Starting phenix.real_space_refine on Fri Jul 3 08:53:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7td0_25819/07_2026/7td0_25819_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7td0_25819/07_2026/7td0_25819.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.83 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7td0_25819/07_2026/7td0_25819_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7td0_25819/07_2026/7td0_25819_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7td0_25819/07_2026/7td0_25819.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7td0_25819/07_2026/7td0_25819.map" } resolution = 2.83 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= -0.000 sd= 0.963 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: 6 Type Number sf(0) Gaussians P 1 5.49 5 S 56 5.16 5 C 4363 2.51 5 N 1148 2.21 5 O 1269 1.98 5 H 6471 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13308 Number of models: 1 Model: "" Number of chains: 5 Chain: "R" Number of atoms: 4397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 4397 Classifications: {'peptide': 290} Link IDs: {'PTRANS': 7, 'TRANS': 282} Chain breaks: 1 Unresolved non-hydrogen bonds: 107 Unresolved non-hydrogen angles: 130 Unresolved non-hydrogen dihedrals: 88 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'PHE:plan': 1, 'ASN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 6, 'HIS:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 64 Chain: "B" Number of atoms: 4797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 4797 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 118 Unresolved non-hydrogen angles: 143 Unresolved non-hydrogen dihedrals: 93 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 4, 'GLN:plan1': 5, 'ARG:plan': 6, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 85 Chain: "A" Number of atoms: 3358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 3358 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 215} Chain breaks: 2 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "G" Number of atoms: 727 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 727 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 4, 'TRANS': 51} Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 22 Chain: "R" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 29 Unusual residues: {'NKP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.12, per 1000 atoms: 0.16 Number of scatterers: 13308 At special positions: 0 Unit cell: (96.824, 95.76, 126.616, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 56 16.00 P 1 15.00 O 1269 8.00 N 1148 7.00 C 4363 6.00 H 6471 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 24 " - pdb=" SG CYS R 190 " distance=2.02 Simple disulfide: pdb=" SG CYS R 188 " - pdb=" SG CYS R 195 " distance=2.33 Simple disulfide: pdb=" SG CYS R 284 " - pdb=" SG CYS R 287 " distance=1.89 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.15 Conformation dependent library (CDL) restraints added in 420.2 milliseconds 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1712 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 8 sheets defined 45.0% alpha, 17.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'R' and resid 29 through 37 removed outlier: 3.601A pdb=" N PHE R 33 " --> pdb=" O SER R 29 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N SER R 37 " --> pdb=" O PHE R 33 " (cutoff:3.500A) Processing helix chain 'R' and resid 46 through 77 Processing helix chain 'R' and resid 82 through 106 Processing helix chain 'R' and resid 109 through 116 Processing helix chain 'R' and resid 117 through 151 removed outlier: 3.589A pdb=" N PHE R 151 " --> pdb=" O HIS R 147 " (cutoff:3.500A) Processing helix chain 'R' and resid 161 through 185 removed outlier: 3.979A pdb=" N VAL R 165 " --> pdb=" O ASN R 161 " (cutoff:3.500A) Proline residue: R 182 - end of helix Processing helix chain 'R' and resid 203 through 238 removed outlier: 4.595A pdb=" N ARG R 238 " --> pdb=" O GLN R 234 " (cutoff:3.500A) Processing helix chain 'R' and resid 252 through 284 removed outlier: 3.662A pdb=" N PHE R 267 " --> pdb=" O VAL R 263 " (cutoff:3.500A) Proline residue: R 273 - end of helix Processing helix chain 'R' and resid 292 through 311 removed outlier: 3.593A pdb=" N PHE R 296 " --> pdb=" O TYR R 292 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N SER R 304 " --> pdb=" O ALA R 300 " (cutoff:3.500A) Proline residue: R 308 - end of helix Processing helix chain 'R' and resid 315 through 322 Processing helix chain 'B' and resid 3 through 25 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'A' and resid 10 through 32 removed outlier: 4.048A pdb=" N GLU A 14 " --> pdb=" O LYS A 10 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ARG A 15 " --> pdb=" O ALA A 11 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 54 removed outlier: 3.512A pdb=" N LYS A 54 " --> pdb=" O VAL A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 216 Processing helix chain 'A' and resid 228 through 231 removed outlier: 3.939A pdb=" N ASP A 231 " --> pdb=" O SER A 228 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 228 through 231' Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 270 through 278 Processing helix chain 'A' and resid 282 through 286 removed outlier: 3.926A pdb=" N ILE A 285 " --> pdb=" O PRO A 282 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N CYS A 286 " --> pdb=" O LEU A 283 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 282 through 286' Processing helix chain 'A' and resid 295 through 310 removed outlier: 4.079A pdb=" N LEU A 310 " --> pdb=" O GLN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 351 Processing helix chain 'G' and resid 9 through 24 removed outlier: 3.812A pdb=" N MET G 21 " --> pdb=" O GLU G 17 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLU G 22 " --> pdb=" O GLN G 18 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'G' and resid 45 through 48 removed outlier: 3.802A pdb=" N ASP G 48 " --> pdb=" O ALA G 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 45 through 48' Processing sheet with id=AA1, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.366A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.803A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 100 through 104 removed outlier: 6.872A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.635A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 187 through 192 removed outlier: 4.051A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.473A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.416A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 185 through 191 removed outlier: 6.447A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 8.553A pdb=" N ALA A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 8.012A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) 372 hydrogen bonds defined for protein. 1065 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: 2.78 Time building geometry restraints manager: 1.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 6446 1.03 - 1.23: 41 1.23 - 1.42: 2936 1.42 - 1.62: 3938 1.62 - 1.81: 82 Bond restraints: 13443 Sorted by residual: bond pdb=" OAD NKP R 401 " pdb=" PAC NKP R 401 " ideal model delta sigma weight residual 1.696 1.508 0.188 2.00e-02 2.50e+03 8.80e+01 bond pdb=" OAB NKP R 401 " pdb=" PAC NKP R 401 " ideal model delta sigma weight residual 1.683 1.507 0.176 2.00e-02 2.50e+03 7.73e+01 bond pdb=" CAH NKP R 401 " pdb=" OBC NKP R 401 " ideal model delta sigma weight residual 1.468 1.398 0.070 2.00e-02 2.50e+03 1.21e+01 bond pdb=" C PHE R 25 " pdb=" O PHE R 25 " ideal model delta sigma weight residual 1.235 1.200 0.035 1.14e-02 7.69e+03 9.36e+00 bond pdb=" N CYS R 24 " pdb=" CA CYS R 24 " ideal model delta sigma weight residual 1.454 1.490 -0.036 1.29e-02 6.01e+03 7.64e+00 ... (remaining 13438 not shown) Histogram of bond angle deviations from ideal: 0.00 - 11.39: 24123 11.39 - 22.78: 2 22.78 - 34.17: 0 34.17 - 45.56: 0 45.56 - 56.95: 1 Bond angle restraints: 24126 Sorted by residual: angle pdb=" OAB NKP R 401 " pdb=" PAC NKP R 401 " pdb=" OAD NKP R 401 " ideal model delta sigma weight residual 53.21 110.16 -56.95 3.00e+00 1.11e-01 3.60e+02 angle pdb=" OAA NKP R 401 " pdb=" PAC NKP R 401 " pdb=" OAB NKP R 401 " ideal model delta sigma weight residual 128.27 109.59 18.68 3.00e+00 1.11e-01 3.88e+01 angle pdb=" OAA NKP R 401 " pdb=" PAC NKP R 401 " pdb=" OAD NKP R 401 " ideal model delta sigma weight residual 121.86 109.63 12.23 3.00e+00 1.11e-01 1.66e+01 angle pdb=" CA PHE R 25 " pdb=" C PHE R 25 " pdb=" O PHE R 25 " ideal model delta sigma weight residual 120.57 116.07 4.50 1.26e+00 6.30e-01 1.27e+01 angle pdb=" CAL NKP R 401 " pdb=" CAK NKP R 401 " pdb=" OAJ NKP R 401 " ideal model delta sigma weight residual 108.66 119.06 -10.40 3.00e+00 1.11e-01 1.20e+01 ... (remaining 24121 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.71: 5967 17.71 - 35.42: 332 35.42 - 53.13: 87 53.13 - 70.84: 22 70.84 - 88.54: 7 Dihedral angle restraints: 6415 sinusoidal: 3282 harmonic: 3133 Sorted by residual: dihedral pdb=" CA ASP A 341 " pdb=" CB ASP A 341 " pdb=" CG ASP A 341 " pdb=" OD1 ASP A 341 " ideal model delta sinusoidal sigma weight residual -30.00 -86.48 56.48 1 2.00e+01 2.50e-03 1.07e+01 dihedral pdb=" CA ASP B 258 " pdb=" CB ASP B 258 " pdb=" CG ASP B 258 " pdb=" OD1 ASP B 258 " ideal model delta sinusoidal sigma weight residual -30.00 -86.35 56.35 1 2.00e+01 2.50e-03 1.07e+01 dihedral pdb=" CB GLU A 297 " pdb=" CG GLU A 297 " pdb=" CD GLU A 297 " pdb=" OE1 GLU A 297 " ideal model delta sinusoidal sigma weight residual 0.00 88.54 -88.54 1 3.00e+01 1.11e-03 1.04e+01 ... (remaining 6412 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 1011 0.068 - 0.135: 93 0.135 - 0.203: 6 0.203 - 0.271: 0 0.271 - 0.338: 1 Chirality restraints: 1111 Sorted by residual: chirality pdb=" CAH NKP R 401 " pdb=" CAG NKP R 401 " pdb=" CAI NKP R 401 " pdb=" OBC NKP R 401 " both_signs ideal model delta sigma weight residual False -2.84 -2.51 -0.34 2.00e-01 2.50e+01 2.86e+00 chirality pdb=" CA PHE R 25 " pdb=" N PHE R 25 " pdb=" C PHE R 25 " pdb=" CB PHE R 25 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.87e-01 chirality pdb=" CA MET A 53 " pdb=" N MET A 53 " pdb=" C MET A 53 " pdb=" CB MET A 53 " both_signs ideal model delta sigma weight residual False 2.51 2.65 -0.14 2.00e-01 2.50e+01 4.86e-01 ... (remaining 1108 not shown) Planarity restraints: 2077 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN A 52 " -0.011 2.00e-02 2.50e+03 2.28e-02 5.18e+00 pdb=" C GLN A 52 " 0.039 2.00e-02 2.50e+03 pdb=" O GLN A 52 " -0.015 2.00e-02 2.50e+03 pdb=" N MET A 53 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN A 52 " -0.010 2.00e-02 2.50e+03 1.76e-02 3.09e+00 pdb=" N MET A 53 " 0.030 2.00e-02 2.50e+03 pdb=" CA MET A 53 " -0.008 2.00e-02 2.50e+03 pdb=" H MET A 53 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR R 26 " -0.009 2.00e-02 2.50e+03 1.73e-02 2.98e+00 pdb=" N ASN R 27 " 0.030 2.00e-02 2.50e+03 pdb=" CA ASN R 27 " -0.008 2.00e-02 2.50e+03 pdb=" H ASN R 27 " -0.013 2.00e-02 2.50e+03 ... (remaining 2074 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.18: 492 2.18 - 2.79: 26340 2.79 - 3.39: 36314 3.39 - 4.00: 47620 4.00 - 4.60: 73831 Nonbonded interactions: 184597 Sorted by model distance: nonbonded pdb=" O ALA B 106 " pdb=" H GLY B 109 " model vdw 1.580 2.450 nonbonded pdb=" OD1 ASP B 254 " pdb=" H ALA B 257 " model vdw 1.639 2.450 nonbonded pdb=" O VAL A 342 " pdb="HD21 ASN A 346 " model vdw 1.674 2.450 nonbonded pdb=" HH TYR A 320 " pdb=" OD1 ASP A 341 " model vdw 1.675 2.450 nonbonded pdb=" HZ1 LYS B 57 " pdb=" OE1 GLU A 216 " model vdw 1.677 2.450 ... (remaining 184592 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 1.610 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: 0.090 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.840 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 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:7.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7206 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 0.300 6975 Z= 0.301 Angle : 0.823 56.945 9486 Z= 0.360 Chirality : 0.040 0.338 1111 Planarity : 0.003 0.042 1199 Dihedral : 12.959 88.544 2389 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 0.72 % Allowed : 8.93 % Favored : 90.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.88 (0.25), residues: 889 helix: -0.14 (0.24), residues: 376 sheet: -1.51 (0.35), residues: 174 loop : -2.30 (0.30), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 150 TYR 0.016 0.001 TYR R 26 PHE 0.009 0.001 PHE B 151 TRP 0.012 0.001 TRP B 82 HIS 0.002 0.001 HIS A 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00429 / 0.22 ( 6972) covalent geometry : angle 0.81090 / 0.35 ( 9480) SS BOND : bond 0.19260 / 9.26 ( 3) SS BOND : angle 5.60075 / 2.88 ( 6) hydrogen bonds : bond 0.11971 / 8.60 ( 372) hydrogen bonds : angle 5.42163 / 3.85 ( 1065) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 47 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue ILE 61 is missing expected H atoms. Skipping. Residue LEU 65 is missing expected H atoms. Skipping. Residue LEU 68 is missing expected H atoms. Skipping. Residue VAL 72 is missing expected H atoms. Skipping. Residue ILE 74 is missing expected H atoms. Skipping. Residue MET 159 is missing expected H atoms. Skipping. Residue THR 173 is missing expected H atoms. Skipping. Residue MET 237 is missing expected H atoms. Skipping. Residue MET 254 is missing expected H atoms. Skipping. Residue LYS 316 is missing expected H atoms. Skipping. Residue SER 2 is missing expected H atoms. Skipping. Residue LEU 4 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue ILE 33 is missing expected H atoms. Skipping. Residue SER 108 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue MET 262 is missing expected H atoms. Skipping. Residue MET 325 is missing expected H atoms. Skipping. Residue LYS 10 is missing expected H atoms. Skipping. Residue LYS 17 is missing expected H atoms. Skipping. Residue MET 18 is missing expected H atoms. Skipping. Residue LYS 51 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue MET 240 is missing expected H atoms. Skipping. Residue LYS 280 is missing expected H atoms. Skipping. Residue THR 327 is missing expected H atoms. Skipping. Residue LYS 330 is missing expected H atoms. Skipping. Residue SER 8 is missing expected H atoms. Skipping. Residue ILE 9 is missing expected H atoms. Skipping. Residue LEU 15 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Evaluate side-chains 180 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 175 time to evaluate : 0.343 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 71 MET cc_start: 0.7065 (mtp) cc_final: 0.6756 (mtp) REVERT: R 77 ASN cc_start: 0.6978 (m-40) cc_final: 0.6525 (m-40) REVERT: B 49 ARG cc_start: 0.7785 (ttm110) cc_final: 0.7451 (ttm-80) REVERT: B 118 ASP cc_start: 0.7274 (p0) cc_final: 0.7009 (p0) REVERT: B 256 ARG cc_start: 0.8247 (mtm-85) cc_final: 0.8025 (mtm-85) REVERT: B 323 ASP cc_start: 0.6327 (t0) cc_final: 0.6039 (t0) REVERT: A 209 LYS cc_start: 0.7929 (tmtt) cc_final: 0.7708 (ptpt) REVERT: A 261 ASP cc_start: 0.7605 (p0) cc_final: 0.7322 (p0) REVERT: A 306 GLN cc_start: 0.7654 (mm-40) cc_final: 0.7337 (mm-40) REVERT: G 58 GLU cc_start: 0.6822 (mm-30) cc_final: 0.5930 (pm20) outliers start: 5 outliers final: 2 residues processed: 178 average time/residue: 0.7575 time to fit residues: 144.8523 Evaluate side-chains 145 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 143 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 109 THR Chi-restraints excluded: chain B residue 67 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 0.5980 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 74 optimal weight: 0.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.176013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.141985 restraints weight = 23300.772| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 2.28 r_work: 0.3345 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3205 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.1590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 6975 Z= 0.237 Angle : 0.551 4.869 9486 Z= 0.308 Chirality : 0.042 0.141 1111 Planarity : 0.004 0.046 1199 Dihedral : 7.211 81.686 990 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 3.03 % Allowed : 15.99 % Favored : 80.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.75 (0.27), residues: 889 helix: 0.95 (0.25), residues: 387 sheet: -1.00 (0.38), residues: 162 loop : -1.92 (0.32), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 314 TYR 0.012 0.002 TYR A 296 PHE 0.016 0.002 PHE B 151 TRP 0.013 0.002 TRP B 82 HIS 0.003 0.001 HIS G 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00529 / 0.24 ( 6972) covalent geometry : angle 0.54886 / 0.31 ( 9480) SS BOND : bond 0.00733 / 0.38 ( 3) SS BOND : angle 1.80130 / 1.07 ( 6) hydrogen bonds : bond 0.05309 / 3.60 ( 372) hydrogen bonds : angle 4.69973 / 3.45 ( 1065) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 47 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue ILE 61 is missing expected H atoms. Skipping. Residue LEU 65 is missing expected H atoms. Skipping. Residue LEU 68 is missing expected H atoms. Skipping. Residue VAL 72 is missing expected H atoms. Skipping. Residue ILE 74 is missing expected H atoms. Skipping. Residue MET 159 is missing expected H atoms. Skipping. Residue THR 173 is missing expected H atoms. Skipping. Residue MET 237 is missing expected H atoms. Skipping. Residue MET 254 is missing expected H atoms. Skipping. Residue LYS 316 is missing expected H atoms. Skipping. Residue SER 2 is missing expected H atoms. Skipping. Residue LEU 4 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue ILE 33 is missing expected H atoms. Skipping. Residue SER 108 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue MET 262 is missing expected H atoms. Skipping. Residue MET 325 is missing expected H atoms. Skipping. Residue LYS 10 is missing expected H atoms. Skipping. Residue LYS 17 is missing expected H atoms. Skipping. Residue MET 18 is missing expected H atoms. Skipping. Residue LYS 51 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue MET 240 is missing expected H atoms. Skipping. Residue LYS 280 is missing expected H atoms. Skipping. Residue THR 327 is missing expected H atoms. Skipping. Residue LYS 330 is missing expected H atoms. Skipping. Residue SER 8 is missing expected H atoms. Skipping. Residue ILE 9 is missing expected H atoms. Skipping. Residue LEU 15 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Evaluate side-chains 170 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 149 time to evaluate : 0.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 71 MET cc_start: 0.7477 (mtp) cc_final: 0.7028 (mtp) REVERT: R 113 THR cc_start: 0.8194 (OUTLIER) cc_final: 0.7848 (t) REVERT: R 189 ILE cc_start: 0.7997 (mt) cc_final: 0.7732 (tt) REVERT: R 204 ASP cc_start: 0.7362 (m-30) cc_final: 0.7149 (m-30) REVERT: B 155 ASN cc_start: 0.7546 (OUTLIER) cc_final: 0.7318 (t0) REVERT: B 323 ASP cc_start: 0.7309 (t0) cc_final: 0.7107 (t0) REVERT: A 29 LYS cc_start: 0.7251 (ttmt) cc_final: 0.6964 (tppp) REVERT: A 209 LYS cc_start: 0.8102 (tmtt) cc_final: 0.7724 (ptpt) REVERT: A 241 ASN cc_start: 0.7536 (p0) cc_final: 0.7217 (p0) REVERT: A 261 ASP cc_start: 0.8292 (p0) cc_final: 0.8053 (p0) REVERT: G 58 GLU cc_start: 0.7239 (mm-30) cc_final: 0.5815 (pm20) outliers start: 21 outliers final: 9 residues processed: 162 average time/residue: 0.7745 time to fit residues: 135.4504 Evaluate side-chains 146 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 135 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 49 SER Chi-restraints excluded: chain R residue 109 THR Chi-restraints excluded: chain R residue 113 THR Chi-restraints excluded: chain R residue 169 VAL Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 155 ASN Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain A residue 297 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 23 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 30 optimal weight: 6.9990 chunk 3 optimal weight: 2.9990 chunk 70 optimal weight: 0.9980 chunk 47 optimal weight: 0.8980 chunk 57 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 chunk 75 optimal weight: 0.9980 chunk 82 optimal weight: 0.9990 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 75 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.174851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.140193 restraints weight = 23501.109| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 2.32 r_work: 0.3356 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3216 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.1871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 6975 Z= 0.162 Angle : 0.495 5.138 9486 Z= 0.275 Chirality : 0.040 0.148 1111 Planarity : 0.004 0.058 1199 Dihedral : 6.535 78.486 989 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 3.31 % Allowed : 17.87 % Favored : 78.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.28), residues: 889 helix: 1.53 (0.25), residues: 386 sheet: -0.87 (0.38), residues: 162 loop : -1.78 (0.32), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 134 TYR 0.009 0.001 TYR A 296 PHE 0.012 0.001 PHE B 151 TRP 0.014 0.001 TRP B 82 HIS 0.002 0.001 HIS R 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.16 ( 6972) covalent geometry : angle 0.49179 / 0.27 ( 9480) SS BOND : bond 0.00766 / 0.40 ( 3) SS BOND : angle 2.17773 / 1.29 ( 6) hydrogen bonds : bond 0.04694 / 3.17 ( 372) hydrogen bonds : angle 4.47724 / 3.28 ( 1065) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 47 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue ILE 61 is missing expected H atoms. Skipping. Residue LEU 65 is missing expected H atoms. Skipping. Residue LEU 68 is missing expected H atoms. Skipping. Residue VAL 72 is missing expected H atoms. Skipping. Residue ILE 74 is missing expected H atoms. Skipping. Residue MET 159 is missing expected H atoms. Skipping. Residue THR 173 is missing expected H atoms. Skipping. Residue MET 237 is missing expected H atoms. Skipping. Residue MET 254 is missing expected H atoms. Skipping. Residue LYS 316 is missing expected H atoms. Skipping. Residue SER 2 is missing expected H atoms. Skipping. Residue LEU 4 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue ILE 33 is missing expected H atoms. Skipping. Residue SER 108 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue MET 262 is missing expected H atoms. Skipping. Residue MET 325 is missing expected H atoms. Skipping. Residue LYS 10 is missing expected H atoms. Skipping. Residue LYS 17 is missing expected H atoms. Skipping. Residue MET 18 is missing expected H atoms. Skipping. Residue LYS 51 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue MET 240 is missing expected H atoms. Skipping. Residue LYS 280 is missing expected H atoms. Skipping. Residue THR 327 is missing expected H atoms. Skipping. Residue LYS 330 is missing expected H atoms. Skipping. Residue SER 8 is missing expected H atoms. Skipping. Residue ILE 9 is missing expected H atoms. Skipping. Residue LEU 15 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Evaluate side-chains 166 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 143 time to evaluate : 0.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 36 ARG cc_start: 0.7345 (tpp-160) cc_final: 0.7071 (tpp80) REVERT: R 53 MET cc_start: 0.8102 (ttp) cc_final: 0.7896 (ttt) REVERT: R 71 MET cc_start: 0.7483 (mtp) cc_final: 0.7046 (mtp) REVERT: R 204 ASP cc_start: 0.7221 (m-30) cc_final: 0.6986 (m-30) REVERT: B 49 ARG cc_start: 0.8343 (OUTLIER) cc_final: 0.8103 (ttm110) REVERT: B 75 GLN cc_start: 0.7362 (OUTLIER) cc_final: 0.7161 (tt0) REVERT: B 134 ARG cc_start: 0.7581 (mtm110) cc_final: 0.7098 (mtp85) REVERT: B 155 ASN cc_start: 0.7526 (OUTLIER) cc_final: 0.7319 (t0) REVERT: A 29 LYS cc_start: 0.7190 (ttmt) cc_final: 0.6889 (tppp) REVERT: A 209 LYS cc_start: 0.8077 (tmtt) cc_final: 0.7658 (ptpt) REVERT: A 241 ASN cc_start: 0.7262 (p0) cc_final: 0.6962 (p0) REVERT: A 349 LYS cc_start: 0.7765 (tttm) cc_final: 0.7371 (ttmm) REVERT: G 58 GLU cc_start: 0.7258 (mm-30) cc_final: 0.5883 (pm20) outliers start: 23 outliers final: 11 residues processed: 156 average time/residue: 0.7541 time to fit residues: 127.3497 Evaluate side-chains 152 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 138 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 49 SER Chi-restraints excluded: chain R residue 113 THR Chi-restraints excluded: chain R residue 135 SER Chi-restraints excluded: chain R residue 169 VAL Chi-restraints excluded: chain R residue 318 MET Chi-restraints excluded: chain B residue 49 ARG Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 155 ASN Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 331 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 62 optimal weight: 0.9990 chunk 6 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 53 optimal weight: 0.7980 chunk 80 optimal weight: 0.5980 chunk 73 optimal weight: 0.7980 chunk 16 optimal weight: 0.9990 chunk 83 optimal weight: 9.9990 chunk 23 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 chunk 57 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 75 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.175192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.140901 restraints weight = 23254.495| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 2.29 r_work: 0.3358 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3219 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 moved from start: 0.2005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6975 Z= 0.138 Angle : 0.478 4.474 9486 Z= 0.265 Chirality : 0.040 0.149 1111 Planarity : 0.004 0.048 1199 Dihedral : 6.254 76.297 988 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 3.31 % Allowed : 19.16 % Favored : 77.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.28), residues: 889 helix: 1.87 (0.26), residues: 387 sheet: -0.77 (0.38), residues: 162 loop : -1.76 (0.32), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 134 TYR 0.012 0.001 TYR B 59 PHE 0.011 0.001 PHE B 151 TRP 0.013 0.001 TRP B 82 HIS 0.002 0.001 HIS B 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.14 ( 6972) covalent geometry : angle 0.47623 / 0.26 ( 9480) SS BOND : bond 0.01176 / 0.62 ( 3) SS BOND : angle 1.82183 / 1.08 ( 6) hydrogen bonds : bond 0.04358 / 2.92 ( 372) hydrogen bonds : angle 4.34989 / 3.19 ( 1065) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 47 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue ILE 61 is missing expected H atoms. Skipping. Residue LEU 65 is missing expected H atoms. Skipping. Residue LEU 68 is missing expected H atoms. Skipping. Residue VAL 72 is missing expected H atoms. Skipping. Residue ILE 74 is missing expected H atoms. Skipping. Residue MET 159 is missing expected H atoms. Skipping. Residue THR 173 is missing expected H atoms. Skipping. Residue MET 237 is missing expected H atoms. Skipping. Residue MET 254 is missing expected H atoms. Skipping. Residue LYS 316 is missing expected H atoms. Skipping. Residue SER 2 is missing expected H atoms. Skipping. Residue LEU 4 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue ILE 33 is missing expected H atoms. Skipping. Residue SER 108 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue MET 262 is missing expected H atoms. Skipping. Residue MET 325 is missing expected H atoms. Skipping. Residue LYS 10 is missing expected H atoms. Skipping. Residue LYS 17 is missing expected H atoms. Skipping. Residue MET 18 is missing expected H atoms. Skipping. Residue LYS 51 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue MET 240 is missing expected H atoms. Skipping. Residue LYS 280 is missing expected H atoms. Skipping. Residue THR 327 is missing expected H atoms. Skipping. Residue LYS 330 is missing expected H atoms. Skipping. Residue SER 8 is missing expected H atoms. Skipping. Residue ILE 9 is missing expected H atoms. Skipping. Residue LEU 15 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Evaluate side-chains 166 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 143 time to evaluate : 0.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 36 ARG cc_start: 0.7354 (tpp-160) cc_final: 0.7097 (tpp80) REVERT: R 71 MET cc_start: 0.7547 (mtp) cc_final: 0.7091 (mtp) REVERT: R 212 ILE cc_start: 0.7309 (mt) cc_final: 0.7000 (mm) REVERT: B 49 ARG cc_start: 0.8331 (OUTLIER) cc_final: 0.8085 (ttm110) REVERT: B 134 ARG cc_start: 0.7585 (mtm110) cc_final: 0.7245 (mtm180) REVERT: B 155 ASN cc_start: 0.7504 (OUTLIER) cc_final: 0.7282 (t0) REVERT: A 29 LYS cc_start: 0.7173 (ttmt) cc_final: 0.6910 (tppp) REVERT: A 209 LYS cc_start: 0.8064 (tmtt) cc_final: 0.7632 (ptpt) REVERT: A 349 LYS cc_start: 0.7726 (tttm) cc_final: 0.7325 (ttmm) REVERT: G 58 GLU cc_start: 0.7205 (mm-30) cc_final: 0.5882 (pm20) outliers start: 23 outliers final: 15 residues processed: 155 average time/residue: 0.7603 time to fit residues: 127.3388 Evaluate side-chains 154 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 137 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 113 THR Chi-restraints excluded: chain R residue 135 SER Chi-restraints excluded: chain R residue 169 VAL Chi-restraints excluded: chain R residue 306 MET Chi-restraints excluded: chain R residue 318 MET Chi-restraints excluded: chain B residue 49 ARG Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 155 ASN Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 331 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 47 optimal weight: 1.9990 chunk 48 optimal weight: 0.5980 chunk 25 optimal weight: 1.9990 chunk 55 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 29 optimal weight: 5.9990 chunk 74 optimal weight: 0.9990 chunk 84 optimal weight: 8.9990 chunk 59 optimal weight: 2.9990 chunk 17 optimal weight: 0.0870 chunk 12 optimal weight: 1.9990 overall best weight: 0.9162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.176613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.142854 restraints weight = 23368.948| |-----------------------------------------------------------------------------| r_work (start): 0.3478 rms_B_bonded: 2.27 r_work: 0.3343 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3203 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.2157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6975 Z= 0.155 Angle : 0.485 4.494 9486 Z= 0.269 Chirality : 0.040 0.148 1111 Planarity : 0.004 0.048 1199 Dihedral : 6.159 75.550 988 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 4.03 % Allowed : 19.02 % Favored : 76.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.28), residues: 889 helix: 1.95 (0.26), residues: 388 sheet: -0.83 (0.37), residues: 169 loop : -1.64 (0.33), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 32 TYR 0.007 0.001 TYR A 296 PHE 0.011 0.001 PHE B 151 TRP 0.013 0.001 TRP B 82 HIS 0.002 0.001 HIS B 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.15 ( 6972) covalent geometry : angle 0.48427 / 0.27 ( 9480) SS BOND : bond 0.00393 / 0.21 ( 3) SS BOND : angle 0.89100 / 0.54 ( 6) hydrogen bonds : bond 0.04449 / 2.98 ( 372) hydrogen bonds : angle 4.35934 / 3.20 ( 1065) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 47 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue ILE 61 is missing expected H atoms. Skipping. Residue LEU 65 is missing expected H atoms. Skipping. Residue LEU 68 is missing expected H atoms. Skipping. Residue VAL 72 is missing expected H atoms. Skipping. Residue ILE 74 is missing expected H atoms. Skipping. Residue MET 159 is missing expected H atoms. Skipping. Residue THR 173 is missing expected H atoms. Skipping. Residue MET 237 is missing expected H atoms. Skipping. Residue MET 254 is missing expected H atoms. Skipping. Residue LYS 316 is missing expected H atoms. Skipping. Residue SER 2 is missing expected H atoms. Skipping. Residue LEU 4 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue ILE 33 is missing expected H atoms. Skipping. Residue SER 108 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue MET 262 is missing expected H atoms. Skipping. Residue MET 325 is missing expected H atoms. Skipping. Residue LYS 10 is missing expected H atoms. Skipping. Residue LYS 17 is missing expected H atoms. Skipping. Residue MET 18 is missing expected H atoms. Skipping. Residue LYS 51 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue MET 240 is missing expected H atoms. Skipping. Residue LYS 280 is missing expected H atoms. Skipping. Residue THR 327 is missing expected H atoms. Skipping. Residue LYS 330 is missing expected H atoms. Skipping. Residue SER 8 is missing expected H atoms. Skipping. Residue ILE 9 is missing expected H atoms. Skipping. Residue LEU 15 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Evaluate side-chains 172 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 144 time to evaluate : 0.325 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 36 ARG cc_start: 0.7352 (tpp-160) cc_final: 0.7049 (tpt90) REVERT: R 53 MET cc_start: 0.7964 (ttt) cc_final: 0.7710 (ttp) REVERT: R 71 MET cc_start: 0.7547 (mtp) cc_final: 0.7118 (mtp) REVERT: R 212 ILE cc_start: 0.7282 (mt) cc_final: 0.6991 (mm) REVERT: B 49 ARG cc_start: 0.8369 (OUTLIER) cc_final: 0.8135 (ttm110) REVERT: B 134 ARG cc_start: 0.7583 (mtm110) cc_final: 0.7257 (mtm180) REVERT: B 155 ASN cc_start: 0.7513 (OUTLIER) cc_final: 0.7290 (t0) REVERT: B 170 ASP cc_start: 0.7212 (t0) cc_final: 0.7000 (t70) REVERT: A 29 LYS cc_start: 0.7191 (ttmt) cc_final: 0.6927 (tppp) REVERT: A 209 LYS cc_start: 0.8090 (tmtt) cc_final: 0.7696 (ptpt) REVERT: A 349 LYS cc_start: 0.7720 (tttm) cc_final: 0.7322 (ttmm) REVERT: G 47 GLU cc_start: 0.7605 (mt-10) cc_final: 0.7265 (mt-10) REVERT: G 58 GLU cc_start: 0.7191 (mm-30) cc_final: 0.5882 (pm20) outliers start: 28 outliers final: 19 residues processed: 163 average time/residue: 0.7637 time to fit residues: 134.5872 Evaluate side-chains 169 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 148 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 49 SER Chi-restraints excluded: chain R residue 113 THR Chi-restraints excluded: chain R residue 135 SER Chi-restraints excluded: chain R residue 169 VAL Chi-restraints excluded: chain R residue 210 TRP Chi-restraints excluded: chain R residue 261 VAL Chi-restraints excluded: chain R residue 263 VAL Chi-restraints excluded: chain R residue 306 MET Chi-restraints excluded: chain B residue 49 ARG Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 155 ASN Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 331 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 57 optimal weight: 0.9980 chunk 29 optimal weight: 7.9990 chunk 23 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 80 optimal weight: 0.8980 chunk 81 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 chunk 60 optimal weight: 0.1980 chunk 7 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.174111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.139868 restraints weight = 23275.851| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 2.29 r_work: 0.3355 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3214 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.2275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6975 Z= 0.141 Angle : 0.476 4.463 9486 Z= 0.264 Chirality : 0.040 0.148 1111 Planarity : 0.003 0.048 1199 Dihedral : 5.991 73.915 988 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 3.89 % Allowed : 20.03 % Favored : 76.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.28), residues: 889 helix: 2.09 (0.26), residues: 387 sheet: -0.83 (0.37), residues: 171 loop : -1.59 (0.33), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 32 TYR 0.006 0.001 TYR A 296 PHE 0.011 0.001 PHE B 151 TRP 0.013 0.001 TRP B 82 HIS 0.002 0.001 HIS B 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.14 ( 6972) covalent geometry : angle 0.47588 / 0.26 ( 9480) SS BOND : bond 0.00276 / 0.14 ( 3) SS BOND : angle 0.50319 / 0.32 ( 6) hydrogen bonds : bond 0.04287 / 2.87 ( 372) hydrogen bonds : angle 4.27908 / 3.14 ( 1065) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 47 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue ILE 61 is missing expected H atoms. Skipping. Residue LEU 65 is missing expected H atoms. Skipping. Residue LEU 68 is missing expected H atoms. Skipping. Residue VAL 72 is missing expected H atoms. Skipping. Residue ILE 74 is missing expected H atoms. Skipping. Residue MET 159 is missing expected H atoms. Skipping. Residue THR 173 is missing expected H atoms. Skipping. Residue MET 237 is missing expected H atoms. Skipping. Residue MET 254 is missing expected H atoms. Skipping. Residue LYS 316 is missing expected H atoms. Skipping. Residue SER 2 is missing expected H atoms. Skipping. Residue LEU 4 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue ILE 33 is missing expected H atoms. Skipping. Residue SER 108 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue MET 262 is missing expected H atoms. Skipping. Residue MET 325 is missing expected H atoms. Skipping. Residue LYS 10 is missing expected H atoms. Skipping. Residue LYS 17 is missing expected H atoms. Skipping. Residue MET 18 is missing expected H atoms. Skipping. Residue LYS 51 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue MET 240 is missing expected H atoms. Skipping. Residue LYS 280 is missing expected H atoms. Skipping. Residue THR 327 is missing expected H atoms. Skipping. Residue LYS 330 is missing expected H atoms. Skipping. Residue SER 8 is missing expected H atoms. Skipping. Residue ILE 9 is missing expected H atoms. Skipping. Residue LEU 15 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Evaluate side-chains 175 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 148 time to evaluate : 0.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 36 ARG cc_start: 0.7361 (tpp-160) cc_final: 0.7066 (tpt90) REVERT: R 71 MET cc_start: 0.7540 (mtp) cc_final: 0.7102 (mtp) REVERT: R 145 GLU cc_start: 0.8380 (OUTLIER) cc_final: 0.8011 (tt0) REVERT: R 212 ILE cc_start: 0.7258 (mt) cc_final: 0.6977 (mm) REVERT: B 49 ARG cc_start: 0.8365 (OUTLIER) cc_final: 0.8121 (ttm110) REVERT: B 134 ARG cc_start: 0.7605 (mtm110) cc_final: 0.7270 (mtm180) REVERT: B 155 ASN cc_start: 0.7506 (OUTLIER) cc_final: 0.7294 (t0) REVERT: A 29 LYS cc_start: 0.7166 (ttmt) cc_final: 0.6911 (tppp) REVERT: A 209 LYS cc_start: 0.8115 (tmtt) cc_final: 0.7737 (ptpt) REVERT: A 349 LYS cc_start: 0.7709 (tttm) cc_final: 0.7312 (ttmm) REVERT: G 47 GLU cc_start: 0.7645 (mt-10) cc_final: 0.7279 (mt-10) REVERT: G 58 GLU cc_start: 0.7229 (mm-30) cc_final: 0.5931 (pm20) outliers start: 27 outliers final: 19 residues processed: 166 average time/residue: 0.7408 time to fit residues: 132.8515 Evaluate side-chains 163 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 141 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 49 SER Chi-restraints excluded: chain R residue 109 THR Chi-restraints excluded: chain R residue 113 THR Chi-restraints excluded: chain R residue 135 SER Chi-restraints excluded: chain R residue 145 GLU Chi-restraints excluded: chain R residue 169 VAL Chi-restraints excluded: chain R residue 210 TRP Chi-restraints excluded: chain R residue 261 VAL Chi-restraints excluded: chain R residue 263 VAL Chi-restraints excluded: chain R residue 306 MET Chi-restraints excluded: chain B residue 49 ARG Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 155 ASN Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 331 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 66 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 chunk 27 optimal weight: 0.0980 chunk 45 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 chunk 33 optimal weight: 0.7980 chunk 43 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 72 optimal weight: 0.0670 chunk 26 optimal weight: 0.9990 overall best weight: 0.5922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.175137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.140801 restraints weight = 23432.870| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 2.31 r_work: 0.3355 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3212 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7505 moved from start: 0.2309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 6975 Z= 0.115 Angle : 0.459 4.937 9486 Z= 0.253 Chirality : 0.039 0.150 1111 Planarity : 0.003 0.047 1199 Dihedral : 5.790 70.385 988 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 3.17 % Allowed : 21.04 % Favored : 75.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.29), residues: 889 helix: 2.25 (0.26), residues: 388 sheet: -0.73 (0.38), residues: 166 loop : -1.55 (0.33), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 32 TYR 0.006 0.001 TYR A 296 PHE 0.010 0.001 PHE B 151 TRP 0.013 0.001 TRP B 82 HIS 0.002 0.000 HIS R 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.11 ( 6972) covalent geometry : angle 0.45869 / 0.25 ( 9480) SS BOND : bond 0.00244 / 0.13 ( 3) SS BOND : angle 0.39552 / 0.26 ( 6) hydrogen bonds : bond 0.04013 / 2.68 ( 372) hydrogen bonds : angle 4.18359 / 3.06 ( 1065) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 47 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue ILE 61 is missing expected H atoms. Skipping. Residue LEU 65 is missing expected H atoms. Skipping. Residue LEU 68 is missing expected H atoms. Skipping. Residue VAL 72 is missing expected H atoms. Skipping. Residue ILE 74 is missing expected H atoms. Skipping. Residue MET 159 is missing expected H atoms. Skipping. Residue THR 173 is missing expected H atoms. Skipping. Residue MET 237 is missing expected H atoms. Skipping. Residue MET 254 is missing expected H atoms. Skipping. Residue LYS 316 is missing expected H atoms. Skipping. Residue SER 2 is missing expected H atoms. Skipping. Residue LEU 4 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue ILE 33 is missing expected H atoms. Skipping. Residue SER 108 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue MET 262 is missing expected H atoms. Skipping. Residue MET 325 is missing expected H atoms. Skipping. Residue LYS 10 is missing expected H atoms. Skipping. Residue LYS 17 is missing expected H atoms. Skipping. Residue MET 18 is missing expected H atoms. Skipping. Residue LYS 51 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue MET 240 is missing expected H atoms. Skipping. Residue LYS 280 is missing expected H atoms. Skipping. Residue THR 327 is missing expected H atoms. Skipping. Residue LYS 330 is missing expected H atoms. Skipping. Residue SER 8 is missing expected H atoms. Skipping. Residue ILE 9 is missing expected H atoms. Skipping. Residue LEU 15 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Evaluate side-chains 167 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 145 time to evaluate : 0.448 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 36 ARG cc_start: 0.7352 (tpp-160) cc_final: 0.7049 (tpp80) REVERT: R 71 MET cc_start: 0.7563 (mtp) cc_final: 0.7103 (mtp) REVERT: R 145 GLU cc_start: 0.8254 (OUTLIER) cc_final: 0.7887 (tt0) REVERT: R 212 ILE cc_start: 0.7219 (mt) cc_final: 0.6943 (mm) REVERT: B 49 ARG cc_start: 0.8367 (OUTLIER) cc_final: 0.8125 (ttm110) REVERT: B 134 ARG cc_start: 0.7602 (mtm110) cc_final: 0.7264 (mtm180) REVERT: B 155 ASN cc_start: 0.7406 (OUTLIER) cc_final: 0.7162 (t0) REVERT: A 29 LYS cc_start: 0.7107 (ttmt) cc_final: 0.6845 (tppp) REVERT: A 209 LYS cc_start: 0.8080 (tmtt) cc_final: 0.7697 (ptpt) REVERT: G 47 GLU cc_start: 0.7703 (mt-10) cc_final: 0.7415 (mt-10) REVERT: G 58 GLU cc_start: 0.7212 (mm-30) cc_final: 0.5920 (pm20) outliers start: 22 outliers final: 15 residues processed: 160 average time/residue: 0.8088 time to fit residues: 140.3248 Evaluate side-chains 159 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 141 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 49 SER Chi-restraints excluded: chain R residue 113 THR Chi-restraints excluded: chain R residue 135 SER Chi-restraints excluded: chain R residue 145 GLU Chi-restraints excluded: chain R residue 169 VAL Chi-restraints excluded: chain R residue 261 VAL Chi-restraints excluded: chain R residue 306 MET Chi-restraints excluded: chain B residue 49 ARG Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 155 ASN Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 329 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 48 optimal weight: 0.9990 chunk 19 optimal weight: 0.7980 chunk 20 optimal weight: 0.9980 chunk 17 optimal weight: 0.2980 chunk 9 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 82 optimal weight: 1.9990 chunk 85 optimal weight: 4.9990 chunk 5 optimal weight: 4.9990 chunk 67 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.174122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.139798 restraints weight = 23301.627| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 2.31 r_work: 0.3341 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3199 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 moved from start: 0.2389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 6975 Z= 0.141 Angle : 0.478 6.189 9486 Z= 0.264 Chirality : 0.039 0.150 1111 Planarity : 0.003 0.047 1199 Dihedral : 5.814 69.596 988 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 3.89 % Allowed : 21.04 % Favored : 75.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.29), residues: 889 helix: 2.23 (0.26), residues: 387 sheet: -0.74 (0.37), residues: 166 loop : -1.54 (0.33), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 32 TYR 0.006 0.001 TYR A 296 PHE 0.011 0.001 PHE B 151 TRP 0.012 0.001 TRP B 82 HIS 0.002 0.001 HIS R 147 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.14 ( 6972) covalent geometry : angle 0.47791 / 0.26 ( 9480) SS BOND : bond 0.00207 / 0.11 ( 3) SS BOND : angle 0.31348 / 0.21 ( 6) hydrogen bonds : bond 0.04227 / 2.83 ( 372) hydrogen bonds : angle 4.23864 / 3.11 ( 1065) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 47 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue ILE 61 is missing expected H atoms. Skipping. Residue LEU 65 is missing expected H atoms. Skipping. Residue LEU 68 is missing expected H atoms. Skipping. Residue VAL 72 is missing expected H atoms. Skipping. Residue ILE 74 is missing expected H atoms. Skipping. Residue MET 159 is missing expected H atoms. Skipping. Residue THR 173 is missing expected H atoms. Skipping. Residue MET 237 is missing expected H atoms. Skipping. Residue MET 254 is missing expected H atoms. Skipping. Residue LYS 316 is missing expected H atoms. Skipping. Residue SER 2 is missing expected H atoms. Skipping. Residue LEU 4 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue ILE 33 is missing expected H atoms. Skipping. Residue SER 108 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue MET 262 is missing expected H atoms. Skipping. Residue MET 325 is missing expected H atoms. Skipping. Residue LYS 10 is missing expected H atoms. Skipping. Residue LYS 17 is missing expected H atoms. Skipping. Residue MET 18 is missing expected H atoms. Skipping. Residue LYS 51 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue MET 240 is missing expected H atoms. Skipping. Residue LYS 280 is missing expected H atoms. Skipping. Residue THR 327 is missing expected H atoms. Skipping. Residue LYS 330 is missing expected H atoms. Skipping. Residue SER 8 is missing expected H atoms. Skipping. Residue ILE 9 is missing expected H atoms. Skipping. Residue LEU 15 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Evaluate side-chains 169 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 142 time to evaluate : 0.480 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 36 ARG cc_start: 0.7354 (tpp-160) cc_final: 0.7078 (tpp80) REVERT: R 71 MET cc_start: 0.7575 (mtp) cc_final: 0.7125 (mtp) REVERT: R 145 GLU cc_start: 0.8349 (OUTLIER) cc_final: 0.8009 (tt0) REVERT: R 212 ILE cc_start: 0.7228 (mt) cc_final: 0.6955 (mm) REVERT: B 49 ARG cc_start: 0.8386 (OUTLIER) cc_final: 0.8145 (ttm110) REVERT: A 29 LYS cc_start: 0.7076 (ttmt) cc_final: 0.6834 (tppp) REVERT: A 209 LYS cc_start: 0.8054 (tmtt) cc_final: 0.7661 (ptpt) REVERT: A 241 ASN cc_start: 0.7095 (p0) cc_final: 0.6793 (p0) REVERT: G 47 GLU cc_start: 0.7709 (mt-10) cc_final: 0.7415 (mt-10) REVERT: G 58 GLU cc_start: 0.7216 (mm-30) cc_final: 0.5910 (pm20) outliers start: 27 outliers final: 19 residues processed: 162 average time/residue: 0.8112 time to fit residues: 142.5668 Evaluate side-chains 160 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 139 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 49 SER Chi-restraints excluded: chain R residue 113 THR Chi-restraints excluded: chain R residue 135 SER Chi-restraints excluded: chain R residue 145 GLU Chi-restraints excluded: chain R residue 169 VAL Chi-restraints excluded: chain R residue 210 TRP Chi-restraints excluded: chain R residue 261 VAL Chi-restraints excluded: chain R residue 263 VAL Chi-restraints excluded: chain R residue 306 MET Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 49 ARG Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 331 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 41 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 75 optimal weight: 0.5980 chunk 87 optimal weight: 0.1980 chunk 33 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 78 optimal weight: 0.9990 chunk 9 optimal weight: 0.9980 chunk 35 optimal weight: 0.3980 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.172785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.137705 restraints weight = 23488.946| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 2.32 r_work: 0.3341 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3199 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 moved from start: 0.2434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 6975 Z= 0.120 Angle : 0.470 6.930 9486 Z= 0.257 Chirality : 0.039 0.151 1111 Planarity : 0.005 0.108 1199 Dihedral : 5.683 66.274 988 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 3.31 % Allowed : 21.90 % Favored : 74.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.29), residues: 889 helix: 2.36 (0.26), residues: 388 sheet: -0.70 (0.37), residues: 166 loop : -1.51 (0.33), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG B 134 TYR 0.006 0.001 TYR A 296 PHE 0.010 0.001 PHE B 151 TRP 0.013 0.001 TRP B 82 HIS 0.002 0.001 HIS R 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 ( 6972) covalent geometry : angle 0.47046 / 0.26 ( 9480) SS BOND : bond 0.00212 / 0.11 ( 3) SS BOND : angle 0.29061 / 0.21 ( 6) hydrogen bonds : bond 0.03993 / 2.66 ( 372) hydrogen bonds : angle 4.15155 / 3.04 ( 1065) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 47 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue ILE 61 is missing expected H atoms. Skipping. Residue LEU 65 is missing expected H atoms. Skipping. Residue LEU 68 is missing expected H atoms. Skipping. Residue VAL 72 is missing expected H atoms. Skipping. Residue ILE 74 is missing expected H atoms. Skipping. Residue MET 159 is missing expected H atoms. Skipping. Residue THR 173 is missing expected H atoms. Skipping. Residue MET 237 is missing expected H atoms. Skipping. Residue MET 254 is missing expected H atoms. Skipping. Residue LYS 316 is missing expected H atoms. Skipping. Residue SER 2 is missing expected H atoms. Skipping. Residue LEU 4 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue ILE 33 is missing expected H atoms. Skipping. Residue SER 108 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue MET 262 is missing expected H atoms. Skipping. Residue MET 325 is missing expected H atoms. Skipping. Residue LYS 10 is missing expected H atoms. Skipping. Residue LYS 17 is missing expected H atoms. Skipping. Residue MET 18 is missing expected H atoms. Skipping. Residue LYS 51 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue MET 240 is missing expected H atoms. Skipping. Residue LYS 280 is missing expected H atoms. Skipping. Residue THR 327 is missing expected H atoms. Skipping. Residue LYS 330 is missing expected H atoms. Skipping. Residue SER 8 is missing expected H atoms. Skipping. Residue ILE 9 is missing expected H atoms. Skipping. Residue LEU 15 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Evaluate side-chains 164 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 141 time to evaluate : 0.418 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 36 ARG cc_start: 0.7369 (tpp-160) cc_final: 0.7065 (tpp80) REVERT: R 49 SER cc_start: 0.8219 (OUTLIER) cc_final: 0.7705 (t) REVERT: R 71 MET cc_start: 0.7568 (mtp) cc_final: 0.7119 (mtp) REVERT: R 145 GLU cc_start: 0.8271 (OUTLIER) cc_final: 0.7906 (tt0) REVERT: R 212 ILE cc_start: 0.7248 (mt) cc_final: 0.6983 (mm) REVERT: B 49 ARG cc_start: 0.8363 (OUTLIER) cc_final: 0.8124 (ttm110) REVERT: B 134 ARG cc_start: 0.7505 (mtm110) cc_final: 0.6957 (mtp-110) REVERT: A 29 LYS cc_start: 0.7112 (ttmt) cc_final: 0.6856 (tppp) REVERT: A 209 LYS cc_start: 0.8071 (tmtt) cc_final: 0.7692 (ptpt) REVERT: A 241 ASN cc_start: 0.7040 (p0) cc_final: 0.6759 (p0) REVERT: G 47 GLU cc_start: 0.7625 (mt-10) cc_final: 0.7337 (mt-10) REVERT: G 58 GLU cc_start: 0.7221 (mm-30) cc_final: 0.5912 (pm20) outliers start: 23 outliers final: 18 residues processed: 158 average time/residue: 0.8095 time to fit residues: 138.8063 Evaluate side-chains 166 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 145 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 49 SER Chi-restraints excluded: chain R residue 109 THR Chi-restraints excluded: chain R residue 113 THR Chi-restraints excluded: chain R residue 135 SER Chi-restraints excluded: chain R residue 145 GLU Chi-restraints excluded: chain R residue 169 VAL Chi-restraints excluded: chain R residue 210 TRP Chi-restraints excluded: chain R residue 261 VAL Chi-restraints excluded: chain R residue 263 VAL Chi-restraints excluded: chain R residue 306 MET Chi-restraints excluded: chain B residue 49 ARG Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 331 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 56 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 8 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 chunk 16 optimal weight: 0.3980 chunk 55 optimal weight: 0.4980 chunk 9 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.174715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.140761 restraints weight = 23399.011| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 2.30 r_work: 0.3340 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3198 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 moved from start: 0.2521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6975 Z= 0.128 Angle : 0.483 8.695 9486 Z= 0.263 Chirality : 0.039 0.151 1111 Planarity : 0.004 0.100 1199 Dihedral : 5.613 64.435 988 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 2.88 % Allowed : 23.20 % Favored : 73.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.29), residues: 889 helix: 2.39 (0.26), residues: 388 sheet: -0.72 (0.37), residues: 166 loop : -1.51 (0.33), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG B 134 TYR 0.007 0.001 TYR A 296 PHE 0.011 0.001 PHE B 151 TRP 0.012 0.001 TRP B 82 HIS 0.002 0.001 HIS R 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.13 ( 6972) covalent geometry : angle 0.48272 / 0.26 ( 9480) SS BOND : bond 0.00201 / 0.11 ( 3) SS BOND : angle 0.26552 / 0.19 ( 6) hydrogen bonds : bond 0.04043 / 2.70 ( 372) hydrogen bonds : angle 4.15420 / 3.05 ( 1065) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 47 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue ILE 61 is missing expected H atoms. Skipping. Residue LEU 65 is missing expected H atoms. Skipping. Residue LEU 68 is missing expected H atoms. Skipping. Residue VAL 72 is missing expected H atoms. Skipping. Residue ILE 74 is missing expected H atoms. Skipping. Residue MET 159 is missing expected H atoms. Skipping. Residue THR 173 is missing expected H atoms. Skipping. Residue MET 237 is missing expected H atoms. Skipping. Residue MET 254 is missing expected H atoms. Skipping. Residue LYS 316 is missing expected H atoms. Skipping. Residue SER 2 is missing expected H atoms. Skipping. Residue LEU 4 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue ILE 33 is missing expected H atoms. Skipping. Residue SER 108 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue MET 262 is missing expected H atoms. Skipping. Residue MET 325 is missing expected H atoms. Skipping. Residue LYS 10 is missing expected H atoms. Skipping. Residue LYS 17 is missing expected H atoms. Skipping. Residue MET 18 is missing expected H atoms. Skipping. Residue LYS 51 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue MET 240 is missing expected H atoms. Skipping. Residue LYS 280 is missing expected H atoms. Skipping. Residue THR 327 is missing expected H atoms. Skipping. Residue LYS 330 is missing expected H atoms. Skipping. Residue SER 8 is missing expected H atoms. Skipping. Residue ILE 9 is missing expected H atoms. Skipping. Residue LEU 15 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Evaluate side-chains 165 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 145 time to evaluate : 0.371 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 36 ARG cc_start: 0.7326 (tpp-160) cc_final: 0.7045 (tpp80) REVERT: R 49 SER cc_start: 0.8244 (OUTLIER) cc_final: 0.7712 (t) REVERT: R 71 MET cc_start: 0.7545 (mtp) cc_final: 0.7128 (mtp) REVERT: R 145 GLU cc_start: 0.8321 (OUTLIER) cc_final: 0.7972 (tt0) REVERT: R 212 ILE cc_start: 0.7237 (mt) cc_final: 0.6976 (mm) REVERT: B 49 ARG cc_start: 0.8378 (OUTLIER) cc_final: 0.8145 (ttm110) REVERT: B 134 ARG cc_start: 0.7552 (mtm110) cc_final: 0.7039 (mtp-110) REVERT: A 29 LYS cc_start: 0.7157 (ttmt) cc_final: 0.6903 (tppp) REVERT: A 209 LYS cc_start: 0.8086 (tmtt) cc_final: 0.7691 (ptpt) REVERT: G 58 GLU cc_start: 0.7239 (mm-30) cc_final: 0.5929 (pm20) outliers start: 20 outliers final: 17 residues processed: 161 average time/residue: 0.8451 time to fit residues: 146.8011 Evaluate side-chains 154 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 134 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 49 SER Chi-restraints excluded: chain R residue 113 THR Chi-restraints excluded: chain R residue 135 SER Chi-restraints excluded: chain R residue 145 GLU Chi-restraints excluded: chain R residue 169 VAL Chi-restraints excluded: chain R residue 210 TRP Chi-restraints excluded: chain R residue 261 VAL Chi-restraints excluded: chain R residue 263 VAL Chi-restraints excluded: chain R residue 306 MET Chi-restraints excluded: chain B residue 49 ARG Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 331 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 32 optimal weight: 2.9990 chunk 29 optimal weight: 7.9990 chunk 51 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 78 optimal weight: 0.9990 chunk 55 optimal weight: 0.0570 chunk 4 optimal weight: 0.9980 chunk 14 optimal weight: 0.4980 chunk 60 optimal weight: 0.9980 chunk 16 optimal weight: 0.9980 chunk 8 optimal weight: 0.7980 overall best weight: 0.6698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 52 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.173765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.139744 restraints weight = 23427.923| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 2.29 r_work: 0.3344 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3204 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 moved from start: 0.2554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6975 Z= 0.124 Angle : 0.479 8.405 9486 Z= 0.261 Chirality : 0.039 0.150 1111 Planarity : 0.004 0.096 1199 Dihedral : 5.503 62.135 988 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.59 % Allowed : 23.63 % Favored : 73.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.60 (0.29), residues: 889 helix: 2.43 (0.26), residues: 388 sheet: -0.69 (0.38), residues: 166 loop : -1.53 (0.33), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG B 134 TYR 0.006 0.001 TYR A 296 PHE 0.010 0.001 PHE B 151 TRP 0.013 0.001 TRP B 82 HIS 0.002 0.001 HIS A 213 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 ( 6972) covalent geometry : angle 0.47956 / 0.26 ( 9480) SS BOND : bond 0.00195 / 0.10 ( 3) SS BOND : angle 0.25900 / 0.19 ( 6) hydrogen bonds : bond 0.03977 / 2.66 ( 372) hydrogen bonds : angle 4.13196 / 3.03 ( 1065) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5351.76 seconds wall clock time: 91 minutes 17.62 seconds (5477.62 seconds total)