_updated.pdb" } resolution = 2.7 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= 0.002 sd= 0.033 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 67 5.16 5 C 5697 2.51 5 N 1507 2.21 5 O 1660 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "S TYR 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 8931 Number of models: 1 Model: "" Number of chains: 6 Chain: "R" Number of atoms: 2234 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2234 Classifications: {'peptide': 283} Link IDs: {'PTRANS': 11, 'TRANS': 271} Chain breaks: 1 Chain: "A" Number of atoms: 1811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1811 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 2, 'TRANS': 222} Chain breaks: 1 Chain: "B" Number of atoms: 2607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2607 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 333} Chain: "G" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 444 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 4, 'TRANS': 53} Chain: "S" Number of atoms: 1795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1795 Classifications: {'peptide': 234} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 223} Chain breaks: 1 Chain: "R" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 40 Unusual residues: {'9FI': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.11, per 1000 atoms: 0.57 Number of scatterers: 8931 At special positions: 0 Unit cell: (106.47, 126.75, 111.54, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 67 16.00 O 1660 8.00 N 1507 7.00 C 5697 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 115 " - pdb=" SG CYS R 193 " 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=2.03 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: 3.27 Conformation dependent library (CDL) restraints added in 1.7 seconds 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2126 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 25 helices and 15 sheets defined 34.9% alpha, 22.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.65 Creating SS restraints... Processing helix chain 'R' and resid 42 through 68 Processing helix chain 'R' and resid 77 through 104 Proline residue: R 97 - end of helix removed outlier: 4.043A pdb=" N ALA R 100 " --> pdb=" O LEU R 96 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N MET R 101 " --> pdb=" O PRO R 97 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N GLN R 102 " --> pdb=" O PHE R 98 " (cutoff:3.500A) Processing helix chain 'R' and resid 113 through 144 removed outlier: 3.891A pdb=" N PHE R 127 " --> pdb=" O GLY R 123 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ILE R 130 " --> pdb=" O GLN R 126 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N PHE R 131 " --> pdb=" O PHE R 127 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N CYS R 132 " --> pdb=" O THR R 128 " (cutoff:3.500A) Processing helix chain 'R' and resid 149 through 153 removed outlier: 4.198A pdb=" N TRP R 153 " --> pdb=" O LYS R 149 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 149 through 153' Processing helix chain 'R' and resid 156 through 180 removed outlier: 3.888A pdb=" N ILE R 174 " --> pdb=" O SER R 170 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N LEU R 175 " --> pdb=" O LEU R 171 " (cutoff:3.500A) Proline residue: R 176 - end of helix Processing helix chain 'R' and resid 203 through 242 removed outlier: 5.273A pdb=" N VAL R 219 " --> pdb=" O LEU R 215 " (cutoff:3.500A) Proline residue: R 220 - end of helix Processing helix chain 'R' and resid 247 through 281 Proline residue: R 271 - end of helix Processing helix chain 'R' and resid 288 through 313 removed outlier: 3.752A pdb=" N SER R 305 " --> pdb=" O THR R 301 " (cutoff:3.500A) Proline residue: R 309 - end of helix Processing helix chain 'R' and resid 317 through 326 removed outlier: 3.841A pdb=" N SER R 322 " --> pdb=" O ASN R 318 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N ASN R 325 " --> pdb=" O LYS R 321 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N VAL R 326 " --> pdb=" O SER R 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 7 through 31 removed outlier: 3.550A pdb=" N GLU A 28 " --> pdb=" O ARG A 24 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LYS A 29 " --> pdb=" O GLU A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 53 removed outlier: 3.733A pdb=" N VAL A 50 " --> pdb=" O LYS A 46 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N MET A 53 " --> pdb=" O ILE A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 210 No H-bonds generated for 'chain 'A' and resid 208 through 210' Processing helix chain 'A' and resid 212 through 215 removed outlier: 3.605A pdb=" N PHE A 215 " --> pdb=" O ILE A 212 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 212 through 215' Processing helix chain 'A' and resid 242 through 254 Processing helix chain 'A' and resid 271 through 278 Processing helix chain 'A' and resid 283 through 285 No H-bonds generated for 'chain 'A' and resid 283 through 285' Processing helix chain 'A' and resid 296 through 310 removed outlier: 3.761A pdb=" N LEU A 310 " --> pdb=" O GLN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 351 Processing helix chain 'B' and resid 4 through 25 Processing helix chain 'B' and resid 30 through 36 removed outlier: 5.516A pdb=" N ASN B 36 " --> pdb=" O GLN B 32 " (cutoff:3.500A) Processing helix chain 'G' and resid 6 through 23 Processing helix chain 'G' and resid 30 through 43 Processing helix chain 'S' and resid 29 through 31 No H-bonds generated for 'chain 'S' and resid 29 through 31' Processing helix chain 'S' and resid 88 through 90 No H-bonds generated for 'chain 'S' and resid 88 through 90' Processing helix chain 'S' and resid 221 through 223 No H-bonds generated for 'chain 'S' and resid 221 through 223' Processing sheet with id= A, first strand: chain 'R' and resid 181 through 183 Processing sheet with id= B, first strand: chain 'A' and resid 319 through 323 removed outlier: 6.580A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 7.970A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N PHE A 189 " --> pdb=" O PHE A 196 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.827A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.740A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.750A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 221 through 223 removed outlier: 4.365A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.705A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N SER B 245 " --> pdb=" O THR B 249 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.513A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 46 through 51 removed outlier: 3.736A pdb=" N ARG B 46 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'S' and resid 3 through 7 Processing sheet with id= K, first strand: chain 'S' and resid 10 through 12 Processing sheet with id= L, first strand: chain 'S' and resid 95 through 99 removed outlier: 5.843A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N ALA S 40 " --> pdb=" O LEU S 45 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N LEU S 45 " --> pdb=" O ALA S 40 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'S' and resid 146 through 148 removed outlier: 6.859A pdb=" N LYS S 244 " --> pdb=" O VAL S 147 " (cutoff:3.500A) No H-bonds generated for sheet with id= M Processing sheet with id= N, first strand: chain 'S' and resid 155 through 160 Processing sheet with id= O, first strand: chain 'S' and resid 226 through 231 removed outlier: 3.679A pdb=" N ILE S 189 " --> pdb=" O TRP S 176 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N LEU S 178 " --> pdb=" O LEU S 187 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N LEU S 187 " --> pdb=" O LEU S 178 " (cutoff:3.500A) 410 hydrogen bonds defined for protein. 1188 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: 2.55 Time building geometry restraints manager: 3.58 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: 1444 1.30 - 1.43: 2413 1.43 - 1.56: 5163 1.56 - 1.69: 1 1.69 - 1.82: 98 Bond restraints: 9119 Sorted by residual: bond pdb=" C19 9FI R 401 " pdb=" N1 9FI R 401 " ideal model delta sigma weight residual 1.369 1.492 -0.123 2.00e-02 2.50e+03 3.78e+01 bond pdb=" C11 9FI R 401 " pdb=" N1 9FI R 401 " ideal model delta sigma weight residual 1.455 1.571 -0.116 2.00e-02 2.50e+03 3.37e+01 bond pdb=" C20 9FI R 401 " pdb=" N3 9FI R 401 " ideal model delta sigma weight residual 1.444 1.334 0.110 2.00e-02 2.50e+03 3.00e+01 bond pdb=" C12 9FI R 401 " pdb=" N1 9FI R 401 " ideal model delta sigma weight residual 1.456 1.347 0.109 2.00e-02 2.50e+03 2.97e+01 bond pdb=" C PHE R 127 " pdb=" O PHE R 127 " ideal model delta sigma weight residual 1.235 1.168 0.067 1.33e-02 5.65e+03 2.53e+01 ... (remaining 9114 not shown) Histogram of bond angle deviations from ideal: 86.16 - 95.81: 1 95.81 - 105.46: 136 105.46 - 115.11: 5599 115.11 - 124.77: 6455 124.77 - 134.42: 159 Bond angle restraints: 12350 Sorted by residual: angle pdb=" C22 9FI R 401 " pdb=" C20 9FI R 401 " pdb=" N3 9FI R 401 " ideal model delta sigma weight residual 110.53 86.16 24.37 3.00e+00 1.11e-01 6.60e+01 angle pdb=" N ILE R 124 " pdb=" CA ILE R 124 " pdb=" C ILE R 124 " ideal model delta sigma weight residual 111.81 105.17 6.64 8.60e-01 1.35e+00 5.96e+01 angle pdb=" C6 9FI R 401 " pdb=" C12 9FI R 401 " pdb=" N1 9FI R 401 " ideal model delta sigma weight residual 111.52 127.12 -15.60 3.00e+00 1.11e-01 2.70e+01 angle pdb=" N ALA R 307 " pdb=" CA ALA R 307 " pdb=" C ALA R 307 " ideal model delta sigma weight residual 111.36 116.61 -5.25 1.09e+00 8.42e-01 2.32e+01 angle pdb=" C TYR R 302 " pdb=" N ALA R 303 " pdb=" CA ALA R 303 " ideal model delta sigma weight residual 120.28 126.19 -5.91 1.34e+00 5.57e-01 1.94e+01 ... (remaining 12345 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.36: 4880 16.36 - 32.72: 432 32.72 - 49.07: 94 49.07 - 65.43: 16 65.43 - 81.79: 7 Dihedral angle restraints: 5429 sinusoidal: 2132 harmonic: 3297 Sorted by residual: dihedral pdb=" CA LEU R 105 " pdb=" C LEU R 105 " pdb=" N VAL R 106 " pdb=" CA VAL R 106 " ideal model delta harmonic sigma weight residual -180.00 -161.70 -18.30 0 5.00e+00 4.00e-02 1.34e+01 dihedral pdb=" CA GLU B 130 " pdb=" C GLU B 130 " pdb=" N GLY B 131 " pdb=" CA GLY B 131 " ideal model delta harmonic sigma weight residual 180.00 162.01 17.99 0 5.00e+00 4.00e-02 1.30e+01 dihedral pdb=" CA TYR S 190 " pdb=" C TYR S 190 " pdb=" N ARG S 191 " pdb=" CA ARG S 191 " ideal model delta harmonic sigma weight residual 180.00 163.54 16.46 0 5.00e+00 4.00e-02 1.08e+01 ... (remaining 5426 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 1231 0.069 - 0.138: 158 0.138 - 0.207: 6 0.207 - 0.275: 7 0.275 - 0.344: 2 Chirality restraints: 1404 Sorted by residual: chirality pdb=" CA ASN R 125 " pdb=" N ASN R 125 " pdb=" C ASN R 125 " pdb=" CB ASN R 125 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.96e+00 chirality pdb=" CA THR R 128 " pdb=" N THR R 128 " pdb=" C THR R 128 " pdb=" CB THR R 128 " both_signs ideal model delta sigma weight residual False 2.53 2.25 0.28 2.00e-01 2.50e+01 1.92e+00 chirality pdb=" CB ILE R 174 " pdb=" CA ILE R 174 " pdb=" CG1 ILE R 174 " pdb=" CG2 ILE R 174 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.27 2.00e-01 2.50e+01 1.85e+00 ... (remaining 1401 not shown) Planarity restraints: 1550 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 9FI R 401 " -0.007 2.00e-02 2.50e+03 5.42e-01 8.07e+03 pdb=" C10 9FI R 401 " 0.025 2.00e-02 2.50e+03 pdb=" C14 9FI R 401 " -0.004 2.00e-02 2.50e+03 pdb=" C16 9FI R 401 " 0.010 2.00e-02 2.50e+03 pdb=" C17 9FI R 401 " -0.010 2.00e-02 2.50e+03 pdb=" C18 9FI R 401 " 0.002 2.00e-02 2.50e+03 pdb=" C21 9FI R 401 " -0.003 2.00e-02 2.50e+03 pdb=" C23 9FI R 401 " 0.008 2.00e-02 2.50e+03 pdb=" C25 9FI R 401 " -0.015 2.00e-02 2.50e+03 pdb=" C5 9FI R 401 " -1.274 2.00e-02 2.50e+03 pdb=" C6 9FI R 401 " 1.266 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C11 9FI R 401 " -0.004 2.00e-02 2.50e+03 2.87e-02 1.44e+01 pdb=" C12 9FI R 401 " -0.028 2.00e-02 2.50e+03 pdb=" C19 9FI R 401 " 0.017 2.00e-02 2.50e+03 pdb=" C20 9FI R 401 " -0.050 2.00e-02 2.50e+03 pdb=" N1 9FI R 401 " 0.002 2.00e-02 2.50e+03 pdb=" N3 9FI R 401 " 0.040 2.00e-02 2.50e+03 pdb=" O1 9FI R 401 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE R 127 " 0.035 2.00e-02 2.50e+03 2.61e-02 1.19e+01 pdb=" CG PHE R 127 " -0.051 2.00e-02 2.50e+03 pdb=" CD1 PHE R 127 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE R 127 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE R 127 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 PHE R 127 " -0.009 2.00e-02 2.50e+03 pdb=" CZ PHE R 127 " 0.029 2.00e-02 2.50e+03 ... (remaining 1547 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 525 2.73 - 3.27: 8623 3.27 - 3.82: 14639 3.82 - 4.36: 17221 4.36 - 4.90: 30803 Nonbonded interactions: 71811 Sorted by model distance: nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.192 2.440 nonbonded pdb=" OE2 GLU A 8 " pdb=" OH TYR S 175 " model vdw 2.244 2.440 nonbonded pdb=" OG SER G 57 " pdb=" OE1 GLU G 58 " model vdw 2.252 2.440 nonbonded pdb=" O HIS R 146 " pdb=" OG SER R 150 " model vdw 2.302 2.440 nonbonded pdb=" NH1 ARG B 48 " pdb=" O ARG G 62 " model vdw 2.307 2.520 ... (remaining 71806 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: 0.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.940 Check model and map are aligned: 0.210 Set scattering table: 0.130 Process input model: 26.750 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.030 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:13.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7352 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 : 0.006 0.123 9119 Z= 0.414 Angle : 0.746 24.373 12350 Z= 0.383 Chirality : 0.048 0.344 1404 Planarity : 0.014 0.542 1550 Dihedral : 13.302 81.791 3294 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.26), residues: 1123 helix: 1.86 (0.27), residues: 398 sheet: 0.93 (0.32), residues: 282 loop : -0.39 (0.29), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 108 HIS 0.003 0.001 HIS A 188 PHE 0.051 0.001 PHE R 127 TYR 0.016 0.001 TYR R 211 ARG 0.007 0.000 ARG B 251 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 187 time to evaluate : 1.011 Fit side-chains revert: symmetry clash REVERT: A 28 GLU cc_start: 0.7294 (mp0) cc_final: 0.6651 (mp0) REVERT: B 135 VAL cc_start: 0.8506 (t) cc_final: 0.8177 (p) REVERT: B 217 MET cc_start: 0.6505 (ppp) cc_final: 0.6131 (ppp) outliers start: 0 outliers final: 1 residues processed: 187 average time/residue: 1.1905 time to fit residues: 237.4387 Evaluate side-chains 176 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 175 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 2.9990 chunk 84 optimal weight: 0.8980 chunk 46 optimal weight: 0.3980 chunk 28 optimal weight: 3.9990 chunk 56 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 87 optimal weight: 0.0010 chunk 33 optimal weight: 4.9990 chunk 52 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 100 optimal weight: 4.9990 overall best weight: 1.4590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 125 ASN A 188 HIS B 176 GLN B 220 GLN B 239 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7406 moved from start: 0.1023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 9119 Z= 0.311 Angle : 0.927 57.193 12350 Z= 0.387 Chirality : 0.045 0.262 1404 Planarity : 0.004 0.044 1550 Dihedral : 6.260 66.294 1266 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.43 % Allowed : 9.72 % Favored : 88.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.25), residues: 1123 helix: 1.96 (0.27), residues: 398 sheet: 0.82 (0.31), residues: 278 loop : -0.39 (0.29), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP R 108 HIS 0.006 0.001 HIS A 188 PHE 0.027 0.002 PHE R 92 TYR 0.030 0.002 TYR S 190 ARG 0.006 0.000 ARG B 251 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 180 time to evaluate : 0.921 Fit side-chains revert: symmetry clash REVERT: A 28 GLU cc_start: 0.7295 (mp0) cc_final: 0.6400 (mp0) REVERT: A 53 MET cc_start: 0.5276 (mmp) cc_final: 0.5010 (mmp) REVERT: B 135 VAL cc_start: 0.8680 (t) cc_final: 0.8391 (p) REVERT: S 140 MET cc_start: 0.8244 (OUTLIER) cc_final: 0.7836 (mtp) outliers start: 14 outliers final: 8 residues processed: 182 average time/residue: 1.1797 time to fit residues: 228.7350 Evaluate side-chains 187 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 178 time to evaluate : 1.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 58 LEU Chi-restraints excluded: chain R residue 209 ILE Chi-restraints excluded: chain R residue 229 LEU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 328 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain S residue 93 MET Chi-restraints excluded: chain S residue 140 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 56 optimal weight: 1.9990 chunk 31 optimal weight: 0.5980 chunk 83 optimal weight: 2.9990 chunk 68 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 chunk 100 optimal weight: 4.9990 chunk 109 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 chunk 81 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 ASN B 176 GLN B 220 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7413 moved from start: 0.1307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9119 Z= 0.281 Angle : 0.903 57.062 12350 Z= 0.374 Chirality : 0.044 0.230 1404 Planarity : 0.004 0.043 1550 Dihedral : 6.058 71.220 1264 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.84 % Allowed : 11.36 % Favored : 86.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.25), residues: 1123 helix: 2.19 (0.26), residues: 397 sheet: 0.81 (0.31), residues: 279 loop : -0.42 (0.29), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP R 108 HIS 0.004 0.001 HIS S 35 PHE 0.020 0.001 PHE R 92 TYR 0.027 0.002 TYR S 190 ARG 0.005 0.000 ARG B 251 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 186 time to evaluate : 1.017 Fit side-chains revert: symmetry clash REVERT: A 53 MET cc_start: 0.5232 (mmp) cc_final: 0.4938 (mmp) REVERT: B 135 VAL cc_start: 0.8725 (t) cc_final: 0.8490 (p) REVERT: S 140 MET cc_start: 0.8229 (OUTLIER) cc_final: 0.7835 (mtp) outliers start: 18 outliers final: 9 residues processed: 189 average time/residue: 1.1942 time to fit residues: 240.6890 Evaluate side-chains 191 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 181 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain S residue 93 MET Chi-restraints excluded: chain S residue 140 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 75 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 11 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 101 optimal weight: 20.0000 chunk 107 optimal weight: 4.9990 chunk 96 optimal weight: 0.5980 chunk 28 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 60 optimal weight: 0.4980 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 132 ASN B 176 GLN B 220 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7422 moved from start: 0.1503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 9119 Z= 0.303 Angle : 0.906 57.175 12350 Z= 0.377 Chirality : 0.044 0.231 1404 Planarity : 0.004 0.043 1550 Dihedral : 6.041 78.484 1264 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.87 % Allowed : 11.98 % Favored : 85.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.25), residues: 1123 helix: 2.21 (0.26), residues: 397 sheet: 0.87 (0.30), residues: 281 loop : -0.48 (0.30), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP R 108 HIS 0.004 0.001 HIS S 35 PHE 0.012 0.001 PHE B 234 TYR 0.026 0.002 TYR S 190 ARG 0.006 0.000 ARG B 214 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 174 time to evaluate : 0.945 Fit side-chains revert: symmetry clash REVERT: B 135 VAL cc_start: 0.8727 (t) cc_final: 0.8514 (p) REVERT: S 140 MET cc_start: 0.8233 (OUTLIER) cc_final: 0.7750 (mtp) outliers start: 28 outliers final: 12 residues processed: 181 average time/residue: 1.2021 time to fit residues: 231.8790 Evaluate side-chains 191 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 178 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 301 THR Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain S residue 140 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 1 optimal weight: 3.9990 chunk 79 optimal weight: 3.9990 chunk 44 optimal weight: 0.9990 chunk 91 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 54 optimal weight: 2.9990 chunk 96 optimal weight: 0.9990 chunk 27 optimal weight: 8.9990 chunk 36 optimal weight: 0.0770 chunk 21 optimal weight: 0.9990 overall best weight: 1.2146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 132 ASN B 220 GLN B 340 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7416 moved from start: 0.1576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9119 Z= 0.266 Angle : 0.897 57.263 12350 Z= 0.370 Chirality : 0.043 0.220 1404 Planarity : 0.004 0.043 1550 Dihedral : 6.015 84.688 1264 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.97 % Allowed : 12.90 % Favored : 84.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.26), residues: 1123 helix: 2.24 (0.26), residues: 397 sheet: 0.89 (0.30), residues: 281 loop : -0.48 (0.30), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP R 108 HIS 0.004 0.001 HIS S 35 PHE 0.011 0.001 PHE B 234 TYR 0.023 0.001 TYR S 190 ARG 0.004 0.000 ARG B 251 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 181 time to evaluate : 1.064 Fit side-chains revert: symmetry clash REVERT: R 53 VAL cc_start: 0.5621 (OUTLIER) cc_final: 0.5371 (t) REVERT: A 53 MET cc_start: 0.5361 (mmp) cc_final: 0.5143 (mmp) REVERT: S 140 MET cc_start: 0.8231 (OUTLIER) cc_final: 0.7860 (mtp) outliers start: 29 outliers final: 18 residues processed: 190 average time/residue: 1.1707 time to fit residues: 237.6908 Evaluate side-chains 195 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 175 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 53 VAL Chi-restraints excluded: chain R residue 164 MET Chi-restraints excluded: chain R residue 209 ILE Chi-restraints excluded: chain R residue 229 LEU Chi-restraints excluded: chain R residue 301 THR Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain S residue 140 MET Chi-restraints excluded: chain S residue 234 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 62 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 chunk 107 optimal weight: 0.4980 chunk 89 optimal weight: 5.9990 chunk 49 optimal weight: 0.9990 chunk 8 optimal weight: 0.9990 chunk 35 optimal weight: 5.9990 chunk 56 optimal weight: 0.9980 chunk 103 optimal weight: 0.0030 chunk 12 optimal weight: 1.9990 chunk 61 optimal weight: 0.6980 overall best weight: 0.6392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN B 340 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7395 moved from start: 0.1587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9119 Z= 0.173 Angle : 0.877 57.215 12350 Z= 0.357 Chirality : 0.042 0.195 1404 Planarity : 0.003 0.042 1550 Dihedral : 5.806 78.680 1264 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.56 % Allowed : 14.23 % Favored : 83.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.26), residues: 1123 helix: 2.35 (0.26), residues: 397 sheet: 0.99 (0.31), residues: 280 loop : -0.43 (0.30), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 169 HIS 0.003 0.000 HIS S 35 PHE 0.009 0.001 PHE B 234 TYR 0.020 0.001 TYR S 190 ARG 0.002 0.000 ARG B 251 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 180 time to evaluate : 0.927 Fit side-chains revert: symmetry clash REVERT: R 53 VAL cc_start: 0.5568 (OUTLIER) cc_final: 0.5345 (t) REVERT: S 140 MET cc_start: 0.8192 (OUTLIER) cc_final: 0.7823 (mtp) outliers start: 25 outliers final: 14 residues processed: 187 average time/residue: 1.1947 time to fit residues: 238.4448 Evaluate side-chains 194 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 178 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 41 THR Chi-restraints excluded: chain R residue 53 VAL Chi-restraints excluded: chain R residue 229 LEU Chi-restraints excluded: chain R residue 301 THR Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain S residue 140 MET Chi-restraints excluded: chain S residue 174 LEU Chi-restraints excluded: chain S residue 234 GLU 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: 2.9990 chunk 90 optimal weight: 1.9990 chunk 59 optimal weight: 0.5980 chunk 106 optimal weight: 4.9990 chunk 66 optimal weight: 0.9980 chunk 65 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 42 optimal weight: 0.0570 chunk 63 optimal weight: 0.7980 chunk 32 optimal weight: 2.9990 overall best weight: 0.8900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN B 259 GLN B 340 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7401 moved from start: 0.1633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9119 Z= 0.212 Angle : 0.882 57.343 12350 Z= 0.360 Chirality : 0.042 0.202 1404 Planarity : 0.003 0.042 1550 Dihedral : 5.700 74.625 1264 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.87 % Allowed : 14.23 % Favored : 82.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.37 (0.26), residues: 1123 helix: 2.35 (0.26), residues: 397 sheet: 0.90 (0.31), residues: 283 loop : -0.41 (0.30), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP R 108 HIS 0.003 0.001 HIS S 35 PHE 0.009 0.001 PHE B 234 TYR 0.021 0.001 TYR S 190 ARG 0.005 0.000 ARG B 49 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 180 time to evaluate : 0.958 Fit side-chains revert: symmetry clash REVERT: R 53 VAL cc_start: 0.5570 (OUTLIER) cc_final: 0.5336 (t) REVERT: S 140 MET cc_start: 0.8235 (OUTLIER) cc_final: 0.7866 (mtp) outliers start: 28 outliers final: 19 residues processed: 187 average time/residue: 1.2397 time to fit residues: 246.7671 Evaluate side-chains 201 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 180 time to evaluate : 1.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 41 THR Chi-restraints excluded: chain R residue 53 VAL Chi-restraints excluded: chain R residue 164 MET Chi-restraints excluded: chain R residue 209 ILE Chi-restraints excluded: chain R residue 229 LEU Chi-restraints excluded: chain R residue 301 THR Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain S residue 140 MET Chi-restraints excluded: chain S residue 174 LEU Chi-restraints excluded: chain S residue 234 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 21 optimal weight: 2.9990 chunk 20 optimal weight: 0.0570 chunk 68 optimal weight: 1.9990 chunk 72 optimal weight: 5.9990 chunk 52 optimal weight: 0.9990 chunk 9 optimal weight: 0.7980 chunk 84 optimal weight: 3.9990 chunk 97 optimal weight: 4.9990 chunk 102 optimal weight: 4.9990 chunk 93 optimal weight: 3.9990 chunk 99 optimal weight: 0.9990 overall best weight: 0.9704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7402 moved from start: 0.1657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9119 Z= 0.224 Angle : 0.894 57.436 12350 Z= 0.366 Chirality : 0.042 0.206 1404 Planarity : 0.003 0.043 1550 Dihedral : 5.642 70.314 1264 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.97 % Allowed : 14.53 % Favored : 82.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.26), residues: 1123 helix: 2.31 (0.26), residues: 397 sheet: 0.91 (0.31), residues: 283 loop : -0.41 (0.30), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP R 108 HIS 0.003 0.001 HIS S 35 PHE 0.010 0.001 PHE A 274 TYR 0.020 0.001 TYR S 190 ARG 0.004 0.000 ARG B 49 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 182 time to evaluate : 1.041 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 53 VAL cc_start: 0.5568 (OUTLIER) cc_final: 0.5336 (t) REVERT: R 172 LEU cc_start: 0.6778 (tt) cc_final: 0.6436 (tp) REVERT: S 6 GLU cc_start: 0.7801 (mp0) cc_final: 0.7581 (mp0) REVERT: S 140 MET cc_start: 0.8242 (OUTLIER) cc_final: 0.7865 (mtp) outliers start: 29 outliers final: 21 residues processed: 190 average time/residue: 1.2520 time to fit residues: 253.0682 Evaluate side-chains 204 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 181 time to evaluate : 1.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 41 THR Chi-restraints excluded: chain R residue 53 VAL Chi-restraints excluded: chain R residue 120 THR Chi-restraints excluded: chain R residue 164 MET Chi-restraints excluded: chain R residue 209 ILE Chi-restraints excluded: chain R residue 229 LEU Chi-restraints excluded: chain R residue 301 THR Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 328 ASP Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain S residue 140 MET Chi-restraints excluded: chain S residue 174 LEU Chi-restraints excluded: chain S residue 234 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 102 optimal weight: 6.9990 chunk 60 optimal weight: 0.7980 chunk 43 optimal weight: 0.0000 chunk 78 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 90 optimal weight: 0.8980 chunk 94 optimal weight: 1.9990 chunk 99 optimal weight: 4.9990 chunk 65 optimal weight: 0.9980 chunk 105 optimal weight: 2.9990 chunk 64 optimal weight: 0.7980 overall best weight: 0.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN B 340 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7389 moved from start: 0.1662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9119 Z= 0.180 Angle : 0.888 57.393 12350 Z= 0.361 Chirality : 0.042 0.194 1404 Planarity : 0.003 0.042 1550 Dihedral : 5.541 64.649 1264 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.87 % Allowed : 14.84 % Favored : 82.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.26), residues: 1123 helix: 2.39 (0.27), residues: 397 sheet: 0.90 (0.30), residues: 284 loop : -0.38 (0.30), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 169 HIS 0.003 0.001 HIS S 35 PHE 0.009 0.001 PHE R 92 TYR 0.019 0.001 TYR S 190 ARG 0.006 0.000 ARG B 251 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 178 time to evaluate : 1.087 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 53 VAL cc_start: 0.5561 (OUTLIER) cc_final: 0.5338 (t) REVERT: R 172 LEU cc_start: 0.6787 (tt) cc_final: 0.6444 (tp) REVERT: S 140 MET cc_start: 0.8190 (OUTLIER) cc_final: 0.7838 (mtp) outliers start: 28 outliers final: 17 residues processed: 188 average time/residue: 1.3100 time to fit residues: 262.1917 Evaluate side-chains 199 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 180 time to evaluate : 1.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 41 THR Chi-restraints excluded: chain R residue 53 VAL Chi-restraints excluded: chain R residue 164 MET Chi-restraints excluded: chain R residue 229 LEU Chi-restraints excluded: chain R residue 301 THR Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 328 ASP Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain S residue 140 MET Chi-restraints excluded: chain S residue 204 SER Chi-restraints excluded: chain S residue 234 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 50 optimal weight: 5.9990 chunk 73 optimal weight: 0.8980 chunk 110 optimal weight: 0.9990 chunk 101 optimal weight: 9.9990 chunk 88 optimal weight: 5.9990 chunk 9 optimal weight: 0.5980 chunk 68 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 93 optimal weight: 0.5980 chunk 26 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 132 ASN B 220 GLN B 340 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7390 moved from start: 0.1696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9119 Z= 0.194 Angle : 0.891 57.440 12350 Z= 0.363 Chirality : 0.042 0.195 1404 Planarity : 0.003 0.042 1550 Dihedral : 5.445 57.282 1264 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.05 % Allowed : 15.97 % Favored : 81.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.37 (0.26), residues: 1123 helix: 2.35 (0.27), residues: 398 sheet: 0.79 (0.30), residues: 289 loop : -0.34 (0.30), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 169 HIS 0.003 0.001 HIS S 35 PHE 0.009 0.001 PHE R 92 TYR 0.019 0.001 TYR S 190 ARG 0.006 0.000 ARG B 251 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 185 time to evaluate : 1.030 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 53 VAL cc_start: 0.5556 (OUTLIER) cc_final: 0.5339 (t) REVERT: R 172 LEU cc_start: 0.6837 (tt) cc_final: 0.6490 (tp) REVERT: S 140 MET cc_start: 0.8213 (OUTLIER) cc_final: 0.7854 (mtp) outliers start: 20 outliers final: 16 residues processed: 191 average time/residue: 1.1893 time to fit residues: 242.5831 Evaluate side-chains 204 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 186 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 41 THR Chi-restraints excluded: chain R residue 53 VAL Chi-restraints excluded: chain R residue 99 LEU Chi-restraints excluded: chain R residue 164 MET Chi-restraints excluded: chain R residue 229 LEU Chi-restraints excluded: chain R residue 301 THR Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 328 ASP Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain S residue 140 MET Chi-restraints excluded: chain S residue 234 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 81 optimal weight: 3.9990 chunk 13 optimal weight: 0.0970 chunk 24 optimal weight: 0.9980 chunk 88 optimal weight: 5.9990 chunk 36 optimal weight: 0.4980 chunk 90 optimal weight: 0.7980 chunk 11 optimal weight: 0.9990 chunk 16 optimal weight: 0.5980 chunk 77 optimal weight: 0.5980 chunk 5 optimal weight: 0.0270 chunk 63 optimal weight: 0.9990 overall best weight: 0.3636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN B 340 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.138620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.119033 restraints weight = 12146.992| |-----------------------------------------------------------------------------| r_work (start): 0.3543 rms_B_bonded: 1.86 r_work: 0.3438 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3295 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.1731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9119 Z= 0.138 Angle : 0.877 57.301 12350 Z= 0.354 Chirality : 0.041 0.201 1404 Planarity : 0.003 0.041 1550 Dihedral : 5.319 53.312 1264 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.64 % Allowed : 16.38 % Favored : 81.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.26), residues: 1123 helix: 2.44 (0.27), residues: 398 sheet: 0.86 (0.30), residues: 288 loop : -0.29 (0.31), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 169 HIS 0.002 0.000 HIS S 35 PHE 0.010 0.001 PHE R 92 TYR 0.017 0.001 TYR S 190 ARG 0.006 0.000 ARG B 251 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4207.72 seconds wall clock time: 75 minutes 21.56 seconds (4521.56 seconds total)